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1
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Gordon MG, Kathail P, Choy B, Kim MC, Mazumder T, Gearing M, Ye CJ. Population Diversity at the Single-Cell Level. Annu Rev Genomics Hum Genet 2024; 25. [PMID: 38382493 DOI: 10.1146/annurev-genom-021623-083207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Population-scale single-cell genomics is a transformative approach for unraveling the intricate links between genetic and cellular variation. This approach is facilitated by cutting-edge experimental methodologies, including the development of high-throughput single-cell multiomics and advances in multiplexed environmental and genetic perturbations. Examining the effects of natural or synthetic genetic variants across cellular contexts provides insights into the mutual influence of genetics and the environment in shaping cellular heterogeneity. The development of computational methodologies further enables detailed quantitative analysis of molecular variation, offering an opportunity to examine the respective roles of stochastic, intercellular, and interindividual variation. Future opportunities lie in leveraging long-read sequencing, refining disease-relevant cellular models, and embracing predictive and generative machine learning models. These advancements hold the potential for a deeper understanding of the genetic architecture of human molecular traits, which in turn has important implications for understanding the genetic causes of human disease. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 25 is August 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | - Pooja Kathail
- Center for Computational Biology, University of California, Berkeley, California, USA
| | - Bryson Choy
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Min Cheol Kim
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Thomas Mazumder
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Melissa Gearing
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
- Bakar Computational Health Sciences Institute, Gladstone-UCSF Institute of Genomic Immunology, Parker Institute for Cancer Immunotherapy, Department of Epidemiology and Biostatistics, Department of Microbiology and Immunology, and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA;
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2
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Strober BJ, Tayeb K, Popp J, Qi G, Gordon MG, Perez R, Ye CJ, Battle A. SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models. Genome Biol 2024; 25:28. [PMID: 38254214 PMCID: PMC10801966 DOI: 10.1186/s13059-023-03152-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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: 12/22/2022] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Genetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and environmental conditions. We developed SURGE, a method for unsupervised discovery of context-specific expression quantitative trait loci (eQTLs) from single-cell transcriptomic data. This allows discovery of the contexts or cell types modulating genetic regulation without prior knowledge. Applied to peripheral blood single-cell eQTL data, SURGE contexts capture continuous representations of distinct cell types and groupings of biologically related cell types. We demonstrate the disease-relevance of SURGE context-specific eQTLs using colocalization analysis and stratified LD-score regression.
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Affiliation(s)
- Benjamin J Strober
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Karl Tayeb
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Joshua Popp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Guanghao Qi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - M Grace Gordon
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Richard Perez
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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3
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Oelen R, de Vries DH, Brugge H, Gordon MG, Vochteloo M, Ye CJ, Westra HJ, Franke L, van der Wijst MGP. Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure. Nat Commun 2022; 13:3267. [PMID: 35672358 PMCID: PMC9174272 DOI: 10.1038/s41467-022-30893-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [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: 06/14/2021] [Accepted: 05/24/2022] [Indexed: 12/15/2022] Open
Abstract
The host's gene expression and gene regulatory response to pathogen exposure can be influenced by a combination of the host's genetic background, the type of and exposure time to pathogens. Here we provide a detailed dissection of this using single-cell RNA-sequencing of 1.3M peripheral blood mononuclear cells from 120 individuals, longitudinally exposed to three different pathogens. These analyses indicate that cell-type-specificity is a more prominent factor than pathogen-specificity regarding contexts that affect how genetics influences gene expression (i.e., eQTL) and co-expression (i.e., co-expression QTL). In monocytes, the strongest responder to pathogen stimulations, 71.4% of the genetic variants whose effect on gene expression is influenced by pathogen exposure (i.e., response QTL) also affect the co-expression between genes. This indicates widespread, context-specific changes in gene expression level and its regulation that are driven by genetics. Pathway analysis on the CLEC12A gene that exemplifies cell-type-, exposure-time- and genetic-background-dependent co-expression interactions, shows enrichment of the interferon (IFN) pathway specifically at 3-h post-exposure in monocytes. Similar genetic background-dependent association between IFN activity and CLEC12A co-expression patterns is confirmed in systemic lupus erythematosus by in silico analysis, which implies that CLEC12A might be an IFN-regulated gene. Altogether, this study highlights the importance of context for gaining a better understanding of the mechanisms of gene regulation in health and disease.
