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1.
Mol Psychiatry ; 29(3): 782-792, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38145985

RESUMEN

Enhancers play an essential role in the etiology of schizophrenia; however, the dysregulation of enhancer activity and its impact on the regulome in schizophrenia remains understudied. To address this gap in our knowledge, we assessed enhancer and gene expression in 1,382 brain samples comprising cases with schizophrenia and unaffected controls. Dysregulation of enhancer expression was concordant with changes in gene expression, and was more closely associated with schizophrenia polygenic risk, suggesting that enhancer dysregulation is proximal to the genetic etiology of the disease. Modeling the shared variance of cis-coordinated genes and enhancers revealed a gene regulatory program that was highly associated with genetic vulnerability to schizophrenia. By integrating coordinated factors with evolutionary constraints, we found that enhancers acquired during human evolution are more likely to regulate genes that are implicated in neuropsychiatric disorders and, thus, hold potential as therapeutic targets. Our analysis provides a systematic view of regulome dysregulation in schizophrenia and highlights its convergence with schizophrenia polygenic risk and human-gained enhancers.


Asunto(s)
Elementos de Facilitación Genéticos , Predisposición Genética a la Enfermedad , Herencia Multifactorial , Esquizofrenia , Humanos , Esquizofrenia/genética , Herencia Multifactorial/genética , Predisposición Genética a la Enfermedad/genética , Elementos de Facilitación Genéticos/genética , Masculino , Femenino , Estudio de Asociación del Genoma Completo/métodos , Encéfalo/metabolismo , Regulación de la Expresión Génica/genética , Factores de Riesgo , Polimorfismo de Nucleótido Simple/genética , Adulto
2.
Bioinformatics ; 37(2): 192-201, 2021 04 19.
Artículo en Inglés | MEDLINE | ID: mdl-32730587

RESUMEN

SUMMARY: Large-scale transcriptome studies with multiple samples per individual are widely used to study disease biology. Yet, current methods for differential expression are inadequate for cross-individual testing for these repeated measures designs. Most problematic, we observe across multiple datasets that current methods can give reproducible false-positive findings that are driven by genetic regulation of gene expression, yet are unrelated to the trait of interest. Here, we introduce a statistical software package, dream, that increases power, controls the false positive rate, enables multiple types of hypothesis tests, and integrates with standard workflows. In 12 analyses in 6 independent datasets, dream yields biological insight not found with existing software while addressing the issue of reproducible false-positive findings. AVAILABILITY AND IMPLEMENTATION: Dream is available within the variancePartition Bioconductor package at http://bioconductor.org/packages/variancePartition. CONTACT: gabriel.hoffman@mssm.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Perfilación de la Expresión Génica , Programas Informáticos , Regulación de la Expresión Génica , Transcriptoma
3.
Am J Hum Genet ; 102(6): 1169-1184, 2018 06 07.
Artículo en Inglés | MEDLINE | ID: mdl-29805045

RESUMEN

Causal genes and variants within genome-wide association study (GWAS) loci can be identified by integrating GWAS statistics with expression quantitative trait loci (eQTL) and determining which variants underlie both GWAS and eQTL signals. Most analyses, however, consider only the marginal eQTL signal, rather than dissect this signal into multiple conditionally independent signals for each gene. Here we show that analyzing conditional eQTL signatures, which could be important under specific cellular or temporal contexts, leads to improved fine mapping of GWAS associations. Using genotypes and gene expression levels from post-mortem human brain samples (n = 467) reported by the CommonMind Consortium (CMC), we find that conditional eQTL are widespread; 63% of genes with primary eQTL also have conditional eQTL. In addition, genomic features associated with conditional eQTL are consistent with context-specific (e.g., tissue-, cell type-, or developmental time point-specific) regulation of gene expression. Integrating the 2014 Psychiatric Genomics Consortium schizophrenia (SCZ) GWAS and CMC primary and conditional eQTL data reveals 40 loci with strong evidence for co-localization (posterior probability > 0.8), including six loci with co-localization of conditional eQTL. Our co-localization analyses support previously reported genes, identify novel genes associated with schizophrenia risk, and provide specific hypotheses for their functional follow-up.


