1
|
Arthur TD, Joshua IN, Nguyen JP, D'Antonio-Chronowska A, Frazer KA, D'Antonio M. IFN-γ activates an immune-like regulatory network in the cardiac vascular endothelium. bioRxiv 2024:2024.05.03.592380. [PMID: 38746472 PMCID: PMC11092750 DOI: 10.1101/2024.05.03.592380] [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: 05/16/2024]
Abstract
The regulatory mechanisms underlying the response to pro-inflammatory cytokines during myocarditis are poorly understood. Here, we use iPSC-derived cardiovascular progenitor cells (CVPCs) to model the response to interferon gamma (IFN-γ) during myocarditis. We generate RNA-seq and ATAC-seq for four CVPCs that were treated with IFN-γ and compare them with paired untreated controls. Transcriptional differences after treatment show that IFN-γ initiates an innate immune cell-like response in the vascular cardiac endothelium. IFN-γ treatment also shifts the CVPC transcriptome towards the adult coronary artery and aorta profiles and expands the relative endothelial cell population in all four CVPC lines. Analysis of the accessible chromatin shows that IFN-γ is a potent chromatin remodeler and establishes an IRF-STAT immune-cell like regulatory network. Our findings reveal insights into the endothelial-specific protective mechanisms during myocarditis.
Collapse
|
2
|
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 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] [What about the content of this article? (0)] [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.
Collapse
|
3
|
Arthur TD, Nguyen JP, D'Antonio-Chronowska A, Matsui H, Silva NS, Joshua IN, Luchessi AD, Greenwald WWY, D'Antonio M, Pera MF, Frazer KA. Complex regulatory networks influence pluripotent cell state transitions in human iPSCs. Nat Commun 2024; 15:1664. [PMID: 38395976 PMCID: PMC10891157 DOI: 10.1038/s41467-024-45506-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing hundreds of hiPSCs derived from different individuals, we show the proportions of these pluripotent states vary considerably across lines. We discover 13 gene network modules (GNMs) and 13 regulatory network modules (RNMs), which are highly correlated with each other suggesting that the coordinated co-accessibility of regulatory elements in the RNMs likely underlie the coordinated expression of genes in the GNMs. Epigenetic analyses reveal that regulatory networks underlying self-renewal and pluripotency are more complex than previously realized. Genetic analyses identify thousands of regulatory variants that overlapped predicted transcription factor binding sites and are associated with chromatin accessibility in the hiPSCs. We show that the master regulator of pluripotency, the NANOG-OCT4 Complex, and its associated network are significantly enriched for regulatory variants with large effects, suggesting that they play a role in the varying cellular proportions of pluripotency states between hiPSCs. Our work bins tens of thousands of regulatory elements in hiPSCs into discrete regulatory networks, shows that pluripotency and self-renewal processes have a surprising level of regulatory complexity, and suggests that genetic factors may contribute to cell state transitions in human iPSC lines.
Collapse
Affiliation(s)
- Timothy D Arthur
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Division of Biomedical Informatics, University of California, San Diego, 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
| | | | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Nayara S Silva
- Northeast Biotechnology Network (RENORBIO), Graduate Program in Biotechnology, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Isaac N Joshua
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - André D Luchessi
- Northeast Biotechnology Network (RENORBIO), Graduate Program in Biotechnology, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte, Natal, Brazil
| | - William W Young Greenwald
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Matteo D'Antonio
- 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
| | | | - 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.
| |
Collapse
|
4
|
Jindal GA, Bantle AT, Solvason JJ, Grudzien JL, D'Antonio-Chronowska A, Lim F, Le SH, Song BP, Ragsac MF, Klie A, Larsen RO, Frazer KA, Farley EK. Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development. Dev Cell 2023; 58:2206-2216.e5. [PMID: 37848026 PMCID: PMC10720985 DOI: 10.1016/j.devcel.2023.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/07/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023]
Abstract
Transcriptional enhancers direct precise gene expression patterns during development and harbor the majority of variants associated with phenotypic diversity, evolutionary adaptations, and disease. Pinpointing which enhancer variants contribute to changes in gene expression and phenotypes is a major challenge. Here, we find that suboptimal or low-affinity binding sites are necessary for precise gene expression during heart development. Single-nucleotide variants (SNVs) can optimize the affinity of ETS binding sites, causing gain-of-function (GOF) gene expression, cell migration defects, and phenotypes as severe as extra beating hearts in the marine chordate Ciona robusta. In human induced pluripotent stem cell (iPSC)-derived cardiomyocytes, a SNV within a human GATA4 enhancer increases ETS binding affinity and causes GOF enhancer activity. The prevalence of suboptimal-affinity sites within enhancers creates a vulnerability whereby affinity-optimizing SNVs can lead to GOF gene expression, changes in cellular identity, and organismal-level phenotypes that could contribute to the evolution of novel traits or diseases.
Collapse
Affiliation(s)
- Granton A Jindal
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexis T Bantle
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joe J Solvason
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, 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
| | - Jessica L Grudzien
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Fabian Lim
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sophia H Le
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Benjamin P Song
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michelle F Ragsac
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, 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
| | - Adam Klie
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Reid O Larsen
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kelly A Frazer
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emma K Farley
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
5
|
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] [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: 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.
Collapse
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.
| |
Collapse
|
6
|
Arthur TD, Nguyen JP, D'Antonio-Chronowska A, Matsui H, Silva NS, Joshua IN, Luchessi AD, Young Greenwald WW, D'Antonio M, Pera MF, Frazer KA. Analysis of regulatory network modules in hundreds of human stem cell lines reveals complex epigenetic and genetic factors contribute to pluripotency state differences between subpopulations. bioRxiv 2023:2023.05.20.541447. [PMID: 37292794 PMCID: PMC10245835 DOI: 10.1101/2023.05.20.541447] [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: 06/10/2023]
Abstract
Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing hundreds of hiPSCs derived from different individuals, we show the proportions of these pluripotent states vary considerably across lines. We discovered 13 gene network modules (GNMs) and 13 regulatory network modules (RNMs), which were highly correlated with each other suggesting that the coordinated co-accessibility of regulatory elements in the RNMs likely underlied the coordinated expression of genes in the GNMs. Epigenetic analyses revealed that regulatory networks underlying self-renewal and pluripotency have a surprising level of complexity. Genetic analyses identified thousands of regulatory variants that overlapped predicted transcription factor binding sites and were associated with chromatin accessibility in the hiPSCs. We show that the master regulator of pluripotency, the NANOG-OCT4 Complex, and its associated network were significantly enriched for regulatory variants with large effects, suggesting that they may play a role in the varying cellular proportions of pluripotency states between hiPSCs. Our work captures the coordinated activity of tens of thousands of regulatory elements in hiPSCs and bins these elements into discrete functionally characterized regulatory networks, shows that regulatory elements in pluripotency networks harbor variants with large effects, and provides a rich resource for future pluripotent stem cell research.
Collapse
|
7
|
D'Antonio M, Nguyen JP, Arthur TD, Matsui H, D'Antonio-Chronowska A, Frazer KA. Author Correction: Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease. Nat Commun 2023; 14:4370. [PMID: 37474502 PMCID: PMC10359269 DOI: 10.1038/s41467-023-40048-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023] Open
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.
| |
Collapse
|
8
|
Frazer KA, Schork NJ. The human pangenome reference anticipates equitable and fundamental genomic insights. Cell Genom 2023; 3:100360. [PMID: 37492100 PMCID: PMC10363913 DOI: 10.1016/j.xgen.2023.100360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
For the past few years, researchers in the Human Pangenome Reference Consortium (HPRC) have been working to catalog almost all human genomic diversity. Frazer and Schork preview an article recently published in Nature, "A draft human pangenome reference,"1 which represents the initial release of 47 fully phased diploid assemblies of genomes of individuals with diverse ancestries.
Collapse
Affiliation(s)
- 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
| | - Nicholas J. Schork
- Quantitative Medicine and Systems Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
- Departments Molecular and Cellular Biology and Population Sciences, City of Hope National Medical Center, Duarte, CA 91010, USA
| |
Collapse
|
9
|
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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
Collapse
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.
| |
Collapse
|
10
|
Benaglio P, Zhu H, Okino ML, Yan J, Elgamal R, Nariai N, Beebe E, Korgaonkar K, Qiu Y, Donovan MK, Chiou J, Wang G, Newsome J, Kaur J, Miller M, Preissl S, Corban S, Aylward A, Taipale J, Ren B, Frazer KA, Sander M, Gaulton KJ. Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines. Cell Genom 2022; 2:100214. [PMID: 36778047 PMCID: PMC9903835 DOI: 10.1016/j.xgen.2022.100214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 06/17/2022] [Accepted: 10/15/2022] [Indexed: 11/13/2022]
Abstract
We combined functional genomics and human genetics to investigate processes that affect type 1 diabetes (T1D) risk by mediating beta cell survival in response to proinflammatory cytokines. We mapped 38,931 cytokine-responsive candidate cis-regulatory elements (cCREs) in beta cells using ATAC-seq and snATAC-seq and linked them to target genes using co-accessibility and HiChIP. Using a genome-wide CRISPR screen in EndoC-βH1 cells, we identified 867 genes affecting cytokine-induced survival, and genes promoting survival and up-regulated in cytokines were enriched at T1D risk loci. Using SNP-SELEX, we identified 2,229 variants in cytokine-responsive cCREs altering transcription factor (TF) binding, and variants altering binding of TFs regulating stress, inflammation, and apoptosis were enriched for T1D risk. At the 16p13 locus, a fine-mapped T1D variant altering TF binding in a cytokine-induced cCRE interacted with SOCS1, which promoted survival in cytokine exposure. Our findings reveal processes and genes acting in beta cells during inflammation that modulate T1D risk.
Collapse
Affiliation(s)
- Paola Benaglio
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Han Zhu
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mei-Lin Okino
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jian Yan
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Ruth Elgamal
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Naoki Nariai
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elisha Beebe
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Katha Korgaonkar
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Yunjiang Qiu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Joshua Chiou
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Gaowei Wang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jacklyn Newsome
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jaspreet Kaur
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Michael Miller
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Sierra Corban
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Anthony Aylward
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Kelly A. Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Maike Sander
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| |
Collapse
|
11
|
den Hollander AI, Mullins RF, Orozco LD, Voigt AP, Chen HH, Strunz T, Grassmann F, Haines JL, Kuiper JJW, Tumminia SJ, Allikmets R, Hageman GS, Stambolian D, Klaver CCW, Boeke JD, Chen H, Honigberg L, Katti S, Frazer KA, Weber BHF, Gorin MB. Systems genomics in age-related macular degeneration. Exp Eye Res 2022; 225:109248. [PMID: 36108770 PMCID: PMC10150562 DOI: 10.1016/j.exer.2022.109248] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/29/2022] [Accepted: 09/07/2022] [Indexed: 12/29/2022]
Abstract
Genomic studies in age-related macular degeneration (AMD) have identified genetic variants that account for the majority of AMD risk. An important next step is to understand the functional consequences and downstream effects of the identified AMD-associated genetic variants. Instrumental for this next step are 'omics' technologies, which enable high-throughput characterization and quantification of biological molecules, and subsequent integration of genomics with these omics datasets, a field referred to as systems genomics. Single cell sequencing studies of the retina and choroid demonstrated that the majority of candidate AMD genes identified through genomic studies are expressed in non-neuronal cells, such as the retinal pigment epithelium (RPE), glia, myeloid and choroidal cells, highlighting that many different retinal and choroidal cell types contribute to the pathogenesis of AMD. Expression quantitative trait locus (eQTL) studies in retinal tissue have identified putative causal genes by demonstrating a genetic overlap between gene regulation and AMD risk. Linking genetic data to complement measurements in the systemic circulation has aided in understanding the effect of AMD-associated genetic variants in the complement system, and supports that protein QTL (pQTL) studies in plasma or serum samples may aid in understanding the effect of genetic variants and pinpointing causal genes in AMD. A recent epigenomic study fine-mapped AMD causal variants by determing regulatory regions in RPE cells differentiated from induced pluripotent stem cells (iPSC-RPE). Another approach that is being employed to pinpoint causal AMD genes is to produce synthetic DNA assemblons representing risk and protective haplotypes, which are then delivered to cellular or animal model systems. Pinpointing causal genes and understanding disease mechanisms is crucial for the next step towards clinical translation. Clinical trials targeting proteins encoded by the AMD-associated genomic loci C3, CFB, CFI, CFH, and ARMS2/HTRA1 are currently ongoing, and a phase III clinical trial for C3 inhibition recently showed a modest reduction of lesion growth in geographic atrophy. The EYERISK consortium recently developed a genetic test for AMD that allows genotyping of common and rare variants in AMD-associated genes. Polygenic risk scores (PRS) were applied to quantify AMD genetic risk, and may aid in predicting AMD progression. In conclusion, genomic studies represent a turning point in our exploration of AMD. The results of those studies now serve as a driving force for several clinical trials. Expanding to omics and systems genomics will further decipher function and causality from the associations that have been reported, and will enable the development of therapies that will lessen the burden of AMD.