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Affiliation(s)
- Roy Oelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Dylan H de Vries
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Harm Brugge
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - M Grace Gordon
- Biological and Medical Informatics Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- UCSF Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Martijn Vochteloo
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Chun J Ye
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- UCSF Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Harm-Jan Westra
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Monique G P van der Wijst
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
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4
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Perez RK, Gordon MG, Subramaniam M, Kim MC, Hartoularos GC, Targ S, Sun Y, Ogorodnikov A, Bueno R, Lu A, Thompson M, Rappoport N, Dahl A, Lanata CM, Matloubian M, Maliskova L, Kwek SS, Li T, Slyper M, Waldman J, Dionne D, Rozenblatt-Rosen O, Fong L, Dall’Era M, Balliu B, Regev A, Yazdany J, Criswell LA, Zaitlen N, Ye CJ. Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus. Science 2022; 376:eabf1970. [PMID: 35389781 PMCID: PMC9297655 DOI: 10.1126/science.abf1970] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [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] [Indexed: 12/13/2022]
Abstract
Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Knowledge of circulating immune cell types and states associated with SLE remains incomplete. We profiled more than 1.2 million peripheral blood mononuclear cells (162 cases, 99 controls) with multiplexed single-cell RNA sequencing (mux-seq). Cases exhibited elevated expression of type 1 interferon-stimulated genes (ISGs) in monocytes, reduction of naïve CD4+ T cells that correlated with monocyte ISG expression, and expansion of repertoire-restricted cytotoxic GZMH+ CD8+ T cells. Cell type-specific expression features predicted case-control status and stratified patients into two molecular subtypes. We integrated dense genotyping data to map cell type-specific cis-expression quantitative trait loci and to link SLE-associated variants to cell type-specific expression. These results demonstrate mux-seq as a systematic approach to characterize cellular composition, identify transcriptional signatures, and annotate genetic variants associated with SLE.
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Affiliation(s)
- Richard K. Perez
- School of Medicine, University of California, San Francisco, CA, USA
| | - M. Grace Gordon
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Meena Subramaniam
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Min Cheol Kim
- School of Medicine, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, CA, USA
- UC Berkeley–UCSF Graduate Program in Bioengineering, San Francisco, CA, USA
| | - George C. Hartoularos
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Sasha Targ
- School of Medicine, University of California, San Francisco, CA, USA
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, CA, USA
| | - Yang Sun
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Anton Ogorodnikov
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Raymund Bueno
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Andrew Lu
- UCLA-Caltech Medical Scientist Training Program, Los Angeles, CA, USA
| | - Mike Thompson
- Department of Computer Science, University of California, Los Angeles, CA, USA
| | - Nadav Rappoport
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Andrew Dahl
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Cristina M. Lanata
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, CA, USA
| | - Mehrdad Matloubian
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, CA, USA
| | - Lenka Maliskova
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Serena S. Kwek
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Tony Li
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | | | - Lawrence Fong
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Maria Dall’Era
- School of Medicine, University of California, San Francisco, CA, USA
| | - Brunilda Balliu
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jinoos Yazdany
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Lindsey A. Criswell
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, CA, USA
| | - Noah Zaitlen
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
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5
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Yazar S, Alquicira-Hernandez J, Wing K, Senabouth A, Gordon MG, Andersen S, Lu Q, Rowson A, Taylor TRP, Clarke L, Maccora K, Chen C, Cook AL, Ye CJ, Fairfax KA, Hewitt AW, Powell JE. Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease. Science 2022; 376:eabf3041. [PMID: 35389779 DOI: 10.1126/science.abf3041] [Citation(s) in RCA: 118] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The human immune system displays substantial variation between individuals, leading to differences in susceptibility to autoimmune disease. We present single-cell RNA sequencing (scRNA-seq) data from 1,267,758 peripheral blood mononuclear cells from 982 healthy human subjects. For 14 cell types, we identified 26,597 independent cis-expression quantitative trait loci (eQTLs) and 990 trans-eQTLs, with most showing cell type-specific effects on gene expression. We subsequently show how eQTLs have dynamic allelic effects in B cells that are transitioning from naïve to memory states and demonstrate how commonly segregating alleles lead to interindividual variation in immune function. Finally, using a Mendelian randomization approach, we identify the causal route by which 305 risk loci contribute to autoimmune disease at the cellular level. This work brings together genetic epidemiology with scRNA-seq to uncover drivers of interindividual variation in the immune system.
