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Qi T, Song L, Guo Y, Chen C, Yang J. From genetic associations to genes: methods, applications, and challenges. Trends Genet 2024:S0168-9525(24)00095-7. [PMID: 38734482 DOI: 10.1016/j.tig.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/13/2024]
Abstract
Genome-wide association studies (GWASs) have identified numerous genetic loci associated with human traits and diseases. However, pinpointing the causal genes remains a challenge, which impedes the translation of GWAS findings into biological insights and medical applications. In this review, we provide an in-depth overview of the methods and technologies used for prioritizing genes from GWAS loci, including gene-based association tests, integrative analysis of GWAS and molecular quantitative trait loci (xQTL) data, linking GWAS variants to target genes through enhancer-gene connection maps, and network-based prioritization. We also outline strategies for generating context-dependent xQTL data and their applications in gene prioritization. We further highlight the potential of gene prioritization in drug repurposing. Lastly, we discuss future challenges and opportunities in this field.
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Affiliation(s)
- Ting Qi
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China.
| | - Liyang Song
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Yazhou Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Chang Chen
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Jian Yang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China.
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2
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Hemerich D, Svenstrup V, Obrero VD, Preuss M, Moscati A, Hirschhorn JN, Loos RJF. An integrative framework to prioritize genes in more than 500 loci associated with body mass index. Am J Hum Genet 2024:S0002-9297(24)00131-9. [PMID: 38754426 DOI: 10.1016/j.ajhg.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Obesity is a major risk factor for a myriad of diseases, affecting >600 million people worldwide. Genome-wide association studies (GWASs) have identified hundreds of genetic variants that influence body mass index (BMI), a commonly used metric to assess obesity risk. Most variants are non-coding and likely act through regulating genes nearby. Here, we apply multiple computational methods to prioritize the likely causal gene(s) within each of the 536 previously reported GWAS-identified BMI-associated loci. We performed summary-data-based Mendelian randomization (SMR), FINEMAP, DEPICT, MAGMA, transcriptome-wide association studies (TWASs), mutation significance cutoff (MSC), polygenic priority score (PoPS), and the nearest gene strategy. Results of each method were weighted based on their success in identifying genes known to be implicated in obesity, ranking all prioritized genes according to a confidence score (minimum: 0; max: 28). We identified 292 high-scoring genes (≥11) in 264 loci, including genes known to play a role in body weight regulation (e.g., DGKI, ANKRD26, MC4R, LEPR, BDNF, GIPR, AKT3, KAT8, MTOR) and genes related to comorbidities (e.g., FGFR1, ISL1, TFAP2B, PARK2, TCF7L2, GSK3B). For most of the high-scoring genes, however, we found limited or no evidence for a role in obesity, including the top-scoring gene BPTF. Many of the top-scoring genes seem to act through a neuronal regulation of body weight, whereas others affect peripheral pathways, including circadian rhythm, insulin secretion, and glucose and carbohydrate homeostasis. The characterization of these likely causal genes can increase our understanding of the underlying biology and offer avenues to develop therapeutics for weight loss.
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Affiliation(s)
- Daiane Hemerich
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Bristol Myers Squibb, Summit, NJ, USA
| | - Victor Svenstrup
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Virginia Diez Obrero
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Regeneron Genetics Center, Tarrytown, NY, USA
| | - Joel N Hirschhorn
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Wang Y, Sarnowski C, Lin H, Pitsillides AN, Heard‐Costa NL, Choi SH, Wang D, Bis JC, Blue EE, Boerwinkle E, De Jager PL, Fornage M, Wijsman EM, Seshadri S, Dupuis J, Peloso GM, DeStefano AL. Key variants via the Alzheimer's Disease Sequencing Project whole genome sequence data. Alzheimers Dement 2024; 20:3290-3304. [PMID: 38511601 PMCID: PMC11095439 DOI: 10.1002/alz.13705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 03/22/2024]
Abstract
INTRODUCTION Genome-wide association studies (GWAS) have identified loci associated with Alzheimer's disease (AD) but did not identify specific causal genes or variants within those loci. Analysis of whole genome sequence (WGS) data, which interrogates the entire genome and captures rare variations, may identify causal variants within GWAS loci. METHODS We performed single common variant association analysis and rare variant aggregate analyses in the pooled population (N cases = 2184, N controls = 2383) and targeted analyses in subpopulations using WGS data from the Alzheimer's Disease Sequencing Project (ADSP). The analyses were restricted to variants within 100 kb of 83 previously identified GWAS lead variants. RESULTS Seventeen variants were significantly associated with AD within five genomic regions implicating the genes OARD1/NFYA/TREML1, JAZF1, FERMT2, and SLC24A4. KAT8 was implicated by both single variant and rare variant aggregate analyses. DISCUSSION This study demonstrates the utility of leveraging WGS to gain insights into AD loci identified via GWAS.
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Affiliation(s)
- Yanbing Wang
- Department of BiostatisticsBoston University, School of Public HealthBostonMassachusettsUSA
| | - Chloé Sarnowski
- Department of BiostatisticsBoston University, School of Public HealthBostonMassachusettsUSA
- Human Genetics CenterDepartment of EpidemiologySchool of Public HealthThe University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Honghuang Lin
- Department of MedicineUniversity of Massachusetts Chan Medical SchoolWorcesterMassachusettsUSA
| | | | - Nancy L. Heard‐Costa
- Department of BiostatisticsBoston University, School of Public HealthBostonMassachusettsUSA
- The Framingham Heart StudyFraminghamMassachusettsUSA
| | - Seung Hoan Choi
- Department of BiostatisticsBoston University, School of Public HealthBostonMassachusettsUSA
| | - Dongyu Wang
- Department of BiostatisticsBoston University, School of Public HealthBostonMassachusettsUSA
| | - Joshua C. Bis
- Cardiovascular Health Research UnitDepartment of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Elizabeth E. Blue
- Department of MedicineDivision of Medical GeneticsUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty InstituteSeattleWashingtonUSA
| | | | - Eric Boerwinkle
- Human Genetics CenterDepartment of EpidemiologySchool of Public HealthThe University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Philip L. De Jager
- Center for Translational & Computational NeuroimmunologyDepartment of NeurologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Myriam Fornage
- Human Genetics CenterDepartment of EpidemiologySchool of Public HealthThe University of Texas Health Science Center at HoustonHoustonTexasUSA
- Brown Foundation Institute of Molecular MedicineMcGovern Medical SchoolUniversity of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Ellen M. Wijsman
- Division of Medical Genetics and Department Biostatistics Statistical Genetics LabUniversity of WashingtonHans Rosling Center for Population HealthSeattleWashingtonUSA
| | - Sudha Seshadri
- The Framingham Heart StudyFraminghamMassachusettsUSA
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative DiseasesThe University of Texas Health Science Center at San AntonioSan AntonioTexasUSA
- Department of NeurologyBoston University School of MedicineBostonMassachusettsUSA
| | - Josée Dupuis
- Department of BiostatisticsBoston University, School of Public HealthBostonMassachusettsUSA
- Department of Epidemiology, Biostatistics and Occupational HealthSchool of Population and Global HealthMcGill UniversityMontrealQuebecCanada
| | - Gina M. Peloso
- Department of BiostatisticsBoston University, School of Public HealthBostonMassachusettsUSA
| | - Anita L. DeStefano
- Department of BiostatisticsBoston University, School of Public HealthBostonMassachusettsUSA
- The Framingham Heart StudyFraminghamMassachusettsUSA
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Hudgins AD, Zhou S, Arey RN, Rosenfeld MG, Murphy CT, Suh Y. A systems biology-based identification and in vivo functional screening of Alzheimer's disease risk genes reveal modulators of memory function. Neuron 2024:S0896-6273(24)00247-2. [PMID: 38692279 DOI: 10.1016/j.neuron.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 10/18/2023] [Accepted: 04/08/2024] [Indexed: 05/03/2024]
Abstract
Genome-wide association studies (GWASs) have uncovered over 75 genomic loci associated with risk for late-onset Alzheimer's disease (LOAD), but identification of the underlying causal genes remains challenging. Studies of induced pluripotent stem cell (iPSC)-derived neurons from LOAD patients have demonstrated the existence of neuronal cell-intrinsic functional defects. Here, we searched for genetic contributions to neuronal dysfunction in LOAD using an integrative systems approach that incorporated multi-evidence-based gene mapping and network-analysis-based prioritization. A systematic perturbation screening of candidate risk genes in Caenorhabditis elegans (C. elegans) revealed that neuronal knockdown of the LOAD risk gene orthologs vha-10 (ATP6V1G2), cmd-1 (CALM3), amph-1 (BIN1), ephx-1 (NGEF), and pho-5 (ACP2) alters short-/intermediate-term memory function, the cognitive domain affected earliest during LOAD progression. These results highlight the impact of LOAD risk genes on evolutionarily conserved memory function, as mediated through neuronal endosomal dysfunction, and identify new targets for further mechanistic interrogation.
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Affiliation(s)
- Adam D Hudgins
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Shiyi Zhou
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Rachel N Arey
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael G Rosenfeld
- Department of Medicine, School of Medicine, University of California, La Jolla, CA, USA; Howard Hughes Medical Institute, University of California, La Jolla, CA, USA
| | - Coleen T Murphy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA; LSI Genomics, Princeton University, Princeton, NJ, USA.
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.
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Luo L, Pang T, Zheng H, Liufu C, Chang S. xWAS analysis in neuropsychiatric disorders by integrating multi-molecular phenotype quantitative trait loci and GWAS summary data. J Transl Med 2024; 22:387. [PMID: 38664746 PMCID: PMC11044291 DOI: 10.1186/s12967-024-05065-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/05/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Integrating quantitative trait loci (QTL) data related to molecular phenotypes with genome-wide association study (GWAS) data is an important post-GWAS strategic approach employed to identify disease-associated molecular features. Various types of molecular phenotypes have been investigated in neuropsychiatric disorders. However, these findings pertaining to distinct molecular features are often independent of each other, posing challenges for having an overview of the mapped genes. METHODS In this study, we comprehensively summarized published analyses focusing on four types of risk-related molecular features (gene expression, splicing transcriptome, protein abundance, and DNA methylation) across five common neuropsychiatric disorders. Subsequently, we conducted supplementary analyses with the latest GWAS dataset and corresponding deficient molecular phenotypes using Functional Summary-based Imputation (FUSION) and summary data-based Mendelian randomization (SMR). Based on the curated and supplemented results, novel reliable genes and their functions were explored. RESULTS Our findings revealed that eQTL exhibited superior ability in prioritizing risk genes compared to the other QTL, followed by sQTL. Approximately half of the genes associated with splicing transcriptome, protein abundance, and DNA methylation were successfully replicated by eQTL-associated genes across all five disorders. Furthermore, we identified 436 novel reliable genes, which enriched in pathways related with neurotransmitter transportation such as synaptic, dendrite, vesicles, axon along with correlations with other neuropsychiatric disorders. Finally, we identified ten multiple molecular involved regulation patterns (MMRP), which may provide valuable insights into understanding the contribution of molecular regulation network targeting these disease-associated genes. CONCLUSIONS The analyses prioritized novel and reliable gene sets related with five molecular features based on published and supplementary results for five common neuropsychiatric disorders, which were missed in the original GWAS analysis. Besides, the involved MMRP behind these genes could be given priority for further investigation to elucidate the pathogenic molecular mechanisms underlying neuropsychiatric disorders in future studies.
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Affiliation(s)
- Lingxue Luo
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 51 Huayuan Bei Road, Beijing, 100191, China
| | - Tao Pang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 51 Huayuan Bei Road, Beijing, 100191, China
| | - Haohao Zheng
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 51 Huayuan Bei Road, Beijing, 100191, China
| | - Chao Liufu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 51 Huayuan Bei Road, Beijing, 100191, China
| | - Suhua Chang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 51 Huayuan Bei Road, Beijing, 100191, China.
- Research Units of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Beijing, 100191, China.
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Jiang Y, Chen P, Zhao Y, Zhang Y. Association of Cadherin-Related Family Member 1 with Traumatic Brain Injury. Cell Mol Neurobiol 2024; 44:41. [PMID: 38656449 PMCID: PMC11043179 DOI: 10.1007/s10571-024-01476-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
The cadherin family plays a pivotal role in orchestrating synapse formation in the central nervous system. Cadherin-related family member 1 (CDHR1) is a photoreceptor-specific calmodulin belonging to the expansive cadherin superfamily. However, its role in traumatic brain injury (TBI) remains largely unknown. CDHR1 expression across various brain tissue sites was analyzed using the GSE104687 dataset. Employing a summary-data-based Mendelian Randomization (SMR) approach, integrated analyses were performed by amalgamating genome-wide association study abstracts from TBI with public data on expressed quantitative trait loci and DNA methylation QTL from both blood and diverse brain tissues. CDHR1 expression and localization in different brain tissues were meticulously delineated using western blotting, immunohistochemistry, and enzyme-linked immunosorbent assay. CDHR1 expression was consistently elevated in the TBI group compared to that in the sham group across multiple tissues. The inflammatory response emerged as a crucial biological mechanism, and pro-inflammatory and anti-inflammatory factors were not expressed in either group. Integrated SMR analyses encompassing both blood and brain tissues substantiated the heightened CDHR1 expression profiles, with methylation modifications emerging as potential contributing factors for increased TBI risk. This was corroborated by western blotting and immunohistochemistry, confirming augmented CDHR1 expression following TBI. This multi-omics-based genetic association study highlights the elevated TBI risk associated with CDHR1 expression coupled with putative methylation modifications. These findings provide compelling evidence for future targeted investigations and offer promising avenues for developing interventional therapies for TBI.
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Affiliation(s)
- Yong'An Jiang
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
- Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Peng Chen
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
- Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - YangYang Zhao
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
- Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Yan Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China.
