Schizophrenia Research Forum - A Catalyst for Creative Thinking

Schizophrenia Genetics 3: Rare Events Share Stage With Common Variants

In SRF's schizophrenia genetics overview, writer Pat McCaffrey surveys the range of experimentation and opinion in the field in a five-part series.

See Part 1, Linkage; Part 2, GWAS, Part 4, Bigger Genetics, Part 5, From Genes to Biology…and Therapies. Read a PDF of the entire series.


19 March 2010. Automated genotyping on single-nucleotide polymorphism (SNP) chips provided researchers with an unexpected view of genetic variation when they began to notice that the signal for some of these SNPs was less intense than expected, or in some cases stronger. The reason, they found, was that the genome is peppered with submicroscopic deletions and duplications that have the potential to disrupt genes or add extra copies. Too small to be detected by the traditional cytogenetic techniques that led to DISC1 and other gene candidates (see SRF related news story), these copy number variants (CNVs) were just recently recognized as a major source of genetic variation among people (see SRF related news story), and have been strongly linked to autism (see SRF related news story).

In the last two years, data have accumulated quickly, suggesting an important role for CNVs in schizophrenia: people with schizophrenia are reported to have elevated incidence of CNVs (see SRF related news story), including CNVs that are not inherited but have arisen in individuals (de novo CNVs; see SRF related news story). Last year, genomewide association studies found a handful of recurrent CNVs that were linked to schizophrenia in large samples (see SRF related news story). The CNVs in those studies showed effect sizes that far outstrip the modest contributions of common variants.

Nevertheless, the operative word is “rare”—so far, CNVs that appear to be causative have only been found in a fraction of a percent of schizophrenia cases. Still, they have grabbed attention as possible windows into pathophysiology and as a potential explanation for the missing portion of the genetic risk for schizophrenia that could not be explained by common variants.

Rare birds?
The involvement of CNVs in schizophrenia is, in fact, old news: gross genomic changes were associated with the disease nearly two decades ago, when David St. Clair and colleagues at the University of Edinburgh, Scotland, found a balanced translocation between chromosomes 1 and 11 that invariably led to schizophrenia and other mental disorders in a Scottish family (St. Clair et al., 1990). David Porteous’s group at the University of Edinburgh subsequently identified a novel gene, disrupted-in-schizophrenia 1 (DISC1), at the breakpoint (Millar et al., 2000), and DISC1 is now the most researched gene in the field (e.g., see SRF meeting report from Neuroscience 2009).

Also, schizophrenia occurs frequently in velo-cardio-facial syndrome (VCFS, also called DiGeorge syndrome), which results from deletion of multiple genes at 22q11.2, a region implicated by several early schizophrenia linkage scans. VCFS can include cleft palate, heart defects, characteristic facial appearance, learning disorders, and speech and feeding problems. Children with VCFS have a 25-times increased risk of schizophrenia (see SRF related news story), and about one-third of all babies born with the deletion will go on to develop schizophrenia (see, e.g., Murphy et al., 1999 ).

The DISC1 translocation and the 22q11.2 deletion were both found by classic cytogenetics techniques, and Porteous's group has since found other genes using the same methods. DISC1 interacts with PDE4B, which his lab identified as disrupted by translocation in another individual with schizophrenia and a cousin with psychosis. Using cytogenetics, Porteous and colleagues also linked schizophrenia with disruptions in the genes for NPAS3 (a brain-enriched transcription factor) and for GRIK4 (a glutamate receptor gene; see SRF related news story), two additional genes that are known to have important roles in neurogenesis and in neurosignaling. “So using cytogenetics, our lab alone has identified four clear-cut gene hits,” said Porteous. That number is now up to five, with their recent findings on the ABCA13 gene (see SRF related news story).

But are those genes relevant to the wider population of people with schizophrenia who do not carry the rare mistakes? Porteous argues that they are. “Each one of those has then been confirmed by doing a genewide association analysis looking in the general population of schizophrenia and bipolar disorder," he said. "We asked, if we look specifically at SNPs in the DISC1 locus or the PD4B locus or NPAS3 or GRIK 4, do we find evidence of association in the general population? The answer in each and every case has been, yes.”

The bottom line, Porteous said, is “We’ve got some real candidates, and genes that are beyond candidates. Certainly for DISC1, there is no question for most people who know the field well that this gene is causally related to psychosis, and there’s a wealth of information now about the biology that backs up that supposition.” Recent work in a mouse model of DISC1 deletion has revealed the gene’s role in neurogenesis (see, e.g., SRF related news story), cortical development (see, e.g., SRF related news story), and in biochemical pathways related to depression (see SRF related news story). In addition, it has pointed to the kinase GSK3, downstream from DISC1, as a candidate therapeutic target for depression and schizophrenia.

…or a whole flock?
The advent of SNP chips opened a window on genetic variation that was hidden to cytogenetics. Using the raw signal intensity data from the chips, researchers could detect submicroscopic insertions and deletions. Genomewide analysis of the CNVs identified this way, or with dedicated CNV chips, in schizophrenia patients led to some key insights. First, several studies consistently found a higher load of copy number variation in individuals with schizophrenia compared to unaffected individuals (see SRF related news story on Walsh et al., 2008). The excess was seen not only in familial cases, but also in de novo CNVs in sporadic disease (see SRF related news story). The increase was small, but appeared specific to schizophrenia compared to bipolar disorder. In total, the data support the idea that rare mutations, either inherited or newly arisen, have a role in the etiology of schizophrenia.

Second, while CNVs are in aggregate more common in people with schizophrenia, individually they are rare and occur all over the genome, consistent with the apparent genetic heterogeneity of the disease. Some larger deletions appear more frequently, and two studies looking at genomewide association of CNVs with schizophrenia came up with recurrent deletions in four regions that were statistically associated with the disease: 22q11.2, (the VCFS deletion region), 1q21.1 (previously linked to schizophrenia), 15q13.3, and 15q11.2 (see SRF related news story).

Finally, genomewide analysis of CNVs suggests that some rare mutations confer a high risk for schizophrenia. Compared to common variants, which carry odds ratios between 1.08 and 1.5, the effect sizes of these recurrent CNVs range from 5 to 20.

Jonathan Sebat, University of California, San Diego, sees these insights as fundamental lessons, but maybe not so surprising. “In hindsight, when we look back on it, we might say we’ve rediscovered something we already knew. When you introduce a severe mutation in a gene involved in brain development, you produce a severe cognitive phenotype. Once you have technologies that allow you to find these severe mutations, you have really impressive power to learn something about the biology of this disorder.”

Chasing down biology might mean going back to patients who have rare deletions to look for more defined phenotypes or endophenotypes (for example, see SRF related news story on the 1q21.1 deletion and head circumference and SRF related news story). Or, researchers might create animal models, like the mouse models of VCFS (see SRF related news story) or DISC1 knockdown (Kim et al., 2009, and see SRF related news story).

“This is something that you can’t do with a common risk allele that has an odds ratio of 1.1 and is present on 60 percent of chromosomes, Sebat said. “I’m not sure that it makes sense to study the biology of that genetic variant in patients. You might as well go around the lab and collect samples, because it’s the most common polymorphism in the population, and its effect on disease risk in an individual is small.” On the other hand, CNV discovery leads to genes and to plausible testable biological hypotheses, Sebat said. “That’s what makes [CNVs] such an excellent approach.”

The best example of a CNV hit in schizophrenia so far is the neurexin gene. Both seminal studies on CNVs in schizophrenia identified single cases of schizophrenia with deletions involving the NRXN1 gene (Kirov et al., 2008 and Walsh et al., 2008, and see SRF related news story). Later, the large SGENE Consortium study found a statistically significant association with deletions in the coding region of the NRXN1 gene and schizophrenia (see SRF related news story).

“I think the field would regard this as still a preliminary finding, but we’ve replicated it and others have replicated it, too, so it will not be preliminary much longer,” said Sebat. “This is a site where you have deletions of a single gene, and they have a very predictable effect on the function of that gene. This gets you into biology very quickly, because the function of this gene has been studied for quite some time now.”

Porteous is looking for that kind of biological follow-up to the other CNV findings. “I think that the onus now is on the CNV practitioners to take some of their findings and seek additional supportive evidence, either to demonstrate that if you do, indeed, increase or decrease the level of expression of one of these genes in a model system, that it has a biological effect consistent with it being causally related to schizophrenia.” he said. “But it may need people other than those who are doing the discovery studies just now, because very often the labs that do the handle-turning, large-scale GWAS and CNV work are not the ones who are best suited to doing this next exercise in biology,” he added.

The neurexin example is the rarest of the rare, where deletions affect a single gene. Most deletions and insertions are not as informative because they span multiple genes. In the case of the 22q11.2 deletion syndrome, no fewer than 27 genes are involved. Although several genes in this region have some positive single-candidate results (see SchizophreniaGene Chromosome 22 overview), and the COMT gene has a positive meta-analysis at the time of this writing, genomewide association studies of the region found no common variants that affect disease risk in any of those genes (International Schizophrenia Consortium, Purcell et al., 2009). Despite a large amount of work aimed at dissecting the biological functions of those genes, and the nomination of multiple candidate genes, the path from genes to schizophrenia remains unclear (see SRF related news story). Recent work only adds to the complexity of the problem, by suggesting that CNVs may affect the expression of genes at a distance from the affected regions (Henrichsen et al., 2009).

Overlapping domains
Another fundamental insight that has come from CNV research is the shared susceptibility for psychiatric diseases. For example, the studies have complemented recent epidemiological findings of a shared inheritance between schizophrenia and bipolar disorder (see SRF related news story) and helped to provide concrete evidence that genetic risk can span several diseases. Neurexin deletions were originally tied to autism, and the family in which DISC1 was identified has a high incidence of both schizophrenia and unipolar depression. Other common effects of some of the “schizophrenia” CNVs include mental retardation, attention deficit-hyperactivity disorder (ADHD), and epilepsy.

That leads some researchers to question whether some of the common deletions, such as 1q21.1 or 22q11, are truly risk factors for schizophrenia. They argue that the defects could cause an endophenotype common to several diseases, or even a pervasive brain developmental disorder that manifests as any one of a number of conditions depending on environmental or other genetic factors (for more on this topic, see SRF related news story, SRF news story, SRF news story, and SRF news story with related interview with author Evan Eichler, University of Washington, Seattle).

“There are a bunch of these deletion syndromes like VCFS, and it looks like overall maybe as many as 3 to 5 percent of people who carry the diagnosis 'schizophrenia' have one of these diagnosable, definable chromosomal syndromes,” said Daniel Weinberger, National Institute of Mental Health, Bethesda, Maryland. “Are these cases schizophrenia, or are these cases with mild mental deficiency as the fundamental effect of these chromosomal abnormalities, which have accessory symptomatology that we can’t differentiate from schizophrenia?"

As Kenneth Kendler, Virginia Commonwealth University, Richmond, put it, “The least exciting interpretation of the CNVs is that you have broad syndromal cases where something quite large is disrupted in the brain, giving an increased risk of schizophrenia. If you reach your hand into a computer, and grab some wires and yank them out, the thing doesn’t work right, but that’s not very informative. Are deletions that take out 30 or 50 genes at a time biologically significant, or are they just like reaching in and yanking out the wires? I don’t think that’s been decided yet.”

Getting the whole picture
What remains to be seen is how much of the risk of schizophrenia in the population is tied up in rare, or even unique, structural variants. The CNVs discovered to date account for just a few percent of schizophrenia cases, but David St. Clair, now at the University of Aberdeen, Scotland, estimates that that number may increase to 10-20 percent, as more novel loci are discovered (St. Clair, 2008). By some estimates, at least half of the larger CNVs (50-100 kb) in the genome cannot be detected by the SNP technology currently used. And as yet, there are no data on other types of rare variants, such as small insertions and deletions of fewer than 1,000 bases, which are thought to be 10 times more common than CNVs. This situation directly contrasts with that involving common variants, where St. Clair writes that researchers have probably seen what there is to be seen.

A deeper understanding of genetic risk will require a full cataloging of disease-causing alleles, said Markus Nöthen, Bonn University, Germany. “We now have a genomewide picture of common variants and, through the same chip-based technology, have the first glimpse of rare variants that confer higher penetrance. But that is only part of the picture,” he said. “From a genetic point of view, what’s really important will be to see the whole allelic spectrum.”

That spectrum includes yet-to-be-discovered CNVs, but also smaller structural changes, right down to rare SNPs and point mutations. There is only one way to get that big picture, and that is large-scale sequencing of individual genomes, an effort some researchers are calling for (see SRF related news story), and some are already starting. Is the field on the verge of its own genomic revolution? For more on that question, stay tuned for Part 4 of the SRF genetics series.—Pat McCaffrey.

See Part 1, Linkage; Part 2, GWAS, Part 4, Bigger Genetics, Part 5, From Genes to Biology…and Therapies. Read a PDF of the entire series.

Comments on Related News


Related News: Chromosome 22 Link to Schizophrenia Strengthened

Comment by:  Anthony Grace, SRF Advisor (Disclosure)
Submitted 5 November 2005
Posted 5 November 2005

The fact that the PRODH alteration studied in Gogos et al. leads to alterations in glutamate release, and this corresponds to deficits in associative learning and response to psychotomimetics, provides a nice parallel to the human condition. The Reiss paper examines humans with the 22q11.2 deletion, and shows that the COMT low-activity allele of this deletion syndrome correlates with cognitive decline, PFC volume, and development of psychotic symptoms. This is a nice addition to the Weinberger and Bilder papers about how COMT can lead to psychosis vulnerability.

View all comments by Anthony Grace

Related News: Chromosome 22 Link to Schizophrenia Strengthened

Comment by:  Caterina Merendino
Submitted 5 November 2005
Posted 5 November 2005
  I recommend the Primary Papers

Related News: Chromosome 22 Link to Schizophrenia Strengthened

Comment by:  Leboyer Marion
Submitted 6 November 2005
Posted 6 November 2005
  I recommend the Primary Papers

Related News: Chromosome 22 Link to Schizophrenia Strengthened

Comment by:  Anne Bassett
Submitted 7 November 2005
Posted 7 November 2005
  I recommend the Primary Papers

I echo Jeff Lieberman's comment regarding previous reports of a weak association between the Val COMT functional allele and schizophrenia. Notably, the most recent meta-analysis (Munafo et al., 2005) shows no significant association. Even in 22q11.2 deletion syndrome (22qDS), our group (unpublished) and Murphy et al. (1999) have reported that there is no association between COMT genotype and schizophrenia, and Bearden et al. reported that Val-hemizygous patients performed significantly worse than Met-hemizygous patients on executive cognition ( 2004) and childhood behavioral problems (2005). Though important as an initial prospective study, there is a risk in the Gothelf et al. small sample size and multiple testing for type 1 errors. Certainly, there is little evidence, even in 22qDS, for COMT (or PRODH) as “key” risk factors for schizophrenia. There may be some evidence for small effects on cognitive or other measures. Regardless, there is not “extreme deficiency” in COMT activity in the many individuals with Met-hemizygosity in 22qDS, or Met-Met homozygosity in the general population.

Regarding the news item, there are a few widely held misconceptions about 22qDS. Our recent article (Bassett et al., 2005) shows that, accounting for ascertainment bias, the rate of schizophrenia was 23 percent, and congenital heart defects was 26 percent. Of the other 41 common lifetime features of 22qDS (found in 5 percent or more patients), neuromuscular palatal anomalies were common but overt cleft palate was so rare it did not meet inclusion criteria; intellectual disabilities ranged from severe mental retardation (rare) to average intellect (rare) with most patients falling in the borderline range of intellect; and on average, patients had nine of 43 common features. We propose clinical practice guidelines for adults with 22qDS which may be directly applicable to the 1-2 percent of patients with a 22qDS form of schizophrenia.

References:
Bassett AS, Chow EWC, Husted J, Weksberg R, Caluseriu O, Webb GD, Gatzoulis MA. Clinical features of 78 adults with 22q11 Deletion Syndrome. Am J Med Genet A. 2005 Nov 1;138(4):307-13. Abstract

Bearden CE, Jawad AF, Lynch DR, Sokol S, Kanes SJ, McDonald-McGinn DM, Saitta SC, Harris SE, Moss E, Wang PP, Zackai E, Emanuel BS, Simon TJ. Effects of a functional COMT polymorphism on prefrontal cognitive function in patients with 22q11.2 deletion syndrome. Am J Psychiatry . 2004 Sep;161(9):1700-2. Abstract

Bearden CE, Jawad AF, Lynch DR, Monterossso JR, Sokol S, McDonald-McGinn DM, Saitta SC, Harris SE, Moss E, Wang PP, Zackai E, Emanuel BS, Simon TJ. Effects of COMT genotype on behavioral symptomatology in the 22q11.2 Deletion Syndrome. Neuropsychol Dev Cogn C Child Neuropsychol. 2005 Feb;11(1):109-17. Abstract

Munafo MR, Bowes L, Clark TG, Flint J. Lack of association of the COMT (Val158/108 Met) gene and schizophrenia: a meta-analysis of case-control studies. Mol Psychiatry. 2005 Aug;10(8):765-70. Abstract

Murphy KC, Jones LA, Owen MJ. High rates of schizophrenia in adults with velo-cardio-facial syndrome. Arch Gen Psychiatry. 1999 Oct 1;56(10):940-5. Abstract

View all comments by Anne Bassett

Related News: New Human Genome Map Shows Extensive Copy Number Variation

Comment by:  Jonathan Sebat
Submitted 27 November 2006
Posted 27 November 2006

This study is the first to systematically map large-scale copy number variation (CNV) across a large sample representing different populations. The investigators have significantly enhanced our knowledge of genomic diversity by identifying approximately 1,000 CNVs that had not been previously reported in the literature, thereby almost doubling the catalogue of published structural variants in healthy individuals. This data set will serve as the framework for a genomic resource on structural variation. It will continue to be refined through continued efforts of many groups and may soon be a very comprehensive map. It is currently just the tip of the iceberg.

View all comments by Jonathan Sebat

Related News: Autism Genes: A Handful, or More?

Comment by:  Daniel Weinberger, SRF Advisor
Submitted 19 March 2007
Posted 19 March 2007

Sense and Nonsense: General Lessons from Genetic Studies of Autism
The capability to characterize genetic variation across the entire genome in one fell swoop has generated considerable enthusiasm and expectation that the important genes for mental illness will “finally” be found. Whole genome association (WGA) is being touted as the path to genetic success in psychiatry. Is this sensible? Before considering the likely successes and limitations of this new capability, it is worth reminding ourselves of how we got here.

With respect to schizophrenia, over 50 years of studies of twin samples and of infants adopted away at birth have demonstrated that the lion’s share of risk for schizophrenia is determined by genes, to the tune of over 70 percent of the variance in liability (“heritability”). Family segregation studies have shown that the pattern of relative risk across relationships is most consistent with at minimum oligogenic inheritance, and more likely polygenic inheritance (Gottesman, I. I., Schizophrenia Genesis: The Origin of Madness, New York: W.H. Freeman.1991). After over a decade of linkage studies, it is clear that across diverse family samples, schizophrenia is not related to a common genetic locus, and no locus accounts for more than a fraction of risk for illness. Because we know that schizophrenia is highly heritable, the failure of linkage to reveal a chromosomal locus providing a highly significant LOD score in most samples is not because there are no genetic variations accounting for the heritability, but because, among other reasons, there is just too much locus heterogeneity across samples.

If we accept that schizophrenia is polygenic and genetically heterogeneous, meaning that in any sample under study, some cases will be ill because they have risk genes W, X, Y, and Z, while other cases will be ill because they have risk genes C, D, E, and F, then any common linkage signals will be diluted by this genetic heterogeneity if these genes are spread throughout the genome. In light of this situation, why, then, have some recent linkage studies of schizophrenia revealed significant and replicable linkage regions? Notwithstanding improvement in ascertainment methods and the informativeness of DNA marker sets, it is likely that linkage has worked in some regions of the genome because some of the genetic heterogeneity is concentrated in these areas, meaning that heterogeneity across families does not necessarily dilute the linkage signal at these loci. For example, in the 8p linkage peak, there are at least five genes that have been found to show association with schizophrenia in various samples: NRG1, PCM1, PPP3CC, DRP2, and FZD3, so if 10 percent of the families have risk alleles in NRG1 that contribute to their risk profile, and even if 10 percent have no NRG1 risk alleles but PCM1 alleles, and the same for PPP3CC and so on, this genetic heterogeneity will not dilute the linkage signal and the 8p locus containing these five genes will be positive in these families. Of course, in a subsequent association study, samples will be positive or negative for any one of these individual genes depending on which alleles happen to be enriched in that sample. This is how heterogeneity affects the prospects for positive linkage and association. Many observers of psychiatric genetics who argue against the validity of linkage and association in psychiatry like to talk about multifactorial medical illnesses such as heart disease and schizophrenia being genetically heterogeneous, but they do not like the walk when it comes to acknowledging the implications for finding association, positive or negative.

Heterogeneity has obvious implications for studies that attempt to survey variation in the entire genome and compare allele frequencies across ill and well samples. Heterogeneity in such studies dilutes the statistical effect of any single DNA polymorphism in the entire sample. Because literally hundreds of thousands of variations may be typed at one time, many of which have no prior probability of being related to the phenotype of interest, it is critical to employ some approach to statistical correction for the possibility of random positive associations. If one were to correct for 500,000 tests, the likelihood that any SNP related to a condition like schizophrenia will survive this level of correction, at least to the extent that the illness is polygenic and heterogeneous, is very small. Based on the strength of the existing data, none of the well-supported candidate susceptibility genes for schizophrenia that have been identified to date (e.g., DTNPB1, NRG1, DISC1, etc.) would survive such correction. It has been argued that the solution to this conundrum is the collection of very large datasets. This may increase power and generate impressive p values for a few genes, but the effect size of the association does not change with sample size, only the p value. It is also important to remember that the larger the sample size, the greater the potential for heterogeneity, because the collection of very large samples often requires multiple collection centers, each with their own ascertainment quirks. Thus, this approach runs the risk of a paradoxical reduction in the strength of linkage and association (see Brzustowicz, 2007).

These considerations have implications for studies of the genetic origins of other neuropsychiatric disorders, such as depression, bipolar disorder, anxiety disorders, and autism. Two recent important papers related to autism illustrate each of these points and offer important lessons for WGA studies that will be emerging soon related to schizophrenia and other psychiatric disorders.

The paper by the Autism Genome Project Consortium (AGPC) reports the largest linkage study of families (over 1,490 families) with children having the autism spectrum syndrome and the most informative set of linkage markers yet reported. This study illustrates in dramatic detail the complications alluded to above. Many areas of the genome show evidence of linkage, i.e., locus heterogeneity, but the individual signals are statistically weak. Indeed, using strict criteria for statistical analysis, no region would have been considered positive, and the region that was closest (11p12-13) was not identified as a promising region in earlier linkage studies.