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Affiliation(s)
- Seyhan Yazar
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Jose Alquicira-Hernandez
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Kristof Wing
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.,Department of Ophthalmology, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Anne Senabouth
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - M Grace Gordon
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Stacey Andersen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Qinyi Lu
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Antonia Rowson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.,Department of Surgery, School of Clinical Science at Monash Health, Monash University, VIC, Australia
| | - Thomas R P Taylor
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Linda Clarke
- Centre for Eye Research Australia, University of Melbourne, East Melbourne, VIC, Australia
| | - Katia Maccora
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.,Department of Surgery, School of Clinical Science at Monash Health, Monash University, VIC, Australia
| | - Christine Chen
- Department of Surgery, School of Clinical Science at Monash Health, Monash University, VIC, Australia
| | - Anthony L Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.,Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Kirsten A Fairfax
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.,Department of Ophthalmology, Royal Hobart Hospital, Hobart, TAS, Australia.,Centre for Eye Research Australia, University of Melbourne, East Melbourne, VIC, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW, Australia
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Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulos-Soares I, Yosef N, Ye CJ, Pollard KS, Shendure J, Kircher M, Ahituv N. Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nat Protoc 2020; 16:3736. [PMID: 33128032 DOI: 10.1038/s41596-020-00422-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- M Grace Gordon
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.,Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA. .,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
| | | | - Max Schubach
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Vikram Agarwal
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Sean Whalen
- Gladstone Institutes, San Francisco, CA, USA
| | - Shiyun Feng
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Tal Ashuach
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ryan Ziffra
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Anat Kreimer
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.,Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ilias Georgakopoulos-Soares
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.,Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.,Chan-Zuckerberg Biohub, San Francisco, CA, USA.,Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Katherine S Pollard
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.,Gladstone Institutes, San Francisco, CA, USA.,Chan-Zuckerberg Biohub, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics and Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA. .,Howard Hughes Medical Institute, Seattle, WA, USA. .,Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA.
| | - Martin Kircher
- Berlin Institute of Health (BIH), Berlin, Germany. .,Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA. .,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
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Crawford ED, Acosta I, Ahyong V, Anderson EC, Arevalo S, Asarnow D, Axelrod S, Ayscue P, Azimi CS, Azumaya CM, Bachl S, Bachmutsky I, Bhaduri A, Brown JB, Batson J, Behnert A, Boileau RM, Bollam SR, Bonny AR, Booth D, Borja MJB, Brown D, Buie B, Burnett CE, Byrnes LE, Cabral KA, Cabrera JP, Caldera S, Canales G, Castañeda GR, Chan AP, Chang CR, Charles-Orszag A, Cheung C, Chio U, Chow ED, Citron YR, Cohen A, Cohn LB, Chiu C, Cole MA, Conrad DN, Constantino A, Cote A, Crayton-Hall T, Darmanis S, Detweiler AM, Dial RL, Dong S, Duarte EM, Dynerman D, Egger R, Fanton A, Frumm SM, Fu BXH, Garcia VE, Garcia J, Gladkova C, Goldman M, Gomez-Sjoberg R, Gordon MG, Grove JCR, Gupta S, Haddjeri-Hopkins A, Hadley P, Haliburton J, Hao SL, Hartoularos G, Herrera N, Hilberg M, Ho KYE, Hoppe N, Hosseinzadeh S, Howard CJ, Hussmann JA, Hwang E, Ingebrigtsen D, Jackson JR, Jowhar ZM, Kain D, Kim JYS, Kistler A, Kreutzfeld O, Kulsuptrakul J, Kung AF, Langelier C, Laurie MT, Lee L, Leng K, Leon KE, Leonetti MD, Levan SR, Li S, Li AW, Liu J, Lubin HS, Lyden A, Mann J, Mann S, Margulis G, Marquez DM, Marsh BP, Martyn C, McCarthy EE, McGeever A, Merriman AF, Meyer LK, Miller S, Moore MK, Mowery CT, Mukhtar T, Mwakibete LL, Narez N, Neff NF, Osso LA, Oviedo D, Peng S, Phelps M, Phong K, Picard P, Pieper LM, Pincha N, Pisco AO, Pogson A, Pourmal S, Puccinelli RR, Puschnik AS, Rackaityte E, Raghavan P, Raghavan M, Reese J, Replogle JM, Retallack H, Reyes H, Rose D, Rosenberg MF, Sanchez-Guerrero E, Sattler SM, Savy L, See SK, Sellers KK, Serpa PH, Sheehy M, Sheu J, Silas S, Streithorst JA, Strickland J, Stryke D, Sunshine S, Suslow P, Sutanto R, Tamura S, Tan M, Tan J, Tang A, Tato CM, Taylor JC, Tenvooren I, Thompson EM, Thornborrow EC, Tse E, Tung T, Turner ML, Turner VS, Turnham RE, Turocy MJ, Vaidyanathan TV, Vainchtein ID, Vanaerschot M, Vazquez SE, Wandler AM, Wapniarski A, Webber JT, Weinberg ZY, Westbrook A, Wong AW, Wong E, Worthington G, Xie F, Xu A, Yamamoto T, Yang Y, Yarza F, Zaltsman Y, Zheng T, DeRisi JL. Rapid deployment of SARS-CoV-2 testing: The CLIAHUB. PLoS Pathog 2020; 16:e1008966. [PMID: 33112933 PMCID: PMC7592773 DOI: 10.1371/journal.ppat.1008966] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Emily D. Crawford
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Department of Microbiology and Immunology, San Francisco, California, United States of America
