1
|
Hodonsky CJ, Turner AW, Khan MD, Barrientos NB, Methorst R, Ma L, Lopez NG, Mosquera JV, Auguste G, Farber E, Ma WF, Wong D, Onengut-Gumuscu S, Kavousi M, Peyser PA, van der Laan SW, Leeper NJ, Kovacic JC, Björkegren JLM, Miller CL. Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci. Cell Genom 2024; 4:100465. [PMID: 38190101 PMCID: PMC10794848 DOI: 10.1016/j.xgen.2023.100465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/07/2023] [Accepted: 11/19/2023] [Indexed: 01/09/2024]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in GWASs, and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotypes to identify quantitative trait loci for expression (eQTLs) and splicing (sQTLs) in coronary arteries from 138 ancestrally diverse Americans. Of 2,132 eQTL-associated genes (eGenes), 47% were previously unreported in coronary artery; 19% exhibited cell-type-specific expression. Colocalization revealed subgroups of eGenes unique to CAD and blood pressure GWAS. Fine-mapping highlighted additional eGenes, including TBX20 and IL5. We also identified sQTLs for 1,690 genes, among which TOR1AIP1 and ULK3 sQTLs demonstrated the importance of evaluating splicing to accurately identify disease-relevant isoform expression. Our work provides a patient-derived coronary artery eQTL resource and exemplifies the need for diverse study populations and multifaceted approaches to characterize gene regulation in disease processes.
Collapse
Affiliation(s)
- Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Mohammad Daud Khan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Nelson B Barrientos
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ruben Methorst
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicolas G Lopez
- Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Gaëlle Auguste
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Emily Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Wei Feng Ma
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Medical Scientist Training Program, Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48019, USA
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Nicholas J Leeper
- Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Jason C Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA 94305, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA.
| |
Collapse
|
2
|
Mosquera JV, Auguste G, Wong D, Turner AW, Hodonsky CJ, Alvarez-Yela AC, Song Y, Cheng Q, Lino Cardenas CL, Theofilatos K, Bos M, Kavousi M, Peyser PA, Mayr M, Kovacic JC, Björkegren JLM, Malhotra R, Stukenberg PT, Finn AV, van der Laan SW, Zang C, Sheffield NC, Miller CL. Integrative single-cell meta-analysis reveals disease-relevant vascular cell states and markers in human atherosclerosis. Cell Rep 2023; 42:113380. [PMID: 37950869 DOI: 10.1016/j.celrep.2023.113380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 09/12/2023] [Accepted: 10/20/2023] [Indexed: 11/13/2023] Open
Abstract
Coronary artery disease (CAD) is characterized by atherosclerotic plaque formation in the arterial wall. CAD progression involves complex interactions and phenotypic plasticity among vascular and immune cell lineages. Single-cell RNA-seq (scRNA-seq) studies have highlighted lineage-specific transcriptomic signatures, but human cell phenotypes remain controversial. Here, we perform an integrated meta-analysis of 22 scRNA-seq libraries to generate a comprehensive map of human atherosclerosis with 118,578 cells. Besides characterizing granular cell-type diversity and communication, we leverage this atlas to provide insights into smooth muscle cell (SMC) modulation. We integrate genome-wide association study data and uncover a critical role for modulated SMC phenotypes in CAD, myocardial infarction, and coronary calcification. Finally, we identify fibromyocyte/fibrochondrogenic SMC markers (LTBP1 and CRTAC1) as proxies of atherosclerosis progression and validate these through omics and spatial imaging analyses. Altogether, we create a unified atlas of human atherosclerosis informing cell state-specific mechanistic and translational studies of cardiovascular diseases.
