Research Questions

Journal Published
npj Schizophrenia volume 5, Article number: 5

Year Published
2019

Authors / Collaborators
Vanessa Kiyomi Ota, Patricia Natalia Moretti, Marcos Leite Santoro, Fernanda Talarico, Leticia Maria Spindola, Gabriela Xavier, Carolina Muniz Carvalho, Diogo Ferri Marques, Giovany Oliveira Costa, Renata Pellegrino, Simone de Jong, Quirino Cordeiro, Hakon Hakonarson, Gerome Breen, Cristiano Noto, Rodrigo Affonseca Bressan, Ary Gadelha, Jair de Jesus Mari & Sintia I. Belangero

Full Article
GeneZExpressionZOverZTheZCourseZofZSchizophrenia.pdf

Hypothesis

To find genes related to a prepsychotic stage (i.e., genes differentially expressed in CHR compared to other groups), to an acute psychotic stage (i.e., genes differentially expressed in FEP compared to other groups), to a long-term psychotic state, or following a long exposure to antipsychotics (i.e., genes differentially expressed in CSZ compared to the other groups). The aim of the study is to determine whether patients with schizophrenia (SZ) at different clinical stages may help clarify what effects could be due to the disease itself, to the pharmacological treatment, or to the disease progression.

They further verified whether single-nucleotide polymorphisms (SNPs) could be related to gene expression differences. 

Background

• Schizophrenia (SZ) is a heterogenous disorder, with a wide array of clinical, functional, and cognitive outcomes.
• The different disease trajectories, in which a patient can present distinct clinical and biological features of disease progression, are a one major source of heterogeneity.
• Clinical staging models have been proposed, but relatively few studies compare biological measures in the distinct stages.
• Although the heritability of schizophrenia is very high (~80%), genetics still lack a major impact in clinical practice.
• Gene expression, the transcription of a gene’s DNA information into an RNA copy, is also influenced by a combination of environmental and genetic factors, such as expression quantitative trait loci (eQTLs), which are genomic loci that contribute to variation in expression levels.
• Schizophrenia risk loci have been noted as being enriched for eQTLs.
• Although many studies have investigated gene expression in the blood of patients with schizophrenia, most were performed in patients with a long time of treatment and disease.
• Our previous studies have shown that antipsychotics affect gene expression and DNA methylation, suggesting that gene expression may be influenced by the time of treatment and disease.
• Other studies have investigated prodromal or FEP patients, but no study has compared RNA expression between patients in different stages.

Journal Published
Research in Translation

Year Published
2017

Full Article
GeneticsZofZSchizophrenia.png

Hypothesis

The study will provide a high-level review of progress, its limitations, and the implications for clinical research and clinical practice.

Background

• There has been progress on research into the etiology of schizophrenia but particularly regarding the molecular genetics of this complex disorder of mind and brain.
• A number of critically important and unresolved issues remain that qualify the ultimate clinical and scientific validity of the results.

References

Full Article
TheZRoleZofZGeneticsZinZtheZEtiologyZofZSchizophrenia.pdf

Hypothesis

The aim of the study is to introduce the reader to the genetics of schizophrenia - its background, the status of a variety of genetic findings, new developments and current and future 

Background

• Genome-wide experiments  have discovered uncommon copy number variations (mainly deletions) associated with schizophrenia as well as common SNPs with alleles associated with schizophrenia.
• The aggregate data provide initial support for polygenic inheritance and for genetic overlap of schizophrenia with autism and with bipolar disorder.
• It is anticipated that  the application of a myriad of tools from systems biology will lead to a delineation of biological pathways involved in the pathophysiology of schizophrenia and eventually to new therapies as genetic discoveries accumulate challenges.

University or Organisation
Johns Hopkins University

School, Department or Faculty
Institute of Genetic Medicine & Department of Psychiatry

Journal Published
Molecular Neuropsychiatry

Year Published
2018

Authors / Collaborators
Dimitrios Avramopoulos

Full Article
RecentZAdvancesZinZtheZGeneticsZofZSchizophreniaZPDF.pdf

Hypothesis

• Focus on genetic variation showing robust associations with schizophrenia including high-penetrance rare variants and low penetrance common variants
• Describe transcriptomics work
• Provide an alternative approach to the genetics of the disease
• The use of alternative phenotypes termed endophenotypes, which is widening our understanding of the dimensionality of mental illness.
• Discuss how cutting-edge technologies are opening new directions in the ways we can experimentally model Schizophrenia

Background

• The last decade brought tremendous progress in the field of schizophrenia genetics.
• As a result of extensive collaborations and multiple technological advances, we now recognize many types of genetic variants that increase the risk. These include:

1. Large copy number variants
2. Rare coding inherited 
3. De novο variants
4. Over 100 loci harboring common risk variants.