| | - Irene Acosta
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Erika C. Anderson
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Shaun Arevalo
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Daniel Asarnow
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Shannon Axelrod
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Patrick Ayscue
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Camillia S. Azimi
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Caleigh M. Azumaya
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Stefanie Bachl
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Iris Bachmutsky
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Aparna Bhaduri
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Jeremy Bancroft Brown
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Joshua Batson
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Astrid Behnert
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Ryan M. Boileau
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Saumya R. Bollam
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Alain R. Bonny
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - David Booth
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | | | - David Brown
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Bryan Buie
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Cassandra E. Burnett
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Lauren E. Byrnes
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Katelyn A. Cabral
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- University of California San Francisco, Institute for Neurodegenerative Diseases, San Francisco, California, United States of America
| | - Joana P. Cabrera
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Saharai Caldera
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Division of Infectious Disease, San Francisco, California, United States of America
| | - Gabriela Canales
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Agnes Protacio Chan
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Christopher R. Chang
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Arthur Charles-Orszag
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Carly Cheung
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Unseng Chio
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Eric D. Chow
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Y. Rose Citron
- University of California, Berkeley, California, United States of America
| | - Allison Cohen
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Lillian B. Cohn
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Department of Experimental Medicine, San Francisco, California, United States of America
| | - Charles Chiu
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Mitchel A. Cole
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Daniel N. Conrad
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Angela Constantino
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Andrew Cote
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Spyros Darmanis
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | | | - Rebekah L. Dial
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Shen Dong
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Elias M. Duarte
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - David Dynerman
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Rebecca Egger
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Alison Fanton
- University of California, Berkeley, California, United States of America
| | - Stacey M. Frumm
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Becky Xu Hua Fu
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Valentina E. Garcia
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Julie Garcia
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Christina Gladkova
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Miriam Goldman
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - M. Grace Gordon
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - James C. R. Grove
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Shweta Gupta
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Alexis Haddjeri-Hopkins
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Pierce Hadley
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- University of California San Francisco, Institute for Neurodegenerative Diseases, San Francisco, California, United States of America
| | - John Haliburton
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Samantha L. Hao
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - George Hartoularos
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Nadia Herrera
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Melissa Hilberg
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Kit Ying E. Ho
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Nicholas Hoppe
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Conor J. Howard
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Jeffrey A. Hussmann
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Elizabeth Hwang
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Danielle Ingebrigtsen
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Julia R. Jackson
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Ziad M. Jowhar
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Danielle Kain
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - James Y. S. Kim
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Oriana Kreutzfeld
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Andrew F. Kung
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Charles Langelier
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Division of Infectious Disease, San Francisco, California, United States of America
| | - Matthew T. Laurie
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Lena Lee