Asunto(s)
Estudio de Asociación del Genoma Completo , Corteza Prefrontal/patología , Sitios de Carácter Cuantitativo/genética , Esquizofrenia/genética , Células Cultivadas , Epigénesis Genética , Genoma Humano , Humanos
4.
Bioinformatics ; 36(9): 2856-2861, 2020 05 01.
Artículo en Inglés | MEDLINE | ID: mdl-32003784

RESUMEN

MOTIVATION: Identifying correlated epigenetic features and finding differences in correlation between individuals with disease compared to controls can give novel insight into disease biology. This framework has been successful in analysis of gene expression data, but application to epigenetic data has been limited by the computational cost, lack of scalable software and lack of robust statistical tests. RESULTS: Decorate, differential epigenetic correlation test, identifies correlated epigenetic features and finds clusters of features that are differentially correlated between two or more subsets of the data. The software scales to genome-wide datasets of epigenetic assays on hundreds of individuals. We apply decorate to four large-scale datasets of DNA methylation, ATAC-seq and histone modification ChIP-seq. AVAILABILITY AND IMPLEMENTATION: decorate R package is available from https://github.com/GabrielHoffman/decorate. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Biología Computacional , Programas Informáticos , Epigénesis Genética , Epigenómica , Genoma , Humanos
5.
Nucleic Acids Res ; 47(20): 10597-10611, 2019 11 18.
Artículo en Inglés | MEDLINE | ID: mdl-31544924

RESUMEN

Identifying functional variants underlying disease risk and adoption of personalized medicine are currently limited by the challenge of interpreting the functional consequences of genetic variants. Predicting the functional effects of disease-associated protein-coding variants is increasingly routine. Yet, the vast majority of risk variants are non-coding, and predicting the functional consequence and prioritizing variants for functional validation remains a major challenge. Here, we develop a deep learning model to accurately predict locus-specific signals from four epigenetic assays using only DNA sequence as input. Given the predicted epigenetic signal from DNA sequence for the reference and alternative alleles at a given locus, we generate a score of the predicted epigenetic consequences for 438 million variants observed in previous sequencing projects. These impact scores are assay-specific, are predictive of allele-specific transcription factor binding and are enriched for variants associated with gene expression and disease risk. Nucleotide-level functional consequence scores for non-coding variants can refine the mechanism of known functional variants, identify novel risk variants and prioritize downstream experiments.


Asunto(s)
Ensamble y Desensamble de Cromatina , Aprendizaje Profundo , Estudio de Asociación del Genoma Completo/métodos , Código de Histonas , Polimorfismo Genético , Análisis de Secuencia de ADN/métodos , Epigénesis Genética , Humanos
6.
Mol Psychiatry ; 24(1): 49-66, 2019 01.
Artículo en Inglés | MEDLINE | ID: mdl-29483625

RESUMEN

The development of human-induced pluripotent stem cells (hiPSCs) has made possible patient-specific modeling across the spectrum of human disease. Here, we discuss recent advances in psychiatric genomics and post-mortem studies that provide critical insights concerning cell-type composition and sample size that should be considered when designing hiPSC-based studies of complex genetic disease. We review recent hiPSC-based models of SZ, in light of our new understanding of critical power limitations in the design of hiPSC-based studies of complex genetic disorders. Three possible solutions are a movement towards genetically stratified cohorts of rare variant patients, application of CRISPR technologies to engineer isogenic neural cells to study the impact of common variants, and integration of advanced genetics and hiPSC-based datasets in future studies. Overall, we emphasize that to advance the reproducibility and relevance of hiPSC-based studies, stem cell biologists must contemplate statistical and biological considerations that are already well accepted in the field of genetics. We conclude with a discussion of the hypothesis of biological convergence of disease-through molecular, cellular, circuit, and patient level phenotypes-and how this might emerge through hiPSC-based studies.