• While the type and contribution to the risk vary among genetic variants, there is concordance in the functions of genes they implicate, such as those whose RNA binds the fragile X-related protein FMRP and members of the activity-regulated cytoskeletal complex involved in learning and memory.
• Gene expression studies add important information on the biology of the disease and recapitulate the same functional gene groups.
• Studies of alternative phenotypes help us widen our understanding of the genetic architecture of mental function and dysfunction, how diseases overlap not only with each other but also with non-disease phenotypes.
• The challenge is to apply this new knowledge to prevention and treatment and help patients.
• The data generated so far and emerging technologies, including new methods in cell engineering, offer significant promise that in the next decade we will unlock the translational potential of these significant discoveries.

Description

• Bipolar disorder, schizoaffective disorder and schizophrenia share some phenotypic aspects in common, both in terms of symptoms and also therapeutics with all responding to antipsychotic drugs.
• Emil Kraepelin defined dementia praecox as a group of psychotic conditions with a tendency toward poor prognosis. He grouped under the term manic-depressive psychoses a set of conditions that included periodic and circular insanity, simple mania, and melancholia which he thought did not result in deterioration. Kraepelin believed that dementia praecox and manic-depressive psychoses had specific and separate causes.
• However, reality proved to be more complex and in 1933 Jacob Kasanin coined the term schizoaffective psychosis to refer to a disorder with mixed features of schizophrenia and affective disorder.
• Compared to the general population, family studies show that the clinically intermediate diagnosis of schizoaffective disorder is more common in families ascertained from probands with schizophrenia as well as in families ascertained from probands with bipolar disorder.
• The diagnostic distinction between schizophrenia or bipolar disorder and schizoaffective disorder is not reliable.
• The specific time criterion for affective symptoms relative to the schizophrenic symptoms is not well defined and varies in different modern classifications.

Source
The Role of Genetics in the Etiology of Schizophrenia

Journal
Psychiatr Clin North Am

Year
2010

Website
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826121/pdf/nihms164007.pdf

Description

• Schizophrenia belongs to a group of pathologies known as complex genetic disorders.
• Our understanding of complex genetic disorders is still evolving as new experiments uncover novel mechanisms of disease.
• It is commonly thought that many genes are involved in each disorder with each gene conferring only a small effect on the phenotype.
• The individual risk variants are thus without diagnostic predictive value and any estimations of risk are probably going to change in the future as large epidemiological samples become available for analysis.
• Epistatic interactions between these genes and among their products and interactions with environmental risk factors are considered highly plausible, however the study of genetic interactions utilizing genome-wide data remains largely unexplored because of need to correct for an enormous number of statistical comparisons.
• Our knowledge is shifting from oligogenic models to a polygenic model of schizophrenia, but its genetic architecture still remains largely unknown.
• The current evidence strongly suggests that the mutation frequency spectrum comprises a mix of many common and rare mutations.
• The idea that complex disorders do not result from abnormal function of individual genes but from dysfunction of entire molecular networks, the concept of system disorder, is making strong inroads in the literature . Whether this applies to schizophrenia is still an empirical question that remains to be addressed.
• It has traditionally been assumed that changes in DNA sequence are solely responsible for the transmission of schizophrenia, however twin studies show that it is also conceivable that an epigenetic mechanism may contribute to the transmission of schizophrenia.
• The possibility of a role for epigenetics (i.e. changes in phenotype not explained by DNA sequence was raised first as an explanation of the incomplete concordance for schizophrenia in monozygotic twins, but still remains little tested due to methodological difficulties.

Source
The Role of Genetics in the Etiology of Schizophrenia

Journal
Psychiatr Clin North Am

Year
2010

Website
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826121/pdf/nihms164007.pdf

Description

• Ernst Rüdin conducted the first systematic family study for a psychiatric disorder.
• He realized that the data would not fit a model of simple monogenic Mendelian transmission but missed the evidence for additional complexity.
• Many family studies of schizophrenia were conducted since then, with the available evidence showing that the child of a parent with schizophrenia has an elevated empirical risk about tenfold over the general population risk
• The risk of a disease in a type of relative compared to that in the general population is often called λ (if the risk is conferred by an allelic variant, it is further specified as an allele specific λ).
• The relative risk to siblings resulting from having a proband with the illness is called λs 41.
• Common disorders have a smaller λs than rare disorders even with similar overall genetic effects (e.g. the respective λs for the autosomal dominant Huntington disease (assuming population prevalence 0.0001), the autosomal recessive cystic fibrosis (assuming population prevalence 0.0004) and autism are 5,000, 625, and 60–100, though the λs for major adult psychiatric disorders of the adult typically are under 10 (λs is ~10 for schizophrenia).
• The risk for schizophrenia to a relative of an affected proband decays much more rapidly than the proportion of genes shared between them. 
• Still most cases of schizophrenia in the general population are sporadic, which may seem surprising at first glance.
• Assuming polygenic inheritance (which explains the molecular findings of schizophrenia better than other models, for a disease with a prevalence of 1% and 90% heritability, more sporadic than familial cases are expected.

