1
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Clark IC, Fontanez KM, Meltzer RH, Xue Y, Hayford C, May-Zhang A, D'Amato C, Osman A, Zhang JQ, Hettige P, Ishibashi JSA, Delley CL, Weisgerber DW, Replogle JM, Jost M, Phong KT, Kennedy VE, Peretz CAC, Kim EA, Song S, Karlon W, Weissman JS, Smith CC, Gartner ZJ, Abate AR. Microfluidics-free single-cell genomics with templated emulsification. Nat Biotechnol 2023; 41:1557-1566. [PMID: 36879006 PMCID: PMC10635830 DOI: 10.1038/s41587-023-01685-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [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: 05/18/2022] [Accepted: 01/20/2023] [Indexed: 03/08/2023]
Abstract
Current single-cell RNA-sequencing approaches have limitations that stem from the microfluidic devices or fluid handling steps required for sample processing. We develop a method that does not require specialized microfluidic devices, expertise or hardware. Our approach is based on particle-templated emulsification, which allows single-cell encapsulation and barcoding of cDNA in uniform droplet emulsions with only a vortexer. Particle-templated instant partition sequencing (PIP-seq) accommodates a wide range of emulsification formats, including microwell plates and large-volume conical tubes, enabling thousands of samples or millions of cells to be processed in minutes. We demonstrate that PIP-seq produces high-purity transcriptomes in mouse-human mixing studies, is compatible with multiomics measurements and can accurately characterize cell types in human breast tissue compared to a commercial microfluidic platform. Single-cell transcriptional profiling of mixed phenotype acute leukemia using PIP-seq reveals the emergence of heterogeneity within chemotherapy-resistant cell subsets that were hidden by standard immunophenotyping. PIP-seq is a simple, flexible and scalable next-generation workflow that extends single-cell sequencing to new applications.
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Affiliation(s)
- Iain C Clark
- Department of Bioengineering, University of California, Berkeley, California Institute for Quantitative Biosciences, Berkeley, CA, USA
| | | | | | - Yi Xue
- Fluent Biosciences, Watertown, MA, USA
| | | | | | | | | | | | | | | | - Cyrille L Delley
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel W Weisgerber
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Marco Jost
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Kiet T Phong
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Vanessa E Kennedy
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Cheryl A C Peretz
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Esther A Kim
- Division of Plastic and Reconstructive Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Siyou Song
- Division of Plastic and Reconstructive Surgery, University of California San Francisco, San Francisco, CA, USA
| | - William Karlon
- Departments of Pathology and Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Catherine C Smith
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
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2
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Koblan LW, Arbab M, Shen MW, Hussmann JA, Anzalone AV, Doman JL, Newby GA, Yang D, Mok B, Replogle JM, Xu A, Sisley TA, Weissman JS, Adamson B, Liu DR. Author Correction: Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning. Nat Biotechnol 2023; 41:1655. [PMID: 37853259 DOI: 10.1038/s41587-023-02028-8] [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: 10/20/2023]
Affiliation(s)
- Luke W Koblan
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Mandana Arbab
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Max W Shen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew V Anzalone
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jordan L Doman
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Dian Yang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Beverly Mok
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Albert Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Tyler A Sisley
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA.
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Britt Adamson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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3
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Guna A, Page KR, Replogle JM, Esantsi TK, Wang ML, Weissman JS, Voorhees RM. A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens. BMC Genomics 2023; 24:651. [PMID: 37904134 PMCID: PMC10614335 DOI: 10.1186/s12864-023-09754-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Mapping genetic interactions is essential for determining gene function and defining novel biological pathways. We report a simple to use CRISPR interference (CRISPRi) based platform, compatible with Fluorescence Activated Cell Sorting (FACS)-based reporter screens, to query epistatic relationships at scale. This is enabled by a flexible dual-sgRNA library design that allows for the simultaneous delivery and selection of a fixed sgRNA and a second randomized guide, comprised of a genome-wide library, with a single transduction. We use this approach to identify epistatic relationships for a defined biological pathway, showing both increased sensitivity and specificity than traditional growth screening approaches.
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Affiliation(s)
- Alina Guna
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Katharine R Page
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Maxine L Wang
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA.
- Howard Hughes Medical Institute Freeman Hrabowski Scholar, California Institute of Technology, Pasadena, CA, 91125, USA.
