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Exome Sequencing Highlights Chromatin Remodeling in Schizophrenia

May 19, 2014. People with schizophrenia carry 3.5 times more spontaneously occurring point mutations than healthy controls do, according to exome sequencing results published online April 29 in Molecular Psychiatry. The researchers, led by Dick McCombie of Cold Spring Harbor Laboratory, New York, and Aiden Corvin of Trinity College Dublin, Ireland, were also able to show that the mutations they identified were likely to be damaging to the genes involved, rather than being innocuous.

The study implicates genes involved in chromatin remodeling (CHD8, MECP2, HUWE1), which suggests that the processes by which genes are made available for transcription go awry in schizophrenia. Several genes hit by mutations in the study have also been implicated in autism and intellectual disability, further underscoring genetic overlaps between schizophrenia and other neurodevelopmental disorders.

The study bolsters a role for new, damaging mutations in the protein-coding part of the genome in schizophrenia. The study’s convergence on chromatin remodeling also fits with the theme that disrupted brain development increases risk for schizophrenia (see SRF related news report; SRF news report). Chromatin is the compact package of DNA wound around proteins, which allows our very long genomes to fit inside a cell’s nucleus. To be expressed, a gene needs to be unwound from these proteins and sufficiently exposed so that transcriptional machinery can get to it. Problems with this process could derail the precise transcriptional choreography that goes on during brain development.

Because it is focused on the protein-coding parts of the genome, exome sequencing can point directly to genes with higher resolution than studies of common variants or copy number variation (see SRF related news report). But the promise of this approach has given way to some dismay, as sequencing turns up plenty of suspicious mutations in cases and controls alike. This means that, after all the hard work of sequencing, geneticists are faced with the task of coming up with principled, unbiased ways of discerning which variants contribute to a disorder (MacArthur et al., 2014).

This problem is compounded for schizophrenia, which is thought to arise through many different genetic variants, some of which may be very rare. To bolster the case for the rare mutations found in the study, first author Shane McCarthy and colleagues used tools that score genes on how sensitive their protein products are to mutation, that is, whether their function would tolerate mutation (Petrovski et al., 2013) or whether loss of a gene copy would be noticed in the phenotype (Huang et al., 2010).

Categorizing de novos
Like previous studies, the new study focused on “de novo” variants, which are more likely to be deleterious because they arise anew in sperm or egg cells and so haven’t yet been weeded out by natural selection. The researchers found these by sequencing the exomes of 57 people with schizophrenia and both their parents. Fifteen of these trios were deemed “familial” cases, in that there was a history of psychosis in first- or second-degree relatives; the remaining majority were termed “sporadic.” With over 90 percent of the exome sequenced 10 times or more, a total of 59 de novo variants turned up, 47 of which occurred in sporadic cases. The mutation rates were within the range reported for de novo mutation in other studies (e.g., 1.62 x 10-8 per base per generation for sporadic cases).

Most of these were “missense” mutations, in that they coded for a different amino acid (28 of 47 of the mutations were found in sporadic cases). But the more damaging kind of “nonsense” mutations were also identified: Five of 47 mutations encoded a premature stop codon, which presumably truncates the resulting protein at a different location. Though these five mutations may not seem like much, they constituted a statistically significant, 3.5-fold increase over the number of de novo, nonsense mutations found in controls in autism studies (see SRF related news report). Nonsense mutations were not identified in the familial trios.

This increased rate of de novo, deleterious mutation looks pretty serious on its own, but the researchers looked for further evidence with methods that score genes on how sensitive they are to mutation. One method scored genes on haploinsufficiency, meaning how necessary it is to have two working copies of a gene to maintain normal function (Huang et al., 2010). The researchers found that the genes hit by nonsense variants were more likely to be rated as haploinsufficient (i.e., unable to get by with only one working copy) than comparable genes in the genome. Another method underscored the sensitivity of these genes to mutation, as four were in the top tier of “intolerant-to-variation” scores (Petrovski et al., 2013).

Of the genes hit by nonsense mutation, the researchers highlighted CHD8, AUTS2, and MLL2. Both CHD8 and MLL2 are chromatin modifiers, and more involvement with chromatin was found among missense mutations in the Rett syndrome genes MECP2 and HUWE1, both transcriptional regulators.