Source
The Role of Genetics in the Etiology of Schizophrenia

Journal
Psychiatr Clin North Am

Year
2010

Website
https://www.theglobalnowproject.com/dc/studies-full-article/TheZRoleZofZGeneticsZinZtheZEtiologyZofZSchizophrenia.pdf

Description

• Schizophrenia is a disease with remarkable phenotypic heterogeneity.  
• Each patient's symptoms lead to an overall highly heterogeneous phenotype.
• Heterogeneity also manifests in the patients’ response to medication, frequently resulting in multiple changes in treatment strategy during the course of the illness as patients navigate through ineffective treatments  
• It is clear that schizophrenic patients would benefit considerably from a robust prediction of their response through individualized medicine.
• A good understanding of the underlying genetics, the importance of environmental factors and the interaction of the two, along with careful clinical characterization may achieve that in the not so distant future.

Source
Recent Advances in the Genetics of Schizophrenia

Journal
2018, Vol.4, No. 1 June 2018 Vol.4, No. 1 June 2018

Year
2018

Website
https://www.karger.com/Article/FullText/488679

Description

• In addition to the importance of genetics, the environment also plays a major role in the risk to develop schizophrenia.
• Environmental factors explain the significant non-heritable fraction of the disease variance
• Multiple studies have already implicated a diverse array of environmental factors that increase the risk to develop schizophrenia. These include social factors such as:

1. Migrant status
2. Urban environment
3. Re- and perinatal factors such as maternal malnutrition
4. Birth month (i.e. those born in winter or spring)

• There are many studies suggesting increased risk accompanying infections such as toxoplasmosis, rubella, influenza, herpes and others. 
• It appears from these associations that stress, whether in utero, at birth, or during life, is an important determinant of risk for schizophrenia.
• These environmental factors are also likely to interact with genetic variation, increasing the risk only in their presence.
• One such replicated example has been reported for CMV infection and common variants near the CTNNA3 gene.
• Knowing these relationships will become increasingly important as we learn more about the genetics of the disease, allowing us to achieve individualized prevention and treatment strategies and move precision medicine into psychiatry.

Source
Recent Advances in the Genetics of Schizophrenia

Journal
Molecular Neuropsychiatry Vol.4, No. 1

Year
2018

Website
https://www.karger.com/Article/FullText/488679

Description

• Patients with schizophrenia have significantly fewer children compared to the general population

• In theory, this should be generating an enormous negative selective pressure quickly removing risk alleles from the population; however, the disease maintains a relatively high heritability and prevalence at ∼1%.

• The reasons for this paradox remain unclear and have sparked much debate and speculation.

• Among possible explanations are balancing selection favoring genotype diversity; advantage for those who carry the allele but do not get sick; changing environments that expose or protect cryptic variation; or quick replenishment by new mutations, in view of the possibility that disruption of thousands of different genes may be able to lead to disease

• The results of genome-wide association studies (GWAS) that we will discuss below support this highly polygenic architecture.

• In addition, GWAS results are consistent with theoretical predictions that common schizophrenia alleles can only show low odds ratios because of this negative selection. This observation, which has the consequence that GWAS variants explain very little genetic variance, has led some health scientists to challenge the value of GWAS. This, however, is a narrow view of the value of these results.

• Common variants that survive selection might have small effects on risk, but pharmacological interventions can be designed to have a larger effect on the gene regulation, its product or the related pathway, providing major benefits.

Source
Recent Advances in the Genetics of Schizophrenia

Journal
Molecular Neuropsychiatry 2018, Vol.4, No. 1

Year
2018

Website
https://www.karger.com/Article/FullText/488679

Description

• The polygenic nature of schizophrenia has been suspected and debated for a long time
• Hoping that at least some families might segregate a single disease-causing variant, or that the overall number of such variants is limited, numerous linkage studies have tested both parametric and non-parametric approaches.
• Starting as early as 1972 possible linkage of schizophrenia was reported with specific blood groups, and many other linkage studies followed.
• Unfortunately, most were met with disappointment, almost always showing weak results and often failing to replicate one another.
• The same was true for the first association studies that focused on candidate genes or followed up previous linkage results.
• At the time, we did not appreciate the large number of risk variants underlying schizophrenia and the small contribution these variants have on the risk.
• The studies of the era were vastly underpowered and often produced no or false positive results.
• Only now that we have succeeded in identifying true schizophrenia risk variants have we come to appreciate the serious limitations of earlier work.
• Very few of the early gene findings remain under investigation today, and those that do are not because of robust evidence for a role in the disease, but rather because of continuing interest in their function revealed by the work initially triggered by the associations.

Source
Recent Advances in the Genetics of Schizophrenia

Journal
Molecular Neuropsychiatry Vol.4, No. 1

Year
2018

Website
https://www.karger.com/Article/FullText/488679

Description

• There is strong link between a deletion syndrome and schizophrenia

• A recurrent deletion in chromosomal band 22q11.2 causing a phenotype called velo-cardio-facial syndrome (VCFS) was noted to be often accompanied by psychosis

• Following the reports of this comorbidity, deletion screening of schizophrenia patients showed that some had the 22q deletion but were not diagnosed with VCFS because of their mild features

• Most recently, this deletion was determined to increase the risk of carriers 68-fold and to be present in 0.3% of individuals diagnosed with schizophrenia.

