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Broadaway KA, Brotman SM, Rosen JD, Currin KW, Alkhawaja AA, Etheridge AS, Wright F, Gallins P, Jima D, Zhou YH, Love MI, Innocenti F, Mohlke KL. Liver eQTL meta-analysis illuminates potential molecular mechanisms of cardiometabolic traits. Am J Hum Genet 2024; 111:1899-1913. [PMID: 39173627 PMCID: PMC11393674 DOI: 10.1016/j.ajhg.2024.07.017] [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: 01/04/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/24/2024] Open
Abstract
Understanding the molecular mechanisms of complex traits is essential for developing targeted interventions. We analyzed liver expression quantitative-trait locus (eQTL) meta-analysis data on 1,183 participants to identify conditionally distinct signals. We found 9,013 eQTL signals for 6,564 genes; 23% of eGenes had two signals, and 6% had three or more signals. We then integrated the eQTL results with data from 29 cardiometabolic genome-wide association study (GWAS) traits and identified 1,582 GWAS-eQTL colocalizations for 747 eGenes. Non-primary eQTL signals accounted for 17% of all colocalizations. Isolating signals by conditional analysis prior to coloc resulted in 37% more colocalizations than using marginal eQTL and GWAS data, highlighting the importance of signal isolation. Isolating signals also led to stronger evidence of colocalization: among 343 eQTL-GWAS signal pairs in multi-signal regions, analyses that isolated the signals of interest resulted in higher posterior probability of colocalization for 41% of tests. Leveraging allelic heterogeneity, we predicted causal effects of gene expression on liver traits for four genes. To predict functional variants and regulatory elements, we colocalized eQTL with liver chromatin accessibility QTL (caQTL) and found 391 colocalizations, including 73 with non-primary eQTL signals and 60 eQTL signals that colocalized with both a caQTL and a GWAS signal. Finally, we used publicly available massively parallel reporter assays in HepG2 to highlight 14 eQTL signals that include at least one expression-modulating variant. This multi-faceted approach to unraveling the genetic underpinnings of liver-related traits could lead to therapeutic development.
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Affiliation(s)
- K Alaine Broadaway
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sarah M Brotman
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jonathan D Rosen
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kevin W Currin
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Abdalla A Alkhawaja
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Amy S Etheridge
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Fred Wright
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA; Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA; Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA
| | - Paul Gallins
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
| | - Dereje Jima
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
| | - Yi-Hui Zhou
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA; Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Federico Innocenti
- Eshelman School of Pharmacy, Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
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2
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Nikpay M. Genome-wide search identified DNA methylation sites that regulate the metabolome. Front Genet 2023; 14:1093882. [PMID: 37274792 PMCID: PMC10233745 DOI: 10.3389/fgene.2023.1093882] [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: 11/09/2022] [Accepted: 05/09/2023] [Indexed: 06/07/2023] Open
Abstract
Background: Identifying DNA methylation sites that regulate the metabolome is important for several purposes. In this study, publicly available GWAS data were integrated to find methylation sites that impact metabolome through a discovery and replication scheme and by using Mendelian randomization. Results: The outcome of analyses revealed 107 methylation sites associated with 84 metabolites at the genome-wide significance level (p<5e-8) at both the discovery and replication stages. A large percentage of the observed associations (85%) were with lipids, significantly higher than expected (p = 0.0003). A number of CpG (methylation) sites showed specificity e.g., cg20133200 within PFKP was associated with glucose only and cg10760299 within GATM impacted the level of creatinine; in contrast, there were sites associated with numerous metabolites e.g., cg20102877 on the 2p23.3 region was associated with 39 metabolites. Integrating transcriptome data enabled identifying genes (N = 82) mediating the impact of methylation sites on the metabolome and cardiometabolic traits. For example, PABPC4 mediated the impact of cg15123755-HDL on type-2 diabetes. KCNK7 mediated the impact of cg21033440-lipids on hypertension. POC5, ILRUN, FDFT1, and NEIL2 mediated the impact of CpG sites on obesity through metabolic pathways. Conclusion: This study provides a catalog of DNA methylation sites that regulate the metabolome for downstream applications.