Diagnostic overlaps
Several of these genes have also been flagged in studies of autism, including CHD8, AUTS2, MECP2, and HUWE1. Using the NEUROCARTA database, which links genes with phenotypes to explore this more systematically, the researchers found that the genes hit by all protein-altering mutations in schizophrenia were over-represented in genes linked to autism and intellectual disability. This echoes other genetic and epidemiology studies, which find shared risk among these disorders (see SRF related news report; SRF news report; SRF news report).

While other exome findings are sure to come in the future, this study shores up a role for new, damaging mutations in schizophrenia. It also provides a meditation on the importance of epigenetic factors in risk. Understanding how transcriptional mishaps during brain development reverberate throughout brain circuitry may yield clues to the beginnings of schizophrenia.—Michele Solis.

Reference:
McCarthy SE, Gillis J, Kramer M, Lihm J, Yoon S, Berstein Y, Mistry M, Pavlidis P, Solomon R, Ghiban E, Antoniou E, Kelleher E, O'Brien C, Donohoe G, Gill M, Morris DW, McCombie WR, Corvin A. De novo mutations in schizophrenia implicate chromatin remodeling and support a genetic overlap with autism and intellectual disability. Mol Psychiatry. 2014 Apr 29. Abstract

Comments on Related News


Related News: Autism Exome: Lessons for Schizophrenia?

Comment by:  Patrick Sullivan, SRF Advisor
Submitted 20 April 2012
Posted 23 April 2012
  I recommend the Primary Papers

Fascinating papers that likely presage work in the pipeline from multiple groups for schizophrenia. Truly groundbreaking work by some of the best groups in the business. Required reading for those interested in psychiatric genomics.

The identified loci provide important new windows into the neurobiology of ASD.

The results also pertain to the longstanding debate about the nature of ASD: does it result from many individually rare, Mendelian-like variants (potentially a different one in each person) and/or from the summation of the effects of many different common variants of subtle effects?

The multiple rare variant model now seems unlikely for ASD as, contrary to the expectations of some, ASD did not readily resolve into a handful of Mendelian-like diseases. (This comment is of course qualified by the limits of the technologies - which have, however, identified causal mutations for many monogenetic disorders.)

Readers might also want to read Ben Neale's comments on these papers at the Genomes Unzipped website.

View all comments by Patrick Sullivan

Related News: Chromosomal Mishaps in Autism Harbor Schizophrenia Candidate Genes

Comment by:  Ben Pickard
Submitted 23 May 2012
Posted 24 May 2012

The paper by Talkowski and colleagues describes the application of cutting edge genomics techniques to the molecular characterisation of multiple balanced chromosomal abnormalities (BCAs) linked to autism, autism spectrum disorders, and general neurodevelopmental disorders. In a single publication it has probably assigned more candidate genes than the entire conventional cytogenetic output from schizophrenia and autism in the preceding 15 years.

The authors carry out a great deal of complementary genomic analyses which add to the strength of their argument that these genes are indeed causally involved in illness. Without these additional data there would be one potential criticism of the paper in that the same power of analysis was not applied to BCAs in healthy controls. This is an important ascertainment issue because previous studies have not only identified disrupted genes in the healthy population (Baptista et al., 2005) but also shown that CNVs deregulating specific genes may only show an increased—as opposed to exclusive—representation in the ill population.

The observed overlaps between some of the identified BCA genes in ASD/neurodevelopmental disorders and those identified in GWAS studies of schizophrenia and bipolar disorder is fascinating but may be a double-edged sword. On the one hand, support for rare genetic contributors (CNVs/sequence variants/BCAs) to complex genetic disorders has often been drawn from those that are co-incident between studies. In that respect, this study is remarkable for highlighting the same genes from methods that detect very different mutation types. I’m genuinely surprised that there appears to be a convergence of ancient (read subject to evolutionary selection/population effects) and recent (meaning random) mutations. On the other hand, there is the disconcerting possibility that schizophrenia GWAS are only powered to detect the causes of blunt neurodevelopmental disturbances (which are perhaps less sensitive to issues of diagnostic categorisation) and not the fine-grained genetic hits that determine a precise clinical endpoint. If this is the case then we could end up with a situation where the genotypic distance between disorders is apparently much less than the phenotypic distance. This is most likely an extreme outcome that will be remedied once the genomic analysis of complex genetic disorders is able to factor in the composite effects of BCAs, CNVs, rare SNPs, and common SNPs—at the level of the single individual, and perhaps conditioned on the presence of big neurodevelopmental hits.