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Katsumata Y, Fardo DW, Shade LMP, Wu X, Karanth SD, Hohman TJ, Schneider JA, Bennett DA, Farfel JM, Gauthreaux K, Mock C, Kukull WA, Abner EL, Nelson PT. Genetic associations with dementia-related proteinopathy: Application of item response theory. Alzheimers Dement 2024; 20:2906-2921. [PMID: 38460116 PMCID: PMC11032554 DOI: 10.1002/alz.13741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 03/11/2024]
Abstract
INTRODUCTION Although dementia-related proteinopathy has a strong negative impact on public health, and is highly heritable, understanding of the related genetic architecture is incomplete. METHODS We applied multidimensional generalized partial credit modeling (GPCM) to test genetic associations with dementia-related proteinopathies. Data were analyzed to identify candidate single nucleotide variants for the following proteinopathies: Aβ, tau, α-synuclein, and TDP-43. RESULTS Final included data comprised 966 participants with neuropathologic and WGS data. Three continuous latent outcomes were constructed, corresponding to TDP-43-, Aβ/Tau-, and α-synuclein-related neuropathology endophenotype scores. This approach helped validate known genotype/phenotype associations: for example, TMEM106B and GRN were risk alleles for TDP-43 pathology; and GBA for α-synuclein/Lewy bodies. Novel suggestive proteinopathy-linked alleles were also discovered, including several (SDHAF1, TMEM68, and ARHGEF28) with colocalization analyses and/or high degrees of biologic credibility. DISCUSSION A novel methodology using GPCM enabled insights into gene candidates for driving misfolded proteinopathies. HIGHLIGHTS Latent factor scores for proteinopathies were estimated using a generalized partial credit model. The three latent continuous scores corresponded well with proteinopathy severity. Novel genes associated with proteinopathies were identified. Several genes had high degrees of biologic credibility for dementia risk factors.
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Affiliation(s)
- Yuriko Katsumata
- Department of BiostatisticsUniversity of KentuckyLexingtonKentuckyUSA
- Sanders‐Brown Center on AgingUniversity of KentuckyLexingtonKentuckyUSA
| | - David W. Fardo
- Department of BiostatisticsUniversity of KentuckyLexingtonKentuckyUSA
- Sanders‐Brown Center on AgingUniversity of KentuckyLexingtonKentuckyUSA
| | | | - Xian Wu
- Department of BiostatisticsUniversity of KentuckyLexingtonKentuckyUSA
- Sanders‐Brown Center on AgingUniversity of KentuckyLexingtonKentuckyUSA
| | - Shama D. Karanth
- Department of SurgeryCollege of MedicineUniversity of FloridaGainesvilleFloridaUSA
- UF Health Cancer CenterUniversity of FloridaGainesvilleFloridaUSA
| | - Timothy J. Hohman
- Vanderbilt Memory and Alzheimer's CenterVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Julie A. Schneider
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
- Department of PathologyRush University Medical CenterChicagoIllinoisUSA
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | - David A. Bennett
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
- Department of PathologyRush University Medical CenterChicagoIllinoisUSA
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | - Jose M. Farfel
- Department of PathologyRush University Medical CenterChicagoIllinoisUSA
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | - Kathryn Gauthreaux
- National Alzheimer's Coordinating CenterDepartment of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Charles Mock
- National Alzheimer's Coordinating CenterDepartment of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Walter A. Kukull
- National Alzheimer's Coordinating CenterDepartment of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Erin L. Abner
- Sanders‐Brown Center on AgingUniversity of KentuckyLexingtonKentuckyUSA
- Department of Epidemiology and Environmental HealthUniversity of KentuckyLexingtonKentuckyUSA
| | - Peter T. Nelson
- Sanders‐Brown Center on AgingUniversity of KentuckyLexingtonKentuckyUSA
- Department of PathologyDivision of NeuropathologyUniversity of KentuckyLexingtonKentuckyUSA
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Fujita M, Gao Z, Zeng L, McCabe C, White CC, Ng B, Green GS, Rozenblatt-Rosen O, Phillips D, Amir-Zilberstein L, Lee H, Pearse RV, Khan A, Vardarajan BN, Kiryluk K, Ye CJ, Klein HU, Wang G, Regev A, Habib N, Schneider JA, Wang Y, Young-Pearse T, Mostafavi S, Bennett DA, Menon V, De Jager PL. Cell subtype-specific effects of genetic variation in the Alzheimer's disease brain. Nat Genet 2024; 56:605-614. [PMID: 38514782 DOI: 10.1038/s41588-024-01685-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/08/2024] [Indexed: 03/23/2024]
Abstract
The relationship between genetic variation and gene expression in brain cell types and subtypes remains understudied. Here, we generated single-nucleus RNA sequencing data from the neocortex of 424 individuals of advanced age; we assessed the effect of genetic variants on RNA expression in cis (cis-expression quantitative trait loci) for seven cell types and 64 cell subtypes using 1.5 million transcriptomes. This effort identified 10,004 eGenes at the cell type level and 8,099 eGenes at the cell subtype level. Many eGenes are only detected within cell subtypes. A new variant influences APOE expression only in microglia and is associated with greater cerebral amyloid angiopathy but not Alzheimer's disease pathology, after adjusting for APOEε4, providing mechanistic insights into both pathologies. Furthermore, only a TMEM106B variant affects the proportion of cell subtypes. Integration of these results with genome-wide association studies highlighted the targeted cell type and probable causal gene within Alzheimer's disease, schizophrenia, educational attainment and Parkinson's disease loci.
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Affiliation(s)
- Masashi Fujita
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Zongmei Gao
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Lu Zeng
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charles C White
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Bernard Ng
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Gilad Sahar Green
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Devan Phillips
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | | | - Hyo Lee
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Richard V Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Atlas Khan
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Badri N Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Hans-Ulrich Klein
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Gao Wang
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Naomi Habib
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Tracy Young-Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sara Mostafavi
- Department of Statistics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA.
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9
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Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X, Bakken TE, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard JF, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman GE, Huang A, Jiang Y, Jin T, Jorstad NL, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran JR, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan AS, Riesenmy TR, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini KJ, Wamsley B, Wang G, Xia Y, Xiao S, Yang AC, Zheng S, Gandal MJ, Lee D, Lein ES, Roussos P, Sestan N, Weng Z, White KP, Won H, Girgenti MJ, Zhang J, Wang D, Geschwind D, Gerstein M. Single-cell genomics and regulatory networks for 388 human brains. bioRxiv 2024:2024.03.18.585576. [PMID: 38562822 PMCID: PMC10983939 DOI: 10.1101/2024.03.18.585576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multi-omics datasets into a resource comprising >2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.
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Affiliation(s)
- Prashant S Emani
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jason J Liu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Declan Clarke
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Matthew Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jonathan Warrell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Chirag Gupta
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Ran Meng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Che Yu Lee
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Siwei Xu
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Cagatay Dursun
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Shaoke Lou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Yuhang Chen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Zhiyuan Chu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Ahyeon Hwang
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
- Mathematical, Computational and Systems Biology, University of California, Irvine, CA, 92697, USA
| | - Yunyang Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Computer Science, Yale University, New Haven, CT, 06520, USA
| | - Pengyu Ni
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Xiao Zhou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | | | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lucy Bicks
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Tanima Chatterjee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | | | - Yuyan Cheng
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Opthalmology, Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yi Dai
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Ziheng Duan
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | | | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Gancz
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Diego Garrido-Martín
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, 08028, Spain
| | - Sophia Gaynor-Gillett
- Tempus Labs, Inc., Chicago, IL, 60654, USA
- Department of Biology, Cornell College, Mount Vernon, IA, 52314, USA
| | - Jennifer Grundman
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Natalie Hawken
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Ella Henry
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Ao Huang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Ting Jin
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | | | - Riki Kawaguchi
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA, 90095, USA
| | - Saniya Khullar
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Jianyin Liu
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Junhao Liu
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Shuang Liu
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale University, New Haven, CT, 06510, USA
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Michael Margolis
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Samantha Mazariegos
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Jill Moore
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | | | - Eric Nguyen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Nishigandha Phalke
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Milos Pjanic
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Henry Pratt
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Diana Quintero
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | | | - Tiernon R Riesenmy
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA
| | - Nicole Shedd
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Manman Shi
- Tempus Labs, Inc., Chicago, IL, 60654, USA
| | | | - Rosemarie Terwilliger
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA
| | | | - Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Gaoyuan Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Yan Xia
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Shaohua Xiao
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Andrew C Yang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Suchen Zheng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Michael J Gandal
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Donghoon Lee
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, 98109, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University, New Haven, CT, 06510, USA
| | - Zhiping Weng
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Kevin P White
- Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Matthew J Girgenti
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA
- Wu Tsai Institute, Yale University, New Haven, CT, 06520, USA
- Clinical Neuroscience Division, National Center for Posttraumatic Stress Disorder, Veterans Affairs Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Daifeng Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Daniel Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Computer Science, Yale University, New Haven, CT, 06520, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA
- Department of Biomedical Informatics & Data Science, Yale University, New Haven, CT, 06520, USA
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10
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Das Adhikari S, Cui Y, Wang J. BayesKAT: bayesian optimal kernel-based test for genetic association studies reveals joint genetic effects in complex diseases. Brief Bioinform 2024; 25:bbae182. [PMID: 38653490 PMCID: PMC11036342 DOI: 10.1093/bib/bbae182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/10/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
Genome-wide Association Studies (GWAS) methods have identified individual single-nucleotide polymorphisms (SNPs) significantly associated with specific phenotypes. Nonetheless, many complex diseases are polygenic and are controlled by multiple genetic variants that are usually non-linearly dependent. These genetic variants are marginally less effective and remain undetected in GWAS analysis. Kernel-based tests (KBT), which evaluate the joint effect of a group of genetic variants, are therefore critical for complex disease analysis. However, choosing different kernel functions in KBT can significantly influence the type I error control and power, and selecting the optimal kernel remains a statistically challenging task. A few existing methods suffer from inflated type 1 errors, limited scalability, inferior power or issues of ambiguous conclusions. Here, we present a new Bayesian framework, BayesKAT (https://github.com/wangjr03/BayesKAT), which overcomes these kernel specification issues by selecting the optimal composite kernel adaptively from the data while testing genetic associations simultaneously. Furthermore, BayesKAT implements a scalable computational strategy to boost its applicability, especially for high-dimensional cases where other methods become less effective. Based on a series of performance comparisons using both simulated and real large-scale genetics data, BayesKAT outperforms the available methods in detecting complex group-level associations and controlling type I errors simultaneously. Applied on a variety of groups of functionally related genetic variants based on biological pathways, co-expression gene modules and protein complexes, BayesKAT deciphers the complex genetic basis and provides mechanistic insights into human diseases.
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Affiliation(s)
- Sikta Das Adhikari
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
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11
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Qiu S, Sun M, Xu Y, Hu Y. Integrating multi-omics data to reveal the effect of genetic variant rs6430538 on Alzheimer's disease risk. Front Neurosci 2024; 18:1277187. [PMID: 38562299 PMCID: PMC10982421 DOI: 10.3389/fnins.2024.1277187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction Growing evidence highlights a potential genetic overlap between Alzheimer's disease (AD) and Parkinson's disease (PD); however, the role of the PD risk variant rs6430538 in AD remains unclear. Methods In Stage 1, we investigated the risk associated with the rs6430538 C allele in seven large-scale AD genome-wide association study (GWAS) cohorts. In Stage 2, we performed expression quantitative trait loci (eQTL) analysis to calculate the cis-regulated effect of rs6430538 on TMEM163 in both AD and neuropathologically normal samples. Stage 3 involved evaluating the differential expression of TMEM163 in 4 brain tissues from AD cases and controls. Finally, in Stage 4, we conducted a transcriptome-wide association study (TWAS) to identify any association between TMEM163 expression and AD. Results The results showed that genetic variant rs6430538 C allele might increase the risk of AD. eQTL analysis revealed that rs6430538 up-regulated TMEM163 expression in AD brain tissue, but down-regulated its expression in normal samples. Interestingly, TMEM163 showed differential expression in entorhinal cortex (EC) and temporal cortex (TCX). Furthermore, the TWAS analysis indicated strong associations between TMEM163 and AD in various tissues. Discussion In summary, our findings suggest that rs6430538 may influence AD by regulating TMEM163 expression. These discoveries may open up new opportunities for therapeutic strategies targeting AD.
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Affiliation(s)
- Shizheng Qiu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Meili Sun
- Beidahuang Industry Group General Hospital, Harbin, China
| | - Yanwei Xu
- Beidahuang Group Neuropsychiatric Hospital, Jiamusi, China
| | - Yang Hu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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Arruda AL, Khandaker GM, Morris AP, Smith GD, Huckins LM, Zeggini E. Genomic insights into the comorbidity between type 2 diabetes and schizophrenia. Schizophrenia (Heidelb) 2024; 10:22. [PMID: 38383672 PMCID: PMC10881980 DOI: 10.1038/s41537-024-00445-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024]
Abstract
Multimorbidity represents an increasingly important public health challenge with far-reaching implications for health management and policy. Mental health and metabolic diseases have a well-established epidemiological association. In this study, we investigate the genetic intersection between type 2 diabetes and schizophrenia. We use Mendelian randomization to examine potential causal relationships between the two conditions and related endophenotypes. We report no compelling evidence that type 2 diabetes genetic liability potentially causally influences schizophrenia risk and vice versa. Our findings show that increased body mass index (BMI) has a protective effect against schizophrenia, in contrast to the well-known risk-increasing effect of BMI on type 2 diabetes risk. We identify evidence of colocalization of association signals for these two conditions at 11 genomic loci, six of which have opposing directions of effect for type 2 diabetes and schizophrenia. To elucidate these colocalizing signals, we integrate multi-omics data from bulk and single-cell gene expression studies, along with functional information. We identify putative effector genes and find that they are enriched for homeostasis and lipid-related pathways. We also highlight drug repurposing opportunities including N-methyl-D-aspartate (NMDA) receptor antagonists. Our findings provide insights into shared biological mechanisms for type 2 diabetes and schizophrenia, highlighting common factors that influence the risk of the two conditions in opposite directions and shedding light on the complex nature of this comorbidity.
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Affiliation(s)
- Ana Luiza Arruda
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Munich School for Data Science, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Technical University of Munich (TUM), TUM School of Medicine and Health, Graduate School of Experimental Medicine, Munich, 81675, Germany
| | - Golam M Khandaker
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
- Centre for Academic Mental Health, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
- Avon and Wiltshire Mental Health Partnership NHS Trust, Bristol, UK
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, M13 9PT, United Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Laura M Huckins
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany.
- TUM School of Medicine and Health, Technical University of Munich and Klinikum Rechts der Isar, Munich, 81675, Germany.