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4
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Sunshine S, Puschnik AS, Replogle JM, Laurie MT, Liu J, Zha BS, Nuñez JK, Byrum JR, McMorrow AH, Frieman MB, Winkler J, Qiu X, Rosenberg OS, Leonetti MD, Ye CJ, Weissman JS, DeRisi JL, Hein MY. Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq. Nat Commun 2023; 14:6245. [PMID: 37803001 PMCID: PMC10558542 DOI: 10.1038/s41467-023-41788-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/30/2023] [Accepted: 09/15/2023] [Indexed: 10/08/2023] Open
Abstract
Genomic and proteomic screens have identified numerous host factors of SARS-CoV-2, but efficient delineation of their molecular roles during infection remains a challenge. Here we use Perturb-seq, combining genetic perturbations with a single-cell readout, to investigate how inactivation of host factors changes the course of SARS-CoV-2 infection and the host response in human lung epithelial cells. Our high-dimensional data resolve complex phenotypes such as shifts in the stages of infection and modulations of the interferon response. However, only a small percentage of host factors showed such phenotypes upon perturbation. We further identified the NF-κB inhibitor IκBα (NFKBIA), as well as the translation factors EIF4E2 and EIF4H as strong host dependency factors acting early in infection. Overall, our study provides massively parallel functional characterization of host factors of SARS-CoV-2 and quantitatively defines their roles both in virus-infected and bystander cells.
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Affiliation(s)
- Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | | | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Matthew T Laurie
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- University of California, Berkeley-UCSF Joint Graduate Program in Bioengineering, San Francisco, CA, USA
| | - Beth Shoshana Zha
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Janie R Byrum
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | | | - Matthew B Frieman
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Juliane Winkler
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Oren S Rosenberg
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
| | - Marco Y Hein
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- Medical University of Vienna, Center for Medical Biochemistry, Vienna, Austria.
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5
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Guna A, Page KR, Replogle JM, Esantsi TK, Wang ML, Weissman JS, Voorhees RM. A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens. bioRxiv 2023:2023.01.22.525086. [PMID: 36711738 PMCID: PMC9882262 DOI: 10.1101/2023.01.22.525086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mapping genetic interactions is essential for determining gene function and defining novel biological pathways. We report a simple to use CRISPR interference (CRISPRi) based platform, compatible with Fluorescence Activated Cell Sorting (FACS)-based reporter screens, to query epistatic relationships at scale. This is enabled by a flexible dual-sgRNA library design that allows for the simultaneous delivery and selection of a fixed sgRNA and a second randomized guide, comprised of a genome-wide library, with a single transduction. We use this approach to identify epistatic relationships for a defined biological pathway, showing both increased sensitivity and specificity than traditional growth screening approaches.
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Affiliation(s)
- Alina Guna
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave., Pasadena, CA 91125, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Katharine R Page
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave., Pasadena, CA 91125, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Maxine L Wang
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave., Pasadena, CA 91125, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA,02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave., Pasadena, CA 91125, USA
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6
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Guna A, Stevens TA, Inglis AJ, Replogle JM, Esantsi TK, Muthukumar G, Shaffer KCL, Wang ML, Pogson AN, Jones JJ, Lomenick B, Chou TF, Weissman JS, Voorhees RM. MTCH2 is a mitochondrial outer membrane protein insertase. Science 2022; 378:317-322. [PMID: 36264797 PMCID: PMC9674023 DOI: 10.1126/science.add1856] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [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] [Indexed: 11/23/2022]
Abstract
In the mitochondrial outer membrane, α-helical transmembrane proteins play critical roles in cytoplasmic-mitochondrial communication. Using genome-wide CRISPR screens, we identified MTCH2, and its paralog MTCH1, and showed that it is required for insertion of biophysically diverse tail-anchored (TA), signal-anchored, and multipass proteins, but not outer membrane β-barrel proteins. Purified MTCH2 was sufficient to mediate insertion into reconstituted proteoliposomes. Functional and mutational studies suggested that MTCH2 has evolved from a solute carrier transporter. MTCH2 uses membrane-embedded hydrophilic residues to function as a gatekeeper for the outer membrane, controlling mislocalization of TAs into the endoplasmic reticulum and modulating the sensitivity of leukemia cells to apoptosis. Our identification of MTCH2 as an insertase provided a mechanistic explanation for the diverse phenotypes and disease states associated with MTCH2 dysfunction. We showed that MTCH2 was both necessary and sufficient for insertion of diverse α-helical proteins into the mitochondrial outer membrane, and was the defining member of a family of insertases that have co-opted the SLC25 transporter fold.