Collapse
Affiliation(s)
- Jose Verdezoto Mosquera
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Gaëlle Auguste
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Doris Wong
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | | | - Yipei Song
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Computer Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Qi Cheng
- CVPath Institute, Gaithersburg, MD 20878, USA
| | - Christian L Lino Cardenas
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | | | - Maxime Bos
- Department of Epidemiology, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48019, USA
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, London WC2R 2LS, UK; National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Jason C Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Rajeev Malhotra
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - P Todd Stukenberg
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | | | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Chongzhi Zang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Nathan C Sheffield
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Clint L Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA.
| |
Collapse
|
3
|
Wong D, Auguste G, Cardenas CLL, Turner AW, Chen Y, Song Y, Ma L, Perry RN, Aherrahrou R, Kuppusamy M, Yang C, Mosquera JV, Dube CJ, Khan MD, Palmore M, Kalra JK, Kavousi M, Peyser PA, Matic L, Hedin U, Manichaikul A, Sonkusare SK, Civelek M, Kovacic JC, Björkegren JL, Malhotra R, Miller CL. FHL5 Controls Vascular Disease-Associated Gene Programs in Smooth Muscle Cells. Circ Res 2023; 132:1144-1161. [PMID: 37017084 PMCID: PMC10147587 DOI: 10.1161/circresaha.122.321692] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 03/21/2023] [Indexed: 04/06/2023]
Abstract
BACKGROUND Genome-wide association studies have identified hundreds of loci associated with common vascular diseases, such as coronary artery disease, myocardial infarction, and hypertension. However, the lack of mechanistic insights for many GWAS loci limits their translation into the clinic. Among these loci with unknown functions is UFL1-four-and-a-half LIM (LIN-11, Isl-1, MEC-3) domain 5 (FHL5; chr6q16.1), which reached genome-wide significance in a recent coronary artery disease/ myocardial infarction GWAS meta-analysis. UFL1-FHL5 is also associated with several vascular diseases, consistent with the widespread pleiotropy observed for GWAS loci. METHODS We apply a multimodal approach leveraging statistical fine-mapping, epigenomic profiling, and ex vivo analysis of human coronary artery tissues to implicate FHL5 as the top candidate causal gene. We unravel the molecular mechanisms of the cross-phenotype genetic associations through in vitro functional analyses and epigenomic profiling experiments in coronary artery smooth muscle cells. RESULTS We prioritized FHL5 as the top candidate causal gene at the UFL1-FHL5 locus through expression quantitative trait locus colocalization methods. FHL5 gene expression was enriched in the smooth muscle cells and pericyte population in human artery tissues with coexpression network analyses supporting a functional role in regulating smooth muscle cell contraction. Unexpectedly, under procalcifying conditions, FHL5 overexpression promoted vascular calcification and dysregulated processes related to extracellular matrix organization and calcium handling. Lastly, by mapping FHL5 binding sites and inferring FHL5 target gene function using artery tissue gene regulatory network analyses, we highlight regulatory interactions between FHL5 and downstream coronary artery disease/myocardial infarction loci, such as FOXL1 and FN1 that have roles in vascular remodeling. CONCLUSIONS Taken together, these studies provide mechanistic insights into the pleiotropic genetic associations of UFL1-FHL5. We show that FHL5 mediates vascular disease risk through transcriptional regulation of downstream vascular remodeling gene programs. These transacting mechanisms may explain a portion of the heritable risk for complex vascular diseases.