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13
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Casazza W, Inkster AM, Del Gobbo GF, Yuan V, Delahaye F, Marsit C, Park YP, Robinson WP, Mostafavi S, Dennis JK. Sex-dependent placental methylation quantitative trait loci provide insight into the prenatal origins of childhood onset traits and conditions. iScience 2024; 27:109047. [PMID: 38357671 PMCID: PMC10865402 DOI: 10.1016/j.isci.2024.109047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 06/19/2023] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
Molecular quantitative trait loci (QTLs) allow us to understand the biology captured in genome-wide association studies (GWASs). The placenta regulates fetal development and shows sex differences in DNA methylation. We therefore hypothesized that placental methylation QTL (mQTL) explain variation in genetic risk for childhood onset traits, and that effects differ by sex. We analyzed 411 term placentas from two studies and found 49,252 methylation (CpG) sites with mQTL and 2,489 CpG sites with sex-dependent mQTL. All mQTL were enriched in regions that typically affect gene expression in prenatal tissues. All mQTL were also enriched in GWAS results for growth- and immune-related traits, but male- and female-specific mQTL were more enriched than cross-sex mQTL. mQTL colocalized with trait loci at 777 CpG sites, with 216 (28%) specific to males or females. Overall, mQTL specific to male and female placenta capture otherwise overlooked variation in childhood traits.
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Affiliation(s)
- William Casazza
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital, Vancouver, BC, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Amy M. Inkster
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Giulia F. Del Gobbo
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Victor Yuan
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | | | - Carmen Marsit
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Yongjin P. Park
- Department of Statistics, University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Wendy P. Robinson
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Sara Mostafavi
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital, Vancouver, BC, Canada
- Paul Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Jessica K. Dennis
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital, Vancouver, BC, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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14
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Archer DB, Eissman JM, Mukherjee S, Lee ML, Choi S, Scollard P, Trittschuh EH, Mez JB, Bush WS, Kunkle BW, Naj AC, Gifford KA, Cuccaro ML, Pericak‐Vance MA, Farrer LA, Wang L, Schellenberg GD, Mayeux RP, Haines JL, Jefferson AL, Kukull WA, Keene CD, Saykin AJ, Thompson PM, Martin ER, Bennett DA, Barnes LL, Schneider JA, Crane PK, Dumitrescu L, Hohman TJ. Longitudinal change in memory performance as a strong endophenotype for Alzheimer's disease. Alzheimers Dement 2024; 20:1268-1283. [PMID: 37985223 PMCID: PMC10896586 DOI: 10.1002/alz.13508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 11/22/2023]
Abstract
INTRODUCTION Although large-scale genome-wide association studies (GWAS) have been conducted on AD, few have been conducted on continuous measures of memory performance and memory decline. METHODS We conducted a cross-ancestry GWAS on memory performance (in 27,633 participants) and memory decline (in 22,365 participants; 129,201 observations) by leveraging harmonized cognitive data from four aging cohorts. RESULTS We found high heritability for two ancestry backgrounds. Further, we found a novel ancestry locus for memory decline on chromosome 4 (rs6848524) and three loci in the non-Hispanic Black ancestry group for memory performance on chromosomes 2 (rs111471504), 7 (rs4142249), and 15 (rs74381744). In our gene-level analysis, we found novel genes for memory decline on chromosomes 1 (SLC25A44), 11 (BSX), and 15 (DPP8). Memory performance and memory decline shared genetic architecture with AD-related traits, neuropsychiatric traits, and autoimmune traits. DISCUSSION We discovered several novel loci, genes, and genetic correlations associated with late-life memory performance and decline. HIGHLIGHTS Late-life memory has high heritability that is similar across ancestries. We discovered four novel variants associated with late-life memory. We identified four novel genes associated with late-life memory. Late-life memory shares genetic architecture with psychiatric/autoimmune traits.
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15
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Lin S, Wu S, Zhao W, Fang Z, Kang H, Liu X, Pan S, Yu F, Bao Y, Jia P. TargetGene: a comprehensive database of cell-type-specific target genes for genetic variants. Nucleic Acids Res 2024; 52:D1072-D1081. [PMID: 37870478 PMCID: PMC10767789 DOI: 10.1093/nar/gkad901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/27/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023] Open
Abstract
Annotating genetic variants to their target genes is of great importance in unraveling the causal variants and genetic mechanisms that underlie complex diseases. However, disease-associated genetic variants are often located in non-coding regions and manifest context-specific effects, making it challenging to accurately identify the target genes and regulatory mechanisms. Here, we present TargetGene (https://ngdc.cncb.ac.cn/targetgene/), a comprehensive database reporting target genes for human genetic variants from various aspects. Specifically, we collected a comprehensive catalog of multi-omics data at the single-cell and bulk levels and from various human tissues, cell types and developmental stages. To facilitate the identification of Single Nucleotide Polymorphism (SNP)-to-gene connections, we have implemented multiple analytical tools based on chromatin co-accessibility, 3D interaction, enhancer activities and quantitative trait loci, among others. We applied the pipeline to evaluate variants from nearly 1300 Genome-wide association studies (GWAS) and assembled a comprehensive atlas of multiscale regulation of genetic variants. TargetGene is equipped with user-friendly web interfaces that enable intuitive searching, navigation and browsing through the results. Overall, TargetGene provides a unique resource to empower researchers to study the regulatory mechanisms of genetic variants in complex human traits.
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Affiliation(s)
- Shiqi Lin
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Wu
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Wei Zhao
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zhanjie Fang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongen Kang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinxuan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siyu Pan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fudong Yu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200237, China
| | - Yiming Bao
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Ge YJ, Wu BS, Zhang Y, Chen SD, Zhang YR, Kang JJ, Deng YT, Ou YN, He XY, Zhao YL, Kuo K, Ma Q, Banaschewski T, Barker GJ, Bokde ALW, Desrivières S, Flor H, Grigis A, Garavan H, Gowland P, Heinz A, Brühl R, Martinot JL, Martinot MLP, Artiges E, Nees F, Orfanos DP, Lemaitre H, Paus T, Poustka L, Hohmann S, Millenet S, Fröhner JH, Smolka MN, Vaidya N, Walter H, Whelan R, Feng JF, Tan L, Dong Q, Schumann G, Cheng W, Yu JT. Genetic architectures of cerebral ventricles and their overlap with neuropsychiatric traits. Nat Hum Behav 2024; 8:164-180. [PMID: 37857874 DOI: 10.1038/s41562-023-01722-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/12/2023] [Indexed: 10/21/2023]
Abstract
The cerebral ventricles are recognized as windows into brain development and disease, yet their genetic architectures, underlying neural mechanisms and utility in maintaining brain health remain elusive. Here we aggregated genetic and neuroimaging data from 61,974 participants (age range, 9 to 98 years) in five cohorts to elucidate the genetic basis of ventricular morphology and examined their overlap with neuropsychiatric traits. Genome-wide association analysis in a discovery sample of 31,880 individuals identified 62 unique loci and 785 candidate genes associated with ventricular morphology. We replicated over 80% of loci in a well-matched cohort of lateral ventricular volume. Gene set analysis revealed enrichment of ventricular-trait-associated genes in biological processes and disease pathogenesis during both early brain development and degeneration. We explored the age-dependent genetic associations in cohorts of different age groups to investigate the possible roles of ventricular-trait-associated loci in neurodevelopmental and neurodegenerative processes. We describe the genetic overlap between ventricular and neuropsychiatric traits through comprehensive integrative approaches under correlative and causal assumptions. We propose the volume of the inferior lateral ventricles as a heritable endophenotype to predict the risk of Alzheimer's disease, which might be a consequence of prodromal Alzheimer's disease. Our study provides an advance in understanding the genetics of the cerebral ventricles and demonstrates the potential utility of ventricular measurements in tracking brain disorders and maintaining brain health across the lifespan.
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Affiliation(s)
- Yi-Jun Ge
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bang-Sheng Wu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Zhang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shi-Dong Chen
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ya-Ru Zhang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ju-Jiao Kang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Yue-Ting Deng
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ya-Nan Ou
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Xiao-Yu He
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yong-Li Zhao
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Kevin Kuo
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qing Ma
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Tobias Banaschewski
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Gareth J Barker
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Arun L W Bokde
- Discipline of Psychiatry, School of Medicine and Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Sylvane Desrivières
- Centre for Population Neuroscience and Precision Medicine, Institute of Psychiatry, Psychology & Neuroscience, SGDP Centre, King's College London, London, UK
| | - Herta Flor
- Institute of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Psychology, School of Social Sciences, University of Mannheim, Mannheim, Germany
| | - Antoine Grigis
- NeuroSpin, CEA, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hugh Garavan
- Departments of Psychiatry and Psychology, University of Vermont, Burlington, VT, USA
| | - Penny Gowland
- Sir Peter Mansfield Imaging Centre, School of Physics and Astronomy, University of Nottingham, Nottingham, UK
| | - Andreas Heinz
- Department of Psychiatry and Psychotherapy CCM, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Rüdiger Brühl
- Physikalisch-Technische Bundesanstalt, Braunschweig and Berlin, Germany
| | - Jean-Luc Martinot
- Institut National de la Santé et de la Recherche Médicale, INSERM U 1299 'Trajectoires développementales & psychiatrie', University Paris-Saclay, CNRS; Ecole Normale Supérieure Paris-Saclay, Centre Borelli, Gif-sur-Yvette, France
| | - Marie-Laure Paillère Martinot
- Institut National de la Santé et de la Recherche Médicale, INSERM U 1299 'Trajectoires développementales & psychiatrie', University Paris-Saclay, CNRS; Ecole Normale Supérieure Paris-Saclay, Centre Borelli, Gif-sur-Yvette, France
- AP-HP, Sorbonne University, Department of Child and Adolescent Psychiatry, Pitié-Salpêtrière Hospital, Paris, France
| | - Eric Artiges
- Institut National de la Santé et de la Recherche Médicale, INSERM U 1299 'Trajectoires développementales & psychiatrie', University Paris-Saclay, CNRS; Ecole Normale Supérieure Paris-Saclay, Centre Borelli, Gif-sur-Yvette, France
- Psychiatry Department, EPS Barthélémy Durand, Etampes, France
| | - Frauke Nees
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Institute of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Institute of Medical Psychology and Medical Sociology, University Medical Center Schleswig Holstein, Kiel University, Kiel, Germany
| | | | - Herve Lemaitre
- NeuroSpin, CEA, Université Paris-Saclay, Gif-sur-Yvette, France
- Institut des Maladies Neurodégénératives, UMR 5293, CNRS, CEA, Université de Bordeaux, Bordeaux, France
| | - Tomáš Paus
- Departments of Psychiatry and Neuroscience, Faculty of Medicine and Centre Hospitalier Universitaire Sainte-Justine, University of Montreal, Montreal, Quebec, Canada
- Departments of Psychiatry and Psychology, University of Toronto, Toronto, Ontario, Canada
| | - Luise Poustka
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Medical Centre Göttingen, Göttingen, Germany
| | - Sarah Hohmann
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Sabina Millenet
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Juliane H Fröhner
- Department of Psychiatry and Neuroimaging Center, Technische Universität Dresden, Dresden, Germany
| | - Michael N Smolka
- Department of Psychiatry and Neuroimaging Center, Technische Universität Dresden, Dresden, Germany
| | - Nilakshi Vaidya
- Centre for Population Neuroscience and Stratified Medicine, Department of Psychiatry and Neuroscience, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Henrik Walter
- Department of Psychiatry and Psychotherapy CCM, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Robert Whelan
- School of Psychology and Global Brain Health Institute, Trinity College Dublin, Dublin, Ireland
| | - Jian-Feng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Beijing, China
- Fudan ISTBI-ZJNU Algorithm Centre for Brain-Inspired Intelligence, Zhejiang Normal University, Jinhua, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Shanghai, China
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Qiang Dong
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gunter Schumann
- Centre for Population Neuroscience and Stratified Medicine, Department of Psychiatry and Neuroscience, Charité Universitätsmedizin Berlin, Berlin, Germany
- Centre for Population Neuroscience and Precision Medicine, Institute for Science and Technology of Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Wei Cheng
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Beijing, China.
- Fudan ISTBI-ZJNU Algorithm Centre for Brain-Inspired Intelligence, Zhejiang Normal University, Jinhua, China.
- Shanghai Medical College and Zhongshan Hospital Immunotherapy Technology Transfer 79 Center, Shanghai, China.
| | - Jin-Tai Yu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.
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17
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Karunakaran KB, Amemori KI. Spatiotemporal expression patterns of anxiety disorder-associated genes. Transl Psychiatry 2023; 13:385. [PMID: 38092764 PMCID: PMC10719387 DOI: 10.1038/s41398-023-02693-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 11/25/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023] Open
Abstract
Anxiety disorders (ADs) are the most common form of mental disorder that affects millions of individuals worldwide. Although physiological studies have revealed the neural circuits related to AD symptoms, how AD-associated genes are spatiotemporally expressed in the human brain still remains unclear. In this study, we integrated genome-wide association studies of four human AD subtypes-generalized anxiety disorder, social anxiety disorder, panic disorder, and obsessive-compulsive disorder-with spatial gene expression patterns. Our investigation uncovered a novel division among AD-associated genes, marked by significant and distinct expression enrichments in the cerebral nuclei, limbic, and midbrain regions. Each gene cluster was associated with specific anxiety-related behaviors, signaling pathways, region-specific gene networks, and cell types. Notably, we observed a significant negative correlation in the temporal expression patterns of these gene clusters during various developmental stages. Moreover, the specific brain regions enriched in each gene group aligned with neural circuits previously associated with negative decision-making and anxious temperament. These results suggest that the two distinct gene clusters may underlie separate neural systems involved in anxiety. As a result, our findings bridge the gap between genes and neural circuitry, shedding light on the mechanisms underlying AD-associated behaviors.
