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Wen Y, Yang H, Hong Y. Transcriptomic Approaches to Cardiomyocyte-Biomaterial Interactions: A Review. ACS Biomater Sci Eng 2024. [PMID: 38934720 DOI: 10.1021/acsbiomaterials.4c00303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Biomaterials, essential for supporting, enhancing, and repairing damaged tissues, play a critical role in various medical applications. This Review focuses on the interaction of biomaterials and cardiomyocytes, emphasizing the unique significance of transcriptomic approaches in understanding their interactions, which are pivotal in cardiac bioengineering and regenerative medicine. Transcriptomic approaches serve as powerful tools to investigate how cardiomyocytes respond to biomaterials, shedding light on the gene expression patterns, regulatory pathways, and cellular processes involved in these interactions. Emerging technologies such as bulk RNA-seq, single-cell RNA-seq, single-nucleus RNA-seq, and spatial transcriptomics offer promising avenues for more precise and in-depth investigations. Longitudinal studies, pathway analyses, and machine learning techniques further improve the ability to explore the complex regulatory mechanisms involved. This review also discusses the challenges and opportunities of utilizing transcriptomic techniques in cardiomyocyte-biomaterial research. Although there are ongoing challenges such as costs, cell size limitation, sample differences, and complex analytical process, there exist exciting prospects in comprehensive gene expression analyses, biomaterial design, cardiac disease treatment, and drug testing. These multimodal methodologies have the capacity to deepen our understanding of the intricate interaction network between cardiomyocytes and biomaterials, potentially revolutionizing cardiac research with the aim of promoting heart health, and they are also promising for studying interactions between biomaterials and other cell types.
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Affiliation(s)
- Yufeng Wen
- Department of Bioengineering, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Huaxiao Yang
- Department of Biomedical Engineering, University of North Texas, Denton, Texas 76207, United States
| | - Yi Hong
- Department of Bioengineering, University of Texas at Arlington, Arlington, Texas 76019, United States
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2
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Glenn RA, Do SC, Guruvayurappan K, Corrigan EK, Santini L, Medina-Cano D, Singer S, Cho H, Liu J, Broman K, Czechanski A, Reinholdt L, Koche R, Furuta Y, Kunz M, Vierbuchen T. A PLURIPOTENT STEM CELL PLATFORM FOR IN VITRO SYSTEMS GENETICS STUDIES OF MOUSE DEVELOPMENT. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597758. [PMID: 38895226 PMCID: PMC11185710 DOI: 10.1101/2024.06.06.597758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The directed differentiation of pluripotent stem cells (PSCs) from panels of genetically diverse individuals is emerging as a powerful experimental system for characterizing the impact of natural genetic variation on developing cell types and tissues. Here, we establish new PSC lines and experimental approaches for modeling embryonic development in a genetically diverse, outbred mouse stock (Diversity Outbred mice). We show that a range of inbred and outbred PSC lines can be stably maintained in the primed pluripotent state (epiblast stem cells -- EpiSCs) and establish the contribution of genetic variation to phenotypic differences in gene regulation and directed differentiation. Using pooled in vitro fertilization, we generate and characterize a genetic reference panel of Diversity Outbred PSCs (n = 230). Finally, we demonstrate the feasibility of pooled culture of Diversity Outbred EpiSCs as "cell villages", which can facilitate the differentiation of large numbers of EpiSC lines for forward genetic screens. These data can complement and inform similar efforts within the stem cell biology and human genetics communities to model the impact of natural genetic variation on phenotypic variation and disease-risk.
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Affiliation(s)
- Rachel A. Glenn
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cell and Developmental Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Stephanie C. Do
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Emily K. Corrigan
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Present address: Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA and Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Laura Santini
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Medina-Cano
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah Singer
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hyein Cho
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jing Liu
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karl Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI USA
| | | | | | - Richard Koche
- Center for Epigenetics Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yasuhide Furuta
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meik Kunz
- The Bioinformatics CRO, Sanford Florida, 32771 USA
| | - Thomas Vierbuchen
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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3
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Nieto-Caballero VE, Reijneveld JF, Ruvalcaba A, Innocenzi G, Abeydeera N, Asgari S, Lopez K, Iwany SK, Luo Y, Nathan A, Fernandez-Salinas D, Chiñas M, Huang CC, Zhang Z, León SR, Calderon RI, Lecca L, Budzik JM, Murray M, Van Rhijn I, Raychaudhuri S, Moody DB, Suliman S, Gutierrez-Arcelus M. History of tuberculosis disease is associated with genetic regulatory variation in Peruvians. PLoS Genet 2024; 20:e1011313. [PMID: 38870230 PMCID: PMC11208071 DOI: 10.1371/journal.pgen.1011313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 06/26/2024] [Accepted: 05/21/2024] [Indexed: 06/15/2024] Open
Abstract
A quarter of humanity is estimated to have been exposed to Mycobacterium tuberculosis (Mtb) with a 5-10% risk of developing tuberculosis (TB) disease. Variability in responses to Mtb infection could be due to host or pathogen heterogeneity. Here, we focused on host genetic variation in a Peruvian population and its associations with gene regulation in monocyte-derived macrophages and dendritic cells (DCs). We recruited former household contacts of TB patients who previously progressed to TB (cases, n = 63) or did not progress to TB (controls, n = 63). Transcriptomic profiling of monocyte-derived DCs and macrophages measured the impact of genetic variants on gene expression by identifying expression quantitative trait loci (eQTL). We identified 330 and 257 eQTL genes in DCs and macrophages (False Discovery Rate (FDR) < 0.05), respectively. Four genes in DCs showed interaction between eQTL variants and TB progression status. The top eQTL interaction for a protein-coding gene was with FAH, the gene encoding fumarylacetoacetate hydrolase, which mediates the last step in mammalian tyrosine catabolism. FAH expression was associated with genetic regulatory variation in cases but not controls. Using public transcriptomic and epigenomic data of Mtb-infected monocyte-derived dendritic cells, we found that Mtb infection results in FAH downregulation and DNA methylation changes in the locus. Overall, this study demonstrates effects of genetic variation on gene expression levels that are dependent on history of infectious disease and highlights a candidate pathogenic mechanism through pathogen-response genes. Furthermore, our results point to tyrosine metabolism and related candidate TB progression pathways for further investigation.
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Affiliation(s)
- Victor E. Nieto-Caballero
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Undergraduate Program in Genomic Sciences, Center for Genomic Sciences, Universidad Nacional Autónoma de México (UNAM), Morelos, Mexico
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Josephine F. Reijneveld
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Angel Ruvalcaba
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Gabriel Innocenzi
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Nalin Abeydeera
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Samira Asgari
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Kattya Lopez
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Socios En Salud Sucursal Peru, Lima, Peru
| | - Sarah K. Iwany
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yang Luo
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Aparna Nathan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniela Fernandez-Salinas
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Marcos Chiñas
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Chuan-Chin Huang
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Zibiao Zhang
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Segundo R. León
- Socios En Salud Sucursal Peru, Lima, Peru
- Medical Technology School and Global Health Research Institute, San Juan Bautista Private University, Lima, Perú
| | | | | | - Jonathan M. Budzik
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Soumya Raychaudhuri
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - D. Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sara Suliman
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Gladstone-UCSF Institute of Genomic Immunology, University of California San Francisco, San Francisco, California, United States of America
- Chan Zuckerberg Initiative Biohub, San Francisco, California, United States of America
| | - Maria Gutierrez-Arcelus
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
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4
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Keener R, Chhetri SB, Connelly CJ, Taub MA, Conomos MP, Weinstock J, Ni B, Strober B, Aslibekyan S, Auer PL, Barwick L, Becker LC, Blangero J, Bleecker ER, Brody JA, Cade BE, Celedon JC, Chang YC, Cupples LA, Custer B, Freedman BI, Gladwin MT, Heckbert SR, Hou L, Irvin MR, Isasi CR, Johnsen JM, Kenny EE, Kooperberg C, Minster RL, Naseri T, Viali S, Nekhai S, Pankratz N, Peyser PA, Taylor KD, Telen MJ, Wu B, Yanek LR, Yang IV, Albert C, Arnett DK, Ashley-Koch AE, Barnes KC, Bis JC, Blackwell TW, Boerwinkle E, Burchard EG, Carson AP, Chen Z, Chen YDI, Darbar D, de Andrade M, Ellinor PT, Fornage M, Gelb BD, Gilliland FD, He J, Islam T, Kaab S, Kardia SLR, Kelly S, Konkle BA, Kumar R, Loos RJF, Martinez FD, McGarvey ST, Meyers DA, Mitchell BD, Montgomery CG, North KE, Palmer ND, Peralta JM, Raby BA, Redline S, Rich SS, Roden D, Rotter JI, Ruczinski I, Schwartz D, Sciurba F, Shoemaker MB, Silverman EK, Sinner MF, Smith NL, Smith AV, Tiwari HK, Vasan RS, Weiss ST, Williams LK, Zhang Y, Ziv E, Raffield LM, Reiner AP, Arvanitis M, Greider CW, Mathias RA, Battle A. Validation of human telomere length multi-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as human telomere length regulation genes. Nat Commun 2024; 15:4417. [PMID: 38789417 PMCID: PMC11126610 DOI: 10.1038/s41467-024-48394-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Genome-wide association studies (GWAS) have become well-powered to detect loci associated with telomere length. However, no prior work has validated genes nominated by GWAS to examine their role in telomere length regulation. We conducted a multi-ancestry meta-analysis of 211,369 individuals and identified five novel association signals. Enrichment analyses of chromatin state and cell-type heritability suggested that blood/immune cells are the most relevant cell type to examine telomere length association signals. We validated specific GWAS associations by overexpressing KBTBD6 or POP5 and demonstrated that both lengthened telomeres. CRISPR/Cas9 deletion of the predicted causal regions in K562 blood cells reduced expression of these genes, demonstrating that these loci are related to transcriptional regulation of KBTBD6 and POP5. Our results demonstrate the utility of telomere length GWAS in the identification of telomere length regulation mechanisms and validate KBTBD6 and POP5 as genes affecting telomere length regulation.