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Kun Leng
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Kristoffer E. Leon
- Gladstone Institute, San Francisco, California, United States of America
| | - Manuel D. Leonetti
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Sophia R. Levan
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Sam Li
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Aileen W. Li
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Jamin Liu
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Heidi S. Lubin
- eSix Development, Oakland, California, United States of America
| | - Amy Lyden
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Jennifer Mann
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Sabrina Mann
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Gorica Margulis
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Diana M. Marquez
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Bryan P. Marsh
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Calla Martyn
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Elizabeth E. McCarthy
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Aaron McGeever
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | | | - Lauren K. Meyer
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Steve Miller
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Megan K. Moore
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Cody T. Mowery
- Gladstone Institute, San Francisco, California, United States of America
| | - Tanzila Mukhtar
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Noelle Narez
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Norma F. Neff
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Lindsay A. Osso
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Diter Oviedo
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Suping Peng
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Maira Phelps
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Kiet Phong
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Peter Picard
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Lindsey M. Pieper
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Neha Pincha
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Angela Pogson
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Sergei Pourmal
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | | | | | - Elze Rackaityte
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Preethi Raghavan
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Madhura Raghavan
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - James Reese
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Joseph M. Replogle
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Hanna Retallack
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Helen Reyes
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Donald Rose
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Marci F. Rosenberg
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Sydney M. Sattler
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Laura Savy
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Stephanie K. See
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Kristin K. Sellers
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Paula Hayakawa Serpa
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Division of Infectious Disease, San Francisco, California, United States of America
| | - Maureen Sheehy
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Jonathan Sheu
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Sukrit Silas
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Jessica A. Streithorst
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Jack Strickland
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Doug Stryke
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Sara Sunshine
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Peter Suslow
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Renaldo Sutanto
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Serena Tamura
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Michelle Tan
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Jiongyi Tan
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Alice Tang
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Cristina M. Tato
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Jack C. Taylor
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Iliana Tenvooren
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Erin M. Thompson
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Edward C. Thornborrow
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Eric Tse
- Joint Bioengineering Graduate Program, University of California, Berkeley, California, United States of America
| | - Tony Tung
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Marc L. Turner
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Victoria S. Turner
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Rigney E. Turnham
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Mary J. Turocy
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Trisha V. Vaidyanathan
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Ilia D. Vainchtein
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Manu Vanaerschot
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Sara E. Vazquez
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Anica M. Wandler
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Anne Wapniarski
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - James T. Webber
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Zara Y. Weinberg
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Alexandra Westbrook
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Allison W. Wong
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Emily Wong
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Gajus Worthington
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Fang Xie