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Affiliation(s)
- Alina Guna
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Taylor A Stevens
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Alison J Inglis
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA.,Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Gayathri Muthukumar
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kelly C L Shaffer
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Maxine L Wang
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Angela N Pogson
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jeff J Jones
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Brett Lomenick
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
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7
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Yang D, Jones MG, Naranjo S, Rideout WM, Min KHJ, Ho R, Wu W, Replogle JM, Page JL, Quinn JJ, Horns F, Qiu X, Chen MZ, Freed-Pastor WA, McGinnis CS, Patterson DM, Gartner ZJ, Chow ED, Bivona TG, Chan MM, Yosef N, Jacks T, Weissman JS. Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution. Cell 2022; 185:1905-1923.e25. [PMID: 35523183 DOI: 10.1016/j.cell.2022.04.015] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [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: 09/21/2021] [Revised: 02/09/2022] [Accepted: 04/08/2022] [Indexed: 12/19/2022]
Abstract
Tumor evolution is driven by the progressive acquisition of genetic and epigenetic alterations that enable uncontrolled growth and expansion to neighboring and distal tissues. The study of phylogenetic relationships between cancer cells provides key insights into these processes. Here, we introduced an evolving lineage-tracing system with a single-cell RNA-seq readout into a mouse model of Kras;Trp53(KP)-driven lung adenocarcinoma and tracked tumor evolution from single-transformed cells to metastatic tumors at unprecedented resolution. We found that the loss of the initial, stable alveolar-type2-like state was accompanied by a transient increase in plasticity. This was followed by the adoption of distinct transcriptional programs that enable rapid expansion and, ultimately, clonal sweep of stable subclones capable of metastasizing. Finally, tumors develop through stereotypical evolutionary trajectories, and perturbing additional tumor suppressors accelerates progression by creating novel trajectories. Our study elucidates the hierarchical nature of tumor evolution and, more broadly, enables in-depth studies of tumor progression.
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Affiliation(s)
- Dian Yang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Matthew G Jones
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Santiago Naranjo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - William M Rideout
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kyung Hoi Joseph Min
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Raymond Ho
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jennifer L Page
- Cell and Genome Engineering Core, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jeffrey J Quinn
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Felix Horns
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xiaojie Qiu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Michael Z Chen
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Medical Scientist Training Program, Harvard Medical School, Boston, MA 02115, USA
| | - William A Freed-Pastor
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Christopher S McGinnis
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David M Patterson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg BioHub Investigator, University of California, San Francisco, San Francisco, CA 94158, USA; Center for Cellular Construction, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Center for Advanced Technology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michelle M Chan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg BioHub Investigator, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Electrical Engineering and Computer Science, University of California Berkeley, Berkeley, CA 94720, USA; Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, USA.
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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8
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Qiu X, Zhang Y, Martin-Rufino JD, Weng C, Hosseinzadeh S, Yang D, Pogson AN, Hein MY, Hoi Joseph Min K, Wang L, Grody EI, Shurtleff MJ, Yuan R, Xu S, Ma Y, Replogle JM, Lander ES, Darmanis S, Bahar I, Sankaran VG, Xing J, Weissman JS. Mapping transcriptomic vector fields of single cells. Cell 2022; 185:690-711.e45. [PMID: 35108499 PMCID: PMC9332140 DOI: 10.1016/j.cell.2021.12.045] [Citation(s) in RCA: 116] [Impact Index Per Article: 58.0] [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: 02/12/2021] [Revised: 10/08/2021] [Accepted: 12/28/2021] [Indexed: 01/03/2023]
Abstract
Single-cell (sc)-RNA-seq, together with RNA-velocity and metabolic labeling, reveals cellular states and transitions at unprecedented resolution. Fully exploiting these data, however, requires kinetic models capable of unveiling governing regulatory functions. Here, we introduce an analytical framework dynamo, that infers absolute RNA velocity, reconstructs continuous vector-field functions that predict cell fates, employs differential geometry to extract underlying regulations, and ultimately predicts optimal reprogramming paths and perturbation outcomes. We highlight dynamo’s power to overcome fundamental limitations of conventional splicing-based RNA velocity analyses to enable accurate velocity estimations on a metabolically-labeled human hematopoiesis scRNA-seq dataset. Furthermore, differential geometry analyses reveal mechanisms driving early megakaryocyte appearance and elucidate asymmetrical regulation within the PU.1–GATA1 circuit. Leveraging the Least-Action-Path method, dynamo accurately predicts drivers of numerous hematopoietic transitions. Finally, in silico perturbations predict cell-fate diversions induced by gene perturbations. Dynamo thus represents an important step in advancing quantitative and predictive theories of cell-state transitions.