Collapse
Affiliation(s)
- Anneke I den Hollander
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands; AbbVie, Genomics Research Center, Cambridge, MA, USA.
| | - Robert F Mullins
- The University of Iowa Institute for Vision Research, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | | | - Andrew P Voigt
- The University of Iowa Institute for Vision Research, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | | | - Tobias Strunz
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | | | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA; Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, the Netherlands; Center of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Rando Allikmets
- Department of Ophthalmology, Columbia University, NY, USA; Department of Pathology and Cell Biology, Columbia University, NY, USA
| | - Gregory S Hageman
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, Department of Ophthalmology & Visual Sciences, University of Utah, Salt Lake City, UT, USA
| | - Dwight Stambolian
- Departments of Ophthalmology and Human Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Caroline C W Klaver
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands; Departments of Ophthalmology and Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands; Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, NY, USA; Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, NY, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
| | - Hao Chen
- Genentech, South San Francisco, CA, USA
| | | | | | - Kelly A Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, USA
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany; Institute of Clinical Human Genetics, University Hospital Regensburg, Regensburg, Germany
| | - Michael B Gorin
- Departments of Ophthalmology and Human Genetics, University of California, Los Angeles, CA, USA
| |
Collapse
|
12
|
D'Antonio M, Nguyen JP, Arthur TD, Matsui H, D'Antonio-Chronowska A, Frazer KA. SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues. Cell Rep 2022; 39:110968. [PMID: 35705058 PMCID: PMC9195561 DOI: 10.1016/j.celrep.2022.110968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|
13
|
Liu R, Lee J, Tchoe Y, Pre D, Bourhis AM, D'Antonio-Chronowska A, Robin G, Lee SH, Ro YG, Vatsyayan R, Tonsfeldt KJ, Hossain LA, Phipps ML, Yoo J, Nogan J, Martinez JS, Frazer KA, Bang AG, Dayeh SA. Ultra-Sharp Nanowire Arrays Natively Permeate, Record, and Stimulate Intracellular Activity in Neuronal and Cardiac Networks. Adv Funct Mater 2022; 32:2108378. [PMID: 35603230 PMCID: PMC9122115 DOI: 10.1002/adfm.202108378] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Indexed: 05/25/2023]
Abstract
We report innovative scalable, vertical, ultra-sharp nanowire arrays that are individually addressable to enable long-term, native recordings of intracellular potentials. Stable amplitudes of intracellular potentials from 3D tissue-like networks of neurons and cardiomyocytes are obtained. Individual electrical addressability is necessary for high-fidelity intracellular electrophysiological recordings. This study paves the way toward predictive, high-throughput, and low-cost electrophysiological drug screening platforms.
Collapse
Affiliation(s)
- Ren Liu
- Integrated Electronics and Biointerfaces Laboratory, Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jihwan Lee
- Integrated Electronics and Biointerfaces Laboratory, Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Youngbin Tchoe
- Integrated Electronics and Biointerfaces Laboratory, Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Deborah Pre
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Andrew M Bourhis
- Integrated Electronics and Biointerfaces Laboratory, Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | | | - Gaelle Robin
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sang Heon Lee
- Integrated Electronics and Biointerfaces Laboratory, Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yun Goo Ro
- Integrated Electronics and Biointerfaces Laboratory, Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Ritwik Vatsyayan
- Integrated Electronics and Biointerfaces Laboratory, Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Karen J Tonsfeldt
- Integrated Electronics and Biointerfaces Laboratory, Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Reproductive Science and Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Lorraine A Hossain
- Integrated Electronics and Biointerfaces Laboratory, Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - M Lisa Phipps
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jinkyoung Yoo
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - John Nogan
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Jennifer S Martinez
- Center for Materials Interfaces in Research and Applications and Department of Applied Physics and Materials Science, Northern Arizona University, 624 S. Knoles Dr. Flagstaff, AZ 86011
| | - Kelly A Frazer
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Anne G Bang
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Shadi A Dayeh
- Integrated Electronics and Biointerfaces Laboratory, Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| |
Collapse
|
14
|
D'Antonio M, Nguyen JP, Arthur TD, Matsui H, D'Antonio-Chronowska A, Frazer KA. SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues. Cell Rep 2021; 37:110020. [PMID: 34762851 PMCID: PMC8563343 DOI: 10.1016/j.celrep.2021.110020] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 05/24/2021] [Revised: 10/06/2021] [Accepted: 10/28/2021] [Indexed: 01/08/2023] Open
Abstract
Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types.
Collapse
Affiliation(s)
- Matteo D'Antonio
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Jennifer P Nguyen
- Department 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
- 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
| | - 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.
| |
Collapse
|
15
|
Biswas P, Villanueva AL, Soto-Hermida A, Duncan JL, Matsui H, Borooah S, Kurmanov B, Richard G, Khan SY, Branham K, Huang B, Suk J, Bakall B, Goldberg JL, Gabriel L, Khan NW, Raghavendra PB, Zhou J, Devalaraja S, Huynh A, Alapati A, Zawaydeh Q, Weleber RG, Heckenlively JR, Hejtmancik JF, Riazuddin S, Sieving PA, Riazuddin SA, Frazer KA, Ayyagari R. Deciphering the genetic architecture and ethnographic distribution of IRD in three ethnic populations by whole genome sequence analysis. PLoS Genet 2021; 17:e1009848. [PMID: 34662339 PMCID: PMC8589175 DOI: 10.1371/journal.pgen.1009848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 11/12/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
Patients with inherited retinal dystrophies (IRDs) were recruited from two understudied populations: Mexico and Pakistan as well as a third well-studied population of European Americans to define the genetic architecture of IRD by performing whole-genome sequencing (WGS). Whole-genome analysis was performed on 409 individuals from 108 unrelated pedigrees with IRDs. All patients underwent an ophthalmic evaluation to establish the retinal phenotype. Although the 108 pedigrees in this study had previously been examined for mutations in known IRD genes using a wide range of methodologies including targeted gene(s) or mutation(s) screening, linkage analysis and exome sequencing, the gene mutations responsible for IRD in these 108 pedigrees were not determined. WGS was performed on these pedigrees using Illumina X10 at a minimum of 30X depth. The sequence reads were mapped against hg19 followed by variant calling using GATK. The genome variants were annotated using SnpEff, PolyPhen2, and CADD score; the structural variants (SVs) were called using GenomeSTRiP and LUMPY. We identified potential causative sequence alterations in 61 pedigrees (57%), including 39 novel and 54 reported variants in IRD genes. For 57 of these pedigrees the observed genotype was consistent with the initial clinical diagnosis, the remaining 4 had the clinical diagnosis reclassified based on our findings. In seven pedigrees (12%) we observed atypical causal variants, i.e. unexpected genotype(s), including 4 pedigrees with causal variants in more than one IRD gene within all affected family members, one pedigree with intrafamilial genetic heterogeneity (different affected family members carrying causal variants in different IRD genes), one pedigree carrying a dominant causative variant present in pseudo-recessive form due to consanguinity and one pedigree with a de-novo variant in the affected family member. Combined atypical and large structural variants contributed to about 20% of cases. Among the novel mutations, 75% were detected in Mexican and 50% found in European American pedigrees and have not been reported in any other population while only 20% were detected in Pakistani pedigrees and were not previously reported. The remaining novel IRD causative variants were listed in gnomAD but were found to be very rare and population specific. Mutations in known IRD associated genes contributed to pathology in 63% Mexican, 60% Pakistani and 45% European American pedigrees analyzed. Overall, contribution of known IRD gene variants to disease pathology in these three populations was similar to that observed in other populations worldwide. This study revealed a spectrum of mutations contributing to IRD in three populations, identified a large proportion of novel potentially causative variants that are specific to the corresponding population or not reported in gnomAD and shed light on the genetic architecture of IRD in these diverse global populations. The study was performed to identify the underlying cause of inherited retinal degeneration (IRD) in 409 individuals from 108 families. Primarily, these families were recruited from three different geographic regions: Mexico, Pakistan and European Americans from the United States. Blood samples were collected from all individuals for genome analysis. This analysis detected causative variants in 61 out of the 108 pedigrees. A total of 93 gene variants were found in the 61 families. Among these, 54 were previously reported as causative variants and the remaining 39 have not been reported in IRD pedigrees. Interestingly, 54% of these novel variants were not listed in gnomAD. In addition to these findings, complex causative genotypes were observed in 20% of pedigrees. Overall, causative variants were detected in 63% Mexican, 60% Pakistani and 45% European American pedigrees. This study revealed the distribution of IRD causative variants in pedigrees with diverse ethnic and geographic backgrounds.
Collapse
Affiliation(s)
- Pooja Biswas
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India
| | - Adda L. Villanueva
- Retina and Genomics Institute, Yucatán, México
- Laboratoire de Diagnostic Moleculaire, Hôpital Maisonneuve Rosemont, Montreal, Quebec, Canada
| | - Angel Soto-Hermida
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Jacque L. Duncan
- Ophthalmology, University of California San Francisco, San Francisco, California, United States of America
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Shyamanga Borooah
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Berzhan Kurmanov
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | | | - Shahid Y. Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kari Branham
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - Bonnie Huang
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - John Suk
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Benjamin Bakall
- Ophthalmology, University of Arizona College of Medicine Phoenix, Phoenix, Arizona, United States of America
| | - Jeffrey L. Goldberg
- Byers Eye Institute, Stanford, Palo Alto, California, United States of America
| | - Luis Gabriel
- Genetics and Ophthalmology, Genelabor, Goiânia, Brazil
| | - Naheed W. Khan
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - Pongali B. Raghavendra
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India
- School of Regenerative Medicine, Manipal University, Bengaluru, Karnataka, India
| | - Jason Zhou
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Sindhu Devalaraja
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Andrew Huynh
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Akhila Alapati
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Qais Zawaydeh
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Richard G. Weleber
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - John R. Heckenlively
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | - Paul A. Sieving
- National Eye Institute, Bethesda, Maryland, United States of America
- Ophthalmology & Vision Science, UC Davis Medical Center, California, United States of America
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (RA); (KAF); (SAR)
| | - Kelly A. Frazer
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, Rady Children’s Hospital, Division of Genome Information Sciences, San Diego, California, United States of America
- * E-mail: (RA); (KAF); (SAR)
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (RA); (KAF); (SAR)
| |
Collapse
|
16
|
Rawat P, Brummel SS, Singh KK, Kim J, Frazer KA, Nichols S, Seage GR, Williams PL, Van Dyke RB, Harismendy O, Trout RN, Spector SA. Genomics Links Inflammation With Neurocognitive Impairment in Children Living With Human Immunodeficiency Virus Type-1. J Infect Dis 2021; 224:870-880. [PMID: 33373444 PMCID: PMC8408770 DOI: 10.1093/infdis/jiaa792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/22/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND We identified host single-nucleotide variants (SNVs) associated with neurocognitive impairment (NCI) in perinatally HIV-infected (PHIV) children. METHODS Whole-exome sequencing (WES) was performed on 217 PHIV with cognitive score for age (CSA) < 70 and 247 CSA ≥ 70 (discovery cohort [DC]). SNVs identified in DC were evaluated in 2 validation cohorts (VC). Logistic regression was used to estimate adjusted odds ratios (ORs) for NCI. A human microglia NLRP3 inflammasome assay characterized the role of identified genes. RESULTS Twenty-nine SNVs in 24 genes reaching P ≤ .002 and OR ≥ 1.5 comparing CSA < 70 to CSA ≥ 70 were identified in the DC, of which 3 SNVs were identified in VCs for further study. Combining the 3 cohorts, SNV in CCRL2 (rs3204849) was associated with decreased odds of NCI (P < .0001); RETREG1/FAM134B (rs61733811) and YWHAH (rs73884247) were associated with increased risk of NCI (P < .0001 and P < .001, respectively). Knockdown of CCRL2 led to decreased microglial release of IL-1β following exposure to ssRNA40 while knockdown of RETREG1 and YWHAH resulted in increased IL-1β release. CONCLUSIONS Using WES and 2 VCs, and gene silencing of microglia we identified 3 genetic variants associated with NCI and inflammation in HIV-infected children.
Collapse
Affiliation(s)
- Pratima Rawat
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Sean S Brummel
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Kumud K Singh
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Jihoon Kim
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Kelly A Frazer
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Sharon Nichols
- Department of Neuroscience, University of California San Diego, La Jolla, California, USA
| | - George R Seage
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Paige L Williams
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Russell B Van Dyke
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Olivier Harismendy
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Rodney N Trout
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Stephen A Spector
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Rady Children’s Hospital San Diego, San Diego, California, USA
| |
Collapse
|
17
|
Oh S, Shao J, Mitra J, Xiong F, D'Antonio M, Wang R, Garcia-Bassets I, Ma Q, Zhu X, Lee JH, Nair SJ, Yang F, Ohgi K, Frazer KA, Zhang ZD, Li W, Rosenfeld MG. Enhancer release and retargeting activates disease-susceptibility genes. Nature 2021; 595:735-740. [PMID: 34040254 DOI: 10.1038/s41586-021-03577-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 04/23/2021] [Indexed: 02/04/2023]
Abstract
The functional engagement between an enhancer and its target promoter ensures precise gene transcription1. Understanding the basis of promoter choice by enhancers has important implications for health and disease. Here we report that functional loss of a preferred promoter can release its partner enhancer to loop to and activate an alternative promoter (or alternative promoters) in the neighbourhood. We refer to this target-switching process as 'enhancer release and retargeting'. Genetic deletion, motif perturbation or mutation, and dCas9-mediated CTCF tethering reveal that promoter choice by an enhancer can be determined by the binding of CTCF at promoters, in a cohesin-dependent manner-consistent with a model of 'enhancer scanning' inside the contact domain. Promoter-associated CTCF shows a lower affinity than that at chromatin domain boundaries and often lacks a preferred motif orientation or a partnering CTCF at the cognate enhancer, suggesting properties distinct from boundary CTCF. Analyses of cancer mutations, data from the GTEx project and risk loci from genome-wide association studies, together with a focused CRISPR interference screen, reveal that enhancer release and retargeting represents an overlooked mechanism that underlies the activation of disease-susceptibility genes, as exemplified by a risk locus for Parkinson's disease (NUCKS1-RAB7L1) and three loci associated with cancer (CLPTM1L-TERT, ZCCHC7-PAX5 and PVT1-MYC).
Collapse
Affiliation(s)
- Soohwan Oh
- Howard Hughes Medical Institute, Department and School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jiaofang Shao
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Joydeep Mitra
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Feng Xiong
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Matteo D'Antonio
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ruoyu Wang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
- Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX, USA
| | - Ivan Garcia-Bassets
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qi Ma
- Howard Hughes Medical Institute, Department and School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Xiaoyu Zhu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Joo-Hyung Lee
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Sreejith J Nair
- Howard Hughes Medical Institute, Department and School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Feng Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kenneth Ohgi
- Howard Hughes Medical Institute, Department and School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kelly A Frazer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.
- Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX, USA.
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department and School of Medicine, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
18
|
D’Antonio M, Arthur TD, Nguyen JP, Matsui H, D’Antonio-Chronowska A, Frazer KA. Insights into genetic factors contributing to variability in SARS-CoV-2 susceptibility and COVID-19 disease severity. medRxiv 2021:2021.05.10.21256423. [PMID: 34013287 PMCID: PMC8132261 DOI: 10.1101/2021.05.10.21256423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we applied colocalization to compare summary statistics for 16 GWASs from the COVID-19 Host Genetics Initiative to investigate similarities and differences in their genetic signals. We identified 9 loci associated with susceptibility (one with two independent GWAS signals; one with an ethnicity-specific signal), 14 associated with severity (one with two independent GWAS signals; two with ethnicity-specific signals) and one harboring two discrepant GWAS signals (one for susceptibility; one for severity). Utilizing colocalization we also identified 45 GTEx tissues that had eQTL(s) for 18 genes strongly associated with GWAS signals in eleven loci (1-4 genes per locus). Some of these genes showed tissue-specific altered expression and others showed altered expression in up to 41 different tissue types. Our study provides insights into the complex molecular mechanisms underlying inherited predispositions to COVID-19-disease phenotypes.
Collapse
Affiliation(s)
- Matteo D’Antonio
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Timothy D. Arthur
- Biomedical Sciences 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
| | - Jennifer P. Nguyen
- Department 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
| | - 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
| |
Collapse
|
19
|
Bonder MJ, Smail C, Gloudemans MJ, Frésard L, Jakubosky D, D'Antonio M, Li X, Ferraro NM, Carcamo-Orive I, Mirauta B, Seaton DD, Cai N, Vakili D, Horta D, Zhao C, Zastrow DB, Bonner DE, Wheeler MT, Kilpinen H, Knowles JW, Smith EN, Frazer KA, Montgomery SB, Stegle O. Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. Nat Genet 2021; 53:313-321. [PMID: 33664507 PMCID: PMC7944648 DOI: 10.1038/s41588-021-00800-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 10/04/2019] [Accepted: 01/25/2021] [Indexed: 12/18/2022]
Abstract
Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental contexts. However, in their pluripotent state, the disease impact of genetic variants is less known. Here, we integrate data from 1,367 human iPSC lines to comprehensively map common and rare regulatory variants in human pluripotent cells. Using this population-scale resource, we report hundreds of novel colocalization events for human traits specific to iPSCs, and find increased power to identify rare regulatory variants compared with somatic tissues. Finally, we demonstrate how iPSCs enable the identification of causal genes for rare diseases.
Collapse
Affiliation(s)
- Marc Jan Bonder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Craig Smail
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA. .,Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA.
| | - Michael J Gloudemans
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Laure Frésard
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - David Jakubosky
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA.,Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA
| | - Matteo D'Antonio
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA, USA
| | - Xin Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Nicole M Ferraro
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Ivan Carcamo-Orive
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Bogdan Mirauta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Daniel D Seaton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Na Cai
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK.,Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.,Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Dara Vakili
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK.,Faculty of Medicine, Imperial College London, London, UK
| | - Danilo Horta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Chunli Zhao
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Diane B Zastrow
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Devon E Bonner
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | | | | | | | | | - Matthew T Wheeler
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Helena Kilpinen
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.,UCL Great Ormond Street Institute of Child Health, University College London, London, UK.,Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Joshua W Knowles
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Erin N Smith
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kelly A Frazer
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
| |
Collapse
|
20
|
Yan J, Qiu Y, Ribeiro Dos Santos AM, Yin Y, Li YE, Vinckier N, Nariai N, Benaglio P, Raman A, Li X, Fan S, Chiou J, Chen F, Frazer KA, Gaulton KJ, Sander M, Taipale J, Ren B. Systematic analysis of binding of transcription factors to noncoding variants. Nature 2021; 591:147-151. [PMID: 33505025 PMCID: PMC9367673 DOI: 10.1038/s41586-021-03211-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 12/11/2020] [Indexed: 12/30/2022]
Abstract
Many sequence variants have been linked to complex human traits and diseases1, but deciphering their biological functions remains challenging, as most of them reside in noncoding DNA. Here we have systematically assessed the binding of 270 human transcription factors to 95,886 noncoding variants in the human genome using an ultra-high-throughput multiplex protein-DNA binding assay, termed single-nucleotide polymorphism evaluation by systematic evolution of ligands by exponential enrichment (SNP-SELEX). The resulting 828 million measurements of transcription factor-DNA interactions enable estimation of the relative affinity of these transcription factors to each variant in vitro and evaluation of the current methods to predict the effects of noncoding variants on transcription factor binding. We show that the position weight matrices of most transcription factors lack sufficient predictive power, whereas the support vector machine combined with the gapped k-mer representation show much improved performance, when assessed on results from independent SNP-SELEX experiments involving a new set of 61,020 sequence variants. We report highly predictive models for 94 human transcription factors and demonstrate their utility in genome-wide association studies and understanding of the molecular pathways involved in diverse human traits and diseases.
Collapse
Affiliation(s)
- Jian Yan
- School of Medicine, Northwest University, Xi'an, China.
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - André M Ribeiro Dos Santos
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Universidade Federal do Pará, Institute of Biological Sciences, Belém, Brazil
| | - Yimeng Yin
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Yang E Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Nick Vinckier
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Naoki Nariai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Paola Benaglio
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Anugraha Raman
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Xiaoyu Li
- School of Medicine, Northwest University, Xi'an, China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Shicai Fan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua Chiou
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Fulin Chen
- School of Medicine, Northwest University, Xi'an, China
| | - Kelly A Frazer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kyle J Gaulton
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Maike Sander
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland.
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
21
|
D'Antonio M, D'Antonio-Chronowska A, Frazer KA. Revealing Instability: Genetic Variation Underlies Variability in mESC Pluripotency. Cell Stem Cell 2021; 27:347-349. [PMID: 32888420 DOI: 10.1016/j.stem.2020.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
mESCs can self-renew indefinitely in vitro. However, depending on culture conditions some strains are more unstable than others. In this issue of Cell Stem Cell, Skelly et al. (2020) and Ortmann et al. (2020) shed light into the role genetic variation plays in control of ground state pluripotency.
Collapse
Affiliation(s)
- Matteo D'Antonio
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Kelly A Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
22
|
Biswas P, Borooah S, Matsui H, Voronchikhina M, Zhou J, Zawaydeh Q, Raghavendra PB, Ferreyra H, Riazuddin SA, Wahlin K, Frazer KA, Ayyagari R. Cover, Volume 42, Issue 2. Hum Mutat 2021. [DOI: 10.1002/humu.24168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Pooja Biswas
- Shiley Eye Institute University of California San Diego La Jolla California USA
- REVA University Bengaluru Karnataka India
| | - Shyamanga Borooah
- Shiley Eye Institute University of California San Diego La Jolla California USA
| | - Hiroko Matsui
- Institute for Genomic Medicine University of California, San Diego La Jolla California USA
| | | | - Jason Zhou
- Shiley Eye Institute University of California San Diego La Jolla California USA
| | - Qais Zawaydeh
- Shiley Eye Institute University of California San Diego La Jolla California USA
| | - Pongali B. Raghavendra
- REVA University Bengaluru Karnataka India
- School of Regenerative Medicine Manipal University‐MAHE Bangalore India
| | - Henry Ferreyra
- Shiley Eye Institute University of California San Diego La Jolla California USA
| | - S. Amer Riazuddin
- Wilmer Eye Institute Johns Hopkins Univesity School of Medicine Baltimore Maryland USA
| | - Karl Wahlin
- Shiley Eye Institute University of California San Diego La Jolla California USA
| | - Kelly A. Frazer
- Institute for Genomic Medicine University of California, San Diego La Jolla California USA
- Department of Pediatrics Rady Children's Hospital, Division of Genome Information Sciences San Diego California USA
| | - Radha Ayyagari
- Shiley Eye Institute University of California San Diego La Jolla California USA
| |
Collapse
|
23
|
Biswas P, Borooah S, Matsui H, Voronchikhina M, Zhou J, Zawaydeh Q, Raghavendra PB, Ferreyra H, Riazuddin SA, Wahlin K, Frazer KA, Ayyagari R. Detection and validation of novel mutations in MERTK in a simplex case of retinal degeneration using WGS and hiPSC-RPEs model. Hum Mutat 2020; 42:189-199. [PMID: 33252167 DOI: 10.1002/humu.24146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/03/2020] [Accepted: 11/24/2020] [Indexed: 12/30/2022]
Abstract
Inherited retinal degenerations (IRDs) are a group of genetically heterogeneous conditions with a broad phenotypic heterogeneity. Here, we report detection and validation of the underlying cause of progressive retinal degeneration in a nuclear family of European descent with a single affected individual. Whole genome sequencing of the proband and her unaffected sibling identified a novel intron 8 donor splice site variant (c.1296 + 1G>A) and a novel 731 base pair deletion encompassing exon 9 (Chr2:g.112751488_112752218 del) resulting in c.1297_1451del; p.K433_G484fsTer3 in the Mer tyrosine kinase protooncogene (MERTK), which is highly expressed in the retinal pigment epithelium (RPE). The proband carried both variants in the heterozygous state, which segregated with disease in the pedigree. These MERTK variants are predicted to result in the defective splicing of exon 8 and loss of exon 9 respectively. To evaluate the impact of these novel variants, peripheral blood mononuclear cells of the proband and her parents were reprogrammed to humaninduced pluripotent stem cell (hiPSC) lines, which were subsequently differentiated to hiPSC-RPE. Analysis of the proband's hiPSC-RPE revealed the absence of both MERTK transcript and its respective protein as well as abnormal phagocytosis when compared with the parental hiPSC-RPE. In summary, whole genome sequencing identified novel compound heterozygous variants in MERTK as the underlying cause of progressive retinal degeneration in a simplex case. Further, analysis using an hiPSC-RPE model established the functional impact of novel MERTK mutations and revealed the potential mechanism underlying pathology in the proband.
Collapse
Affiliation(s)
- Pooja Biswas
- Shiley Eye Institute, University of California San Diego, La Jolla, California, USA.,REVA University, Bengaluru, Karnataka, India
| | - Shyamanga Borooah
- Shiley Eye Institute, University of California San Diego, La Jolla, California, USA
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA
| | - Marina Voronchikhina
- Shiley Eye Institute, University of California San Diego, La Jolla, California, USA
| | - Jason Zhou
- Shiley Eye Institute, University of California San Diego, La Jolla, California, USA
| | - Qais Zawaydeh
- Shiley Eye Institute, University of California San Diego, La Jolla, California, USA
| | - Pongali B Raghavendra
- REVA University, Bengaluru, Karnataka, India.,School of Regenerative Medicine, Manipal University-MAHE, Bangalore, India
| | - Henry Ferreyra
- Shiley Eye Institute, University of California San Diego, La Jolla, California, USA
| | - S Amer Riazuddin
- Wilmer Eye Institute, Johns Hopkins Univesity School of Medicine, Baltimore, Maryland, USA
| | - Karl Wahlin
- Shiley Eye Institute, University of California San Diego, La Jolla, California, USA
| | - Kelly A Frazer
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA.,Department of Pediatrics, Rady Children's Hospital, Division of Genome Information Sciences, San Diego, California, USA
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, California, USA
| |
Collapse
|
24
|
D’Antonio-Chronowska A, D’Antonio M, Frazer KA. In vitro Differentiation of Human iPSC-derived Cardiovascular Progenitor Cells (iPSC-CVPCs). Bio Protoc 2020; 10:e3755. [PMID: 33659414 PMCID: PMC7853936 DOI: 10.21769/bioprotoc.3755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 12/14/2022] Open
Abstract
Induced pluripotent stem cell derived cardiovascular progenitor cells (iPSC-CVPCs) provide an unprecedented platform for examining the molecular underpinnings of cardiac development and disease etiology, but also have great potential to play pivotal roles in the future of regenerative medicine and pharmacogenomic studies. Biobanks like iPSCORE ( Stacey et al., 2013 ; Panopoulos et al., 2017 ), which contain iPSCs generated from hundreds of genetically and ethnically diverse individuals, are an invaluable resource for conducting these studies. Here, we present an optimized, cost-effective and highly standardized protocol for large-scale derivation of human iPSC-CVPCs using small molecules and purification using metabolic selection. We have successfully applied this protocol to derive iPSC-CVPCs from 154 different iPSCORE iPSC lines obtaining large quantities of highly pure cardiac cells. An important component of our protocol is Cell confluency estimates (ccEstimate), an automated methodology for estimating the time when an iPSC monolayer will reach 80% confluency, which is optimal for initiating iPSC-CVPC derivation, and enables the protocol to be readily used across iPSC lines with different growth rates. Moreover, we showed that cellular heterogeneity across iPSC-CVPCs is due to varying proportions of two distinct cardiac cell types: cardiomyocytes (CMs) and epicardium-derived cells (EPDCs), both of which have been shown to have a critical function in heart regeneration. This protocol eliminates the need of iPSC line-to-line optimization and can be easily adapted and scaled to high-throughput studies or to generate large quantities of cells suitable for regenerative medicine applications.