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Affiliation(s)
- Kalyani B Karunakaran
- Institute for the Advanced Study of Human Biology, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Ken-Ichi Amemori
- Institute for the Advanced Study of Human Biology, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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18
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Stacey SN, Zink F, Halldorsson GH, Stefansdottir L, Gudjonsson SA, Einarsson G, Hjörleifsson G, Eiriksdottir T, Helgadottir A, Björnsdottir G, Thorgeirsson TE, Olafsdottir TA, Jonsdottir I, Gretarsdottir S, Tragante V, Magnusson MK, Jonsson H, Gudmundsson J, Olafsson S, Holm H, Gudbjartsson DF, Sulem P, Helgason A, Thorsteinsdottir U, Tryggvadottir L, Rafnar T, Melsted P, Ulfarsson MÖ, Vidarsson B, Thorleifsson G, Stefansson K. Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis. Nat Genet 2023; 55:2149-2159. [PMID: 37932435 PMCID: PMC10703693 DOI: 10.1038/s41588-023-01555-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/28/2023] [Indexed: 11/08/2023]
Abstract
Clonal hematopoiesis (CH) arises when a substantial proportion of mature blood cells is derived from a single hematopoietic stem cell lineage. Using whole-genome sequencing of 45,510 Icelandic and 130,709 UK Biobank participants combined with a mutational barcode method, we identified 16,306 people with CH. Prevalence approaches 50% in elderly participants. Smoking demonstrates a dosage-dependent impact on risk of CH. CH associates with several smoking-related diseases. Contrary to published claims, we find no evidence that CH is associated with cardiovascular disease. We provide evidence that CH is driven by genes that are commonly mutated in myeloid neoplasia and implicate several new driver genes. The presence and nature of a driver mutation alters the risk profile for hematological disorders. Nevertheless, most CH cases have no known driver mutations. A CH genome-wide association study identified 25 loci, including 19 not implicated previously in CH. Splicing, protein and expression quantitative trait loci were identified for CD164 and TCL1A.
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Affiliation(s)
| | | | - Gisli H Halldorsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | - Thorunn A Olafsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Immunology, Landspitali University Hospital, Reykjavik, Iceland
| | | | | | - Magnus K Magnusson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Agnar Helgason
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Pall Melsted
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Magnus Ö Ulfarsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Brynjar Vidarsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Hematology, Landspitali University Hospital, Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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19
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Moore A, Marks JA, Quach BC, Guo Y, Bierut LJ, Gaddis NC, Hancock DB, Page GP, Johnson EO. Evaluating 17 methods incorporating biological function with GWAS summary statistics to accelerate discovery demonstrates a tradeoff between high sensitivity and high positive predictive value. Commun Biol 2023; 6:1199. [PMID: 38001305 PMCID: PMC10673847 DOI: 10.1038/s42003-023-05413-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 10/03/2023] [Indexed: 11/26/2023] Open
Abstract
Where sufficiently large genome-wide association study (GWAS) samples are not currently available or feasible, methods that leverage increasing knowledge of the biological function of variants may illuminate discoveries without increasing sample size. We comprehensively evaluated 17 functional weighting methods for identifying novel associations. We assessed the performance of these methods using published results from multiple GWAS waves across each of five complex traits. Although no method achieved both high sensitivity and positive predictive value (PPV) for any trait, a subset of methods utilizing pleiotropy and expression quantitative trait loci nominated variants with high PPV (>75%) for multiple traits. Application of functionally weighting methods to enhance GWAS power for locus discovery is unlikely to circumvent the need for larger sample sizes in truly underpowered GWAS, but these results suggest that applying functional weighting to GWAS can accurately nominate additional novel loci from available samples for follow-up studies.
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Affiliation(s)
- Amy Moore
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, 27709, USA.
| | - Jesse A Marks
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, 27709, USA
| | - Bryan C Quach
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, 27709, USA
| | - Yuelong Guo
- GeneCentric Therapeutics, Inc., Cary, NC, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Nathan C Gaddis
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, 27709, USA
| | - Dana B Hancock
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, 27709, USA
| | - Grier P Page
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, 27709, USA
- Fellow Program, RTI International, Research Triangle Park, NC, 27709, USA
| | - Eric O Johnson
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, 27709, USA.
- Fellow Program, RTI International, Research Triangle Park, NC, 27709, USA.
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20
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Du Z, Iyyanki T, Lessard S, Chao M, Asbrand C, Nassar D, Klinger K, de Rinaldis E, Khader S, Chatelain C. Genome-wide association study analysis of disease severity in Acne reveals novel biological insights. medRxiv 2023:2023.11.13.23298473. [PMID: 38014089 PMCID: PMC10680891 DOI: 10.1101/2023.11.13.23298473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Acne vulgaris is a common skin disease that affects >85% of teenage young adults among which >8% develop severe lesions that leaves permanent scars. Genetic heritability studies of acne in twin cohorts have estimated that the heritability for acne is 80%. Previous genome-wide association studies (GWAS) have identified 50 genetic loci associated with increased risk of developing acne when compared to healthy individuals. However only a few studies have investigated genetic association with disease severity. GWAS of disease progression may provide a more effective approach to unveil potential disease modifying therapeutic targets. Here, we performed a multi-ethnic GWAS analysis to capture disease severity in acne patients by using individuals with normal acne as a control. Our cohort consists of a total of 2,956 participants, including 290 severe acne cases and 930 normal acne controls from FinnGen, and 522 cases and 1,214 controls from BioVU. We also performed mendelian randomization (MR), colocalization analyses and transcriptome-wide association study (TWAS) to identify putative causal genes. Lastly, we performed gene-set enrichment analysis using MAGMA to implicate biological pathways that drive disease severity in Acne. We identified two new loci associated with acne severity at the genome-wide significance level, six novel associated genes by MR, colocalization and TWAS analyses, including genes CDC7, SLC7A1, ADAM23, TTLL10, CDK20 and DNAJA4 , and 5 novel pathways by MAGMA analyses. Our study suggests that the etiologies of acne susceptibility and severity have limited overlap, with only 26% of known acne risk loci presenting nominal association with acne severity and none of the novel severity associated genes reported as associated with acne risk in previous GWAS.
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21
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Zhu Z, Chen X, Zhang S, Yu R, Qi C, Cheng L, Zhang X. Leveraging molecular quantitative trait loci to comprehend complex diseases/traits from the omics perspective. Hum Genet 2023; 142:1543-1560. [PMID: 37755483 DOI: 10.1007/s00439-023-02602-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023]
Abstract
Comprehending the molecular basis of quantitative genetic variation is a principal goal for complex diseases or traits. Molecular quantitative trait loci (molQTLs) have made it possible to investigate the effects of genetic variants hiding behind large-scale omics data. A deeper understanding of molQTL is urgently required in light of the multi-dimensionalization of omics data to more fully elucidate the pertinent biological mechanisms. Herein, we reviewed molQTLs with the corresponding resource from the omics perspective and further discussed the integrative strategy of GWAS-molQTL to infer their causal effects. Subsequently, we described the opportunities and challenges encountered by molQTL. The case studies showed that molQTL is essential for complex diseases and traits, whether single- or multi-omics QTLs. Overall, we highlighted the functional significance of genetic variants to employ the discovery of molQTL in complex diseases and traits.
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Affiliation(s)
- Zijun Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xinyu Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Sainan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Rui Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Changlu Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
- NHC Key Laboratory of Molecular Probe and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150028, Heilongjiang, China.
| | - Xue Zhang
- NHC Key Laboratory of Molecular Probe and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150028, Heilongjiang, China
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
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22
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Zhou J, Xia Y, Li M, Chen Y, Dai J, Liu C, Chen C. A higher dysregulation burden of brain DNA methylation in female patients implicated in the sex bias of Schizophrenia. Mol Psychiatry 2023; 28:4842-4852. [PMID: 37696874 PMCID: PMC10925554 DOI: 10.1038/s41380-023-02243-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/13/2023]
Abstract
Sex differences are pervasive in schizophrenia (SCZ), but the extent and magnitude of DNA methylation (DNAm) changes underlying these differences remain uncharacterized. In this study, sex-stratified differential DNAm analysis was performed in postmortem brain samples from 117 SCZ and 137 controls, partitioned into discovery and replication datasets. Three differentially methylated positions (DMPs) were identified (adj.p < 0.05) in females and 29 DMPs in males without overlap between them. Over 81% of these sex-stratified DMPs were directionally consistent between sexes but with different effect sizes. Females experienced larger magnitude of DNAm changes and more DMPs (based on data of equal sample size) than males, contributing to a higher dysregulation burden of DNAm in females SCZ. Additionally, despite similar proportions of female-related DMPs (fDMPs, 8%) being under genetic control compared with males (10%), significant enrichment of DMP-related single nucleotide polymorphisms (SNPs) in signals of genome-wide association studies was identified only in fDMPs. One DMP in each sex connected the SNPs and gene expression of CALHM1 in females and CCDC149 in males. PPI subnetworks revealed that both female- and male-related differential DNAm interacted with synapse-related dysregulation. Immune-related pathways were unique for females and neuron-related pathways were associated with males. This study reveals remarkable quantitative differences in DNAm-related sexual dimorphism in SCZ and that females have a higher dysregulation burden of SCZ-associated DNAm than males.
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Affiliation(s)
- Jiaqi Zhou
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and the Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yan Xia
- Department of Medicine, Harvard Medical School, Boston, MA, 02114, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02114, USA.
- Analytic and Translational Genetics unit, Massachusetts General Hospital, Boston, MA, 02114, USA.
| | - Miao Li
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and the Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
| | - Yu Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and the Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02114, USA
| | - Jiacheng Dai
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and the Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and the Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and the Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan, 410078, China.
- National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
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23
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Chen Q, Aguirre L, Zhao H, Borrego F, de Rojas I, Su L, Li PP, Zhang B, Kokovay E, Lechleiter JD, Göring HH, De Jager PL, Kleinman JE, Hyde TM, Ruiz A, Weinberger DR, Seshadri S, Ma L. Identification of a specific APOE transcript and functional elements associated with Alzheimer's disease. medRxiv 2023:2023.10.30.23297431. [PMID: 37961425 PMCID: PMC10635228 DOI: 10.1101/2023.10.30.23297431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
INTRODUCTION The APOE gene is the strongest genetic risk factor for late-onset Alzheimer's Disease (LOAD). However, the gene regulatory mechanisms at this locus have not been fully characterized. METHODS To identify novel AD-linked functional elements within the APOE locus, we integrated SNP variants with RNA-seq, DNA methylation, and ChIP-seq data from human postmortem brains. RESULTS We identified an AD-linked APOE transcript (jxn1.2.2) observed in the dorsolateral prefrontal cortex (DLPFC). The APOE jxn1.2.2 transcript is associated with brain neuropathological features in DLPFC. We prioritized an independent functional SNP, rs157580, significantly associated with jxn1.2.2 transcript abundance and DNA methylation levels. rs157580 is located within active chromatin regions and predicted to affect brain-related transcriptional factors binding affinity. rs157580 shared the effects on the jxn1.2.2 transcript between European and African ethnic groups. DISCUSSION The novel APOE functional elements provide potential therapeutic targets with mechanistic insight into the disease's etiology.
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24
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Sarnowski C, Huan T, Ma Y, Joehanes R, Beiser A, DeCarli CS, Heard-Costa NL, Levy D, Lin H, Liu CT, Liu C, Meigs JB, Satizabal CL, Florez JC, Hivert MF, Dupuis J, De Jager PL, Bennett DA, Seshadri S, Morrison AC. Multi-tissue epigenetic analysis identifies distinct associations underlying insulin resistance and Alzheimer's disease at CPT1A locus. Clin Epigenetics 2023; 15:173. [PMID: 37891690 PMCID: PMC10612362 DOI: 10.1186/s13148-023-01589-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Insulin resistance (IR) is a major risk factor for Alzheimer's disease (AD) dementia. The mechanisms by which IR predisposes to AD are not well-understood. Epigenetic studies may help identify molecular signatures of IR associated with AD, thus improving our understanding of the biological and regulatory mechanisms linking IR and AD. METHODS We conducted an epigenome-wide association study of IR, quantified using the homeostatic model assessment of IR (HOMA-IR) and adjusted for body mass index, in 3,167 participants from the Framingham Heart Study (FHS) without type 2 diabetes at the time of blood draw used for methylation measurement. We identified DNA methylation markers associated with IR at the genome-wide level accounting for multiple testing (P < 1.1 × 10-7) and evaluated their association with neurological traits in participants from the FHS (N = 3040) and the Religious Orders Study/Memory and Aging Project (ROSMAP, N = 707). DNA methylation profiles were measured in blood (FHS) or dorsolateral prefrontal cortex (ROSMAP) using the Illumina HumanMethylation450 BeadChip. Linear regressions (ROSMAP) or mixed-effects models accounting for familial relatedness (FHS) adjusted for age, sex, cohort, self-reported race, batch, and cell type proportions were used to assess associations between DNA methylation and neurological traits accounting for multiple testing. RESULTS We confirmed the strong association of blood DNA methylation with IR at three loci (cg17901584-DHCR24, cg17058475-CPT1A, cg00574958-CPT1A, and cg06500161-ABCG1). In FHS, higher levels of blood DNA methylation at cg00574958 and cg17058475 were both associated with lower IR (P = 2.4 × 10-11 and P = 9.0 × 10-8), larger total brain volumes (P = 0.03 and P = 9.7 × 10-4), and smaller log lateral ventricular volumes (P = 0.07 and P = 0.03). In ROSMAP, higher levels of brain DNA methylation at the same two CPT1A markers were associated with greater risk of cognitive impairment (P = 0.005 and P = 0.02) and higher AD-related indices (CERAD score: P = 5 × 10-4 and 0.001; Braak stage: P = 0.004 and P = 0.01). CONCLUSIONS Our results suggest potentially distinct epigenetic regulatory mechanisms between peripheral blood and dorsolateral prefrontal cortex tissues underlying IR and AD at CPT1A locus.
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Affiliation(s)
- Chloé Sarnowski
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Tianxiao Huan
- Population Sciences Branch, National Heart, Lung and Blood Institutes of Health, Bethesda, MD, USA
| | - Yiyi Ma
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Roby Joehanes
- Population Sciences Branch, National Heart, Lung and Blood Institutes of Health, Bethesda, MD, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Alexa Beiser
- The Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | | | - Nancy L Heard-Costa
- The Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Daniel Levy
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Honghuang Lin
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ching-Ti Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Chunyu Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - James B Meigs
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claudia L Satizabal
- The Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Department of Population Health Sciences, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jose C Florez
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Harvard University, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Josée Dupuis
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University, Montreal, Canada
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Sudha Seshadri
- The Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
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Das Adhikari S, Cui Y, Wang J. BayesKAT: Bayesian Optimal Kernel-based Test for genetic association studies reveals joint genetic effects in complex diseases. bioRxiv 2023:2023.10.18.562824. [PMID: 37905124 PMCID: PMC10614916 DOI: 10.1101/2023.10.18.562824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
GWAS methods have identified individual SNPs significantly associated with specific phenotypes. Nonetheless, many complex diseases are polygenic and are controlled by multiple genetic variants that are usually non-linearly dependent. These genetic variants are marginally less effective and remain undetected in GWAS analysis. Kernel-based tests (KBT), which evaluate the joint effect of a group of genetic variants, are therefore critical for complex disease analysis. However, choosing different kernel functions in KBT can significantly influence the type I error control and power, and selecting the optimal kernel remains a statistically challenging task. A few existing methods suffer from inflated type 1 errors, limited scalability, inferior power, or issues of ambiguous conclusions. Here, we present a new Bayesian framework, BayesKAT( https://github.com/wangjr03/BayesKAT ), which overcomes these kernel specification issues by selecting the optimal composite kernel adaptively from the data while testing genetic associations simultaneously. Furthermore, BayesKAT implements a scalable computational strategy to boost its applicability, especially for high-dimensional cases where other methods become less effective. Based on a series of performance comparisons using both simulated and real large-scale genetics data, BayesKAT outperforms the available methods in detecting complex group-level associations and controlling type I errors simultaneously. Applied on a variety of groups of functionally related genetic variants based on biological pathways, co-expression gene modules, and protein complexes, BayesKAT deciphers the complex genetic basis and provides mechanistic insights into human diseases.