In a series of exploratory post-hoc reanalyses of the data, trying to create more theoretically homogeneous clinical samples (e.g., gender specific, narrower diagnosis), several linkage signals became slightly more positive, but also involving regions of the genome not highlighted in earlier linkage studies. Does this failure to find an impressive statistical result in such an impressively large sample mean that this study is negative? Not if we expect autism to be genetically complex in the ways enumerated above. The results are exactly what would be predicted. Indeed, similar results have been reported before (Risch et al., 1999). The AGPC study also discovered regions where evidence of genomic structural changes, so-called sequence copy number variations (CNVs), might be associated with clinical diagnosis. Their data suggest that as many as 253 CNVs were discovered in 196 cases. The CNVs were found in many chromosomal regions (i.e., locus heterogeneity); involved duplications more often than deletions; varied considerably from one family to another; were spontaneous in most cases but inherited in some; and were most often found only in one individual, though recurrences occurred across ill subjects in some instances. It is very difficult to determine from these data how much of the genetic contribution to autism in this sample is explained by these copy number variations. In a few families, where multiple affected individuals had the same deletion, the data look convincing. However, it appears that CNVs were just as frequent, just as large (average 3.4 Mb) and just as likely to be duplications or deletions in the unaffected siblings of the children with autism.

The paper by Sebat and colleagues surveys the genome exclusively for evidence of structural changes related to variable copy numbers of DNA sequences and uses a putatively more sensitive method. They discovered submicroscopic deletions of 17 chromosomal regions in 14 children with autism spectrum disorder (7 percent of their ill sample). By design, all of the deletions described in this report were de novo, or spontaneous, meaning they were not found in the parents of the affected offspring and were thus not inherited. In other words, these deletions do not explain the very substantial heritability of autism, nor did they map to the regions of the genome that have shown up in linkage studies, which look specifically for loci that contribute to heritable risk (including the regions in the AGPC), nor did they highlight genes that have emerged from linkage studies as likely candidates accounting for the heritability of autism. Moreover, with one exception, all of the deletions were private, meaning they occurred in only one individual. As Sebat and colleagues point out, however, the infrequency of these copy number variations does not preclude them from pointing to more generalizable insights about genetic risk factors that operate in other cases. The genes affected by these infrequent structural variations may in other cases show common variations (e.g., SNPs) that contribute more widely to genetic liability. It is not clear how much overlap there is between the findings of these two studies, but clearly there are major differences.

The bottom line here is that genetic heterogeneity appears to be the rule in autism. While most cases are related to a complex set of inherited risk factors, some may be related to spontaneous genetic lesions, with many different lesions producing a similar clinical phenotype. None of this should surprise us, as diverse congenital encephalopathies can manifest the autism syndrome, e.g., fragile X syndrome, Rett syndrome, tuberous sclerosis. From a genetic point of view, autism is a syndrome that can be reached from many directions, along many paths. It is not likely that autism is any more of a discrete disease entity than, say, blindness or mental retardation.

So where does this leave us with respect to the goal of fully defining the genetic origins of mental disorders such as schizophrenia? The current list of promising candidate genes for schizophrenia is growing rapidly, and some already are leading to insights about potential pathophysiologic mechanisms and potential treatment targets (Straub and Weinberger, 2006). Genome variation scans will hopefully uncover many more novel genes that contribute to the risk for schizophrenia, and regardless of their outcome, these types of studies will be very important. It is likely that within the next 5 years we will have a good sense of all the common genetic variants that contribute to schizophrenia across many world samples. It is also likely that some cases will be related to structural variations (e.g., the 22q11 deletion associated with the velocardiofacial syndrome [VCFS]), both spontaneous and inherited. But, a phoenix rising from this newest chapter of investigation is not likely. Rather, as the recent autism studies illustrate, many genetic loci and many genes, again each accounting for only a relatively small percentage of ill subjects, will likely be the legacy of these studies. It is the legacy of all the work up to this point, and it is not likely to be different now that we can do many more of the same SNP assays all at one time. I doubt that genes that are discovered via WGA or related approaches will show greater effect sizes than the current top candidates, but there certainly will be more of them. Schizophrenia, like autism, is almost certainly a disorder that can be reached from many directions, along many paths. This being said, is it likely that a few genes with “highly significant” p values will be observed in a few of the multitude of WGA studies that will hit the press over the next year or two? Of course it is. Will these be the most important genes? Not necessarily. The challenge for our using these new data will be to make strategic choices about which of the various signals to pursue further and how to pursue them. The most important genes will be the ones that can be translated into meaningful information about disease mechanisms, therapeutic target identification, and clinical prediction.

View all comments by Daniel Weinberger

Related News: Autism Genes: A Handful, or More?

Comment by:  Paul Patterson
Submitted 21 March 2007
Posted 22 March 2007

Regarding the very high "heritability" of schizophrenia and autism: these values are usually based on twin studies, and there is good reason to be skeptical about these numbers.

For instance, the frequency of schizophrenia in dizygotic twins is twice as high as for siblings, suggesting a role for the fetal environment. Second, the concordance for monozygotic twins is 60 percent if they share a placenta, but only 11 percent if they have separate placentas, again highlighting the importance of the fetal environment. (Two-thirds of monozygotic twins share a placenta.) It is also relevant that roughly two-thirds of schizophrenia subjects do not have a primary or secondary relative with the disorder.

No one questions that genes play a role in the risk for schizophrenia and autism, but twins share a fetal environment as well as genes. The importance of the fetal environment is very well illustrated by the work of Brown and colleagues in their studies of the risk factor, maternal respiratory infection.

References:

Phelps J, Davis J, Schartz K. Nature, Nurture, and Twin Research Strategies. Curr. Directions in Pyschol. Sci. 1997;6:117-120.

Brown AS. Prenatal infection as a risk factor for schizophrenia. Schizophr Bull. 2006 Apr;32(2):200-2. Epub 2006 Feb 9. Abstract

Brown AS, Susser ES. In utero infection and adult schizophrenia. Ment Retard Dev Disabil Res Rev. 2002;8(1):51-7. Review.

Ryan B, Vandenbergh J. Intrauterine position effects. Neuroscience and Biobehavioral Reviews. 2002;26:665–678. Abstract

View all comments by Paul Patterson

Related News: Autism Genes: A Handful, or More?

Comment by:  Ben Pickard
Submitted 24 March 2007
Posted 24 March 2007

The Curious Incident of the Gap in the Chromosome
Our bodies are accustomed to a double dose of genes. The cellular ecosystem has been evolutionarily fine-tuned to this baseline of gene expression. Even the exceptions to the rule such as the sex-specific imbalance of X/Y chromosomes or the set of imprinted genes serve to highlight the compensatory mechanisms that have allowed the cell to adapt. Therefore, it is not surprising that chromosomal dosage changes are associated with disease states.

An ever-increasing appreciation of the link between disease and gene copy number has followed closely behind advances in techniques that have enabled the measurement of copy number variation at ever-greater resolution and sensitivity. Starting with Giemsa-stained chromosomes in classical cytogenetics, which identified visible aneuploidies such as trisomy 21, the field has progressed through fluorescence in situ hybridization (FISH) studies which pinpointed finer abnormalities, including those discovered through comparative genomic hybridization and sub-telomeric analysis, to today’s chip-based approaches, which can survey the whole genome at once. (In fact, as an aside, the sensitivity of the current state-of-the-art techniques is only likely to be truly improved upon with the advent of whole-genome sequencing—realistically, that is not likely for a decade or so.)

Despite this progress, the one-off nature and scarcity of many chromosome abnormalities have often led to their dismissal as genetic quirks and not relevant to disease biology at the population level. Perhaps the tide is now turning in their favor as recent studies of sub-microscopic gene copy number changes have yielded intriguing and provocative discoveries. The two papers summarized on this site asked whether a proportion of autism spectrum disorders are caused by CNVs. The same question could, and doubtless will, be asked of schizophrenia, bipolar disorder, and other psychiatric conditions and so is worthy of discussion in this forum. The answer for autism seems to be a resounding “yes,” and this is likely to precipitate a sea change in autism research, both at the genetic and biological levels. Sebat et al. (Science, 15 March, 2007) and The Autism Genome Project Consortium (“AGPC,” Nature Genetics, 18 February, 2007) used slightly different variations on the chip theme in their studies: the former had the advantage of a more discrete output for copy number compared to the continuous distribution from the latter approach. This had consequences for the setting of statistical detection thresholds, but both groups were quite thorough in the confirmation of many of their findings using secondary detection approaches.

Understanding the Consequences of Experimental Design: Choice of Samples and Assessment
The samples chosen for analysis by both research groups focused on nominally family-based collections rather than sporadic cases. Thus, the mutations represented are highly likely to be of higher penetrance and relatively rare. In my opinion, the high level of locus heterogeneity that accompanies such a sample set makes the multiple-family linkage approach unlikely to yield practical dividends—indeed, the linkage component from the AGPC group is the least impressive aspect of their paper. The main linkage peak at 11p12-p13 was not a replication of the typical autism linkage findings (e.g., chromosome 7q, etc.; for review see Klauck, 2006). Additionally, above-threshold LOD scores were not significantly improved when diagnostic boundaries were changed or CNV carriers removed from the data. In fact, one of the most impressive features of the Sebat paper was the enlightened subdivision of the samples based not on phenotype, but rather by the nature of the inheritance patterns of autistic spectrum disorders within the families (the same may be true for the AGPC data, but the information is not explicitly categorized). This stratification into “simplex” (single case within the family) and “multiplex” (more than one affected individual) must be telling us something about the genetic architecture of complex genetic disorders. The results indicate that de novo CNVs were four times more common in the simplex families than multiplex. Let’s examine a hypothetical explanation for this finding. First, the simplex families may not be, or rather may not go on to be, true “families” in the genetic sense—their mutations are of the lower penetrance, “susceptibility altering” class. Such CNV mutations would not produce the densely affected families that are so attractive to gene mappers and so will never be collected and categorized as “multiplex.” The fact that three CNV regions (2q37.3, 3p14.2, and 20p13) are independently present twice in the Sebat simplex group adds weight to these CNVs being “common” risk variants—perhaps they are ripe candidates for a case-control association study in a larger simplex/sporadic cohort? The type of CNVs present in the multiplex families are, by definition, of sufficient penetrance for the multiplex classification to become possible: this class of mutations will probably be rarer. One supportive observation for the distinction between the two CNV types rests on the fact that there is no overlap between identified multiplex and simplex CNV regions—will that remain the case as further studies are carried out? Another, from the AGPC paper, is that many of their familial CNVs lie over previously identified linkage hotspots or known balanced chromosomal rearrangements (breakpoints, see below).

However, two mysteries remain: the predominance of CNV deletions in the Sebat paper compared to the stated overrepresentation of duplications in the AGPC paper. Whether this is a technical or family sample choice issue remains to be elucidated. Secondly, and perhaps more vague a problem, is the seldom addressed nature of the mutations identified in neuropsychiatric disorders. The archetypal mutations we learn about in undergraduate lectures, primarily in the context of neoplasms, include gain-of-function (oncogenes), loss-of-function (tumor suppressors), dominant negative and so on. Chromosome abnormalities in general, and CNVs in particular, seem to suggest that autism spectrum disorder (ASD), schizophrenia, and bipolar disorder are diseases in which gene dosage changes are the only pathological mechanism. Is this a real biological phenomenon or merely a methodological ascertainment bias? If the latter, how might we better adapt our gene hunting strategies to target other forms of mutation?

A Gene in the Hand Is Worth 50 Under a Linkage Peak
In the warm afterglow of an experimental tour-de-force, the biological ramifications can sometimes be sidelined. What genes have these CNVs affected and what does this tell us about the biology of autism spectrum disorder, we can ask, not forgetting that this work should be considered in the context of the history of other genetic and biological studies on ASD.

The first, and perhaps most impressive, finding is that of a CNV covering the Neurexin 1 (NRXN1) gene. The protein encoded by this gene interacts with a family of receptors called Neuroligins. Interestingly, Neuroligin 3 (NLGN3) and Neuroligin 4 (NLGN4) have been linked to ASD through chromosome abnormalities and mutations detected in rare cases. Moreover, SHANK3 has recently been identified as an ASD candidate through the study of cytogenetic abnormalities and several point mutations. SHANK3 protein has also been demonstrated to bind to neuroligins. This amazing convergence is reminiscent of another recent celebrity pairing in the schizophrenia field: the discovery of DISC1 and PDE4B through independent chromosome abnormalities followed by the discovery that their proteins functionally interact. The identification of these four ASD candidate genes is likely to stimulate much research into this nascent signaling pathway, particularly in the context of its supposed role in synaptogenesis.

Many of the CNVs affect gene clusters, and only by analyzing multiple overlapping deletions or systematically examining the gene candidates individually will the causative ASD genes be identified. This seems to be the case for the genes ZFP42 and PACRG, which have been found both in large CNVs with multiple genes affected and singly in smaller CNVs. Several additional CNVs were identified which were small enough, or within large enough genes (large size seems to be a anecdotally reported feature of genes identified through a variety of cytogenetic approaches) to implicate just that gene. These include SLC4A10, FLJ16237, A2BP1, NFIA, GAB2, PCDH7, PCDH9, CDH8, C18orf58, FHOD3, C2orf10, MAN2A1, CSMD1, and TRPM3 as a conservative selection. Two aspects of biology immediately spring to mind when viewing these genes. Firstly, the three members of the cadherin family identified fall into the same biological role as the neuroligins, namely cell adhesion. A related gene, FAT, has also been implicated in familial bipolar disorder. Secondly, the identification of MAN2A1 encoding a component enzyme in the pathway which post-translationally modifies proteins through glycosylation adds another gene from this process to a list including ALG9/DIBD1 and MGAT5 , both of which have been implicated in psychiatric illness. Together with the list of genes identified through CNV analysis, one can add USP6, NBEA, ST7, AUTS2, SSBP1, GRPR, and SHANK3, discovered in previous studies of autism spectrum disorder chromosome abnormalities. These candidates (and those identified in the psychoses) provide a wealth of resources for future functional and genetic studies. However, on the journey to a more rigorous biological definition of ASD, it may be a mistake to attempt to squeeze the functions of these genes into one unifying but unhelpfully vague cellular grouping, e.g., “signal transduction” or “metabolism.” Rather, biological investigations might benefit from trying to place these disparate genes in the context of their roles in the functioning of the brain regions or subsystems in which they are expressed. A hard task undoubtedly, but an endeavor that is likely to provide us with a more holistic understanding of the conditions.

View all comments by Ben Pickard

Related News: DISC1: A Maestro of Adult Hippocampal Neurogenesis?

Comment by:  Barbara K. Lipska
Submitted 9 September 2007
Posted 9 September 2007

Several recent studies on disruptions of the DISC1 gene in mice illustrate the great potential of genetic approaches to studying functions of putative schizophrenia susceptibility genes but also signal the complexity of the problem. An initial rationale for studying the effects of mutations in DISC1 came from the discovery of the chromosomal translocation, resulting in a breakpoint in the DISC1 gene that co-segregated with major mental illness in a Scottish family (reviewed by Porteous et al., 2006). These clinical findings were followed by a number of association studies, which reported that numerous SNPs across the gene were associated with schizophrenia and mood disorders and a variety of intermediate phenotypes, suggesting that other problems in the DISC1 gene may exist in other subjects/populations.

Recent animal models designed to mimic partial loss of DISC1 function suggested that DISC1 is necessary to support development of the cerebral cortex as its loss resulted in impaired neurite outgrowth and the spectrum of behavioral abnormalities characteristic of major mental disorders ( Kamiya et al., 2005; Koike et al., 2006; Clapcote et al., 2007; Hikida et al. 2007). Unexpectedly, however, the paper by Duan et al., 2007, is showing that DISC1 may also function as a brake and master regulator of neuronal development, and that its partial loss could lead to the opposite effects than previously described, i.e., dendritic overgrowth and accelerated synapse formation and faster maturation of newly generated neurons. In contrast to previous studies, they have used the DISC1 knockdown model achieved by RNA interference in a subpopulation of single cells of the dentate gyrus. Other emerging studies continue to reveal the highly complex nature of the DISC1 gene with multiple isoforms exhibiting different functions, perhaps depending on localization, timing, and interactions with a multitude of other genes’ products, some of which confer susceptibility to mental illness independent of DISC1. Similar molecular complexity has also emerged in other susceptibility genes for schizophrenia: GRM3 (Sartorius et al., 2006), NRG1 (Tan et al., 2007), and COMT (Tunbridge et al., 2007). With the growing knowledge about transcript complexity, it becomes increasingly clear that subtle disturbances of isoform(s) of susceptibility gene products and disruptions of intricate interactions between the susceptibility genes may account for the etiology of neuropsychiatric disorders. Research in animals will have a critical role in disentangling this web of interwoven genetic pathways.

View all comments by Barbara K. Lipska

Related News: DISC1: A Maestro of Adult Hippocampal Neurogenesis?

Comment by:  Akira Sawa, SRF Advisor
Submitted 13 September 2007
Posted 13 September 2007

I am very glad that our colleagues at Johns Hopkins University have published a very intriguing paper in Cell, showing a novel role for DISC1 in adult hippocampus. This is very consistent with previous publications (Miyoshi et al., 2003; Kamiya et al., 2005; and others; reviewed by Ishizuka et al., 2006), and adds a new insight into a key role for DISC1 during neurodevelopment. In short, DISC1 is a very important regulator in various phases of neurodevelopment, which is reinforced in this study. Specifically, DISC1 is crucial for regulating neuronal migration and dendritic development—for acceleration in the developing cerebral cortex, and for braking in the adult hippocampus.

There is precedence for signaling molecules playing the same role in different contexts, with the resulting molecular activity going in different directions. For example, FOXO3 (a member of the Forkhead transcription factor family) plays a role in cell survival/death in a bidirectional manner (Brunet et al., 2004). FOXO3 endows cells with resistance to oxidative stress in some contexts, and induces apoptosis in other contexts. SIRT1 (known as a key modulator of organismal lifespan) deacetylates FOXO3 and tips FOXO3-dependent responses away from apoptosis and toward stress resistance. In analogy to FOXO3, context-dependent post-translational modifications, such as phosphorylation, may be an underlying mechanism for DISC1 to function in a bidirectional manner. Indeed, a collaborative team at Johns Hopkins, including Pletnikov's lab, Song's lab, and ours, has started exploring, in both cell and animal models, the molecular switch that makes DISC1's effects bidirectional.

References:

Brunet A, Sweeney LB, Sturgill JF, Chua KF, Greer PL, Lin Y, Tran H, Ross SE, Mostoslavsky R, Cohen HY, Hu LS, Cheng HL, Jedrychowski MP, Gygi SP, Sinclair DA, Alt FW, Greenberg ME. Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. Science. 2004 Mar 26;303(5666):2011-5. Abstract

View all comments by Akira Sawa

Related News: DISC1: A Maestro of Adult Hippocampal Neurogenesis?

Comment by:  Sharon Eastwood
Submitted 14 September 2007
Posted 14 September 2007

Recent findings, including the interactome study by Camargo et al., 2007, and this beautiful study by Duan and colleagues, implicate DISC1 (a leading candidate schizophrenia susceptibility gene) in synaptic function, consistent with prevailing ideas of the disorder as one of the synapse and connectivity (see Stephan et al., 2006). As we learn more about DISC1 and its protein partners, evidence demonstrating the importance of microtubules in the regulation of several neuronal processes (see Eastwood et al., 2006, for review) suggests that DISC1’s interactions with microtubule associated proteins (MAPs) may underpin its pathogenic influence.

DISC1 has been shown to bind to several MAPs (e.g., MAP1A, MIPT3) and other proteins important in regulating microtubule function (see Kamiya et al., 2005; Porteous et al., 2006). As a key component of the cell cytoskeleton, microtubules are involved in many cellular processes including mitosis, motility, vesicle transport, and morphology, and their dynamics are regulated by MAPs, which modulate microtubule polymerization, stability, and arrangement. Decreased microtubule stability in mutant mice for one MAP, stable tubule only polypeptide (STOP; MAP6), results in behavioral changes relevant to schizophrenia and altered synaptic protein expression (Andrieux et al., 2002; Eastwood et al., 2006), indicating the importance of microtubules in synaptic function and suggesting that they may be a molecular mechanism contributing to the pathogenesis of schizophrenia. Likewise, DISC1 mutant mice exhibit behavioral alterations characteristic of psychiatric disorders (e.g., Clapcote et al., 2007), and altered microtubule dynamics are thought to underlie perturbations in cerebral cortex development and neurite outgrowth caused by decreased DISC1 expression or that of a schizophrenia-associated DISC1 mutation (Kamiya et al., 2005).

Our interpretation of the possible functions of DISC1 has been complicated by the unexpected findings of Duan and colleagues that DISC1 downregulation during adult hippocampal neurogenesis leads to overextended neuronal migration and accelerated dendritic outgrowth and synaptic formation. In terms of neuronal positioning, they suggest that their results indicate that DISC1 may relay positional signals to the intracellular machinery, rather than directly mediate migration. In this way, decreased DISC1 expression may result in the mispositioning of newly formed neurons rather than a simple decrease or increase in their migratory distance. Of note, MAP1B, a neuron-specific MAP important in regulating microtubule stability and the crosstalk between microtubules and actin, is required for neurons to correctly respond to netrin 1 signaling during neuronal migration and axonal guidance (Del Rio et al., 2004), and DISC1 may function similarly during migration. Reconciling differences between the effect of decreased DISC1 expression upon neurite outgrowth during neurodevelopment and adult neurogenesis is more difficult, but could be due to differences in the complement of MAPs expressed by different neuronal populations at different times. Regardless, the results of Duan and colleagues have provided additional evidence implicating DISC1 in neuronal functions thought to go awry in schizophrenia. Further characterization of DISC1’s interactions with microtubules and MAPs may lead to a better understanding of the role of DISC1 in the pathogenesis of psychiatric disorders.