• The deleted region includes more than 50 genes including the highly cited catecholamine-degrading enzyme gene COMT.

• The deletion is recurrent and is due to flanking low copy repeats that mediate unequal meiotic crossing over

• There are multiple repeats in the 22q11.2 region so the deletion can vary in size, the most common (90%) being ∼3 Mb followed by ∼1.5 Mb deletions.

• Interestingly, the reciprocal duplication has been reported to be protective against schizophrenia.

• While the 22q11.2 deletion was the first to be discussed in schizophrenia, the ever-increasing use of microarrays, whether for CNV detection or for genotyping, provided data that allowed us to recognize more and smaller copy number variants (CNVs). As a result, many additional CNVs have now been reported to be associated with schizophrenia.

• The 16p11.2 region first received attention after an association of its deletion with autism Later, it was shown that the reciprocal duplication is associated with schizophrenia.

• Interestingly, the deletion and duplication show opposite effects on intracranial volume, brain size, compartmental measures of gray and white matter, subcortical structures, and the cerebellum also show reciprocal effects on head circumference [40] visual evoked potential amplitude and BMI phenotypes

• It has been suggested that the major driver of the neuroanatomical phenotypes may be the gene KCTD13 which has been implicated in long-term positioning and dendritic maturation of cerebral cortical neurons.

• A more distal and smaller region on 16p11.2 has also been implicated in schizophrenia when deleted, as well as in developmental delay and obesity  

• The 2p16.3 deletion was first identified by comparative genome hybridization and disrupts the NRXN1 gene encoding neurexin 1 a presynaptic cell adhesion molecule which interacts with neuroligins to induce synapse formation and maturation. The initial association with schizophrenia was confirmed soon after by a larger SNP array-based study.

• The deletion at 15q13.3 was reported to cause mental retardation and seizures before being associated with schizophrenia

• Two childhood-onset schizophrenia cases with duplications at this locus have also been reporte. It contains the CHRNA7 gene encoding the A7 nicotinic acetylcholine receptor, previously linked to many psychiatric phenotypes including schizophrenia.

• The 1q21.1 CNV was first reported by the International Schizophrenia Consortium to increase the risk when deleted and later the reciprocal duplication was also found in excess in schizophrenia patients.

• Like the 16p11.2 CNV, reciprocal phenotypes have been described for the 1q21.1 CNV.

• Deletion and duplication cause microcephaly and macrocephaly, respectively, and schizophrenia is only one of many associated neurodevelopmental phenotypes.

• The 3q29 deletion was first described to cause mental retardation, with slight dysmorphic facial features [55] and in some cases autism and was later linked to schizophrenia.

• The 7q11.23 duplication is reciprocal to the Williams-Beuren syndrome deletion and in addition to schizophrenia has been associated with autism, language delay, and mental retardation

•  Tyhe 15q11.2 is also associated with developmental and language delay, mild dysmorphic features, autism, and seizures in addition to schizophrenia.

• Many additional, perhaps more rare CNVs or CNVs with smaller odds ratios are likely to be below our current detection threshold and are not on this list. Their existence however is supported by the overall enrichment for CNVs in cases compared to controls, even after exclud ing those reaching significance.

• Additionally, it is thought, largely due to the likely negative selection of these high-risk variants, that CNV leading to schizophrenia often occur de novo and can be recurrent due to flanking low copy repeats, which has been directly demonstrated.

• An important observation is that these CNVs include both gains and losses of genetic material, and are often also associated with autism and/or intellectual disability.

• The associations are often with reciprocal alleles (22q, 16p) but sometimes they are with the same CNV allele. This not only supports the notion of genetic overlap between psychiatric disorders (see below) but also adds a level of complexity showing that for specific loci the allelic effects can be different.

• Overall, within CNV regions in schizophrenia there is excess of genes involved in axon guidance, nervous system development, genes coding for targets of the RNA-binding protein FMRP (responsible for Fragile X syndrome) and for proteins of the activity-regulated cytoskeletal (ARC) complex involved in learning and memory.

• A special case of chromosomal rearrangement that has been linked to schizophrenia is the DISC1 locus.

• A balanced 1q43: 11q14 translocation has been described in a large Scottish pedigree with multiple psychiatric phenotypes including schizophrenia.

• The pedigree showed significant genetic linkage between the disease and the translocation which disrupted two genes, DISC1 on chromosome 1 and DISC2 on chromosome 11. Of the two, DISC1 is the gene that appears most relevant.

• A later study also identified a frameshift mutation in DISC1 segregating in an American family with schizophrenia and schizoaffective disorder, and there has been a significant volume of research on the gene’s function supporting its importance in cortical development.

• The initial DISC1 report has also been followed by numerous association studies with mixed results and significant controversy regarding its role in schizophrenia.

