Contribution of common and rare variants to bipolar disorder susceptibility in extended pedigrees from population isolates

Heterogeneity analysis provides evidence for a genetically homogeneous subtype of bipolar-disorder

Bipolar Disorder (BD) is a complex disease. It is heterogeneous, both at the phenotypic and genetic level, although the extent and impact of this heterogeneity is not fully understood. One way to assess this heterogeneity is to look for patterns in the subphenotype data, identify a more phenotypically homogeneous set of subjects, and perform a genome-wide association-study (GWAS) and subsequent secondary analyses restricted to this homogeneous subset. Because of the variability in how phenotypic data was collected by the various BD studies over the years, homogenizing the phenotypic data is a challenging task, and so is replication. As members of the Psychiatric Genomics Consortium (PGC), we have access to the raw genotypes of 18,711 BD cases and 29,738 controls. This amount of data makes it possible for us to set aside the intricacies of phenotype and allow the genetic data itself to determine which subjects define a homogeneous genetic subgroup. In this paper, we leverage recent advances in heterogeneity analysis to look for distinct homogeneous genetic BD subgroups (or biclusters) that manifest the broad phenotype we think of as Bipolar Disorder. As our data was generated by 27 studies and genotyped on a variety of platforms (OMEX, Affymetrix, Illumina), we use a biclustering algorithm capable of covariate-correction. Covariate-correction is critical if we wish to distinguish disease-related signals from those which are a byproduct of ancestry, study or genotyping platform. We rely on the raw genotyped data and do not include any data generated through imputation. We first apply this covariate-corrected biclustering algorithm to a cohort of 2524 BD cases and 4106 controls from the Bipolar Disease Research Network (BDRN: OMEX). We find evidence of genetic heterogeneity delineating a statistically significant bicluster comprising a subset of BD cases which exhibits a disease-specific pattern of differential-expression across a subset of SNPs. This pattern replicates across the remaining data-sets collected by the PGC containing 5781/8289 (OMEX), 3581/7591 (Illumina), and 6825/9752(Affymetrix) cases/controls, respectively. This bicluster includes subjects diagnosed with bipolar type-I, as well as subjects diagnosed with bipolar type-II. However, the bicluster is enriched for bipolar type-I over type-II and may represent a collection of correlated genetic risk-factors. By investigating the bicluster-informed polygenic-risk-scoring (PRS), we find that the disease-specific pattern highlighted by the bicluster can be leveraged to eliminate noise from our GWAS analyses and improve not only risk prediction, particularly when using only a relatively small subset (e.g., ~ 1%) of the available SNPs, but also SNP replication. Though our primary focus is only the analysis of disease-related signal, we also identify replicable control-related heterogeneity. Covariate-corrected biclustering of raw genetic data appears to be a promising route for untangling heterogeneity and identifying replicable homogeneous genetic subtypes of complex disease. It may also prove useful in identifying protective effects within the control group. This approach circumvents some of the difficulties presented by subphenotype data collected by meta-analyses or 23 andMe, e.g., missingness, assessment variation, and reliance on self-report.

rvTWAS: identifying gene-trait association using sequences by utilizing transcriptome-directed feature selection

Toward the identification of genetic basis of complex traits, transcriptome-wide association study (TWAS) is successful in integrating transcriptome data. However, TWAS is only applicable for common variants, excluding rare variants in exome or whole-genome sequences. This is partly because of the inherent limitation of TWAS protocols that rely on predicting gene expressions. Our previous research has revealed the insight into TWAS: the 2 steps in TWAS, building and applying the expression prediction models, are essentially genetic feature selection and aggregations that do not have to involve predictions. Based on this insight disentangling TWAS, rare variants' inability of predicting expression traits is no longer an obstacle. Herein, we developed "rare variant TWAS," or rvTWAS, that first uses a Bayesian model to conduct expression-directed feature selection and then uses a kernel machine to carry out feature aggregation, forming a model leveraging expressions for association mapping including rare variants. We demonstrated the performance of rvTWAS by thorough simulations and real data analysis in 3 psychiatric disorders, namely schizophrenia, bipolar disorder, and autism spectrum disorder. We confirmed that rvTWAS outperforms existing TWAS protocols and revealed additional genes underlying psychiatric disorders. Particularly, we formed a hypothetical mechanism in which zinc finger genes impact all 3 disorders through transcriptional regulations. rvTWAS will open a door for sequence-based association mappings integrating gene expressions.