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Albert Xu
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Terrina Yamamoto
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Ying Yang
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Fauna Yarza
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Yefim Zaltsman
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Tina Zheng
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
- * E-mail:
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Newberry RW, Arhar T, Costello J, Hartoularos GC, Maxwell AM, Naing ZZC, Pittman M, Reddy NR, Schwarz DMC, Wassarman DR, Wu TS, Barrero D, Caggiano C, Catching A, Cavazos TB, Estes LS, Faust B, Fink EA, Goldman MA, Gomez YK, Gordon MG, Gunsalus LM, Hoppe N, Jaime-Garza M, Johnson MC, Jones MG, Kung AF, Lopez KE, Lumpe J, Martyn C, McCarthy EE, Miller-Vedam LE, Navarro EJ, Palar A, Pellegrino J, Saylor W, Stephens CA, Strickland J, Torosyan H, Wankowicz SA, Wong DR, Wong G, Redding S, Chow ED, DeGrado WF, Kampmann M. Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding. ACS Chem Biol 2020; 15:2137-2153. [PMID: 32786289 DOI: 10.1021/acschembio.0c00339] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein conformations are shaped by cellular environments, but how environmental changes alter the conformational landscapes of specific proteins in vivo remains largely uncharacterized, in part due to the challenge of probing protein structures in living cells. Here, we use deep mutational scanning to investigate how a toxic conformation of α-synuclein, a dynamic protein linked to Parkinson's disease, responds to perturbations of cellular proteostasis. In the context of a course for graduate students in the UCSF Integrative Program in Quantitative Biology, we screened a comprehensive library of α-synuclein missense mutants in yeast cells treated with a variety of small molecules that perturb cellular processes linked to α-synuclein biology and pathobiology. We found that the conformation of α-synuclein previously shown to drive yeast toxicity-an extended, membrane-bound helix-is largely unaffected by these chemical perturbations, underscoring the importance of this conformational state as a driver of cellular toxicity. On the other hand, the chemical perturbations have a significant effect on the ability of mutations to suppress α-synuclein toxicity. Moreover, we find that sequence determinants of α-synuclein toxicity are well described by a simple structural model of the membrane-bound helix. This model predicts that α-synuclein penetrates the membrane to constant depth across its length but that membrane affinity decreases toward the C terminus, which is consistent with orthogonal biophysical measurements. Finally, we discuss how parallelized chemical genetics experiments can provide a robust framework for inquiry-based graduate coursework.
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Affiliation(s)
- Robert W. Newberry
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Taylor Arhar
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, California 94143, United States
| | - Jean Costello
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - George C. Hartoularos
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Alison M. Maxwell
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, California 94143, United States
| | - Zun Zar Chi Naing
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Maureen Pittman
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Nishith R. Reddy
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Daniel M. C. Schwarz
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, California 94143, United States
| | - Douglas R. Wassarman
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, California 94143, United States
| | - Taia S. Wu
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, California 94143, United States
| | - Daniel Barrero
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Christa Caggiano
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Adam Catching
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Taylor B. Cavazos
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Laurel S. Estes
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Bryan Faust
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Elissa A. Fink
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Miriam A. Goldman
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Yessica K. Gomez
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - M. Grace Gordon
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Laura M. Gunsalus
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Nick Hoppe
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Maru Jaime-Garza
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Matthew C. Johnson
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Matthew G. Jones
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Andrew F. Kung
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Kyle E. Lopez
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Jared Lumpe
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Calla Martyn
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Elizabeth E. McCarthy
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Lakshmi E. Miller-Vedam
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Erik J. Navarro
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Aji Palar
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Jenna Pellegrino
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Wren Saylor
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Christina A. Stephens
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Jack Strickland
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Hayarpi Torosyan
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Stephanie A. Wankowicz
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Daniel R. Wong
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Garrett Wong