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Affiliation(s)
- Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Yan Zhang
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA; Joint CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jorge D Martin-Rufino
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Chen Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Shayan Hosseinzadeh
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Dian Yang
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Angela N Pogson
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Marco Y Hein
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | - Kyung Hoi Joseph Min
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Li Wang
- Department of Mathematics, University of Texas at Arlington, Arlington, TX, USA
| | | | | | - Ruoshi Yuan
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | | | - Yian Ma
- Halıcıoğlu Data Science Institute, University of California San Diego, San Diego, CA, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA; Medical Scientist Training Program, University of California, San Francisco, CA, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Systems Biology Harvard Medical School, Boston, MA 02125, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Ivet Bahar
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA; Joint CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vijay G Sankaran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jianhua Xing
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA; Joint CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA, USA; UPMC-Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA; Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA; Koch Institute For Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA.
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9
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Replogle JM, Bonnar JL, Pogson AN, Liem CR, Maier NK, Ding Y, Russell BJ, Wang X, Leng K, Guna A, Norman TM, Pak RA, Ramos DM, Ward ME, Gilbert LA, Kampmann M, Weissman JS, Jost M. Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors. eLife 2022; 11:81856. [PMID: 36576240 PMCID: PMC9829409 DOI: 10.7554/elife.81856] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
CRISPR interference (CRISPRi) enables programmable, reversible, and titratable repression of gene expression (knockdown) in mammalian cells. Initial CRISPRi-mediated genetic screens have showcased the potential to address basic questions in cell biology, genetics, and biotechnology, but wider deployment of CRISPRi screening has been constrained by the large size of single guide RNA (sgRNA) libraries and challenges in generating cell models with consistent CRISPRi-mediated knockdown. Here, we present next-generation CRISPRi sgRNA libraries and effector expression constructs that enable strong and consistent knockdown across mammalian cell models. First, we combine empirical sgRNA selection with a dual-sgRNA library design to generate an ultra-compact (1-3 elements per gene), highly active CRISPRi sgRNA library. Next, we compare CRISPRi effectors to show that the recently published Zim3-dCas9 provides an excellent balance between strong on-target knockdown and minimal non-specific effects on cell growth or the transcriptome. Finally, we engineer a suite of cell lines with stable expression of Zim3-dCas9 and robust on-target knockdown. Our results and publicly available reagents establish best practices for CRISPRi genetic screening.
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Affiliation(s)
- Joseph M Replogle
- Medical Scientist Training Program, University of California, San FranciscoSan FranciscoUnited States,Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States,Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States,Whitehead Institute for Biomedical ResearchCambridgeUnited States
| | - Jessica L Bonnar
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States,Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States,Whitehead Institute for Biomedical ResearchCambridgeUnited States
| | - Angela N Pogson
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States,Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States,Whitehead Institute for Biomedical ResearchCambridgeUnited States
| | - Christina R Liem
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Nolan K Maier
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
| | - Yufang Ding
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
| | - Baylee J Russell
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
| | - Xingren Wang
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
| | - Kun Leng
- Medical Scientist Training Program, University of California, San FranciscoSan FranciscoUnited States,Institute for Neurodegenerative Disease, University of California, San FranciscoSan FranciscoUnited States
| | - Alina Guna
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States,Whitehead Institute for Biomedical ResearchCambridgeUnited States
| | - Thomas M Norman
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Ryan A Pak
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Daniel M Ramos
- Center for Alzheimer's Disease and Related Dementias, National Institutes of HealthBethesdaUnited States,National Institute on Aging, National Institutes of HealthBethesdaUnited States
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaUnited States
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States,Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States,Arc InstitutePalo AltoUnited States
| | - Martin Kampmann
- Institute for Neurodegenerative Disease, University of California, San FranciscoSan FranciscoUnited States,Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States,Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States,Whitehead Institute for Biomedical ResearchCambridgeUnited States,Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Marco Jost