Collapse
Affiliation(s)
- Doris Wong
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
| | - Gaëlle Auguste
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Christian L. Lino Cardenas
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Adam W. Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Yixuan Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Yipei Song
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - R. Noah Perry
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Redouane Aherrahrou
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Maniselvan Kuppusamy
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
| | - Chaojie Yang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Jose Verdezoto Mosquera
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Collin J. Dube
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Mohammad Daud Khan
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Meredith Palmore
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Jaspreet K. Kalra
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, The Netherlands
| | | | - Ljubica Matic
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ani Manichaikul
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - Swapnil K. Sonkusare
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Mete Civelek
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Jason C. Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- St. Vincent’s Clinical School, University of New South Wales, Sydney, Australia
| | - Johan L.M. Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Rajeev Malhotra
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Clint L. Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
4
|
Zhang M, Li J, Wang Q, Urabe G, Tang R, Huang Y, Mosquera JV, Kent KC, Wang B, Miller CL, Guo LW. Gene-repressing epigenetic reader EED unexpectedly enhances cyclinD1 gene activation. Mol Ther Nucleic Acids 2023; 31:717-729. [PMID: 36923952 PMCID: PMC10009644 DOI: 10.1016/j.omtn.2023.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 02/16/2023] [Indexed: 02/23/2023]
Abstract
Epigenetically switched, proliferative vascular smooth muscle cells (SMCs) form neointima, engendering stenotic diseases. Histone-3 lysine-27 trimethylation (H3K27me3) and acetylation (H3K27ac) marks are associated with gene repression and activation, respectively. The polycomb protein embryonic ectoderm development (EED) reads H3K27me3 and also enhances its deposition, hence is a canonical gene repressor. However, herein we found an unexpected role for EED in activating the bona fide pro-proliferative gene Ccnd1 (cyclinD1). EED overexpression in SMCs increased Ccnd1 mRNA, seemingly contradicting its gene-repressing function. However, consistently, EED co-immunoprecipitated with gene-activating H3K27ac reader BRD4, and they co-occupied at both mitogen-activated Ccnd1 and mitogen-repressed P57 (bona fide anti-proliferative gene), as indicated by chromatin immunoprecipitation qPCR. These results were abolished by an inhibitor of either the EED/H3K27me3 or BRD4/H3K27ac reader function. In accordance, elevating BRD4 increased H3K27me3. In vivo, while EED was upregulated in rat and human neointimal lesions, selective EED inhibition abated angioplasty-induced neointima and reduced cyclinD1 in rat carotid arteries. Thus, results uncover a previously unknown role for EED in Ccnd1 activation, likely via its cooperativity with BRD4 that enhances each other's reader function; i.e., activating pro-proliferative Ccnd1 while repressing anti-proliferative P57. As such, this study confers mechanistic implications for the epigenetic intervention of neointimal pathology.
Collapse
Affiliation(s)
- Mengxue Zhang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Jing Li
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Qingwei Wang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Go Urabe
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Runze Tang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Yitao Huang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Jose Verdezoto Mosquera
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.,Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - K Craig Kent
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Bowen Wang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Clint L Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.,Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA.,Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA.,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Lian-Wang Guo
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA 22908, USA.,Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| |
Collapse
|
5
|
Sakamoto A, Kawakami R, Mori M, Guo L, Paek KH, Mosquera JV, Cornelissen A, Ghosh SKB, Kawai K, Konishi T, Fernandez R, Fuller DT, Xu W, Vozenilek AE, Sato Y, Jinnouchi H, Torii S, Turner AW, Akahori H, Kuntz S, Weinkauf CC, Lee PJ, Kutys R, Harris K, Killey AL, Mayhew CM, Ellis M, Weinstein LM, Gadhoke NV, Dhingra R, Ullman J, Dikongue A, Romero ME, Kolodgie FD, Miller CL, Virmani R, Finn AV. CD163+ macrophages restrain vascular calcification, promoting the development of high-risk plaque. JCI Insight 2023; 8:e154922. [PMID: 36719758 PMCID: PMC10077470 DOI: 10.1172/jci.insight.154922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/20/2023] [Indexed: 02/01/2023] Open
Abstract
Vascular calcification (VC) is concomitant with atherosclerosis, yet it remains uncertain why rupture-prone high-risk plaques do not typically show extensive calcification. Intraplaque hemorrhage (IPH) deposits erythrocyte-derived cholesterol, enlarging the necrotic core and promoting high-risk plaque development. Pro-atherogenic CD163+ alternative macrophages engulf hemoglobin:haptoglobin (HH) complexes at IPH sites. However, their role in VC has never been examined to our knowledge. Here we show, in human arteries, the distribution of CD163+ macrophages correlated inversely with VC. In vitro experiments using vascular smooth muscle cells (VSMCs) cultured with HH-exposed human macrophage - M(Hb) - supernatant reduced calcification, while arteries from ApoE-/- CD163-/- mice showed greater VC. M(Hb) supernatant-exposed VSMCs showed activated NF-κB, while blocking NF-κB attenuated the anticalcific effect of M(Hb) on VSMCs. CD163+ macrophages altered VC through NF-κB-induced transcription of hyaluronan synthase (HAS), an enzyme that catalyzes the formation of the extracellular matrix glycosaminoglycan, hyaluronan, within VSMCs. M(Hb) supernatants enhanced HAS production in VSMCs, while knocking down HAS attenuated its anticalcific effect. NF-κB blockade in ApoE-/- mice reduced hyaluronan and increased VC. In human arteries, hyaluronan and HAS were increased in areas of CD163+ macrophage presence. Our findings highlight an important mechanism by which CD163+ macrophages inhibit VC through NF-κB-induced HAS augmentation and thus promote the high-risk plaque development.