References:

Andrieux A, Salin PA, Vernet M, Kujala P, Baratier J, Gory Faure S, Bosc C, Pointu H, Proietto D, Schweitzer A, Denarier E, Klumperman J, Job D (2002). The suppression of brain cold-stable microtubules in mice induces synaptic deficits associated with neuroleptic-sensitive behavioural disorders. Genes Dev. 16: 2350-2364. Abstract

Camargo LM, Collura V, Rain JC, Mizuguchi K, Hermjakob H, Kerrien S, Bonnert TP, Whiting PJ, Brandon NJ (2007). Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia. Mol. Psychiatry 12: 74-86. Abstract

Clapcote SJ, Lipina TV, Millar JK, Mackie S, Christie S, Ogawa F, Lerch JP, Trimble K, Uchiyama M, Sakuraba Y, Kaneda H, Shiroishi T, Houslay MD, Henkelman RM, Sled JG, Gondo Y, Porteous DJ, Roder JC (2007). Behavioral phenotypes of Disc1 missense mutations in mice. Neuron 54: 387-402. Abstract

Del Rio, J.A., Gonzalez-Billault, C., Urena, J.M., Jimenez, E.M., Barallobre, M.J., Pascual, M., Pujadas, L., Simo, S., La Torre, A., Wandosell, F., Avila, J. and Soriano, E. (2004). MAP1B is required for netrin 1 signaling in neuronal migration and axonal guidance. Cur. Biol. 14: 840-850. Abstract

Eastwood SL, Lyon L, George L, Andrieux A, Job D, Harrison PJ (2006). Altered expression of synaptic protein mRNAs in STOP (MAP6) mutant mice. J. Psychopharm. 21: 635-644. Abstract

Kamiya A, Kubo K, Tomoda T, Takaki M, Youn R, Ozeki Y, Sawamura N, Park U, Kudo C, Okawa M, Ross CA, Hatten ME, Nakajima K, Sawa A. A schizophrenia-associated mutation of DISC1 perturbs cerebral cortex development. Nat Cell Biol. 2005 Dec;7(12):1167-78. Epub 2005 Nov 20. Erratum in: Nat Cell Biol. 2006 Jan;8(1):100. Abstract

Porteous DJ, Thomson P, Brandon NJ, Millar JK (2006). The genetics and biology of DISC1-an emerging role in psychosis and cognition. Biol. Psychiatry 60: 123-131. Abstract

Stephan KE, Baldeweg T, Friston KJ (2006). Synaptic plasticity and disconnection in schizophrenia. Biol. Psychiatry 59: 929-939. Abstract

View all comments by Sharon Eastwood

Related News: Copy Number Variations in Schizophrenia: Rare But Powerful?

Comment by:  Daniel Weinberger, SRF Advisor
Submitted 27 March 2008
Posted 27 March 2008

The paper by Walsh et al. is an important addition to the expanding literature on copy number variations in the human genome and their potential role in causing neuropsychiatric disorders. It is clear that copy number variations are important aspects of human genetic variation and that deletions and duplications in diverse genes throughout the genome are likely to affect the function of these genes and possibly the development and function of the human brain. So-called private variations, such as those described in this paper, i.e., changes in the genome found in only a single individual, as all of these variations are, are difficult to establish as pathogenic factors, because it is hard to know how much they contribute to the complex problem of human behavioral variation in a single individual. If the change is private, i.e., only in one case and not enriched in cases as a group, as are common genetic polymorphisms such as SNPs, how much they account for case status is very difficult to prove.

An assumption implicit in this paper is that these private variations may be major factors in the case status of the individuals who have them. The data of this paper suggest, however, this is actually not the case, at least for the childhood onset cases. Here’s why: mentioned in the paper is a statement that only two of the CNVs in the childhood cases are de novo, i.e., spontaneous and not inherited (and one of these is on the Y chromosome, making its functional implications obscure). If most of the CNVs are inherited, they can’t be causing illness per se as major effect players because they are coming from well parents.

Also, if you add up all CNVs in transmitted and non-transmitted chromosomes of the parents, it’s something like 31 gene-based CNVs in 154 parents (i.e., 20 percent of the parents have a gene-based deletion or duplication in the very illness-related pathways that are highlighted in the cases), which is at least as high a frequency as in the adult-onset schizophrenia sample in this study…and three times the frequency as found in the adult controls. This is not to say that such variants might not represent susceptibility genetic factors, or show variable penetrance between individuals, like other polymorphisms, and contribute to the complex genetic risk architecture, like other genetic variations that have been more consistently associated with schizophrenia. However, the CNV literature has tended to seek a more major effect connotation to the findings.

View all comments by Daniel Weinberger

Related News: Copy Number Variations in Schizophrenia: Rare But Powerful?

Comment by:  William Honer
Submitted 28 March 2008
Posted 28 March 2008
  I recommend the Primary Papers

As new technologies are applied to understanding the etiology and pathophysiology of schizophrenia, considering the clinical features of the cases studied and the implications of the findings is of value. The conclusion of the Walsh et al. paper, “these results suggest that schizophrenia can be caused by rare mutations….“ is worth considering carefully.

What evidence is needed to link an observation in the laboratory or clinic to cause? Recent recommendations for the content of papers in epidemiology (von Elm et al., 2008) remind us of the suggestions of A.V. Hill (Hill, 1965). To discern the implications of a finding, or association, for causality, Hill suggests assessment of the following:

1. Strength of the association: this is not the observed p-value, but a measure of the magnitude of the association. In the Walsh et al. study, the primary outcome measure, structural variants duplicating or deleting genes was observed in 15 percent of cases, and 5 percent of controls. But what is the association with? The diagnostic entity of schizophrenia, or some risk factor for the illness? Of interest, and noted in the Supporting Online Material, these variants were present in 7/15 (47 percent) of the cases with presumed IQ <80, but only 15/135 (11 percent) of the cases with IQ >80. Are the structural variants more strongly associated with mental retardation (within schizophrenia 47 percent vs. 11 percent) than with diagnosis (11 percent vs. 5 percent of controls, assuming normal IQ)? This is of particular interest in the context of the speculation in the paper concerning the importance of genes putatively involved with brain development in the etiology of schizophrenia.

2. Consistency of results in the literature across studies and research groups: there are now several papers examining copy number variation in schizophrenia, including a report from our group (Wilson et al., 2006). The authors of the present paper state that each variant observed was unique, and so consistency of the specific findings could be argued to be irrelevant, if the model is of novel mutations (more on models below). Undoubtedly, future meta-analyses and accumulating databases help determine if there is anything consistent in the findings, other than a higher frequency of any abnormalities in cases rather than controls.

3. Specificity of the findings to the illness in question: this was not addressed experimentally in the paper. However, the findings of more abnormalities in the putative low IQ cases, and the similarity of the findings to reports in autism and mental retardation, suggest that this criterion for supporting causality is unlikely to be met.

4. Temporality: the abnormalities should precede the illness. If DNA from terminally differentiated neurons harbors the same variants as DNA from constantly renewed populations of lymphocytes, then clearly this condition is met. While it seems highly likely that this is the case, it is worthwhile considering the possibility that DNA structure may vary between tissue types, or between cell populations. Even within human brain there is some evidence for chromosomal heterogeneity (Rehen et al., 2005).

5. Biological gradient: presence of a “dose-response” curve strengthens the likelihood of a causal relationship. This condition is not met within cases: only 1/115 appeared to have more than one variant. However, in the presumably more severe childhood onset form of schizophrenia, four individuals carried multiple variants, and the observation of a higher prevalence of variants overall. Still, the question of what the observations of CNV are associated with is relevant, since one of the inclusion/exclusion criteria for COS allowed IQ 65-80, and it is uncertain how many of these cases had some degree of intellectual deficit.

6. Plausibility: biological likelihood—quite difficult to satisfy as a criterion, in the context of the limits of knowledge concerning the mechanisms of illness of schizophrenia.

7. Coherence of the observation with known facts about the illness: the genetic basis of schizophrenia is quite well studied, and there is no dearth of theories concerning genetic architecture. However, a coherent model remains lacking. As examples, the suggestion is made that the observations concerning inherited CNVs in the COS cases are linked with a severe family history in this type of illness. This appears inconsistent with a high penetrance model for CNVs as suggested in the opening of the paper (presuming the parents in COS families are unaffected, as would seem likely). Elsewhere, CNVs are proposed by the authors to be related to de novo events, and an interaction with an environmental modifier, folate (and exposure to famine), is posited (McClellan et al., 2006). A model of the effects of CNVs, which generates falsifiable hypotheses is needed.

8. Experiment: the ability to intervene clinically to modify the effects of CNVs disrupting genes seems many years away.

9. Analogy: the novelty of the CNV findings is both intriguing, but limiting in understanding the likelihood of causal relationships.

The intersection of clinical realities and novel laboratory technologies will fuel the need for better translational research in schizophrenia for many, many more years.

References:

von Elm E, Altman DG, Egger M, Pocock SJ, Gøtzsche PC, Vandenbroucke JP. Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: guidelines for reporting observational studies. J Clin Epidemiol. 2008 Apr 1;61(4):344-349. Abstract

HILL AB. THE ENVIRONMENT AND DISEASE: ASSOCIATION OR CAUSATION? Proc R Soc Med. 1965 May 1;58():295-300. Abstract

Wilson GM, Flibotte S, Chopra V, Melnyk BL, Honer WG, Holt RA. DNA copy-number analysis in bipolar disorder and schizophrenia reveals aberrations in genes involved in glutamate signaling. Hum Mol Genet. 2006 Mar 1;15(5):743-9. Abstract

Rehen SK, Yung YC, McCreight MP, Kaushal D, Yang AH, Almeida BSV, Kingsbury MA, Cabral KMS, McConnell MJ, Anliker B, Fontanoz M, Chun J: Constitutional aneuploidy in the normal human brain. J Neurosci 2005; 25:2176-2180. Abstract

McClellan JM, ESusser E, King M-C: Maternal famine, de novo mutations, and schizophrenia. JAMA 2006; 296:582-584. Abstract

View all comments by William Honer

Related News: Copy Number Variations in Schizophrenia: Rare But Powerful?

Comment by:  Todd LenczAnil Malhotra (SRF Advisor)
Submitted 30 March 2008
Posted 30 March 2008

The new study by Walsh et al. (2008), as well as recent data from other groups working in schizophrenia, autism, and mental retardation, make a strong case for including copy number variants as an important source of risk for neurodevelopmental phenotypes. These findings raise several intriguing new questions for future research, including: the degree of causality/penetrance that can be attributed to individual CNVs; diagnostic specificity; and recency of their origins. While these questions are difficult to address in the context of private mutations, one potential source of additional information is the examination of common, recurrent CNVs, which have not yet been systematically studied as potential risk factors for schizophrenia.

Still, the association of rare CNVs with schizophrenia provides additional evidence that genetic transmission patterns may be a complex hybrid of common, low-penetrant alleles and rare, highly penetrant variants. In diseases ranging from Parkinson's to colon cancer, the literature demonstrates that rare penetrant loci are frequently embedded within an otherwise complex disease. Perhaps the most well-known example involves mutations in amyloid precursor protein and the presenilins in Alzheimer’s disease (AD). Although extremely rare, accounting for <1 percent of all cases of AD, identification of these autosomal dominant subtypes greatly enhanced understanding of pathophysiology. Similarly, a study of consanguineous families in Iran has very recently identified a rare autosomal recessive form of mental retardation (MR) caused by glutamate receptor (GRIK2) mutations, thereby opening new avenues of research (Motazacker et al., 2007). In schizophrenia, we have recently employed a novel, case-control approach to homozygosity mapping (Lencz et al., 2007), resulting in several candidate loci that may harbor highly penetrant recessive variants. Taken together, these results suggest that a diversity of methodological approaches will be needed to parse genetic heterogeneity in schizophrenia.

References:

Motazacker MM, Rost BR, Hucho T, Garshasbi M, Kahrizi K, Ullmann R, Abedini SS, Nieh SE, Amini SH, Goswami C, Tzschach A, Jensen LR, Schmitz D, Ropers HH, Najmabadi H, Kuss AW. (2007) A defect in the ionotropic glutamate receptor 6 gene (GRIK2) is associated with autosomal recessive mental retardation. Am J Hum Genet. 81(4):792-8. Abstract

Lencz T, Lambert C, DeRosse P, Burdick KE, Morgan TV, Kane JM, Kucherlapati R,Malhotra AK (2007). Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc Natl Acad Sci U S A. 104(50):19942-7. Abstract

View all comments by Todd Lencz
View all comments by Anil Malhotra

Related News: Copy Number Variations in Schizophrenia: Rare But Powerful?

Comment by:  Ben Pickard
Submitted 31 March 2008
Posted 31 March 2008

In my mind, the study of CNVs in autism (and likely soon in schizophrenia/bipolar disorder, which are a little behind) is likely to put biological meat on the bones of illness etiology and finally lay to rest the annoyingly persistent taunts that genetics hasn’t delivered on its promises for psychiatric illness.

I don’t think it’s necessary at the moment to wring our hands at any inconsistencies between the Walsh et al. and previous studies of CNV in schizophrenia (e.g., Kirov et al., 2008). There are a number of factors which I think are going to influence the frequency, type, and identity of CNVs found in any given study.

1. CNVs are going to be found at the rare/penetrant/familial end of the disease allele spectrum—in direct contrast to the common risk variants which are the targets of recent GWAS studies. In the short term, we are likely to see a large number of different CNVs identified. The nature of this spectrum, however, is that there will be more common pathological CNVs which should be replicated sooner—NRXN1, APBA2 (Kirov et al., 2008), CNTNAP2 (Friedman et al., 2008)—and may be among some of these “low hanging fruit.” For the rarer CNVs, proving a pathological role is going to be a real headache. Large studies or meta-analyses are never going to yield significant p-values for rare CNVs which, nevertheless, may be the chief causes of illness for those few individuals who carry them. Showing clear segregation with illness in families is likely to be the only means to judge their role. However, we must not expect a pure cause-and-effect role for all CNVs: even in the Scottish t(1;11) family disrupting the DISC1 gene, there are several instances of healthy carriers.

2. Sample selection is also likely to be critical. In the Kirov paper, samples were chosen to represent sporadic and family history-positive cases equally. In the Walsh paper, samples were taken either from hospital patients (the majority) or a cohort of childhood onset schizophrenia. Detailed evidence for family history on a case-by-case basis was not given but appeared far stronger in the childhood onset cases. CNVs appeared to be more prevalent, and as expected, more familial, in the latter cohort. A greater frequency was also observed in the Kirov study familial subset.

3. Inclusion criteria are likely to be important—particularly in the more sporadic cases without family history. This is because CNVs found in this group may be commoner and less penetrant—they will be more frequent in cases than in controls but not exclusively found in cases. Any strategy, such as that used in the Kirov paper, which discounts a CNV based on its presence—even singly—in the control group is likely to bias against this class.

4. Technical issues. Certainly, the coverage/sensitivity of the method of choice for the “event discovery” stage is going to influence the minimum size of CNV detectable. However, a more detailed coverage often comes with a greater false-positive rate. Technique choice may also have more general issues. In both of the papers, the primary detection method is based on hybridization of case and pooled control genomes prior to detection on a chip. Thus, a more continuously distributed output may result—and the extra round of hybridization might bias against certain sequences. More direct primary approaches such as Illumina arrays or a second-hand analysis of SNP genotyping arrays may provide a more discrete copy number output, but these, too, can suffer from interpretational issues.

The other major implication of these and other CNV studies is the observation that certain genes “ignore” traditional disease boundaries. For example, NRXN1 CNVs have now been identified in autism and schizophrenia, and CNTNAP2 translocations/CNVs have been described in autism, Gilles de la Tourette syndrome, and schizophrenia/epilepsy. This mirrors the observation of common haplotypes altering risk across the schizophrenia-bipolar divide in numerous association studies. It might be the case that these more promiscuous genes are likely to be involved in more fundamental CNS processes or developmental stages—with the precise phenotypic outcome being defined by other variants or environment. The presence of mental retardation comorbid with psychiatric diagnoses in a number of CNV studies suggests that this might be the case. I look forward to the Venn diagrams of the future which show us the shared neuropsychiatric and disease-specific genes/gene alleles. It will also be interesting to see if the large deletions/duplications involving numerous genes give rise to more severe, familial, and diagnostically more defined syndromes or, alternatively, a more diffuse phenotype. Certainly, it has not been easy to dissect out individual gene contributions to phenotype in VCFS or the minimal region in Down syndrome.

References:

Friedman JI, Vrijenhoek T, Markx S, Janssen IM, van der Vliet WA, Faas BH, Knoers NV, Cahn W, Kahn RS, Edelmann L, Davis KL, Silverman JM, Brunner HG, van Kessel AG, Wijmenga C, Ophoff RA, Veltman JA. CNTNAP2 gene dosage variation is associated with schizophrenia and epilepsy. Mol Psychiatry. 2008 Mar 1;13(3):261-6. Abstract

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Related News: Copy Number Variations in Schizophrenia: Rare But Powerful?

Comment by:  Christopher RossRussell L. Margolis
Submitted 3 April 2008
Posted 3 April 2008

We agree with the comments of Weinberger, Lencz and Malhotra, and Pickard, and the question raised by Honer about the extent to which the association may be more to mental retardation than schizophrenia. These new studies of copy number variation represent important advances, but need to be interpreted carefully.

We are now getting two different kinds of data on schizophrenia, which can be seen as two opposite poles. The first is from association studies with common variants, in which large numbers of people are required to see significance, and the strengths of the associations are quite modest. These kinds of vulnerability factors would presumably contribute a very modest increase in risk, and many taken together would cause the disease. By contrast, the “private” mutations, as identified by the Sebat study, could potentially be completely causative, but because they are present in only single individuals or very small numbers of individuals, it is difficult to be certain of causality. Furthermore, since some of them in the early-onset schizophrenia patients were present in unaffected parents, one might have to assume the contribution of a common variant vulnerability (from the other parent) as well.

If a substantial number of the private structural mutations are causal, then one might expect to have seen multiple small Mendelian families segregating a structural variant. The situation would then be reminiscent of the autosomal dominant spinocerebellar ataxis, in which mutations (currently about 30 identified loci) in multiple different genes result in similar clinical syndromes. The existence of many small Mendelian families would be less likely if either 1) structural variants that cause schizophrenia nearly always abolish fertility, or 2) some of the SVs detected by Walsh et al. are risk factors, but are usually not sufficient to cause disease. The latter seems more likely.

We think these two poles highlight the continued importance of segregation studies, as have been used for the DISC1 translocation. In order to validate these very rare “private” copy number variations, we believe that it would be important to look for sequence variations in the same genes in large numbers of schizophrenia and control subjects, and ideally to do so in family studies.

One very exciting result of the new copy number studies is the implication of whole pathways rather than just single genes. This highlights the importance of a better understanding of pathogenesis. The study of candidate pathways should help facilitate better pathogenic understanding, which should result in better biomarkers and potentially improve classification and treatment. In genetic studies, development of pathway analysis will be fruitful. Convergent evidence can come from studies of pathogenesis in cell and animal models, but this will need to be interpreted with caution, as it is possible to make a plausible story for so many different pathways (Ross et al., 2006). The genetic evidence will remain critical.

References:

Ross CA, Margolis RL, Reading SA, Pletnikov M, Coyle JT. Neurobiology of schizophrenia. Neuron. 2006 Oct 5;52(1):139-53. Abstract

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Related News: Copy Number Variations in Schizophrenia: Rare But Powerful?

Comment by:  Michael Owen, SRF AdvisorMichael O'Donovan (SRF Advisor)George Kirov
Submitted 15 April 2008
Posted 15 April 2008

The idea that a proportion of schizophrenia is associated with rare chromosomal abnormalities has been around for some time, but it has been difficult to be sure whether such events are pathogenic given that most are rare. Two instances where a pathogenic role seems likely are first, the balanced ch1:11 translocation that breaks DISC1, where pathogenesis seems likely due to co-segregation with disease in a large family, and second, deletion of chromosome 22q11, which is sufficiently common for rates of psychosis to be compared with that in the general population. This association came to light because of the recognizable physical phenotype associated with deletion of 22q11, and the field has been waiting for the availability of genome-wide detection methods that would allow the identification of other sub-microscopic chromosomal abnormalities that might be involved, but whose presence is not predicted by non-psychiatric syndromal features. This technology is now upon us in the form of various microarray-based methods, and we can expect a slew of studies addressing this hypothesis in the coming months.

Structural chromosomal abnormalities can take a variety of forms, in particular, deletions, duplication, inversions, and translocations. Generally speaking, these can disrupt gene function by, in the case of deletions, insertions and unbalanced translocations, altering the copy number of individual genes. These are sometimes called copy number variations (CNVs). Structural chromosomal abnormalities can also disrupt a gene sequence, and such disruptions include premature truncation, internal deletion, gene fusion, or disruption of regulatory or promoter elements.

It is, however, worth pointing out that structural chromosomal variation in the genome is common—it has been estimated that any two individuals on average differ in copy number by a total of around 6 Mb, and that the frequency of individual duplications or deletions can range from common through rare to unique, much in the same way as other DNA variation. Also similar to other DNA variation, many structural variants, indeed almost certainly most, may have no phenotypic effects (and this includes those that span genes), while others may be disastrous for fetal viability. Walsh and colleagues have focused upon rare structural variants, and by rare they mean events that might be specific to single cases or families. For this reason, they specifically targeted CNVs that had not previously been described in the published literature or in the Database of Genomic Variants. The reasonable assumption was made that this would enrich for CNVs that are highly penetrant for the disorder. Indeed, Walsh et al. favor the hypothesis that genetic susceptibility to schizophrenia is conferred not by relatively common disease alleles but by a large number of individually rare alleles of high penetrance, including structural variants. As we have argued elsewhere (Craddock et al., 2007), it seems entirely plausible that schizophrenia reflects a spectrum of alleles of varying effect sizes including common alleles of small effect and rare alleles of larger effect, but data from genetic epidemiology do not support the hypothesis that the majority of the disorder reflects rare alleles of large effect.

Walsh et al. found that individuals with schizophrenia were >threefold more likely than controls to harbor rare CNVs that impacted on genes, but in contrast, found no significant difference in the proportions of cases and controls carrying rare mutations that did not impact upon genes. They also found a similar excess of rare structural variants that deleted or duplicated one or more genes in an independent series of cases and controls, using a cohort with childhood onset schizophrenia (COS).

The results of the Walsh study are important, and clearly suggest a role for structural variation in the etiology of schizophrenia. There are, however, a number of caveats and issues to consider. First, it would be unwise on the basis of that study to speculate on the likely contribution of rare variants to schizophrenia as a whole. It is likely correct that, due to selection pressures, highly penetrant alleles for disorders (like schizophrenia) that impair reproductive fitness are more likely to be of low frequency than they are to be common, but this does not imply that the converse is true. That is, one cannot assume that the penetrance of low frequency alleles is more likely to be high than low. Thus, and as pointed out by Walsh et al., it is not possible to know which or how many of the unique events observed in their study are individually pathogenic. Whether individual loci contribute to pathogenesis (and their penetrances) is, as we have seen, hard to establish. Estimating penetrance by association will require accurate measurement of frequencies in case and control populations, which for rare alleles, will have to be very large. Alternatively, more biased estimates of penetrance can be estimated from the degree of co-segregation with disease in highly multiplex pedigrees, but these are themselves fairly rare in schizophrenia, and pedigrees segregating any given rare CNV obviously even more so.