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3
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Tribolet L, Brice AM, Fulford TS, Layton DS, Godfrey DI, Bean AGD, Stewart CR. Identification of a novel role for the immunomodulator ILRUN in the development of several T cell subsets in mice. Immunobiology 2023; 228:152380. [PMID: 37031606 DOI: 10.1016/j.imbio.2023.152380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/20/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023]
Abstract
Inflammation and lipid regulator with UBA-like and NBR1-like domains (ILRUN) is a protein-encoding gene associated with innate immune signaling, lipid metabolism and cancer. In the context of innate immunity, ILRUN inhibits IRF3-mediated transcription of antimicrobial and proinflammatory cytokines by inducing degradation of the transcriptional coactivators CBP and p300. There remains a paucity of information, however, regarding the innate immune roles of ILRUN beyond in vitro analyses. To address this, we utilize a knockout mouse model to investigate the effect of ILRUN on cytokine expression in splenocytes and on the development of immune cell populations in the spleen and thymus. We show elevated production of tumor necrosis factor and interleukin-6 cytokines in ILRUN-deficient splenocytes following stimulation with the innate immune ligands polyinosinic:polycytidylic acid or lipopolysaccharide. Differences were also observed in the populations of several T cell subsets, including regulatory, mucosal-associated invariant and natural killer. These data identify novel functions for ILRUN in the development of certain immune cell populations and support previous in vitro findings that ILRUN negatively regulates the synthesis of pathogen-stimulated cytokines. This establishes the ILRUN knockout mouse model as a valuable resource for further study of the functions of ILRUN in health and disease.
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Affiliation(s)
- Leon Tribolet
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong 3220, Victoria, Australia
| | - Aaron M Brice
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong 3220, Victoria, Australia
| | - Thomas S Fulford
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Victoria, Australia
| | - Daniel S Layton
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong 3220, Victoria, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Victoria, Australia
| | - Andrew G D Bean
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong 3220, Victoria, Australia
| | - Cameron R Stewart
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong 3220, Victoria, Australia.
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4
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Hong-Le T, Crouse WL, Keele GR, Holl K, Seshie O, Tschannen M, Craddock A, Das SK, Szalanczy AM, McDonald B, Grzybowski M, Klotz J, Sharma NK, Geurts AM, Key CCC, Hawkins G, Valdar W, Mott R, Solberg Woods LC. Genetic Mapping of Multiple Traits Identifies Novel Genes for Adiposity, Lipids, and Insulin Secretory Capacity in Outbred Rats. Diabetes 2023; 72:135-148. [PMID: 36219827 PMCID: PMC9797320 DOI: 10.2337/db22-0252] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 10/04/2022] [Indexed: 01/21/2023]
Abstract
Despite the successes of human genome-wide association studies, the causal genes underlying most metabolic traits remain unclear. We used outbred heterogeneous stock (HS) rats, coupled with expression data and mediation analysis, to identify quantitative trait loci (QTLs) and candidate gene mediators for adiposity, glucose tolerance, serum lipids, and other metabolic traits. Physiological traits were measured in 1,519 male HS rats, with liver and adipose transcriptomes measured in >410 rats. Genotypes were imputed from low-coverage whole-genome sequencing. Linear mixed models were used to detect physiological and expression QTLs (pQTLs and eQTLs, respectively), using both single nucleotide polymorphism (SNP)- and haplotype-based models for pQTL mapping. Genes with cis-eQTLs that overlapped pQTLs were assessed as causal candidates through mediation analysis. We identified 14 SNP-based pQTLs and 19 haplotype-based pQTLs, of which 10 were in common. Using mediation, we identified the following genes as candidate mediators of pQTLs: Grk5 for fat pad weight and serum triglyceride pQTLs on Chr1, Krtcap3 for fat pad weight and serum triglyceride pQTLs on Chr6, Ilrun for a fat pad weight pQTL on Chr20, and Rfx6 for a whole pancreatic insulin content pQTL on Chr20. Furthermore, we verified Grk5 and Ktrcap3 using gene knockdown/out models, thereby shedding light on novel regulators of obesity.