Quite logically, the presence of genes spanning diagnoses has been explained in terms of shared predisposition derived from early neurodevelopmental insults that are subsequently pushed down diagnostic pathways by other genetic or environmental factors. However, this assumption needs formal testing. The problem is reminiscent of the debate that circled the early use of constitutive mouse knockouts: how is it possible to disentangle developmental from adult functional phenotypes in a null? The advent of inducible Cre-LoxP technologies allowed that question to be directly addressed and may be the means to test the neurodevelopmental contribution of diagnosis-spanning candidate genes such as TCF4.

Could the approach detailed in this paper be applied directly to schizophrenia? It would certainly add substantially to the ‘confirmed’ gene list and would detect any reciprocal relationships with ASD/neurodevelopmental disorders. One issue is that ASD appears to have a higher overall incidence of chromosomal and genomic structural rearrangements than schizophrenia, but perhaps the greater question is availability of an appropriate sample set. The concerted cytogenetic screening that took place in Scotland coupled with an ability to cross-reference these findings with incidence of psychiatric disorder was instrumental in the discovery of DISC1 and other genes in Scotland (Muir et al., 2008) but this resource is now largely exhausted of relevant BCAs. To my knowledge, the Danish registry represents the best bet for such an approach to succeed for schizophrenia (Bache et al., 2006).

References:

Baptista J, Prigmore E, Gribble SM, Jacobs PA, Carter NP, Crolla JA. Molecular cytogenetic analyses of breakpoints in apparently balanced reciprocal translocations carried by phenotypically normal individuals. Eur J Hum Genet. 2005 Nov;13(11):1205-12. Abstract

Muir WJ, Pickard BS, Blackwood DH. Disrupted-in-Schizophrenia-1. Curr Psychiatry Rep. 2008 Apr;10(2):140-7. Abstract

Bache I, Hjorth M, Bugge M, Holstebroe S, Hilden J, Schmidt L, Brondum-Nielsen K, Bruun-Petersen G, Jensen PK, Lundsteen C, Niebuhr E, Rasmussen K, Tommerup N. Systematic re-examination of carriers of balanced reciprocal translocations: a strategy to search for candidate regions for common and complex diseases. Eur J Hum Genet. 2006 Apr;14(4):410-7. Abstract

View all comments by Ben Pickard

Related News: Chromosomal Mishaps in Autism Harbor Schizophrenia Candidate Genes

Comment by:  Patrick Sullivan, SRF AdvisorJin Szatkiewicz
Submitted 29 May 2012
Posted 29 May 2012
  I recommend the Primary Papers

In this exceptional paper, the authors combined new technology with old-school genomics to deliver convergent data about the genomic regions that predispose to neuropsychiatric disorders. The first goal of psychiatric genetics is to identify the “parts list,” an enumeration of the genes and genetic loci whose alteration clearly and unequivocally alters risk. The results of this intriguing paper connect rare and powerful genomic disruptions with loci identified via common variant genomewide association screens.

A classical approach in human genetics is to study affected individuals with balanced translocations. Using next-generation sequencing, these authors identified the precise locations of 38 rare balanced chromosomal abnormalities in subjects with neurodevelopmental disorders. They identified 33 disrupted genes, of which 22 were novel risk loci for autism and neurodevelopmental disorders. The other disrupted genes included many that had previously been identified by genomic searches for rare variation and common variation (e.g., AUTS2, CHD8, TCF4, and ZNF804A).

The authors then sought secondary genomic support for disease association with these 33 risk loci by analyzing a large collection of psychiatric GWAS data. They found an increased burden of copy number variants (CNVs) among cases as well as a significant enrichment of common risk alleles among both autism and schizophrenia cases. This research suggests that autism and neurodevelopmental disorders may have commonalities with psychiatric disorders such as schizophrenia at the molecular level, underscoring the complexity of genetic contribution to these conditions.

CNVs discovered from microarrays are mainly large, rare CNVs spanning multiple genes. Exome sequencing is limited to coding regions of the genome. In contrast, as illustrated in Talkowski et al. (2012), it is possible to identify individual lesions with nucleotide resolution in both coding and non-coding regions. Thus, this research suggests that sequencing individuals with pathogenic balanced translocations could provide a complementary strategy for mutation identification and gene discovery.