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Grants
- 5K12GM123914 U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- R01AG069120 U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- R35GM139580 U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- R01 DK071891 NIDDK NIH HHS
- R01HL153805 U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- R01AG081244 U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- R35CA209974 U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- R01HL105756 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01HL68959 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01HL079915 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01HL87681 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL153805 NHLBI NIH HHS
- R01HL-120393 U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
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Affiliation(s)
- Rebecca Keener
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Surya B Chhetri
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Carla J Connelly
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
| | - Margaret A Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Matthew P Conomos
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Joshua Weinstock
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Bohan Ni
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Benjamin Strober
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | | | - Paul L Auer
- Division of Biostatistics, Institute for Health & Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Lucas Barwick
- LTRC Data Coordinating Center, The Emmes Company, LLC, Rockville, MD, USA
| | - Lewis C Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Eugene R Bleecker
- Department of Medicine, Division of Genetics, Genomics and Precision Medicine, University of Arizona, Tucson, AZ, USA
- Division of Pharmacogenomics, University of Arizona, Tucson, AZ, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Juan C Celedon
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yi-Cheng Chang
- Department of Internal Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- The National Heart, Lung, and Blood Institute, Boston University's Framingham Heart Study, Framingham, MA, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Barry I Freedman
- Internal Medicine - Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Mark T Gladwin
- School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama Birmingham, Birmingham, AL, USA
| | - Carmen R Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jill M Johnsen
- Department of Medicine and Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Eimear E Kenny
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ryan L Minster
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Take Naseri
- Naseri & Associates Public Health Consultancy Firm and Family Health Clinic, Apia, Samoa
- International Health Institute, School of Public Health, Brown University, Providence, RI, USA
| | - Satupa'itea Viali
- Oceania University of Medicine, Apia, Samoa
- School of Medicine, National University of Samoa, Apia, Samoa
- Department of Chronic Disease Epidemiology, Yale University School of Public Health, New Haven, CT, USA
| | - Sergei Nekhai
- Center for Sickle Cell Disease and Department of Medicine, College of Medicine, Howard University, Washington DC, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marilyn J Telen
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Baojun Wu
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ivana V Yang
- Departments of Biomedical Informatics, Medicine, and Epidemiology, University of Colorado, Boulder, CO, USA
| | - Christine Albert
- Harvard Medical School, Boston, MA, USA
- Division of Cardiovascular, Brigham and Women's Hospital, Boston, MA, USA
| | - Donna K Arnett
- Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC, USA
| | | | - Kathleen C Barnes
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Thomas W Blackwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MI, USA
| | - Zhanghua Chen
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Dawood Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL, USA
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine, New York, NY, USA
| | - Frank D Gilliland
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jiang He
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Talat Islam
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stefan Kaab
- Department of Cardiology, University Hospital, LMU Munich, Munich, Germany
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Shannon Kelly
- Vitalant Research Institute, San Francisco, CA, USA
- University of California San Francisco Benioff Children's Hospital, Oakland, CA, USA
| | - Barbara A Konkle
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Rajesh Kumar
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- The Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fernando D Martinez
- Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Stephen T McGarvey
- Department of Epidemiology & International Health Institute, Brown University School of Public Health, Providence, RI, USA
| | - Deborah A Meyers
- Department of Medicine, Division of Genetics, Genomics and Precision Medicine, University of Arizona, Tucson, AZ, USA
- Division of Pharmacogenomics, University of Arizona, Tucson, AZ, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Courtney G Montgomery
- Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Juan M Peralta
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Benjamin A Raby
- Division of Pulmonary and Critical Care, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Susan Redline
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Dan Roden
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - David Schwartz
- Departments of Medicine and Immunology, University of Colorado, Boulder, CO, USA
| | - Frank Sciurba
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - M Benjamin Shoemaker
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Moritz F Sinner
- Department of Cardiology, University Hospital, LMU Munich, Munich, Germany
| | - Nicholas L Smith
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Hemant K Tiwari
- Department of Biostatistics, University of Alabama Birmingham, Birmingham, AL, USA
| | | | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Yingze Zhang
- Division of Pulmonary Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Elad Ziv
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Marios Arvanitis
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, USA
| | - Carol W Greider
- Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- University Professor Johns Hopkins University, Baltimore, MD, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA.
- Data Science and AI Institute, Johns Hopkins University, Baltimore, MD, USA.
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5
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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] [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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6
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Popp JM, Rhodes K, Jangi R, Li M, Barr K, Tayeb K, Battle A, Gilad Y. Cell-type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592174. [PMID: 38746382 PMCID: PMC11092595 DOI: 10.1101/2024.05.02.592174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Identifying the molecular effects of human genetic variation across cellular contexts is crucial for understanding the mechanisms underlying disease-associated loci, yet many cell-types and developmental stages remain underexplored. Here we harnessed the potential of heterogeneous differentiating cultures ( HDCs ), an in vitro system in which pluripotent cells asynchronously differentiate into a broad spectrum of cell-types. We generated HDCs for 53 human donors and collected single-cell RNA-sequencing data from over 900,000 cells. We identified expression quantitative trait loci in 29 cell-types and characterized regulatory dynamics across diverse differentiation trajectories. This revealed novel regulatory variants for genes involved in key developmental and disease-related processes while replicating known effects from primary tissues, and dynamic regulatory effects associated with a range of complex traits.
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7
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Randolph HE, Aracena KA, Lin YL, Mu Z, Barreiro LB. Shaping immunity: The influence of natural selection on population immune diversity. Immunol Rev 2024; 323:227-240. [PMID: 38577999 DOI: 10.1111/imr.13329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Humans exhibit considerable variability in their immune responses to the same immune challenges. Such variation is widespread and affects individual and population-level susceptibility to infectious diseases and immune disorders. Although the factors influencing immune response diversity are partially understood, what mechanisms lead to the wide range of immune traits in healthy individuals remain largely unexplained. Here, we discuss the role that natural selection has played in driving phenotypic differences in immune responses across populations and present-day susceptibility to immune-related disorders. Further, we touch on future directions in the field of immunogenomics, highlighting the value of expanding this work to human populations globally, the utility of modeling the immune response as a dynamic process, and the importance of considering the potential polygenic nature of natural selection. Identifying loci acted upon by evolution may further pinpoint variants critically involved in disease etiology, and designing studies to capture these effects will enrich our understanding of the genetic contributions to immunity and immune dysregulation.
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Affiliation(s)
- Haley E Randolph
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Yen-Lung Lin
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Zepeng Mu
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Luis B Barreiro
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
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8
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Xia J, Li Y, Zhu H, Xue F, Shi F, Li N. A Bayesian Change Point Model for Dynamic Alternative Transcription Start Site Usage During Cellular Differentiation. J Comput Biol 2024; 31:445-457. [PMID: 38752891 DOI: 10.1089/cmb.2023.0174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024] Open
Abstract
ABSTRACT An alternative transcription start site (ATSS) is a major driving force for increasing the complexity of transcripts in human tissues. As a transcriptional regulatory mechanism, ATSS has biological significance. Many studies have confirmed that ATSS plays an important role in diseases and cell development and differentiation. However, exploration of its dynamic mechanisms remains insufficient. Identifying ATSS change points during cell differentiation is critical for elucidating potential dynamic mechanisms. For relative ATSS usage as percentage data, the existing methods lack sensitivity to detect the change point for ATSS longitudinal data. In addition, some methods have strict requirements for data distribution and cannot be applied to deal with this problem. In this study, the Bayesian change point detection model was first constructed using reparameterization techniques for two parameters of a beta distribution for the percentage data type, and the posterior distributions of parameters and change points were obtained using Markov Chain Monte Carlo (MCMC) sampling. With comprehensive simulation studies, the performance of the Bayesian change point detection model is found to be consistently powerful and robust across most scenarios with different sample sizes and beta distributions. Second, differential ATSS events in the real data, whose change points were identified using our method, were clustered according to their change points. Last, for each change point, pathway and transcription factor motif analyses were performed on its differential ATSS events. The results of our analyses demonstrated the effectiveness of the Bayesian change point detection model and provided biological insights into cell differentiation.
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Affiliation(s)
- Juan Xia
- Department of Mathematics, College of Informatics, Huazhong Agricultural University, Wuhan, P.R. China
| | - Yuxia Li
- Department of Mathematics, College of Informatics, Huazhong Agricultural University, Wuhan, P.R. China
| | - Haotian Zhu
- College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, P.R. China
| | - Feiyang Xue
- College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, P.R. China
| | - Feng Shi
- Department of Mathematics, College of Informatics, Huazhong Agricultural University, Wuhan, P.R. China
| | - Nana Li
- Department of Mathematics, College of Informatics, Huazhong Agricultural University, Wuhan, P.R. China
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9
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Farbehi N, Neavin DR, Cuomo ASE, Studer L, MacArthur DG, Powell JE. Integrating population genetics, stem cell biology and cellular genomics to study complex human diseases. Nat Genet 2024; 56:758-766. [PMID: 38741017 DOI: 10.1038/s41588-024-01731-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/20/2024] [Indexed: 05/16/2024]
Abstract
Human pluripotent stem (hPS) cells can, in theory, be differentiated into any cell type, making them a powerful in vitro model for human biology. Recent technological advances have facilitated large-scale hPS cell studies that allow investigation of the genetic regulation of molecular phenotypes and their contribution to high-order phenotypes such as human disease. Integrating hPS cells with single-cell sequencing makes identifying context-dependent genetic effects during cell development or upon experimental manipulation possible. Here we discuss how the intersection of stem cell biology, population genetics and cellular genomics can help resolve the functional consequences of human genetic variation. We examine the critical challenges of integrating these fields and approaches to scaling them cost-effectively and practically. We highlight two areas of human biology that can particularly benefit from population-scale hPS cell studies, elucidating mechanisms underlying complex disease risk loci and evaluating relationships between common genetic variation and pharmacotherapeutic phenotypes.
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Affiliation(s)
- Nona Farbehi
- Garvan Weizmann Center for Cellular Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA
| | - Drew R Neavin
- Garvan Weizmann Center for Cellular Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Anna S E Cuomo
- Garvan Weizmann Center for Cellular Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research, University of New South Wales, Sydney, New South Wales, Australia
| | - Lorenz Studer
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA
- The Center for Stem Cell Biology and Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research, University of New South Wales, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Joseph E Powell
- Garvan Weizmann Center for Cellular Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA.
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia.
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10
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Yang L, Bu X, Lu X, Wan J, Zhang X, Zhang W, Zhong L. SERS-based long-term mitochondrial pH monitoring during differentiation of human induced pluripotent stem cells to neural progenitor cells. BIOMEDICAL OPTICS EXPRESS 2024; 15:2926-2936. [PMID: 38855674 PMCID: PMC11161384 DOI: 10.1364/boe.519931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 06/11/2024]
Abstract
As one of the important organelles in the process of cell differentiation, mitochondria regulate the whole process of differentiation by participating in energy supply and information transmission. Mitochondrial pH value is a key indicator of mitochondrial function. Therefore, real-time monitoring of mitochondrial pH value during cell differentiation is of great significance for understanding cell biochemical processes and exploring differentiation mechanisms. In this study, Surface-enhanced Raman scattering (SERS) technology was used to achieve the real-time monitoring of mitochondrial pH during induced pluripotent stem cells (iPSCs) differentiation into neural progenitor cells (NPCs). The results showed that the variation trend of mitochondrial pH in normal and abnormal differentiated batches was different. The mitochondrial pH value of normal differentiated cells continued to decline from iPSCs to embryoid bodies (EB) day 4, and continued to rise from EB day 4 to the NPCs stage, and the mitochondrial microenvironment of iPSCs to NPCs differentiation became acidic. In contrast, the mitochondrial pH value of abnormally differentiated cells declined continuously during differentiation. This study improves the information on acid-base balance during cell differentiation and may provide a basis for further understanding of the changes and regulatory mechanisms of mitochondrial metabolism during cell differentiation. This also helps to improve more accurate and useful differentiation protocols based on the microenvironment within the mitochondria, improving the efficiency of cell differentiation.