Collapse
Affiliation(s)
| | | | | | - Liang Guo
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | - Ka Hyun Paek
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | - Jose Verdezoto Mosquera
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | | | | | - Kenji Kawai
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | | | | | | | - Weili Xu
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | | | - Yu Sato
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | | | - Sho Torii
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | - Adam W. Turner
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Hirokuni Akahori
- Department of Cardiovascular and Renal Medicine, Hyogo Medical University, Nishinomiya, Hyogo, Japan
| | - Salome Kuntz
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | - Craig C. Weinkauf
- Division of Vascular and Endovascular Surgery, University of Arizona, Tucson, Arizona, USA
| | | | - Robert Kutys
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | - Kathryn Harris
- University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | | | | - Roma Dhingra
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | | | | | | | | | - Clint L. Miller
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Renu Virmani
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | - Aloke V. Finn
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
- University of Maryland School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
6
|
Hodonsky CJ, Turner AW, Khan MD, Barrientos NB, Methorst R, Ma L, Lopez NG, Mosquera JV, Auguste G, Farber E, Ma WF, Wong D, Onengut-Gumuscu S, Kavousi M, Peyser PA, van der Laan SW, Leeper NJ, Kovacic JC, Björkegren JLM, Miller CL. Integrative multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci. medRxiv 2023:2023.02.09.23285622. [PMID: 36824883 PMCID: PMC9949190 DOI: 10.1101/2023.02.09.23285622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Genome-wide association studies (GWAS) have identified hundreds of genetic risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in GWAS and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotype information to identify quantitative trait loci (QTL) for gene expression and splicing in coronary arteries obtained from 138 ancestrally diverse Americans. Of 2,132 eQTL-associated genes (eGenes), 47% were previously unreported in coronary arteries and 19% exhibited cell-type-specific expression. Colocalization analysis with GWAS identified subgroups of eGenes unique to CAD and blood pressure. Fine-mapping highlighted additional eGenes of interest, including TBX20 and IL5 . Splicing (s)QTLs for 1,690 genes were also identified, among which TOR1AIP1 and ULK3 sQTLs demonstrated the importance of evaluating splicing events to accurately identify disease-relevant gene expression. Our work provides the first human coronary artery eQTL resource from a patient sample and exemplifies the necessity of diverse study populations and multi-omic approaches to characterize gene regulation in critical disease processes. Study Design Overview
Collapse
|
7
|
Ma WF, Turner AW, Gancayco C, Wong D, Song Y, Mosquera JV, Auguste G, Hodonsky CJ, Prabhakar A, Ekiz HA, van der Laan SW, Miller CL. PlaqView 2.0: A comprehensive web portal for cardiovascular single-cell genomics. Front Cardiovasc Med 2022; 9:969421. [PMID: 36003902 PMCID: PMC9393487 DOI: 10.3389/fcvm.2022.969421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Single-cell RNA-seq (scRNA-seq) is a powerful genomics technology to interrogate the cellular composition and behaviors of complex systems. While the number of scRNA-seq datasets and available computational analysis tools have grown exponentially, there are limited systematic data sharing strategies to allow rapid exploration and re-analysis of single-cell datasets, particularly in the cardiovascular field. We previously introduced PlaqView, an open-source web portal for the exploration and analysis of published atherosclerosis single-cell datasets. Now, we introduce PlaqView 2.0 (www.plaqview.com), which provides expanded features and functionalities as well as additional cardiovascular single-cell datasets. We showcase improved PlaqView functionality, backend data processing, user-interface, and capacity. PlaqView brings new or improved tools to explore scRNA-seq data, including gene query, metadata browser, cell identity prediction, ad hoc RNA-trajectory analysis, and drug-gene interaction prediction. PlaqView serves as one of the largest central repositories for cardiovascular single-cell datasets, which now includes data from human aortic aneurysm, gene-specific mouse knockouts, and healthy references. PlaqView 2.0 brings advanced tools and high-performance computing directly to users without the need for any programming knowledge. Lastly, we outline steps to generalize and repurpose PlaqView's framework for single-cell datasets from other fields.