The experimental procedures were technically well done; all BCA breakpoints were confirmed by PCR and capillary sequencing. In seeking the secondary genomic support, the authors were keen on evaluating and eliminating the possibility for any confounding factors that may cause spurious association. For example, CNV burden analysis was conducted with respect to differential sensitivities from microarrays, and all results remained robust to various subset analyses and to one million simulations designed to establish empirical significance. To examine the potential for spurious enrichment of common risk alleles, the authors additionally conducted identical analysis in phenotype-permuted datasets from well-powered GWAS data for schizophrenia and autism as well as in well-powered GWAS data for eight unrelated traits, and therefore eliminated unforeseen confounders.

Impressively, many of the loci identified here now have convergent genomic results with support across multiple different samples and technical approaches. For example, TCF4 harbors common variation identified via GWAS, a Mendelian disorder, and now a gene disruption. These convergent genomic results markedly increase confidence that TCF4 is truly in the “parts list” for neurodevelopmental disorders. In contrast, there remain multiple questions about the genomic evidence for DISC1, where such convergence has not been achieved.

This paper also provides important results relevant to resolving the rare “versus” common variation debate. This appears to be a false dichotomy where, often, both rare and common variations contribute to the parts lists for these disorders.

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View all comments by Jin Szatkiewicz

Related News: Chromosomal Mishaps in Autism Harbor Schizophrenia Candidate Genes

Comment by:  Bernard Crespi
Submitted 29 May 2012
Posted 29 May 2012
  I recommend the Primary Papers

Balanced chromosomal abnormalities (BCAs) provide extremely useful alterations for linking of specific loci with psychiatric conditions, because they exert penetrant effects and localize to specific genes. The recent study by Talkowski et al. (2012) used direct sequencing of breakpoints, based on 38 subjects, to generate a set of genes with putative links to different neurodevelopmental disorders, broadly construed as including autism spectrum disorders, intellectual disability, and/or developmental and other delays.

One of the most striking results from their study was the presence, in their set of breakpoint-altered genes, of five genes that have been associated from other work with schizophrenia and related psychotic-affective spectrum disorders (such as bipolar disorder and major depression), including TCF4, ZNF804A, PDE10A, GRIN2B, and ANK3. These results suggest, according to the authors, the presence of shared genetic etiology for ASD, schizophrenia, and other neurodevelopmental disorders (mainly developmental delays). The authors also show overlap of their gene list with results from CNV and GWAS of autism and schizophrenia, further suggesting genetic links between these two conditions.

Do these results mean that autism and schizophrenia share genetic risk factors? Perhaps, but also perhaps not. Two important caveats apply.

First, schizophrenia involves well-documented premorbidity, in a substantial proportion of cases, that centers on developmental, social, and language deficits and delays (e.g., Saracco-Alvarez et al., 2009; Gibson et al., 2010). In children, premorbidity to schizophrenia most commonly involves "negative" symptoms, including deficits in social interaction (Remschmidt et al., 1994; Tandon et al., 2009), which can overlap with symptoms of autism spectrum disorders (Goldstein et al., 2002; Sheitman et al., 2004; Tjordman, 2008; King and Lord, 2011). Males are more severely affected, as in autism (Sobin et al., 2001; Rapoport et al., 2009; Tandon et al., 2009). Schizophrenia mediated by CNVs, or BCAs, is likely to exhibit relatively high levels of premorbidity, due to the penetrant, syndromic, and deleterious nature of these alterations (Bassett et al., 2010; Vassos et al., 2010). A recent study by Sahoo et al. (Sahoo et al., 2011) provides evidence consistent with such premorbidity, in that of over 38,000 individuals (predominantly children) referred for developmental delay, intellectual disability, autism spectrum disorders, or multiple congenital anomalies, 704 exhibited one of seven CNVs (del 1q21.1, dup 1q21.1, del 15q11.2, del 15q13.3, dup 16p11.2, dup 16p13.11, and del 22q11.2) that have been statistically associated with schizophrenia in studies of adults (Levinson et al., 2011).

These findings suggest that the subjects in Talkowski et al. (Talkowski et al., 2012), (most of them children, for individuals with age data given) who harbor alterations to schizophrenia-associated genes may, in fact, be severely premorbid for schizophrenia. Diagnoses of ASD (commonly PDD-NOS) in such individuals may represent either false positives (Eliez, 2007 ; Feinstein and Singh, 2007), or true positives, with ASD as a developmental stage followed, in some individuals, by schizophrenia. This latter conceptualization considers autism as akin to childhood schizophrenia, a view which contrasts sharply with the classic criteria derived from Kanner (Kanner, 1943), Asperger (1991) and Rutter (Rutter, 2000, Rutter, 1972, Rutter, 1978), who consider autism as a lifelong condition present from early childhood. Of course, diagnosing premorbidity to schizophrenia as such is challenging, but if any data can help, it is data from highly penetrant alterations such as CNVs and BCAs, as well as from biological and neurological (rather than just behavioral) phenotypes.