Asunto(s)
Células Madre Pluripotentes Inducidas/fisiología , Trastornos Mentales/metabolismo , Trastornos Mentales/fisiopatología , Diferenciación Celular , Humanos , Modelos Biológicos , Neuronas , Fenotipo , Reproducibilidad de los Resultados
7.
Genes Immun ; 20(7): 577-588, 2019 09.
Artículo en Inglés | MEDLINE | ID: mdl-30692607

RESUMEN

Genome-wide association studies have identified ~170 loci associated with Crohn's disease (CD) and defining which genes drive these association signals is a major challenge. The primary aim of this study was to define which CD locus genes are most likely to be disease related. We developed a gene prioritization regression model (GPRM) by integrating complementary mRNA expression datasets, including bulk RNA-Seq from the terminal ileum of 302 newly diagnosed, untreated CD patients and controls, and in stimulated monocytes. Transcriptome-wide association and co-expression network analyses were performed on the ileal RNA-Seq datasets, identifying 40 genome-wide significant genes. Co-expression network analysis identified a single gene module, which was substantially enriched for CD locus genes and most highly expressed in monocytes. By including expression-based and epigenetic information, we refined likely CD genes to 2.5 prioritized genes per locus from an average of 7.8 total genes. We validated our model structure using cross-validation and our prioritization results by protein-association network analyses, which demonstrated significantly higher CD gene interactions for prioritized compared with non-prioritized genes. Although individual datasets cannot convey all of the information relevant to a disease, combining data from multiple relevant expression-based datasets improves prediction of disease genes and helps to further understanding of disease pathogenesis.


Asunto(s)
Enfermedad de Crohn/genética , Monocitos/patología , Análisis de Secuencia de ADN/métodos , Adolescente , Algoritmos , Estudios de Casos y Controles , Niño , Preescolar , Enfermedad de Crohn/metabolismo , Femenino , Redes Reguladoras de Genes/genética , Predisposición Genética a la Enfermedad/genética , Estudio de Asociación del Genoma Completo , Humanos , Masculino , Monocitos/metabolismo , Polimorfismo de Nucleótido Simple/genética , Sitios de Carácter Cuantitativo/genética , Programas Informáticos , Transcriptoma/genética
9.
Hum Mol Genet ; 24(14): 4147-57, 2015 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-25935003

RESUMEN

Genome-wide association studies in Crohn's disease (CD) have identified 140 genome-wide significant loci. However, identification of genes driving association signals remains challenging. Furthermore, genome-wide significant thresholds limit false positives at the expense of decreased sensitivity. In this study, we explored gene features contributing to CD pathogenicity, including gene-based association data from CD and autoimmune (AI) diseases, as well as gene expression features (eQTLs, epigenetic markers of expression and intestinal gene expression data). We developed an integrative model based on a CD reference gene set. This integrative approach outperformed gene-based association signals alone in identifying CD-related genes based on statistical validation, gene ontology enrichment, differential expression between M1 and M2 macrophages and a validation using genes causing monogenic forms of inflammatory bowel disease as a reference. Besides gene-level CD association P-values, association with AI diseases was the strongest predictor, highlighting generalized mechanisms of inflammation, and the interferon-γ pathway particularly. Within the 140 high-confidence CD regions, 598 of 1328 genes had low prioritization scores, highlighting genes unlikely to contribute to CD pathogenesis. For select regions, comparably high integrative model scores were observed for multiple genes. This is particularly evident for regions having extensive linkage disequilibrium such as the IBD5 locus. Our analyses provide a standardized reference for prioritizing potential CD-related genes, in regions with both highly significant and nominally significant gene-level association P-values. Our integrative model may be particularly valuable in prioritizing rare, potentially private, missense variants for which genome-wide evidence for association may be unattainable.


Asunto(s)
Enfermedad de Crohn/genética , Expresión Génica , Estudios de Casos y Controles , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Humanos , Interferón gamma/metabolismo , Intestinos , Desequilibrio de Ligamiento , Modelos Logísticos , Macrófagos , Análisis por Micromatrices , Polimorfismo de Nucleótido Simple , Sitios de Carácter Cuantitativo , Análisis de Secuencia de ARN
10.
Gastroenterology ; 150(5): 1196-1207, 2016 05.
Artículo en Inglés | MEDLINE | ID: mdl-26836588