• The gene also shows no association with schizophrenia in large GWAS, which suggests it contains no common alleles that increase the risk, but does not exclude its involvement in disease through rare highly penetrant variation like the 1q43: 11q14 translocation and the reported frameshift mutations.

• The strong linkage results, but most importantly the large volume of functional information that has now accumulated and linked the gene to brain development, certainly makes its study worthwhile.

Source
Recent Advances in the Genetics of Schizophrenia

Journal
Molecular Neuropsychiatry Vol.4, No. 1

Year
2018

Website
https://www.karger.com/Article/FullText/488679

Description

• In the last decade, new technologies have made sequencing of the entire exome or genome much more affordable, having a significant impact on the strategies used to study complex diseases including schizophrenia.

• Hypothesizing the existence of rare or de novo variants that have a strong impact on the risk, many investigators have sought them by sequencing case/control cohorts or parent-patient trios. However, despite the recent price reduction, the cost of sequencing remains significant and the size of the sequenced cohorts lags behind those studied in GWAS. This, along with the low frequency of such variants, leads to insufficient power at the gene level.

• Investigators have worked around this limitation by exploring the burden of likely functional variants across schizophrenia-related gene groups.

• In addition to the limitations of the “candidate pathway” approach and the uncertainties regarding gene group membership, a number of arbitrary thresholds are typically set to filter the variants by allele frequency and evidence of function.

• Nevertheless, there have been interesting results that are consistent with the results of both CNV and GWAS studies.

• In one of the first exome sequencing studies, the exomes of 14 schizophrenia probands and their parents and reported an excess of exonic de novo mutations, the higher prevalence of gene-disruptive de novo mutations and reporting recurrent mutations in four genes (LAMA2, DPYD, TRRAP, and VPS39).

• Increased de novo mutation burden in select groups of genes, namely those encoding proteins closely associated with N-methyl-D-aspartate (NMDA) receptors and proteins that interact with the activity-regulated cytoskeleton-associated protein ARC, reiterating the results of CNV studies.

• They also reported recurrence for the TAF13 gene.

• De novo mutations in genes involved in chromatin remodeling and previously implicated in autism and intellectual disability, re-iterating the disease overlaps reported for CNVs.

• Synonymous variants that overlap brain-derived DNase hypersensitivity sites, genomic sites where chromatin is open, suggesting functional significance.

• One of the genes they identified, SETD1A, showed two loss-of-function and one synonymous de novo mutation.

• The mutated genes were mapped onto transcriptome profiles measured in normal human brains aged between the 13th week of gestation and adulthood.

• Mutated genes mapped on transcriptional coexpression and protein interaction networks involved in regulation of transcription, cellular transport, signaling, neuronal migration, and synaptic transmission.

• Rare variants are unlikely to be a major risk factor for schizophrenia.

• The contribution of recessive and compound heterozygous rare likely functional variants but neither was able to show a significant contribution; however, a number of possible limitations including sample size do not allow definite conclusions from these negative results.  

• Therev is a high polygenic burden of very rare disruptive mutations in schizophrenics.

• While no individual gene test achieved study-wide significance, they showed enrichment in genes related to voltage-gated calcium channels and the ARC-associated proteins, once again supporting the same enrichments observed with CNVs.

• There is highly significant excess of ultra-rare gene-disruptive variants, particularly in genes expressed in neurons.

• The corresponding RNAs included many known to interact with synaptic proteins, so they concluded that these rare genetic variants disrupt synaptic function.

• In schizophrenia, genes intolerant of loss-of-function variation and genes whose RNAs bind FMRP, similar to CNV results, carried an excess of rare alleles with minor allele frequency less than 0.1%.

• The only individual gene to show study-wide significant enrichment for rare loss-of-function variants is SETD1A, specifically suggesting a role for epigenetic dysregulation in the histone H3K4 methylation in schizophrenia

• Overall, the evidence of a role of rare and de novo mutations in schizophrenia is overwhelming, and involves some of the same functional categories with genes implicated by CNVs, although their overall contribution to disease is modest.

• The limited examples of recurrent hits of the same gene with de novo mutations, suggests that the number of genes involved in schizophrenia is quite large.

• The penetrance of these de novo variants and the extent to which their expression depends on the rest of the genome and the environment remains unknown, and requires large sample sizes to study.

• A limitation of current sequencing studies is that although they make a valid point on the involvement of rare or de novo variants, what they show is deviations from the expected number of such variants; they do not yet point to specific variants that increase the risk with enough certainty to warrant investing resources on follow-up. This however is likely to change as sample sizes increase.