Collapse
Affiliation(s)
- Wei Feng Ma
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA, United States
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Adam W. Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Christina Gancayco
- Research Computing, University of Virginia, Charlottesville, VA, United States
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Yipei Song
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Computer Engineering, University of Virginia, Charlottesville, VA, United States
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Research Computing, University of Virginia, Charlottesville, VA, United States
| | - Gaëlle Auguste
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Chani J. Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Ajay Prabhakar
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - H. Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Gülbahçe, Turkey
| | - Sander W. van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Clint L. Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
- *Correspondence: Clint L. Miller
| |
Collapse
|
8
|
Turner AW, Hu SS, Mosquera JV, Ma WF, Hodonsky CJ, Wong D, Auguste G, Song Y, Sol-Church K, Farber E, Kundu S, Kundaje A, Lopez NG, Ma L, Ghosh SKB, Onengut-Gumuscu S, Ashley EA, Quertermous T, Finn AV, Leeper NJ, Kovacic JC, Björkgren JLM, Zang C, Miller CL. Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk. Nat Genet 2022; 54:804-816. [PMID: 35590109 PMCID: PMC9203933 DOI: 10.1038/s41588-022-01069-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 03/31/2022] [Indexed: 12/24/2022]
Abstract
Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across cell types. Genome-wide association studies (GWAS) have identified over 200 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis-regulatory elements (CREs). Here, we applied single-nucleus ATAC-seq to profile 28,316 nuclei across coronary artery segments from 41 patients with varying stages of CAD, which revealed 14 distinct cellular clusters. We mapped ~320,000 accessible sites across all cells, identified cell type-specific elements, transcription factors, and prioritized functional CAD risk variants. . We identified elements in smooth muscle cell (SMC) transition states (e.g. fibromyocytes) and functional variants predicted to alter SMC and macrophage-specific regulation of MRAS (3q22) and LIPA (10q23), respectively. We further nominated key driver transcription factors such as PRDM16 and TBX2. Together, this single nucleus atlas provides a critical step towards interpreting regulatory mechanisms across the continuum of CAD risk.
Collapse
Affiliation(s)
- Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Shengen Shawn Hu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Wei Feng Ma
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Medical Scientist Training Program, University of Virginia, Charlottesville, VA, USA.,Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Gaëlle Auguste
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Yipei Song
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Katia Sol-Church
- Department of Pathology, University of Virginia, Charlottesville, VA, USA.,Genome Analysis & Technology Core, University of Virginia, Charlottesville, VA, USA
| | - Emily Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Genome Sciences Laboratory, University of Virginia, Charlottesville, VA, USA
| | - Soumya Kundu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Nicolas G Lopez
- Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA, USA
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Genome Sciences Laboratory, University of Virginia, Charlottesville, VA, USA.,Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Euan A Ashley
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Thomas Quertermous
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | | | - Nicholas J Leeper
- Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA, USA
| | - Jason C Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Johan L M Björkgren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA. .,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA. .,Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA. .,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA. .,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA. .,Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
| |
Collapse
|
9
|
Kupkova K, Mosquera JV, Smith JP, Stolarczyk M, Danehy TL, Lawson JT, Xue B, Stubbs JT, LeRoy N, Sheffield NC. GenomicDistributions: fast analysis of genomic intervals with Bioconductor. BMC Genomics 2022; 23:299. [PMID: 35413804 PMCID: PMC9003978 DOI: 10.1186/s12864-022-08467-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background Epigenome analysis relies on defined sets of genomic regions output by widely used assays such as ChIP-seq and ATAC-seq. Statistical analysis and visualization of genomic region sets is essential to answer biological questions in gene regulation. As the epigenomics community continues generating data, there will be an increasing need for software tools that can efficiently deal with more abundant and larger genomic region sets. Here, we introduce GenomicDistributions, an R package for fast and easy summarization and visualization of genomic region data. Results GenomicDistributions offers a broad selection of functions to calculate properties of genomic region sets, such as feature distances, genomic partition overlaps, and more. GenomicDistributions functions are meticulously optimized for best-in-class speed and generally outperform comparable functions in existing R packages. GenomicDistributions also offers plotting functions that produce editable ggplot objects. All GenomicDistributions functions follow a uniform naming scheme and can handle either single or multiple region set inputs. Conclusions GenomicDistributions offers a fast and scalable tool for exploratory genomic region set analysis and visualization. GenomicDistributions excels in user-friendliness, flexibility of outputs, breadth of functions, and computational performance. GenomicDistributions is available from Bioconductor (https://bioconductor.org/packages/release/bioc/html/GenomicDistributions.html). Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08467-y.