Collapse
Affiliation(s)
| | - Matteo D’Antonio
- Department of Pediatrics, University of California, San Diego, La Jolla, USA
| | - Kelly A. Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, USA
- Institue for Genomic Medicine, University of California, San Diego, La Jolla, USA
| |
Collapse
|
25
|
Jakubosky D, Smith EN, D'Antonio M, Jan Bonder M, Young Greenwald WW, D'Antonio-Chronowska A, Matsui H, Stegle O, Montgomery SB, DeBoever C, Frazer KA. Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats. Nat Commun 2020; 11:2928. [PMID: 32522985 PMCID: PMC7287045 DOI: 10.1038/s41467-020-16481-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 05/05/2020] [Indexed: 02/07/2023] Open
Abstract
Structural variants (SVs) and short tandem repeats (STRs) are important sources of genetic diversity but are not routinely analyzed in genetic studies because they are difficult to accurately identify and genotype. Because SVs and STRs range in size and type, it is necessary to apply multiple algorithms that incorporate different types of evidence from sequencing data and employ complex filtering strategies to discover a comprehensive set of high-quality and reproducible variants. Here we assemble a set of 719 deep whole genome sequencing (WGS) samples (mean 42×) from 477 distinct individuals which we use to discover and genotype a wide spectrum of SV and STR variants using five algorithms. We use 177 unique pairs of genetic replicates to identify factors that affect variant call reproducibility and develop a systematic filtering strategy to create of one of the most complete and well characterized maps of SVs and STRs to date.
Collapse
Affiliation(s)
- David Jakubosky
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093-0419, USA
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, 92093-0419, USA
| | - Erin N Smith
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Matteo D'Antonio
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Marc Jan Bonder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - William W Young Greenwald
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | | | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Stephen B Montgomery
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Christopher DeBoever
- 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.
| |
Collapse
|
26
|
Jakubosky D, D'Antonio M, Bonder MJ, Smail C, Donovan MKR, Young Greenwald WW, Matsui H, D'Antonio-Chronowska A, Stegle O, Smith EN, Montgomery SB, DeBoever C, Frazer KA. Properties of structural variants and short tandem repeats associated with gene expression and complex traits. Nat Commun 2020; 11:2927. [PMID: 32522982 PMCID: PMC7286898 DOI: 10.1038/s41467-020-16482-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
Structural variants (SVs) and short tandem repeats (STRs) comprise a broad group of diverse DNA variants which vastly differ in their sizes and distributions across the genome. Here, we identify genomic features of SV classes and STRs that are associated with gene expression and complex traits, including their locations relative to eGenes, likelihood of being associated with multiple eGenes, associated eGene types (e.g., coding, noncoding, level of evolutionary constraint), effect sizes, linkage disequilibrium with tagging single nucleotide variants used in GWAS, and likelihood of being associated with GWAS traits. We identify a set of high-impact SVs/STRs associated with the expression of three or more eGenes via chromatin loops and show that they are highly enriched for being associated with GWAS traits. Our study provides insights into the genomic properties of structural variant classes and short tandem repeats that are associated with gene expression and human traits.
Collapse
Affiliation(s)
- David Jakubosky
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093-0419, USA
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, 92093-0419, USA
| | - Matteo D'Antonio
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Marc Jan Bonder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Craig Smail
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University, Stanford, California, 94305, USA
| | - Margaret K R Donovan
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, 92093-0419, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - William W Young Greenwald
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | | | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Erin N Smith
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University, Stanford, California, 94305, USA
- Department of Genetics, Stanford University, Stanford, California, 94305, USA
| | - Christopher DeBoever
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Kelly A Frazer
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
27
|
Kanchan K, Iyer K, Yanek LR, Carcamo-Orive I, Taub MA, Malley C, Baldwin K, Becker LC, Broeckel U, Cheng L, Cowan C, D'Antonio M, Frazer KA, Quertermous T, Mostoslavsky G, Murphy G, Rabinovitch M, Rader DJ, Steinberg MH, Topol E, Yang W, Knowles JW, Jaquish CE, Ruczinski I, Mathias RA. Genomic integrity of human induced pluripotent stem cells across nine studies in the NHLBI NextGen program. Stem Cell Res 2020; 46:101803. [PMID: 32442913 PMCID: PMC7575060 DOI: 10.1016/j.scr.2020.101803] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/11/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022] Open
Abstract
Human induced pluripotent stem cell (hiPSC) lines have previously been generated through the NHLBI sponsored NextGen program at nine individual study sites. Here, we examined the structural integrity of 506 hiPSC lines as determined by copy number variations (CNVs). We observed that 149 hiPSC lines acquired 258 CNVs relative to donor DNA. We identified six recurrent regions of CNVs on chromosomes 1, 2, 3, 16 and 20 that overlapped with cancer associated genes. Furthermore, the genes mapping to regions of acquired CNVs show an enrichment in cancer related biological processes (IL6 production) and signaling cascades (JNK cascade & NFκB cascade). The genomic region of instability on chr20 (chr20q11.2) includes transcriptomic signatures for cancer associated genes such as ID1, BCL2L1, TPX2, PDRG1 and HCK. Of these HCK shows statistically significant differential expression between carrier and non-carrier hiPSC lines. Overall, while a low level of genomic instability was observed in the NextGen generated hiPSC lines, the observation of structural instability in regions with known cancer associated genes substantiates the importance of systematic evaluation of genetic variations in hiPSCs before using them as disease/research models.
Collapse
Affiliation(s)
- Kanika Kanchan
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kruthika Iyer
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Lisa R Yanek
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ivan Carcamo-Orive
- Department of Medicine, Cardiovascular Institute and Diabetes Research Center, Stanford University, School of Medicine, Stanford, CA, USA
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public health, Johns Hopkins University, Baltimore, MD, USA
| | - Claire Malley
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kristin Baldwin
- Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Lewis C Becker
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ulrich Broeckel
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Linzhao Cheng
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Chad Cowan
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Matteo D'Antonio
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kelly A Frazer
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Thomas Quertermous
- Department of Medicine, Cardiovascular Institute and Diabetes Research Center, Stanford University, School of Medicine, Stanford, CA, USA
| | - Gustavo Mostoslavsky
- The Center for Regenerative Medicine, Boston Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - George Murphy
- The Center for Regenerative Medicine, Boston Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Marlene Rabinovitch
- Department of Medicine, Cardiovascular Institute and Diabetes Research Center, Stanford University, School of Medicine, Stanford, CA, USA
| | - Daniel J Rader
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martin H Steinberg
- Department of Medicine, Section of Hematology-Oncology, Boston University School of Medicine, Boston, MA, USA
| | - Eric Topol
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Wenli Yang
- Penn Center for Pulmonary Biology and Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joshua W Knowles
- Department of Medicine, Cardiovascular Institute and Diabetes Research Center, Stanford University, School of Medicine, Stanford, CA, USA
| | | | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public health, Johns Hopkins University, Baltimore, MD, USA
| | - Rasika A Mathias
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| |
Collapse
|
28
|
Koga T, Chaim IA, Benitez JA, Markmiller S, Parisian AD, Hevner RF, Turner KM, Hessenauer FM, D'Antonio M, Nguyen NPD, Saberi S, Ma J, Miki S, Boyer AD, Ravits J, Frazer KA, Bafna V, Chen CC, Mischel PS, Yeo GW, Furnari FB. Author Correction: Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells. Nat Commun 2020; 11:1958. [PMID: 32312984 PMCID: PMC7171109 DOI: 10.1038/s41467-020-15828-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Tomoyuki Koga
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA.,Department of Neurosurgery, University of Minnesota, 420 Delaware St SE, Minneapolis, MN, 55455, USA
| | - Isaac A Chaim
- Department of Cellular and Molecular Medicine, University of California San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92093, USA.,Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Dr., Mail Code 0761, La Jolla, CA, 92093, USA
| | - Jorge A Benitez
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA
| | - Sebastian Markmiller
- Department of Cellular and Molecular Medicine, University of California San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92093, USA
| | - Alison D Parisian
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA.,Department of Pathology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Robert F Hevner
- Department of Pathology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Kristen M Turner
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA
| | - Florian M Hessenauer
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA
| | - Matteo D'Antonio
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Dr., Mail Code 0761, La Jolla, CA, 92093, USA
| | - Nam-Phuong D Nguyen
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., Mail Code 0404, La Jolla, CA, 92093, USA
| | - Shahram Saberi
- Department of Neuroscience, University of California San Diego, 9500 Gilman Dr., Mail Code 0662, La Jolla, CA, 92093, USA
| | - Jianhui Ma
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA
| | - Shunichiro Miki
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA
| | - Antonia D Boyer
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA
| | - John Ravits
- Department of Neuroscience, University of California San Diego, 9500 Gilman Dr., Mail Code 0662, La Jolla, CA, 92093, USA
| | - Kelly A Frazer
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Dr., Mail Code 0761, La Jolla, CA, 92093, USA.,Department of Pediatrics and Rady Children's Hospital, University of California San Diego, 9500 Gilman Dr., Mail Code 0831, La Jolla, CA, 92093, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., Mail Code 0404, La Jolla, CA, 92093, USA
| | - Clark C Chen
- Department of Neurosurgery, University of Minnesota, 420 Delaware St SE, Minneapolis, MN, 55455, USA
| | - Paul S Mischel
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA.,Department of Pathology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92093, USA. .,Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Dr., Mail Code 0761, La Jolla, CA, 92093, USA.
| | - Frank B Furnari
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA. .,Department of Pathology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
| |
Collapse
|
29
|
Donovan MKR, D'Antonio-Chronowska A, D'Antonio M, Frazer KA. Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants. Nat Commun 2020; 11:955. [PMID: 32075962 PMCID: PMC7031340 DOI: 10.1038/s41467-020-14561-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 01/17/2020] [Indexed: 12/31/2022] Open
Abstract
The Genotype-Tissue Expression (GTEx) resource has provided insights into the regulatory impact of genetic variation on gene expression across human tissues; however, thus far has not considered how variation acts at the resolution of the different cell types. Here, using gene expression signatures obtained from mouse cell types, we deconvolute bulk RNA-seq samples from 28 GTEx tissues to quantify cellular composition, which reveals striking heterogeneity across these samples. Conducting eQTL analyses for GTEx liver and skin samples using cell composition estimates as interaction terms, we identify thousands of genetic associations that are cell-type-associated. The skin cell-type associated eQTLs colocalize with skin diseases, indicating that variants which influence gene expression in distinct skin cell types play important roles in traits and disease. Our study provides a framework to estimate the cellular composition of GTEx tissues enabling the functional characterization of human genetic variation that impacts gene expression in cell-type-specific manners.
Collapse
Affiliation(s)
- 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
| | | | - Matteo D'Antonio
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Kelly A Frazer
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA, 92093, USA.
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
30
|
Koga T, Chaim IA, Benitez JA, Markmiller S, Parisian AD, Hevner RF, Turner KM, Hessenauer FM, D'Antonio M, Nguyen NPD, Saberi S, Ma J, Miki S, Boyer AD, Ravits J, Frazer KA, Bafna V, Chen CC, Mischel PS, Yeo GW, Furnari FB. Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells. Nat Commun 2020; 11:550. [PMID: 31992716 PMCID: PMC6987220 DOI: 10.1038/s41467-020-14312-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/20/2019] [Indexed: 12/27/2022] Open
Abstract
Many cellular models aimed at elucidating cancer biology do not recapitulate pathobiology including tumor heterogeneity, an inherent feature of cancer that underlies treatment resistance. Here we introduce a cancer modeling paradigm using genetically engineered human pluripotent stem cells (hiPSCs) that captures authentic cancer pathobiology. Orthotopic engraftment of the neural progenitor cells derived from hiPSCs that have been genome-edited to contain tumor-associated genetic driver mutations revealed by The Cancer Genome Atlas project for glioblastoma (GBM) results in formation of high-grade gliomas. Similar to patient-derived GBM, these models harbor inter-tumor heterogeneity resembling different GBM molecular subtypes, intra-tumor heterogeneity, and extrachromosomal DNA amplification. Re-engraftment of these primary tumor neurospheres generates secondary tumors with features characteristic of patient samples and present mutation-dependent patterns of tumor evolution. These cancer avatar models provide a platform for comprehensive longitudinal assessment of human tumor development as governed by molecular subtype mutations and lineage-restricted differentiation.
Collapse
Affiliation(s)
- Tomoyuki Koga
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA
- Department of Neurosurgery, University of Minnesota, 420 Delaware St SE, Minneapolis, MN, 55455, USA
| | - Isaac A Chaim
- Department of Cellular and Molecular Medicine, University of California San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92093, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Dr. Mail Code 0761, La Jolla, CA, 92093, USA
| | - Jorge A Benitez
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA
| | - Sebastian Markmiller
- Department of Cellular and Molecular Medicine, University of California San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92093, USA
| | - Alison D Parisian
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA
- Department of Pathology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Robert F Hevner
- Department of Pathology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Kristen M Turner
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA
| | - Florian M Hessenauer
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA
| | - Matteo D'Antonio
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Dr. Mail Code 0761, La Jolla, CA, 92093, USA
| | - Nam-Phuong D Nguyen
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., Mail Code 0404, La Jolla, CA, 92093, USA
| | - Shahram Saberi
- Department of Neuroscience, University of California San Diego, 9500 Gilman Dr., Mail Code 0662, La Jolla, CA, 92093, USA
| | - Jianhui Ma
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA
| | - Shunichiro Miki
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA
| | - Antonia D Boyer
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA
| | - John Ravits
- Department of Neuroscience, University of California San Diego, 9500 Gilman Dr., Mail Code 0662, La Jolla, CA, 92093, USA
| | - Kelly A Frazer
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Dr. Mail Code 0761, La Jolla, CA, 92093, USA
- Department of Pediatrics and Rady Children's Hospital, University of California San Diego, 9500 Gilman Dr., Mail Code 0831, La Jolla, CA, 92093, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., Mail Code 0404, La Jolla, CA, 92093, USA
| | - Clark C Chen
- Department of Neurosurgery, University of Minnesota, 420 Delaware St SE, Minneapolis, MN, 55455, USA
| | - Paul S Mischel
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA
- Department of Pathology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92093, USA.
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Dr. Mail Code 0761, La Jolla, CA, 92093, USA.
| | - Frank B Furnari
- Ludwig Cancer Research San Diego Branch, 9500 Gilman Dr., CMM-East Room 3055, La Jolla, CA, 92093, USA.