Source
Recent Advances in the Genetics of Schizophrenia

Journal
Molecular Neuropsychiatry Vol.4, No. 1

Year
2018

Website
https://www.karger.com/Article/FullText/488679

Description

• In complex disorders GWAS have far superior power than genome-wide linkage studies, which is the preferred way to map genes for diseases like schizophrenia.
• The first GWAS for schizophrenia to adequately cover the genome in a relatively large collaborative case/control sample was published in 2008. Following a two-step analysis to reduce genotyping cost, and including BD patients in an effort to increase power, this study reported a single association around the ZNF804A gene, a gene that has been replicated in subsequent studies.
• This was followed by a larger study combining data from multiple others to reach 13,000 cases and 35,000 controls and reporting three genomic loci including the Human Leukocyte Antigen (HLA) region on chromosome 6 and near the genes TCF4 and NRGN on chromosomes 18 and 11, respectively.
• At the same time, the International Schizophrenia Consortium also reported on the HLA association as well as significant genetic overlap with BD.
• After these studies, smaller groups began consolidating collected samples and genotypes of patients and controls into larger consortia.
• Efforts such as the Molecular Genetics of Schizophrenia collection and the Genetic Association Information Network (GAIN) were developed in order to achieve the statistical power necessary for robust discovery.
• The biggest collaborative consortium, the Psychiatric Genomics Consortium (PGC) with its schizophrenia group currently includes over 400 investigators from 40 countries.
• The PGC published its first GWAS in 2011 identifying five new loci for schizophrenia using a discovery sample of 21,856 Europeans and 29,839 independent subjects for replication.
• Many other important papers followed until most recently in 2014 they published on 36,989 cases and 113,075 controls, reporting 108 significant loci that represent 128 independent association signals, 83 of which had not been previously reported.
• The authors mapped the variants onto epigenetic marks characteristic of active enhancers in 56 tissues and cell lines.
• As expected, they found enrichment in brain tissue enhancers (highest in midfrontal and angular gyrus), but also in tissues with important roles in immunity (highest in CD19 and CD20 B cells).
• The same group also developed an analytical framework to use summary statistics data from this GWAS to identify and rank common gene/functional pathways between schizophrenia, BD, and major depressive disorder (MDD). They reported associations for the histone methylation pathway as well as for immune and neuronal signaling and postsynaptic density.
• Li et al. have recently added 30 new loci to the PGC results by adding a large Chinese sample of ∼36,000 individuals and combining them with the PGC data in meta-analysis. The PGC has also continued increasing their sample size and at the 2017 World Congress of Psychiatric Genetics, they reported the identification of 248 genome-wide significant loci, confirming the speculation that a large number of genes are likely involved in schizophrenia, and providing the basis for a tremendous amount of future work on the etiology of schizophrenia.
• While combining samples through consortia has tremendous value, there is also the limitation that it is hard to replicate every finding in an independent comparable sample. However, the persistence of signals constitutes equally strong validation to independent replication, suggesting it is highly unlikely to be a false positive. Each new sample increase brings new candidate associations forward while validating many of the previously reported.
• In addition to identifying multiple reliable associations, the advent of GWAS also has led to a novel approach in the study of the genetics of complex diseases, the development of polygenic risk scores (PRSs).
• The International Schizophrenia Consortium was the first to use PRSs.
• In a paper reporting an early schizophrenia GWAS that identified the HLA locus as mentioned above, the authors performed an additional analysis where they used the GWAS results as a reference dataset to calculate PRSs on other independent datasets.
• In a first step, the method selects variants from the GWAS at some significance threshold and assigns to their alleles the observed effect on risk.
• Then, based on the genotypes of the individuals in the target data set at these loci, it calculates a PRS for each individual. While most of the selected loci are not genome-wide significant, and many are false positives, those will have random effect size and direction; so, final score is mostly driven by true risk loci.
• In the original paper, the author used this method to formally demonstrate a long-suspected genetic overlap between schizophrenia and BD that is also supported by CNV and rare variant data. The polygenic scores also became a tool for other explorations in the genetic architecture of schizophrenia and its relationship to other phenotypes.
• Hamshere et al. showed an overlap of schizophrenia PRS with attention-deficit hyperactivity disorder (ADHD), while the Cross-Disorder Group of the PGC published on overlaps across five disorders, autism, ADHD, BP, MDD, and schizophrenia showing strongest overlaps between schizophrenia BP and MDD.
• Others have shown positive correlations of schizophrenia PRS with the risk for posttraumatic stress disorder, addiction, and cortical thinning in patients.
• In contrast, a large study from Iceland found that an increased score correlated with higher creativity, using membership in artistic societies and creative profession as a proxy.
• It is clear both from PRSs and from the results of CNV and rare variant analyses that the roles of some genes cut across multiple clinical diagnoses.
• It may be that subset variants confer risk for specific diseases while others affect general mental health robustness, while yet others do not increase the risk per se but only the outcome following loss of robustness.
• A recent study on a large sample (n ≈ 14,000) of BD patients and controls showed that only 22 of 107 leading schizophrenia SNPs reached nominal significance. While this is more than expected by chance, it clearly demonstrated that not all variants are important across diseases.
• As the reference GWAS and the target samples become larger, PRSs will gain power that may allow us to understand how behavioral and other phenotypes relate to each other at the level of the gene. 
• Having identified over 100 robust association signals for schizophrenia is a tremendous achievement and demonstrates the power of collaboration in science. However, the true benefits of these discoveries will only be realized once we begin to understand the disease mechanisms that underlie these associations.
• There are a number of obstacles in this path forward. First, most associated variants disrupt regulatory sequences as demonstrated by the lack of coding variation in linkage disequilibrium (LD).
• In contrast to coding sequences, we know very little about the rules governing regulatory sequences and the many association signals per locus due to LD; this makes it difficult to identify the biologically relevant variant.
• It is also often not clear which gene(s) and which isoform(s) are regulated by such variants and under what conditions or at what time during development the regulation is occurring.
• In the GTEx database for example, many of the GWAS variants are not identified as eQTLs in the included tissues, while many others are eQTLs for multiple genes across many tissues.
• Further, eQTLs that only affect splicing or are only active at specific times/conditions may be near invisible.
• Another obstacle is that the effect of GWAS variants on the risk is quite small, with most carriers of risk alleles being healthy.
• It is therefore unlikely to observe a phenotype even if one could imitate the exact same biological effect in a model organism.
• Applying more extreme disruptions such as gene knockouts might give a phenotype but reduces the credibility of the conclusions.
• Despite the obstacles, new disease biology is already emerging from the GWAS results.
• Beyond the group enrichments and network analyses described above, many studies have begun to link variants to specific genes as eQTLs and experimentally follow them up to understand the biological consequences of these variants. Examples include signals near ZNF804A, TCF4, and CACNA1C.
• The most detailed and well publicized such study has been that of Sekar et al.in the HLA region.
• The authors investigated the strongest signal from the PGC GWAS and found that the associated SNPs were proxies for the genomic structure of a nearby gene, C4A, which along with C4B show structurally diverse alleles. These alleles correspond to differences in the expression levels of the genes, which in turn lead to differences in synaptic pruning as the authors demonstrated by modeling in mice.
• A connection between schizophrenia and synaptic pruning was first made hypothetically 35 years ago and the involvement of the complement has also been reported.
• The work of Sekar et al., took advantage of the GWAS results to provide some of the strongest support for this hypothesis to date.
• With 108 loci to investigate and more than twice that expected as the PGC continues to expand their sample size, there is a lot of work to be done.
• The vision of biology-based psychiatry is becoming a reality.
• As we understand the basis of each genetic association, their common elements, the differences between them, and their interplay with the environment, we will likely soon make leaps in prevention, treatment, and management tailored to the individual patient.