Collapse
Affiliation(s)
- Kristyna Kupkova
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA
| | - Jason P Smith
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA
| | - Michał Stolarczyk
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA
| | - Tessa L Danehy
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA
| | - John T Lawson
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA.,Department of Biomedical Engineering, University of Virginia, Charlottesville, USA
| | - Bingjie Xue
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA.,Department of Biomedical Engineering, University of Virginia, Charlottesville, USA
| | - John T Stubbs
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA
| | - Nathan LeRoy
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA.,Department of Biomedical Engineering, University of Virginia, Charlottesville, USA
| | - Nathan C Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA. .,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA. .,Department of Biomedical Engineering, University of Virginia, Charlottesville, USA. .,Department of Public Health Sciences, University of Virginia, Charlottesville, USA.
| |
Collapse
|
10
|
Ma WF, Hodonsky CJ, Turner AW, Wong D, Song Y, Mosquera JV, Ligay AV, Slenders L, Gancayco C, Pan H, Barrientos NB, Mai D, Alencar GF, Owsiany K, Owens GK, Reilly MP, Li M, Pasterkamp G, Mokry M, van der Laan SW, Khomtchouk BB, Miller CL. Enhanced single-cell RNA-seq workflow reveals coronary artery disease cellular cross-talk and candidate drug targets. Atherosclerosis 2022; 340:12-22. [PMID: 34871816 PMCID: PMC8919504 DOI: 10.1016/j.atherosclerosis.2021.11.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND AND AIMS The atherosclerotic plaque microenvironment is highly complex, and selective agents that modulate plaque stability are not yet available. We sought to develop a scRNA-seq analysis workflow to investigate this environment and uncover potential therapeutic approaches. We designed a user-friendly, reproducible workflow that will be applicable to other disease-specific scRNA-seq datasets. METHODS Here we incorporated automated cell labeling, pseudotemporal ordering, ligand-receptor evaluation, and drug-gene interaction analysis into a ready-to-deploy workflow. We applied this pipeline to further investigate a previously published human coronary single-cell dataset by Wirka et al. Notably, we developed an interactive web application to enable further exploration and analysis of this and other cardiovascular single-cell datasets. RESULTS We revealed distinct derivations of fibroblast-like cells from smooth muscle cells (SMCs), and showed the key changes in gene expression along their de-differentiation path. We highlighted several key ligand-receptor interactions within the atherosclerotic environment through functional expression profiling and revealed several avenues for future pharmacological development for precision medicine. Further, our interactive web application, PlaqView (www.plaqview.com), allows lay scientists to explore this and other datasets and compare scRNA-seq tools without prior coding knowledge. CONCLUSIONS This publicly available workflow and application will allow for more systematic and user-friendly analysis of scRNA datasets in other disease and developmental systems. Our analysis pipeline provides many hypothesis-generating tools to unravel the etiology of coronary artery disease. We also highlight potential mechanisms for several drugs in the atherosclerotic cellular environment. Future releases of PlaqView will feature more scRNA-seq and scATAC-seq atherosclerosis-related datasets to provide a critical resource for the field, and to promote data harmonization and biological interpretation.