- Department of Pathology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
| |
Collapse
|
31
|
D’Antonio-Chronowska A, D’Antonio M, Frazer KA. In vitro Differentiation of Human iPSC-derived Retinal Pigment Epithelium Cells (iPSC-RPE). Bio Protoc 2019; 9:e3469. [PMID: 33654959 PMCID: PMC7853967 DOI: 10.21769/bioprotoc.3469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/17/2019] [Accepted: 11/21/2019] [Indexed: 11/02/2022] Open
Abstract
Induced Pluripotent Stem Cells (iPSCs) serve as an excellent model system for studying the molecular underpinnings of tissue development. Human iPSC-derived retinal pigment epithelium (iPSC-RPE) cells have fetal-like molecular profiles. Hence, biobanks like iPSCORE, which contain iPSCs generated from hundreds of individuals, are an invaluable resource for examining how common genetic variants exert their effects during RPE development resulting in individuals having different propensities to develop Age-related Macular Degeneration (AMD) as adults. Here, we present an optimized, cost-effective and highly reproducible protocol for derivation of human iPSC-RPE cells using small molecules under serum-free condition and for their quality control using flow cytometry and immunofluorescence. While most previous protocols have required laborious manual selection to enrich for iPSC-RPE cells, our protocol uses whole culture passaging and yields a large number of iPSC-RPE cells with high purity (88-98.1% ZO-1 and MiTF double positive cells). The simplicity and robustness of this protocol would enable its adaption for high-throughput applications involving the generation of iPSC-RPE samples from hundreds of individuals.
Collapse
Affiliation(s)
| | - Matteo D’Antonio
- Department of Pediatrics, University of California, San Diego, La Jolla, USA
| | - Kelly A. Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, USA
- Institue for Genomic Medicine, University of California, San Diego, La Jolla, USA
| |
Collapse
|
32
|
D'Antonio M, Reyna J, Jakubosky D, Donovan MKR, Bonder MJ, Matsui H, Stegle O, Nariai N, D'Antonio-Chronowska A, Frazer KA. Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease. eLife 2019; 8:e48476. [PMID: 31746734 PMCID: PMC6904215 DOI: 10.7554/elife.48476] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023] Open
Abstract
The MHC region is highly associated with autoimmune and infectious diseases. Here we conduct an in-depth interrogation of associations between genetic variation, gene expression and disease. We create a comprehensive map of regulatory variation in the MHC region using WGS from 419 individuals to call eight-digit HLA types and RNA-seq data from matched iPSCs. Building on this regulatory map, we explored GWAS signals for 4083 traits, detecting colocalization for 180 disease loci with eQTLs. We show that eQTL analyses taking HLA type haplotypes into account have substantially greater power compared with only using single variants. We examined the association between the 8.1 ancestral haplotype and delayed colonization in Cystic Fibrosis, postulating that downregulation of RNF5 expression is the likely causal mechanism. Our study provides insights into the genetic architecture of the MHC region and pinpoints disease associations that are due to differential expression of HLA genes and non-HLA genes.
Collapse
Affiliation(s)
- Matteo D'Antonio
- Institute for Genomic MedicineUniversity of California, San DiegoSan DiegoUnited States
- Department of PediatricsRady Children’s Hospital, University of California, San DiegoSan DiegoUnited States
| | - Joaquin Reyna
- Department of PediatricsRady Children’s Hospital, University of California, San DiegoSan DiegoUnited States
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaUnited States
| | - David Jakubosky
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaUnited States
- Bioinformatics and Systems Biology Graduate ProgramUniversity of California, San DiegoSan DiegoUnited States
| | - Margaret KR Donovan
- Bioinformatics and Systems Biology Graduate ProgramUniversity of California, San DiegoSan DiegoUnited States
- Department of Biomedical InformaticsUniversity of California, San DiegoSan DiegoUnited States
| | - Marc-Jan Bonder
- European Molecular Biology Laboratory, European Bioinformatics InstituteCambridgeUnited Kingdom
| | - Hiroko Matsui
- Institute for Genomic MedicineUniversity of California, San DiegoSan DiegoUnited States
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics InstituteCambridgeUnited Kingdom
| | - Naoki Nariai
- Department of PediatricsRady Children’s Hospital, University of California, San DiegoSan DiegoUnited States
| | - Agnieszka D'Antonio-Chronowska
- Institute for Genomic MedicineUniversity of California, San DiegoSan DiegoUnited States
- Department of PediatricsRady Children’s Hospital, University of California, San DiegoSan DiegoUnited States
| | - Kelly A Frazer
- Institute for Genomic MedicineUniversity of California, San DiegoSan DiegoUnited States
- Department of PediatricsRady Children’s Hospital, University of California, San DiegoSan DiegoUnited States
| |
Collapse
|
33
|
Jin W, Mulas F, Gaertner B, Sui Y, Wang J, Matta I, Zeng C, Vinckier N, Wang A, Nguyen-Ngoc KV, Chiou J, Kaestner KH, Frazer KA, Carrano AC, Shih HP, Sander M. A Network of microRNAs Acts to Promote Cell Cycle Exit and Differentiation of Human Pancreatic Endocrine Cells. iScience 2019; 21:681-694. [PMID: 31733514 PMCID: PMC6889369 DOI: 10.1016/j.isci.2019.10.063] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 10/03/2018] [Revised: 09/30/2019] [Accepted: 10/28/2019] [Indexed: 12/12/2022] Open
Abstract
Pancreatic endocrine cell differentiation is orchestrated by the action of transcription factors that operate in a gene regulatory network to activate endocrine lineage genes and repress lineage-inappropriate genes. MicroRNAs (miRNAs) are important modulators of gene expression, yet their role in endocrine cell differentiation has not been systematically explored. Here we characterize miRNA-regulatory networks active in human endocrine cell differentiation by combining small RNA sequencing, miRNA over-expression, and network modeling approaches. Our analysis identified Let-7g, Let-7a, miR-200a, miR-127, and miR-375 as endocrine-enriched miRNAs that drive endocrine cell differentiation-associated gene expression changes. These miRNAs are predicted to target different transcription factors, which converge on genes involved in cell cycle regulation. When expressed in human embryonic stem cell-derived pancreatic progenitors, these miRNAs induce cell cycle exit and promote endocrine cell differentiation. Our study delineates the role of miRNAs in human endocrine cell differentiation and identifies miRNAs that could facilitate endocrine cell reprogramming.
Collapse
Affiliation(s)
- Wen Jin
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Francesca Mulas
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bjoern Gaertner
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yinghui Sui
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jinzhao Wang
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ileana Matta
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chun Zeng
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicholas Vinckier
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Allen Wang
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kim-Vy Nguyen-Ngoc
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joshua Chiou
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kelly A Frazer
- Department of Pediatrics, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andrea C Carrano
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hung-Ping Shih
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolic Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Maike Sander
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
34
|
D'Antonio-Chronowska A, Donovan MKR, Young Greenwald WW, Nguyen JP, Fujita K, Hashem S, Matsui H, Soncin F, Parast M, Ward MC, Coulet F, Smith EN, Adler E, D'Antonio M, Frazer KA. Association of Human iPSC Gene Signatures and X Chromosome Dosage with Two Distinct Cardiac Differentiation Trajectories. Stem Cell Reports 2019; 13:924-938. [PMID: 31668852 PMCID: PMC6895695 DOI: 10.1016/j.stemcr.2019.09.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 04/12/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 11/30/2022] Open
Abstract
Despite the importance of understanding how variability across induced pluripotent stem cell (iPSC) lines due to non-genetic factors (clone and passage) influences their differentiation outcome, large-scale studies capable of addressing this question have not yet been conducted. Here, we differentiated 191 iPSC lines to generate iPSC-derived cardiovascular progenitor cells (iPSC-CVPCs). We observed cellular heterogeneity across the iPSC-CVPC samples due to varying fractions of two cell types: cardiomyocytes (CMs) and epicardium-derived cells (EPDCs). Comparing the transcriptomes of CM-fated and EPDC-fated iPSCs, we discovered that 91 signature genes and X chromosome dosage differences are associated with these two distinct cardiac developmental trajectories. In an independent set of 39 iPSCs differentiated into CMs, we confirmed that sex and transcriptional differences affect cardiac-fate outcome. Our study provides novel insights into how iPSC transcriptional and X chromosome gene dosage differences influence their response to differentiation stimuli and, hence, cardiac cell fate. Cellular heterogeneity across iPSC-CVPCs due to varying fractions of CMs and EPDCs iPSC non-genetic factors (clone and passage) associated with cardiac cell fate Expression levels of signature genes in iPSCs associated with cardiac lineage fate iPSC donor sex plays a role in cardiac lineage fate
Collapse
Affiliation(s)
| | - Margaret K R Donovan
- Bioinformatics and Systems Biology Graduate Program, UC San Diego, La Jolla, CA 92093, USA
| | | | - Jennifer Phuong Nguyen
- Bioinformatics and Systems Biology Graduate Program, UC San Diego, La Jolla, CA 92093, USA
| | - Kyohei Fujita
- Department of Pediatrics, UC San Diego, La Jolla, CA 92093, USA
| | - Sherin Hashem
- Division of Cardiology, Department of Medicine, UC San Diego, La Jolla, CA 92093, USA
| | - Hiroko Matsui
- Department of Pediatrics, UC San Diego, La Jolla, CA 92093, USA
| | | | - Mana Parast
- Department of Pathology, UC San Diego, La Jolla, CA 92093, USA
| | - Michelle C Ward
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Florence Coulet
- Department of Pediatrics, UC San Diego, La Jolla, CA 92093, USA
| | - Erin N Smith
- Department of Pediatrics, UC San Diego, La Jolla, CA 92093, USA
| | - Eric Adler
- Division of Cardiology, Department of Medicine, UC San Diego, La Jolla, CA 92093, USA
| | - Matteo D'Antonio
- Department of Pediatrics, UC San Diego, La Jolla, CA 92093, USA.
| | - Kelly A Frazer
- Department of Pediatrics, UC San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
35
|
Solomon T, Lapek JD, Jensen SB, Greenwald WW, Hindberg K, Matsui H, Latysheva N, Braekken SK, Gonzalez DJ, Frazer KA, Smith EN, Hansen JB. Identification of Common and Rare Genetic Variation Associated With Plasma Protein Levels Using Whole-Exome Sequencing and Mass Spectrometry. Circ Genom Precis Med 2019; 11:e002170. [PMID: 30562114 DOI: 10.1161/circgen.118.002170] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Identifying genetic variation associated with plasma protein levels, and the mechanisms by which they act, could provide insight into alterable processes involved in regulation of protein levels. Although protein levels can be affected by genetic variants, their estimation can also be biased by missense variants in coding exons causing technical artifacts. Integrating genome sequence genotype data with mass spectrometry-based protein level estimation could reduce bias, thereby improving detection of variation that affects RNA or protein metabolism. METHODS Here, we integrate the blood plasma protein levels of 664 proteins from 165 participants of the Tromsø Study, measured via tandem mass tag mass spectrometry, with whole-exome sequencing data to identify common and rare genetic variation associated with peptide and protein levels (protein quantitative trait loci [pQTLs]). We additionally use literature and database searches to prioritize putative functional variants for each pQTL. RESULTS We identify 109 independent associations (36 protein and 73 peptide) and use genotype data to exclude 49 (4 protein and 45 peptide) as technical artifacts. We describe 2 particular cases of rare variation: 1 associated with the complement pathway and 1 with platelet degranulation. We identify putative functional variants and show that pQTLs act through diverse molecular mechanisms that affect both RNA and protein metabolism. CONCLUSIONS We show that although the majority of pQTLs exert their effects by modulating RNA metabolism, many affect protein levels directly. Our work demonstrates the extent by which pQTL studies are affected by technical artifacts and highlights how prioritizing the functional variant in pQTL studies can lead to insights into the molecular steps by which a protein may be regulated.
Collapse
Affiliation(s)
- Terry Solomon
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla (T.S.)
| | - John D Lapek
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla (J.D.L., D.J.G.)
| | - Søren Beck Jensen
- Department of Clinical Medicine, K.G. Jebsen Thrombosis Research and Expertise Center, UiT-The Arctic University of Norway (S.B.J., K.H., N.L., S.K.B., K.A.F., E.N.S., J.-B.H.)
| | - William W Greenwald
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla (W.W.G.)
| | - Kristian Hindberg
- Department of Clinical Medicine, K.G. Jebsen Thrombosis Research and Expertise Center, UiT-The Arctic University of Norway (S.B.J., K.H., N.L., S.K.B., K.A.F., E.N.S., J.-B.H.)
| | - Hiroko Matsui
- Institue of Genomic Medicine, University of California, San Diego, La Jolla (H.M., K.A.F.)
| | - Nadezhda Latysheva
- Department of Clinical Medicine, K.G. Jebsen Thrombosis Research and Expertise Center, UiT-The Arctic University of Norway (S.B.J., K.H., N.L., S.K.B., K.A.F., E.N.S., J.-B.H.)
| | - Sigrid K Braekken
- Department of Clinical Medicine, K.G. Jebsen Thrombosis Research and Expertise Center, UiT-The Arctic University of Norway (S.B.J., K.H., N.L., S.K.B., K.A.F., E.N.S., J.-B.H.).,Division of Internal Medicine, University Hospital of North Norway, Tromsû (S.K.B., J.-B.H.)
| | - David J Gonzalez
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla (J.D.L., D.J.G.)
| | - Kelly A Frazer
- Institue of Genomic Medicine, University of California, San Diego, La Jolla (H.M., K.A.F.).,Department of Pediatrics, Rady Children's Hospital, University of California, San Diego, La Jolla (K.A.F., E.N.S.).,Department of Clinical Medicine, K.G. Jebsen Thrombosis Research and Expertise Center, UiT-The Arctic University of Norway (S.B.J., K.H., N.L., S.K.B., K.A.F., E.N.S., J.-B.H.)
| | - Erin N Smith
- Department of Pediatrics, Rady Children's Hospital, University of California, San Diego, La Jolla (K.A.F., E.N.S.).,Department of Clinical Medicine, K.G. Jebsen Thrombosis Research and Expertise Center, UiT-The Arctic University of Norway (S.B.J., K.H., N.L., S.K.B., K.A.F., E.N.S., J.-B.H.)