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Affiliation(s)
- Liwei Yang
- Guangdong Provincial Key Laboratory of Nanophotonic Functional Materials and Devices, South China Normal University, Guangzhou 510006, China
| | - Xiaoya Bu
- Guangdong Provincial Key Laboratory of Nanophotonic Functional Materials and Devices, South China Normal University, Guangzhou 510006, China
| | - Xiaoxu Lu
- Guangdong Provincial Key Laboratory of Nanophotonic Functional Materials and Devices, South China Normal University, Guangzhou 510006, China
| | - Jianhui Wan
- Key Laboratory of Photonics Technology for Integrated Sensing and Communication of Ministry of Education, Guangdong University of Technology, Guangzhou 510006, China
| | - Xiao Zhang
- Key Laboratory of Photonics Technology for Integrated Sensing and Communication of Ministry of Education, Guangdong University of Technology, Guangzhou 510006, China
| | - Weina Zhang
- Key Laboratory of Photonics Technology for Integrated Sensing and Communication of Ministry of Education, Guangdong University of Technology, Guangzhou 510006, China
| | - Liyun Zhong
- Key Laboratory of Photonics Technology for Integrated Sensing and Communication of Ministry of Education, Guangdong University of Technology, Guangzhou 510006, China
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11
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Arthur TD, Nguyen JP, D'Antonio-Chronowska A, Jaureguy J, Silva N, Henson B, Panopoulos AD, Belmonte JCI, D'Antonio M, McVicker G, Frazer KA. Multi-omic QTL mapping in early developmental tissues reveals phenotypic and temporal complexity of regulatory variants underlying GWAS loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588874. [PMID: 38645112 PMCID: PMC11030419 DOI: 10.1101/2024.04.10.588874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Most GWAS loci are presumed to affect gene regulation, however, only ∼43% colocalize with expression quantitative trait loci (eQTLs). To address this colocalization gap, we identify eQTLs, chromatin accessibility QTLs (caQTLs), and histone acetylation QTLs (haQTLs) using molecular samples from three early developmental (EDev) tissues. Through colocalization, we annotate 586 GWAS loci for 17 traits by QTL complexity, QTL phenotype, and QTL temporal specificity. We show that GWAS loci are highly enriched for colocalization with complex QTL modules that affect multiple elements (genes and/or peaks). We also demonstrate that caQTLs and haQTLs capture regulatory variations not associated with eQTLs and explain ∼49% of the functionally annotated GWAS loci. Additionally, we show that EDev-unique QTLs are strongly depleted for colocalizing with GWAS loci. By conducting one of the largest multi-omic QTL studies to date, we demonstrate that many GWAS loci exhibit phenotypic complexity and therefore, are missed by traditional eQTL analyses.
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12
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Sakaue S, Weinand K, Isaac S, Dey KK, Jagadeesh K, Kanai M, Watts GFM, Zhu Z, Brenner MB, McDavid A, Donlin LT, Wei K, Price AL, Raychaudhuri S. Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nat Genet 2024; 56:615-626. [PMID: 38594305 DOI: 10.1038/s41588-024-01682-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 02/07/2024] [Indexed: 04/11/2024]
Abstract
Translating genome-wide association study (GWAS) loci into causal variants and genes requires accurate cell-type-specific enhancer-gene maps from disease-relevant tissues. Building enhancer-gene maps is essential but challenging with current experimental methods in primary human tissues. Here we developed a nonparametric statistical method, SCENT (single-cell enhancer target gene mapping), that models association between enhancer chromatin accessibility and gene expression in single-cell or nucleus multimodal RNA sequencing and ATAC sequencing data. We applied SCENT to 9 multimodal datasets including >120,000 single cells or nuclei and created 23 cell-type-specific enhancer-gene maps. These maps were highly enriched for causal variants in expression quantitative loci and GWAS for 1,143 diseases and traits. We identified likely causal genes for both common and rare diseases and linked somatic mutation hotspots to target genes. We demonstrate that application of SCENT to multimodal data from disease-relevant human tissue enables the scalable construction of accurate cell-type-specific enhancer-gene maps, essential for defining noncoding variant function.
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Affiliation(s)
- Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathryn Weinand
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Shakson Isaac
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kushal K Dey
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Karthik Jagadeesh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Masahiro Kanai
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Gerald F M Watts
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhu Zhu
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrew McDavid
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Laura T Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alkes L Price
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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13
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Natri HM, Del Azodi CB, Peter L, Taylor CJ, Chugh S, Kendle R, Chung MI, Flaherty DK, Matlock BK, Calvi CL, Blackwell TS, Ware LB, Bacchetta M, Walia R, Shaver CM, Kropski JA, McCarthy DJ, Banovich NE. Cell-type-specific and disease-associated expression quantitative trait loci in the human lung. Nat Genet 2024; 56:595-604. [PMID: 38548990 PMCID: PMC11018522 DOI: 10.1038/s41588-024-01702-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 02/28/2024] [Indexed: 04/04/2024]
Abstract
Common genetic variants confer substantial risk for chronic lung diseases, including pulmonary fibrosis. Defining the genetic control of gene expression in a cell-type-specific and context-dependent manner is critical for understanding the mechanisms through which genetic variation influences complex traits and disease pathobiology. To this end, we performed single-cell RNA sequencing of lung tissue from 66 individuals with pulmonary fibrosis and 48 unaffected donors. Using a pseudobulk approach, we mapped expression quantitative trait loci (eQTLs) across 38 cell types, observing both shared and cell-type-specific regulatory effects. Furthermore, we identified disease interaction eQTLs and demonstrated that this class of associations is more likely to be cell-type-specific and linked to cellular dysregulation in pulmonary fibrosis. Finally, we connected lung disease risk variants to their regulatory targets in disease-relevant cell types. These results indicate that cellular context determines the impact of genetic variation on gene expression and implicates context-specific eQTLs as key regulators of lung homeostasis and disease.
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Affiliation(s)
- Heini M Natri
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Christina B Del Azodi
- St. Vincent's Institute of Medical Research, Melbourne, Victoria, Australia
- Melbourne Integrative Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Lance Peter
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chase J Taylor
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sagrika Chugh
- St. Vincent's Institute of Medical Research, Melbourne, Victoria, Australia
- Melbourne Integrative Genomics, University of Melbourne, Melbourne, Victoria, Australia
- School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, Victoria, Australia
| | - Robert Kendle
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Mei-I Chung
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - David K Flaherty
- Flow Cytometry Shared Resource, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brittany K Matlock
- Flow Cytometry Shared Resource, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Carla L Calvi
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy S Blackwell
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
| | - Lorraine B Ware
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew Bacchetta
- Department of Cardiac Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rajat Walia
- Department of Thoracic Disease and Transplantation, Norton Thoracic Institute, Phoenix, AZ, USA
| | - Ciara M Shaver
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan A Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
| | - Davis J McCarthy
- St. Vincent's Institute of Medical Research, Melbourne, Victoria, Australia
- Melbourne Integrative Genomics, University of Melbourne, Melbourne, Victoria, Australia
- School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, Victoria, Australia
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14
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Lin W, Wall JD, Li G, Newman D, Yang Y, Abney M, VandeBerg JL, Olivier M, Gilad Y, Cox LA. Genetic regulatory effects in response to a high-cholesterol, high-fat diet in baboons. CELL GENOMICS 2024; 4:100509. [PMID: 38430910 PMCID: PMC10943580 DOI: 10.1016/j.xgen.2024.100509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/20/2023] [Accepted: 02/05/2024] [Indexed: 03/05/2024]
Abstract
Steady-state expression quantitative trait loci (eQTLs) explain only a fraction of disease-associated loci identified through genome-wide association studies (GWASs), while eQTLs involved in gene-by-environment (GxE) interactions have rarely been characterized in humans due to experimental challenges. Using a baboon model, we found hundreds of eQTLs that emerge in adipose, liver, and muscle after prolonged exposure to high dietary fat and cholesterol. Diet-responsive eQTLs exhibit genomic localization and genic features that are distinct from steady-state eQTLs. Furthermore, the human orthologs associated with diet-responsive eQTLs are enriched for GWAS genes associated with human metabolic traits, suggesting that context-responsive eQTLs with more complex regulatory effects are likely to explain GWAS hits that do not seem to overlap with standard eQTLs. Our results highlight the complexity of genetic regulatory effects and the potential of eQTLs with disease-relevant GxE interactions in enhancing the understanding of GWAS signals for human complex disease using non-human primate models.
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Affiliation(s)
- Wenhe Lin
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA.
| | - Jeffrey D Wall
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ge Li
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Deborah Newman
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78229, USA
| | - Yunqi Yang
- Committee on Genetics, Genomics and System Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Mark Abney
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - John L VandeBerg
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA
| | - Michael Olivier
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Yoav Gilad
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA; Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL 60637, USA.
| | - Laura A Cox
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78229, USA.
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15
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Lappalainen T, Li YI, Ramachandran S, Gusev A. Genetic and molecular architecture of complex traits. Cell 2024; 187:1059-1075. [PMID: 38428388 DOI: 10.1016/j.cell.2024.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/20/2023] [Accepted: 01/16/2024] [Indexed: 03/03/2024]
Abstract
Human genetics has emerged as one of the most dynamic areas of biology, with a broadening societal impact. In this review, we discuss recent achievements, ongoing efforts, and future challenges in the field. Advances in technology, statistical methods, and the growing scale of research efforts have all provided many insights into the processes that have given rise to the current patterns of genetic variation. Vast maps of genetic associations with human traits and diseases have allowed characterization of their genetic architecture. Finally, studies of molecular and cellular effects of genetic variants have provided insights into biological processes underlying disease. Many outstanding questions remain, but the field is well poised for groundbreaking discoveries as it increases the use of genetic data to understand both the history of our species and its applications to improve human health.
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Affiliation(s)
- Tuuli Lappalainen
- New York Genome Center, New York, NY, USA; Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Yang I Li
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Sohini Ramachandran
- Ecology, Evolution and Organismal Biology, Center for Computational Molecular Biology, and the Data Science Institute, Brown University, Providence, RI 029129, USA
| | - Alexander Gusev
- Harvard Medical School and Dana-Farber Cancer Institute, Boston, MA, USA
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16
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McIntire E, Barr KA, Gonzales NM, Gilad Y. Guided Differentiation of Pluripotent Stem Cells for Cardiac Cell Diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.21.550072. [PMID: 37502898 PMCID: PMC10370173 DOI: 10.1101/2023.07.21.550072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
We have developed a guided differentiation protocol for induced pluripotent stem cells (iPSCs) that rapidly generates a temporally and functionally diverse set of cardiac-relevant cell types. By leveraging techniques used in embryoid body and cardiac organoid generation, we produce both progenitor and terminal cardiac cell types concomitantly in just 10 days. Our results show that guided differentiation generates functionally relevant cardiac cell types that closely align with the transcriptional profiles of cells from differentiation time-course collections, mature cardiac organoids, and in vivo heart tissue. Guided differentiation prioritizes simplicity by minimizing the number of reagents and steps required, thereby enabling rapid and cost-effective experimental throughput. We expect this approach will provide a scalable cardiac model for population-level studies of gene regulatory variation and gene-by-environment interactions.
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Affiliation(s)
- Erik McIntire
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Kenneth A Barr
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Natalia M Gonzales
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
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17
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Panten J, Heinen T, Ernst C, Eling N, Wagner RE, Satorius M, Marioni JC, Stegle O, Odom DT. The dynamic genetic determinants of increased transcriptional divergence in spermatids. Nat Commun 2024; 15:1272. [PMID: 38341412 PMCID: PMC10858866 DOI: 10.1038/s41467-024-45133-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify allele-specific expression during spermatogenic differentiation at single-cell resolution in an F1 hybrid mouse system, allowing for the comprehensive characterisation of cis- and trans-genetic effects, including their dynamics across cellular differentiation. Collectively, almost half of the genes subject to genetic regulation show evidence for dynamic cis-effects that vary during differentiation. Our system also allows us to robustly identify dynamic trans-effects, which are less pervasive than cis-effects. In aggregate, genetic effects were strongest in round spermatids, which parallels their increased transcriptional divergence we identified between species. Our approach provides a comprehensive quantification of the variability of genetic effects in vivo, and demonstrates a widely applicable strategy to dissect the impact of regulatory variants on gene regulation in dynamic systems.