As Weinberger notes, the case for high penetrance (at the level of being sufficient to cause the disorder) is also undermined by their data from COS, where the majority of variants were inherited from unaffected parents. This accords well with the observation that 22q11DS, whilst conferring a high risk of schizophrenia, is still only associated with psychosis in ~30 percent of cases. It also accords well with the relative rarity of pedigrees segregating schizophrenia in a clearly Mendelian fashion, though the association of CNVs with severe illness of early onset might be expected to reduce the probability of transmission.

Third, there are questions about the generality of the findings. Cases in the case control series were ascertained in a way that enriched for severity and chronicity. Perhaps more importantly, the CNVs were greatly overrepresented in people with low IQ. Thus, one-third of all the potentially pathogenic CNVs in the case control series were seen in the tenth of the sample with IQ less than 80. The association between structural variants and low IQ is well known, as is the association between low IQ and psychotic symptoms, and it seems plausible to assume that forms of schizophrenia accompanied by mental retardation (MR) are likely to be enriched for this type of pathogenesis. The question that arises is whether the CNVs in such cases act simply by influencing IQ, which in turn has a non-specific effect on increasing risk of schizophrenia, or whether there are specific CNVs for MR plus schizophrenia, and some which may indeed increase risk of schizophrenia independent of IQ. In the case of 22q11 deletion, risk of schizophrenia does not seem to be dependent on risk of MR, but more work is needed to establish that this applies more generally.

Another reason to caution about the generality of the effect is that Walsh et al. found that cases with onset of psychotic symptoms at age 18 or younger were particularly enriched for CNVs, being greater than fourfold more likely than controls to harbor such variants. There did remain an excess of CNVs in cases with adult onset, supporting a more general contribution, although it should be noted that even in this group with severe disorder, this excess was not statistically significant (Fisher’s exact test, p = 0.17, 2-tailed, our calculation). The issue of age of onset clearly impacts upon assessing the overall contribution CNVs may make upon psychosis, since onset before 18, while not rare, is also not typical. A particular contribution of CNVs to early onset also appears supported by the second series studied, which had COS. However, this is a particularly unusual form of schizophrenia which is already known to have high rates of chromosomal abnormalities. Future studies of more typical samples will doubtless bear upon these issues.

Even allowing for the fact that many more CNVs may be detected as resolution of the methodology improves, the above considerations suggest it is premature to conclude a substantial proportion of cases of schizophrenia can be attributed to rare, highly penetrant CNVs. Nevertheless, even if it turns out that only a small fraction of the disorder is attributable to CNVs, as seen for other rare contributors to the disorder (e.g., DISC1 translocation), such uncommon events offer enormous opportunities for advancing our knowledge of schizophrenia pathogenesis.

References:

Craddock N, O'Donovan MC, Owen MJ. Phenotypic and genetic complexity of psychosis. Invited commentary on ... Schizophrenia: a common disease caused by multiple rare alleles.Br J Psychiatry. 2007 90:200-3. Abstract

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Related News: Copy Number Variations in Schizophrenia: Rare But Powerful?

Comment by:  Ridha JooberPatricia Boksa
Submitted 2 May 2008
Posted 4 May 2008

Walsh et al. claim that rare and severe chromosomal structural variants (SVs) (i.e., not described in the literature or in the specialized databases as of November 2007) are highly penetrant events each explaining a few, if not singular, cases of schizophrenia.

However, their definition of rareness is questionable. Indeed, it is unclear why SVs that are rare (<1 percent) but previously described should be omitted from their analysis. In addition, contrary to their own definition of rareness, the authors included in the COS sample several SVs that have been previously mentioned in the literature (e.g. “115 kb deletion on chromosome 2p16.3 disrupting NRXN1”). Furthermore, some of these SVs (entire Y chromosome duplication) are certainly not rare (by the authors’ definition), nor highly penetrant with regard to psychosis (Price et al., 1967). Finally, as their definition of rareness depends on a specific date, the results of this study will change over time.

As to the assessment of severity, it can equally be concluded from table 2 and using their statistical approach that "patients with schizophrenia are significantly more likely to harbor rare structural variants (6/150) that do not disrupt any gene compared to controls(2/268) (p = 0.03)", thus contradicting their claim. In fact, had they used criteria in the literature (Lee et al., 2007; (Brewer et al., 1999) (i.e., deletion SVs are more likely than duplications to be pathogenic) and appropriate statistical contrasts, deletions are significantly (p = 0.02) less frequent in patients (5/23) than in controls (9/13) who have SVs. In addition, the assumption of high penetrance is questionable given the high level (13 percent) of non-transmitted SVs in parents of COS patients. Is the rate of psychosis proportionately high in the parents? From the data presented, we know that only 2/27 SVs in COS patients are de novo and that “some” SVs are transmitted. Adding this undetermined number of transmitted SVs to the reported non-transmitted SVs will lead to an even larger proportion of parents carrying SVs. Disclosing the inheritance status of SVs in COS patients along with information on diagnoses in parents from this “rigorously characterised cohort,” represents a major criterion for assessing the risk associated with these SVs.

Consequently, it appears that the argument of rareness is rather idiosyncratic and contains inconsistencies, and the one of severity is very open to interpretation. Most importantly, it should be emphasized that amalgamated gene effects at the population level do not allow one to conclude that any single SV actually contributes to schizophrenia in an individual. Thus it is unclear how this study of grouped events differs from the thousands of controversial and underpowered association studies of single genes.

References:

Price WH, Whatmore PB. Behaviour Disorders and Pattern of Crime among XYY males Identified at a Maximum Security Hospital. Brit Med J 1967;1:533-6.

Lee C, Iafrate AJ, Brothman AR. Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet 2007 July;39(7 Suppl):S48-S54.

Brewer C, Holloway S, Zawalnyski P, Schinzel A, FitzPatrick D. A chromosomal duplication map of malformations: regions of suspected haplo- and triplolethality--and tolerance of segmental aneuploidy--in humans. Am J Hum Genet 1999 June;64(6):1702-8.

View all comments by Ridha Joober
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Related News: More Evidence for CNVs in Schizophrenia Etiology—Jury Still Out on Practical Implications

Comment by:  Christopher RossRussell L. Margolis
Submitted 1 August 2008
Posted 1 August 2008

The two recent papers in Nature, from the Icelandic group (Stefansson et al., 2008), and the International Schizophrenia Consortium (2008) led by Pamela Sklar, represent a landmark in psychiatric genetics. For the first time two large studies have yielded highly significant consistent results using multiple population samples. Furthermore, they arrived at these results using quite different methods. The Icelandic group used transmission screening and focused on de novo events, using the Illumina platform in both a discovery population and a replication population. By contrast, the ISC study was a large population-based case-control study using the Affymetrix platform, which did not specifically search for de novo events.

Both identified the same two regions on chromosome 1 and chromosome 15, as well as replicating the previously well studied VCFS region on chromosome 22. Thus, we now have three copy number variants which are replicated and consistent across studies. This provides data on rare highly penetrant variants complementary to the family based study of DISC1 (Porteous et al., 2006), in which the chromosomal translocation clearly segregates with disease, but in only one family. In addition, they are in general congruent with three other studies (Walsh et al., 2008; Kirov et al., 2008; Xu et al., 2008) which also demonstrate a role for copy number variation in schizophrenia. These studies together should put to rest many of the arguments about the value of genetics in psychiatry, so that future studies can now begin from a firmer base.

However, these studies also raise at least as many questions as they answer. One is the role of copy number variation in schizophrenia in the general population. The number of cases accounted for by the deletions on chromosome 1 and 15 in the ISC and Icelandic studies is extremely small--on the order of 1% or less. The extent to which copy number variation, including very rare or even private de novo variants, will account for the genetic risk for schizophrenia in the general population is still unknown. The ISC study indicated that there is a higher overall load of copy number variations in schizophrenia, broadly consistent with Walsh et al and Xu et al but backed up by a much larger sample size, allowing the results to achieve high statistical significance. The implications of these findings are still undeveloped,

Another issue is the relationship to the phenotype of schizophrenia in the general population. Many more genotype-phenotype studies will need to be done. It will be important to determine whether there is a higher rate of mental retardation in the schizophrenia in these studies than in other populations.

Another question is the relationship between these copy number variations (and other rare events) and the more common variants accounting for smaller increases in risk, as in the recent O’Donovan et al. (2008) association study in Nature Genetics. It is far too early to know, but there may well be some combination of rare mutations plus risk alleles that account for cases in the general population. This would then be highly reminiscent of Alzheimer’s disease, Parkinson’s disease, and other diseases which have been studied for a longer period of time.

For instance, in Alzheimer’s disease there are rare mutations in APP and presenilin, as well as copy number variation in APP, with duplications causing the accelerated Alzheimer’s disease seen in Down syndrome. These appear to interact with the risk allele in APOE, and possibly other risk alleles, and are part of a pathogenic pathway (Tanzi and Bertram, 2005). Similarly in Parkinson’s disease, rare mutations in α-synuclein, LRRK2 and other genes can be causative of PD, though notably the G2019S mutation in LRRK2 has incomplete penetrance. In addition, duplications or triplications of α-synuclein can cause familial PD, and altered expression due to promoter variants may contribute to risk. By contrast, deletions in Parkin cause an early onset Parkinsonian syndrome (Hardy et al., 2006). Finally, much of PD may be due to genetic risk factors or environmental causes that have not yet been identified. Further studies will likely lead to the elucidation of pathogenic pathways. These diseases can provide a paradigm for the study of schizophrenia and other psychiatric diseases. One difference is that the copy number variations in the neurodegenerative diseases are often increases in copies (as in APP and α-synuclein), consistent with gain of function mechanisms, while the schizophrenia associations were predominantly with deletions, suggesting loss of function mechanisms. The hope is that as genes are identified, they can be linked together in pathways, leading to understanding of the neurobiology of schizophrenia (Ross et al., 2006).

The key unanswered questions, of course, are what genes or other functional domains are deleted at the chromosome 1, 15, and 22 loci, whether the deletions at these loci are sufficient in themselves to cause schizophrenia, and, if sufficient, the extent to which the deletions are penetrant. Both of the current studies identified deletions large enough to include several genes. The hope is that at least a subset of copy number variations (unlike SNP associations identified in schizophrenia to date) may be causative, making the identification of the relevant genes or other functional domains—at least in principle—more feasible.

Another tantalizing observation is that the copy number variations associated with schizophrenia were defined by flanking repeat regions. This raises the question of the extent to which undetected smaller insertions, deletions or other copy number variations related to other repetitive motifs, such as long tandem repeats, may also be associated with schizophrenia. Identification and testing of these loci may prove a fruitful approach to finding additional genetic risk factors for schizophrenia.

References:

Hardy J, Cai H, Cookson MR, Gwinn-Hardy K, Singleton A. Genetics of Parkinson's disease and parkinsonism. Ann Neurol. 2006 Oct;60(4):389-98. Abstract

Kirov G, Gumus D, Chen W, Norton N, Georgieva L, Sari M, O'Donovan MC, Erdogan F, Owen MJ, Ropers HH, Ullmann R. Comparative genome hybridization suggests a role for NRXN1 and APBA2 in schizophrenia. Hum Mol Genet . 2008 Feb 1 ; 17(3):458-65. Abstract

Porteous DJ, Thomson P, Brandon NJ, Millar JK. The genetics and biology of DISC1—an emerging role in psychosis and cognition. Biol Psychiatry. 2006 Jul 15;60(2):123-31. Abstract

Ross CA, Margolis RL, Reading SA, Pletnikov M, Coyle JT. Neurobiology of schizophrenia. Neuron. 2006 Oct 5;52(1):139-53. Abstract

Singleton A, Myers A, Hardy J. The law of mass action applied to neurodegenerative disease: a hypothesis concerning the etiology and pathogenesis of complex diseases. Hum Mol Genet. 2004 Apr 1;13 Spec No 1:R123-6. Abstract

Tanzi RE, Bertram L. Twenty years of the Alzheimer's disease amyloid hypothesis: a genetic perspective. Cell. 2005 Feb 25;120(4):545-55. Abstract

Walsh T, McClellan JM, McCarthy SE, Addington AM, Pierce SB, Cooper GM, Nord AS, Kusenda M, Malhotra D, Bhandari A, Stray SM, Rippey CF, Roccanova P, Makarov V, Lakshmi B, Findling RL, Sikich L, Stromberg T, Merriman B, Gogtay N, Butler P, Eckstrand K, Noory L, Gochman P, Long R, Chen Z, Davis S, Baker C, Eichler EE, Meltzer PS, Nelson SF, Singleton AB, Lee MK, Rapoport JL, King MC, Sebat J. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science. 2008 Apr 25;320(5875):539-43. Abstract

Xu B, Roos JL, Levy S, van Rensburg EJ, Gogos JA, Karayiorgou M. Strong association of de novo copy number mutations with sporadic schizophrenia. Nat Genet. 2008 Jul;40(7):880-5. Abstract

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Related News: More Evidence for CNVs in Schizophrenia Etiology—Jury Still Out on Practical Implications

Comment by:  Daniel Weinberger, SRF Advisor
Submitted 3 August 2008
Posted 3 August 2008

Several recent reports have suggested that rare CNVs may be highly penetrant genetic factors in the pathogenesis of schizophrenia, perhaps even singular etiologic events in those cases of schizophrenia who have them. This is potentially of enormous importance, as the definitive identification of such a “causative” factor may be a major step in unraveling the biologic mystery of the condition. I would stress several issues that need to be considered in putting these recent findings into a broader perspective.

It is very difficult to attribute illness to a private CNV, i.e., one found only in a single individual. This point has been potently illustrated by a study of clinically discordant MZ twins who share CNVs (Bruder et al., AJHG, 2008). Inherited CNVs, such as those that made up almost all of the CNVs described in the childhood onset cases of the study by Walsh et al. (Science, 2008), are by definition not highly penetrant (since they are inherited from unaffected parents). The finding by Xu et al. (Nat Gen, 2008) that de novo (i.e., non-inherited) CNVs are much more likely to be associated with cases lacking a family history is provocative but difficult to interpret as no data are given about the size of the families having a family history and those not having such a history. Unless these family samples are of comparable size and obtained by a comparable ascertainment strategy, it is hard to know how conclusive the finding is. Indeed, in the study of Walsh et al., rare CNVs were just as likely to be found in patients with a positive family history. Finally, in contrast to private CNVs, recurrent (but still rare) CNVs, such as those identified on 1q and 15q in the studies of the International Schizophrenia Consortium (Nature, 2008) and Stefansson et al. (Nature, 2008), are strongly implicated as being associated with the diagnosis of schizophrenia and therefore likely involved in the causation of the illnesses in the cases having these CNVs. In all, these new CNV regions, combined with the VCFS region on 22q, suggest that approximately five to 10 patients out of 1,000 who carry the diagnosis of schizophrenia may have a well-defined genetic lesion (i.e., a substantial deletion or duplication).

The overarching question now is how relevant these findings are to the other 99 percent of individuals with this diagnosis who do not have these recurrent CNVs. Before we had the capability to perform high-density DNA hybridization and SNP array analyses, chromosomal anomalies associated with the diagnosis of schizophrenia were identified using cytogenetic techniques. Indeed, VCFS, XXX, XXY (Kleinfelter’s syndrome), and XO (Turner syndrome) have been found with similarly increased frequency in cases with this diagnosis in a number of studies. Now that we have greater resolution to identify smaller structural anomalies, the list of congenital syndromes that increase the possibility that people will manifest symptoms that earn them this diagnosis appears to be growing rapidly. Are we finding causes for the form of schizophrenia that most psychiatrists see in their offices, or are we instead carving out a new set of rare congenital syndromes that share some clinical characteristics, as syphilis was carved out from the diagnosis of schizophrenia at the turn of the twentieth century? Is schizophrenia a primary expression of these anomalies or a secondary manifestation? VCFS is associated with schizophrenia-like phenomena but even more often with mild mental retardation, autism spectrum, and other psychiatric manifestations. The same is true of the aneuploidies that increase the probability of manifesting schizophrenia symptoms. The two new papers in Nature allude to the possibility that epilepsy and intellectual limitations may also be associated with these CNVs. The diagnostic potential of any of these new findings cannot be determined until the full spectrum of their clinical manifestations is clarified.

One of the important insights that might emerge from identification of these new CNV syndromes is the identification of candidate genes that may show association with schizophrenia based on SNPs in these regions. VCFS has been an important source of promising candidate genes with broader clinical relevance (e.g., PRODH, COMT). Stefansson et al. report, however, that none of the 319 SNPs in the CNV regions showed significant association with schizophrenia in quite a large sample of individuals not having deletions in these regions. The Consortium report also presumably has the results of SNP association testing in these regions in their large sample but did not report them. It is very important to explore in greater genetic detail these regions of the genome showing association with the diagnosis of schizophrenia in samples lacking these lesions and to fully characterize the clinical picture of individuals who have them. It is hoped that insights into the pathogenesis of symptoms related to this diagnosis will emerge from these additional studies.

Anyone who has worked in a public state hospital or chronic schizophrenia care facility (where I spent over 20 years) is not surprised to find an occasional patient with a rare congenital or acquired syndrome who expresses symptoms similar to those individuals also diagnosed with schizophrenia who do not have such rare syndromes. Our diagnostic procedures are not precise, and the symptoms that earn someone this diagnosis are not specific. Schizophrenia is not something someone has; it is a diagnosis someone is given. In an earlier comment for SRF on structural variations in the genome related to autism, I suggested that, “From a genetic point of view, autism is a syndrome that can be reached from many directions, along many paths. It is not likely that autism is any more of a discrete disease entity than say, blindness or mental retardation.” These new CNV syndromes manifesting schizophrenia phenomena are probably a reminder that the same is true of what we call schizophrenia.

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Related News: Are Membrane Molecules Unmoored in 22q11DS Mouse?

Comment by:  Doron Gothelf
Submitted 27 October 2008
Posted 27 October 2008

The common theory held until recently regarding the genetic underpinning of neuropsychiatric disorders was based on the “common disease-common variant” model. According to that theory, multiple common alleles in the population contribute small-to-moderate additive or multiplicative effects to the predisposition to neuropsychiatric disorders. With the advances in genetic screening technologies this theory is now being challenged. Recent findings indicate that rare copy number variations (CNVs) may account for a substantial fraction of the overall genetic risk for neuropsychiatric disorders including schizophrenia and autism (Consortium, 2008; Stefansson et al., 2008; Mefford et al., 2008). The 22q11.2 microdeletion was the most common CNV identified in patients with schizophrenia in a recent large scale study of patients with schizophrenia (Consortium, 2008). The 22q11.2 microdeletion is also the most common microdeletion occurring in humans and up to one third of individuals with 22q11.2 deletion syndrome (22q11.2DS) develop schizophrenia by adulthood. Thus the syndrome serves as an important model from which to learn the path leading from a well defined genetic defect to brain development and eventually to the evolution of schizophrenia.

It is still uncertain whether the neuropsychiatric phenotype associated with 22q11.2DS is a result of a strong effect of haploinsufficiency of one or a few genes from the microdeletion region as some studies suggested (Gothelf et al., 2005; Paterlini et al., 2005; Raux et al., 2007; Vorstman et al., 2008), or the result of cumulative small effects of haploinsufficiency of multiple genes, each contributing a small effect, as other studies suggested (Maynard et al., 2003; Meechan et al., 2006).

The current very elegant study by Mukai and colleagues suggests that haploinsufficiency of a single gene from the 22q11.2 deleted region, Zdhhc8, is responsible for the microscopic neural hippocampal abnormalities present in a mouse model of the disease. Remarkably, these abnormalities were prevented with the reintroduction of enzymatically active ZDHHC8 protein. The works of Gogos and his colleagues (Paterlini et al., 2005; Stark et al., 2008) are consistently and brilliantly getting us closer to revealing the complex association between genes from the 22q11.2 region and the neuropsychiatric phenotype. If indeed haploinsuffiency of single genes like Zdhhc8, COMT, or Dgcr8 have a strong effect on abnormal brain development and the eruption of schizophrenia, it conveys an enormous potential for developing novel pathophysiologically based treatments for this refractory disease. Such treatments will target the enzymatic deficit conveyed by the genetic mutation.