Progress and Implications from Genetic Studies of Bipolar Disorder

With the advancements in gene sequencing technologies, including genome-wide association studies, polygenetic risk scores, and high-throughput sequencing, there has been a tremendous advantage in mapping a detailed blueprint for the genetic model of bipolar disorder (BD). To date, intriguing genetic clues have been identified to explain the development of BD, as well as the genetic association that might be applied for the development of susceptibility prediction and pharmacogenetic intervention. Risk genes of BD, such as CACNA1C, ANK3, TRANK1, and CLOCK, have been found to be involved in various pathophysiological processes correlated with BD. Although the specific roles of these genes have yet to be determined, genetic research on BD will help improve the prevention, therapeutics, and prognosis in clinical practice. The latest preclinical and clinical studies, and reviews of the genetics of BD, are analyzed in this review, aiming to summarize the progress in this intriguing field and to provide perspectives for individualized, precise, and effective clinical practice.

Neurite outgrowth deficits caused by rare PLXNB1 mutation in pediatric bipolar disorder

Pediatric bipolar disorder (PBD) is a severe mood dysregulation condition that affects 0.5-1% of children and teens in the United States. It is associated with recurrent episodes of mania and depression and an increased risk of suicidality. However, the genetics and neuropathology of PBD are largely unknown. Here, we used a combinatorial family-based approach to characterize cellular, molecular, genetic, and network-level deficits associated with PBD. We recruited a PBD patient and three unaffected family members from a family with a history of psychiatric illnesses. Using resting-state functional magnetic resonance imaging (rs-fMRI), we detected altered resting-state functional connectivity in the patient as compared to an unaffected sibling. Using transcriptomic profiling of patient and control induced pluripotent stem cell (iPSC)-derived telencephalic organoids, we found aberrant signaling in the molecular pathways related to neurite outgrowth. We corroborated the presence of neurite outgrowth deficits in patient iPSC-derived cortical neurons and identified a rare homozygous loss-of-function PLXNB1 variant (c.1360C>C; p.Ser454Arg) responsible for the deficits in the patient. Expression of wild-type PLXNB1, but not the variant, rescued neurite outgrowth in patient neurons, and expression of the variant caused the neurite outgrowth deficits in cortical neurons from PlxnB1 knockout mice. These results indicate that dysregulated PLXNB1 signaling may contribute to an increased risk of PBD and other mood dysregulation-related disorders by disrupting neurite outgrowth and functional brain connectivity. Overall, this study established and validated a novel family-based combinatorial approach for studying cellular and molecular deficits in psychiatric disorders and identified dysfunctional PLXNB1 signaling and neurite outgrowth as potential risk factors for PBD.

Genetic substrates of bipolar disorder risk in Latino families

Genetic studies of bipolar disorder (BP) have been conducted in the Latin American population, to date, in several countries, including Mexico, the United States, Costa Rica, Colombia, and, to a lesser extent, Brazil. These studies focused primarily on linkage-based designs utilizing families with multiplex cases of BP. Significant BP loci were identified on Chromosomes 18, 5 and 8, and fine mapping suggested several genes of interest underlying these linkage peaks. More recently, studies in these same pedigrees yielded significant linkage loci for BP endophenotypes, including measures of activity, sleep cycles, and personality traits. Building from findings in other populations, candidate gene association analyses in Latinos from Mexican and Central American ancestry confirmed the role of several genes (including CACNA1C and ANK3) in conferring BP risk. Although GWAS, methylation, and deep sequencing studies have only begun in these populations, there is evidence that CNVs and rare SNPs both play a role in BP risk of these populations. Large segments of the Latino populations in the Americas remain largely unstudied regarding BP genetics, but evidence to date has shown that this type of research can be successfully conducted in these populations and that the genetic underpinnings of BP in these cohorts share at least some characteristics with risk genes identified in European and other populations.