| | - John-Bjarne Hansen
- Department of Clinical Medicine, K.G. Jebsen Thrombosis Research and Expertise Center, UiT-The Arctic University of Norway (S.B.J., K.H., N.L., S.K.B., K.A.F., E.N.S., J.-B.H.).,Division of Internal Medicine, University Hospital of North Norway, Tromsû (S.K.B., J.-B.H.)
| |
Collapse
|
36
|
Paulsen B, Skille H, Smith EN, Hveem K, Gabrielsen ME, Brækkan SK, Rosendaal FR, Frazer KA, Gran OV, Hansen JB. Fibrinogen gamma gene rs2066865 and risk of cancer-related venous thromboembolism. Haematologica 2019; 105:1963-1968. [PMID: 31582554 PMCID: PMC7327659 DOI: 10.3324/haematol.2019.224279] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 04/11/2019] [Accepted: 10/03/2019] [Indexed: 12/21/2022] Open
Abstract
Venous thromboembolism (VTE) is a frequent complication in patients with cancer. Homozygous carriers of the fibrinogen gamma gene (FGG) rs2066865 have a moderately increased risk of VTE, but the effect of the FGG variant in cancer is unknown. We aimed to investigate the effect of the FGG variant and active cancer on the risk of VTE. Cases with incident VTE (n=640) and a randomly selected age-weighted sub-cohort (n=3,734) were derived from a population-based cohort (the Tromsø study). Cox-regression was used to estimate hazard ratios (HR) with 95% confidence intervals (CI) for VTE according to categories of cancer and FGG. In those without cancer, homozygosity at the FGG variant was associated with a 70% (HR 1.7, 95% CI: 1.2–2.3) increased risk of VTE compared to non-carriers. Cancer patients homozygous for the FGG variant had a two-fold (HR 2.0, 95% CI: 1.1–3.6) higher risk of VTE than cancer patients without the variant. Moreover, the six-months cumulative incidence of VTE among cancer patients was 6.4% (95% CI: 3.5–11.6) in homozygous carriers of FGG and 3.1% (95% CI: 2.3–4.7) in those without risk alleles. A synergistic effect was observed between rs2066865 and active cancer on the risk of VTE (synergy index: 1.81, 95% CI: 1.02–3.21, attributable proportion: 0.43, 95% CI: 0.11–0.74). In conclusion, homozygosity at the FGG variant and active cancer yielded a synergistic effect on the risk of VTE.
Collapse
Affiliation(s)
- Benedikte Paulsen
- K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Hanne Skille
- K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Erin N Smith
- Department of Pediatrics and Rady's Children's Hospital, University of California, San Diego, La Jolla, CA, USA
| | - Kristian Hveem
- St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.,HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway.,K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health, Norwegian University of Science and Technology, Trondheim, Norway
| | - Maiken E Gabrielsen
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway.,K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sigrid K Brækkan
- K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway.,Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - Frits R Rosendaal
- K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway.,Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Kelly A Frazer
- K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway.,Department of Pediatrics and Rady's Children's Hospital, University of California, San Diego, La Jolla, CA, USA
| | - Olga V Gran
- K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
| | - John-Bjarne Hansen
- K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway.,Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| |
Collapse
|
37
|
Benaglio P, D'Antonio-Chronowska A, Ma W, Yang F, Young Greenwald WW, Donovan MKR, DeBoever C, Li H, Drees F, Singhal S, Matsui H, van Setten J, Sotoodehnia N, Gaulton KJ, Smith EN, D'Antonio M, Rosenfeld MG, Frazer KA. Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits. Nat Genet 2019; 51:1506-1517. [PMID: 31570892 PMCID: PMC6858543 DOI: 10.1038/s41588-019-0499-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 02/21/2018] [Accepted: 08/15/2019] [Indexed: 12/15/2022]
Abstract
The cardiac transcription factor (TF) gene NKX2-5 has been associated with electrocardiographic (EKG) traits through genome-wide association studies (GWASs), but the extent to which differential binding of NKX2-5 at common regulatory variants contributes to these traits has not yet been studied. We analyzed transcriptomic and epigenomic data from induced pluripotent stem cell-derived cardiomyocytes from seven related individuals, and identified ~2,000 single-nucleotide variants associated with allele-specific effects (ASE-SNVs) on NKX2-5 binding. NKX2-5 ASE-SNVs were enriched for altered TF motifs, for heart-specific expression quantitative trait loci and for EKG GWAS signals. Using fine-mapping combined with epigenomic data from induced pluripotent stem cell-derived cardiomyocytes, we prioritized candidate causal variants for EKG traits, many of which were NKX2-5 ASE-SNVs. Experimentally characterizing two NKX2-5 ASE-SNVs (rs3807989 and rs590041) showed that they modulate the expression of target genes via differential protein binding in cardiac cells, indicating that they are functional variants underlying EKG GWAS signals. Our results show that differential NKX2-5 binding at numerous regulatory variants across the genome contributes to EKG phenotypes.
Collapse
Affiliation(s)
- Paola Benaglio
- Department of Pediatrics, Rady Children's Hospital, Division of Genome Information Sciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Wubin Ma
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Feng Yang
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Margaret K R Donovan
- Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA.,Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA
| | - Christopher DeBoever
- Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA
| | - He Li
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Frauke Drees
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sanghamitra Singhal
- Department of Pediatrics, Rady Children's Hospital, Division of Genome Information Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jessica van Setten
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - Nona Sotoodehnia
- Department of Medicine, Cardiovascular Health Research Unit, Division of Cardiology, University of Washington, Seattle, WA, USA.,Department of Epidemiology, Cardiovascular Health Research Unit, Division of Cardiology, University of Washington, Seattle, WA, USA
| | - Kyle J Gaulton
- Department of Pediatrics, Rady Children's Hospital, Division of Genome Information Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Erin N Smith
- Department of Pediatrics, Rady Children's Hospital, Division of Genome Information Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Matteo D'Antonio
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Kelly A Frazer
- Department of Pediatrics, Rady Children's Hospital, Division of Genome Information Sciences, University of California, San Diego, La Jolla, CA, USA. .,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
38
|
Ghia EM, Rassenti LZ, Neuberg DS, Blanco A, Yousif F, Smith EN, McPherson JD, Hudson TJ, Harismendy O, Frazer KA, Kipps TJ. Activation of hedgehog signaling associates with early disease progression in chronic lymphocytic leukemia. Blood 2019; 133:2651-2663. [PMID: 30923040 PMCID: PMC6587306 DOI: 10.1182/blood-2018-09-873695] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 03/11/2019] [Indexed: 12/14/2022] Open
Abstract
Targeted sequencing of 103 leukemia-associated genes in leukemia cells from 841 treatment-naive patients with chronic lymphocytic leukemia (CLL) identified 89 (11%) patients as having CLL cells with mutations in genes encoding proteins that putatively are involved in hedgehog (Hh) signaling. Consistent with this finding, there was a significant association between the presence of these mutations and the expression of GLI1 (χ2 test, P < .0001), reflecting activation of the Hh pathway. However, we discovered that 38% of cases without identified mutations also were GLI1+ Patients with GLI1+ CLL cells had a shorter median treatment-free survival than patients with CLL cells lacking expression of GLI1 independent of IGHV mutation status. We found that GANT61, a small molecule that can inhibit GLI1, was highly cytotoxic for GLI1+ CLL cells relative to that of CLL cells without GLI1. Collectively, this study shows that a large proportion of patients have CLL cells with activated Hh signaling, which is associated with early disease progression and enhanced sensitivity to inhibition of GLI1.
Collapse
MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Disease Progression
- Female
- Gene Expression Regulation, Leukemic/genetics
- Hedgehog Proteins/metabolism
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Middle Aged
- Pyridines/pharmacology
- Pyrimidines/pharmacology
- Signal Transduction/drug effects
- Signal Transduction/physiology
- Zinc Finger Protein GLI1/metabolism
Collapse
Affiliation(s)
- Emanuela M Ghia
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Laura Z Rassenti
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Donna S Neuberg
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Alejandro Blanco
- Programa de Genetica Humana, Universidad de Chile, Santiago, Chile
| | - Fouad Yousif
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Erin N Smith
- Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA
| | - John D McPherson
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA; and
| | | | - Olivier Harismendy
- Moores Cancer Center, University of California San Diego, La Jolla, CA
- Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA
| | - Kelly A Frazer
- Moores Cancer Center, University of California San Diego, La Jolla, CA
- Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA
| | - Thomas J Kipps
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| |
Collapse
|
39
|
Lindström S, Brody JA, Turman C, Germain M, Bartz TM, Smith EN, Chen MH, Puurunen M, Chasman D, Hassler J, Pankratz N, Basu S, Guan W, Gyorgy B, Ibrahim M, Empana JP, Olaso R, Jackson R, Brækkan SK, McKnight B, Deleuze JF, O’Donnell CJ, Jouven X, Frazer KA, Psaty BM, Wiggins KL, Taylor K, Reiner AP, Heckbert SR, Kooperberg C, Ridker P, Hansen JB, Tang W, Johnson AD, Morange PE, Trégouët DA, Kraft P, Smith NL, Kabrhel C. A large-scale exome array analysis of venous thromboembolism. Genet Epidemiol 2019; 43:449-457. [PMID: 30659681 PMCID: PMC6520188 DOI: 10.1002/gepi.22187] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/26/2018] [Accepted: 12/11/2019] [Indexed: 01/12/2023]
Abstract
Although recent Genome-Wide Association Studies have identified novel associations for common variants, there has been no comprehensive exome-wide search for low-frequency variants that affect the risk of venous thromboembolism (VTE). We conducted a meta-analysis of 11 studies comprising 8,332 cases and 16,087 controls of European ancestry and 382 cases and 1,476 controls of African American ancestry genotyped with the Illumina HumanExome BeadChip. We used the seqMeta package in R to conduct single variant and gene-based rare variant tests. In the single variant analysis, we limited our analysis to the 64,794 variants with at least 40 minor alleles across studies (minor allele frequency [MAF] ~0.08%). We confirmed associations with previously identified VTE loci, including ABO, F5, F11, and FGA. After adjusting for multiple testing, we observed no novel significant findings in single variant or gene-based analysis. Given our sample size, we had greater than 80% power to detect minimum odds ratios greater than 1.5 and 1.8 for a single variant with MAF of 0.01 and 0.005, respectively. Larger studies and sequence data may be needed to identify novel low-frequency and rare variants associated with VTE risk.
Collapse
Affiliation(s)
- Sara Lindström
- Department of Epidemiology, University of Washington, Seattle, United States
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Jennifer A. Brody
- Department of Medicine, University of Washington, Seattle, United States
| | - Constance Turman
- Department of Epidemiology Harvard TH Chan School of Public Health, Boston, United States
| | - Marine Germain
- University of Bordeaux, Inserm 1219, Bordeaux Population Health Research Center, Bordeaux, France
| | - Traci M. Bartz
- Department of Medicine, University of Washington, Seattle, United States
- Department of Biostatistics University of Washington, Seattle, United States
| | - Erin N. Smith
- Department of Pediatrics and Rady Children’s Hospital University of California, San Diego, La Jolla, United State
- Department of Clinical Medicine, UiT - The Arctic University of Norway, K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Tromsø, Norway
| | - Ming-Huei Chen
- Population Sciences Branch, National Heart, Lung and Blood Institute’s The Framingham Heart Study, Framingham, United States
| | - Marja Puurunen
- School of Medicine, Boston University, Boston, United States
| | - Daniel Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, United States
| | - Jeffrey Hassler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, USA
| | - Saonli Basu
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, USA
| | - Beata Gyorgy
- Team Genomics & Pathophysiology of Cardiovascular Diseases, Sorbonne Universités, UPMC Univ. Paris 06, INSERM, UMR_S 1166, Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris, France
| | - Manal Ibrahim
- Laboratory of Haematology, La Timone Hospital, Marseille, France
- Aix-Marseille University, INSERM, INSERM, INRA, C2VN, Marseille, France
- CRB Assistance Publique Hopitaux de Marseille HemoVasc, Marseille, France
| | - Jean-Philippe Empana
- Department of Epidemiology, Université Paris Descartes, Sorbonne Paris Cité, INSERM UMR_S 970, Paris, France
- Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), Direction de la Recherche Fondamentale, CEA, Institut de Biologie François Jacob, Evry, France
| | | | - Sigrid K. Brækkan
- Department of Clinical Medicine, UiT - The Arctic University of Norway, K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Tromsø, Norway
- Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - Barbara McKnight
- Department of Biostatistics University of Washington, Seattle, United States
| | - Jean-Francois Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Direction de la Recherche Fondamentale, CEA, Institut de Biologie François Jacob, Evry, France
| | | | - Xavier Jouven
- Department of Epidemiology, Université Paris Descartes, Sorbonne Paris Cité, INSERM UMR_S 970, Paris, France
- Department of Cardiology, Georges Pompidou European Hospital, APHP, Paris, France
| | - Kelly A. Frazer
- Department of Pediatrics and Rady Children’s Hospital University of California, San Diego, La Jolla, United State
- Department of Clinical Medicine, UiT - The Arctic University of Norway, K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Tromsø, Norway
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, United States
| | - Bruce M. Psaty
- Department of Epidemiology, University of Washington, Seattle, United States
- Department of Medicine, University of Washington, Seattle, United States
- Department of Health Services, University of Washington, Seattle, United States
- Kaiser Permanente Washington Research Institute, Kaiser Permanente Washington, Seattle, United States
| | - Kerri L. Wiggins
- Department of Medicine, University of Washington, Seattle, United States
| | | | - Alexander P. Reiner
- Department of Epidemiology, University of Washington, Seattle, United States
| | - Susan R. Heckbert
- Department of Epidemiology, University of Washington, Seattle, United States
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Paul Ridker
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, United States
| | - John-Bjarne Hansen
- Department of Clinical Medicine, UiT - The Arctic University of Norway, K.G. Jebsen Thrombosis Research and Expertise Center (TREC), Tromsø, Norway
- Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - Weihong Tang
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, United States
| | - Andrew D. Johnson
- Population Sciences Branch, National Heart, Lung and Blood Institute’s The Framingham Heart Study, Framingham, United States
| | - Pierre-Emmanuel Morange
- Laboratory of Haematology, La Timone Hospital, Marseille, France
- Aix-Marseille University, INSERM, INSERM, INRA, C2VN, Marseille, France
- CRB Assistance Publique Hopitaux de Marseille HemoVasc, Marseille, France
| | - David A. Trégouët
- University of Bordeaux, Inserm 1219, Bordeaux Population Health Research Center, Bordeaux, France
| | - Peter Kraft
- Department of Epidemiology Harvard TH Chan School of Public Health, Boston, United States
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, United States
| | - Nicholas L. Smith
- Department of Epidemiology, University of Washington, Seattle, United States
- Kaiser Permanente Washington Research Institute, Kaiser Permanente Washington, Seattle, United States
- Department of Veteran Affairs Office of Research and Development, Seattle Epidemiologic Research and Information Center, Seattle, United States
| | - Christopher Kabrhel
- Center for Vascular Emergencies, Department of Emergency Medicine, Massachusetts General Hospital, Boston, United States
- Channing Network Medicine, Brigham and Women’s Hospital, Boston, United States
- Harvard Medical School, Boston, United States
| |
Collapse
|
40
|
Smith EN, D'Antonio-Chronowska A, Greenwald WW, Borja V, Aguiar LR, Pogue R, Matsui H, Benaglio P, Borooah S, D'Antonio M, Ayyagari R, Frazer KA. Human iPSC-Derived Retinal Pigment Epithelium: A Model System for Prioritizing and Functionally Characterizing Causal Variants at AMD Risk Loci. Stem Cell Reports 2019; 12:1342-1353. [PMID: 31080113 PMCID: PMC6565613 DOI: 10.1016/j.stemcr.2019.04.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 10/29/2022] Open
Abstract
We evaluate whether human induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE) cells can be used to prioritize and functionally characterize causal variants at age-related macular degeneration (AMD) risk loci. We generated iPSC-RPE from six subjects and show that they have morphological and molecular characteristics similar to those of native RPE. We generated RNA-seq, ATAC-seq, and H3K27ac ChIP-seq data and observed high similarity in gene expression and enriched transcription factor motif profiles between iPSC-RPE and human fetal RPE. We performed fine mapping of AMD risk loci by integrating molecular data from the iPSC-RPE, adult retina, and adult RPE, which identified rs943080 as the probable causal variant at VEGFA. We show that rs943080 is associated with altered chromatin accessibility of a distal ATAC-seq peak, decreased overall gene expression of VEGFA, and allele-specific expression of a non-coding transcript. Our study thus provides a potential mechanism underlying the association of the VEGFA locus with AMD.