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26
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Lin C, Liu W, Jiang W, Zhao H. Robustness of quantifying mediating effects of genetically regulated expression on complex traits with mediated expression score regression. Biol Methods Protoc 2023; 8:bpad024. [PMID: 37901453 PMCID: PMC10599978 DOI: 10.1093/biomethods/bpad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/08/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023] Open
Abstract
Genetic association signals have been mostly found in noncoding regions through genome-wide association studies (GWAS), suggesting the roles of gene expression regulation in human diseases and traits. However, there has been limited success in colocalizing expression quantitative trait locus (eQTL) with disease-associated variants. Mediated expression score regression (MESC) is a recently proposed method to quantify the proportion of trait heritability mediated by genetically regulated gene expressions (GReX). Applications of MESC to GWAS results have yielded low estimation of mediated heritability for many traits. As MESC relies on stringent independence assumptions between cis-eQTL effects, gene effects, and nonmediated SNP effects, it may fail to characterize the true relationships between those effect sizes, which leads to biased results. Here, we consider the robustness of MESC to investigate whether the low fraction of mediated heritability inferred by MESC reflects biological reality for complex traits or is an underestimation caused by model misspecifications. Our results suggest that MESC may lead to biased estimates of mediated heritability with misspecification of gene annotations leading to underestimation, whereas misspecification of SNP annotations may lead to overestimation. Furthermore, errors in eQTL effect estimates may lead to underestimation of mediated heritability.
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Affiliation(s)
- Chen Lin
- Department of Biostatistics, Yale University, New Haven, CT 06510, United States
| | - Wei Liu
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06510, United States
| | - Wei Jiang
- Department of Biostatistics, Yale University, New Haven, CT 06510, United States
| | - Hongyu Zhao
- Department of Biostatistics, Yale University, New Haven, CT 06510, United States
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06510, United States
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27
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Arruda AL, Khandaker GM, Morris AP, Smith GD, Huckins LM, Zeggini E. Genomic insights into the comorbidity between type 2 diabetes and schizophrenia. medRxiv 2023:2023.10.16.23297073. [PMID: 37905000 PMCID: PMC10615007 DOI: 10.1101/2023.10.16.23297073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Multimorbidity represents an increasingly important public health challenge with far-reaching implications for health management and policy. Mental health and metabolic diseases have a well-established epidemiological association. In this study, we investigate the genetic intersection between type 2 diabetes and schizophrenia. We use Mendelian randomization to examine potential causal relationships between the two conditions and related endophenotypes. We report no compelling evidence that type 2 diabetes genetic liability potentially causally influences schizophrenia risk and vice versa. Our findings show that increased body mass index (BMI) has a protective effect against schizophrenia, in contrast to the well-known risk-increasing effect of BMI on type 2 diabetes risk. We identify evidence of colocalization of association signals for these two conditions at 11 genomic loci, six of which have opposing directions of effect for type 2 diabetes and schizophrenia. To elucidate these colocalizing signals, we integrate multi-omics data from bulk and single-cell gene expression studies, along with functional information. We identify high-confidence effector genes and find that they are enriched for homeostasis and lipid-related pathways. We also highlight drug repurposing opportunities including N-methyl-D-aspartate (NMDA) receptor antagonists. Our findings provide insights into shared biological mechanisms for type 2 diabetes and schizophrenia, highlighting common factors that influence the risk of the two conditions in opposite directions and shedding light on the complex nature of this comorbidity.
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Affiliation(s)
- Ana Luiza Arruda
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, 85764, Germany
- Munich School for Data Science, Helmholtz Munich, Neuherberg, 85764, Germany
- Technical University of Munich (TUM), School of Medicine, Graduate School of Experimental Medicine, Munich, 81675, Germ
| | - Golam M. Khandaker
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
- Centre for Academic Mental Health, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
- Avon and Wiltshire Mental Health Partnership NHS Trust, Bristol, UK
| | - Andrew P. Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, M13 9PT, United Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Laura M. Huckins
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, 85764, Germany
- TUM school of medicine, Technical University Munich and Klinikum Rechts der Isar, Munich, 81675, Germany
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28
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Johansen N, Somasundaram S, Travaglini KJ, Yanny AM, Shumyatcher M, Casper T, Cobbs C, Dee N, Ellenbogen R, Ferreira M, Goldy J, Guzman J, Gwinn R, Hirschstein D, Jorstad NL, Keene CD, Ko A, Levi BP, Ojemann JG, Pham T, Shapovalova N, Silbergeld D, Sulc J, Torkelson A, Tung H, Smith K, Lein ES, Bakken TE, Hodge RD, Miller JA. Interindividual variation in human cortical cell type abundance and expression. Science 2023; 382:eadf2359. [PMID: 37824649 DOI: 10.1126/science.adf2359] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 07/30/2023] [Indexed: 10/14/2023]
Abstract
Single-cell transcriptomic studies have identified a conserved set of neocortical cell types from small postmortem cohorts. We extended these efforts by assessing cell type variation across 75 adult individuals undergoing epilepsy and tumor surgeries. Nearly all nuclei map to one of 125 robust cell types identified in the middle temporal gyrus. However, we found interindividual variance in abundances and gene expression signatures, particularly in deep-layer glutamatergic neurons and microglia. A minority of donor variance is explainable by age, sex, ancestry, disease state, and cell state. Genomic variation was associated with expression of 150 to 250 genes for most cell types. This characterization of cellular variation provides a baseline for cell typing in health and disease.
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Affiliation(s)
| | | | | | | | | | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Charles Cobbs
- Swedish Neuroscience Institute, Seattle,WA 98122, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Richard Ellenbogen
- Department of Neurological Surgery, University of Washington, Seattle, WA 98104, USA
| | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA 98104, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Junitta Guzman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ryder Gwinn
- Swedish Neuroscience Institute, Seattle,WA 98122, USA
| | | | | | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98104, USA
| | - Andrew Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA 98104, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA 98104, USA
| | - Thanh Pham
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Daniel Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA 98104, USA
| | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Amy Torkelson
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kimberly Smith
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
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29
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Huang J, Wang Y, Stein TD, Ang TFA, Zhu Y, Tao Q, Lunetta KL, Mez J, Au R, Farrer LA, Qiu WQ, Zhang X. The impact of blood MCP-1 levels on Alzheimer's disease with genetic variation of UNC5C and NAV3 loci. Res Sq 2023:rs.3.rs-3376348. [PMID: 37841863 PMCID: PMC10571626 DOI: 10.21203/rs.3.rs-3376348/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Background Previous study shows that monocyte chemoattractant protein-1 (MCP-1), which is implicated in the peripheral proinflammatory cascade and blood-brain barrier (BBB) disruption, modulates the genetic risks of AD in established AD loci. Methods In this study, we hypothesized that blood MCP-1 impacts the AD risk of genetic variants beyond known AD loci. We thus performed a genome-wide association study (GWAS) using the logistic regression via generalized estimating equations (GEE) and the Cox proportional-hazards models to examine the interactive effects between single nucleotide polymorphisms (SNPs) and blood MCP-1 level on AD in three cohorts: the Framingham Heart Study (FHS), Alzheimer's Disease Neuroimaging Initiative (ADNI) and Religious Orders Study/Memory and Aging Project (ROSMAP). Results We identified SNPs in two genes, neuron navigator 3 (NAV3, also named Unc-53 Homolog 3, rs696468) (p < 7.55×10- 9) and Unc-5 Netrin Receptor C (UNC5C rs72659964) (p < 1.07×10- 8) that showed an association between increasing levels of blood MCP-1 and AD. Elevating blood MCP-1 concentrations increased AD risk and AD pathology in genotypes of NAV3 (rs696468-CC) and UNC5C (rs72659964-AT + TT), but did not influence the other counterpart genotypes of these variants. Conclusions NAV3 and UNC5C are homologs and may increase AD risk through dysregulating the functions of neurite outgrowth and guidance. Overall, the association of risk alleles of NAV3 and UNC5C with AD is enhanced by peripheral MCP-1 level, suggesting that lowering the level of blood MCP-1 may reduce the risk of developing AD for people with these genotypes.
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Affiliation(s)
- Jinghan Huang
- Boston University Chobanian & Avedisian School of Medicine
| | - Yixuan Wang
- Boston University Chobanian & Avedisian School of Medicine
| | - Thor D Stein
- Boston University Chobanian & Avedisian School of Medicine
| | | | - Yibo Zhu
- Boston University Chobanian & Avedisian School of Medicine
| | - Qiushan Tao
- Boston University Chobanian & Avedisian School of Medicine
| | | | - Jesse Mez
- Boston University Chobanian & Avedisian School of Medicine
| | - Rhoda Au
- Boston University Chobanian & Avedisian School of Medicine
| | | | - Wei Qiao Qiu
- Boston University Chobanian & Avedisian School of Medicine
| | - Xiaoling Zhang
- Boston University Chobanian & Avedisian School of Medicine
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30
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Koido M. Polygenic modelling and machine learning approaches in pharmacogenomics: Importance in downstream analysis of genome-wide association study data. Br J Clin Pharmacol 2023. [PMID: 37743713 DOI: 10.1111/bcp.15913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified genetic variations associated with adverse drug effects in pharmacogenomics (PGx) research. However, interpreting the biological implications of these associations remains a challenge. This review highlights 2 promising post-GWAS methods for PGx. First, we discuss the polygenic architecture of the PGx traits, especially for drug-induced liver injury. Experimental modelling using multiple donors' human primary hepatocytes and human liver organoids demonstrated the polygenic architecture of drug-induced liver injury susceptibility and found biological vulnerability in genetically high-risk tissue donors. Second, we discuss the challenges of interpreting the roles of variants in noncoding regions. Beyond methods involving expression quantitative trait locus analysis and massively parallel reporter assays, we suggest the use of in silico mutagenesis through machine learning methods to understand the roles of variants in transcriptional regulation. This review underscores the importance of these post-GWAS methods in providing critical insights into PGx, potentially facilitating drug development and personalized treatment.
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Affiliation(s)
- Masaru Koido
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
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31
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Carnes MU, Quach BC, Zhou L, Han S, Tao R, Mandal M, Deep-Soboslay A, Marks JA, Page GP, Maher BS, Jaffe AE, Won H, Bierut LJ, Hyde TM, Kleinman JE, Johnson EO, Hancock DB. Smoking-informed methylation and expression QTLs in human brain and colocalization with smoking-associated genetic loci. medRxiv 2023:2023.09.18.23295431. [PMID: 37790540 PMCID: PMC10543041 DOI: 10.1101/2023.09.18.23295431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Smoking is a leading cause of preventable morbidity and mortality. Smoking is heritable, and genome-wide association studies (GWAS) of smoking behaviors have identified hundreds of significant loci. Most GWAS-identified variants are noncoding with unknown neurobiological effects. We used genome-wide genotype, DNA methylation, and RNA sequencing data in postmortem human nucleus accumbens (NAc) to identify cis-methylation/expression quantitative trait loci (meQTLs/eQTLs), investigate variant-by-cigarette smoking interactions across the genome, and overlay QTL evidence at smoking GWAS-identified loci to evaluate their regulatory potential. Active smokers (N=52) and nonsmokers (N=171) were defined based on cotinine biomarker levels and next-of-kin reporting. We simultaneously tested variant and variant-by-smoking interaction effects on methylation and expression, separately, adjusting for biological and technical covariates and using a two-stage multiple testing approach with eigenMT and Bonferroni corrections. We found >2 million significant meQTL variants (padj<0.05) corresponding to 41,695 unique CpGs. Results were largely driven by main effects; five meQTLs, mapping to NUDT12, FAM53B, RNF39, and ADRA1B, showed a significant interaction with smoking. We found 57,683 significant eQTLs for 958 unique eGenes (padj<0.05) and no smoking interactions. Colocalization analyses identified loci with smoking-associated GWAS variants that overlapped meQTLs/eQTLs, suggesting that these heritable factors may influence smoking behaviors through functional effects on methylation/expression. One locus containing MUSTIN1 and ITIH4 colocalized across all data types (GWAS + meQTL + eQTL). In this first genome-wide meQTL map in the human NAc, the enriched overlap with smoking GWAS-identified genetic loci provides evidence that gene regulation in the brain helps explain the neurobiology of smoking behaviors.
