Dataset Information

Identification of rare and common variants in BNIP3L: a schizophrenia susceptibility gene.

ABSTRACT: BACKGROUND:Schizophrenia is a chronic and severe mental disorder, and it has been predicted to be highly polygenic. Common SNPs located in or near BNIP3L were found to be genome-wide significantly associated with schizophrenia in recent genome-wide association studies. The purpose of our study is to investigate potential causal variants in BNIP3L gene. RESULTS:We performed targeted sequencing for all exons and un-translated regions of BNIP3L gene among 1806 patients with schizophrenia and 998 healthy controls of Han Chinese origin. Three rare nonsynonymous mutations, BNIP3L (NM_004331): c.52A>G, c.167G>A and c.313A>T, were identified in schizophrenia cases, and two of them were newly reported. The frequencies of these rare nonsynonymous mutations were significantly different between schizophrenia cases and healthy controls. For the common variants, rs147389989 achieved significance in both allelic and genotypic distributions with schizophrenia. Rs1042992 and rs17310286 were significantly associated with schizophrenia in meta-analyses using PGC, CLOZUK, and our new datasets in this study. CONCLUSIONS:Our findings provided further evidence that BNIP3L gene is a susceptibility gene of schizophrenia and revealed functional and potential causal mutations in BNIP3L. However, more functional validations are suggested to better understand the role of BNIP3L in the etiology of schizophrenia.

SUBMITTER: Zhou J

PROVIDER: S-EPMC7212671 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Identification of rare and common variants in BNIP3L: a schizophrenia susceptibility gene.

Zhou Juan J Ma Chuanchuan C Wang Ke K Li Xiuli X Jian Xuemin X Zhang Han H Yuan Jianmin J Yin Jiajun J Chen Jianhua J Shi Yongyong Y

Human genomics 20200511 1

<h4>Background</h4>Schizophrenia is a chronic and severe mental disorder, and it has been predicted to be highly polygenic. Common SNPs located in or near BNIP3L were found to be genome-wide significantly associated with schizophrenia in recent genome-wide association studies. The purpose of our study is to investigate potential causal variants in BNIP3L gene.<h4>Results</h4>We performed targeted sequencing for all exons and un-translated regions of BNIP3L gene among 1806 patients with schizophr ...[more]

PMID: 32393399

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Project description:BackgroundCopy-number variations (CNVs) have been associated with rare and debilitating genomic disorders (GDs) but their impact on health later in life in the general population remains poorly described.MethodsAssessing four modes of CNV action, we performed genome-wide association scans (GWASs) between the copy-number of CNV-proxy probes and 60 curated ICD-10 based clinical diagnoses in 331,522 unrelated white British UK Biobank (UKBB) participants with replication in the Estonian Biobank.ResultsWe identified 73 signals involving 40 diseases, all of which indicating that CNVs increased disease risk and caused earlier onset. We estimated that 16% of these associations are indirect, acting by increasing body mass index (BMI). Signals mapped to 45 unique, non-overlapping regions, nine of which being linked to known GDs. Number and identity of genes affected by CNVs modulated their pathogenicity, with many associations being supported by colocalization with both common and rare single-nucleotide variant association signals. Dissection of association signals provided insights into the epidemiology of known gene-disease pairs (e.g., deletions in BRCA1 and LDLR increased risk for ovarian cancer and ischemic heart disease, respectively), clarified dosage mechanisms of action (e.g., both increased and decreased dosage of 17q12 impacted renal health), and identified putative causal genes (e.g., ABCC6 for kidney stones). Characterization of the pleiotropic pathological consequences of recurrent CNVs at 15q13, 16p13.11, 16p12.2, and 22q11.2 in adulthood indicated variable expressivity of these regions and the involvement of multiple genes. Finally, we show that while the total burden of rare CNVs-and especially deletions-strongly associated with disease risk, it only accounted for ~ 0.02% of the UKBB disease burden. These associations are mainly driven by CNVs at known GD CNV regions, whose pleiotropic effect on common diseases was broader than anticipated by our CNV-GWAS.ConclusionsOur results shed light on the prominent role of rare CNVs in determining common disease susceptibility within the general population and provide actionable insights for anticipating later-onset comorbidities in carriers of recurrent CNVs.

Project description:Abstract Schizophrenia (SZ) is a debilitating psychiatric disorder for which the complex genetic mechanisms underlying the disease state remain unclear. Whereas highly penetrant variants have proven well-suited to human induced pluripotent stem cell (hiPSC)-based models, the power of hiPSC-based studies to resolve the much smaller effects of common variants within the size of cohorts that can be realistically assembled remains uncertain. Overall, we consider the successes and limitations in applying human induced pluripotent stem cell (hiPSC)-based models to study the impact of rare and common variants in SZ risk. To explore the neuronal impact of rare variants, we investigated the relationship between heterozygous 2p16.3 deletions, alternative splicing of NRXN1, and perturbations in neuronal activity, finding some commonalities with idiopathic SZ. We identified ~100 NRXN1α isoforms in control hiPSC neurons; patient-derived 2p16.3 neurons show perturbed NRXN1 isoform repertoires, reduced neuronal branching and decreased neuronal activity, which unexpectedly can be partially ameliorated by overexpression of a single NRXN1 isoform. Second, we present a genetics-driven hiPSC-based CRISPR-mediated approach for the functional validation of common variants and genes associated with SZ, evaluating the impact of one putative causal SZ SNP (FURIN rs4702) and two SZ-associated genes (SNAP91 and TSNARE1) on global gene expression patterns and synaptic function. We predict a growing convergence between hiPSC and post-mortem studies as both approaches expand to larger cohort sizes. We demonstrate a systematic and scalable strategy to interpret and evaluate the growing number of SZ-associated variants and genes across neural cell types and genetic backgrounds. Altogether, our objective is to dissect the genetic origins of SZ while developing a precision medicine approach to screen for novel therapeutics with which to prevent or reverse disease course. Concurrent Symposia

Dataset Information

Identification of rare and common variants in BNIP3L: a schizophrenia susceptibility gene.

Publications

Identification of rare and common variants in BNIP3L: a schizophrenia susceptibility gene.

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