Second, association to an overlapping set of genes need not make two disorders similar, or similar in their genetic etiology. For example, as noted by Talkowski et al. (Talkowski et al., 2012), variation in TCF4 has been associated with both Pitt-Hopkins syndrome and schizophrenia, but these conditions show essentially no overlap in phenotypes. Similar considerations apply to CACNA1C, linked to the autism-associated Timothy syndrome (via an apparent gain of function) as well as to schizophrenia and bipolar disorder. A key to sorting out the huge clinical and genetic heterogeneity in autism, and in schizophrenia, is subsetting of cases by similarity in alterations to pathways and phenotypes. Lumping of autism with schizophrenia, based on overlap in risk loci without consideration of the nature of the overlap, will make such subsetting all the more difficult.

Data on genes disrupted by balanced translocations are tremendously useful, but their usefulness will, as for other data such as CNVs, be circumscribed by diagnostic considerations, especially when the subjects are children. Bearing in mind the possibility that some childhood diagnoses may represent false positives, and that overlap in genes need not mean overlap in causation, should help in moving the study of both autism and schizophrenia forward.

References:

Asperger H; translated and annotated by Frith U (1991) [1944]. Autistic psychopathy' in childhood. In Frith, U. Autism and Asperger syndrome. Cambridge University Press. pp. 37-92.

Bassett AS, Scherer SW, Brzustowicz LM. Copy number variations in schizophrenia: critical review and new perspectives on concepts of genetics and disease. Am J Psychiatry. 2010;167(8):899-914. Abstract

Eliez S. Autism in children with 22q11.2 deletion syndrome. J Am Acad Child Adolesc Psychiatry. 2007;46(4):433-4. Abstract

Feinstein C, Singh S. Social phenotypes in neurogenetic syndromes. Child Adolesc Psychiatr Clin N Am. 2007;16(3):631-47. Abstract

Gibson CM, Penn DL, Prinstein MJ, Perkins DO, Belger A. Social skill and social cognition in adolescents at genetic risk for psychosis. Schizophr Res. 2010;122(1-3):179-84. Abstract

Kanner L. 1968;2:217–250. Abstract

King BH, Lord C. Is schizophrenia on the autism spectrum? Brain Res. 2011;1380:34-41. Abstract

Levinson DF, Duan J, Oh S, Wang K, Sanders AR, Shi J, et al., Copy number variants in schizophrenia: confirmation of five previous findings and new evidence for 3q29 microdeletions and VIPR2 duplications. Am J Psychiatry. 2011;168(3):302-16. Abstract

Rapoport J, Chavez A, Greenstein D, Addington A, Gogtay N. Autism spectrum disorders and childhood-onset schizophrenia: clinical and biological contributions to a relation revisited. J Am Acad Child Adolesc Psychiatry. 2009;48(1):10-8. Abstract

Remschmidt HE, Schulz E, Martin M, Warnke A, Trott GE. Childhood-onset schizophrenia: history of the concept and recent studies. Schizophr Bull. 1994;20(4):727-45. Abstract

Rutter ML. Relationships between child and adult psychiatric disorders. Some research considerations. Acta Psychiatr Scand. 1972;48(1):3-21. Abstract

Rutter M. Diagnosis and definition of childhood autism. J Autism Child Schizophr. 1978;8(2):139-61. Abstract

Rutter M. Genetic studies of autism: from the 1970s into the millennium. J Abnorm Child Psychol. 2000;28(1):3-14. Abstract

Saracco-Alvarez R, Rodríguez-Verdugo S, García-Anaya M, Fresán A. Premorbid adjustment in schizophrenia and schizoaffective disorder. Psychiatry Res. 2009;165(3):234-40. Abstract

Sahoo T, Theisen A, Rosenfeld JA, Lamb AN, Ravnan JB, Schultz RA, et al., Copy number variants of schizophrenia susceptibility loci are associated with a spectrum of speech and developmental delays and behavior problems. Genet Med. 2011; 13(10):868-80. Abstract