Whole exome sequencing in dense families suggests genetic pleiotropy amongst Mendelian and complex neuropsychiatric syndromes

Whole Exome Sequencing (WES) studies provide important insights into the genetic architecture of serious mental illness (SMI). Genes that are central to the shared biology of SMIs may be identified by WES in families with multiple affected individuals with diverse SMI (F-SMI). We performed WES in 220 individuals from 75 F-SMI families and 60 unrelated controls. Within pedigree prioritization employed criteria of rarity, functional consequence, and sharing by ≥ 3 affected members. Across the sample, gene and gene-set-wide case-control association analysis was performed with Sequence Kernel Association Test (SKAT). In 14/16 families with ≥ 3 sequenced affected individuals, we identified a total of 78 rare predicted deleterious variants in 78 unique genes shared by ≥ 3 members with SMI. Twenty (25%) genes were implicated in monogenic CNS syndromes in OMIM (OMIM-CNS), a fraction that is a significant overrepresentation (Fisher's Exact test OR = 2.47, p = 0.001). In gene-set SKAT, statistically significant association was noted for OMIM-CNS gene-set (SKAT-p = 0.005) but not the synaptic gene-set (SKAT-p = 0.17). In this WES study in F-SMI, we identify private, rare, protein altering variants in genes previously implicated in Mendelian neuropsychiatric syndromes; suggesting pleiotropic influences in neurodevelopment between complex and Mendelian syndromes.

Rare genetic variants explain missing heritability in smoking

Common genetic variants explain less variation in complex phenotypes than inferred from family-based studies, and there is a debate on the source of this 'missing heritability'. We investigated the contribution of rare genetic variants to tobacco use with whole-genome sequences from up to 26,257 unrelated individuals of European ancestries and 11,743 individuals of African ancestries. Across four smoking traits, single-nucleotide-polymorphism-based heritability ([Formula: see text]) was estimated from 0.13 to 0.28 (s.e., 0.10-0.13) in European ancestries, with 35-74% of it attributable to rare variants with minor allele frequencies between 0.01% and 1%. These heritability estimates are 1.5-4 times higher than past estimates based on common variants alone and accounted for 60% to 100% of our pedigree-based estimates of narrow-sense heritability ([Formula: see text], 0.18-0.34). In the African ancestry samples, [Formula: see text] was estimated from 0.03 to 0.33 (s.e., 0.09-0.14) across the four smoking traits. These results suggest that rare variants are important contributors to the heritability of smoking.

Ten challenges for clinical translation in psychiatric genetics

Genome-wide association studies have identified hundreds of robust genetic associations underlying psychiatric disorders and provided important biological insights into disease onset and progression. There is optimism that genetic findings will pave the way to precision psychiatry by facilitating the development of more effective treatments and the identification of groups of patients that these treatments should be targeted toward. However, there are several challenges that must be addressed before genetic findings can be translated into the clinic. In this Perspective, we highlight ten challenges for the field of psychiatric genetics, focused on the robust and generalizable detection of genetic risk factors, improved definition and assessment of psychopathology and achieving better clinical indicators. We discuss recent advancements in the field that will improve the explanatory and predictive power of genetic data and ultimately contribute to improving the management and treatment of patients with a psychiatric disorder.

Haplotype phasing of a bipolar disorder pedigree revealed rare multiple mutations of SPOCD1 gene in the 1p36-35 susceptibility locus

BACKGROUND

The etiology of bipolar disorder (BD) is poorly understood. Considering the complexity of BD, pedigree-based sequencing studies focusing on haplotypes at specific loci may be practical to discover high-impact risk variants. This study comprehensively examined the haplotype sequence at 1p36-35 BD and recurrent depressive disorder (RDD) susceptibility loci.

METHODS

We surveyed BD families in Okinawa, Japan. We performed linkage analysis and determined the phased sequence of the affected haplotype using whole genome sequencing. We filtered rare missense variants on the haplotype. For validation, we conducted a case-control genetic association study on approximately 3000 Japanese subjects.