- Integrative Program in Quantitative Biology, University of California, San Francisco, California 94143, United States
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, United States
| | - Eric D. Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, United States
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Martin Kampmann
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, United States
- Institute for Neurodegenerative Disease, University of California, San Francisco, California 94143, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulos-Soares I, Yosef N, Ye CJ, Pollard KS, Shendure J, Kircher M, Ahituv N. lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nat Protoc 2020; 15:2387-2412. [PMID: 32641802 PMCID: PMC7550205 DOI: 10.1038/s41596-020-0333-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [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: 01/08/2020] [Accepted: 04/17/2020] [Indexed: 12/22/2022]
Abstract
Massively parallel reporter assays (MPRAs) can simultaneously measure the function of thousands of candidate regulatory sequences (CRSs) in a quantitative manner. In this method, CRSs are cloned upstream of a minimal promoter and reporter gene, alongside a unique barcode, and introduced into cells. If the CRS is a functional regulatory element, it will lead to the transcription of the barcode sequence, which is measured via RNA sequencing and normalized for cellular integration via DNA sequencing of the barcode. This technology has been used to test thousands of sequences and their variants for regulatory activity, to decipher the regulatory code and its evolution, and to develop genetic switches. Lentivirus-based MPRA (lentiMPRA) produces 'in-genome' readouts and enables the use of this technique in hard-to-transfect cells. Here, we provide a detailed protocol for lentiMPRA, along with a user-friendly Nextflow-based computational pipeline-MPRAflow-for quantifying CRS activity from different MPRA designs. The lentiMPRA protocol takes ~2 months, which includes sequencing turnaround time and data processing with MPRAflow.
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Affiliation(s)
- M Grace Gordon
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Max Schubach
- Berlin Institute of Health (BIH), Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Vikram Agarwal
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Sean Whalen
- Gladstone Institutes, San Francisco, CA, USA
| | - Shiyun Feng
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Tal Ashuach
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ryan Ziffra
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Anat Kreimer
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ilias Georgakopoulos-Soares
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Katherine S Pollard
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics and Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA.
| | - Martin Kircher
- Berlin Institute of Health (BIH), Berlin, Germany.
- Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
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10
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Gu F, Wu A, Gordon MG, Vlahos L, Macnamara S, Burke E, Malicdan MC, Adams DR, Tifft CJ, Toro C, Gahl WA, Markello TC. A suite of automated sequence analyses reduces the number of candidate deleterious variants and reveals a difference between probands and unaffected siblings. Genet Med 2019; 21:1772-1780. [PMID: 30700791 PMCID: PMC6669106 DOI: 10.1038/s41436-019-0434-0] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 01/03/2019] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Develop an automated exome analysis workflow that can produce a very small number of candidate variants yet still detect different numbers of deleterious variants between probands and unaffected siblings. METHODS Ninety-seven outbred nuclear families from the Undiagnosed Diseases Program/Network included single probands and the corresponding unaffected sibling(s). Single-nucleotide polymorphism (SNP) chip and exome analyses were performed on all, with proband and unaffected sibling considered independently as the target. The total burden of candidate genetic variants was summed for probands and siblings over all considered disease models. RESULTS Exome analysis workflow include automated programs for ethnicity-matched genotype calling, salvage pathway for Mendelian inconsistency, compound heterozygous recessive detection, BAM file regional curation, population frequency filtering, pedigree-aware BAM file noise evaluation, and exon deletion filtration. This workflow relied heavily on BAM file analysis. A greater average pathogenic variant number was found compared with unaffected siblings. This was significant (p < 0.05) when using published recommended thresholds, and implies that causal variants are retained in many probands' lists. CONCLUSION Using Mendelian and non-Mendelian models, this agnostic exome analysis shows a difference between a small group of probands and their unaffected siblings. This workflow produces candidate lists small enough to pursue with laboratory validation.
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Affiliation(s)
- Fangning Gu
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Anchi Wu
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - M Grace Gordon
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Lukas Vlahos
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Shane Macnamara
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth Burke
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - May C Malicdan
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J Tifft
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Camilo Toro
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - William A Gahl
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Thomas C Markello
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA.