References:

[No authors listed]. Rare chromosomal deletions and duplications increase risk of schizophrenia. Nature. 2008 Sep 11;455(7210):237-41. Abstract

Stefansson H, Rujescu D, Cichon S, Pietiläinen OP, Ingason A, Steinberg S, Fossdal R, Sigurdsson E, Sigmundsson T, Buizer-Voskamp JE, Hansen T, Jakobsen KD, Muglia P, Francks C, Matthews PM, Gylfason A, Halldorsson BV, Gudbjartsson D, Thorgeirsson TE, Sigurdsson A, Jonasdottir A, Jonasdottir A, Bjornsson A, Mattiasdottir S, Blondal T, Haraldsson M, Magnusdottir BB, Giegling I, Möller HJ, Hartmann A, Shianna KV, Ge D, Need AC, Crombie C, Fraser G, Walker N, Lonnqvist J, Suvisaari J, Tuulio-Henriksson A, Paunio T, Toulopoulou T, Bramon E, Di Forti M, Murray R, Ruggeri M, Vassos E, Tosato S, Walshe M, Li T, Vasilescu C, Mühleisen TW, Wang AG, Ullum H, Djurovic S, Melle I, Olesen J, Kiemeney LA, Franke B, Sabatti C, Freimer NB, Gulcher JR, Thorsteinsdottir U, Kong A, Andreassen OA, Ophoff RA, Georgi A, Rietschel M, Werge T, Petursson H, Goldstein DB, Nöthen MM, Peltonen L, Collier DA, St Clair D, Stefansson K, Kahn RS, Linszen DH, van Os J, Wiersma D, Bruggeman R, Cahn W, de Haan L, Krabbendam L, Myin-Germeys I. Large recurrent microdeletions associated with schizophrenia. Nature. 2008 Sep 11;455(7210):232-6. Abstract

Mefford HC, Sharp AJ, Baker C, Itsara A, Jiang Z, Buysse K, Huang S, Maloney VK, Crolla JA, Baralle D, Collins A, Mercer C, Norga K, de Ravel T, Devriendt K, Bongers EM, de Leeuw N, Reardon W, Gimelli S, Bena F, Hennekam RC, Male A, Gaunt L, Clayton-Smith J, Simonic I, Park SM, Mehta SG, Nik-Zainal S, Woods CG, Firth HV, Parkin G, Fichera M, Reitano S, Lo Giudice M, Li KE, Casuga I, Broomer A, Conrad B, Schwerzmann M, Räber L, Gallati S, Striano P, Coppola A, Tolmie JL, Tobias ES, Lilley C, Armengol L, Spysschaert Y, Verloo P, De Coene A, Goossens L, Mortier G, Speleman F, van Binsbergen E, Nelen MR, Hochstenbach R, Poot M, Gallagher L, Gill M, McClellan J, King MC, Regan R, Skinner C, Stevenson RE, Antonarakis SE, Chen C, Estivill X, Menten B, Gimelli G, Gribble S, Schwartz S, Sutcliffe JS, Walsh T, Knight SJ, Sebat J, Romano C, Schwartz CE, Veltman JA, de Vries BB, Vermeesch JR, Barber JC, Willatt L, Tassabehji M, Eichler EE. Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med. 2008 Oct 16;359(16):1685-99. Abstract

Gothelf D, Eliez S, Thompson T, Hinard C, Penniman L, Feinstein C, Kwon H, Jin S, Jo B, Antonarakis SE, Morris MA, Reiss AL. COMT genotype predicts longitudinal cognitive decline and psychosis in 22q11.2 deletion syndrome. Nat Neurosci. 2005 Nov 1;8(11):1500-2. Abstract

Paterlini M, Zakharenko SS, Lai WS, Qin J, Zhang H, Mukai J, Westphal KG, Olivier B, Sulzer D, Pavlidis P, Siegelbaum SA, Karayiorgou M, Gogos JA. Transcriptional and behavioral interaction between 22q11.2 orthologs modulates schizophrenia-related phenotypes in mice. Nat Neurosci. 2005 Nov 1;8(11):1586-94. Abstract

Raux G, Bumsel E, Hecketsweiler B, van Amelsvoort T, Zinkstok J, Manouvrier-Hanu S, Fantini C, Brévière GM, Di Rosa G, Pustorino G, Vogels A, Swillen A, Legallic S, Bou J, Opolczynski G, Drouin-Garraud V, Lemarchand M, Philip N, Gérard-Desplanches A, Carlier M, Philippe A, Nolen MC, Heron D, Sarda P, Lacombe D, Coizet C, Alembik Y, Layet V, Afenjar A, Hannequin D, Demily C, Petit M, Thibaut F, Frebourg T, Campion D. Involvement of hyperprolinemia in cognitive and psychiatric features of the 22q11 deletion syndrome. Hum Mol Genet. 2007 Jan 1;16(1):83-91. Abstract

Vorstman JA, Chow EW, Ophoff RA, van Engeland H, Beemer FA, Kahn RS, Sinke RJ, Bassett AS. Association of the PIK4CA schizophrenia-susceptibility gene in adults with the 22q11.2 deletion syndrome. Am J Med Genet B Neuropsychiatr Genet. 2008 Jul 21; Abstract

Maynard TM, Haskell GT, Peters AZ, Sikich L, Lieberman JA, LaMantia AS. A comprehensive analysis of 22q11 gene expression in the developing and adult brain. Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):14433-8. Abstract

Meechan DW, Maynard TM, Wu Y, Gopalakrishna D, Lieberman JA, LaMantia AS. Gene dosage in the developing and adult brain in a mouse model of 22q11 deletion syndrome. Mol Cell Neurosci. 2006 Dec 1;33(4):412-28. Abstract

Stark KL, Xu B, Bagchi A, Lai WS, Liu H, Hsu R, Wan X, Pavlidis P, Mills AA, Karayiorgou M, Gogos JA. Altered brain microRNA biogenesis contributes to phenotypic deficits in a 22q11-deletion mouse model. Nat Genet. 2008 Jun 1;40(6):751-60. Abstract

View all comments by Doron Gothelf

Related News: Mixed Message: 15q13.3 Deletions Confer Risk, But for What?

Comment by:  Ben Pickard
Submitted 21 January 2009
Posted 21 January 2009

Before Christmas, an insightful discussion between SRF's Pete Farley and researchers Heather Mefford and Evan Eichler delved into the complex interplay between genotype (copy number variant status at 1q21.1) and phenotype (psychiatric illness, autism, mental retardation, and congenital abnormalities) (see SRF related news story). The upshot was that although deletions at this locus were statistically associated with pathologies, the severity and nature of those pathologies was extremely variable. This raised questions about whether researchers and clinicians should focus on the disease or the deletion, and what the mechanisms that determine the clinical endpoint might be. This is becoming a clear trend. Another CNV region at 16p11.2 has also been variously associated with both autism and schizophrenia. Deletions of just a single gene, CNTNAP2, as opposed to a gene cluster, have also shown this phenomenon of variable phenotype expression—deletion carriers have been diagnosed with autism, Gilles de la Tourette/obsessive compulsive disorder, schizophrenia/epilepsy, or remain entirely healthy (Bakkaloglu et al., 2008; Friedman et al., 2008; Verkerk et al., 2003; Belloso et al., 2007).

In the same vein, this new paper by Helbig and colleagues describes yet another example of a discrete copy number variant (microdeletion) that was originally linked with psychiatric phenotypes but is now also shown to give rise to idiopathic generalized epilepsy (IGE). The deletion is at 15q13.3, which encompasses the candidate neurotransmitter receptor gene, CHRNA7, among others. In fact, with a frequency of 1 percent in the IGE population and absence in controls, the deletion is the strongest genetic risk factor for this condition and is more prevalent in IGE than in either mental retardation or schizophrenia.

Although the study of CNVs has highlighted this genotype-phenotype issue, it has been observed previously in the context of the overlap of linkage hotspots between schizophrenia and bipolar disorder (Berrettini, 2003), in case-control association studies linking the same gene to multiple disorders (Chubb et al., 2008), and in the case of the Scottish family with the t(1;11) translocation disrupting DISC1, in which carrier phenotypes ranged from healthy to major depression, bipolar disorder, and schizophrenia (Blackwood et al., 2001).

So we are now faced with complex genetic disorders that really live up to their name. As such, two particular issues warrant further discussion.

The first issue is that clinicians seem to observe discrete rather than continuous disorder phenotypes. Despite the current diagnostic manuals leaving little room for diagnostic leeway, it seems that the majority of case phenotypes tend toward a limited number of outcomes such as schizophrenia, bipolar disorder, mental retardation, autism, and epilepsy. Moreover, no psychiatrist can distinguish DISC1 schizophrenia from 1q21.1 schizophrenia or NRG1 schizophrenia without recourse to genetic methodologies, suggesting that there is a positive biological drive towards the endpoint. To borrow what may be a useful analogy from physics, the system is “chaotic” (in terms of its genetic input and its effect on cellular biology) but tends toward “strange attractors” (a limited set of diagnoses) [http://en.wikipedia.org/wiki/Attractor]. Why might this be so? It may be that there are several higher order functional bottlenecks within the brain such as synaptic transmission efficiency, cortical development, astrocyte/oligodendrocyte function, hippocampal neurogenesis, higher order communication between brain regions, etc. These act to “sum” the expected environmental, genetic, and cellular complexity present within an individual and transform it into a limited set of potential outcomes—in essence, these are the strange attractors.

The next issue is how the same mutation can give rise to two (or more) different conditions. It may be useful to think of the Knudson “two-hit” hypothesis of cancer in which environment and other genetic factors act subsequent to a “deep” genetic fault (Knudson, 1971).

The CNV examples above may represent such fundamental disruptions and most probably impinge on neurodevelopmental pathways, priming the brain to be tipped over the threshold into a disease state. In fact, the t(1:11) translocation carriers present evidence for such a phenomenon as both healthy and affected carriers show abnormal P300 brain response activities suggesting this endophenotype highlights an underlying brain dysfunction (Blackwood et al., 2001).

We have to postulate that the additional genetic or environmental influences (modifiers) not only determine entry into the disease state but also dictate the final outcome. Possible candidates for modifiers of the deletions above are the remaining single copy alleles at the CNV locus—exposed recessive mutations, imprinting, or epigenetic modification could all alter expressivity and penetrance of the deletion phenotype. However, limited studies by Eichler’s group seem to discount this possibility (Mefford et al., 2008).

In any case, genomewide association and CNV studies suggest that there is plenty of scope for a sufficient burden of genetic modifiers outside the CNV region. This may also fit in with the seemingly disparate concepts of rare/familial variants exposed by linkage and common/low odds ratio variants revealed by association. Both act causally with the former potentially acting as the “first hit.”

As time progresses, we will move towards the definition of the range of phenotypes potentially resulting from each genotype and the spectrum of genotypes causing each phenotype. CNVs represent a pretty blunt tool to dissect finer relationships between genotype and phenotype, so it is to be expected that rare but penetrant point mutations that emerge from resequencing projects will be of greater use in dissecting function-phenotype links—as has been seen with the connexin gene family, for example (Rabionet et al., 2002).

In summary, it is to be hoped that the clinical and research communities are able to embrace these complexities for what they offer—a deeper understanding of these disorders, one that is intimately linked to the development and function of the brain.

References:

Bakkaloglu B, O'roak BJ, Louvi A, Gupta AR, Abelson JF, Morgan TM, Chawarska K, Klin A, Ercan-Sencicek AG, Stillman AA, Tanriover G, Abrahams BS, Duvall JA, Robbins EM, Geschwind DH, Biederer T, Gunel M, Lifton RP, State MW. Molecular cytogenetic analysis and resequencing of contactin associated protein-like 2 in autism spectrum disorders. Am J Hum Genet. 2008 Jan 1;82(1):165-73. Abstract

Friedman JI, Vrijenhoek T, Markx S, Janssen IM, van der Vliet WA, Faas BH, Knoers NV, Cahn W, Kahn RS, Edelmann L, Davis KL, Silverman JM, Brunner HG, van Kessel AG, Wijmenga C, Ophoff RA, Veltman JA. CNTNAP2 gene dosage variation is associated with schizophrenia and epilepsy. Mol Psychiatry. 2008 Mar 1;13(3):261-6. Abstract

Verkerk AJ, Mathews CA, Joosse M, Eussen BH, Heutink P, Oostra BA, . CNTNAP2 is disrupted in a family with Gilles de la Tourette syndrome and obsessive compulsive disorder. Genomics. 2003 Jul 1;82(1):1-9. Abstract

Belloso JM, Bache I, Guitart M, Caballin MR, Halgren C, Kirchhoff M, Ropers HH, Tommerup N, Tümer Z. Disruption of the CNTNAP2 gene in a t(7;15) translocation family without symptoms of Gilles de la Tourette syndrome. Eur J Hum Genet. 2007 Jun 1;15(6):711-3. Abstract

Berrettini W. Evidence for shared susceptibility in bipolar disorder and schizophrenia. Am J Med Genet C Semin Med Genet. 2003 Nov 15;123C(1):59-64. Abstract

Chubb JE, Bradshaw NJ, Soares DC, Porteous DJ, Millar JK. The DISC locus in psychiatric illness. Mol Psychiatry. 2008 Jan 1;13(1):36-64. Abstract

Blackwood DH, Fordyce A, Walker MT, St Clair DM, Porteous DJ, Muir WJ. Schizophrenia and affective disorders--cosegregation with a translocation at chromosome 1q42 that directly disrupts brain-expressed genes: clinical and P300 findings in a family. Am J Hum Genet. 2001 Aug 1;69(2):428-33. Abstract

Knudson AG. Mutation and cancer: statistical study of retinoblastoma. Proc Natl Acad Sci U S A. 1971 Apr 1;68(4):820-3. Abstract

Mefford HC, Sharp AJ, Baker C, Itsara A, Jiang Z, Buysse K, Huang S, Maloney VK, Crolla JA, Baralle D, Collins A, Mercer C, Norga K, de Ravel T, Devriendt K, Bongers EM, de Leeuw N, Reardon W, Gimelli S, Bena F, Hennekam RC, Male A, Gaunt L, Clayton-Smith J, Simonic I, Park SM, Mehta SG, Nik-Zainal S, Woods CG, Firth HV, Parkin G, Fichera M, Reitano S, Lo Giudice M, Li KE, Casuga I, Broomer A, Conrad B, Schwerzmann M, Räber L, Gallati S, Striano P, Coppola A, Tolmie JL, Tobias ES, Lilley C, Armengol L, Spysschaert Y, Verloo P, De Coene A, Goossens L, Mortier G, Speleman F, van Binsbergen E, Nelen MR, Hochstenbach R, Poot M, Gallagher L, Gill M, McClellan J, King MC, Regan R, Skinner C, Stevenson RE, Antonarakis SE, Chen C, Estivill X, Menten B, Gimelli G, Gribble S, Schwartz S, Sutcliffe JS, Walsh T, Knight SJ, Sebat J, Romano C, Schwartz CE, Veltman JA, de Vries BB, Vermeesch JR, Barber JC, Willatt L, Tassabehji M, Eichler EE. Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med. 2008 Oct 16;359(16):1685-99. Abstract

Rabionet R, López-Bigas N, Arbonès ML, Estivill X. Connexin mutations in hearing loss, dermatological and neurological disorders. Trends Mol Med. 2002 May 1;8(5):205-12. Abstract

View all comments by Ben Pickard

Related News: Copy-number Variants, Interacting Alleles, or Both?

Comment by:  David J. Porteous, SRF Advisor
Submitted 11 February 2009
Posted 12 February 2009

The answer is unequivocally, “yes”
In co-highlighting the papers from Need et al., 2009, and Tomppo et al., 2009, you pose the question “CNV’s, interacting loci or both?” to which my immediate answer is an unequivocal “yes,” but it actually goes further than that. These two studies, interesting in their own rights, add just two more pieces of evidence now accumulated from case only, case-control, and family-based linkage on the genetic architecture of schizophrenia. Thus, we can reject with confidence a single evolutionary and genetic origin for schizophrenia. If it were so, it would have been found already by the plethora of genomewide studies now completed, studies specifically designed to detect causal variants, should they exist, which are both common to most if not all subjects and ancient in origin—the Common Disease, Common Variant (CDCV) hypothesis.

Moreover, for DISC1, NRG1, NRXN1, and a few others, the criteria for causality are met in some subjects, but none of these is the sole cause of schizophrenia. Their net contributions to individual and population risk remain uncertain and await large scale resequencing as well as SNP and CNV studies to capture the totality of genetic variation and how that contributes to the incidence of major mental illness. Meanwhile, nosological and epidemiological evidence has also forced a re-evaluation of the categorical distinction between schizophrenia and bipolar disorder, let alone schizoaffective disorder (Lichtenstein et al., 2009).

In this regard, DISC1 serves again as an instructive paradigm, with good evidence for genetic association to schizophrenia, BP, schizoaffective disorder, and beyond (Chubb et al., 2008). The study by Hennah et al. (2008) added a further nuance to the DISC1 story by demonstrating intra-allelic interaction. Tomppo et al. (2009) now build upon their earlier evidence to show that DISC1 variants affect subcomponents of the psychiatric phenotype, treated now as a quantitative than a dichotomous trait. In much the same way and just as would be predicted, DISC1 variation also contributes to normal variation in human brain development and behavior (e.g., Callicott et al., 2005). Self-evidently, different classes of genetic variants (SNP or CNV, regulatory or coding) will have different biological and therefore psychiatric consequences (Porteous, 2008).

That Need et al. (2009) failed to replicate previous genomewide association studies (or find support for DISC1, NRG1, and the rest) is just further proof, if any were needed, that there is extensive genetic heterogeneity and that common variants of ancient origin are not major determinants of individual or population risk (Porteous, 2008). Variable penetrance, expressivity, and gene-gene interaction (epistasis) all need to be considered, but these intrinsic aspects of genetic influence are best addressed by family studies (currently lacking for CNV studies) and poorly addressed by large-scale case-control genomewide association studies. Power to test the CDCV hypothesis may increase with increasing numbers of subjects, but so does the inherent heterogeneity, both genetic and diagnostic.

That said, genetics is without doubt the most incisive tool we have to dissect the etiology of major mental illness. The criteria for success (and certainly for causality, rather than mere correlation) must be less about the number of noughts after the “p” and much more about the connection between candidate gene, gene variant, and the biological consequences for brain development and function. In this regard, both studies have something to say and offer.

References:

Lichtenstein P, Yip BH, Björk C, Pawitan Y, Cannon TD, Sullivan PF, Hultman CM. Common genetic determinants of schizophrenia and bipolar disorder in Swedish families: a population-based study. 2009 Lancet 373:234-9. Abstract

Chubb JE, Bradshaw NJ, Soares DC, Porteous DJ, Millar JK. Mol Psychiatry. The DISC locus in psychiatric illness. 2008 Jan;13(1):36-64. Epub 2007 Oct 2. Abstract

Callicott JH, Straub RE, Pezawas L, Egan MF, Mattay VS, Hariri AR, Verchinski BA,Meyer-Lindenberg A, Balkissoon R, Kolachana B, Goldberg TE, Weinberger DR. Variation in DISC1 affects hippocampal structure and function and increases risk for schizophrenia. 2005 Proc Natl Acad Sci U S A. 2005 102:8627-32. Abstract

Porteous D. Genetic causality in schizophrenia and bipolar disorder: out with the old and in with the new. 2008 Curr Opin Genet Dev. 18:229-34. Abstract

View all comments by David J. Porteous

Related News: Copy-number Variants, Interacting Alleles, or Both?

Comment by:  Pamela DeRosseAnil Malhotra (SRF Advisor)
Submitted 19 February 2009
Posted 22 February 2009

The results reported by Tomppo et al. and Need et al. collectively instantiate the complexities of the genetic architecture underlying risk for psychiatric illness. Paradoxically, however, while the results of Need et al. suggest that the answer to the complex question of risk genes for schizophrenia (SZ) may be found by searching a very select population for rare changes in genetic sequence, the results of Tomppo et al. suggest that the answer may be found by searching for common variants in large heterogeneous populations. So which is it? Is SZ the result of rare, novel genetic mutations or an accumulation of common ones? Such a conundrum is not a novel predicament in the process of scientific inquiry and such conundrums are often resolved by the reconciliation of both opposing views. Thus, if we allow history to serve as our guide it seems reasonable that the answer to the current question of what genetic mechanisms are responsible for SZ, is that SZ is caused by both rare and common variants.

Although considerable efforts, by our lab and others, are currently being directed towards seeking the type of rare variants that Need et al. suggest may be responsible for risk for SZ, a less concerted effort is being directed towards parsing the effects of more specific, common genetic variations. To date, there are limited data seeking to elucidate the effects of previously identified risk variants for SZ on phenotypic variation within the diagnostic group. The data that are available, however, suggest that risk variants do influence phenotypic variation. Our work with DISC1, for example, has produced relatively robust, and replicated findings linking variation in the gene to cognitive dysfunction (Burdick et al., 2005) as well as an increased risk for persecutory delusions in SZ (DeRosse et al., 2007). Similarly, our work with DTNBP1 indicates a strong association between variants in the gene and both cognitive dysfunction (Burdick et al., 2006) and negative symptoms in SZ (DeRosse et al., 2006). Moreover, the risk for cognitive dysfunction associated with the DTNBP1 risk genotype was also observed in a sample of healthy individuals. Thus, it seems conceivable that genetic variation associated with phenotypic variation within a diagnostic group may also be associated with similar, sub-syndromal phenotypes in non-clinical samples.

The data reported by Tomppo et al. provide support for the utility of parsing the specific effects of genetic variants on phenotypic variation and extend this approach to populations with sub-syndromal psychiatric symptoms. Such an approach is attractive in that it allows us to study the effects of genotype on phenotype without the confound imposed by psychotropic medications. Although the current data linking genes to specific dimensions of psychiatric illness are provocative, the study groups utilized are comprised of patients undergoing varying degrees of pharmacological intervention. Thus, in these analyses quantitative assessment of psychosis is to some extent confounded by treatment history and response. By measuring lifetime history of symptoms, which for most patients includes substantial periods without effective medication, many studies (including our own) may partially overcome this limitation. Still, assessment of the relation between genetic variation and dimensions of psychosis in study groups not undergoing treatment with pharmacological agents would be a compelling source of confirmation for these preliminary findings.

Perhaps most importantly, the data reported by Tomppo et al. suggest that previously identified risk genes should not be marginalized but rather, should be studied in non-clinical samples to identity phenotypic variation that may be related to the signs and symptoms of psychiatric illness.

References:

Burdick KE, Hodgkinson CA, Szeszko PR, Lencz T, Ekholm JM, Kane JM, Goldman D, Malhotra AK. DISC1 and neurocognitive function in schizophrenia. Neuroreport. 2005; 16(12):1399-402. Abstract

Burdick KE, Lencz T, Funke B, Finn CT, Szeszko PR, Kane JM, Kucherlapati R, Malhotra AK. Genetic variation in DTNBP1 influences general cognitive ability. Hum Mol Genet. 2006; 15(10):1563-8. Abstract

DeRosse P, Hodgkinson CA, Lencz T, Burdick KE, Kane JM, Goldman D, Malhotra AK. Disrupted in schizophrenia 1 genotype and positive symptoms in schizophrenia. Biol Psychiatry. 2007; 61(10):1208-10. Abstract

DeRosse P, Funke B, Burdick KE, Lencz T, Ekholm JM, Kane JM, Kucherlapati R, Malhotra AK. Dysbindin genotype and negative symptoms in schizophrenia. Am J Psychiatry. 2006; 163(3):532-4. Abstract

View all comments by Pamela DeRosse
View all comments by Anil Malhotra

Related News: Copy-number Variants, Interacting Alleles, or Both?

Comment by:  James L. Kennedy, SRF Advisor (Disclosure)
Submitted 25 February 2009
Posted 25 February 2009

Has anyone considered the possibility that the CNVs found to be elevated in schizophrenia versus controls could be a peripheral effect and perhaps not present in brain tissue? For example, the diet of the typical schizophrenia patient is poor, and it is conceivable that chronic folate deficiency could predispose to problems in DNA structure or repair in lymphocytes. Thus, the CNVs could be an effect of the illness, and not a cause. Someone needs to do the experiment that compares CNVs in blood to those in the brain of the same individual. And then we need studies of the stability of CNVs over the lifetime of an individual.

View all comments by James L. Kennedy

Related News: Copy-number Variants, Interacting Alleles, or Both?

Comment by:  Kevin J. Mitchell
Submitted 2 March 2009
Posted 2 March 2009

The papers by Need et al. and Tomppo et al. seem to present conflicting evidence for the involvement of common or rare variants in the etiology of schizophrenia.

On the one hand, Need et al., in a very large and well-powered sample, find no evidence for involvement of any common SNPs or CNVs. Importantly, they show that while any one SNP with a small effect and modest allelic frequency might be missed by their analysis, the likelihood that all such putative SNPs would be missed is vanishingly small. They come to the reasonable conclusion that common variants are unlikely to play a major role in the etiology of schizophrenia, except under a highly specific and implausible genetic model. Does this sound the death knell for the common variants, polygenic model of schizophrenia? Yes and no. These and other empirical data are consistent with theoretical analyses which show that the currently popular purely polygenic model, without some gene(s) of large effect, cannot explain familial risk patterns (Hemminki et al., 2007; Hemminki et al., 2008; Bodmer and Bonilla, 2008). It has been suggested that epistatic interactions may generate discontinuous risk from a continuous distribution of common alleles; however, while comparisons of risk in monozygotic and dizygotic twins are consistent with some contribution from epistasis, they are not consistent with the massive levels that would be required to rescue a purely polygenic mechanism, whether through a multiplicative or (biologically unrealistic) threshold model.