RESUMEN

BACKGROUND & AIMS: Severe forms of inflammatory bowel disease (IBD) that develop in very young children can be caused by variants in a single gene. We performed whole-exome sequence (WES) analysis to identify genetic factors that might cause granulomatous colitis and severe perianal disease, with recurrent bacterial and viral infections, in an infant of consanguineous parents. METHODS: We performed targeted WES analysis of DNA collected from the patient and her parents. We validated our findings by a similar analysis of DNA from 150 patients with very-early-onset IBD not associated with known genetic factors analyzed in Toronto, Oxford, and Munich. We compared gene expression signatures in inflamed vs noninflamed intestinal and rectal tissues collected from patients with treatment-resistant Crohn's disease who participated in a trial of ustekinumab. We performed functional studies of identified variants in primary cells from patients and cell culture. RESULTS: We identified a homozygous variant in the tripartite motif containing 22 gene (TRIM22) of the patient, as well as in 2 patients with a disease similar phenotype. Functional studies showed that the variant disrupted the ability of TRIM22 to regulate nucleotide binding oligomerization domain containing 2 (NOD2)-dependent activation of interferon-beta signaling and nuclear factor-κB. Computational studies demonstrated a correlation between the TRIM22-NOD2 network and signaling pathways and genetic factors associated very early onset and adult-onset IBD. TRIM22 is also associated with antiviral and mycobacterial effectors and markers of inflammation, such as fecal calprotectin, C-reactive protein, and Crohn's disease activity index scores. CONCLUSIONS: In WES and targeted exome sequence analyses of an infant with severe IBD characterized by granulomatous colitis and severe perianal disease, we identified a homozygous variant of TRIM22 that affects the ability of its product to regulate NOD2. Combined computational and functional studies showed that the TRIM22-NOD2 network regulates antiviral and antibacterial signaling pathways that contribute to inflammation. Further study of this network could lead to new disease markers and therapeutic targets for patients with very early and adult-onset IBD.


Asunto(s)
Enfermedad de Crohn/genética , Variación Genética , Antígenos de Histocompatibilidad Menor/genética , Proteína Adaptadora de Señalización NOD2/metabolismo , Proteínas Represoras/genética , Transducción de Señal , Proteínas de Motivos Tripartitos/genética , Edad de Inicio , Australia , Células Cultivadas , Biología Computacional , Consanguinidad , Enfermedad de Crohn/diagnóstico , Enfermedad de Crohn/metabolismo , Enfermedad de Crohn/terapia , Bases de Datos Genéticas , Inglaterra , Exoma , Femenino , Perfilación de la Expresión Génica/métodos , Redes Reguladoras de Genes , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Alemania , Homocigoto , Humanos , Recién Nacido , Antígenos de Histocompatibilidad Menor/metabolismo , Ontario , Linaje , Fenotipo , Mapas de Interacción de Proteínas , Proteínas Represoras/metabolismo , Índice de Severidad de la Enfermedad , Transfección , Proteínas de Motivos Tripartitos/metabolismo
11.
Bioinformatics ; 32(12): i101-i110, 2016 06 15.
Artículo en Inglés | MEDLINE | ID: mdl-27307606

RESUMEN

MOTIVATION: Underrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability. To the best of our knowledge, our work is the first attempt to perform comparative, population-scale analyses of disease networks across three different populations, namely Caucasian (EA), African American (AA) and Hispanic/Latino (HL). RESULTS: We compared susceptibility profiles and temporal connectivity patterns for 1988 diseases and 37 282 disease pairs represented in a clinical population of 1 025 573 patients. Accordingly, we revealed appreciable differences in disease susceptibility, temporal patterns, network structure and underlying disease connections between EA, AA and HL populations. We found 2158 significantly comorbid diseases for the EA cohort, 3265 for AA and 672 for HL. We further outlined key disease pair associations unique to each population as well as categorical enrichments of these pairs. Finally, we identified 51 key 'hub' diseases that are the focal points in the race-centric networks and of particular clinical importance. Incorporating race-specific disease comorbidity patterns will produce a more accurate and complete picture of the disease landscape overall and could support more precise understanding of disease relationships and patient management towards improved clinical outcomes. CONTACTS: rong.chen@mssm.edu or joel.dudley@mssm.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Registros Electrónicos de Salud , Negro o Afroamericano , Bases de Datos Factuales , Hispánicos o Latinos , Humanos , Población Blanca
12.
BMC Bioinformatics ; 17(1): 483, 2016 Nov 25.
Artículo en Inglés | MEDLINE | ID: mdl-27884101

RESUMEN

BACKGROUND: As large-scale studies of gene expression with multiple sources of biological and technical variation become widely adopted, characterizing these drivers of variation becomes essential to understanding disease biology and regulatory genetics. RESULTS: We describe a statistical and visualization framework, variancePartition, to prioritize drivers of variation based on a genome-wide summary, and identify genes that deviate from the genome-wide trend. Using a linear mixed model, variancePartition quantifies variation in each expression trait attributable to differences in disease status, sex, cell or tissue type, ancestry, genetic background, experimental stimulus, or technical variables. Analysis of four large-scale transcriptome profiling datasets illustrates that variancePartition recovers striking patterns of biological and technical variation that are reproducible across multiple datasets. CONCLUSIONS: Our open source software, variancePartition, enables rapid interpretation of complex gene expression studies as well as other high-throughput genomics assays. variancePartition is available from Bioconductor: http://bioconductor.org/packages/variancePartition .