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11
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Sawyer EM, Brunner EC, Hwang Y, Ivey LE, Brown O, Bannon M, Akrobetu D, Sheaffer KE, Morgan O, Field CO, Suresh N, Gordon MG, Gunnell ET, Regruto LA, Wood CG, Fuller MT, Hales KG. Testis-specific ATP synthase peripheral stalk subunits required for tissue-specific mitochondrial morphogenesis in Drosophila. BMC Cell Biol 2017; 18:16. [PMID: 28335714 PMCID: PMC5364652 DOI: 10.1186/s12860-017-0132-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/15/2017] [Indexed: 12/13/2022] Open
Abstract
Background In Drosophila early post-meiotic spermatids, mitochondria undergo dramatic shaping into the Nebenkern, a spherical body with complex internal structure that contains two interwrapped giant mitochondrial derivatives. The purpose of this study was to elucidate genetic and molecular mechanisms underlying the shaping of this structure. Results The knotted onions (knon) gene encodes an unconventionally large testis-specific paralog of ATP synthase subunit d and is required for internal structure of the Nebenkern as well as its subsequent disassembly and elongation. Knon localizes to spermatid mitochondria and, when exogenously expressed in flight muscle, alters the ratio of ATP synthase complex dimers to monomers. By RNAi knockdown we uncovered mitochondrial shaping roles for other testis-expressed ATP synthase subunits. Conclusions We demonstrate the first known instance of a tissue-specific ATP synthase subunit affecting tissue-specific mitochondrial morphogenesis. Since ATP synthase dimerization is known to affect the degree of inner mitochondrial membrane curvature in other systems, the effect of Knon and other testis-specific paralogs of ATP synthase subunits may be to mediate differential membrane curvature within the Nebenkern.
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Affiliation(s)
- Eric M Sawyer
- Department of Biology, Davidson College, Davidson, NC, USA
| | | | - Yihharn Hwang
- Department of Biology, Davidson College, Davidson, NC, USA
| | - Lauren E Ivey
- Department of Biology, Davidson College, Davidson, NC, USA
| | - Olivia Brown
- Department of Biology, Davidson College, Davidson, NC, USA
| | - Megan Bannon
- Department of Biology, Davidson College, Davidson, NC, USA
| | | | | | - Oshauna Morgan
- Department of Biology, Davidson College, Davidson, NC, USA
| | - Conroy O Field
- Department of Biology, Davidson College, Davidson, NC, USA
| | - Nishita Suresh
- Department of Biology, Davidson College, Davidson, NC, USA
| | - M Grace Gordon
- Department of Biology, Davidson College, Davidson, NC, USA
| | | | | | - Cricket G Wood
- Departments of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Margaret T Fuller
- Departments of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Karen G Hales
- Department of Biology, Davidson College, Davidson, NC, USA. .,Departments of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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12
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Kudrov MK, Sandrikov VA, Gordon MG, Klimenko VS. [Variations of cardiac cycle length in patients with coronary heart disease before and after aortic coronary bypass surgery]. Vestn Ross Akad Med Nauk 1998:28-32. [PMID: 9771111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
It is well known that variations in cardiac cycle length or heart rates may be used for noninvasive evaluation of autonomic cardiovascular control. The investigation uses an original procedure. The data for analysis of cardiac cycle length variations (CCLV) are those obtained regularly at follow-up intervals, random 24-hour Holter 2-lead ECG recordings for 5 sec, and simultaneously calculated continuous sequence of mean heart rate. With the procedure, the correlations of CCLV with the parameters reflecting the early postoperative status of patients with CHD, including acute myocardial infarction, acute heart failure, rhythm and conduction disturbances, as well as age, operative stress, concurrent diseases. The findings are of both diagnostic and predictive value at subsequent stages of CHD treatment.
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13
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Wright JT, Waterson EJ, Barrison IG, Toplis PJ, Lewis IG, Gordon MG, MacRae KD, Morris NF, Murray-Lyon IM. Alcohol consumption, pregnancy, and low birthweight. Lancet 1983; 1:663-5. [PMID: 6132033 DOI: 10.1016/s0140-6736(83)91964-5] [Citation(s) in RCA: 117] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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