RESULTS

We identified a three-generation multiplex pedigree with BD and RDD. Strikingly, we identified a significant linkage with mood disorders (logarithm of odds [LOD] = 3.61) at 1p36-35, supported in other ancestry studies. Finally, we determined the entire sequence of the 6.4-Mb haplotype shared by all affected subjects. Moreover, we found a rare triplet of missense variants in the SPOCD1 gene on the haplotype. Notably, despite the rare frequency, one heterozygote with multiple SPOCD1 variants was identified in an independent set of 88 BD type I genotyping samples.

LIMITATIONS

The 1p36-35 sequence was obtained from only a single pedigree. The replicate sample was small. Short-read sequencing might miss structural variants. A polygenic risk score was not analyzed.

CONCLUSION

The 1p36-35 haplotype sequence may be valuable for future BD variant studies. In particular, SPOCD1 is a promising candidate gene and should be validated.

Genomic and neuroimaging approaches to bipolar disorder

BACKGROUND

To date, besides genome-wide association studies, a variety of other genetic analyses (e.g. polygenic risk scores, whole-exome sequencing and whole-genome sequencing) have been conducted, and a large amount of data has been gathered for investigating the involvement of common, rare and very rare types of DNA sequence variants in bipolar disorder. Also, non-invasive neuroimaging methods can be used to quantify changes in brain structure and function in patients with bipolar disorder.

AIMS

To provide a comprehensive assessment of genetic findings associated with bipolar disorder, based on the evaluation of different genomic approaches and neuroimaging studies.

METHOD

We conducted a PubMed search of all relevant literatures from the beginning to the present, by querying related search strings.

RESULTS

ANK3, CACNA1C, SYNE1, ODZ4 and TRANK1 are five genes that have been replicated as key gene candidates in bipolar disorder pathophysiology, through the investigated studies. The percentage of phenotypic variance explained by the identified variants is small (approximately 4.7%). Bipolar disorder polygenic risk scores are associated with other psychiatric phenotypes. The ENIGMA-BD studies show a replicable pattern of lower cortical thickness, altered white matter integrity and smaller subcortical volumes in bipolar disorder.

CONCLUSIONS

The low amount of explained phenotypic variance highlights the need for further large-scale investigations, especially among non-European populations, to achieve a more complete understanding of the genetic architecture of bipolar disorder and the missing heritability. Combining neuroimaging data with genetic data in large-scale studies might help researchers acquire a better knowledge of the engaged brain regions in bipolar disorder.

What Do We Know About the Genetic Architecture of Psychopathology?

In the second half of the twentieth century, twin and family studies established beyond a reasonable doubt that all forms of psychopathology are substantially heritable and highly polygenic. These conclusions were simultaneously an important theoretical advance and a difficult methodological obstacle, as it became clear that heritability is universal and undifferentiated across forms of psychopathology, and the radical polygenicity of genetic effects limits the biological insight provided by genetically informed studies at the phenotypic level. The paradigm-shifting revolution brought on by the Human Genome Project has recapitulated the great methodological promise and the profound theoretical difficulties of the twin study era. We review these issues using the rubric of genetic architecture, which we define as a search for specific genetic insight that adds to the general conclusion that psychopathology is heritable and polygenic. Although significant problems remain, we see many promising avenues for progress.

Expected final online publication date for the Annual Review of Clinical Psychology, Volume 18 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Genetic contributions to bipolar disorder: current status and future directions

Bipolar disorder (BD) is a highly heritable mental disorder and is estimated to affect about 50 million people worldwide. Our understanding of the genetic etiology of BD has greatly increased in recent years with advances in technology and methodology as well as the adoption of international consortiums and large population-based biobanks. It is clear that BD is also highly heterogeneous and polygenic and shows substantial genetic overlap with other psychiatric disorders. Genetic studies of BD suggest that the number of associated loci is expected to substantially increase in larger future studies and with it, improved genetic prediction of the disorder. Still, a number of challenges remain to fully characterize the genetic architecture of BD. First among these is the need to incorporate ancestrally-diverse samples to move research away from a Eurocentric bias that has the potential to exacerbate health disparities already seen in BD. Furthermore, incorporation of population biobanks, registry data, and electronic health records will be required to increase the sample size necessary for continued genetic discovery, while increased deep phenotyping is necessary to elucidate subtypes within BD. Lastly, the role of rare variation in BD remains to be determined. Meeting these challenges will enable improved identification of causal variants for the disorder and also allow for equitable future clinical applications of both genetic risk prediction and therapeutic interventions.