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Affiliation(s)
- Jasper Panten
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
| | - Tobias Heinen
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Faculty of Mathematics and Computer Science, Heidelberg University, Heidelberg, Germany
- European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany
| | - Christina Ernst
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Nils Eling
- University of Zurich, Department of Quantitative Biomedicine, Zurich, 8057, Switzerland
- ETH Zurich, Institute for Molecular Health Sciences, Zurich, 8093, Switzerland
| | - Rebecca E Wagner
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
- Division of Mechanisms Regulating Gene Expression, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Maja Satorius
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Oliver Stegle
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany.
- European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.
| | - Duncan T Odom
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany.
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
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18
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Boye C, Kalita CA, Findley AS, Alazizi A, Wei J, Wen X, Pique-Regi R, Luca F. Characterization of caffeine response regulatory variants in vascular endothelial cells. eLife 2024; 13:e85235. [PMID: 38334359 PMCID: PMC10901511 DOI: 10.7554/elife.85235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/08/2024] [Indexed: 02/10/2024] Open
Abstract
Genetic variants in gene regulatory sequences can modify gene expression and mediate the molecular response to environmental stimuli. In addition, genotype-environment interactions (GxE) contribute to complex traits such as cardiovascular disease. Caffeine is the most widely consumed stimulant and is known to produce a vascular response. To investigate GxE for caffeine, we treated vascular endothelial cells with caffeine and used a massively parallel reporter assay to measure allelic effects on gene regulation for over 43,000 genetic variants. We identified 665 variants with allelic effects on gene regulation and 6 variants that regulate the gene expression response to caffeine (GxE, false discovery rate [FDR] < 5%). When overlapping our GxE results with expression quantitative trait loci colocalized with coronary artery disease and hypertension, we dissected their regulatory mechanisms and showed a modulatory role for caffeine. Our results demonstrate that massively parallel reporter assay is a powerful approach to identify and molecularly characterize GxE in the specific context of caffeine consumption.
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Affiliation(s)
- Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Cynthia A Kalita
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Anthony S Findley
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Xiaoquan Wen
- Department of Biostatistics, University of MichiganAnn ArborUnited States
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
- Department of Obstetrics and Gynecology, Wayne State UniversityDetroitUnited States
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
- Department of Obstetrics and Gynecology, Wayne State UniversityDetroitUnited States
- Department of Biology, University of Rome Tor VergataRomeItaly
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19
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Strober BJ, Tayeb K, Popp J, Qi G, Gordon MG, Perez R, Ye CJ, Battle A. SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models. Genome Biol 2024; 25:28. [PMID: 38254214 PMCID: PMC10801966 DOI: 10.1186/s13059-023-03152-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Genetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and environmental conditions. We developed SURGE, a method for unsupervised discovery of context-specific expression quantitative trait loci (eQTLs) from single-cell transcriptomic data. This allows discovery of the contexts or cell types modulating genetic regulation without prior knowledge. Applied to peripheral blood single-cell eQTL data, SURGE contexts capture continuous representations of distinct cell types and groupings of biologically related cell types. We demonstrate the disease-relevance of SURGE context-specific eQTLs using colocalization analysis and stratified LD-score regression.
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Affiliation(s)
- Benjamin J Strober
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Karl Tayeb
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Joshua Popp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Guanghao Qi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - M Grace Gordon
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Richard Perez
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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20
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Boocock J, Alexander N, Tapia LA, Walter-McNeill L, Munugala C, Bloom JS, Kruglyak L. Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570640. [PMID: 38106186 PMCID: PMC10723400 DOI: 10.1101/2023.12.07.570640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Expression quantitative trait loci (eQTLs) provide a key bridge between noncoding DNA sequence variants and organismal traits. The effects of eQTLs can differ among tissues, cell types, and cellular states, but these differences are obscured by gene expression measurements in bulk populations. We developed a one-pot approach to map eQTLs in Saccharomyces cerevisiae by single-cell RNA sequencing (scRNA-seq) and applied it to over 100,000 single cells from three crosses. We used scRNA-seq data to genotype each cell, measure gene expression, and classify the cells by cell-cycle stage. We mapped thousands of local and distant eQTLs and identified interactions between eQTL effects and cell-cycle stages. We took advantage of single-cell expression information to identify hundreds of genes with allele-specific effects on expression noise. We used cell-cycle stage classification to map 20 loci that influence cell-cycle progression. One of these loci influenced the expression of genes involved in the mating response. We showed that the effects of this locus arise from a common variant (W82R) in the gene GPA1, which encodes a signaling protein that negatively regulates the mating pathway. The 82R allele increases mating efficiency at the cost of slower cell-cycle progression and is associated with a higher rate of outcrossing in nature. Our results provide a more granular picture of the effects of genetic variants on gene expression and downstream traits.
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Affiliation(s)
- James Boocock
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Noah Alexander
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Leslie Alamo Tapia
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Laura Walter-McNeill
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Chetan Munugala
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Joshua S Bloom
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Leonid Kruglyak
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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21
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Abe H, Lin P, Zhou D, Ruderfer DM, Gamazon ER. Mapping the landscape of lineage-specific dynamic regulation of gene expression using single-cell transcriptomics and application to genetics of complex disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.24.23297476. [PMID: 37961453 PMCID: PMC10635195 DOI: 10.1101/2023.10.24.23297476] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Single-cell transcriptome data can provide insights into how genetic variation influences biological processes involved in human biology and disease. However, the identification of gene-level associations in distinct cell types faces several challenges, including the limited reference resource from population scale studies, data sparsity in single-cell RNA sequencing, and the complex cell-state pattern of expression within individual cell types. Here we develop genetic models of cell type specific and cell state adjusted gene expression in mid-brain neurons in the process of specializing from induced pluripotent stem cells. The resulting framework quantifies the dynamics of the genetic regulation of gene expression and estimates its cell type specificity. As an application, we show that the approach detects known and new genes associated with schizophrenia and enables insights into context-dependent disease mechanisms. We provide a genomic resource from a phenome-wide application of our models to more than 1500 phenotypes from the UK Biobank. Using longitudinal genetically determined expression, we implement a predictive causality framework, evaluating the prediction of future values of a target gene expression using prior values of a putative regulatory gene. Collectively, this work demonstrates the insights that can be gained into the molecular underpinnings of diseases by quantifying the genetic control of gene expression at single-cell resolution.
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Affiliation(s)
- Hanna Abe
- Vanderbilt University, Nashville, TN
| | - Phillip Lin
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Dan Zhou
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Douglas M Ruderfer
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Biomedical Informatics and Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Clare Hall, University of Cambridge, Cambridge, England
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22
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Adegunsoye A, Gonzales NM, Gilad Y. Induced Pluripotent Stem Cells in Disease Biology and the Evidence for Their In Vitro Utility. Annu Rev Genet 2023; 57:341-360. [PMID: 37708421 DOI: 10.1146/annurev-genet-022123-090319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Many human phenotypes are impossible to recapitulate in model organisms or immortalized human cell lines. Induced pluripotent stem cells (iPSCs) offer a way to study disease mechanisms in a variety of differentiated cell types while circumventing ethical and practical issues associated with finite tissue sources and postmortem states. Here, we discuss the broad utility of iPSCs in genetic medicine and describe how they are being used to study musculoskeletal, pulmonary, neurologic, and cardiac phenotypes. We summarize the particular challenges presented by each organ system and describe how iPSC models are being used to address them. Finally, we discuss emerging iPSC-derived organoid models and the potential value that they can bring to studies of human disease.
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Affiliation(s)
- Ayodeji Adegunsoye
- Genetics, Genomics, and Systems Biology, Section of Pulmonary and Critical Care, and the Department of Medicine, University of Chicago, Chicago, Illinois, USA;
| | - Natalia M Gonzales
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA; ,
| | - Yoav Gilad
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA; ,
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
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23
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Lin W, Wall JD, Li G, Newman D, Yang Y, Abney M, VandeBerg JL, Olivier M, Gilad Y, Cox LA. Genetic regulatory effects in response to a high cholesterol, high fat diet in baboons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551489. [PMID: 37577666 PMCID: PMC10418186 DOI: 10.1101/2023.08.01.551489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Steady-state expression quantitative trait loci (eQTLs) explain only a fraction of disease-associated loci identified through genome-wide association studies (GWAS), while eQTLs involved in gene-by-environment (GxE) interactions have rarely been characterized in humans due to experimental challenges. Using a baboon model, we found hundreds of eQTLs that emerge in adipose, liver, and muscle after prolonged exposure to high dietary fat and cholesterol. Diet-responsive eQTLs exhibit genomic localization and genic features that are distinct from steady-state eQTLs. Furthermore, the human orthologs associated with diet-responsive eQTLs are enriched for GWAS genes associated with human metabolic traits, suggesting that context-responsive eQTLs with more complex regulatory effects are likely to explain GWAS hits that do not seem to overlap with standard eQTLs. Our results highlight the complexity of genetic regulatory effects and the potential of eQTLs with disease-relevant GxE interactions in enhancing the understanding of GWAS signals for human complex disease using nonhuman primate models.
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Affiliation(s)
- Wenhe Lin
- Department of Human Genetics, The University of Chicago, Chicago, USA
| | - Jeffrey D. Wall
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Present address: Galatea Bio, Hialeah, FL, USA
| | - Ge Li
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Deborah Newman
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Yunqi Yang
- Committee on Genetics, Genomics and System Biology, The University of Chicago, Chicago, USA
| | - Mark Abney
- Department of Human Genetics, The University of Chicago, Chicago, USA
| | - John L. VandeBerg
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grand Valley, Brownsville, TX, USA
| | - Michael Olivier
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Yoav Gilad
- Department of Human Genetics, The University of Chicago, Chicago, USA
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA
- Lead contact
| | - Laura A. Cox
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
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24
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Renganaath K, Albert FW. Trans -eQTL hotspots shape complex traits by modulating cellular states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567054. [PMID: 38014174 PMCID: PMC10680915 DOI: 10.1101/2023.11.14.567054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Regulatory genetic variation shapes gene expression, providing an important mechanism connecting DNA variation and complex traits. The causal relationships between gene expression and complex traits remain poorly understood. Here, we integrated transcriptomes and 46 genetically complex growth traits in a large cross between two strains of the yeast Saccharomyces cerevisiae . We discovered thousands of genetic correlations between gene expression and growth, suggesting functional connections. Local regulatory variation was a minor source of these genetic correlations. Instead, genetic correlations tended to arise from multiple independent trans -acting regulatory loci. Trans -acting hotspots that affect the expression of numerous genes accounted for particularly large fractions of genetic growth variation and of genetic correlations between gene expression and growth. Genes with genetic correlations were enriched for similar biological processes across traits, but with heterogeneous direction of effect. Our results reveal how trans -acting regulatory hotspots shape complex traits by altering cellular states.