Thus, it seems most parsimonious to conclude that most cases of schizophrenia will involve a variant of large effect. As such variants are likely to be rapidly selected against, they are also likely to be quite rare. The findings of specific, gene-disrupting CNVs or mutations in individual genes in schizophrenia cases by Need et al. and numerous other groups support this idea. Excitingly, they also have highlighted specific molecules and biological pathways that provide molecular entry points to elucidate pathogenic mechanisms. The possible convergence on genes interacting with DISC1, including PCM1 and NDE1 in the current study, provides further support for the importance of this pathway, though, clearly, there may be many other ways to disrupt neural development or function that could lead to schizophrenia. (Conversely, it is becoming clearer that many of the putative causative mutations identified so far predispose to multiple psychiatric or neurological conditions.)

Despite the likely involvement of rare variants in most cases of schizophrenia, it remains possible that common alleles could have a modifying influence on risk—indeed, one early paper commonly cited as supporting a polygenic model for schizophrenia actually provided strong support for a model of a single gene of large effect and two to three modifiers (Risch, 1990). A rare variants/common modifiers model would be consistent with the body of literature on modifying genes in model organisms, where effects of genetic background on the phenotypic expression of particular mutations are quite common and can sometimes be large (Nadeau, 2001). Whether such genetic background effects would be mediated by common or rare variants is another question—there is certainly good reason to think that rare or even private mutations may make a larger contribution to phenotypic variance than previously suspected (Ng et al., 2008; Ji et al., 2008).

Nevertheless, common variants are also likely to be involved, and these effects might be detectable in large association studies, though they would be expected to be diluted across genotypes. This might explain inconsistent findings of association of common variants with disease state for various genes, including COMT, BDNF, and DISC1, for example. This issue has led some to look for association of variants in these genes with endophenotypes of schizophrenia in the general population—psychological or physiological traits that are heritable and affected by the symptoms of the disease, such as working memory, executive function, or, in the study by Tomppo et al., social interaction.

These approaches have tended to lead to statistically stronger and more consistent associations and are undoubtedly revealing genes and mechanisms contributing to normal variation in many psychological traits. How this relates to their potential involvement in disease etiology is far from clear, however. The implication of the endophenotype model is that the disorder itself emerges due to the combination of minor effects on multiple symptom parameters (Gottesman and Gould, 2003; Meyer-Lindenberg and Weinberger, 2006). An alternative interpretation is that these common variants may modify the phenotypic expression of some other rare variant, either due to their demonstrated effect on the psychological trait in question or through a more fundamental biochemical interaction, but that in the absence of such a variant of large effect, no combination of common alleles would lead to disease.

References:

Hemminki K, Försti A, Bermejo JL. The 'common disease-common variant' hypothesis and familial risks. PLoS ONE. 2008 Jun 18;3(6):e2504. Abstract

Hemminki K, Bermejo JL. Constraints for genetic association studies imposed by attributable fraction and familial risk. Carcinogenesis. 2007 Mar;28(3):648-56. Abstract

Bodmer W, Bonilla C. Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet. 2008 Jun;40(6):695-701. Abstract

Risch N. Linkage strategies for genetically complex traits. I. Multilocus models. Am J Hum Genet. 1990 Feb;46(2):222-8. Abstract

Nadeau JH. Modifier genes in mice and humans. Nat Rev Genet. 2001 Mar;2(3):165-74. Abstract

Ng PC, Levy S, Huang J, Stockwell TB, Walenz BP, Li K, Axelrod N, Busam DA, Strausberg RL, Venter JC. Genetic variation in an individual human exome. PLoS Genet. 2008 Aug 15;4(8):e1000160. Abstract

Ji W, Foo JN, O'Roak BJ, Zhao H, Larson MG, Simon DB, Newton-Cheh C, State MW, Levy D, Lifton RP. Rare independent mutations in renal salt handling genes contribute to blood pressure variation. Nat Genet. 2008 May;40(5):592-9. Abstract

Gottesman II, Gould TD. The endophenotype concept in psychiatry: etymology and strategic intentions. Am J Psychiatry. 2003 Apr;160(4):636-45. Abstract

Meyer-Lindenberg A, Weinberger DR. Intermediate phenotypes and genetic mechanisms of psychiatric disorders. Nat Rev Neurosci. 2006 Oct;7(10):818-27. Abstract

View all comments by Kevin J. Mitchell

Related News: DISC1: A Matter of Life or Death for Neural Progenitors

Comment by:  Khaled Rahman
Submitted 26 March 2009
Posted 26 March 2009

Mao and colleagues present an impressive body of work implicating GSK3β/β-catenin signaling in the function of Disc1. However, several key experimental controls are missing that detract from the impact of their study, and it is unclear whether this function of Disc1 among its many others is the critical link between the t(1;11) translocation and psychopathology in the Scottish family.

The results of Mao et al. suggest that acute knockdown of Disc1 in embryonic brain causes premature exit from the proliferative cell cycle and premature differentiation into neurons. In fact, they observe fewer GFP+ cells in the VZ/SVZ and greater GFP+ cells within the cortical plate. This is in contrast to the study by Kamiya et al. (2005), in which they find that knocking down Disc1 caused greater retention of cells in the VZ/SVZ and fewer in the cortical plate, suggesting retarded migration. Although the timing of electroporation (E13 vs. E14.5) and examination (E15 vs. P2) differed between the two studies, these results are not easily reconciled.

The authors also suggest that they can rescue the deficits in proliferation by overexpressing human wild-type DISC1, stabilizing β-catenin expression, or inhibiting GSK3β activity, and thus conclude that Disc1 is acting through this pathway. This conclusion, however, rests on an error in logic. If increasing X causes an increase in Y, and decreasing Z causes a decrease in Y, this does not mean that X and Z are operating via the same mechanism. In fact, overexpressing WT-DISC1, stabilizing β-catenin, or inhibiting GSK3β activity all increase proliferation in control cells. Thus, the fact that these manipulations also work in progenitors with Disc1 silenced only tells us that these effects are independent or downstream of Disc1. What are needed are studies that show a differential sensitivity of Disc1-silenced cells to manipulations of β-catenin or GSK3β. In other words, is there a shift in the dose response curves? This is what is to be expected given that Mao et al. show changes in β-catenin levels and changes in the phosphorylation of GSK3β substrates in Disc1 silenced cells.

Furthermore, it is surprising that a restricted silencing of Disc1 in the adult dentate gyrus produces changes in affective behaviors, when total ablation of dentate neurogenesis in the adult produces little effects on depression-related behaviors (Santarelli et al., 2003; Airen et al., 2007). The fact that inhibiting GSK3β increases proliferation in both control and Disc1 knockdown animals to a similar degree suggests that the “rescue” of any behavioral deficits is independent of the drug’s effects on proliferation. Correlating measures of proliferation with behavioral performance would help address this issue.

How this study will lead to new or improved therapeutic interventions is also an open question. Lithium is well known for its mood-stabilizing properties, and this study may point to better, more efficient ways to address these symptoms. However, it is also known that lithium does little for, if not worsens, cognitive symptoms in patients (Pachet and Wisniewski, 2003), and it is this symptom domain that is in dire need of drug development.

It is also important to keep in mind that acute silencing of Disc1 in a restricted set of cells will not necessarily recapitulate the pathogenetic process of a disease-associated mutation. It remains to be seen if similar results are obtained in animal models of the Disc1 mutation (Clapcote et al., 2007; Hikida et al., 2007; Li et al., 2007).

References:

Kamiya A, Kubo K, Tomoda T, Takaki M, Youn R, Ozeki Y, Sawamura N, Park U, Kudo C, Okawa M, Ross CA, Hatten ME, Nakajima K, Sawa A. A schizophrenia-associated mutation of DISC1 perturbs cerebral cortex development. Nat Cell Biol. 2005 Dec 1;7(12):1167-78. Abstract

Santarelli, L. et al. Requirement of hippocampal neurogenesis for the behavioral effects of antidepressants. Science 301, 805–809 (2003). Abstract

Airan, R.D. et al. High-speed imaging reveals neurophysiological links to behavior in an animal model of depression. Science 317, 819-23 (2007). Abstract

Pachet AK, Wisniewski AM. The effects of lithium on cognition: an updated review. Psychopharmacology (Berl). 2003 Nov;170(3):225-34. Review. Abstract

Clapcote SJ, Lipina TV, Millar JK, Mackie S, Christie S, et al. (2007) Behavioral phenotypes of Disc1 missense mutations in mice. Neuron 54: 387–402. Abstract

Hikida T, Jaaro-Peled H, Seshadri S, Oishi K, Hookway C, et al. (2007) Dominant-negative DISC1 transgenic mice display schizophrenia-associated phenotypes detected by measures translatable to humans. Proc Natl Acad Sci U S A 104: 14501–14506. Abstract

Li W, Zhou Y, Jentsch JD, Brown RA, Tian X, et al. (2007) Specific developmental disruption of disrupted-in-schizophrenia-1 function results in schizophrenia-related phenotypes in mice. Proc Natl Acad Sci U S A 104: 18280–18285. Abstract

View all comments by Khaled Rahman

Related News: DISC1: A Matter of Life or Death for Neural Progenitors

Comment by:  Simon Lovestone
Submitted 27 March 2009
Posted 27 March 2009

This is an intriguing paper that builds on a growing body of evidence implicating wnt regulation of GSK3 signaling in psychotic illness (Lovestone et al., 2007).

It is interesting that the authors report that binding of DISC1 to GSK3 results in no change in the inhibitory Ser9 phosphorylation site of GSK3 but a change in Y216 activation site and that this resulted in effects on some but not all GSK3 substrates. This poses a challenge both in terms of understanding the role of GSK3 signaling in schizophrenia and other psychotic disorders and in drug discovery.

The authors cite some of the other evidence for regulation of GSK3 signaling in psychosis, including, for example, the evidence for a role of AKT signaling alteration in schizophrenia and lithium, an inhibitor of GSK3, as a treatment for bipolar disorder. But in both cases, AKT (Cross et al., 1995) and lithium (Jope, 2003), the effect on GSK3 is predominantly via Ser9 phosphorylation and not via Y216. The unstated implication is at least two, possibly three, mechanisms for regulation of GSK3 are all involved in psychotic illness—the auto-phosphorylation at Y216, the exogenous signal transduction regulated Ser9 site inhibition and, if the association of schizophrenia with the wnt inhibitor DKK4 we reported is true (Proitsi et al., 2008), also via the wnt signaling effects on disruption of the macromolecular complex that brings GSK3 together with β-catenin. On the one hand, this might be taken as positive evidence of a role for GSK3 in psychosis—all of its regulatory mechanisms have been implicated; therefore, the case is stronger. On the other hand, GSK3 lies at the intersection point of very many signaling pathways and so is likely to be implicated in many disorders (as it is), and the fact that in cellular and animal models related to psychosis there is no consistent effect on the enzyme is troublesome.

From a drug discovery perspective, those with GSK3 inhibitors in the pipeline will be watching this space carefully. However, it is worth noting that Mao et al. find very selective effects of DISC1 on GSK3 substrates. Despite convincing evidence of an increase in Y216 phosphorylation, which one would expect to increase activity of GSK3 against all substrates, the authors find no evidence of effects on phosphorylation of the GSK3 substrates Ngn2 or C/EBPα. This is somewhat puzzling and merits further attention, especially as in vitro direct binding of a DISC1 fragment to GSK3 inhibited the action of GSK3 on a range of substrates. Might there be more to the direct interaction of DISC1 with GSK3 than a regulation of Y216 autophosphorylation and activation? If, however, GSK3 regulation turns out to be part of the mechanism of schizophrenia or bipolar disorder, then identifying which of the substrates and which of the many activities of GSK3, including on plasticity and hence cognition (Peineau et al., 2007; Hooper et al., 2007), are important in disease will become the critical task.

References:

Lovestone S, Killick R, Di Forti M, Murray R. Schizophrenia as a GSK-3 dysregulation disorder. Trends Neurosci. 2007 Apr 1 ; 30(4):142-9. Abstract

Cross DA, Alessi DR, Cohen P, Andjelkovich M, Hemmings BA. Inhibition of glycogen synthase kinase-3 by insulin mediated by protein kinase B. Nature . 1995 Dec 21-28 ; 378(6559):785-9. Abstract

Jope RS. Lithium and GSK-3: one inhibitor, two inhibitory actions, multiple outcomes. Trends Pharmacol Sci . 2003 Sep 1 ; 24(9):441-3. Abstract

Proitsi P, Li T, Hamilton G, Di Forti M, Collier D, Killick R, Chen R, Sham P, Murray R, Powell J, Lovestone S. Positional pathway screen of wnt signaling genes in schizophrenia: association with DKK4. Biol Psychiatry . 2008 Jan 1 ; 63(1):13-6. Abstract

Peineau S, Taghibiglou C, Bradley C, Wong TP, Liu L, Lu J, Lo E, Wu D, Saule E, Bouschet T, Matthews P, Isaac JT, Bortolotto ZA, Wang YT, Collingridge GL. LTP inhibits LTD in the hippocampus via regulation of GSK3beta. Neuron . 2007 Mar 1 ; 53(5):703-17. Abstract

Hooper C, Markevich V, Plattner F, Killick R, Schofield E, Engel T, Hernandez F, Anderton B, Rosenblum K, Bliss T, Cooke SF, Avila J, Lucas JJ, Giese KP, Stephenson J, Lovestone S. Glycogen synthase kinase-3 inhibition is integral to long-term potentiation. Eur J Neurosci . 2007 Jan 1 ; 25(1):81-6. Abstract

View all comments by Simon Lovestone

Related News: DISC1: A Matter of Life or Death for Neural Progenitors

Comment by:  Nick Brandon (Disclosure)
Submitted 27 March 2009
Posted 30 March 2009
  I recommend the Primary Papers

Li-huei Tsai and colleagues have identified another pathway in which the candidate gene DISC1 looks to have a critical regulatory role, namely the wnt signaling pathway, in progenitor cell proliferation. In recent years we have seen that DISC1 has a vital role at the centrosome (Kamiya et al., 2005), in cAMP signaling (Millar et al., 2005), and in multiple steps of adult hippocampal neurogenesis (Duan et al., 2007). They have shown a pivotal role for DISC1 in neural progenitor cell proliferation through regulation of GSK3 signaling using a spectacular combination of cellular and in utero manipulations with shRNAs and GSK3 inhibitor compounds. These findings clearly implicate DISC1 in another “druggable” pathway but at this stage do not really identify new approach/targets, except perhaps to confirm that manipulating adult neurogenesis and the wnt pathway holds much potential hope for therapeutics. Perhaps understanding the mechanism of inhibition of GSK3 by DISC1 in more detail might reveal more novel approaches or encourage more innovative work around this pathway. In addition, I have read the other comment (by Rahman), and though I agree that this work still leaves many questions to be answered, the paper is much more significant and likely reconcilable with previous papers than appreciated. The commentary from Lovestone was very insightful and brings up additional gaps and issues with the present work. Additional experimentation I am sure will tease out more key facets of the DISC1-wnt interaction in the near future.

There are many avenues now to proceed with this work. In particular, from the DISC1-centric view, a GSK3 binding site on DISC1 overlaps with one of the critical core PDE4 binding site. Mao et al. show that residues 211 to 225 are a core part of a GSK3 binding site. Previously, Miles Houslay had shown very elegantly that residues 191-230 form a common binding site (known as common site 1) for both PDE4B and 4D families (Murdoch et al., 2007). It will be important to understand the relationship between GSK3 and PDE4 related signaling in reference to the activity of DISC1 starting at whether a trimolecular complex among DISC1-PDE4-GSK3 can form. Then it will be critical to understand the regulatory interplay among these molecules. For example, it is known that PKA can regulate GSK3 activity (Torii et al., 2008) and the interaction between DISC1 and PDE4, while both GSK3 and PKA can phosphorylate β-catenin (Taurin et al., 2006). The output of these relationships on progenitor proliferation will further deepen insights into the role of DISC1 complexes in neuronal processes. This type of situation is not really surprising for a molecule (DISC1) which has been shown to interact with >100 proteins (Camargo et al., 2007). The context of these interactions in both normal development and disease is likely to be critical to allow understanding of its complete functional repertoire.

Another area where these new findings need to be exploited is in the study of additional animal models. Though the two behavioral endpoint models used in the paper (amphetamine hyperactivity and forced swim test) provide a tantalizing glimpse of the behavioral importance of the complex, it would be critical to look in additional models relevant for schizophrenia and mood disorders. Furthermore, it will be very interesting to look at the effects of GSK3β inhibitors in some of the DISC1 animal models already available and to see if they can reverse all or a subset of reported behaviors. In reviewing a summary of the phenotypes available to date (Shen et al., 2008) there is clearly a number of lines which share the properties with mice injected with DISC1 shRNA into the dentate gyrus and would be of value to look at.

A very exciting paper which I am sure will drive additional research into understanding the role of DISC1 in psychiatry and hopefully encourage drug discovery efforts around this molecular pathway (Wang et al., 2008).

References:

1. Kamiya A, Kubo K, Tomoda T, Takaki M, Youn R, Ozeki Y, Sawamura N, Park U, Kudo C, Okawa M, Ross CA, Hatten ME, Nakajima K, Sawa A. A schizophrenia-associated mutation of DISC1 perturbs cerebral cortex development. Nat Cell Biol . 2005 Dec 1 ; 7(12):1167-78. Abstract

2. Millar JK, Pickard BS, Mackie S, James R, Christie S, Buchanan SR, Malloy MP, Chubb JE, Huston E, Baillie GS, Thomson PA, Hill EV, Brandon NJ, Rain JC, Camargo LM, Whiting PJ, Houslay MD, Blackwood DH, Muir WJ, Porteous DJ. DISC1 and PDE4B are interacting genetic factors in schizophrenia that regulate cAMP signaling. Science . 2005 Nov 18 ; 310(5751):1187-91. Abstract

3. Duan X, Chang JH, Ge S, Faulkner RL, Kim JY, Kitabatake Y, Liu XB, Yang CH, Jordan JD, Ma DK, Liu CY, Ganesan S, Cheng HJ, Ming GL, Lu B, Song H. Disrupted-In-Schizophrenia 1 regulates integration of newly generated neurons in the adult brain. Cell . 2007 Sep 21 ; 130(6):1146-58. Abstract

4. Murdoch H, Mackie S, Collins DM, Hill EV, Bolger GB, Klussmann E, Porteous DJ, Millar JK, Houslay MD. Isoform-selective susceptibility of DISC1/phosphodiesterase-4 complexes to dissociation by elevated intracellular cAMP levels. J Neurosci . 2007 Aug 29 ; 27(35):9513-24. Abstract

5. Torii K, Nishizawa K, Kawasaki A, Yamashita Y, Katada M, Ito M, Nishimoto I, Terashita K, Aiso S, Matsuoka M. Anti-apoptotic action of Wnt5a in dermal fibroblasts is mediated by the PKA signaling pathways. Cell Signal . 2008 Jul 1 ; 20(7):1256-66. Abstract

6. Taurin S, Sandbo N, Qin Y, Browning D, Dulin NO. Phosphorylation of beta-catenin by cyclic AMP-dependent protein kinase. J Biol Chem . 2006 Apr 14 ; 281(15):9971-6. Abstract

7. Camargo LM, Collura V, Rain JC, Mizuguchi K, Hermjakob H, Kerrien S, Bonnert TP, Whiting PJ, Brandon NJ. Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia. Mol Psychiatry . 2007 Jan 1 ; 12(1):74-86. Abstract

8. Shen S, Lang B, Nakamoto C, Zhang F, Pu J, Kuan SL, Chatzi C, He S, Mackie I, Brandon NJ, Marquis KL, Day M, Hurko O, McCaig CD, Riedel G, St Clair D. Schizophrenia-related neural and behavioral phenotypes in transgenic mice expressing truncated Disc1. J Neurosci . 2008 Oct 22 ; 28(43):10893-904. Abstract

9. Wang Q, Jaaro-Peled H, Sawa A, Brandon NJ. How has DISC1 enabled drug discovery? Mol Cell Neurosci . 2008 Feb 1 ; 37(2):187-95. Abstract

View all comments by Nick Brandon

Related News: Large Family Study Links Genetics of Schizophrenia, Bipolar Disorder

Comment by:  Alastair Cardno
Submitted 7 April 2009
Posted 7 April 2009
  I recommend the Primary Papers

The results of the family/adoption study by Lichtenstein et al. (2009) and our twin study (Cardno et al., 2002) are remarkably similar. Using a non-hierarchical diagnostic approach, the genetic correlation between schizophrenia and bipolar/mania was 0.60 in the family/twin study and 0.68 in the twin study. The heritability estimates were somewhat lower in the family/adoption (~60 percent) than twin study (~80 percent), but can still be said to be substantial and similar for both disorders.

When we adopted a hierarchical approach, with schizophrenia above mania, we found no monozygotic twin pairs where one twin had schizophrenia and the other had bipolar/mania, but with their considerably larger sample, Lichtenstein et al. (2009) were able to confirm a significantly elevated risk for bipolar disorder in siblings of probands with schizophrenia (RR = 2.7), even when individuals with co-occurrence of both disorders were excluded.

I think there is a potentially interesting link between the family/adoption and twin studies focusing mainly on non-hierarchical diagnoses: Owen and Craddock’s (2009) commentary on the family/adoption study, where they advocate a dimensional approach, and Will Carpenter’s SRF comment regarding the value of domains of psychopathology. The non-hierarchical approach (where individuals can have a diagnosis of both schizophrenia and bipolar disorder during their lifetime) could be viewed as a form of dimensional/domains of psychopathology approach, with schizophrenia and bipolar disorder each having a dimension of liability, and there is now evidence from family, twin, and adoption analyses that these dimensions are correlated, i.e., that there is some overlap in etiological influences.

If schizophrenia and bipolar disorder share some causal factors in common, what might be the implications for the unresolved status of schizoaffective disorder? Our twin study suggested that the genetic (but not environmental) liability to schizoaffective disorder is entirely shared with schizophrenia and mania, defined non-hierarchically (Cardno et al., 2002). If so, and if schizophrenia and bipolar disorder share some genetic susceptibility loci in common, while other loci are not shared, then risk of schizoaffective disorder (or perhaps the bipolar subtype) could be elevated either by the coincidental co-occurrence of non-shared susceptibility loci, or by the occurrence of loci that are common to both disorders.