Rare variants in the endocytic pathway are associated with Alzheimer's disease, its related phenotypes, and functional consequences

Late-onset Alzheimer’s disease (LOAD) is the most common type of dementia causing irreversible brain damage to the elderly and presents a major public health challenge. Clinical research and genome-wide association studies have suggested a potential contribution of the endocytic pathway to AD, with an emphasis on common loci. However, the contribution of rare variants in this pathway to AD has not been thoroughly investigated. In this study, we focused on the effect of rare variants on AD by first applying a rare-variant gene-set burden analysis using genes in the endocytic pathway on over 3,000 individuals with European ancestry from three large whole-genome sequencing (WGS) studies. We identified significant associations of rare-variant burden within the endocytic pathway with AD, which were successfully replicated in independent datasets. We further demonstrated that this endocytic rare-variant enrichment is associated with neurofibrillary tangles (NFTs) and age-related phenotypes, increasing the risk of obtaining severer brain damage, earlier age-at-onset, and earlier age-of-death. Next, by aggregating rare variants within each gene, we sought to identify single endocytic genes associated with AD and NFTs. Careful examination using NFTs revealed one significantly associated gene, ANKRD13D. To identify functional associations, we integrated bulk RNA-Seq data from over 600 brain tissues and found two endocytic expression genes (eGenes), HLA-A and SLC26A7, that displayed significant influences on their gene expressions. Differential expressions between AD patients and controls of these three identified genes were further examined by incorporating scRNA-Seq data from 48 post-mortem brain samples and demonstrated distinct expression patterns across cell types. Taken together, our results demonstrated strong rare-variant effect in the endocytic pathway on AD risk and progression and functional effect of gene expression alteration in both bulk and single-cell resolution, which may bring more insight and serve as valuable resources for future AD genetic studies, clinical research, and therapeutic targeting.

Late-onset Alzheimer’s disease (LOAD) is the most common type of dementia and a leading cause of death in the world. Clinical and genetic studies have suggested the potential contribution of the cellular transportation pathway to AD with an emphasis on common variants. In this study, we investigated the effect of rare variants within the cellular transportation pathway and examined three large datasets with over 3,000 individuals with European ancestry. We reported enrichment of rare deleterious variants in the cellular transportation pathway in AD patients from all three datasets. We also observed an elevation of rare deleterious variants in this pathway was associated with individuals with severer brain damages (AD progression), earlier age-at-onset, and earlier age-of-death. By aggregating rare variants in each gene from the cellular transportation pathway, we revealed one gene in which rare variants were significantly associated with the progression of AD. By integrating gene expression data from brain tissues, we identified two additional genes whose rare-variant effect displayed significant influences on gene expression. Taken together, our results demonstrated that rare-variant effect in the cellular transportation pathway is strongly associated with the risk and the progression of AD, which may serve as future clinical and therapeutic targets.

Psychiatric symptoms and syndromes transcending diagnostic boundaries in Indian multiplex families: The cohort of ADBS study

Syndromes of schizophrenia, bipolar disorder, obsessive-compulsive disorder, substance use disorders and Alzheimer's dementia are highly heritable. About 10-20% of subjects have another affected first degree relative (FDR), and thus represent a 'greater' genetic susceptibility. We screened 3583 families to identify 481 families with multiple affected members, assessed 1406 individuals in person, and collected information systematically about other relatives. Within the selected families, a third of all FDRs were affected with serious mental illness. Although similar diagnoses aggregated within families, 62% of the families also had members with other syndromes. Moreover, 15% of affected individuals met criteria for co-occurrence of two or more syndromes, across their lifetime. Using dimensional assessments, we detected a range of symptom clusters in both affected and unaffected individuals, and across diagnostic categories. Our findings suggest that in multiplex families, there is considerable heterogeneity of clinical syndromes, as well as sub-threshold symptoms. These families would help provide an opportunity for further research using both genetic analyses and biomarkers.