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25
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Taylor DJ, Chhetri SB, Tassia MG, Biddanda A, Battle A, McCoy RC. Sources of gene expression variation in a globally diverse human cohort. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.04.565639. [PMID: 37965206 PMCID: PMC10635147 DOI: 10.1101/2023.11.04.565639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Genetic variation influencing gene expression and splicing is a key source of phenotypic diversity. Though invaluable, studies investigating these links in humans have been strongly biased toward participants of European ancestries, diminishing generalizability and hindering evolutionary research. To address these limitations, we developed MAGE, an open-access RNA-seq data set of lymphoblastoid cell lines from 731 individuals from the 1000 Genomes Project spread across 5 continental groups and 26 populations. Most variation in gene expression (92%) and splicing (95%) was distributed within versus between populations, mirroring variation in DNA sequence. We mapped associations between genetic variants and expression and splicing of nearby genes (cis-eQTLs and cis-sQTLs, respective), identifying >15,000 putatively causal eQTLs and >16,000 putatively causal sQTLs that are enriched for relevant epigenomic signatures. These include 1310 eQTLs and 1657 sQTLs that are largely private to previously underrepresented populations. Our data further indicate that the magnitude and direction of causal eQTL effects are highly consistent across populations and that apparent "population-specific" effects observed in previous studies were largely driven by low resolution or additional independent eQTLs of the same genes that were not detected. Together, our study expands understanding of gene expression diversity across human populations and provides an inclusive resource for studying the evolution and function of human genomes.
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Affiliation(s)
- Dylan J. Taylor
- Department of Biology, Johns Hopkins University, Baltimore MD, USA
| | - Surya B. Chhetri
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore MD, USA
| | | | - Arjun Biddanda
- Department of Biology, Johns Hopkins University, Baltimore MD, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore MD, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore MD, USA
| | - Rajiv C. McCoy
- Department of Biology, Johns Hopkins University, Baltimore MD, USA
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26
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You J, Liu Z, Qi Z, Ma Y, Sun M, Su L, Niu H, Peng Y, Luo X, Zhu M, Huang Y, Chang X, Hu X, Zhang Y, Pi R, Liu Y, Meng Q, Li J, Zhang Q, Zhu L, Lin Z, Min L, Yuan D, Grover CE, Fang DD, Lindsey K, Wendel JF, Tu L, Zhang X, Wang M. Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton. Nat Genet 2023; 55:1987-1997. [PMID: 37845354 PMCID: PMC10632151 DOI: 10.1038/s41588-023-01530-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 09/14/2023] [Indexed: 10/18/2023]
Abstract
Polyploidy complicates transcriptional regulation and increases phenotypic diversity in organisms. The dynamics of genetic regulation of gene expression between coresident subgenomes in polyploids remains to be understood. Here we document the genetic regulation of fiber development in allotetraploid cotton Gossypium hirsutum by sequencing 376 genomes and 2,215 time-series transcriptomes. We characterize 1,258 genes comprising 36 genetic modules that control staged fiber development and uncover genetic components governing their partitioned expression relative to subgenomic duplicated genes (homoeologs). Only about 30% of fiber quality-related homoeologs show phenotypically favorable allele aggregation in cultivars, highlighting the potential for subgenome additivity in fiber improvement. We envision a genome-enabled breeding strategy, with particular attention to 48 favorable alleles related to fiber phenotypes that have been subjected to purifying selection during domestication. Our work delineates the dynamics of gene regulation during fiber development and highlights the potential of subgenomic coordination underpinning phenotypes in polyploid plants.
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Affiliation(s)
- Jiaqi You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhengyang Qi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Mengling Sun
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ling Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Hao Niu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yabing Peng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xuanxuan Luo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Mengmeng Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuefan Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xing Chang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiubao Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuqi Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ruizhen Pi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuqi Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qingying Meng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, USA
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, UK
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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Zhang M, Chen C, Lu Z, Cai Y, Li Y, Zhang F, Liu Y, Chen S, Zhang H, Yang S, Gen H, Jiang Y, Ning C, Huang J, Wang W, Fan L, Zhang Y, Jin M, Han J, Xiong Z, Cai M, Liu J, Huang C, Yang X, Xu B, Li H, Li B, Zhu X, Wei Y, Zhu Y, Tian J, Miao X. Genetic Control of Alternative Splicing and its Distinct Role in Colorectal Cancer Mechanisms. Gastroenterology 2023; 165:1151-1167. [PMID: 37541527 DOI: 10.1053/j.gastro.2023.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND & AIMS Dysregulation of alternative splicing is implicated in many human diseases, and understanding the genetic variation underlying transcript splicing is essential to dissect the molecular mechanisms of cancers. We aimed to provide a comprehensive functional dissection of splicing quantitative trait loci (sQTLs) in cancer and focus on elucidating its distinct role in colorectal cancer (CRC) mechanisms. METHODS We performed a comprehensive sQTL analysis to identify genetic variants that control messenger RNA splicing across 33 cancer types from The Cancer Genome Atlas and independently validated in our 154 CRC tissues. Then, large-scale, multicenter, multi-ethnic case-control studies (34,585 cases and 76,023 controls) were conducted to examine the association of these sQTLs with CRC risk. A series of biological experiments in vitro and in vivo were performed to investigate the potential mechanisms of the candidate sQTLs and target genes. RESULTS The molecular characterization of sQTL revealed its distinct role in cancer susceptibility. Tumor-specific sQTL further showed better response to cancer development. In addition, functionally informed polygenic risk score highlighted the potentiality of sQTLs in the CRC prediction. Complemented by large-scale population studies, we identified that the risk allele (T) of a multi-ancestry-associated sQTL rs61746794 significantly increased the risk of CRC in Chinese (odds ratio, 1.20; 95% CI, 1.12-1.29; P = 8.82 × 10-7) and European (odds ratio, 1.11; 95% CI, 1.07-1.16; P = 1.13 × 10-7) populations. rs61746794-T facilitated PRMT7 exon 16 splicing mediated by the RNA-binding protein PRPF8, thus increasing the level of canonical PRMT7 isoform (PRMT7-V2). Overexpression of PRMT7-V2 significantly enhanced the growth of CRC cells and xenograft tumors compared with PRMT7-V1. Mechanistically, PRMT7-V2 functions as an epigenetic writer that catalyzes the arginine methylation of H4R3 and H3R2, subsequently regulating diverse biological processes, including YAP, AKT, and KRAS pathway. A selective PRMT7 inhibitor, SGC3027, exhibited antitumor effects on human CRC cells. CONCLUSIONS Our study provides an informative sQTLs resource and insights into the regulatory mechanisms linking splicing variants to cancer risk and serving as biomarkers and therapeutic targets.
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Affiliation(s)
- Ming Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China; Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Can Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China; Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zequn Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China; Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yimin Cai
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yanmin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Fuwei Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yizhuo Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Shuoni Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Heng Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Shuhui Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Hui Gen
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yuan Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Caibo Ning
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Jinyu Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Wenzhuo Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Linyun Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yi Zhang
- Department of Hygiene Toxicology, School of Public Health, Zunyi Medical University, Zunyi, Guizhou, China
| | - Meng Jin
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jinxin Han
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhen Xiong
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ming Cai
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiuyang Liu
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Chaoqun Huang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Xiaojun Yang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Bin Xu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Heng Li
- Department of Urology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Xu Zhu
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yongchang Wei
- Department of Gastrointestinal Oncology, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China; Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China; Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, China; Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China.
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28
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Mostafavi H, Spence JP, Naqvi S, Pritchard JK. Systematic differences in discovery of genetic effects on gene expression and complex traits. Nat Genet 2023; 55:1866-1875. [PMID: 37857933 DOI: 10.1038/s41588-023-01529-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 09/14/2023] [Indexed: 10/21/2023]
Abstract
Most signals in genome-wide association studies (GWAS) of complex traits implicate noncoding genetic variants with putative gene regulatory effects. However, currently identified regulatory variants, notably expression quantitative trait loci (eQTLs), explain only a small fraction of GWAS signals. Here, we show that GWAS and cis-eQTL hits are systematically different: eQTLs cluster strongly near transcription start sites, whereas GWAS hits do not. Genes near GWAS hits are enriched in key functional annotations, are under strong selective constraint and have complex regulatory landscapes across different tissue/cell types, whereas genes near eQTLs are depleted of most functional annotations, show relaxed constraint, and have simpler regulatory landscapes. We describe a model to understand these observations, including how natural selection on complex traits hinders discovery of functionally relevant eQTLs. Our results imply that GWAS and eQTL studies are systematically biased toward different types of variant, and support the use of complementary functional approaches alongside the next generation of eQTL studies.
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Affiliation(s)
| | | | - Sahin Naqvi
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Biology, Stanford University, Stanford, CA, USA.
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29
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Nobrega M, Farris K, Andersen E, Donkin I, Versteyhe S, Kristiansen VB, Simpson S, Barres R. Splicing across adipocyte differentiation is highly dynamic and impacted by metabolic phenotype. RESEARCH SQUARE 2023:rs.3.rs-3487148. [PMID: 37961160 PMCID: PMC10635361 DOI: 10.21203/rs.3.rs-3487148/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Adipose tissue dysfunction underlies many of the metabolic complications associated with obesity. A better understanding of the gene regulation differences present in metabolically unhealthy adipose tissue can provide insights into the mechanisms underlying adipose tissue dysfunction. Here, we used RNA-seq data collected from a differentiation time course of lean, obese, and obese with type 2 diabetes (T2D) individuals to characterize the role of alterative splicing in adipocyte differentiation and function. We found that splicing was highly dynamic across adipocyte differentiation in all three cohorts, and that the dynamics of splicing were significantly impacted by metabolic phenotype. We also found that there was very little overlap between genes that were differentially spliced in adipocyte differentiation and those that were differentially expressed, positioning alternative splicing as a largely independent gene regulatory mechanism whose impact would be missed when looking at gene expression changes alone. To assess the impact of alternative splicing across adipocyte differentiation on genetic risk for metabolic diseases, we integrated the differential splicing results generated here with genome-wide association study results for body mass index and T2D, and found that variants associated with T2D were enriched in regions that were differentially spliced in early differentiation. These findings provide insight into the role of alternative splicing in adipocyte differentiation and can serve as a resource to guide future variant-to-function studies.
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Affiliation(s)
| | | | | | | | | | | | | | - Romain Barres
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
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30
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Nguyen JP, Arthur TD, Fujita K, Salgado BM, Donovan MKR, Matsui H, Kim JH, D'Antonio-Chronowska A, D'Antonio M, Frazer KA. eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk. Nat Commun 2023; 14:6928. [PMID: 37903777 PMCID: PMC10616100 DOI: 10.1038/s41467-023-42560-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023] Open
Abstract
The impact of genetic regulatory variation active in early pancreatic development on adult pancreatic disease and traits is not well understood. Here, we generate a panel of 107 fetal-like iPSC-derived pancreatic progenitor cells (iPSC-PPCs) from whole genome-sequenced individuals and identify 4065 genes and 4016 isoforms whose expression and/or alternative splicing are affected by regulatory variation. We integrate eQTLs identified in adult islets and whole pancreas samples, which reveal 1805 eQTL associations that are unique to the fetal-like iPSC-PPCs and 1043 eQTLs that exhibit regulatory plasticity across the fetal-like and adult pancreas tissues. Colocalization with GWAS risk loci for pancreatic diseases and traits show that some putative causal regulatory variants are active only in the fetal-like iPSC-PPCs and likely influence disease by modulating expression of disease-associated genes in early development, while others with regulatory plasticity likely exert their effects in both the fetal and adult pancreas by modulating expression of different disease genes in the two developmental stages.
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Affiliation(s)
- Jennifer P Nguyen
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Timothy D Arthur
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Kyohei Fujita
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bianca M Salgado
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Margaret K R Donovan
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Ji Hyun Kim
- Department of Pediatrics, Dongguk University Ilsan Hospital, Goyang, South Korea
| | | | - Matteo D'Antonio
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Kelly A Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA.