Sheitman BB, Kraus JE, Bodfish JW, Carmel H. Are the negative symptoms of schizophrenia consistent with an autistic spectrum illness? Schizophr Res. 2004;69(1):119-20. Abstract

Sobin C, Blundell ML, Conry A, Weiller F, Gavigan C, Haiman C, et al., Early, non-psychotic deviant behavior in schizophrenia: a possible endophenotypic marker for genetic studies. Psychiatry Res. 2001;101(2):101-13. Abstract

Talkowski ME, Rosenfeld JA, Blumenthal I, Pillalamarri V, Chiang C, Heilbut A, Ernst C, Hanscom C, Rossin E, Lindgren AM, Pereira S, Ruderfer D, Kirby A, Ripke S, Harris DJ, Lee JH, Ha K, Kim HG, Solomon BD, Gropman AL, Lucente D, Sims K, Ohsumi TK, Borowsky ML, Loranger S, Quade B, Lage K, Miles J, Wu BL, Shen Y, Neale B, Shaffer LG, Daly MJ, Morton CC, Gusella JF. Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries. Cell. 2012;149(3):525-37. Abstract

Tandon R, Nasrallah HA, Keshavan MS. Schizophrenia, "just the facts" 4. Clinical features and conceptualization. Schizophr Res. 2009;110(1-3):1-23. Abstract

Tjordman S Reunifying autism and early-onset schizophrenia in terms of social communication disorders. Behav Brain Sci. 2008;31(3):278-9.

Vassos E, Collier DA, Holden S, Patch C, Rujescu D, St Clair D, et al., Penetrance for copy number variants associated with schizophrenia. Hum Mol Genet. 2010;19(17):3477-81. Abstract

View all comments by Bernard Crespi

Related News: Family Roots for Autism, Schizophrenia, Bipolar Disorder

Comment by:  Bernard Crespi
Submitted 30 July 2012
Posted 30 July 2012

In a new paper in Archives of General Psychiatry that has received considerable media attention, Sullivan et al. (Sullivan et al., 2012) use register data from Sweden and Israel to show higher rates of ASDs among individuals with family histories of schizophrenia and bipolar disorder. The authors interpret these results as indicating that ASD, schizophrenia, and bipolar disorder share etiology. This is a very interesting hypothesis that, if supported, would have important implications for our understanding of the genetic underpinnings of schizophrenia in relation to other conditions. However, two alternative hypotheses not involving shared causation may, at least in part, help to explain their results.

First, a recent set of studies demonstrates that drug treatments for schizophrenia and bipolar disorder increase the incidence of ASDs, or their biologically based phenotypic correlates, in offspring. Croen et al. (Croen et al., 2011) reported that prenatal exposure to antidepressants (SSRIs) was associated with a twofold increase in risk of ASD. It is also notable that hyperserotoninemia has also been found in about one-third of autism cases (Burgess et al., 2006). Fetal exposure to the mood stabilizer valproate has been associated with a sevenfold increase in ASD risk (Bromley et al., 2008), and also serves as a model system for autism in animal studies. Use of clozapine and olanzapine during pregnancy has been associated with increased offspring head circumference (Bodén et al., 2012), which represents another well-validated correlate of autism (Courchesne et al., 2011). Moreover, environmental exposure to three psychoactive drugs (fluoxetine, venlafaxine, and carbamazepine) has been demonstrated to cause gene-expression changes that resemble those seen only in autism (Thomas and Klaper, 2012).

These results may help to explain mother-offspring and sib-sib associations of schizophrenia and bipolar disorder with ASDs. Such effects might be expected to be higher than those seen for fathers, but data were not presented in the report by Sullivan et al. on such parental sex differences. Effects of pharmacological treatment of fathers on ASD risk in offspring apparently have yet to be investigated, although paternal effects on offspring psychopathology and epigenetic profiles have been reported with regard to such factors as age (Hultman et al., 2011), and stress (Essex et al., 2011).

Second, the authors' data may also be attributable in part to false-positive diagnoses of premorbidity to schizophrenia (or bipolar disorder) as ASD in children, and conflation of schizotypal personality disorder (SPD) with high-functioning autism and Asperger's syndrome. Premorbidity to schizophrenia occurs in a notable proportion of cases, and most usually involves "negative symptoms" such as deficits in social interaction and language (discussed in Crespi, 2011). The clearest apparent evidence regarding this hypothesis comes from Sullivan et al. themselves, who noted that in their Study 1, 2,147 individuals had received a diagnosis of both ASD and (at discharge) schizophrenia or bipolar disorder. The authors excluded these cases as involving "diagnostic uncertainty." However, such uncertainties in the retained data may still influence the analyses. Thus, to the extent that individuals with diagnoses of ASD are under the age of onset for schizophrenia or bipolar disorder, they may exhibit false-positive diagnoses of premorbidity to schizophrenia or bipolar disorder as ASDs. Similar considerations apply to sibs differing in age.