Asunto(s)
Biología Computacional/métodos , Perfilación de la Expresión Génica , Variación Genética/genética , Análisis de Secuencia de ARN/métodos , Programas Informáticos , Algoritmos , Regulación de la Expresión Génica , Genómica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Modelos Lineales
13.
BMC Genomics ; 16: 241, 2015 Mar 25.
Artículo en Inglés | MEDLINE | ID: mdl-25880738

RESUMEN

BACKGROUND: The X chromosome plays an important role in human diseases and traits. However, few X-linked associations have been reported in genome-wide association studies, partly due to analytical complications and low statistical power. RESULTS: In this study, we propose tests of X-linked association that capitalize on variance heterogeneity caused by various factors, predominantly the process of X-inactivation. In the presence of X-inactivation, the expression of one copy of the chromosome is randomly silenced. Due to the consequent elevated randomness of expressed variants, females that are heterozygotes for a quantitative trait locus might exhibit higher phenotypic variance for that trait. We propose three tests that build on this phenomenon: 1) A test for inflated variance in heterozygous females; 2) A weighted association test; and 3) A combined test. Test 1 captures the novel signal proposed herein by directly testing for higher phenotypic variance of heterozygous than homozygous females. As a test of variance it is generally less powerful than standard tests of association that consider means, which is supported by extensive simulations. Test 2 is similar to a standard association test in considering the phenotypic mean, but differs by accounting for (rather than testing) the variance heterogeneity. As expected in light of X-inactivation, this test is slightly more powerful than a standard association test. Finally, test 3 further improves power by combining the results of the first two tests. We applied the these tests to the ARIC cohort data and identified a novel X-linked association near gene AFF2 with blood pressure, which was not significant based on standard association testing of mean blood pressure. CONCLUSIONS: Variance-based tests examine overdispersion, thereby providing a complementary type of signal to a standard association test. Our results point to the potential to improve power of detecting X-linked associations in the presence of variance heterogeneity.


Asunto(s)
Genes Ligados a X , Estudio de Asociación del Genoma Completo , Sitios de Carácter Cuantitativo , Algoritmos , Alelos , Aterosclerosis/etiología , Aterosclerosis/genética , Femenino , Heterocigoto , Humanos , Fenotipo , Polimorfismo de Nucleótido Simple , Factores de Riesgo , Inactivación del Cromosoma X
14.
Bioinformatics ; 30(21): 3134-5, 2014 Nov 01.
Artículo en Inglés | MEDLINE | ID: mdl-25035399

RESUMEN

UNLABELLED: The linear mixed model is the state-of-the-art method to account for the confounding effects of kinship and population structure in genome-wide association studies (GWAS). Current implementations test the effect of one or more genetic markers while including prespecified covariates such as sex. Here we develop an efficient implementation of the linear mixed model that allows composite hypothesis tests to consider genotype interactions with variables such as other genotypes, environment, sex or ancestry. Our R package, lrgpr, allows interactive model fitting and examination of regression diagnostics to facilitate exploratory data analysis in the context of the linear mixed model. By leveraging parallel and out-of-core computing for datasets too large to fit in main memory, lrgpr is applicable to large GWAS datasets and next-generation sequencing data. AVAILABILITY AND IMPLEMENTATION: lrgpr is an R package available from lrgpr.r-forge.r-project.org.