In this case, any loci that influence risk of schizoaffective disorder (bipolar subtype?) should also increase risk of schizophrenia and/or bipolar disorder, and this model would be refuted if any relatively specific susceptibility loci for schizoaffective disorder were confidently identified.

Some further outstanding issues:



References:

Cardno AG, Rijsdijk FV, Sham PC, Murray RM, McGuffin P. A twin study of genetic relationships between psychotic symptoms. American Journal of Psychiatry 2002;159:539-545. Abstract

Lichtenstein P, Yip BH, Björk C, Pawitan Y, Cannon TD, Sullivan PF, Hultman CM. Common genetic determinants of schizophrenia and bipolar disorder in Swedish families: a population-based study. Lancet 2009;373:234-9. Abstract

Owen MJ, Craddock N. Diagnosis of functional psychoses: time to face the future. Lancet 2009;373:190-191. Abstract

View all comments by Alastair Cardno

Related News: DISC1: A Matter of Life or Death for Neural Progenitors

Comment by:  Akira Sawa, SRF Advisor
Submitted 8 April 2009
Posted 8 April 2009

Mao and colleagues’ present outstanding work sheds light on a novel function of DISC1. Because DISC1 is a multifunctional protein, the addition of new functions is not surprising. Thus, for the past several years, the field has focused on how DISC1 can have distinct functions in different cell contexts (for example, progenitor cells vs. postmitotic neurons, or developing cortex vs. adult dentate gyrus). In addition to Mao and colleagues, I understand that several groups, including ours, have obtained preliminary, unpublished evidence that DISC1 regulates progenitor cell proliferation, at least in part via GSK3β. Thus, I am very supportive of this new observation.

If there might be a missing point in this paper, it is unclear whether suppression of GSK3β occurs in several different biological contexts in brain in vivo. In other words, it is uncertain whether DISC1’s actions on GSK3β are constitutive or context-dependent. How can we reconcile differential roles for DISC1 in progenitor cells in contrast to postmitotic neurons? We have already obtained a preliminary promising answer to this question, which is currently being validated very intensively. These two phenotypes (progenitor cell control and postmitotic migration) may compensate for each other in cortical development; thus, overall cortical pathology looks milder in adults, at least in our preliminary unpublished data using DISC1 knockout mice. We are not sure how this novel function of DISC1 may account for the pathology of Scottish cases. Although I have great respect for the Scottish pioneers of DISC1 study, such as St. Clair, Blackwood, and Muir (I believe that the St. Clair et al., 1990 Lancet paper is one of the best publications in psychiatry), now is the time to pay more and more attention to the question of the molecular pathway(s) involving DISC1 in general schizophrenia (see 2009 SRF roundtable discussion). Unlike the role of APP in Alzheimer’s disease, DISC1 is not a key biological target in general schizophrenia, instead being an entry point to explore much more important targets for schizophrenia. There may be no more need to stick to DISC1 itself in the unique Scottish cases in schizophrenia research. In sum, although there may still be key missing points in this study, I wish to congratulate the authors on their outstanding work.

References:

St Clair D, Blackwood D, Muir W, Carothers A, Walker M, Spowart G, Gosden C, Evans HJ. Association within a family of a balanced autosomal translocation with major mental illness. Lancet . 1990 Jul 7 ; 336(8706):13-6. Abstract

View all comments by Akira Sawa

Related News: Putting 2 and 2 Together—Chromosomal Deletions and Neurodevelopment in Schizophrenia Susceptibility

Comment by:  Brian Morris
Submitted 5 October 2009
Posted 5 October 2009

The dramatically increased risk of schizophrenia associated with velocardiofacial/DiGeorge syndromes (VCFS/DGS) can potentially provide us with a unique insight into the causes of the disease. This study is interesting in that it provides further evidence that reduced levels of expression of the genes encoded in this short region of chromosome 22 are sufficient to cause neurodevelopmental impairments in cerebrocortical neurons. It is worth remembering, as noted above, and as emphasized by the authors, that VCFS/DGS are associated with increased risk of a number of mental health problems with a neurodevelopmental component, not just schizophrenia. In fact, the cortical abnormality reported in this paper that can be specifically associated with schizophrenia (altered parvalbumin neuron distribution) is really subtle. Nevertheless, the study suggests that reduced expression of these few genes on chromosome 22 may be sufficient to cause cortical parvalbumin neuron dysfunction. In turn, this provides some support for the theory that cortical GABA interneuron impairments are an early event in the etiology of schizophrenia, and not simply a consequence of the cortical dysfunction arising from other causes.

The number of genes in the VCFS/DGS deletion region is small, and studies using gene-specific knockouts can provide further insight into the mechanisms leading to altered cortical function in schizophrenia.

View all comments by Brian Morris

Related News: DISC1 Players Gird For Adult Neurodevelopment

Comment by:  Kevin J. Mitchell
Submitted 8 October 2009
Posted 8 October 2009

The seminal identification of mutations in DISC1 associated with schizophrenia and other psychiatric disorders raises several obvious questions: what does the DISC1 protein normally do? What are its biochemical and cellular functions, and what processes are affected by its mutation? How do defects in these cellular processes ultimately lead to altered brain function and psychopathology? Which brain systems are affected and how? Similar questions could be asked for the growing number of other genes that have been implicated by the identification of putatively causal mutations, including NRG1, ERBB4, NRXN1, CNTNAP2, and many copy number variants. Finding the points of biochemical or phenotypic convergence for these proteins or mutations may be key to understanding how mutations in so many different genes can lead to a similar clinical phenotype and to suggesting points of common therapeutic intervention.

The papers by Kim et al. and Enomoto et al. add more detail to the complex picture of the biochemical interactions of DISC1 and its diverse cellular functions. The links with Akt and PTEN signaling are especially interesting, given the previous implication of these proteins in schizophrenia and autism. Akt, in particular, may provide a link between Nrg1/ErbB4 signaling and DISC1 intracellular functions.

These studies also reinforce the importance of DISC1 and its interacting partners in neurodevelopment, specifically in cell migration and axonal extension. In particular, they highlight the roles of these proteins in postnatal hippocampal development and adult hippocampal neurogenesis. They also raise the question of which extracellular signals and receptors regulate these processes through these signalling pathways. The Nrg1/ErbB4 pathway has already been implicated, but there are a multitude of other cell migration and axon guidance cues known to regulate hippocampal development, some of which, for example, semaphorins, signal through the PTEN pathway.

Whether or how disruptions in these developmental processes contribute to psychopathology also remains unclear. It seems likely that the effects of mutations in any of these genes will be highly pleiotropic and have effects in many brain systems. The reported pathology in schizophrenia is not restricted to hippocampus but extends to cortex, thalamus, cerebellum, and many other regions. Similarly, while the cognitive deficits receive a justifiably large amount of attention, given that they may have the most clinical impact, motor and sensory deficits are also a stable and consistent part of the syndrome that must be explained. Pleiotropic effects on prenatal and postnatal development, as well as on adult processes, may actually be the one common thread characterizing the genes so far implicated. These new papers represent the first steps in the kinds of detailed biological studies that will be required to make explanatory links from mutations, through biochemical and cellular functions, to effects on neuronal networks and ultimately psychopathology.

View all comments by Kevin J. Mitchell

Related News: DISC1 Players Gird For Adult Neurodevelopment

Comment by:  Peter PenzesMichael Cahill
Submitted 8 October 2009
Posted 8 October 2009

DISC1 disruption by chromosomal translocation cosegregates with several neuropsychiatric disorders, including schizophrenia (Blackwood et al., 2001; Millar et al., 2000). Recent attention has focused on the effects of DISC1 on the structure and function of the dentate gyrus, one of the few brain regions that exhibit neurogenesis throughout life. The downregulation of DISC1 has several deleterious effects on the dentate gyrus, including aberrant neuronal migration (Duan et al., 2007). However, the mechanisms through which DISC1 regulates the structure and function of the dentate gyrus remain unknown. The dentate gyrus and its output to the CA3 area, the mossy fiber, show several abnormalities in schizophrenia and other neuropsychiatric diseases (Kobayashi, 2009). Thus, understanding how a gene associated with neuropsychiatric disease, DISC1, mechanistically impacts the dentate gyrus is an important question with much clinical relevance.

The recent papers by Kim et al. and Enomoto et al. characterize an interaction between DISC1 and girdin (also known as KIAA1212), and reveal how girdin, and the interaction between DISC1 and girdin, impact axon development, dendritic development, and the proper positioning of newborn neurons in the dentate gyrus. Girdin normally stimulates the function of AKT (Anai et al., 2005), and Kim et al. show that DISC1 binds to girdin and inhibits its function. Thus, the loss of DISC1 leaves girdin unopposed, resulting in excessive AKT signaling. Indeed, the developmental defects in neurons lacking DISC1 can be rescued by pharmacologically blocking the activation of an AKT downstream target. However, as shown by Enomoto et al., the loss of girdin produces deleterious effects on neuronal morphology, suggesting that a proper balance of girdin function is crucial.

Collectively, these studies thoroughly characterize the interaction between DISC1 and girdin, and shed much light on the consequences of this interaction on neuronal morphology as well as on the positioning of neurons in the dentate gyrus. The role of girdin in the pathology of neuropsychiatric diseases is unknown, and remains an interesting question for the future. Characterizing the molecules that act up- or downstream of DISC1 remains an important area of investigation and could aid the development of pharmacological interventions in the future. It’s intriguing that DISC1 acting through girdin regulates the activity of AKT as AKT1 was previously identified as a schizophrenia risk gene (Emamian et al., 2004). This suggests a convergence of multiple schizophrenia-associated genes in a shared pathway, and thus it will be important to determine if the DISC1-girdin-AKT1 pathway is particularly vulnerable in neuropsychiatric disorders.

References:

Blackwood DH, Fordyce A, Walker MT, St Clair DM, Porteous DJ, Muir WJ. Schizophrenia and affective disorders--cosegregation with a translocation at chromosome 1q42 that directly disrupts brain-expressed genes: clinical and P300 findings in a family. Am J Hum Genet . 2001 Aug 1 ; 69(2):428-33. Abstract

Millar JK, Christie S, Semple CA, Porteous DJ. Chromosomal location and genomic structure of the human translin-associated factor X gene (TRAX; TSNAX) revealed by intergenic splicing to DISC1, a gene disrupted by a translocation segregating with schizophrenia. Genomics . 2000 Jul 1 ; 67(1):69-77. Abstract

Duan X, Chang JH, Ge S, Faulkner RL, Kim JY, Kitabatake Y, Liu XB, Yang CH, Jordan JD, Ma DK, Liu CY, Ganesan S, Cheng HJ, Ming GL, Lu B, Song H. Disrupted-In-Schizophrenia 1 regulates integration of newly generated neurons in the adult brain. Cell . 2007 Sep 21 ; 130(6):1146-58. Abstract

Kobayashi K. Targeting the hippocampal mossy fiber synapse for the treatment of psychiatric disorders. Mol Neurobiol . 2009 Feb 1 ; 39(1):24-36. Abstract

Anai M, Shojima N, Katagiri H, Ogihara T, Sakoda H, Onishi Y, Ono H, Fujishiro M, Fukushima Y, Horike N, Viana A, Kikuchi M, Noguchi N, Takahashi S, Takata K, Oka Y, Uchijima Y, Kurihara H, Asano T. A novel protein kinase B (PKB)/AKT-binding protein enhances PKB kinase activity and regulates DNA synthesis. J Biol Chem . 2005 May 6 ; 280(18):18525-35. Abstract

Emamian ES, Hall D, Birnbaum MJ, Karayiorgou M, Gogos JA. Convergent evidence for impaired AKT1-GSK3beta signaling in schizophrenia. Nat Genet . 2004 Feb 1 ; 36(2):131-7. Abstract

View all comments by Peter Penzes
View all comments by Michael Cahill

Related News: Genomic Studies Draw Autism and Schizophrenia Back Toward Each Other

Comment by:  Katie Rodriguez
Submitted 7 November 2009
Posted 7 November 2009

If schizophrenia and autism are on a spectrum, how can there be people who are both autistic and schizophrenic? I know of a few people who suffer from both diseases.

View all comments by Katie Rodriguez

Related News: Genomic Studies Draw Autism and Schizophrenia Back Toward Each Other

Comment by:  Bernard Crespi
Submitted 12 November 2009
Posted 12 November 2009

One Hundred Years of Insanity: The Relationship Between Schizophrenia and Autism
The great Colombian author Gabriel García Márquez reified the cyclical nature of history in his Nobel Prize-winning 1967 book, One Hundred Years of Solitude. Eugen Bleuler’s less-famous book Dementia Præcox or the Group of Schizophrenias, originally published in 1911, saw first use of the term “autism,” a form of solitude manifest as withdrawal from reality in schizophrenia. This neologism, about to celebrate its centenary, epitomizes an astonishing cycle of reification and change in nosology, a cycle only now coming into clear view as molecular-genetic data confront the traditional, age-old categories of psychiatric classification.

The term autism was, of course, redefined by Leo Kanner (1943) for a childhood psychiatric condition first considered as a subset of schizophrenia, then regarded as quite distinct (Rutter, 1972) or even opposite to it (Rimland, 1964; Crespi and Badcock, 2008), and most recently seen by some researchers as returning to its original Bluelerian incarnation (e.g., Carroll and Owen, 2009). An outstanding new paper by McCarthy et al. (2009), demonstrating that duplications of the CNV locus 16p11.2 are strongly associated with increased risk of schizophrenia, has brought this question to the forefront of psychiatric inquiry, because deletions of this same CNV are one of the most striking recently-characterized risk factors for autism. Additional CNVs, such as those at 1q21.1 and 22q11.21 have also been associated with autism and schizophrenia in one or more studies (e.g., Mefford et al., 2008; Crespi et al., 2009; Glessner et al., 2009), which has led some authors to infer that since an overlapping set of loci mediates risk of both conditions, autism and schizophrenia must be more similar than previously conceived (e.g., Carroll and Owen, 2009; Guilmatre et al., 2009). Similar considerations apply to several genes, such as CNTNAP2 and NRXN1, various disruptions of which have likewise been linked with both conditions (Iossifov et al., 2008; Kirov et al., 2008; Burbach and van der Zwaag, 2009).

So does this plethora of new molecular-genetic data imply that Blueler was indeed correct, if not prescient, that autism and schizophrenia are manifestations of similar disease processes? The answer may appear tantalizingly close, but will likely remain inaccessible without explicit consideration of alternative hypotheses and targeted tests of their differentiating predictions. This approach is simply Platt’s (1964) classic method of strong inference, which has propelled molecular biology so far and fast but left psychiatry largely by the wayside (Cannon, 2009). The alternative hypotheses in this case are clear: with regard to causation from specific genetic and genomic risk factors, autism and schizophrenia are either: 1) independent and discrete, 2) partially yet broadly overlapping, 3) subsumed with autism as a subset of schizophrenia, or 4) diametrically opposite, with normality in the centre. CNVs are especially useful for testing among such alternative hypotheses, because they naturally involve highly-penetrant perturbations in two opposite directions, due to deletions vs duplications of more or less the same genomic regions. Hypotheses 2), 3) and 4) thus predict that autism and schizophrenia should share CNV risk loci, but 2) and 3) predict specific rearrangements (deletions, duplications, or both) shared across both conditions; by contrast, hypothesis (4) predicts that, as highlighted by McCarthy et al. (2009), reciprocal CNVs at the same locus should mediate risk of autism versus schizophrenia. This general approach was pioneered by Craddock et al. (2005, 2009), in their discussion of explicit alternative hypotheses for the relationship between schizophrenia and bipolar disorder, which are now known to share a notable suite of risk alleles.

A key assumption that underlies tests of hypotheses for the relationship between autism and schizophrenia is accuracy of diagnoses. For schizophrenia, this is seldom at issue. However, diagnoses of autism, or autism spectrum disorders such as PDD-NOS, are normally made at an age well before the first manifestations of schizophrenia in adolescence or early adulthood, which generates a risk for false-positive diagnoses of premorbidity to schizophrenia as autism or autism spectrum (e.g., Eliez, 2007). The tendencies for males to exhibit worse premorbidity to schizophrenia than females (Sobin et al., 2001; Tandon et al., 2009), for CNVs to exert severe effects on diverse aspects of early neurodevelopment (Shinawi et al., 2009), and for schizophrenia of earlier onset to exhibit a higher male sex-ratio bias and a stronger tendency to be associated with CNVs rather than other causes (Remschmidt et al., 1994; Rapoport et al., 2009), all suggest a high risk for false-positive diagnoses of autistic spectrum conditions in individuals with these genomic risk factors (Feinstein and Singh, 2007; Reaven et al., 2008; Sugihara et al., 2008; Starling and Dossetor, 2009). Possible evidence of such risk comes from diagnoses of autism spectrum conditions in children with deletions at 15q11.2, 15q13.3, and 22q11.21, and duplications of 16p11.2, CNVs for which schizophrenia risk has been well established from studies of adults (Antshel et al., 2007; Stefansson et al., 2008; Weiss et al., 2008; Ben-Shachar et al., 2009; Doornbos et al., 2009; McCarthy et al., 2009). By contrast, autism-associated CNVs, such as deletions at 16p11.2 (Kumar et al., 2008), or duplications at 22q11.21 (Glessner et al., 2009; Crespi et al., 2009) have seldom also been reported in individuals diagnosed with schizophrenia, which suggests that false-positive diagnoses of schizophrenia as autism are uncommon.

Differentiating between a hypothesis of false-positive diagnoses of premorbidity to schizophrenia as autism, compared to a hypothesis of specific deletions or duplications shared between autism and schizophrenia, requires some combination of longitudinal studies, judicious use of endophenotypes, and adoption of relatively new diagnostic categories such as multiple complex developmental disorder (Sprong et al., 2008). Moreover, to the degree that such false positives are not uncommon, and autism and schizophrenia are underlain by diametric genetically based risk factors, inclusion of children premorbid for schizophrenia in studies on the genetic bases of autism will substantially dilute the probability of detecting significant results.

Ultimately, robust evaluation of alternative hypotheses for the relationship of autism with schizophrenia will require evidence from studies of common and rare SNP variants as well as CNVs, in-depth analyses of the neurodevelopmental and neuronal-function effects of different alterations to genes such as NRXN1, CNTNAP2, and SHANK3, and integrative data from diverse disciplines other than genetics, especially the neurosciences and psychology. Unless such interdisciplinary studies are deployed—in hypothesis-testing frameworks that use strong inference—we should expect to remain, as penned by García Márquez, in “permanent alternation between excitement and disappointment, doubt and revelation, to such an extreme that no one knows for certain where the limits of reality lay”—for yet another 100 years.

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View all comments by Bernard Crespi

Related News: Genomic Studies Draw Autism and Schizophrenia Back Toward Each Other

Comment by:  Suzanna Russell-SmithDonna BaylissMurray Maybery
Submitted 9 February 2010
Posted 10 February 2010

The Diametric Opposition of Autism and Psychosis: Support From a Study of Cognition
As has been noted previously, Crespi and Badcock’s (2008) theory that autism and schizophrenia are diametrically opposed disorders is certainly a novel and somewhat controversial one. In his recent blog on Psychology Today, Badcock states that the theory stands on two completely different foundations: one in evolution and genetics, and one in psychiatry and cognitive science (Badcock, 2010). While most of the comments posted before ours have addressed the relationship between autism and schizophrenia from a genetic perspective, coming from a psychology background, we note that it is the aspects of Crespi and Badcock’s theory that relate to cognition which have particularly caught our attention. While we can therefore contribute little to the discussion of a relationship between autism and schizophrenia from a genetic standpoint, we present the findings from our recent study (Russell-Smith et al., 2010), which provided the first test of Crespi and Badcock’s claim that autism and psychosis are at opposite ends of the cognitive spectrum.

In placing autism and psychosis at opposite ends of the cognitive spectrum, Crespi and Badcock (2008) propose that autistic and positive schizophrenia traits contrastingly affect preference for local versus global processing, with individuals with autism displaying a preference for local processing and individuals with positive schizophrenia displaying a preference for global processing. That is, these authors claim that while individuals with autism show a tendency to focus on detail or process features in their isolation, individuals with positive schizophrenia show a tendency to look at the bigger picture or process features as an integrated whole. Importantly, since Crespi and Badcock argue for a continuum stretching all the way from autism to psychosis, the same diametric pattern of cognition should be seen in individuals who display only mild variants of autistic and positive schizophrenia traits. This includes typical individuals who score highly on measures such as the Autism Spectrum Quotient (AQ; Baron-Cohen et al., 2001) and the Unusual Experiences subscale of the Oxford-Liverpool Inventory of Experiences (O-LIFE:UE; Mason et al., 2005). These are both reliable and commonly used measures which have been specifically designed to assess the levels of “autistic-like” traits and positive schizotypy traits in typical individuals. Since Crespi and Badcock actually argue their theory is best evaluated with reference to individuals with milder traits of autism and positive schizophrenia, it is with these populations that we investigated their claims.

A task often used to determine whether an individual has a preference for local over global processing is the Embedded Figures Test (EFT; Witkin et al., 1971), which requires individuals to detect hidden shapes within complex figures. As the test requires one to resist experiencing an integrated visual stimulus or gestalt in favor of seeing single elements, it is argued that a local processing style aids successful (i.e., faster) completion of this task (Bolte et al., 2007). Accordingly, from Crespi and Badcock’s (2008) theory, one would expect that relative to individuals with low levels of these traits, individuals with high levels of autistic-like traits should perform better on the EFT, while individuals with positive schizotypy traits should perform worse. To test this claim, our study obtained the AQ and O-LIFE:UE scores for 318 students completing psychology as part of a broader degree (e.g., a BSc or BA). Two pairs of groups (i.e., four groups in total), each consisting of 20 students, were then formed. One of these pairs consisted of High and Low AQ groups, which were selected such that they were separated substantially in their AQ scores but matched as closely as possible on their O-LIFE:UE scores. The other pair of groups, the High and Low O-LIFE:UE groups, were selected such that they were separated in their O-LIFE:UE scores, but matched as closely as possible on their AQ scores. The gender ratio was matched closely across the four groups.

To test the prediction that higher levels of autistic-like traits are associated with more skilled EFT performance, the High and Low AQ groups were compared in terms of their mean response time to accurately locate each of the embedded figures. Individuals in the High AQ group did display more skilled EFT performance than individuals in the Low AQ group, consistent with a greater preference for local over global processing in relation to higher levels of autistic-like traits (see also Almeida et al., 2010; Bolte and Poustka, 2007; Grinter et al., 2009; Grinter et al., 2009). We then compared EFT performance for the O-LIFE:UE groups to test the prediction that higher levels of positive schizotypy traits are associated with less skilled performance on this task. Consistent with a preference for global over local processing in relation to higher levels of positive schizotypy traits, individuals in the High O-LIFE:UE group displayed less skilled EFT performance than individuals in the Low O-LIFE:UE group. Therefore, results from both pairs of groups together provide support for Crespi and Badcock’s (2008) claim that autistic and positive schizophrenia traits are diametrically opposed with regard to their effect on local versus global processing.