Source
Recent Advances in the Genetics of Schizophrenia

Journal
Molecular Neuropsychiatry Vol.4, No. 1

Year
2018

Website
https://www.karger.com/Article/FullText/488679

Description

• The study of the transcriptome has only been possible in the last two decades with the advent of microarray technologies, which have been replaced more recently by transcriptome sequencing.
• There have been numerous studies attempting to characterize the schizophrenia transcriptome, with the first study on postmortem brain tissue of schizophrenics appearing in 2000 and reporting abnormalities in presynaptic function.
• Subsequent studies have shown fairly consistent results incriminating mitochondrial function and energy metabolism , oligodendrocyte function, immunity-related genes and GABA neurotransmission
• A study by Cohen et al. implicated alternative splicing in schizophrenia by showing differential expression of particular exons and 3′ untranslated regions, a result that was supported by an independent study from Oldmeadow et al. and later another independent observation by Takata et al, who found enrichment of splicing QTLs among schizophrenia-associated loci.
• Also studying schizophrenia-associated loci, Birnbaum et al. showed that they were enriched for genes transcribed during fetal life, supporting a developmental origin of the disease.
• The same finding was independently reported a year later by Ohi et al. Jaffe et al. mapped DNA methylation across development and found 2,104 CpGs differing between schizophrenia patients and controls. These were enriched for brain development and neuronal differentiation genes, and were often located at GWAS schizophrenia risk loci.
• Ellis et al. studying both autism and schizophrenia brains found significant excess of shared sets of downregulated genes between them, adding to the evidence of etiological overlaps between psychiatric disorder.
• Finally, using data from the CommonMind Consortium, Fromer et al. showed that ∼20% of schizophrenia loci have variants that alter gene expression.
• In cases where a single gene was involved (FURIN, TSNARE1, CNTN4), they showed that altering its expression changed neurodevelopment in zebrafish.
• Using gene coexpression network analysis, they showed support for gene networks involved in neurobiological functions that had already been suggested by other studies like the ARC protein complex, targets of FMRP, neuronal markers, postsynaptic density proteins, and NMDA receptors.
• Most recently, Gandal et al. applied transcriptomic analysis to further explore the overlap between psychiatric disorders.
• They identified patterns of both shared and distinct gene expression perturbations and similar to reported polygenic overlaps, they found strong overlaps with BD autism and MDD in order of overlap strength and reported specific expression patterns.
• Three other studies have used the transcriptome as a readout to characterize the biological consequences of schizophrenia-associated genes.
• Chen et al.studied the ZNF804A gene by analyzing the effects of a gene knockdown in neurons derived from human induced pluripotent stem cells and reported enrichment of downregulated genes involved in interferon signaling.
• Pham et al., following up on their own linkage, association, and functional data, modified an isoform-specific promoter of the DPYSL2 gene by CRISPR/Cas9 and found a complementary effect to transcriptomic changes induced by antipsychotics, enrichment in immune system process genes, as well as a significant overlap with the results of Chen et al.
• This last point is of interest as it connects ZNF804A and DPYSL2, two genes that have no other known functional connection other than their associations with schizophrenia.
• Finally, Hill et al. knocked down the schizophrenia-associated gene TCF4 and reported that this resulted in RNA-level changes of genes involved in the cell cycle and the proliferation of human cortical progenitor cells.
• Across different study designs exploring CNVs, rare variants, de novo variants, common variants, or the disease transcriptome, it is clear that certain gene groups and pathways appear repeatedly. 