Asunto(s)
Estudio de Asociación del Genoma Completo/métodos , Programas Informáticos , Genotipo , Modelos Lineales
15.
PLoS Genet ; 8(4): e1002641, 2012.
Artículo en Inglés | MEDLINE | ID: mdl-22570615

RESUMEN

African Pygmy groups show a distinctive pattern of phenotypic variation, including short stature, which is thought to reflect past adaptation to a tropical environment. Here, we analyze Illumina 1M SNP array data in three Western Pygmy populations from Cameroon and three neighboring Bantu-speaking agricultural populations with whom they have admixed. We infer genome-wide ancestry, scan for signals of positive selection, and perform targeted genetic association with measured height variation. We identify multiple regions throughout the genome that may have played a role in adaptive evolution, many of which contain loci with roles in growth hormone, insulin, and insulin-like growth factor signaling pathways, as well as immunity and neuroendocrine signaling involved in reproduction and metabolism. The most striking results are found on chromosome 3, which harbors a cluster of selection and association signals between approximately 45 and 60 Mb. This region also includes the positional candidate genes DOCK3, which is known to be associated with height variation in Europeans, and CISH, a negative regulator of cytokine signaling known to inhibit growth hormone-stimulated STAT5 signaling. Finally, pathway analysis for genes near the strongest signals of association with height indicates enrichment for loci involved in insulin and insulin-like growth factor signaling.


Asunto(s)
Evolución Biológica , Estatura/genética , Enanismo , Etnicidad/genética , Adaptación Biológica , África Occidental , Población Negra , Mapeo Cromosómico , Enanismo/genética , Estudios de Asociación Genética , Genoma Humano , Hormona del Crecimiento/genética , Factores de Intercambio de Guanina Nucleótido/genética , Humanos , Factor I del Crecimiento Similar a la Insulina/genética , Proteínas del Tejido Nervioso/genética , Polimorfismo de Nucleótido Simple , Selección Genética , Proteínas Supresoras de la Señalización de Citocinas/genética
16.
PLoS Comput Biol ; 9(6): e1003101, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23825936

RESUMEN

Penalized Multiple Regression (PMR) can be used to discover novel disease associations in GWAS datasets. In practice, proposed PMR methods have not been able to identify well-supported associations in GWAS that are undetectable by standard association tests and thus these methods are not widely applied. Here, we present a combined algorithmic and heuristic framework for PUMA (Penalized Unified Multiple-locus Association) analysis that solves the problems of previously proposed methods including computational speed, poor performance on genome-scale simulated data, and identification of too many associations for real data to be biologically plausible. The framework includes a new minorize-maximization (MM) algorithm for generalized linear models (GLM) combined with heuristic model selection and testing methods for identification of robust associations. The PUMA framework implements the penalized maximum likelihood penalties previously proposed for GWAS analysis (i.e. Lasso, Adaptive Lasso, NEG, MCP), as well as a penalty that has not been previously applied to GWAS (i.e. LOG). Using simulations that closely mirror real GWAS data, we show that our framework has high performance and reliably increases power to detect weak associations, while existing PMR methods can perform worse than single marker testing in overall performance. To demonstrate the empirical value of PUMA, we analyzed GWAS data for type 1 diabetes, Crohns's disease, and rheumatoid arthritis, three autoimmune diseases from the original Wellcome Trust Case Control Consortium. Our analysis replicates known associations for these diseases and we discover novel etiologically relevant susceptibility loci that are invisible to standard single marker tests, including six novel associations implicating genes involved in pancreatic function, insulin pathways and immune-cell function in type 1 diabetes; three novel associations implicating genes in pro- and anti-inflammatory pathways in Crohn's disease; and one novel association implicating a gene involved in apoptosis pathways in rheumatoid arthritis. We provide software for applying our PUMA analysis framework.


Asunto(s)
Estudio de Asociación del Genoma Completo , Modelos Teóricos , Análisis de Regresión , Humanos
17.
Res Sq ; 2024 Apr 04.
Artículo en Inglés | MEDLINE | ID: mdl-38645177

RESUMEN

Our understanding of the sex-specific role of the non-coding genome in serious mental illness remains largely incomplete. To address this gap, we explored sex differences in 1,393 chromatin accessibility profiles, derived from neuronal and non-neuronal nuclei of two distinct cortical regions from 234 cases with serious mental illness and 235 controls. We identified sex-specific enhancer-promoter interactions and showed that they regulate genes involved in X-chromosome inactivation (XCI). Examining chromosomal conformation allowed us to identify sex-specific cis- and trans-regulatory domains (CRDs and TRDs). Co-localization of sex-specific TRDs with schizophrenia common risk variants pinpointed male-specific regulatory regions controlling a number of metabolic pathways. Additionally, enhancers from female-specific TRDs were found to regulate two genes known to escape XCI, (XIST and JPX), underlying the importance of TRDs in deciphering sex differences in schizophrenia. Overall, these findings provide extensive characterization of sex differences in the brain epigenome and disease-associated regulomes.