However, the support our study offers for Crespi and Badcock’s (2008) theory was tempered slightly by our failure to find the expected contrasting patterns of non-verbal relative to verbal ability for our two pairs of groups. To display the expected patterns, relative to individuals with low levels of these traits, individuals with high levels of autistic-like traits should have displayed higher non-verbal ability relative to verbal ability, whereas individuals with high levels of positive schizotypy traits should have displayed lower non-verbal relative to verbal ability. While visual inspection of mean verbal and non-verbal scores for the O-LIFE:UE groups revealed a trend consistent with what would be expected based on Crespi and Badcock’s theory, none of the group differences was statistically significant. However, as we pointed out in our article, a study which offers a more complete assessment of this aspect of the theory is warranted. In particular, since the use of a student sample in our study no doubt led to a restriction in the range of IQ scores (especially with reference to verbal IQ), a test of community-based samples would be useful.

Therefore, while Crespi and Badcock’s (2008) theory has passed its first major test at the level of cognition, with our results indicating a contrasting effect of autistic-like and positive schizotypy traits with regard to preference for local versus global processing, further investigation of these authors’ theory at both the cognitive and genetic levels is required.

References:

Almeida, R., Dickinson, J., Maybery, M., Badcock, J., Badcock, D. A new step toward understanding Embedded Figures Test performance in the autism spectrum: The radial frequency search task. Neuropsychologia. 2010 Jan;48(2):374-81. Abstract

Badcock, C. (2010). Diametric cognition passes its first lab test. Psychology Today. Retrieved February 8, from http://www.psychologytoday.com/blog/the-imprinted-brain/201002/diametric-cognition-passes-its-first-lab-test.

Baron-Cohen, S., Wheelwright, S., Skinner, R., Martin, J., Clubley, E. (2001). The Autism-Spectrum Quotient (AQ): Evidence from Asperger Syndrome/High-Functioning Autism, males and females, scientists and mathematicians. Journal of Autism and Developmental Disorders, 31, 5-17. Abstract

Bolte, S., Holtmann, M., Poustka, F., Scheurich, A., Schmidt, L. (2007). Gestalt perception and local-global processing in High-Functioning Autism. Journal of Autism and Developmental Disorders, 37, 1493-1504. Abstract

Bolte, S., Poustka, F. (2006). The broader cognitive phenotype of autism in parents: How specific is the tendency for local processing and executive function. Journal of Child Psychology and Psychiatry, 47, 639-645. Abstract

Crespi, B., Badcock, C. (2008). Psychosis and autism as diametrical disorders of the social brain. Behavioral and Brain Sciences, 31, 241-261. Abstract

Grinter, E., Maybery, M., Van Beek, P., Pellicano, E., Badcock, J., Badcock, D. (2009). Global visual processing and self-rated autistic-like traits. Journal of Autism and Developmental Disorders, 39, 1278-1290. Abstract

Grinter, E., Van Beek, P., Maybery, M., Badcock, D. (2009). Brief Report: Visuospatial analysis and self-rated autistic-like traits. Journal of Autism and Developmental Disorders, 39, 670–677. Abstract

Mason, O., Linney, Y., Claridge, G. (2005). Short scales for measuring schizotypy. Schizophrenia Research, 78, 293-296. Abstract

Russell-Smith, S., Maybery, M., Bayliss, D. Are the autism and positive schizotypy spectra diametrically opposed in local versus global processing? Journal of Autism and Developmental Disorders. 2010 Jan 28. Abstract

Witkin, H., Oltman, P., Raskin, E., Karp, S. (1971). A manual for the Embedded Figures Test. Palo Alto, CA: Consulting Psychologists Press.

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Related News: CNV “Double Whammies” May Account for Variable Neuropsychiatric Phenotypes

Comment by:  Ben Pickard
Submitted 25 February 2010
Posted 25 February 2010

In their Nature Genetics paper, Girirajan et al. contribute to the slow shift of focus in the field of complex genetic disorders, away from population risks towards the risks specific to the individual. The driving force of this shift is the ongoing discovery of mutations more penetrant than the common single nucleotide polymorphisms (SNPs) studied in case-control association studies. Copy number variants (CNVs) and coding variants are the two principal classes of these mutations, typified by their relative rarity, frequent familiality, and generally higher odds ratio (OR) values indicative of their impact.

Considerable evidence from increased levels of comorbidity, dysmorphic features, brain structural changes, and latent endophenotypes suggests that early neurodevelopmental deficits can predispose to later neuropsychiatric conditions (Ross et al., 2006). This paper demonstrates how the phenotype in a single individual can be more closely linked with the causative genotype when the simultaneous action of two CNVs is considered. This provides some concrete evidence to explain how seemingly disparate diagnoses (for example, epilepsy, autism, schizophrenia and mental retardation) and variable penetrance can occur in different individuals who ostensibly carry the same pathogenic CNV (van Bon et al., 2009; Mefford et al., 2008)—specifically, it appears that a second CNV can translate a generalized neurodevelopmental pathology into a more specific, severe, and reproducible final clinical endpoint. Hence, the authors invoke a “two-hit” hypothesis, as originally applied by Knudson to explain the observed progression of familial forms of cancer (Knudson, 1971).

From a semantic point of view, the use of the “two-hit” terminology is a little loosely applied here. Originally, this described an inherited predisposition to cancer in the form of a tumor suppressor mutation which was coupled with a later, somatic, “second hit” oncogenic mutation that resulted in the tumor. In the current application of the term, both mutational changes are germline, present from the outset, and even a single CNV “hit” can still produce a phenotype. However, the comprehensive data in the paper and the analogy used are thought-provoking, as they highlight three etiological issues, outlined below, which may have wide applicability to complex genetic disorders.

1. A key observation from this paper is that the hypothetical Venn diagrams illustrating the overlapping relationships between the varied diagnoses and also between diagnoses and genomic variation would be highly complex. The phenotypic reach of each CNV may also be considerably greater than we currently suppose—limited by the developmental or neurological conditions that have yet to be comprehensively studied by comparative genomic hybridization. Conversely, the interpretation of shared genetic risk in association and epidemiological studies may have to be reassessed in the light of this paper’s findings. For example, the demonstration of a component of genetic contribution shared between bipolar disorder and schizophrenia may not be such a simple story (Lichtenstein et al., 2009). That component may be just a genetic contribution to generalized neurodevelopmental failure which predisposes to neuropsychiatric disorders in the context of “second hit,” disease-specific mutations (schizophrenia or bipolar disorder, in this case). Can a gene truly be called a “schizophrenia gene” if you haven’t discounted its role in other conditions first? This is reminiscent of the shared genetic contribution to underlying autoimmunity processes which is emerging from the genomewide association studies of diagnostically discrete disorders such as type I diabetes, Crohn’s disease, and rheumatoid arthritis (Baranzini, 2009).

2. The two-hit terminology and the involvement of neurodevelopmental deficits clearly imply a sequential pattern of CNV effect—early predisposition followed by later resolution of diagnosis. Mouse gene knockouts have shown that such staged action is indeed possible, and its confounding effects on animal models of disease led to the development of spatially and temporally controllable transgenic technologies (Gingrich et al., 1998). However, to prove this in the context of the CNV model will require both the individual spatiotemporal expression profiles of the deleted genes and also some measure of individual gene dosage sensitivity to be correlated with the apparent mode of CNV action (developmental or “modifier”).

3. The model’s restriction to just two contributory CNVs as presented here is, in my opinion, a by-product of CNV scarcity, visibility, and sample size, rather than a genuine biological phenomenon. As the authors state, the accuracy of genotype-phenotype correlations at the level of the individual will undoubtedly increase when common and rare SNP variation is also taken into account—potentially to the point where predictive diagnosis is realistic. Likewise, the authors’ suggestion that the second CNV has a “modifier” effect on the foundation CNV is enticing, and backed up by the ubiquity of the 16p12.1 across several genomic disorders, but it is still difficult at this stage to discount the equally compelling explanation that two CNVs just represent a simple increase in mutational load. However, this latter explanation has its own problems, as it suggests a continuum of illness dictated by additive genetic risk. Does this continuum start with mild developmental delay and end with neuropsychiatric illness—or vice versa?

Finally, it must not be forgotten that schizophrenia, bipolar, autism, and epilepsy can exist without comorbid traits and without evidence for developmental issues. Is this, then, an important dimension to be considered in the future sub-categorization of these disorders?

References:

Ross CA, Margolis RL, Reading SA, Pletnikov M, Coyle JT. Neurobiology of schizophrenia. Neuron . 2006 Oct 5 ; 52(1):139-53. Abstract

van Bon BW, Mefford HC, Menten B, Koolen DA, Sharp AJ, Nillesen WM, Innis JW, de Ravel TJ, Mercer CL, Fichera M, Stewart H, Connell LE, Ounap K, Lachlan K, Castle B, Van der Aa N, van Ravenswaaij C, Nobrega MA, Serra-Juhé C, Simonic I, de Leeuw N, Pfundt R, Bongers EM, Baker C, Finnemore P, Huang S, Maloney VK, Crolla JA, van Kalmthout M, Elia M, Vandeweyer G, Fryns JP, Janssens S, Foulds N, Reitano S, Smith K, Parkel S, Loeys B, Woods CG, Oostra A, Speleman F, Pereira AC, Kurg A, Willatt L, Knight SJ, Vermeesch JR, Romano C, Barber JC, Mortier G, Pérez-Jurado LA, Kooy F, Brunner HG, Eichler EE, Kleefstra T, de Vries BB. Further delineation of the 15q13 microdeletion and duplication syndromes: a clinical spectrum varying from non-pathogenic to a severe outcome. J Med Genet . 2009 Aug 1 ; 46(8):511-23. Abstract

Mefford HC, Sharp AJ, Baker C, Itsara A, Jiang Z, Buysse K, Huang S, Maloney VK, Crolla JA, Baralle D, Collins A, Mercer C, Norga K, de Ravel T, Devriendt K, Bongers EM, de Leeuw N, Reardon W, Gimelli S, Bena F, Hennekam RC, Male A, Gaunt L, Clayton-Smith J, Simonic I, Park SM, Mehta SG, Nik-Zainal S, Woods CG, Firth HV, Parkin G, Fichera M, Reitano S, Lo Giudice M, Li KE, Casuga I, Broomer A, Conrad B, Schwerzmann M, Räber L, Gallati S, Striano P, Coppola A, Tolmie JL, Tobias ES, Lilley C, Armengol L, Spysschaert Y, Verloo P, De Coene A, Goossens L, Mortier G, Speleman F, van Binsbergen E, Nelen MR, Hochstenbach R, Poot M, Gallagher L, Gill M, McClellan J, King MC, Regan R, Skinner C, Stevenson RE, Antonarakis SE, Chen C, Estivill X, Menten B, Gimelli G, Gribble S, Schwartz S, Sutcliffe JS, Walsh T, Knight SJ, Sebat J, Romano C, Schwartz CE, Veltman JA, de Vries BB, Vermeesch JR, Barber JC, Willatt L, Tassabehji M, Eichler EE. Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med . 2008 Oct 16 ; 359(16):1685-99. Abstract

Knudson AG. Mutation and cancer: statistical study of retinoblastoma. Proc Natl Acad Sci U S A . 1971 Apr 1 ; 68(4):820-3. Abstract

Lichtenstein P, Yip BH, Björk C, Pawitan Y, Cannon TD, Sullivan PF, Hultman CM. Common genetic determinants of schizophrenia and bipolar disorder in Swedish families: a population-based study. Lancet . 2009 Jan 17 ; 373(9659):234-9. Abstract

Baranzini SE. The genetics of autoimmune diseases: a networked perspective. Curr Opin Immunol . 2009 Dec 1 ; 21(6):596-605. Abstract

Gingrich JR, Roder J. Inducible gene expression in the nervous system of transgenic mice. Annu Rev Neurosci . 1998 Jan 1 ; 21():377-405. Abstract

View all comments by Ben Pickard

Related News: Schizophrenia Genetics 2: The Rise of GWAS

Comment by:  Chris Carter
Submitted 7 April 2010
Posted 8 April 2010

I wonder whether the relative lack of success in schizophrenia GWAS may be because the origin of schizophrenia may lie not so much in the genetic make-up of people with schizophrenia themselves, but in their prenatal experience, and possibly with the genes of the mother rather than with those of the offspring. Famine, rubella, influenza, herpes (HSV1 and HSV2), and poliovirus infection as well as high fever during pregnancy have all been listed as risk factors for the offspring developing schizophrenia in later life, as have maternal preeclampsia and obstetric complications. (See page at Polygenic Pathways for the many references.)

Maternal resistance to these effects is likely to be gene-dependent. Is it worth considering GWAS in the mothers rather than in the offspring?

View all comments by Chris Carter

Related News: Exome Sequencing Hints at Prenatal Genes in Schizophrenia

Comment by:  Sven CichonMarcella RietschelMarkus M. Nöthen
Submitted 5 October 2012
Posted 5 October 2012

The new exome sequencing study by Xu et al. confirms previous results by the same research group (Xu et al., 2011) and by an independent group (Girard et al., 2011) that a significantly higher frequency of protein-altering de novo single nucleotide variants (SNVs) and in/dels is found in sporadic patients with schizophrenia. It is certainly reassuring that this observation has now been confirmed in an independent and considerably larger sample (134 patient-parent trios and 34 control-parent trios).

A closer look also reveals differences between this study and the study by Girard et al.: Xu et al. do not find a significantly higher overall de novo mutation rate per base per generation when comparing schizophrenia and control trios (1.73 x 10-08 vs. 1.28 x 10-08). In contrast, the Girard study found 2.59 x 10-08 de novo mutations in schizophrenia trios as opposed to the 1.1 x 10-08 events reported in the general population by the 1000 Genomes Project. The larger sample size in the new study by Xu et al., however, suggests that their estimation of the de novo mutation rates may be more precise now.

What eventually seems to count is the quality of the de novo mutations in the sporadic schizophrenia patients. The function of the genes hit by the non-synonymous/deleterious (as defined by in-silico scores) mutations is diverse and shows similarity with functions reported for common risk genes for schizophrenia identified by GWAS. Interestingly, there is an overrepresentation of genes that are predominantly expressed during embryogenesis, strongly highlighting a possible effect of neurodevelopmental disturbances in the etiology of schizophrenia (and nicely supporting what has already been concluded from GWAS).

It would probably be very interesting to estimate the penetrance of such de novo mutations to get a feeling for their individual impact on the development of the disease. In the absence of a reasonable number of individuals with the same mutation, however, this will be a difficult task.

Another aspect that is missing in the current paper, but is accessible to investigation, is the frequency/quality of de novo mutations in trios with a family history of schizophrenia and comparison to the figures seen in the sporadic trios. That might (or might not) support the authors’ conclusion that de novo events play a strong role in sporadic cases (and not in familial cases).

References:

Xu B, Roos JL, Dexheimer P, Boone B, Plummer B, Levy S, Gogos JA, Karayiorgou M. Exome sequencing supports a de novo mutational paradigm for schizophrenia. Nat Genet . 2011 Sep ; 43(9):864-8. Abstract

Girard SL, Gauthier J, Noreau A, Xiong L, Zhou S, Jouan L, Dionne-Laporte A, Spiegelman D, Henrion E, Diallo O, Thibodeau P, Bachand I, Bao JY, Tong AH, Lin CH, Millet B, Jaafari N, Joober R, Dion PA, Lok S, Krebs MO, Rouleau GA. Increased exonic de novo mutation rate in individuals with schizophrenia. Nat Genet . 2011 Sep ; 43(9):860-3. Abstract

View all comments by Sven Cichon
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Related News: Exome Sequencing Hints at Prenatal Genes in Schizophrenia

Comment by:  Patrick Sullivan, SRF Advisor
Submitted 5 October 2012
Posted 5 October 2012

This paper by the productive group at Columbia increases our knowledge of the role of rare exon mutations in schizophrenia. The authors applied exome sequencing—a newish high-throughput sequencing technology—to trios consisting of both parents plus an offspring with schizophrenia. The authors focused on a subset of the genome (the “exome,” genetic regions believed to code for protein) on a subset of genetic variants (SNPs and insertion/deletion variants) of predicted functional significance, and on one type of inheritance (“de novo“ mutations, those absent in both parents and present in the offspring with schizophrenia).

The sample sizes are the largest yet reported for schizophrenia—231 affected trios and 34 controls. About 28 percent of these samples were reported in 2011 (Xu et al., 2011). A recent schizophrenia sequencing study (N = 166) from the Duke group was unrevealing (Need et al., 2012). The numbers in the Xu, 2012 paper are small compared to the three Nature trio studies for autism (see SRF related news story), an approximately threefold larger trio study for schizophrenia (in preparation), a case-control exome sequencing study for schizophrenia (total N ~5,000, in preparation), and a case-control exome chip study for schizophrenia (total N ~11,000, in preparation).

The authors reported:

more mutations with older fathers, as has been reported before (see SRF related news story). Note that advanced paternal age is an established risk factor for schizophrenia.

more de novo/predicted functional/exonic mutations in schizophrenia than in controls. However, the difference was slight, one-sided P = 0.03. One can quibble with the use of a one-tailed test (should never be used, in my opinion), but it is difficult to interpret this result unless paternal age is included as a covariate in this critical test.

an impressive set of bioinformatic and integrative analyses—see the paper for the large amount of work they did.

as might be predicted given the small sample size and the rarity of these sorts of mutations, there was no statistically significant pile-up of variants in specific genes. Hence, to my reading, the authors do not compellingly implicate any specific genes in the pathophysiology of schizophrenia. This conclusion is consistent with Need et al., 2012, and I note that the autism work implicated only a few genes (e.g., CHD8 and KATNAL2).

Note that the authors would disagree with the above, as they chose to focus on a set of genes that they thought stood out (reporting an aggregate P of 0.002), and the last third of the paper focuses on these genes. However, the human genetics community now insists on two critical points for implicating specific genes in associations with a disorder. The first is statistical significance, and the critical P value for an exome sequencing study is on the order of 1E-6. The second is replication. In my view, neither of these standards are achieved. However, their observations are intriguing, and may well eventually move us forward.

The key observation in this paper is the increased rate of de novo variation in schizophrenia cases. Is the increased rate indeed part of an etiological process? In other words, older fathers have an increased chance of exonic mutations, and these, in turn, increase risk for schizophrenia? Or are these merely hitch-hikers of no particularly biological import?

A major issue with exome studies is that there are so many predicted functional variants in apparently normal people. We all carry on the order of 100 exonic variants of predicted functional consequences with on the order of 20 genes that are probable knockouts. If part of the risk for schizophrenia indeed resides in the exome, very large studies will be required to identify such loci confidently. Moreover, published work on autism and unpublished work for type 2 diabetes, coronary artery disease, and schizophrenia suggest that this will require very large sample sizes, on the order of 100 times more than reported here. And, it is possible that the exome is not all that important for schizophrenia.

References:

Xu B, Roos JL, Dexheimer P, Boone B, Plummer B, Levy S, Gogos JA, Karayiorgou M. Exome sequencing supports a de novo mutational paradigm for schizophrenia. Nat Genet . 2011 Sep ; 43(9):864-8. Abstract

Need AC, McEvoy JP, Gennarelli M, Heinzen EL, Ge D, Maia JM, Shianna KV, He M, Cirulli ET, Gumbs CE, Zhao Q, Campbell CR, Hong L, Rosenquist P, Putkonen A, Hallikainen T, Repo-Tiihonen E, Tiihonen J, Levy DL, Meltzer HY, Goldstein DB. Exome sequencing followed by large-scale genotyping suggests a limited role for moderately rare risk factors of strong effect in schizophrenia. Am J Hum Genet . 2012 Aug 10 ; 91(2):303-12. Abstract

View all comments by Patrick Sullivan

Related News: Cognitive Deficits Found in Controls Carrying Neuropsychiatric Risk CNVs

Comment by:  Daniel Weinberger, SRF Advisor
Submitted 19 December 2013
Posted 19 December 2013

The latest important result from the Icelandic population genetic study confirms from a new vantage point what has been clear from over two decades of research: that genetic risk for schizophrenia is associated with cognitive deficits independent of the presence of illness. The earlier work to identify this association included studies of discordant monozygotic twins (Goldberg et al., 1990; Cannon et al., 2000) and more studies of healthy siblings (Egan et al., 2001). These results are consistent with the view that susceptibility genes for developmental neuropsychiatric disorders are genes that influence brain development and function. Cognitive assays are proxies for integrative neural functions that reflect these effects.

The interpretation of the imaging data is less clear, however. While reduced measures of gray matter volume in cingulate and insula have been found in some studies of first-episode psychosis, these findings are not typical in patients with schizophrenia diagnoses and are generally not found in healthy relatives (Honea et al., 2008; Owens et al., 2012), suggesting that they are not associated with genetic risk for schizophrenia in the general population. Indeed, data linking increased genetic risk for schizophrenia with measurements made on structural MRI scans have been unconvincing, even in much larger samples.

References:

Goldberg TE, Ragland JD, Torrey EF, Gold J, Bigelow LB and Weinberger DR. Neuropsychological assessment of monozygotic twins discordant for schizophrenia. Arch Gen Psychiatry. 1990;47:1066-1072. Abstract

Cannon TD, Huttunen MO, Lonnqvist J, Tuulio-Henriksson A, Pirkola T, Glahn D, Finkelstein J, Hietanen M, Kaprio J, Koskenvuo M. The inheritance of neuropsychological dysfunction in twins discordant for schizophrenia Am J Hum Genet. 2000;67:369–382. Abstract

Egan MF, Goldberg TE, Gscheidle T, Weirich M, Rawlings R, Hyde TM, Bigelow L and Weinberger DR. Relative risk for cognitive impairments in siblings of patients with schizophrenia. Biol Psychiatry. 2001;50:98-107. Abstract

Honea RA, Meyer-Lindenberg A, Hobbs KB, Pezawas L, Mattay VS, Egan MF, Verchinski B, Passingham RE, Weinberger DR and Callicott JH. Is gray matter volume an intermediate phenotype for schizophrenia? A VBM study of patients with schizophrenia and their healthy siblings. Biol Psychiatry. 2008;63:465-474. Abstract

Owens SF, Picchioni MM, Ettinger U, McDonald C, Walshe M, Schmechtig A, Murray RM, Rijsdijk F, Toulopoulou T. Prefrontal deviations in function but not volume are putative endophenotypes for schizophrenia. Brain. 2012;135:2231–2244. Abstract

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