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Affiliation(s)
- Megan Ulmer Carnes
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Bryan C. Quach
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Linran Zhou
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Shizhong Han
- Lieber Institute for Brain Development (LIBD), Baltimore, Maryland
| | - Ran Tao
- Lieber Institute for Brain Development (LIBD), Baltimore, Maryland
| | - Meisha Mandal
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | | | - Jesse A. Marks
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Grier P. Page
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
- Fellow Program, RTI International, Research Triangle Park, North Carolina
| | - Brion S. Maher
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, Maryland
| | - Andrew E. Jaffe
- Lieber Institute for Brain Development (LIBD), Baltimore, Maryland
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Laura J. Bierut
- Department of Psychiatry, Washington University in St. Louis, Missouri
| | - Thomas M. Hyde
- Lieber Institute for Brain Development (LIBD), Baltimore, Maryland
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, Maryland
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland
| | - Joel E. Kleinman
- Lieber Institute for Brain Development (LIBD), Baltimore, Maryland
| | - Eric O. Johnson
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
- Fellow Program, RTI International, Research Triangle Park, North Carolina
| | - Dana B. Hancock
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
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32
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Paryani F, Kwon JS, Ng CW, Madden N, Ofori K, Tang A, Lu H, Li J, Mahajan A, Davidson SM, Basile A, McHugh C, Vonsattel JP, Hickman R, Zody M, Houseman DE, Goldman JE, Yoo AS, Menon V, Al-Dalahmah O. Multi-OMIC analysis of Huntington disease reveals a neuroprotective astrocyte state. bioRxiv 2023:2023.09.08.556867. [PMID: 37745577 PMCID: PMC10515780 DOI: 10.1101/2023.09.08.556867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Huntington disease (HD) is an incurable neurodegenerative disease characterized by neuronal loss and astrogliosis. One hallmark of HD is the selective neuronal vulnerability of striatal medium spiny neurons. To date, the underlying mechanisms of this selective vulnerability have not been fully defined. Here, we employed a multi-omic approach including single nucleus RNAseq (snRNAseq), bulk RNAseq, lipidomics, HTT gene CAG repeat length measurements, and multiplexed immunofluorescence on post-mortem brain tissue from multiple brain regions of HD and control donors. We defined a signature of genes that is driven by CAG repeat length and found it enriched in astrocytic and microglial genes. Moreover, weighted gene correlation network analysis showed loss of connectivity of astrocytic and microglial modules in HD and identified modules that correlated with CAG-repeat length which further implicated inflammatory pathways and metabolism. We performed lipidomic analysis of HD and control brains and identified several lipid species that correlate with HD grade, including ceramides and very long chain fatty acids. Integration of lipidomics and bulk transcriptomics identified a consensus gene signature that correlates with HD grade and HD lipidomic abnormalities and implicated the unfolded protein response pathway. Because astrocytes are critical for brain lipid metabolism and play important roles in regulating inflammation, we analyzed our snRNAseq dataset with an emphasis on astrocyte pathology. We found two main astrocyte types that spanned multiple brain regions; these types correspond to protoplasmic astrocytes, and fibrous-like - CD44-positive, astrocytes. HD pathology was differentially associated with these cell types in a region-specific manner. One protoplasmic astrocyte cluster showed high expression of metallothionein genes, the depletion of this cluster positively correlated with the depletion of vulnerable medium spiny neurons in the caudate nucleus. We confirmed that metallothioneins were increased in cingulate HD astrocytes but were unchanged or even decreased in caudate astrocytes. We combined existing genome-wide association studies (GWAS) with a GWA study conducted on HD patients from the original Venezuelan cohort and identified a single-nucleotide polymorphism in the metallothionein gene locus associated with delayed age of onset. Functional studies found that metallothionein overexpressing astrocytes are better able to buffer glutamate and were neuroprotective of patient-derived directly reprogrammed HD MSNs as well as against rotenone-induced neuronal death in vitro. Finally, we found that metallothionein-overexpressing astrocytes increased the phagocytic activity of microglia in vitro and increased the expression of genes involved in fatty acid binding. Together, we identified an astrocytic phenotype that is regionally-enriched in less vulnerable brain regions that can be leveraged to protect neurons in HD.
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Affiliation(s)
- Fahad Paryani
- Department of Neurology, Columbia University Irving Medical Center
| | - Ji-Sun Kwon
- Washington University School of Medicine in St. Louis
| | - Chris W Ng
- Massachusetts Institute of Technology, Department of Biological Engineering
| | - Nacoya Madden
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Kenneth Ofori
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Alice Tang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Hong Lu
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Juncheng Li
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Aayushi Mahajan
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Shawn M. Davidson
- Princeton University, Lewis-Sigler Institute for Integrative Genomics
| | | | | | - Jean Paul Vonsattel
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Richard Hickman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | | | - David E. Houseman
- Massachusetts Institute of Technology, Department of Biological Engineering
| | - James E. Goldman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Andrew S. Yoo
- Washington University School of Medicine in St. Louis
| | - Vilas Menon
- Department of Neurology, Columbia University Irving Medical Center
| | - Osama Al-Dalahmah
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
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33
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Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K. eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs. PLoS Genet 2023; 19:e1010932. [PMID: 37721944 PMCID: PMC10538656 DOI: 10.1371/journal.pgen.1010932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/28/2023] [Accepted: 08/22/2023] [Indexed: 09/20/2023] Open
Abstract
The eQTL Catalogue is an open database of uniformly processed human molecular quantitative trait loci (QTLs). We are continuously updating the resource to further increase its utility for interpreting genetic associations with complex traits. Over the past two years, we have increased the number of uniformly processed studies from 21 to 31 and added X chromosome QTLs for 19 compatible studies. We have also implemented Leafcutter to directly identify splice-junction usage QTLs in all RNA sequencing datasets. Finally, to improve the interpretability of transcript-level QTLs, we have developed static QTL coverage plots that visualise the association between the genotype and average RNA sequencing read coverage in the region for all 1.7 million fine mapped associations. To illustrate the utility of these updates to the eQTL Catalogue, we performed colocalisation analysis between vitamin D levels in the UK Biobank and all molecular QTLs in the eQTL Catalogue. Although most GWAS loci colocalised both with eQTLs and transcript-level QTLs, we found that visual inspection could sometimes be used to distinguish primary splicing QTLs from those that appear to be secondary consequences of large-effect gene expression QTLs. While these visually confirmed primary splicing QTLs explain just 6/53 of the colocalising signals, they are significantly less pleiotropic than eQTLs and identify a prioritised causal gene in 4/6 cases.
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Affiliation(s)
- Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ralf Tambets
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - James D. Hayhurst
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ida Rahu
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Peep Kolberg
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Uku Raudvere
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Ivan Kuzmin
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Anshika Chowdhary
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Andreas Vija
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Hans J. Teras
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jacob Ulirsch
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - John Hardy
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sebastian Guelfi
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Daniah Trabzuni
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sarah Kim-Hellmuth
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital LMU Munich, Munich, Germany
| | - William Rayner
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Hilary Finucane
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Abayomi Mosaku
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Helen Parkinson
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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Wang H, Makowski C, Zhang Y, Qi A, Kaufmann T, Smeland OB, Fiecas M, Yang J, Visscher PM, Chen CH. Chromosomal inversion polymorphisms shape human brain morphology. Cell Rep 2023; 42:112896. [PMID: 37505983 PMCID: PMC10508191 DOI: 10.1016/j.celrep.2023.112896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 06/27/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
The impact of chromosomal inversions on human brain morphology remains underexplored. We studied 35 common inversions classified from genotypes of 33,018 adults with European ancestry. The inversions at 2p22.3, 16p11.2, and 17q21.31 reach genome-wide significance, followed by 8p23.1 and 6p21.33, in their association with cortical and subcortical morphology. The 17q21.31, 8p23.1, and 16p11.2 regions comprise the LRRC37, OR7E, and NPIP duplicated gene families. We find the 17q21.31 MAPT inversion region, known for harboring neurological risk, to be the most salient locus among common variants for shaping and patterning the cortex. Overall, we observe the inverted orientations decreasing brain size, with the exception that the 2p22.3 inversion is associated with increased subcortical volume and the 8p23.1 inversion is associated with increased motor cortex. These significant inversions are in the genomic hotspots of neuropsychiatric loci. Our findings are generalizable to 3,472 children and demonstrate inversions as essential genetic variation to understand human brain phenotypes.
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Affiliation(s)
- Hao Wang
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA 92093, USA
| | - Carolina Makowski
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA 92093, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Anna Qi
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA 92093, USA
| | - Tobias Kaufmann
- Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, 72076 Tübingen, Germany; Norwegian Centre for Mental Disorders Research, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway
| | - Olav B Smeland
- Norwegian Centre for Mental Disorders Research, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway
| | - Mark Fiecas
- Division of Biostatistics, University of Minnesota School of Public Health, Minneapolis, MN 55455, USA
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Chi-Hua Chen
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA 92093, USA.
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Wang Y, Sarnowski C, Lin H, Pitsillides AN, Heard-Costa NL, Choi SH, Wang D, Bis JC, Blue EE, Boerwinkle E, De Jager PL, Fornage M, Wijsman EM, Seshadri S, Dupuis J, Peloso GM, DeStefano AL. Key variants via Alzheimer's Disease Sequencing Project whole genome sequence data. medRxiv 2023:2023.08.28.23294631. [PMID: 37693453 PMCID: PMC10491364 DOI: 10.1101/2023.08.28.23294631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
INTRODUCTION Genome-wide association studies (GWAS) have identified loci associated with Alzheimer's disease (AD) but did not identify specific causal genes or variants within those loci. Analysis of whole genome sequence (WGS) data, which interrogates the entire genome and captures rare variations, may identify causal variants within GWAS loci. METHODS We performed single common variant association analysis and rare variant aggregate analyses in the pooled population (N cases=2,184, N controls=2,383) and targeted analyses in sub-populations using WGS data from the Alzheimer's Disease Sequencing Project (ADSP). The analyses were restricted to variants within 100 kb of 83 previously identified GWAS lead variants. RESULTS Seventeen variants were significantly associated with AD within five genomic regions implicating the genes OARD1/NFYA/TREML1, JAZF1, FERMT2, and SLC24A4. KAT8 was implicated by both single variant and rare variant aggregate analyses. DISCUSSION This study demonstrates the utility of leveraging WGS to gain insights into AD loci identified via GWAS.
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Affiliation(s)
- Yanbing Wang
- Department of Biostatistics, Boston University, School of Public Health, Boston, MA, USA
| | - Chloé Sarnowski
- Department of Biostatistics, Boston University, School of Public Health, Boston, MA, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Honghuang Lin
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Nancy L Heard-Costa
- Department of Biostatistics, Boston University, School of Public Health, Boston, MA, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Seung Hoan Choi
- Department of Biostatistics, Boston University, School of Public Health, Boston, MA, USA
| | - Dongyu Wang
- Department of Biostatistics, Boston University, School of Public Health, Boston, MA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Elizabeth E Blue
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
- Brotman Baty Institute, Seattle, WA, USA
| | | | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ellen M Wijsman
- Div. of Medical Genetics and Dept. Biostatistics Statistical Genetics Lab, University of Washington, Seattle, WA, USA
| | - Sudha Seshadri
- The Framingham Heart Study, Framingham, MA, USA
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Boston University School of Medicine, Department of Neurology, Boston, MA, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University, School of Public Health, Boston, MA, USA
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University, Montreal, Canada
| | - Gina M Peloso
- Department of Biostatistics, Boston University, School of Public Health, Boston, MA, USA
| | - Anita L DeStefano
- Department of Biostatistics, Boston University, School of Public Health, Boston, MA, USA
- The Framingham Heart Study, Framingham, MA, USA
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36
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Villicaña S, Castillo-Fernandez J, Hannon E, Christiansen C, Tsai PC, Maddock J, Kuh D, Suderman M, Power C, Relton C, Ploubidis G, Wong A, Hardy R, Goodman A, Ong KK, Bell JT. Genetic impacts on DNA methylation help elucidate regulatory genomic processes. Genome Biol 2023; 24:176. [PMID: 37525248 PMCID: PMC10391992 DOI: 10.1186/s13059-023-03011-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 07/10/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Pinpointing genetic impacts on DNA methylation can improve our understanding of pathways that underlie gene regulation and disease risk. RESULTS We report heritability and methylation quantitative trait locus (meQTL) analysis at 724,499 CpGs profiled with the Illumina Infinium MethylationEPIC array in 2358 blood samples from three UK cohorts. Methylation levels at 34.2% of CpGs are affected by SNPs, and 98% of effects are cis-acting or within 1 Mbp of the tested CpG. Our results are consistent with meQTL analyses based on the former Illumina Infinium HumanMethylation450 array. Both SNPs and CpGs with meQTLs are overrepresented in enhancers, which have improved coverage on this platform compared to previous approaches. Co-localisation analyses across genetic effects on DNA methylation and 56 human traits identify 1520 co-localisations across 1325 unique CpGs and 34 phenotypes, including in disease-relevant genes, such as USP1 and DOCK7 (total cholesterol levels), and ICOSLG (inflammatory bowel disease). Enrichment analysis of meQTLs and integration with expression QTLs give insights into mechanisms underlying cis-meQTLs (e.g. through disruption of transcription factor binding sites for CTCF and SMC3) and trans-meQTLs (e.g. through regulating the expression of ACD and SENP7 which can modulate DNA methylation at distal sites). CONCLUSIONS Our findings improve the characterisation of the mechanisms underlying DNA methylation variability and are informative for prioritisation of GWAS variants for functional follow-ups. The MeQTL EPIC Database and viewer are available online at https://epicmeqtl.kcl.ac.uk .
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Affiliation(s)
- Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | | | | | - Colette Christiansen
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jane Maddock
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, UK
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Christine Power
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - George Ploubidis
- Centre for Longitudinal Studies, Institute of Education, University College London, London, UK
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, UK
| | - Rebecca Hardy
- School of Sport, Exercise & Health Sciences, Loughborough University, Loughborough, UK
- UCL Social Research Institute, University College London, London, UK
| | - Alissa Goodman
- Centre for Longitudinal Studies, Institute of Education, University College London, London, UK
| | - Ken K Ong
- MRC Epidemiology Unit and Department of Paediatrics, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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International Multiple Sclerosis Genetics Consortium, MultipleMS Consortium. Locus for severity implicates CNS resilience in progression of multiple sclerosis. Nature 2023; 619:323-31. [PMID: 37380766 DOI: 10.1038/s41586-023-06250-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 05/23/2023] [Indexed: 06/30/2023]
Abstract
Multiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS) that results in significant neurodegeneration in the majority of those affected and is a common cause of chronic neurological disability in young adults1,2. Here, to provide insight into the potential mechanisms involved in progression, we conducted a genome-wide association study of the age-related MS severity score in 12,584 cases and replicated our findings in a further 9,805 cases. We identified a significant association with rs10191329 in the DYSF-ZNF638 locus, the risk allele of which is associated with a shortening in the median time to requiring a walking aid of a median of 3.7 years in homozygous carriers and with increased brainstem and cortical pathology in brain tissue. We also identified suggestive association with rs149097173 in the DNM3-PIGC locus and significant heritability enrichment in CNS tissues. Mendelian randomization analyses suggested a potential protective role for higher educational attainment. In contrast to immune-driven susceptibility3, these findings suggest a key role for CNS resilience and potentially neurocognitive reserve in determining outcome in MS.