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Affiliation(s)
- Thu Hong-Le
- Genetics Institute, University College London, London, U.K
| | - Wesley L. Crouse
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Katie Holl
- Medical College of Wisconsin, Milwaukee, WI
| | - Osborne Seshie
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | | | - Ann Craddock
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Swapan K. Das
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Alexandria M. Szalanczy
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Bailey McDonald
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | | | | | - Neeraj K. Sharma
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | | | - Chia-Chi Chuang Key
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Gregory Hawkins
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Richard Mott
- Genetics Institute, University College London, London, U.K
| | - Leah C. Solberg Woods
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
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Bi X, Stankov S, Lee PC, Wang Z, Wu X, Li L, Ko YA, Cheng L, Zhang H, Hand NJ, Rader DJ. ILRUN Promotes Atherosclerosis Through Lipid-Dependent and Lipid-Independent Factors. Arterioscler Thromb Vasc Biol 2022; 42:1139-1151. [PMID: 35861973 PMCID: PMC9420832 DOI: 10.1161/atvbaha.121.317156] [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: 02/04/2023]
Abstract
BACKGROUND Common genetic variation in close proximity to the ILRUN gene are significantly associated with coronary artery disease as well as with plasma lipid traits. We recently demonstrated that hepatic inflammation and lipid regulator with ubiquitin-associated domain-like and NBR1-like domains (ILRUN) regulates lipoprotein metabolism in vivo in mice. However, whether ILRUN, which is expressed in vascular cells, directly impacts atherogenesis remains unclear. We sought to determine the role of ILRUN in atherosclerosis development in mice. METHODS For our study, we generated global Ilrun-deficient (IlrunKO) male and female mice on 2 hyperlipidemic backgrounds: low density lipoprotein receptor knockout (LdlrKO) and apolipoprotein E knockout (ApoeKO; double knockout [DKO]). RESULTS Compared with littermate control mice (single LdlrKO or ApoeKO), deletion of Ilrun in DKO mice resulted in significantly attenuated both early and advanced atherosclerotic lesion development, as well as reduced necrotic area. DKO mice also had significantly decreased plasma cholesterol levels, primarily attributable to non-HDL (high-density lipoprotein) cholesterol. Hepatic-specific reconstitution of ILRUN in DKO mice on the ApoeKO background normalized plasma lipids, but atherosclerotic lesion area and necrotic area remained reduced in DKO mice. Further analysis showed that loss of Ilrun increased efferocytosis receptor MerTK expression in macrophages, enhanced in vitro efferocytosis, and significantly improved in situ efferocytosis in advanced lesions. CONCLUSIONS Our results support ILRUN as an important novel regulator of atherogenesis that promotes lesion progression and necrosis. It influences atherosclerosis through both plasma lipid-dependent and lipid-independent mechanisms. These findings support ILRUN as the likely causal gene responsible for genetic association of variants with coronary artery disease at this locus and suggest that suppression of ILRUN activity might be expected to reduce atherosclerosis.
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Affiliation(s)
- Xin Bi
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sylvia Stankov
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul C. Lee
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ziyi Wang
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Xun Wu
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Li Li
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yi-An Ko
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lan Cheng
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hanrui Zhang
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicholas J. Hand
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J. Rader
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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6
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Getz GS, Reardon CA. ILRUNing to Atherosclerosis. Arterioscler Thromb Vasc Biol 2022; 42:1152-1153. [PMID: 35924556 DOI: 10.1161/atvbaha.122.318107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Godfrey S Getz
- Department of Pathology, University of Chicago, IL (G.S.G.)
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7
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ILRUN Downregulates ACE2 Expression and Blocks Infection of Human Cells by SARS-CoV-2. J Virol 2021; 95:e0032721. [PMID: 33963054 DOI: 10.1128/jvi.00327-21] [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: 11/20/2022] Open
Abstract
The human protein-coding gene ILRUN (inflammation and lipid regulator with UBA-like and NBR1-like domains; previously C6orf106) was identified as a proviral factor for Hendra virus infection and was recently characterized to function as an inhibitor of type I interferon expression. Here, we have utilized transcriptome sequencing (RNA-seq) to define cellular pathways regulated by ILRUN in the context of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of Caco-2 cells. We find that inhibition of ILRUN expression by RNA interference alters transcription profiles of numerous cellular pathways, including upregulation of the SARS-CoV-2 entry receptor ACE2 and several other members of the renin-angiotensin aldosterone system. In addition, transcripts of the SARS-CoV-2 coreceptors TMPRSS2 and CTSL were also upregulated. Inhibition of ILRUN also resulted in increased SARS-CoV-2 replication, while overexpression of ILRUN had the opposite effect, identifying ILRUN as a novel antiviral factor for SARS-CoV-2 replication. This represents, to our knowledge, the first report of ILRUN as a regulator of the renin-angiotensin-aldosterone system (RAAS). IMPORTANCE There is no doubt that the current rapid global spread of COVID-19 has had significant and far-reaching impacts on our health and economy and will continue to do so. Research in emerging infectious diseases, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is growing rapidly, with new breakthroughs in the understanding of host-virus interactions to assist with the development of innovative and exciting therapeutic strategies. Here, we present the first evidence that modulation of the human protein-coding gene ILRUN functions as an antiviral factor for SARS-CoV-2 infection, likely through its newly identified role in regulating the expression of SARS-CoV-2 entry receptors ACE2, TMPRSS2, and CTSL. These data improve our understanding of biological pathways that regulate host factors critical to SARS-CoV-2 infection, contributing to the development of antiviral strategies to deal with the current SARS-CoV-2 pandemic.