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
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31
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Weinstock JS, Arce MM, Freimer JW, Ota M, Marson A, Battle A, Pritchard JK. Gene regulatory network inference from CRISPR perturbations in primary CD4+ T cells elucidates the genomic basis of immune disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.17.557749. [PMID: 37745614 PMCID: PMC10516010 DOI: 10.1101/2023.09.17.557749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The effects of genetic variation on complex traits act mainly through changes in gene regulation. Although many genetic variants have been linked to target genes in cis, the trans-regulatory cascade mediating their effects remains largely uncharacterized. Mapping trans-regulators based on natural genetic variation, including eQTL mapping, has been challenging due to small effects. Experimental perturbation approaches offer a complementary and powerful approach to mapping trans-regulators. We used CRISPR knockouts of 84 genes in primary CD4+ T cells to perturb an immune cell gene network, targeting both inborn error of immunity (IEI) disease transcription factors (TFs) and background TFs matched in constraint and expression level, but without a known immune disease association. We developed a novel Bayesian structure learning method called Linear Latent Causal Bayes (LLCB) to estimate the gene regulatory network from perturbation data and observed 211 directed edges among the genes which could not be detected in existing CD4+ trans-eQTL data. We used LLCB to characterize the differences between the IEI and background TFs, finding that the gene groups were highly interconnected, but that IEI TFs were much more likely to regulate immune cell specific pathways and immune GWAS genes. We further characterized nine coherent gene programs based on downstream effects of the TFs and linked these modules to regulation of GWAS genes, finding that canonical JAK-STAT family members are regulated by KMT2A, a global epigenetic regulator. These analyses reveal the trans-regulatory cascade from upstream epigenetic regulator to intermediate TFs to downstream effector cytokines and elucidate the logic linking immune GWAS genes to key signaling pathways.
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Affiliation(s)
- Joshua S. Weinstock
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD
- Department of Genetics, Stanford University, Stanford, CA
| | - Maya M. Arce
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Jacob W. Freimer
- Department of Genetics, Stanford University, Stanford, CA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA
| | - Mineto Ota
- Department of Genetics, Stanford University, Stanford, CA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA
- Department of Medicine, University of California, San Francisco, San Francisco, CA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA, 94143
- Diabetes Center, University of California, San Francisco, San Francisco, CA, 94143
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, 94129
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, 94143
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94158
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD
- Department of Computer Science, Johns Hopkins University, Baltimore, MD
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD
| | - Jonathan K. Pritchard
- Department of Genetics, Stanford University, Stanford, CA
- Department of Biology, Stanford University, Stanford, CA
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32
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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] [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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33
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Amarasinghe HE, Zhang P, Whalley JP, Allcock A, Migliorini G, Brown AC, Scozzafava G, Knight JC. Mapping the epigenomic landscape of human monocytes following innate immune activation reveals context-specific mechanisms driving endotoxin tolerance. BMC Genomics 2023; 24:595. [PMID: 37805492 PMCID: PMC10559536 DOI: 10.1186/s12864-023-09663-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/08/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND Monocytes are key mediators of innate immunity to infection, undergoing profound and dynamic changes in epigenetic state and immune function which are broadly protective but may be dysregulated in disease. Here, we aimed to advance understanding of epigenetic regulation following innate immune activation, acutely and in endotoxin tolerant states. METHODS We exposed human primary monocytes from healthy donors (n = 6) to interferon-γ or differing combinations of endotoxin (lipopolysaccharide), including acute response (2 h) and two models of endotoxin tolerance: repeated stimulations (6 + 6 h) and prolonged exposure to endotoxin (24 h). Another subset of monocytes was left untreated (naïve). We identified context-specific regulatory elements based on epigenetic signatures for chromatin accessibility (ATAC-seq) and regulatory non-coding RNAs from total RNA sequencing. RESULTS We present an atlas of differential gene expression for endotoxin and interferon response, identifying widespread context specific changes. Across assayed states, only 24-29% of genes showing differential exon usage are also differential at the gene level. Overall, 19.9% (6,884 of 34,616) of repeatedly observed ATAC peaks were differential in at least one condition, the majority upregulated on stimulation and located in distal regions (64.1% vs 45.9% of non-differential peaks) within which sequences were less conserved than non-differential peaks. We identified enhancer-derived RNA signatures specific to different monocyte states that correlated with chromatin accessibility changes. The endotoxin tolerance models showed distinct chromatin accessibility and transcriptomic signatures, with integrated analysis identifying genes and pathways involved in the inflammatory response, detoxification, metabolism and wound healing. We leveraged eQTL mapping for the same monocyte activation states to link potential enhancers with specific genes, identifying 1,946 unique differential ATAC peaks with 1,340 expression associated genes. We further use this to inform understanding of reported GWAS, for example involving FCHO1 and coronary artery disease. CONCLUSION This study reports context-specific regulatory elements based on transcriptomic profiling and epigenetic signatures for enhancer-derived RNAs and chromatin accessibility in immune tolerant monocyte states, and demonstrates the informativeness of linking such elements and eQTL to inform future mechanistic studies aimed at defining therapeutic targets of immunosuppression and diseases.
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Affiliation(s)
- Harindra E Amarasinghe
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK.
| | - Ping Zhang
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK
| | - Justin P Whalley
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Alice Allcock
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Gabriele Migliorini
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Andrew C Brown
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Giuseppe Scozzafava
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK.
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK.
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34
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Kang JB, Raveane A, Nathan A, Soranzo N, Raychaudhuri S. Methods and Insights from Single-Cell Expression Quantitative Trait Loci. Annu Rev Genomics Hum Genet 2023; 24:277-303. [PMID: 37196361 PMCID: PMC10784788 DOI: 10.1146/annurev-genom-101422-100437] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Recent advancements in single-cell technologies have enabled expression quantitative trait locus (eQTL) analysis across many individuals at single-cell resolution. Compared with bulk RNA sequencing, which averages gene expression across cell types and cell states, single-cell assays capture the transcriptional states of individual cells, including fine-grained, transient, and difficult-to-isolate populations at unprecedented scale and resolution. Single-cell eQTL (sc-eQTL) mapping can identify context-dependent eQTLs that vary with cell states, including some that colocalize with disease variants identified in genome-wide association studies. By uncovering the precise contexts in which these eQTLs act, single-cell approaches can unveil previously hidden regulatory effects and pinpoint important cell states underlying molecular mechanisms of disease. Here, we present an overview of recently deployed experimental designs in sc-eQTL studies. In the process, we consider the influence of study design choices such as cohort, cell states, and ex vivo perturbations. We then discuss current methodologies, modeling approaches, and technical challenges as well as future opportunities and applications.
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Affiliation(s)
- Joyce B Kang
- Center for Data Sciences and Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; ,
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA;
| | | | - Aparna Nathan
- Center for Data Sciences and Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; ,
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA;
| | - Nicole Soranzo
- Human Technopole, Milan, Italy; ,
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
- British Heart Foundation Centre of Research Excellence and Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Soumya Raychaudhuri
- Center for Data Sciences and Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; ,
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA;
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester, Manchester, United Kingdom
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35
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Lo EKW, Velazquez JJ, Peng D, Kwon C, Ebrahimkhani MR, Cahan P. Platform-agnostic CellNet enables cross-study analysis of cell fate engineering protocols. Stem Cell Reports 2023; 18:1721-1742. [PMID: 37478860 PMCID: PMC10444577 DOI: 10.1016/j.stemcr.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/23/2023] Open
Abstract
Optimization of cell engineering protocols requires standard, comprehensive quality metrics. We previously developed CellNet, a computational tool to quantitatively assess the transcriptional fidelity of engineered cells compared with their natural counterparts, based on bulk-derived expression profiles. However, this platform and others were limited in their ability to compare data from different sources, and no current tool makes it easy to compare new protocols with existing state-of-the-art protocols in a standardized manner. Here, we utilized our prior application of the top-scoring pair transformation to build a computational platform, platform-agnostic CellNet (PACNet), to address both shortcomings. To demonstrate the utility of PACNet, we applied it to thousands of samples from over 100 studies that describe dozens of protocols designed to produce seven distinct cell types. We performed an in-depth examination of hepatocyte and cardiomyocyte protocols to identify the best-performing methods, characterize the extent of intra-protocol and inter-lab variation, and identify common off-target signatures, including a surprising neural/neuroendocrine signature in primary liver-derived organoids. We have made PACNet available as an easy-to-use web application, allowing users to assess their protocols relative to our database of reference engineered samples, and as open-source, extensible code.
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Affiliation(s)
- Emily K W Lo
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jeremy J Velazquez
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Da Peng
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Chulan Kwon
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mo R Ebrahimkhani
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA; McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Patrick Cahan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.
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36
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Cuomo ASE, Nathan A, Raychaudhuri S, MacArthur DG, Powell JE. Single-cell genomics meets human genetics. Nat Rev Genet 2023; 24:535-549. [PMID: 37085594 PMCID: PMC10784789 DOI: 10.1038/s41576-023-00599-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2023] [Indexed: 04/23/2023]
Abstract
Single-cell genomic technologies are revealing the cellular composition, identities and states in tissues at unprecedented resolution. They have now scaled to the point that it is possible to query samples at the population level, across thousands of individuals. Combining single-cell information with genotype data at this scale provides opportunities to link genetic variation to the cellular processes underpinning key aspects of human biology and disease. This strategy has potential implications for disease diagnosis, risk prediction and development of therapeutic solutions. But, effectively integrating large-scale single-cell genomic data, genetic variation and additional phenotypic data will require advances in data generation and analysis methods. As single-cell genetics begins to emerge as a field in its own right, we review its current state and the challenges and opportunities ahead.
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Affiliation(s)
- Anna S E Cuomo
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Divisions of Rheumatology and Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Divisions of Rheumatology and Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Joseph E Powell
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia.
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia.
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37
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Shevade K, Peddada S, Mader K, Przybyla L. Functional genomics in stem cell models: considerations and applications. Front Cell Dev Biol 2023; 11:1236553. [PMID: 37554308 PMCID: PMC10404852 DOI: 10.3389/fcell.2023.1236553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023] Open
Abstract
Protocols to differentiate human pluripotent stem cells have advanced in terms of cell type specificity and tissue-level complexity over the past 2 decades, which has facilitated human disease modeling in the most relevant cell types. The ability to generate induced PSCs (iPSCs) from patients further enables the study of disease mutations in an appropriate cellular context to reveal the mechanisms that underlie disease etiology and progression. As iPSC-derived disease models have improved in robustness and scale, they have also been adopted more widely for use in drug screens to discover new therapies and therapeutic targets. Advancement in genome editing technologies, in particular the discovery of CRISPR-Cas9, has further allowed for rapid development of iPSCs containing disease-causing mutations. CRISPR-Cas9 technologies have now evolved beyond creating single gene edits, aided by the fusion of inhibitory (CRISPRi) or activation (CRISPRa) domains to a catalytically dead Cas9 protein, enabling inhibition or activation of endogenous gene loci. These tools have been used in CRISPR knockout, CRISPRi, or CRISPRa screens to identify genetic modifiers that synergize or antagonize with disease mutations in a systematic and unbiased manner, resulting in identification of disease mechanisms and discovery of new therapeutic targets to accelerate drug discovery research. However, many technical challenges remain when applying large-scale functional genomics approaches to differentiated PSC populations. Here we review current technologies in the field of iPSC disease modeling and CRISPR-based functional genomics screens and practical considerations for implementation across a range of modalities, applications, and disease areas, as well as explore CRISPR screens that have been performed in iPSC models to-date and the insights and therapies these screens have produced.