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Gedik H, Nguyen TH, Peterson RE, Chatzinakos C, Vladimirov VI, Riley BP, Bacanu SA. Identifying potential risk genes and pathways for neuropsychiatric and substance use disorders using intermediate molecular mediator information. Front Genet 2023; 14:1191264. [PMID: 37415601 PMCID: PMC10320396 DOI: 10.3389/fgene.2023.1191264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/23/2023] [Indexed: 07/08/2023] Open
Abstract
Neuropsychiatric and substance use disorders (NPSUDs) have a complex etiology that includes environmental and polygenic risk factors with significant cross-trait genetic correlations. Genome-wide association studies (GWAS) of NPSUDs yield numerous association signals. However, for most of these regions, we do not yet have a firm understanding of either the specific risk variants or the effects of these variants. Post-GWAS methods allow researchers to use GWAS summary statistics and molecular mediators (transcript, protein, and methylation abundances) infer the effect of these mediators on risk for disorders. One group of post-GWAS approaches is commonly referred to as transcriptome/proteome/methylome-wide association studies, which are abbreviated as T/P/MWAS (or collectively as XWAS). Since these approaches use biological mediators, the multiple testing burden is reduced to the number of genes (∼20,000) instead of millions of GWAS SNPs, which leads to increased signal detection. In this work, our aim is to uncover likely risk genes for NPSUDs by performing XWAS analyses in two tissues-blood and brain. First, to identify putative causal risk genes, we performed an XWAS using the Summary-data-based Mendelian randomization, which uses GWAS summary statistics, reference xQTL data, and a reference LD panel. Second, given the large comorbidities among NPSUDs and the shared cis-xQTLs between blood and the brain, we improved XWAS signal detection for underpowered analyses by performing joint concordance analyses between XWAS results i) across the two tissues and ii) across NPSUDs. All XWAS signals i) were adjusted for heterogeneity in dependent instruments (HEIDI) (non-causality) p-values and ii) used to test for pathway enrichment. The results suggest that there were widely shared gene/protein signals within the major histocompatibility complex region on chromosome 6 (BTN3A2 and C4A) and elsewhere in the genome (FURIN, NEK4, RERE, and ZDHHC5). The identification of putative molecular genes and pathways underlying risk may offer new targets for therapeutic development. Our study revealed an enrichment of XWAS signals in vitamin D and omega-3 gene sets. So, including vitamin D and omega-3 in treatment plans may have a modest but beneficial effect on patients with bipolar disorder.
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Affiliation(s)
- Huseyin Gedik
- Integrative Life Sciences, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States
| | - Tan Hoang Nguyen
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States
| | - Roseann E. Peterson
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY, United States
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, United States
| | - Christos Chatzinakos
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Psychiatry, McLean Hospital and Harvard Medical School, Belmont, MA, United States
| | - Vladimir I. Vladimirov
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ, United States
| | - Brien P. Riley
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States
| | - Silviu-Alin Bacanu
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States
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Pan L, Zheng C, Yang Z, Pawitan Y, Vu TN, Shen X. Hidden Genetic Regulation of Human Complex Traits via Brain Isoforms. Phenomics 2023; 3:217-227. [PMID: 37325708 PMCID: PMC10260721 DOI: 10.1007/s43657-023-00100-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 06/17/2023]
Abstract
Alternative splicing exists in most multi-exonic genes, and exploring these complex alternative splicing events and their resultant isoform expressions is essential. However, it has become conventional that RNA sequencing results have often been summarized into gene-level expression counts mainly due to the multiple ambiguous mapping of reads at highly similar regions. Transcript-level quantification and interpretation are often overlooked, and biological interpretations are often deduced based on combined transcript information at the gene level. Here, for the most variable tissue of alternative splicing, the brain, we estimate isoform expressions in 1,191 samples collected by the Genotype-Tissue Expression (GTEx) Consortium using a powerful method that we previously developed. We perform genome-wide association scans on the isoform ratios per gene and identify isoform-ratio quantitative trait loci (irQTL), which could not be detected by studying gene-level expressions alone. By analyzing the genetic architecture of the irQTL, we show that isoform ratios regulate educational attainment via multiple tissues including the frontal cortex (BA9), cortex, cervical spinal cord, and hippocampus. These tissues are also associated with different neuro-related traits, including Alzheimer's or dementia, mood swings, sleep duration, alcohol intake, intelligence, anxiety or depression, etc. Mendelian randomization (MR) analysis revealed 1,139 pairs of isoforms and neuro-related traits with plausible causal relationships, showing much stronger causal effects than on general diseases measured in the UK Biobank (UKB). Our results highlight essential transcript-level biomarkers in the human brain for neuro-related complex traits and diseases, which could be missed by merely investigating overall gene expressions. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-023-00100-6.
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Affiliation(s)
- Lu Pan
- Biostatistics Group, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 China
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177 Sweden
| | - Chenqing Zheng
- Biostatistics Group, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Zhijian Yang
- Biostatistics Group, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177 Sweden
| | - Trung Nghia Vu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177 Sweden
| | - Xia Shen
- Biostatistics Group, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 China
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177 Sweden
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458 China
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG UK
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40
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Yang Z, Wang C, Liu L, Khan A, Lee A, Vardarajan B, Mayeux R, Kiryluk K, Ionita-Laza I. CARMA is a new Bayesian model for fine-mapping in genome-wide association meta-analyses. Nat Genet 2023; 55:1057-1065. [PMID: 37169873 DOI: 10.1038/s41588-023-01392-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/11/2023] [Indexed: 05/13/2023]
Abstract
Fine-mapping is commonly used to identify putative causal variants at genome-wide significant loci. Here we propose a Bayesian model for fine-mapping that has several advantages over existing methods, including flexible specification of the prior distribution of effect sizes, joint modeling of summary statistics and functional annotations and accounting for discrepancies between summary statistics and external linkage disequilibrium in meta-analyses. Using simulations, we compare performance with commonly used fine-mapping methods and show that the proposed model has higher power and lower false discovery rate (FDR) when including functional annotations, and higher power, lower FDR and higher coverage for credible sets in meta-analyses. We further illustrate our approach by applying it to a meta-analysis of Alzheimer's disease genome-wide association studies where we prioritize putatively causal variants and genes.
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Affiliation(s)
- Zikun Yang
- Department of Biostatistics, Columbia University, New York City, NY, USA
| | - Chen Wang
- Department of Biostatistics, Columbia University, New York City, NY, USA
- Division of Nephrology Department of Medicine College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Linxi Liu
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Atlas Khan
- Division of Nephrology Department of Medicine College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Annie Lee
- Department of Neurology College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Badri Vardarajan
- Department of Neurology College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Richard Mayeux
- Department of Neurology College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Krzysztof Kiryluk
- Division of Nephrology Department of Medicine College of Physicians and Surgeons, Columbia University, New York City, NY, USA
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Xia C, Pickett SJ, Liewald DCM, Weiss A, Hudson G, Hill WD. The contributions of mitochondrial and nuclear mitochondrial genetic variation to neuroticism. Nat Commun 2023; 14:3146. [PMID: 37253732 DOI: 10.1038/s41467-023-38480-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 05/04/2023] [Indexed: 06/01/2023] Open
Abstract
Neuroticism is a heritable trait composed of separate facets, each conferring different levels of protection or risk, to health. By examining mitochondrial DNA in 269,506 individuals, we show mitochondrial haplogroups explain 0.07-0.01% of variance in neuroticism and identify five haplogroup and 15 mitochondria-marker associations across a general factor of neuroticism, and two special factors of anxiety/tension, and worry/vulnerability with effect sizes of the same magnitude as autosomal variants. Within-haplogroup genome-wide association studies identified H-haplogroup-specific autosomal effects explaining 1.4% variance of worry/vulnerability. These H-haplogroup-specific autosomal effects show a pleiotropic relationship with cognitive, physical and mental health that differs from that found when assessing autosomal effects across haplogroups. We identify interactions between chromosome 9 regions and mitochondrial haplogroups at P < 5 × 10-8, revealing associations between general neuroticism and anxiety/tension with brain-specific gene co-expression networks. These results indicate that the mitochondrial genome contributes toward neuroticism and the autosomal links between neuroticism and health.
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Affiliation(s)
- Charley Xia
- Lothian Birth Cohort studies, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Sarah J Pickett
- Wellcome Centre for Mitochondrial Research and Translational and Clinical Research Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - David C M Liewald
- Lothian Birth Cohort studies, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Alexander Weiss
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research and Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - W David Hill
- Lothian Birth Cohort studies, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.
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Aygün N, Liang D, Crouse WL, Keele GR, Love MI, Stein JL. Inferring cell-type-specific causal gene regulatory networks during human neurogenesis. Genome Biol 2023; 24:130. [PMID: 37254169 PMCID: PMC10230710 DOI: 10.1186/s13059-023-02959-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/05/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Genetic variation influences both chromatin accessibility, assessed in chromatin accessibility quantitative trait loci (caQTL) studies, and gene expression, assessed in expression QTL (eQTL) studies. Genetic variants can impact either nearby genes (cis-eQTLs) or distal genes (trans-eQTLs). Colocalization between caQTL and eQTL, or cis- and trans-eQTLs suggests that they share causal variants. However, pairwise colocalization between these molecular QTLs does not guarantee a causal relationship. Mediation analysis can be applied to assess the evidence supporting causality versus independence between molecular QTLs. Given that the function of QTLs can be cell-type-specific, we performed mediation analyses to find epigenetic and distal regulatory causal pathways for genes within two major cell types of the developing human cortex, progenitors and neurons. RESULTS We find that the expression of 168 and 38 genes is mediated by chromatin accessibility in progenitors and neurons, respectively. We also find that the expression of 11 and 12 downstream genes is mediated by upstream genes in progenitors and neurons. Moreover, we discover that a genetic locus associated with inter-individual differences in brain structure shows evidence for mediation of SLC26A7 through chromatin accessibility, identifying molecular mechanisms of a common variant association to a brain trait. CONCLUSIONS In this study, we identify cell-type-specific causal gene regulatory networks whereby the impacts of variants on gene expression were mediated by chromatin accessibility or distal gene expression. Identification of these causal paths will enable identifying and prioritizing actionable regulatory targets perturbing these key processes during neurodevelopment.
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Affiliation(s)
- Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Dan Liang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Wesley L Crouse
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Gregory R Keele
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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Little P, Liu S, Zhabotynsky V, Li Y, Lin DY, Sun W. A computational method for cell type-specific expression quantitative trait loci mapping using bulk RNA-seq data. Nat Commun 2023; 14:3030. [PMID: 37231002 PMCID: PMC10212972 DOI: 10.1038/s41467-023-38795-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
Mapping cell type-specific gene expression quantitative trait loci (ct-eQTLs) is a powerful way to investigate the genetic basis of complex traits. A popular method for ct-eQTL mapping is to assess the interaction between the genotype of a genetic locus and the abundance of a specific cell type using a linear model. However, this approach requires transforming RNA-seq count data, which distorts the relation between gene expression and cell type proportions and results in reduced power and/or inflated type I error. To address this issue, we have developed a statistical method called CSeQTL that allows for ct-eQTL mapping using bulk RNA-seq count data while taking advantage of allele-specific expression. We validated the results of CSeQTL through simulations and real data analysis, comparing CSeQTL results to those obtained from purified bulk RNA-seq data or single cell RNA-seq data. Using our ct-eQTL findings, we were able to identify cell types relevant to 21 categories of human traits.
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Affiliation(s)
- Paul Little
- Biostatistics Program, Public Health Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Si Liu
- Biostatistics Program, Public Health Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Vasyl Zhabotynsky
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dan-Yu Lin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wei Sun
- Biostatistics Program, Public Health Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biostatistics, University of Washington, Seattle, WA, USA.
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Wang H, Li Y, Cao W, Zhang J, Cao M, Meng X, Liu D, Wang Y. Leveraging IgG N-glycosylation to infer the causality between T2D and hypertension. Diabetol Metab Syndr 2023; 15:80. [PMID: 37095539 PMCID: PMC10127371 DOI: 10.1186/s13098-023-01053-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/07/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Observational studies demonstrated a bidirectional association between type 2 diabetes (T2D) and hypertension, whereas Mendelian randomization (MR) analyses supported the causality from T2D to hypertension but not causal from hypertension to T2D. We previously found that IgG N-glycosylation is associated with both T2D and hypertension, and thus IgG N-glycosylation might link the causality between them. METHODS We carried out a genome-wide association study (GWAS) to identify IgG N-glycosylation-quantitative-trait loci (QTLs) integrating GWAS for T2D and hypertension and then performed bidirectional univariable and multivariable MR analyses to infer the causal association among them. The inverse-variance-weighted (IVW) analysis was performed as the primary analysis, followed by some sensitivity analyses to explore the stability of the results. RESULTS Six putatively causal IgG N-glycans for T2D and four for hypertension were identified in the IVW method. Genetically predicted T2D increased the risk of hypertension (odds ratio [OR] = 1.177, 95% confidence interval (95% CI) = 1.037-1.338, P = 0.012) and vice versa (OR = 1.391, 95% CI = 1.081-1.790, P = 0.010). Multivariable MR showed that T2D remained at risk effect with hypertension ([OR] = 1.229, 95% CI = 1.140-1.325, P = 7.817 × 10-8) after conditioning on T2D-related IgG-glycans. Conversely, hypertension was associated with higher T2D risk (OR = 1.287, 95% CI = 1.107-1.497, P = 0.001) after adjusting for related IgG-glycans. No evidence of horizontal pleiotropy was observed, as MR‒Egger regression provided P values for intercept > 0.05. CONCLUSION Our study validated the mutual causality between T2D and hypertension from the perspective of IgG N-glycosylation, further validating the "common soil" hypothesis underlying the pathogenesis of T2D and hypertension.
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Affiliation(s)
- Haotian Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Xitoutiao, Beijing, 100069, China
| | - Yuan Li
- Lianyungang Maternal and Child Health Hospital, Lianyungang, 222062, Jiangsu, China
| | - Weijie Cao
- Centre for Precision Medicine, Edith Cowan University, Perth, 60127, Australia
| | - Jie Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Xitoutiao, Beijing, 100069, China
| | - Mingyang Cao
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Xitoutiao, Beijing, 100069, China
| | - Xiaoni Meng
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Xitoutiao, Beijing, 100069, China
| | - Di Liu
- Centre for Biomedical Information Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, University Town, Nanshan District, Shenzhen, 518055, Guangdong, China.