Collapse
Affiliation(s)
- Wei Feng Ma
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA, 22908, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA , 22908, USA
| | - Yipei Song
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA; Department of Computer Engineering, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA , 22908, USA
| | - Alexandra V Ligay
- Master of Science in Biomedical Informatics (MScBMI) Program, University of Chicago, Chicago, IL, 60637, USA
| | - Lotte Slenders
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584, CX, Utrecht, the Netherlands
| | - Christina Gancayco
- Research Computing, University of Virginia, Charlottesville, VA, 22908, USA
| | - Huize Pan
- Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, 10032, USA
| | - Nelson B Barrientos
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - David Mai
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Gabriel F Alencar
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, 22908, USA
| | - Katherine Owsiany
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA, 22908, USA; Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, 22908, USA
| | - Gary K Owens
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, 22908, USA; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Muredach P Reilly
- Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, 10032, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584, CX, Utrecht, the Netherlands
| | - Michal Mokry
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584, CX, Utrecht, the Netherlands; Department of Experimental Cardiology, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584, CX, Utrecht, the Netherlands
| | - Bohdan B Khomtchouk
- Department of Medicine, Section of Computational Biomedicine and Biomedical Data Science, Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL , 60637, USA.
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA , 22908, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA.
| |
Collapse
|
11
|
Abstract
Fat stored in the form of lipid droplets has long been considered a defining characteristic of cytoplasm. However, recent studies have shown that nuclear lipid droplets occur in multiple cells and tissues, including in human patients with fatty liver disease. The function(s) of stored fat in the nucleus has not been determined, and it is possible that nuclear fat is beneficial in some situations. Conversely, nuclear lipid droplets might instead be deleterious by disrupting nuclear organization or triggering aggregation of hydrophobic proteins. We show here that nuclear lipid droplets occur normally in C. elegans intestinal cells and germ cells, but appear to be associated with damage only in the intestine. Lipid droplets in intestinal nuclei can be associated with novel bundles of microfilaments (nuclear actin) and membrane tubules that might have roles in damage repair. To increase the normal, low frequency of nuclear lipid droplets in wild-type animals, we used a forward genetic screen to isolate mutants with abnormally large or abundant nuclear lipid droplets. Genetic analysis and cloning of three such mutants showed that the genes encode the lipid regulator SEIP-1/seipin, the inner nuclear membrane protein NEMP-1/Nemp1/TMEM194A, and a component of COPI vesicles called COPA-1/α-COP. We present several lines of evidence that the nuclear lipid droplet phenotype of copa-1 mutants results from a defect in retrieving mislocalized membrane proteins that normally reside in the endoplasmic reticulum. The seip-1 mutant causes most germ cells to have nuclear lipid droplets, the largest of which occupy more than a third of the nuclear volume. Nevertheless, the nuclear lipid droplets do not trigger apoptosis, and the germ cells differentiate into gametes that produce viable, healthy progeny. Thus, our results suggest that nuclear lipid droplets are detrimental to intestinal nuclei, but have no obvious deleterious effect on germ nuclei. Several human disorders such as obesity are associated with abnormal fat storage. Cells normally store fat in cytoplasmic organelles called lipid droplets. However, recent studies have shown that fat can also form inside of the cell nucleus, and the effects of nuclear fat are not known. Here we use the cell biology and genetics of the model organism C. elegans to study the causes and consequences of nuclear fat. We show that intestinal cells can contain nuclear fat, particularly during high-low-high changes in cytoplasmic fat that involve de novo fat synthesis. Nuclear fat is associated with multiple changes in intestinal nuclei that appear to represent damage and repair. Germ nuclei that normally differentiate into oocytes can also contain nuclear fat. In germ cells, however, even high levels of nuclear fat appear to cause little or no damage. Our results suggest that intestinal nuclei and germ cell nuclei might have different responses to nuclear fat in part because they differ in chromosomal organization at the nuclear envelope.
Collapse
Affiliation(s)
| | - Meghan C. Bacher
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - James R. Priess
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| |
Collapse
|