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8
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Ding X, Cai M, Wang S, Yang Q, Zheng X, Zuo X, Liu S. Gene-based association analysis identified a novel gene associated with systemic lupus erythematosus. Ann Hum Genet 2021; 85:213-220. [PMID: 34145571 DOI: 10.1111/ahg.12439] [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: 12/05/2020] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is a complex autoimmune disease with strong genetic predisposition. Genome-wide association studies (GWAS) of SLE have identified more than 50 robust susceptibility loci. However, traditional individual SNP-based GWAS have made it difficult to identify variants with small effects. Moreover, variants revealed by GWAS only explain a limited disease heritability, suggesting that many susceptibility genes remain uncovered. METHODS We first curated the published SLE GWAS data from 1047 SLE patients and 1205 healthy controls of Chinese ancestry and performed a gene-based association study. Then quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was conducted to verify novel genes identified above. RESULTS Gene-based association study identified 10 SLE-associated genes, nine of which were reported by previous GWAS, the other one, ILRUN, is a newly identified gene and was further validated by qRT-PCR. Gene expression analysis of Gene Expression Omnibus (GEO) datasets also showed that the expression of ILRUN in patients with SLE was lower than that in normal subjects. CONCLUSION In this study, gene-based association study and qRT-PCR identified that ILRUN is a novel susceptibility gene of SLE. ILRUN may regulate inflammation and antiviral response through its effect on the transcription of type I interferons )I-IFN, and participate in the pathogenesis of SLE.
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Affiliation(s)
- Xian Ding
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Minglong Cai
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Sun Wang
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Qingqing Yang
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Xiaodong Zheng
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Xianbo Zuo
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Shengxiu Liu
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
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9
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Kwon SB, Ernst J. Learning a genome-wide score of human-mouse conservation at the functional genomics level. Nat Commun 2021; 12:2495. [PMID: 33941776 PMCID: PMC8093196 DOI: 10.1038/s41467-021-22653-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 03/24/2021] [Indexed: 01/06/2023] Open
Abstract
Identifying genomic regions with functional genomic properties that are conserved between human and mouse is an important challenge in the context of mouse model studies. To address this, we develop a method to learn a score of evidence of conservation at the functional genomics level by integrating information from a compendium of epigenomic, transcription factor binding, and transcriptomic data from human and mouse. The method, Learning Evidence of Conservation from Integrated Functional genomic annotations (LECIF), trains neural networks to generate this score for the human and mouse genomes. The resulting LECIF score highlights human and mouse regions with shared functional genomic properties and captures correspondence of biologically similar human and mouse annotations. Analysis with independent datasets shows the score also highlights loci associated with similar phenotypes in both species. LECIF will be a resource for mouse model studies by identifying loci whose functional genomic properties are likely conserved.
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Affiliation(s)
- Soo Bin Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, USA
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, USA. .,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California, Los Angeles, CA, USA. .,Computer Science Department, University of California, Los Angeles, CA, USA. .,Department of Computational Medicine, University of California, Los Angeles, CA, USA. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA. .,Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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10
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Rom O, Chen YE, Aviram M. Genetic variants associated with cardiovascular diseases and related risk factors highlight novel potential therapeutic approaches. Curr Opin Lipidol 2021; 32:148-150. [PMID: 33651747 PMCID: PMC7988477 DOI: 10.1097/mol.0000000000000739] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Oren Rom
- Department of Internal Medicine, Frankel Cardiovascular Center, University of Michigan, Ann Arbor, MI, USA
| | - Y. Eugene Chen
- Department of Internal Medicine, Frankel Cardiovascular Center, University of Michigan, Ann Arbor, MI, USA
| | - Michael Aviram
- The Lipid Research Laboratory, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel
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11
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Affiliation(s)
- Michael J Thomas
- Department of Pharmacology & Toxicology (M.J.T., M.G.S.-T.), Section on Endocrinology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Mary G Sorci-Thomas
- Department of Pharmacology & Toxicology (M.J.T., M.G.S.-T.), Section on Endocrinology, Medical College of Wisconsin, Milwaukee, Wisconsin.,Department of Medicine (M.G.S.-T.), Section on Endocrinology, Medical College of Wisconsin, Milwaukee, Wisconsin
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