Collapse
Affiliation(s)
- Erin N Smith
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | | | - William W Greenwald
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Victor Borja
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Lana R Aguiar
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Robert Pogue
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Paola Benaglio
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Shyamanga Borooah
- Centre for Clinical Brain Sciences, School of Clinical Sciences, The University of Edinburgh, Edinburgh, UK; Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Matteo D'Antonio
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Kelly A Frazer
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Cellular and Molecular Medicine East, 9500 Gilman Drive #0761, La Jolla, CA 92093-0761, USA.
| |
Collapse
|
41
|
Rinde LB, Morelli VM, Småbrekke B, Mathiesen EB, Løchen ML, Njølstad I, Wilsgaard T, Smith E, Rosendaal FR, Frazer KA, Braekkan SK, Hansen JB. Effect of prothrombotic genotypes on the risk of venous thromboembolism in patients with and without ischemic stroke. The Tromsø Study. J Thromb Haemost 2019; 17:749-758. [PMID: 30773804 DOI: 10.1111/jth.14410] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 02/09/2019] [Indexed: 11/27/2022]
Abstract
Essentials Prothrombotic genotypes may agument the risk of venous thromboembolism (VTE) after ischemic stroke. We studied this effect in a case-cohort study using a genetic risk score. In stroke patients, a one-category increase in the genetic risk score was associated with a 50% higher relative risk of VTE. The risk of VTE in stroke patients increased with an increasing number of risk alleles. SUMMARY: Background Patients with ischemic stroke have a transiently increased risk of subsequent venous thromboembolism (VTE). Prothrombotic genotypes may augment VTE risk under conditions of high thrombosis risk related to stroke. Aims To investigate the effect of prothrombotic genotypes in patients with ischemic stroke on the risk of VTE in a population-based case-cohort study. Methods Cases with incident VTE (n = 664) and a randomly selected age-weighted subcohort (n = 1817) were sampled from three surveys of the Tromsø Study (1994-2008). Participants were genotyped for ABO (rs8176719), F5 (rs6025), F2 (rs1799963), FGG (rs2066865) and F11 (rs2036914) single-nucleotide polymorphisms (SNPs). Cox regression models were used to calculate hazard ratios (HRs) for incident VTE according to individual SNPs and categories of risk alleles (5-SNP score; 0-1, 2, 3-4 and ≥ 5) in participants with and without ischemic stroke. Results There were 192 patients with incident stroke, of whom 43 developed VTE during a median of 15.2 years of follow-up. The risk alleles of individual SNPs augmented the elevated VTE risk brought about by ischemic stroke. In stroke patients, a one-category increase in the genetic risk score was associated with a 50% higher relative risk of overall VTE (HR 1.5, 95% confidence interval [CI] 1.3-1.8) and an 80% higher relative risk of provoked VTE (HR 1.8, 95% CI 1.5-2.1). Stroke patients with ≥ 5 risk alleles had a 12-fold (HR 11.7, 95% CI 4.1-33.3) higher relative risk of VTE than stroke-free participants with 0-1 risk alleles. Conclusions Prothrombotic genotypes increased the risk of VTE in stroke patients, and the risk increased with an increasing number of risk alleles.
Collapse
Affiliation(s)
- Ludvig B Rinde
- K. G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Vania M Morelli
- K. G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Birgit Småbrekke
- K. G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ellisiv B Mathiesen
- K. G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- Brain and Circulation Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maja-Lisa Løchen
- Epidemiology of Chronic Diseases Research Group, Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Inger Njølstad
- K. G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- Epidemiology of Chronic Diseases Research Group, Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Tom Wilsgaard
- Epidemiology of Chronic Diseases Research Group, Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Erin Smith
- K. G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- Department of Pediatrics and Rady's Children's Hospital, University of California, San Diego, La Jolla, CA, USA
| | - Frits R Rosendaal
- K. G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Kelly A Frazer
- K. G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- Department of Pediatrics and Rady's Children's Hospital, University of California, San Diego, La Jolla, CA, USA
| | - Sigrid K Braekkan
- K. G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - John-Bjarne Hansen
- K. G. Jebsen Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| |
Collapse
|
42
|
Greenwald WW, Li H, Benaglio P, Jakubosky D, Matsui H, Schmitt A, Selvaraj S, D'Antonio M, D'Antonio-Chronowska A, Smith EN, Frazer KA. Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression. Nat Commun 2019; 10:1054. [PMID: 30837461 PMCID: PMC6401380 DOI: 10.1038/s41467-019-08940-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/04/2019] [Indexed: 12/13/2022] Open
Abstract
While genetic variation at chromatin loops is relevant for human disease, the relationships between contact propensity (the probability that loci at loops physically interact), genetics, and gene regulation are unclear. We quantitatively interrogate these relationships by comparing Hi-C and molecular phenotype data across cell types and haplotypes. While chromatin loops consistently form across different cell types, they have subtle quantitative differences in contact frequency that are associated with larger changes in gene expression and H3K27ac. For the vast majority of loci with quantitative differences in contact frequency across haplotypes, the changes in magnitude are smaller than those across cell types; however, the proportional relationships between contact propensity, gene expression, and H3K27ac are consistent. These findings suggest that subtle changes in contact propensity have a biologically meaningful role in gene regulation and could be a mechanism by which regulatory genetic variants in loop anchors mediate effects on expression.
Collapse
Affiliation(s)
- William W Greenwald
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - He Li
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Paola Benaglio
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA, 92093, USA
| | - David Jakubosky
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Biomedical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | | | - Matteo D'Antonio
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Erin N Smith
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Kelly A Frazer
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
43
|
Jensen SB, Hindberg K, Solomon T, Smith EN, Lapek JD, Gonzalez DJ, Latysheva N, Frazer KA, Braekkan SK, Hansen JB. Discovery of novel plasma biomarkers for future incident venous thromboembolism by untargeted synchronous precursor selection mass spectrometry proteomics. J Thromb Haemost 2018; 16:1763-1774. [PMID: 29964323 PMCID: PMC6123273 DOI: 10.1111/jth.14220] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 02/09/2018] [Indexed: 01/08/2023]
Abstract
Essentials Discovery of predictive biomarkers of venous thromboembolism (VTE) may aid risk stratification. A case-control study where plasma was sampled before the occurrence of VTE was established. We generated untargeted plasma proteomic profiles of 200 individuals by use of mass spectrometry. Assessment of the biomarker potential of 501 proteins yielded 46 biomarker candidates. ABSTRACT Background Prophylactic anticoagulant treatment may substantially reduce the incidence of venous thromboembolism (VTE) but entails considerable risk of severe bleeding. Identification of individuals at high risk of VTE through the use of predictive biomarkers is desirable in order to achieve a favorable benefit-to-harm ratio. Objective We aimed to identify predictive protein biomarker candidates of VTE. Methods We performed a case-control study of 200 individuals that participated in the Tromsø Study, a population-based cohort, where blood samples were collected before the VTE events occurred. Untargeted tandem mass tag-synchronous precursor selection-mass spectrometry (TMT-SPS-MS3)-based proteomic profiling was used to study the plasma proteomes of each individual. Results Of the 501 proteins detected in a sufficient number of samples to allow multivariate analysis, 46 proteins were associated with VTE case-control status with P-values below the 0.05 significance threshold. The strongest predictive biomarker candidates, assessed by statistical significance, were transthyretin, vitamin K-dependent protein Z and protein/nucleic acid deglycase DJ-1. Conclusions Our untargeted approach of plasma proteome profiling revealed novel predictive biomarker candidates of VTE and confirmed previously reported candidates, thereby providing conceptual support for the validity of the study. A larger nested case-control study will be conducted to validate our findings.
Collapse
Affiliation(s)
- S B Jensen
- K. G. Jebsen Thrombosis Research and Expertise Center, Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
| | - K Hindberg
- K. G. Jebsen Thrombosis Research and Expertise Center, Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
| | - T Solomon
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | - E N Smith
- K. G. Jebsen Thrombosis Research and Expertise Center, Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
- Department of Pediatrics and Rady's Children's Hospital, University of California San Diego, La Jolla, California, USA
| | - J D Lapek
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - D J Gonzalez
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - N Latysheva
- K. G. Jebsen Thrombosis Research and Expertise Center, Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
| | - K A Frazer
- K. G. Jebsen Thrombosis Research and Expertise Center, Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
- Department of Pediatrics and Rady's Children's Hospital, University of California San Diego, La Jolla, California, USA
- Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - S K Braekkan
- K. G. Jebsen Thrombosis Research and Expertise Center, Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
- Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - J-B Hansen
- K. G. Jebsen Thrombosis Research and Expertise Center, Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
- Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| |
Collapse
|
44
|
Veevers J, Farah EN, Corselli M, Witty AD, Palomares K, Vidal JG, Emre N, Carson CT, Ouyang K, Liu C, van Vliet P, Zhu M, Hegarty JM, Deacon DC, Grinstein JD, Dirschinger RJ, Frazer KA, Adler ED, Knowlton KU, Chi NC, Martin JC, Chen J, Evans SM. Cell-Surface Marker Signature for Enrichment of Ventricular Cardiomyocytes Derived from Human Embryonic Stem Cells. Stem Cell Reports 2018; 11:828-841. [PMID: 30122443 PMCID: PMC6135222 DOI: 10.1016/j.stemcr.2018.07.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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: 04/21/2015] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 01/01/2023] Open
Abstract
To facilitate understanding of human cardiomyocyte (CM) subtype specification, and the study of ventricular CM biology in particular, we developed a broadly applicable strategy for enrichment of ventricular cardiomyocytes (VCMs) derived from human embryonic stem cells (hESCs). A bacterial artificial chromosome transgenic H9 hESC line in which GFP expression was driven by the human ventricular-specific myosin light chain 2 (MYL2) promoter was generated, and screened to identify cell-surface markers specific for MYL2-GFP-expressing VCMs. A CD77+/CD200- cell-surface signature facilitated isolation of >97% cardiac troponin I-positive cells from H9 hESC differentiation cultures, with 65% expressing MYL2-GFP. This study provides a tool for VCM enrichment when using some, but not all, human pluripotent stem cell lines. Tools generated in this study can be utilized toward understanding CM subtype specification, and enriching for VCMs for therapeutic applications.