Schizophrenia exhibits well-established genetic, symptomatic, and epidemiological overlap with both schizotypal personality disorder (SPD) and bipolar disorder (Carpenter et al., 2009). Additionally, first-order relatives of individuals with schizophrenia or affective psychosis show elevated rates of SPD (Schürhoff et al., 2005). These results indicate that SPD may show conflation in epidemiological data with high-functioning autism or Asperger's, due to the presence in both SPD and high-functioning forms of ASD of general social deficits and abnormalities. The possibility of such conflation is supported by: 1) the authors' finding that their familial association "was principally in cases without clinical indication of mental retardation," and 2) studies showing behavioral overlap of SPD with ASDs (based predominantly on questionnaires) (Barneveld et al., 2011), but a striking lack of data on overlap for developmental, physiological, or neurological phenotypes. Such conflation would falsely connect ASDs (which are actually SPD) with schizophrenia or bipolar disorder. It would appear more useful and realistic to consider the possibility and expected effects of diagnostic uncertainties than to presume that they do not exist.

This second set of considerations also applies to studies that would use GWAS data to evaluate hypotheses of how autism and schizophrenia are related to one another; even a rather small degree of false-positive conflation of premorbidity to schizophrenia with ASD could result in incorrect conclusions regarding the genetic etiologies of these sets of conditions. Such potential problems might be minimized by subsetting ASD cases into autism “sensu stricto,” given that PDD-NOS is the diagnostic category most likely to be conflated with schizophrenia premorbidity.

References:

Sullivan PF, Magnusson C, Reichenberg A, Boman M, Dalman C, Davidson M, Fruchter E, Hultman CM, Lundberg M, Lĺngström N, Weiser M, Svensson AC, Lichtenstein P. Family history of schizophrenia and bipolar disorder as risk factors for autism. Arch Gen Psychiatry. 2012 Jul 2:1-5. Abstract

Croen LA, Grether JK, Yoshida CK, Odouli R, Hendrick V. Antidepressant use during pregnancy and childhood autism spectrum disorders. Arch Gen Psychiatry. 2011:68(11):1104-1112. Abstract

Burgess NK, Sweeten TL, McMahon WM, Fujinami RS. Hyperserotoninemia and altered immunity in autism. J Autism Dev Disord. 2006:36(5):697-704. Abstract

Bromley RL, Mawer G, Clayton-Smith J, Baker GA; Liverpool and Manchester Neurodevelopment Group. Autism spectrum disorders following in utero exposure to antiepileptic drugs. Neurology. 2008:71(23):1923-4. Abstract

Bodén R, Lundgren M, Brandt L, Reutfors J, Kieler H. Antipsychotics during pregnancy: relation to fetal and maternal metabolic effects. Arch Gen Psychiatry. 2012:69(7):715-21. Abstract

Courchesne E, Mouton PR, Calhoun ME, Semendeferi K, Ahrens-Barbeau C, Hallet MJ, Barnes CC, Pierce K. Neuron number and size in prefrontal cortex of children with autism. JAMA. 2011:306(18):2001-10. Abstract

Thomas MA, Klaper RD. Psychoactive pharmaceuticals induce fish gene expression profiles associated with human idiopathic autism. PLoS One. 2012;7(6):e32917. Abstract

Hultman CM, Sandin S, Levine SZ, Lichtenstein P, Reichenberg A. Advancing paternal age and risk of autism: new evidence from a population-based study and a meta-analysis of epidemiological studies. Mol Psychiatry. 2011:16(12):1203-12. Abstract

Essex MJ, Thomas Boyce W, Hertzman C, Lam LL, Armstrong JM, Neumann SM, Kobor MS. Epigenetic vestiges of early developmental adversity: childhood stress exposure and DNA methylation in adolescence. Child Dev. 2011 Sep 2. Abstract

Crespi B. One hundred years of insanity: genomic, psychological, and evolutionary models of autism in relation to schizophrenia. In: Ritsner M, ed. Handbook of Schizophrenia Spectrum Disorders, Volume I. New York, NY: Springer; 2011:163-185.