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States,Department of Microbiology, Harvard Medical SchoolBostonUnited States
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10
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Koblan LW, Arbab M, Shen MW, Hussmann JA, Anzalone AV, Doman JL, Newby GA, Yang D, Mok B, Replogle JM, Xu A, Sisley TA, Weissman JS, Adamson B, Liu DR. Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning. Nat Biotechnol 2021; 39:1414-1425. [PMID: 34183861 PMCID: PMC8985520 DOI: 10.1038/s41587-021-00938-z] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [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: 01/04/2021] [Accepted: 04/30/2021] [Indexed: 12/22/2022]
Abstract
Programmable C•G-to-G•C base editors (CGBEs) have broad scientific and therapeutic potential, but their editing outcomes have proved difficult to predict and their editing efficiency and product purity are often low. We describe a suite of engineered CGBEs paired with machine learning models to enable efficient, high-purity C•G-to-G•C base editing. We performed a CRISPR interference (CRISPRi) screen targeting DNA repair genes to identify factors that affect C•G-to-G•C editing outcomes and used these insights to develop CGBEs with diverse editing profiles. We characterized ten promising CGBEs on a library of 10,638 genomically integrated target sites in mammalian cells and trained machine learning models that accurately predict the purity and yield of editing outcomes (R = 0.90) using these data. These CGBEs enable correction to the wild-type coding sequence of 546 disease-related transversion single-nucleotide variants (SNVs) with >90% precision (mean 96%) and up to 70% efficiency (mean 14%). Computational prediction of optimal CGBE-single-guide RNA pairs enables high-purity transversion base editing at over fourfold more target sites than achieved using any single CGBE variant.
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Affiliation(s)
- Luke W Koblan
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Mandana Arbab
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Max W Shen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew V Anzalone
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jordan L Doman
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Dian Yang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Beverly Mok
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Albert Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Tyler A Sisley
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA.
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Britt Adamson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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11
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Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, Kampmann M, Bernstein BE, Hovestadt V, Gilbert LA, Weissman JS. Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell 2021; 184:2503-2519.e17. [PMID: 33838111 PMCID: PMC8376083 DOI: 10.1016/j.cell.2021.03.025] [Citation(s) in RCA: 242] [Impact Index Per Article: 80.7] [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: 08/30/2020] [Revised: 01/28/2021] [Accepted: 03/11/2021] [Indexed: 12/23/2022]
Abstract
A general approach for heritably altering gene expression has the potential to enable many discovery and therapeutic efforts. Here, we present CRISPRoff-a programmable epigenetic memory writer consisting of a single dead Cas9 fusion protein that establishes DNA methylation and repressive histone modifications. Transient CRISPRoff expression initiates highly specific DNA methylation and gene repression that is maintained through cell division and differentiation of stem cells to neurons. Pairing CRISPRoff with genome-wide screens and analysis of chromatin marks establishes rules for heritable gene silencing. We identify single guide RNAs (sgRNAs) capable of silencing the large majority of genes including those lacking canonical CpG islands (CGIs) and reveal a wide targeting window extending beyond annotated CGIs. The broad ability of CRISPRoff to initiate heritable gene silencing even outside of CGIs expands the canonical model of methylation-based silencing and enables diverse applications including genome-wide screens, multiplexed cell engineering, enhancer silencing, and mechanistic exploration of epigenetic inheritance.
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Affiliation(s)
- James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Jin Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Greg C Pommier
- Department of Urology, University of California, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - J Zachery Cogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA; Medical Scientist Training Program, University of California, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142, USA
| | - Carmen Adriaens
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Gokul N Ramadoss
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Avi J Samelson
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158
| | - Angela N Pogson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142, USA
| | - James Y S Kim
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Amanda Chung
- Department of Urology, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA
| | | | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Bradley E Bernstein
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Volker Hovestadt
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215, USA
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA.
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142, USA.