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Xitoutiao, Beijing, 100069, China.
- Centre for Precision Medicine, Edith Cowan University, Perth, 60127, Australia.
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Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K. Systematic visualisation of molecular QTLs reveals variant mechanisms at GWAS loci. bioRxiv 2023:2023.04.06.535816. [PMID: 37066341 PMCID: PMC10104061 DOI: 10.1101/2023.04.06.535816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Splicing quantitative trait loci (QTLs) have been implicated as a common mechanism underlying complex trait associations. However, utilising splicing QTLs in target discovery and prioritisation has been challenging due to extensive data normalisation which often renders the direction of the genetic effect as well as its magnitude difficult to interpret. This is further complicated by the fact that strong expression QTLs often manifest as weak splicing QTLs and vice versa, making it difficult to uniquely identify the underlying molecular mechanism at each locus. We find that these ambiguities can be mitigated by visualising the association between the genotype and average RNA sequencing read coverage in the region. Here, we generate these QTL coverage plots for 1.7 million molecular QTL associations in the eQTL Catalogue identified with five quantification methods. We illustrate the utility of these QTL coverage plots by performing colocalisation between vitamin D levels in the UK Biobank and all molecular QTLs in the eQTL Catalogue. We find that while visually confirmed splicing QTLs explain just 6/53 of the colocalising signals, they are significantly less pleiotropic than eQTLs and identify a prioritised causal gene in 4/6 cases. All our association summary statistics and QTL coverage plots are freely available at https://www.ebi.ac.uk/eqtl/.
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Affiliation(s)
- Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ralf Tambets
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - James D Hayhurst
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ida Rahu
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Peep Kolberg
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Uku Raudvere
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Ivan Kuzmin
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Anshika Chowdhary
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Andreas Vija
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Hans J Teras
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob Ulirsch
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - John Hardy
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Sebastian Guelfi
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Daniah Trabzuni
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Sarah Kim-Hellmuth
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich, Germany
| | - Will Rayner
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Hilary Finucane
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Abayomi Mosaku
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Parkinson
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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46
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Perini S, Filosi M, Domenici E. Candidate biomarkers from the integration of methylation and gene expression in discordant autistic sibling pairs. Transl Psychiatry 2023; 13:109. [PMID: 37012247 PMCID: PMC10070641 DOI: 10.1038/s41398-023-02407-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
While the genetics of autism spectrum disorders (ASD) has been intensively studied, resulting in the identification of over 100 putative risk genes, the epigenetics of ASD has received less attention, and results have been inconsistent across studies. We aimed to investigate the contribution of DNA methylation (DNAm) to the risk of ASD and identify candidate biomarkers arising from the interaction of epigenetic mechanisms with genotype, gene expression, and cellular proportions. We performed DNAm differential analysis using whole blood samples from 75 discordant sibling pairs of the Italian Autism Network collection and estimated their cellular composition. We studied the correlation between DNAm and gene expression accounting for the potential effects of different genotypes on DNAm. We showed that the proportion of NK cells was significantly reduced in ASD siblings suggesting an imbalance in their immune system. We identified differentially methylated regions (DMRs) involved in neurogenesis and synaptic organization. Among candidate loci for ASD, we detected a DMR mapping to CLEC11A (neighboring SHANK1) where DNAm and gene expression were significantly and negatively correlated, independently from genotype effects. As reported in previous studies, we confirmed the involvement of immune functions in the pathophysiology of ASD. Notwithstanding the complexity of the disorder, suitable biomarkers such as CLEC11A and its neighbor SHANK1 can be discovered using integrative analyses even with peripheral tissues.
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Affiliation(s)
- Samuel Perini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
| | - Michele Filosi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
- EURAC Research, Bolzano, Italy
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy.
- Fondazione The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy.
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Abstract
Genome-wide association studies reveal the complex polygenic architecture underlying psychiatric disorder risk, but there is an unmet need to validate causal variants, resolve their target genes(s), and explore their functional impacts on disorder-related mechanisms. Disorder-associated loci regulate transcription of target genes in a cell type- and context-specific manner, which can be measured through expression quantitative trait loci. In this review, we discuss methods and insights from context-specific modeling of genetically and environmentally regulated expression. Human induced pluripotent stem cell-derived cell type and organoid models have uncovered context-specific psychiatric disorder associations by investigating tissue-, cell type-, sex-, age-, and stressor-specific genetic regulation of expression. Techniques such as massively parallel reporter assays and pooled CRISPR (clustered regularly interspaced short palindromic repeats) screens make it possible to functionally fine-map genome-wide association study loci and validate their target genes at scale. Integration of disorder-associated contexts with these patient-specific human induced pluripotent stem cell models makes it possible to uncover gene by environment interactions that mediate disorder risk, which will ultimately improve our ability to diagnose and treat psychiatric disorders.
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Affiliation(s)
- Carina Seah
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York
| | - Laura M Huckins
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York; Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.
| | - Kristen J Brennand
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.
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48
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Wu S, Xue Q, Yang M, Wang Y, Kim P, Zhou X, Huang L. Genetic control of RNA editing in neurodegenerative disease. Brief Bioinform 2023; 24:bbad007. [PMID: 36681936 PMCID: PMC10387301 DOI: 10.1093/bib/bbad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/07/2022] [Accepted: 12/31/2022] [Indexed: 01/23/2023] Open
Abstract
A-to-I RNA editing diversifies human transcriptome to confer its functional effects on the downstream genes or regulations, potentially involving in neurodegenerative pathogenesis. Its variabilities are attributed to multiple regulators, including the key factor of genetic variants. To comprehensively investigate the potentials of neurodegenerative disease-susceptibility variants from the view of A-to-I RNA editing, we analyzed matched genetic and transcriptomic data of 1596 samples across nine brain tissues and whole blood from two large consortiums, Accelerating Medicines Partnership-Alzheimer's Disease and Parkinson's Progression Markers Initiative. The large-scale and genome-wide identification of 95 198 RNA editing quantitative trait loci revealed the preferred genetic effects on adjacent editing events. Furthermore, to explore the underlying mechanisms of the genetic controls of A-to-I RNA editing, several top RNA-binding proteins were pointed out, such as EIF4A3, U2AF2, NOP58, FBL, NOP56 and DHX9, since their regulations on multiple RNA-editing events were probably interfered by these genetic variants. Moreover, these variants may also contribute to the variability of other molecular phenotypes associated with RNA editing, including the functions of 3 proteins, expressions of 277 genes and splicing of 449 events. All the analyses results shown in NeuroEdQTL (https://relab.xidian.edu.cn/NeuroEdQTL/) constituted a unique resource for the understanding of neurodegenerative pathogenesis from genotypes to phenotypes related to A-to-I RNA editing.
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Affiliation(s)
- Sijia Wu
- School of Life Science and Technology, Xidian University, Xi’an 710071, China
| | - Qiuping Xue
- School of Life Science and Technology, Xidian University, Xi’an 710071, China
| | - Mengyuan Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yanfei Wang
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Pora Kim
- Corresponding authors: Liyu Huang, School of Life Science and Technology, Xidian University, Xi’an 710071, China. E-mail: ; Xiaobo Zhou, Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. E-mail: ; Pora Kim, Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. E-mail:
| | - Xiaobo Zhou
- Corresponding authors: Liyu Huang, School of Life Science and Technology, Xidian University, Xi’an 710071, China. E-mail: ; Xiaobo Zhou, Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. E-mail: ; Pora Kim, Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. E-mail:
| | - Liyu Huang
- Corresponding authors: Liyu Huang, School of Life Science and Technology, Xidian University, Xi’an 710071, China. E-mail: ; Xiaobo Zhou, Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. E-mail: ; Pora Kim, Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. E-mail:
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49
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Chen Z, Li X, Cui X, Zhang L, Liu Q, Lu Y, Wang X, Shi H, Ding M, Yang Y, Li W, Lv L. Association of CTNND2 gene polymorphism with schizophrenia: Two-sample case-control study in Chinese Han population. Int J Psychiatry Med 2023:912174231164669. [PMID: 36930964 DOI: 10.1177/00912174231164669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
OBJECTIVES Genetic factors play an important role in the etiology of schizophrenia (SZ). Catenin Delta 2 (CTNND2) is one of the genes regulating neuronal development in the brain. It is unclear whether CTNND2 is involved in SZ. With the hypothesis that CTNND2 may be a risk gene for SZ, we performed a case-control association analysis to investigate if CTNND2 gene single nucleotide polymorphisms (SNPs) are implicated in SZ in a Han Chinese northern population. MATERIALS AND METHODS We recruited subjects from 2010 to 2022 from the Han population of northern Henan and divided them into two case-control samples, including a discovery sample (SZ = 528 and control = 528) and replication sample (SZ = 2458 and control = 6914). Twenty-one SNPs were genotyped on the Illumina BeadStation 500G platform using GoldenGate technology and analyzed by PLINK. Positive and Negative Syndrome Scale (PANSS) was used to assess clinical symptoms. RESULTS Rs16901943, rs7733427, and rs2168878 SNPs were associated with SZ (Chi2 = 7.484, 11.576, and 5.391, respectively, df = 1; p = 0.006, 0.00067, and 0.02, respectively) in two samples. Rs10058868 was associated with SZ in male patients in the discovery sample (Chi2 = 6.264, df = 1, p = .044). Only rs7733427 survived Bonferroni correction. Linkage disequilibrium block three haplotypes were associated with SZ in the discovery and total sample. PANSS analysis of the four SNPs implicated rs10058868 and rs2168878 with symptoms of depression and excitement, respectively, in the SZ patients. CONCLUSION Four SNPs were identified as being correlated with SZ. The CTNND2 gene may be involved in susceptibility to SZ.
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Affiliation(s)
- Zhaonian Chen
- 34727The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Xiaojing Li
- 34727The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Xiangzheng Cui
- 34727The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Luwen Zhang
- 34727The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Qing Liu
- 34727The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Yanli Lu
- 34727The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Xiujuan Wang
- 34727The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Han Shi
- 34727The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Minli Ding
- 34727The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Yongfeng Yang
- 34727The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Wenqiang Li
- 34727The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Luxian Lv
- 34727The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
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50
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Cilleros-Portet A, Lesseur C, Marí S, Cosin-Tomas M, Lozano M, Irizar A, Burt A, García-Santisteban I, Martín DG, Escaramís G, Hernangomez-Laderas A, Soler-Blasco R, Breeze CE, Gonzalez-Garcia BP, Santa-Marina L, Chen J, Llop S, Fernández MF, Vrijhed M, Ibarluzea J, Guxens M, Marsit C, Bustamante M, Bilbao JR, Fernandez-Jimenez N. Potentially causal associations between placental DNA methylation and schizophrenia and other neuropsychiatric disorders. medRxiv 2023:2023.03.07.23286905. [PMID: 36945560 PMCID: PMC10029044 DOI: 10.1101/2023.03.07.23286905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Increasing evidence supports the role of placenta in neurodevelopment and potentially, in the later onset of neuropsychiatric disorders. Recently, methylation quantitative trait loci (mQTL) and interaction QTL (iQTL) maps have proven useful to understand SNP-genome wide association study (GWAS) relationships, otherwise missed by conventional expression QTLs. In this context, we propose that part of the genetic predisposition to complex neuropsychiatric disorders acts through placental DNA methylation (DNAm). We constructed the first public placental cis-mQTL database including nearly eight million mQTLs calculated in 368 fetal placenta DNA samples from the INMA project, ran cell type- and gestational age-imQTL models and combined those data with the summary statistics of the largest GWAS on 10 neuropsychiatric disorders using Summary-based Mendelian Randomization (SMR) and colocalization. Finally, we evaluated the influence of the DNAm sites identified on placental gene expression in the RICHS cohort. We found that placental cis-mQTLs are highly enriched in placenta-specific active chromatin regions, and useful to map the etiology of neuropsychiatric disorders at prenatal stages. Specifically, part of the genetic burden for schizophrenia, bipolar disorder and major depressive disorder confers risk through placental DNAm. The potential causality of several of the observed associations is reinforced by secondary association signals identified in conditional analyses, regional pleiotropic methylation signals associated to the same disorder, and cell type-imQTLs, additionally associated to the expression levels of relevant immune genes in placenta. In conclusion, the genetic risk of several neuropsychiatric disorders could operate, at least in part, through DNAm and associated gene expression in placenta.
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Affiliation(s)
- Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Corina Lesseur
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sergi Marí
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Marta Cosin-Tomas
- ISGlobal, Barcelona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Manuel Lozano
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de Valéncia, Valencia, Spain
- Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine Department, Universitat de València, Valencia, Spain
| | - Amaia Irizar
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Department of Preventive Medicine and Public Health, University of the Basque Country (UPV/EHU), Leioa, Spain
- Biodonostia Health Research Institute, 20013, San Sebastian, Spain
| | - Amber Burt
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Diego Garrido Martín
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona (UB), 08028 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Geòrgia Escaramís
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, Casanova 143, Barcelona, Spain
| | - Alba Hernangomez-Laderas
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Raquel Soler-Blasco
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de Valéncia, Valencia, Spain
- Department of Nursing, Universitat de València, Valencia, Spain
| | - Charles E. Breeze
- UCL Cancer Institute, University College London, 72 Huntley St, London WC1E 6DD, United Kingdom
| | - Bárbara P. Gonzalez-Garcia
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Loreto Santa-Marina
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Biodonostia Health Research Institute, 20013, San Sebastian, Spain
- Department of Health of the Basque Government, Subdirectorate of Public Health of Gipuzkoa, Avenida Navarra 4, 20013, San Sebastian, Spain
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sabrina Llop
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de Valéncia, Valencia, Spain
| | - Mariana F. Fernández
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Biomedical Research Center (CIBM) & Department of Radiology and Physical Medicine, School of Medicine University of Granada, 18016 Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| | - Martine Vrijhed
- ISGlobal, Barcelona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jesús Ibarluzea
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Biodonostia Health Research Institute, 20013, San Sebastian, Spain
- Department of Health of the Basque Government, Subdirectorate of Public Health of Gipuzkoa, Avenida Navarra 4, 20013, San Sebastian, Spain
| | - Mònica Guxens
- ISGlobal, Barcelona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
| | - Carmen Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Mariona Bustamante
- ISGlobal, Barcelona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), Leioa, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), Leioa, Spain
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