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Affiliation(s)
- Kaivalya Shevade
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Sailaja Peddada
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Karl Mader
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Laralynne Przybyla
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
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38
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Wu EY, Singh NP, Choi K, Zakeri M, Vincent M, Churchill GA, Ackert-Bicknell CL, Patro R, Love MI. SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty. Genome Biol 2023; 24:165. [PMID: 37438847 PMCID: PMC10337143 DOI: 10.1186/s13059-023-03003-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 06/29/2023] [Indexed: 07/14/2023] Open
Abstract
Detecting allelic imbalance at the isoform level requires accounting for inferential uncertainty, caused by multi-mapping of RNA-seq reads. Our proposed method, SEESAW, uses Salmon and Swish to offer analysis at various levels of resolution, including gene, isoform, and aggregating isoforms to groups by transcription start site. The aggregation strategies strengthen the signal for transcripts with high uncertainty. The SEESAW suite of methods is shown to have higher power than other allelic imbalance methods when there is isoform-level allelic imbalance. We also introduce a new test for detecting imbalance that varies across a covariate, such as time.
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Affiliation(s)
- Euphy Y Wu
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Noor P Singh
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | | | - Mohsen Zakeri
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | | | | | - Cheryl L Ackert-Bicknell
- Department of Orthopedics, School of Medicine, University of Colorado, Anschutz Campus, Aurora, CO, USA
| | - Rob Patro
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Michael I Love
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.
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39
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Natri HM, Del Azodi CB, Peter L, Taylor CJ, Chugh S, Kendle R, Chung MI, Flaherty DK, Matlock BK, Calvi CL, Blackwell TS, Ware LB, Bacchetta M, Walia R, Shaver CM, Kropski JA, McCarthy DJ, Banovich NE. Cell type-specific and disease-associated eQTL in the human lung. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533161. [PMID: 36993211 PMCID: PMC10055257 DOI: 10.1101/2023.03.17.533161] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Common genetic variants confer substantial risk for chronic lung diseases, including pulmonary fibrosis (PF). Defining the genetic control of gene expression in a cell-type-specific and context-dependent manner is critical for understanding the mechanisms through which genetic variation influences complex traits and disease pathobiology. To this end, we performed single-cell RNA-sequencing of lung tissue from 67 PF and 49 unaffected donors. Employing a pseudo-bulk approach, we mapped expression quantitative trait loci (eQTL) across 38 cell types, observing both shared and cell type-specific regulatory effects. Further, we identified disease-interaction eQTL and demonstrated that this class of associations is more likely to be cell-type specific and linked to cellular dysregulation in PF. Finally, we connected PF risk variants to their regulatory targets in disease-relevant cell types. These results indicate that cellular context determines the impact of genetic variation on gene expression, and implicates context-specific eQTL as key regulators of lung homeostasis and disease.
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40
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Suliman S, Nieto-Caballero VE, Asgari S, Lopez K, Iwany SK, Luo Y, Nathan A, Fernandez-Salinas D, Chiñas M, Huang CC, Zhang Z, León SR, Calderon RI, Lecca L, Murray M, Van Rhijn I, Raychaudhuri S, Moody DB, Gutierrez-Arcelus M. History of tuberculosis disease is associated with genetic regulatory variation in Peruvians. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.20.23291558. [PMID: 37425785 PMCID: PMC10327177 DOI: 10.1101/2023.06.20.23291558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
A quarter of humanity is estimated to be latently infected with Mycobacterium tuberculosis (Mtb) with a 5-10% risk of developing tuberculosis (TB) disease. Variability in responses to Mtb infection could be due to host or pathogen heterogeneity. Here, we focused on host genetic variation in a Peruvian population and its associations with gene regulation in monocyte-derived macrophages and dendritic cells (DCs). We recruited former household contacts of TB patients who previously progressed to TB (cases, n=63) or did not progress to TB (controls, n=63). Transcriptomic profiling of monocyte-derived dendritic cells (DCs) and macrophages measured the impact of genetic variants on gene expression by identifying expression quantitative trait loci (eQTL). We identified 330 and 257 eQTL genes in DCs and macrophages (False Discovery Rate (FDR) < 0.05), respectively. Five genes in DCs showed interaction between eQTL variants and TB progression status. The top eQTL interaction for a protein-coding gene was with FAH, the gene encoding fumarylacetoacetate hydrolase, which mediates the last step in mammalian tyrosine catabolism. FAH expression was associated with genetic regulatory variation in cases but not controls. Using public transcriptomic and epigenomic data of Mtb-infected monocyte-derived dendritic cells, we found that Mtb infection results in FAH downregulation and DNA methylation changes in the locus. Overall, this study demonstrates effects of genetic variation on gene expression levels that are dependent on history of infectious disease and highlights a candidate pathogenic mechanism through pathogen-response genes. Furthermore, our results point to tyrosine metabolism and related candidate TB progression pathways for further investigation.
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Affiliation(s)
- Sara Suliman
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Initiative Biohub, San Francisco, CA, USA
| | - Victor E. Nieto-Caballero
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Undergraduate Program in Genomic Sciences, Center for Genomic Sciences, Universidad Nacional Autónoma de México (UNAM), Morelos 62210, Mexico
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samira Asgari
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kattya Lopez
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Socios En Salud Sucursal Peru, Lima, Peru
| | - Sarah K. Iwany
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Yang Luo
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Aparna Nathan
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Daniela Fernandez-Salinas
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Marcos Chiñas
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chuan-Chin Huang
- Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Zibiao Zhang
- Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Segundo R León
- Socios En Salud Sucursal Peru, Lima, Peru
- Medical Technology School and Global Health Research Institute, San Juan Bautista Private University, Lima, Perú
| | | | | | - Megan Murray
- Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - D. Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Maria Gutierrez-Arcelus
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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41
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Shi FY, Wang Y, Huang D, Liang Y, Liang N, Chen XW, Gao G. Computational Assessment of the Expression-modulating Potential for Non-coding Variants. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:662-673. [PMID: 34890839 PMCID: PMC10787178 DOI: 10.1016/j.gpb.2021.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 10/13/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Large-scale genome-wide association studies (GWAS) and expression quantitative trait locus (eQTL) studies have identified multiple non-coding variants associated with genetic diseases by affecting gene expression. However, pinpointing causal variants effectively and efficiently remains a serious challenge. Here, we developed CARMEN, a novel algorithm to identify functional non-coding expression-modulating variants. Multiple evaluations demonstrated CARMEN's superior performance over state-of-the-art tools. Applying CARMEN to GWAS and eQTL datasets further pinpointed several causal variants other than the reported lead single-nucleotide polymorphisms (SNPs). CARMEN scales well with the massive datasets, and is available online as a web server at http://carmen.gao-lab.org.
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Affiliation(s)
- Fang-Yuan Shi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Biomedical Pioneering Innovative Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, Beijing 100871, China
| | - Yu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Biomedical Pioneering Innovative Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, Beijing 100871, China
| | - Dong Huang
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Yu Liang
- Human Aging Research Institute, School of Life Science, Nanchang University, Nanchang 330031, China
| | - Nan Liang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Biomedical Pioneering Innovative Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, Beijing 100871, China
| | - Xiao-Wei Chen
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Biomedical Pioneering Innovative Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, Beijing 100871, China.
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42
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Ziyani C, Delaneau O, Ribeiro DM. Multimodal single cell analysis infers widespread enhancer co-activity in a lymphoblastoid cell line. Commun Biol 2023; 6:563. [PMID: 37237005 DOI: 10.1038/s42003-023-04954-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Non-coding regulatory elements such as enhancers are key in controlling the cell-type specificity and spatio-temporal expression of genes. To drive stable and precise gene transcription robust to genetic variation and environmental stress, genes are often targeted by multiple enhancers with redundant action. However, it is unknown whether enhancers targeting the same gene display simultaneous activity or whether some enhancer combinations are more often co-active than others. Here, we take advantage of recent developments in single cell technology that permit assessing chromatin status (scATAC-seq) and gene expression (scRNA-seq) in the same single cells to correlate gene expression to the activity of multiple enhancers. Measuring activity patterns across 24,844 human lymphoblastoid single cells, we find that the majority of enhancers associated with the same gene display significant correlation in their chromatin profiles. For 6944 expressed genes associated with enhancers, we predict 89,885 significant enhancer-enhancer associations between nearby enhancers. We find that associated enhancers share similar transcription factor binding profiles and that gene essentiality is linked with higher enhancer co-activity. We provide a set of predicted enhancer-enhancer associations based on correlation derived from a single cell line, which can be further investigated for functional relevance.
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Affiliation(s)
- Chaymae Ziyani
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Diogo M Ribeiro
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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43
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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] [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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Linghu C, An B, Shpokayte M, Celiker OT, Shmoel N, Zhang R, Zhang C, Park D, Park WM, Ramirez S, Boyden ES. Recording of cellular physiological histories along optically readable self-assembling protein chains. Nat Biotechnol 2023; 41:640-651. [PMID: 36593405 PMCID: PMC10188365 DOI: 10.1038/s41587-022-01586-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 10/21/2022] [Indexed: 01/03/2023]
Abstract
Observing cellular physiological histories is key to understanding normal and disease-related processes. Here we describe expression recording islands-a fully genetically encoded approach that enables both continual digital recording of biological information within cells and subsequent high-throughput readout in fixed cells. The information is stored in growing intracellular protein chains made of self-assembling subunits, human-designed filament-forming proteins bearing different epitope tags that each correspond to a different cellular state or function (for example, gene expression downstream of neural activity or pharmacological exposure), allowing the physiological history to be read out along the ordered subunits of protein chains with conventional optical microscopy. We use expression recording islands to record gene expression timecourse downstream of specific pharmacological and physiological stimuli in cultured neurons and in living mouse brain, with a time resolution of a fraction of a day, over periods of days to weeks.
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Affiliation(s)
- Changyang Linghu
- Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Biological Engineering, MIT, Cambridge, MA, USA
- Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Department of Cell and Developmental Biology, Program in Single Cell Spatial Analysis, and Michigan Neuroscience Institute, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Bobae An
- Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Biological Engineering, MIT, Cambridge, MA, USA
- Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
| | - Monika Shpokayte
- Graduate Program for Neuroscience, Boston University, Boston, MA, USA
- Psychological and Brain Sciences, Boston University, Boston, MA, USA
| | - Orhan T Celiker
- Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Biological Engineering, MIT, Cambridge, MA, USA
- Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
| | - Nava Shmoel
- Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Biological Engineering, MIT, Cambridge, MA, USA
- Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
| | - Ruihan Zhang
- Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Biological Engineering, MIT, Cambridge, MA, USA
- Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
| | - Chi Zhang
- Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Biological Engineering, MIT, Cambridge, MA, USA
- Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
| | - Demian Park
- Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Biological Engineering, MIT, Cambridge, MA, USA
- Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
| | - Won Min Park
- Chemical Engineering, Kansas State University, Manhattan, KS, USA
| | - Steve Ramirez
- Psychological and Brain Sciences, Boston University, Boston, MA, USA
| | - Edward S Boyden
- Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
- Biological Engineering, MIT, Cambridge, MA, USA.
- Media Arts and Sciences, MIT, Cambridge, MA, USA.
- McGovern Institute, MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, MIT, Cambridge, MA, USA.
- K Lisa Yang Center for Bionics, MIT, Cambridge, MA, USA.
- Center for Neurobiological Engineering, MIT, Cambridge, MA, USA.
- Koch Institute, MIT, Cambridge, MA, USA.