Collapse
Affiliation(s)
- Jennifer Veevers
- School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Elie N Farah
- School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Mirko Corselli
- BD Biosciences, 11077 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Alec D Witty
- School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Karina Palomares
- School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jason G Vidal
- BD Biosciences, 11077 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Nil Emre
- BD Biosciences, 11077 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | - Kunfu Ouyang
- School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Drug Discovery Center, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Canzhao Liu
- School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Patrick van Vliet
- Skaggs School of Pharmacy, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Maggie Zhu
- Skaggs School of Pharmacy, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jeffrey M Hegarty
- School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Dekker C Deacon
- School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jonathan D Grinstein
- School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Ralf J Dirschinger
- Skaggs School of Pharmacy, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kelly A Frazer
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Eric D Adler
- School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kirk U Knowlton
- School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Neil C Chi
- School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jody C Martin
- BD Biosciences, 11077 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ju Chen
- School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Sylvia M Evans
- School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| |
Collapse
|
45
|
D'Antonio M, Benaglio P, Jakubosky D, Greenwald WW, Matsui H, Donovan MKR, Li H, Smith EN, D'Antonio-Chronowska A, Frazer KA. Insights into the Mutational Burden of Human Induced Pluripotent Stem Cells from an Integrative Multi-Omics Approach. Cell Rep 2018; 24:883-894. [PMID: 30044985 PMCID: PMC6467479 DOI: 10.1016/j.celrep.2018.06.091] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 01/10/2018] [Revised: 04/29/2018] [Accepted: 06/21/2018] [Indexed: 12/16/2022] Open
Abstract
To understand the mutational burden of human induced pluripotent stem cells (iPSCs), we sequenced genomes of 18 fibroblast-derived iPSC lines and identified different classes of somatic mutations based on structure, origin, and frequency. Copy-number alterations affected 295 kb in each sample and strongly impacted gene expression. UV-damage mutations were present in ∼45% of the iPSCs and accounted for most of the observed heterogeneity in mutation rates across lines. Subclonal mutations (not present in all iPSCs within a line) composed 10% of point mutations and, compared with clonal variants, showed an enrichment in active promoters and increased association with altered gene expression. Our study shows that, by combining WGS, transcriptome, and epigenome data, we can understand the mutational burden of each iPSC line on an individual basis and suggests that this information could be used to prioritize iPSC lines for models of specific human diseases and/or transplantation therapy.
Collapse
Affiliation(s)
- Matteo D'Antonio
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Paola Benaglio
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - David Jakubosky
- Biomedical Sciences 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
| | - William W Greenwald
- Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Margaret K R Donovan
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - He Li
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Erin N Smith
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Kelly A Frazer
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
46
|
Chekuri A, Guru AA, Biswas P, Branham K, Borooah S, Soto-Hermida A, Hicks M, Khan NW, Matsui H, Alapati A, Raghavendra PB, Roosing S, Sarangapani S, Mathavan S, Telenti A, Heckenlively JR, Riazuddin SA, Frazer KA, Sieving PA, Ayyagari R. IFT88 mutations identified in individuals with non-syndromic recessive retinal degeneration result in abnormal ciliogenesis. Hum Genet 2018; 137:447-458. [PMID: 29978320 DOI: 10.1007/s00439-018-1897-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/21/2018] [Indexed: 12/26/2022]
Abstract
Whole genome sequencing (WGS) was performed to identify the variants responsible for inherited retinal degeneration (IRD) in a Caucasian family. Segregation analysis of selected rare variants with pathogenic potential identified a set of compound heterozygous changes p.Arg266*:c.796C>T and p.Ala568Thr:c.1702G>A in the intraflagellar transport protein-88 (IFT88) gene segregating with IRD. Expression of IFT88 with the p.Arg266* and p.Ala568Thr mutations in mIMDC3 cells by transient transfection and in HeLa cells by introducing the mutations using CRISPR-cas9 system suggested that both mutations result in the formation of abnormal ciliary structures. The introduction of the IFT88 p.Arg266* variant in the homozygous state in HeLa cells by CRISPR-Cas9 genome-editing revealed that the mutant transcript undergoes nonsense-mediated decay leading to a significant depletion of IFT88 transcript. Additionally, abnormal ciliogenesis was observed in these cells. These observations suggest that the rare and unique combination of IFT88 alleles observed in this study provide insight into the physiological role of IFT88 in humans and the likely mechanism underlying retinal pathology in the pedigree with IRD.
Collapse
Affiliation(s)
- Anil Chekuri
- Shiley Eye Institute, University of California San Diego, 9415 Campus Point Drive, JRC 206, La Jolla, CA, 92093, USA
| | - Aditya A Guru
- Shiley Eye Institute, University of California San Diego, 9415 Campus Point Drive, JRC 206, La Jolla, CA, 92093, USA
| | - Pooja Biswas
- Shiley Eye Institute, University of California San Diego, 9415 Campus Point Drive, JRC 206, La Jolla, CA, 92093, USA.,School of Biotechnology, REVA University, Bengaluru, Karnataka, India
| | - Kari Branham
- Ophthalmology and Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, MI, USA
| | - Shyamanga Borooah
- Shiley Eye Institute, University of California San Diego, 9415 Campus Point Drive, JRC 206, La Jolla, CA, 92093, USA
| | - Angel Soto-Hermida
- Shiley Eye Institute, University of California San Diego, 9415 Campus Point Drive, JRC 206, La Jolla, CA, 92093, USA
| | | | - Naheed W Khan
- Ophthalmology and Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, MI, USA
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Akhila Alapati
- Shiley Eye Institute, University of California San Diego, 9415 Campus Point Drive, JRC 206, La Jolla, CA, 92093, USA
| | - Pongali B Raghavendra
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India.,School of Regenerative Medicine, Manipal University-MAHE, Bangalore, India
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Nijmegen Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | | | | | - John R Heckenlively
- Ophthalmology and Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, MI, USA
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kelly A Frazer
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.,Division of Genome Information Sciences, Department of Pediatrics, Rady Children's Hospital, San Diego, CA, USA
| | - Paul A Sieving
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, 9415 Campus Point Drive, JRC 206, La Jolla, CA, 92093, USA.
| |
Collapse
|
47
|
Benitez JA, Ma J, D'Antonio M, Boyer A, Camargo MF, Zanca C, Kelly S, Khodadadi-Jamayran A, Jameson NM, Andersen M, Miletic H, Saberi S, Frazer KA, Cavenee WK, Furnari FB. Publisher Correction: PTEN regulates glioblastoma oncogenesis through chromatin-associated complexes of DAXX and histone H3.3. Nat Commun 2018; 9:16217. [PMID: 29799523 PMCID: PMC6026911 DOI: 10.1038/ncomms16217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This corrects the article DOI: 10.1038/ncomms15223.
Collapse
|
48
|
Biswas P, Duncan JL, Ali M, Matsui H, Naeem MA, Raghavendra PB, Frazer KA, Arts HH, Riazuddin S, Akram J, Hejtmancik JF, Riazuddin SA, Ayyagari R. A mutation in IFT43 causes non-syndromic recessive retinal degeneration. Hum Mol Genet 2018; 26:4741-4751. [PMID: 28973684 DOI: 10.1093/hmg/ddx356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/12/2017] [Indexed: 01/12/2023] Open
Abstract
The aim of this work is to identify the molecular cause of autosomal recessive early onset retinal degeneration in a consanguineous pedigree. Seventeen members of a four-generation Pakistani family were recruited and underwent a detailed ophthalmic examination. Exomes of four affected and two unaffected individuals were sequenced. Variants were filtered using exomeSuite to identify rare potentially pathogenic variants in genes expressed in the retina and/or brain and consistent with the pattern of inheritance. Effect of the variant observed in the gene Intraflagellar Transport Protein 43 (IFT43) was studied by heterologous expression in mIMCD3 and MDCK cells. Expression and sub-cellular localization of IFT43 in the retina and transiently transfected cells was examined by RT-PCR, western blot analysis, and immunohistochemistry. Affected members were diagnosed with early onset non-syndromic progressive retinal degeneration and the presence of bone spicules distributed throughout the retina at younger ages while the older affected members showed severe central choroidal atrophy. Whole-exome sequencing analysis identified a novel homozygous c.100 G > A change in IFT43 segregating with retinal degeneration and not present in ethnicity-matched controls. Immunostaining showed IFT43 localized in the photoreceptors, and to the tip of the cilia in transfected mIMCD3 and MDCK cells. The cilia in mIMCD3 and MDCK cells expressing mutant IFT43 were found to be significantly shorter (P < 0.001) than cells expressing wild-type IFT43. Our studies identified a novel homozygous mutation in the ciliary protein IFT43 as the underlying cause of recessive inherited retinal degeneration. This is the first report demonstrating the involvement of IFT43 in retinal degeneration.
Collapse
Affiliation(s)
- Pooja Biswas
- Shiley Eye Institute, University of California San Diego, La Jolla, CA, USA.,School of Biotechnology, REVA University, Bengaluru, Karnataka, India
| | - Jacque L Duncan
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
| | - Muhammad Ali
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Pongali B Raghavendra
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India.,School of Regenerative Medicine, Manipal University, Bangalore, India
| | - Kelly A Frazer
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Pediatrics, Division of Genome Information Sciences, Rady Children's Hospital, San Diego, CA, USA
| | - Heleen H Arts
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.,Allama Iqbal Medical College, University of Health Sciences Lahore, Pakistan.,National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Javed Akram
- Allama Iqbal Medical College, University of Health Sciences Lahore, Pakistan.,National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - J Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, MD, USA
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
49
|
Horvei LD, Braekkan SK, Smith EN, Solomon T, Hindberg K, Frazer KA, Rosendaal FR, Hansen JB. Joint effects of prothrombotic genotypes and body height on the risk of venous thromboembolism: the Tromsø study. J Thromb Haemost 2018; 16:83-89. [PMID: 29094466 DOI: 10.1111/jth.13892] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 12/17/2022]
Abstract
Essentials Body height and prothrombotic genotypes are associated with risk of venous thromboembolism (VTE). The joint effect of prothrombotic genotypes and tall stature on VTE risk is scarcely investigated. We investigated the joint effect of prothrombotic genotypes and tall stature on VTE risk. Prothrombotic genotypes did not yield excess risk of VTE in subjects with a tall stature. SUMMARY Background Studies have reported synergistic effects of prothrombotic single-nucleotide polymorphisms (SNPs) and obesity on the risk of venous thromboembolism (VTE). Tall stature is associated with an increased VTE risk, but the joint effect of prothrombotic genotypes and tall stature on the VTE risk is unknown. Aims To investigate the joint effects of prothrombotic genotypes and tall stature on the VTE risk. Methods Cases with incident VTE (n = 676) and a randomly selected age-weighted subcohort (n = 1842) were sampled from the Tromsø study (cohort follow-up: 1994-2012). DNA was genotyped for rs6025 (factor V Leiden), rs1799963 (FII), rs8176719 (ABO blood group), rs2066865 (fibrinogen-γ), and rs2036914 (FIX). Age-adjusted and sex-adjusted hazard ratios (HRs) of VTE were calculated by categories of risk alleles (de Haan 5-SNP score: 0-1, 2-3, and ≥ 4) and body height (< 40th, 40th-80th and > 80th percentiles). Results The VTE risk increased by increasing category of body height, and subjects with height ≥ 178 cm had a two-fold higher VTE risk (HR 2.03; 95% confidence interval [CI] 1.51-2.73) than those with height ≤ 165 cm. The VTE risk also increased across categories of risk alleles. However, the combination of a tall stature and risk alleles, either individual SNPs or risk score, did not result in an excess VTE risk. Subjects with four or more risk alleles and height ≥ 178 cm had a two-fold (HR 2.08; 95% CI 1.24-3.52) higher VTE risk than subjects ≤ 165 cm with no risk allele or one risk allele. Conclusions In contrast to obesity, the presence of prothrombotic genotypes did not result in an excess VTE risk in subjects with a tall stature.
Collapse
Affiliation(s)
- L D Horvei
- Department of Clinical Medicine, K. G. Jebsen Thrombosis Research and Expertise Center (TREC), UiT - The Arctic University of Norway, Tromsø, Norway
- Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - S K Braekkan
- Department of Clinical Medicine, K. G. Jebsen Thrombosis Research and Expertise Center (TREC), UiT - The Arctic University of Norway, Tromsø, Norway
- Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - E N Smith
- Department of Clinical Medicine, K. G. Jebsen Thrombosis Research and Expertise Center (TREC), UiT - The Arctic University of Norway, Tromsø, Norway
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, CA, USA
| | - T Solomon
- Biomedical Sciences Graduate Program, University of California, San Diego, CA, USA
| | - K Hindberg
- Department of Clinical Medicine, K. G. Jebsen Thrombosis Research and Expertise Center (TREC), UiT - The Arctic University of Norway, Tromsø, Norway
| | - K A Frazer
- Department of Clinical Medicine, K. G. Jebsen Thrombosis Research and Expertise Center (TREC), UiT - The Arctic University of Norway, Tromsø, Norway
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, CA, USA
| | - F R Rosendaal
- Department of Clinical Medicine, K. G. Jebsen Thrombosis Research and Expertise Center (TREC), UiT - The Arctic University of Norway, Tromsø, Norway
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - J-B Hansen
- Department of Clinical Medicine, K. G. Jebsen Thrombosis Research and Expertise Center (TREC), UiT - The Arctic University of Norway, Tromsø, Norway
- Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| |
Collapse
|
50
|
Gustafson K, Duncan JL, Biswas P, Soto-Hermida A, Matsui H, Jakubosky D, Suk J, Telenti A, Frazer KA, Ayyagari R. Correction: Gustafson et al., Whole Genome Sequencing Revealed Mutations in Two Independent Genes as the Underlying Cause of Retinal Degeneration in an Ashkenazi Jewish Pedigree. Genes 2017, 8, 210. Genes (Basel) 2017; 8:genes8100286. [PMID: 29065517 PMCID: PMC5664136 DOI: 10.3390/genes8100286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 10/16/2017] [Accepted: 10/16/2017] [Indexed: 12/27/2022] Open
Affiliation(s)
- Kevin Gustafson
- Ophthalmology, University of California, San Francisco, San Francisco, CA 94143-0730, USA.
| | - Jacque L Duncan
- Ophthalmology, University of California, San Francisco, San Francisco, CA 94143-0730, USA.
| | - Pooja Biswas
- REVA University, Bengaluru, Karnataka 560034, India.
- Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92093-0946, USA.
| | - Angel Soto-Hermida
- Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92093-0946, USA.
| | - Hiroko Matsui
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
| | - David Jakubosky
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
| | - John Suk
- Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92093-0946, USA.
| | | | - Kelly A Frazer
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
- Department of Pediatrics, Rady Children's Hospital, Division of Genome Information Sciences, San Diego, CA 92093, USA.
| | - Radha Ayyagari
- Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92093-0946, USA.
| |
Collapse
|