Carpenter WT, Bustillo JR, Thaker GK, van Os J, Krueger RF, Green MJ. The psychoses: cluster 3 of the proposed meta-structure for DSM-V and ICD-11. Psychol Med. 2009: 39(12):2025-42. Abstract

Schürhoff F, Laguerre A, Szöke A, Méary A, Leboyer M. Schizotypal dimensions: continuity between schizophrenia and bipolar disorders. Schizophr Res. 2005:80(2-3):235-42. Abstract

Barneveld PS, Pieterse J, de Sonneville L, van Rijn S, Lahuis B, van Engeland H, Swaab H. Overlap of autistic and schizotypal traits in adolescents with Autism Spectrum Disorders. Schizophr Res. 2011:126(1-3):231-6. Abstract

View all comments by Bernard Crespi

Related News: Family Roots for Autism, Schizophrenia, Bipolar Disorder

Comment by:  William Carpenter, SRF Advisor (Disclosure)
Submitted 30 July 2012
Posted 30 July 2012

Shared risk for ASDs in bipolar and schizophrenia families is important, and the apparent gradient in risk with schizophrenia being greater than bipolar may be informative. From the view that schizophrenia and bipolar disorder are heterogeneous syndromes, the following is surmised:



View all comments by William Carpenter

Related News: Family Roots for Autism, Schizophrenia, Bipolar Disorder

Comment by:  John McGrath, SRF Advisor
Submitted 30 July 2012
Posted 30 July 2012
  I recommend the Primary Papers

This impressive study adds to the growing body of evidence demonstrating that heritable factors are shared among autism, schizophrenia, and bipolar disorder. The authors suggest that genetic factors could underlie the findings, but also remind the reader that environmental factors could play a role. They note that twin-based studies of heritability in schizophrenia and autism have demonstrated appreciable contributions for environmental factors that were shared between the affected individuals—usually referred to as common environmental effects. It should be noted that in this context, the word “common” does not equate with “prevalent.” With respect to shared genetic factors, the growing body of evidence regarding structural variation such as copy number variants is impressive. With respect to non-genetic factors, more work is needed—prenatal infection (which could trigger maternal immune activation) and nutrition (e.g., low vitamin D) might be candidate domains. If there are shared environmental risk factors contributing to schizophrenia, bipolar disorder, and autism, and if these were potentially modifiable, then this would be a very attractive proposition from a public health perspective.

The study is also an excellent demonstration of collaborative epidemiology—three datasets from two nations were used to examine the same research questions. This is an efficient way to do science.

View all comments by John McGrath

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: Ambitious Genetic Integration Analysis of Schizophrenia Points to Early Brain Development

Comment by:  Roger Boshes
Submitted 10 August 2013
Posted 20 August 2013

These data suggest a "stem" circuit that may be common to many patients with schizophrenia, but subsequent de novo mutations may explain the protean manifestations of the disorder. Alternatively, this prefrontal perturbation may be related to a heritable, i.e., not a somatic, mutation that explains 80 percent heritability but not the protean phenotypic expression of the condition. Finally, it may be the link between schizophrenia and some flavors of autism.

References:

Boshes RA, Manschreck TC, Konigsberg W. Genetics of the schizophrenias: a model accounting for their persistence and myriad phenotypes. Harv Rev Psychiatry. 2012 May-Jun; 20(3):119-29. Abstract

View all comments by Roger Boshes

Related News: New Exome Evidence Points to Old Suspect in Schizophrenia

Comment by:  Francis McMahon, SRF Advisor
Submitted 23 January 2014
Posted 28 January 2014

I think these studies do represent real progress. Finding genetic support for particular pathways provides unique evidence for a causative role of these pathways in disease. Why didn't the case-control study point to individual genes? Disorders such as schizophrenia may be more like a plane crash than a typical inherited disease: Since many things can go wrong, each crash is different, but damage to key systems is very likely to lead to a bad outcome. The finding in Fromer et al. that there are 18 genes with recurrent deleterious de novo events should allow scientists to focus on these genes as especially important. The overlaps with autism and intellectual disability are interesting, though not entirely unexpected. Will we also see gene overlaps with illnesses such as bipolar disorder? It wouldn't surprise me if some of the same genes are involved, but with fewer, less deleterious hits.

View all comments by Francis McMahon