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45
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Flores-Díaz A, Escoto-Sandoval C, Cervantes-Hernández F, Ordaz-Ortiz JJ, Hayano-Kanashiro C, Reyes-Valdés H, Garcés-Claver A, Ochoa-Alejo N, Martínez O. Gene Functional Networks from Time Expression Profiles: A Constructive Approach Demonstrated in Chili Pepper ( Capsicum annuum L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1148. [PMID: 36904008 PMCID: PMC10005043 DOI: 10.3390/plants12051148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Gene co-expression networks are powerful tools to understand functional interactions between genes. However, large co-expression networks are difficult to interpret and do not guarantee that the relations found will be true for different genotypes. Statistically verified time expression profiles give information about significant changes in expressions through time, and genes with highly correlated time expression profiles, which are annotated in the same biological process, are likely to be functionally connected. A method to obtain robust networks of functionally related genes will be useful to understand the complexity of the transcriptome, leading to biologically relevant insights. We present an algorithm to construct gene functional networks for genes annotated in a given biological process or other aspects of interest. We assume that there are genome-wide time expression profiles for a set of representative genotypes of the species of interest. The method is based on the correlation of time expression profiles, bound by a set of thresholds that assure both, a given false discovery rate, and the discard of correlation outliers. The novelty of the method consists in that a gene expression relation must be repeatedly found in a given set of independent genotypes to be considered valid. This automatically discards relations particular to specific genotypes, assuring a network robustness, which can be set a priori. Additionally, we present an algorithm to find transcription factors candidates for regulating hub genes within a network. The algorithms are demonstrated with data from a large experiment studying gene expression during the development of the fruit in a diverse set of chili pepper genotypes. The algorithm is implemented and demonstrated in a new version of the publicly available R package "Salsa" (version 1.0).
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Affiliation(s)
- Alan Flores-Díaz
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Christian Escoto-Sandoval
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Felipe Cervantes-Hernández
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - José J. Ordaz-Ortiz
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Corina Hayano-Kanashiro
- Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Hermosillo 83000, Mexico
| | - Humberto Reyes-Valdés
- Department of Plant Breeding, Universidad Autónoma Agraria Antonio Narro, Saltillo 25315, Mexico
| | - Ana Garcés-Claver
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), 50059 Zaragoza, Spain
| | - Neftalí Ochoa-Alejo
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Octavio Martínez
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
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D'Antonio M, Nguyen JP, Arthur TD, Matsui H, D'Antonio-Chronowska A, Frazer KA. Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease. Nat Commun 2023; 14:1132. [PMID: 36854752 PMCID: PMC9975214 DOI: 10.1038/s41467-023-36638-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 02/10/2023] [Indexed: 03/02/2023] Open
Abstract
The causal variants and genes underlying thousands of cardiac GWAS signals have yet to be identified. Here, we leverage spatiotemporal information on 966 RNA-seq cardiac samples and perform an expression quantitative trait locus (eQTL) analysis detecting eQTLs considering both eGenes and eIsoforms. We identify 2,578 eQTLs associated with a specific developmental stage-, tissue- and/or cell type. Colocalization between eQTL and GWAS signals of five cardiac traits identified variants with high posterior probabilities for being causal in 210 GWAS loci. Pulse pressure GWAS loci are enriched for colocalization with fetal- and smooth muscle- eQTLs; pulse rate with adult- and cardiac muscle- eQTLs; and atrial fibrillation with cardiac muscle- eQTLs. Fine mapping identifies 79 credible sets with five or fewer SNPs, of which 15 were associated with spatiotemporal eQTLs. Our study shows that many cardiac GWAS variants impact traits and disease in a developmental stage-, tissue- and/or cell type-specific fashion.
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Affiliation(s)
- Matteo D'Antonio
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA.
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
| | - Jennifer P Nguyen
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Timothy D Arthur
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | | | - Kelly A Frazer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
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47
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Copy number variation-associated lncRNAs may contribute to the etiologies of congenital heart disease. Commun Biol 2023; 6:189. [PMID: 36806749 PMCID: PMC9938258 DOI: 10.1038/s42003-023-04565-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 02/08/2023] [Indexed: 02/19/2023] Open
Abstract
Copy number variations (CNVs) have long been recognized as pathogenic factors for congenital heart disease (CHD). Few CHD associated CNVs could be interpreted as dosage effect due to disruption of coding sequences. Emerging evidences have highlighted the regulatory roles of long noncoding RNAs (lncRNAs) in cardiac development. Whereas it remains unexplored whether lncRNAs within CNVs (CNV-lncRNAs) could contribute to the etiology of CHD associated CNVs. Here we constructed coexpression networks involving CNV-lncRNAs within CHD associated CNVs and protein coding genes using the human organ developmental transcriptomic data, and showed that CNV-lncRNAs within 10 of the non-syndromic CHD associated CNVs clustered in the most significant heart correlated module, and had highly correlated coexpression with multiple key CHD genes. HSALNG0104472 within 15q11.2 region was identified as a hub CNV-lncRNA with heart-biased expression and validated experimentally. Our results indicated that HSALNG0104472 should be a main effector responsible for cardiac defects of 15q11.2 deletion through regulating cardiomyocytes differentiation. Our findings suggested that CNV-lncRNAs could potentially contribute to the pathologies of a maximum proportion of 68.4% (13/19) of non-syndromic CHD associated CNVs. These results indicated that explaining the pathogenesis of CHD associated CNVs should take account of the noncoding regions.
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48
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Song Y, Zhang Y, Qu Q, Zhang X, Lu T, Xu J, Ma W, Zhu M, Huang C, Xiong R. Biomaterials based on hyaluronic acid, collagen and peptides for three-dimensional cell culture and their application in stem cell differentiation. Int J Biol Macromol 2023; 226:14-36. [PMID: 36436602 DOI: 10.1016/j.ijbiomac.2022.11.213] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
In recent decades, three-dimensional (3D) cell culture technologies have been developed rapidly in the field of tissue engineering and regeneration, and have shown unique advantages and great prospects in the differentiation of stem cells. Herein, the article reviews the progress and advantages of 3D cell culture technologies in the field of stem cell differentiation. Firstly, 3D cell culture technologies are divided into two main categories: scaffoldless and scaffolds. Secondly, the effects of hydrogels scaffolds and porous scaffolds on stem cell differentiation in the scaffold category were mainly reviewed. Among them, hydrogels scaffolds are divided into natural hydrogels and synthetic hydrogels. Natural materials include polysaccharides, proteins, and their derivatives, focusing on hyaluronic acid, collagen and polypeptides. Synthetic materials mainly include polyethylene glycol (PEG), polyacrylic acid (PAA), polyvinyl alcohol (PVA), etc. In addition, since the preparation techniques have a large impact on the properties of porous scaffolds, several techniques for preparing porous scaffolds based on different macromolecular materials are reviewed. Finally, the future prospects and challenges of 3D cell culture in the field of stem cell differentiation are reviewed. This review will provide a useful guideline for the selection of materials and techniques for 3D cell culture in stem cell differentiation.
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Affiliation(s)
- Yuanyuan Song
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Yingying Zhang
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Qingli Qu
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Xiaoli Zhang
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Tao Lu
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Jianhua Xu
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Wenjing Ma
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Miaomiao Zhu
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China
| | - Chaobo Huang
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China.
| | - Ranhua Xiong
- Joint Laboratory of Advanced Biomedical Materials (NFU-UGent), Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing 210037, China.
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Bosada FM, van Duijvenboden K, Giovou AE, Rivaud MR, Uhm JS, Verkerk AO, Boukens BJ, Christoffels VM. An atrial fibrillation-associated regulatory region modulates cardiac Tbx5 levels and arrhythmia susceptibility. eLife 2023; 12:80317. [PMID: 36715501 PMCID: PMC9928424 DOI: 10.7554/elife.80317] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 01/29/2023] [Indexed: 01/31/2023] Open
Abstract
Heart development and rhythm control are highly Tbx5 dosage-sensitive. TBX5 haploinsufficiency causes congenital conduction disorders, whereas increased expression levels of TBX5 in human heart samples has been associated with atrial fibrillation (AF). We deleted the conserved mouse orthologues of two independent AF-associated genomic regions in the Tbx5 locus, one intronic (RE(int)) and one downstream (RE(down)) of Tbx5. In both lines, we observed a modest (30%) increase of Tbx5 in the postnatal atria. To gain insight into the effects of slight dosage increase in vivo, we investigated the atrial transcriptional, epigenetic and electrophysiological properties of both lines. Increased atrial Tbx5 expression was associated with induction of genes involved in development, ion transport and conduction, with increased susceptibility to atrial arrhythmias, and increased action potential duration of atrial cardiomyocytes. We identified an AF-associated variant in the human RE(int) that increases its transcriptional activity. Expression of the AF-associated transcription factor Prrx1 was induced in Tbx5RE(int)KO cardiomyocytes. We found that some of the transcriptional and functional changes in the atria caused by increased Tbx5 expression were normalized when reducing cardiac Prrx1 expression in Tbx5RE(int)KO mice, indicating an interaction between these two AF genes. We conclude that modest increases in expression of dose-dependent transcription factors, caused by common regulatory variants, significantly impact on the cardiac gene regulatory network and disease susceptibility.
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Affiliation(s)
- Fernanda M Bosada
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| | - Karel van Duijvenboden
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| | - Alexandra E Giovou
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| | - Mathilde R Rivaud
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| | - Jae-Sun Uhm
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
- Department of Cardiology, Severance Hospital, College of Medicine, Yonsei UniversitySeoulRepublic of Korea
| | - Arie O Verkerk
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| | - Bastiaan J Boukens
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
- Department of Physiology, University of Maastricht, Cardiovascular Research Institute Maastricht, Maastricht University Medical CenterMaastrichtNetherlands
| | - Vincent M Christoffels
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
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50
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Connally NJ, Nazeen S, Lee D, Shi H, Stamatoyannopoulos J, Chun S, Cotsapas C, Cassa CA, Sunyaev SR. The missing link between genetic association and regulatory function. eLife 2022; 11:74970. [PMID: 36515579 PMCID: PMC9842386 DOI: 10.7554/elife.74970] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
The genetic basis of most traits is highly polygenic and dominated by non-coding alleles. It is widely assumed that such alleles exert small regulatory effects on the expression of cis-linked genes. However, despite the availability of gene expression and epigenomic datasets, few variant-to-gene links have emerged. It is unclear whether these sparse results are due to limitations in available data and methods, or to deficiencies in the underlying assumed model. To better distinguish between these possibilities, we identified 220 gene-trait pairs in which protein-coding variants influence a complex trait or its Mendelian cognate. Despite the presence of expression quantitative trait loci near most GWAS associations, by applying a gene-based approach we found limited evidence that the baseline expression of trait-related genes explains GWAS associations, whether using colocalization methods (8% of genes implicated), transcription-wide association (2% of genes implicated), or a combination of regulatory annotations and distance (4% of genes implicated). These results contradict the hypothesis that most complex trait-associated variants coincide with homeostatic expression QTLs, suggesting that better models are needed. The field must confront this deficit and pursue this 'missing regulation.'
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Affiliation(s)
- Noah J Connally
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Sumaiya Nazeen
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Daniel Lee
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Huwenbo Shi
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Epidemiology, Harvard T.H. Chan School of Public HealthBostonUnited States
| | | | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s HospitalBostonUnited States
| | - Chris Cotsapas
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Neurology, Yale Medical SchoolNew HavenUnited States
- Department of Genetics, Yale Medical SchoolNew HavenUnited States
| | - Christopher A Cassa
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
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