18.
Res Sq ; 2024 Jan 26.
Artículo en Inglés | MEDLINE | ID: mdl-38343831

RESUMEN

Microglia are resident immune cells of the brain and are implicated in the etiology of Alzheimer's Disease (AD) and other diseases. Yet the cellular and molecular processes regulating their function throughout the course of the disease are poorly understood. Here, we present the transcriptional landscape of primary microglia from 189 human postmortem brains, including 58 healthy aging individuals and 131 with a range of disease phenotypes, including 63 patients representing the full spectrum of clinical and pathological severity of AD. We identified transcriptional changes associated with multiple AD phenotypes, capturing the severity of dementia and neuropathological lesions. Transcript-level analyses identified additional genes with heterogeneous isoform usage and AD phenotypes. We identified changes in gene-gene coordination in AD, dysregulation of co-expression modules, and disease subtypes with distinct gene expression. Taken together, these data further our understanding of the key role of microglia in AD biology and nominate candidates for therapeutic intervention.

19.
Science ; 384(6698): eadg5136, 2024 May 24.
Artículo en Inglés | MEDLINE | ID: mdl-38781388

RESUMEN

The complexity and heterogeneity of schizophrenia have hindered mechanistic elucidation and the development of more effective therapies. Here, we performed single-cell dissection of schizophrenia-associated transcriptomic changes in the human prefrontal cortex across 140 individuals in two independent cohorts. Excitatory neurons were the most affected cell group, with transcriptional changes converging on neurodevelopment and synapse-related molecular pathways. Transcriptional alterations included known genetic risk factors, suggesting convergence of rare and common genomic variants on neuronal population-specific alterations in schizophrenia. Based on the magnitude of schizophrenia-associated transcriptional change, we identified two populations of individuals with schizophrenia marked by expression of specific excitatory and inhibitory neuronal cell states. This single-cell atlas links transcriptomic changes to etiological genetic risk factors, contextualizing established knowledge within the human cortical cytoarchitecture and facilitating mechanistic understanding of schizophrenia pathophysiology and heterogeneity.


Asunto(s)
Predisposición Genética a la Enfermedad , Neuroglía , Neuronas , Corteza Prefrontal , Esquizofrenia , Análisis de la Célula Individual , Adulto , Femenino , Humanos , Masculino , Estudios de Cohortes , Neuronas/metabolismo , Corteza Prefrontal/metabolismo , Factores de Riesgo , Esquizofrenia/genética , Sinapsis/metabolismo , Transcriptoma , Adulto Joven , Persona de Mediana Edad , Anciano , Anciano de 80 o más Años , Neuroglía/metabolismo
20.
Science ; 384(6698): eadh4265, 2024 May 24.
Artículo en Inglés | MEDLINE | ID: mdl-38781378

RESUMEN

Nucleotide variants in cell type-specific gene regulatory elements in the human brain are risk factors for human disease. We measured chromatin accessibility in 1932 aliquots of sorted neurons and non-neurons from 616 human postmortem brains and identified 34,539 open chromatin regions with chromatin accessibility quantitative trait loci (caQTLs). Only 10.4% of caQTLs are shared between neurons and non-neurons, which supports cell type-specific genetic regulation of the brain regulome. Incorporating allele-specific chromatin accessibility improves statistical fine-mapping and refines molecular mechanisms that underlie disease risk. Using massively parallel reporter assays in induced excitatory neurons, we screened 19,893 brain QTLs and identified the functional impact of 476 regulatory variants. Combined, this comprehensive resource captures variation in the human brain regulome and provides insights into disease etiology.


Asunto(s)
Encefalopatías , Encéfalo , Cromatina , Regulación de la Expresión Génica , Elementos Reguladores de la Transcripción , Humanos , Alelos , Encéfalo/metabolismo , Encefalopatías/genética , Cromatina/metabolismo , Neuronas/metabolismo , Sitios de Carácter Cuantitativo , Masculino , Femenino
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