Translational genomics and beyond in bipolar disorder

Genome-wide association studies (GWAS) have revealed multiple genomic loci conferring risk of bipolar disorder (BD), providing hints for its underlying pathobiology. However, there are still remaining questions to answer. For example, discordance exists between BD heritability estimated with earlier epidemiological evidence and that calculated based on common GWAS variations. Where is the "missing heritability"? How can we explain the biology of the disease based on genetic findings? In this review, we summarize the accomplishments and limitations of current BD GWAS, and discuss potential reasons for the "missing heritability." In addition, progresses of research for the biological mechanisms underlying BD genetic risk using brain tissues, reprogrammed cells, and model animals are reviewed. While our knowledge of BD genetic basis is significantly promoted by these efforts, the complexities of gene regulation in the genome, the spatial-temporal heterogeneity during brain development, and the limitations of different experimental models should always be considered. Notably, several genes have been widely studied given their relatively well-characterized involvement in BD (e.g., CACAN1C and ANK3), and findings of these genes are summarized to both outline possible biological mechanisms of BD and describe examples of translating GWAS discoveries into the pathophysiology.

Copy number variant analysis and expression profiling of the olfactory receptor-rich 11q11 region in obesity predisposition

Genome-wide copy number surveys associated chromosome 11q11 with obesity. As this is an olfactory receptor-rich region, we hypothesize that genetic variation in olfactory receptor genes might be implicated in the pathogenesis of obesity. Multiplex Amplicon Quantification analysis was applied to screen for copy number variants at chromosome 11q11 in 627 patients with obesity and 330 healthy-weight individuals. A ± 80 kb deletion with an internally 1.3 kb retained segment was identified, covering the three olfactory receptor genes OR4C11, OR4P4, and OR4S2. A significant increase in copy number loss(es) was perceived in our patient cohort (MAF = 27%; p = 0.02). Gene expression profiling in metabolic relevant tissues was performed to evaluate the functional impact of the obesity susceptible locus. All three 11q11 genes were present in visceral and subcutaneous adipose tissue while no expression was perceived in the liver. These results support the 'metabolic system' hypothesis and imply that gene disruption of OR4C11, OR4P4, and OR4S2 will negatively influence energy metabolism, ultimately leading to fat accumulation and obesity. Our study thus demonstrates a role for structural variation within olfactory receptor-rich regions in complex diseases and defines the 11q11 deletion as a risk factor for obesity.

Whole-exome sequencing in an Afrikaner family with bipolar disorder

BACKGROUND

Bipolar disorder (BD) has considerable heritability, with genome-wide association studies indicating that multiple common genetic variants contribute to risk. Less work has been undertaken to assess the contribution of rare variation in the development of this complex disorder, particularly in isolated populations. Using whole-exome sequencing (WES), the aim of this study was to identify rare, potentially damaging variants contributing to risk for BD in the Afrikaner population.

METHODS

WES was performed on eight Afrikaner family members, five affected and three unaffected. The analyses focused on i) the identification of rare, damaging variation, and ii) the molecular pathways in which these rare variants play a role using in silico prediction tools such as wANNOVAR and KOBAS 3.0.

RESULTS

Two rare and potentially damaging missense variants in FAM71B and SLC26A9 were shared by affected family members but were absent in unaffected members. In addition, variants in genes that play a role in pathways involved in signal transduction and synaptic transmission were shared by the five affected individuals.

LIMITATIONS

Two main limitations affect this study: the limited number of cases and controls, and the fact that whole-exome sequencing can only capture a small fragment of the genome which may harbor mutations.

CONCLUSION

This is the first WES study of BD in an Afrikaner family, and findings suggest that novel candidate genes may contribute to risk for BD in this population. Future work in larger samples of this population as well as in other populations is needed to fully investigate the role of the candidate genes found here.