Source
Recent Advances in the Genetics of Schizophrenia

Journal
Molecular Neuropsychiatry Vol.4, No. 1

Year
2018

Website
https://www.karger.com/Article/FullText/488679

Description

• Endophenotypes are a concept initially described by Gottesman and Shields as internal phenotypes discoverable by a “biochemical test or microscopic examination.”
• They are phenotypes that are not immediately observable, but can be related to a disease because they are present in patients and sometimes their non-affected relatives as a presumed consequence of higher penetrance of the endophenotype compared to the disease phenotype.
• The initial idea behind their study was that endophenotypes may be the result of a subset of the many disease genes and may have higher expressivity, making it easier to identify these genes.
• This approach has been successfully used in diseases other than schizophrenia.
• A prominent example is the identification of genes for long QT syndrome, an endophenotype for syncope, ventricle arrhythmias, and sudden death.
• Other terms that have been used in place of endophenotype include:

1. Intermediate phenotype
2. Biological marker
3. Subclinical trait and
4. Vulnerability marker.

• The concept is of particular interest for psychiatric diseases for the additional reason that it may provide an objectively measurable phenotype.
• It is closely related to the Research Domain Criteria (RDoC) in psychiatric research, an NIMH project to create a research framework for genomics and neuroscience aimed to eventually inform classification schemes.
• Some of the major endophenotypes that have been studied for schizophrenia are:

1. Sensory motor gating
2. Eye-tracking dysfunction
3. Working memory and
4. Executive cognition.

• There have been many studies looking for linkage and associations between schizophrenia endophenotypes and common genetic variation.
• The largest effort to investigate endophenotypes and identify linkage with schizophrenia has been the Consortium on the Genetics of Schizophrenia (COGS), a 7-site study funded by the National Institute of Mental Health. They have reported on the significant impairment of:

1. P50 inhibition
2. Prepulse inhibition
3. Verbal declarative memory and
4. Working memory in schizophrenic patients and relatives

• Positive but weaker results were also reported for the antisaccade task performance and reduced auditory P300 amplitude
• A linkage analysis of their 12 phenotypes identified a LOD score of 4.0 on chromosome 3p14 for the antisaccade task but no other genome-wide significant result,
• Heritability analysis in the COGS-1 family sample has shown comparable levels between endophenotypes and psychotic disorders
• More recently, the group has reported on new endophenotypes from measures derived from the original endophenotype tests finding nine to be significantly heritable and discriminate between schizophrenia patients and controls.
• As GWAS are currently the state-of-the-art and provide much more reliable results, we will not report on the multiple candidate gene association studies.
• Unfortunately, GWAS for schizophrenia endophenotypes have generally been limited in sample size.
• One of the first GWAS examined 11 cognitive phenotypes in 750 subjects but did not find genome-wide significant associations.
• Hatzimanolis et al  in a GWAS on multiple endophenotypes in young male adults that also did not show genome-wide significant results, reported that schizophrenia polygenic risk influences neurocognitive performance, a result recapitulated by a study in childhood
• Roussos et al also showed that in addition to reduced cognition, increased PRS for schizophrenia was associated with reduced PPI validating this additional endophenotype.
• More recently, a meta-analysis by the Cognitive Genomics Consortium (COGENT) reported on a sample of 35,298 healthy individuals of European ancestry.
• They found polygenic correlations between cognitive performance, educational attainment, several psychiatric disorders, birth length/weight, smoking behavior and the personality trait of openness. Importantly, they also reported on some specific loci significantly associated with general cognitive function.
• Finally, schizophrenia-derived polygenic scores have also been correlated with cortical gyrification, an additional potential schizophrenia endophenotype.
• While endophenotypes were initially considered a way to facilitate disease gene discovery, the results suggest that their genetics are similarly complex. However, these results also highlight the value of polygenic scores in the study of the genetics of schizophrenia and the underlying polygenic architecture.
• With larger samples, we might be able to better understand their relationships to schizophrenia and how it relates to the underlying genetics.
• This multifaceted approach to disease may prove to be key in achieving individualized medicine and extending precision medicine into psychiatry.

Source
Recent Advances in the Genetics of Schizophrenia

Journal
Molecular Neuropsychiatry Vol.4, No. 1

Year
2018

Website
https://www.karger.com/Article/FullText/488679