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12
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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
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California, Berkeley, California, United States of America
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- 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
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- 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
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- 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
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Gladstone Institute, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- eSix Development, Oakland, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Gladstone Institute, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- 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
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- 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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13
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Hickey KL, Dickson K, Cogan JZ, Replogle JM, Schoof M, D'Orazio KN, Sinha NK, Hussmann JA, Jost M, Frost A, Green R, Weissman JS, Kostova KK. GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control. Mol Cell 2020; 79:950-962.e6. [PMID: 32726578 PMCID: PMC7891188 DOI: 10.1016/j.molcel.2020.07.007] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [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: 12/21/2019] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022]
Abstract
Ribosome-associated quality control (RQC) pathways protect cells from toxicity caused by incomplete protein products resulting from translation of damaged or problematic mRNAs. Extensive work in yeast has identified highly conserved mechanisms that lead to degradation of faulty mRNA and partially synthesized polypeptides. Here we used CRISPR-Cas9-based screening to search for additional RQC strategies in mammals. We found that failed translation leads to specific inhibition of translation initiation on that message. This negative feedback loop is mediated by two translation inhibitors, GIGYF2 and 4EHP. Model substrates and growth-based assays established that inhibition of additional rounds of translation acts in concert with known RQC pathways to prevent buildup of toxic proteins. Inability to block translation of faulty mRNAs and subsequent accumulation of partially synthesized polypeptides could explain the neurodevelopmental and neuropsychiatric disorders observed in mice and humans with compromised GIGYF2 function.
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Affiliation(s)
- Kelsey L Hickey
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kimberley Dickson
- Department of Biology, Lawerence University, Appleton, WI 54911, USA
| | - J Zachery Cogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael Schoof
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Karole N D'Orazio
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Niladri K Sinha
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Marco Jost
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adam Frost
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Rachel Green
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Howard Hughes Medical Institute, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Carnegie Institution for Science, Baltimore, MD 21218, USA.
| | - Kamena K Kostova
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
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14
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Replogle JM, Norman TM, Xu A, Hussmann JA, Chen J, Cogan JZ, Meer EJ, Terry JM, Riordan DP, Srinivas N, Fiddes IT, Arthur JG, Alvarado LJ, Pfeiffer KA, Mikkelsen TS, Weissman JS, Adamson B. Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing. Nat Biotechnol 2020; 38:954-961. [PMID: 32231336 PMCID: PMC7416462 DOI: 10.1038/s41587-020-0470-y] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [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: 12/20/2018] [Accepted: 02/26/2020] [Indexed: 12/13/2022]
Abstract
Single-cell CRISPR screens enable the exploration of mammalian gene function and genetic regulatory networks. However, use of this technology has been limited by reliance on indirect indexing of single-guide RNAs (sgRNAs). Here we present direct-capture Perturb-seq, a versatile screening approach in which expressed sgRNAs are sequenced alongside single-cell transcriptomes. Direct-capture Perturb-seq enables detection of multiple distinct sgRNA sequences from individual cells and thus allows pooled single-cell CRISPR screens to be easily paired with combinatorial perturbation libraries that contain dual-guide expression vectors. We demonstrate the utility of this approach for high-throughput investigations of genetic interactions and, leveraging this ability, dissect epistatic interactions between cholesterol biogenesis and DNA repair. Using direct capture Perturb-seq, we also show that targeting individual genes with multiple sgRNAs per cell improves efficacy of CRISPR interference and activation, facilitating the use of compact, highly active CRISPR libraries for single-cell screens. Last, we show that hybridization-based target enrichment permits sensitive, specific sequencing of informative transcripts from single-cell RNA-seq experiments.
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Affiliation(s)
- Joseph M Replogle
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
| | - Thomas M Norman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Albert Xu
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jin Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
| | - J Zachery Cogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA, USA.
| | - Britt Adamson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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15
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Norman TM, Horlbeck MA, Replogle JM, Ge AY, Xu A, Jost M, Gilbert LA, Weissman JS. Exploring genetic interaction manifolds constructed from rich single-cell phenotypes. Science 2019; 365:786-793. [PMID: 31395745 PMCID: PMC6746554 DOI: 10.1126/science.aax4438] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [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: 03/29/2019] [Accepted: 07/29/2019] [Indexed: 12/18/2022]
Abstract
How cellular and organismal complexity emerges from combinatorial expression of genes is a central question in biology. High-content phenotyping approaches such as Perturb-seq (single-cell RNA-sequencing pooled CRISPR screens) present an opportunity for exploring such genetic interactions (GIs) at scale. Here, we present an analytical framework for interpreting high-dimensional landscapes of cell states (manifolds) constructed from transcriptional phenotypes. We applied this approach to Perturb-seq profiling of strong GIs mined from a growth-based, gain-of-function GI map. Exploration of this manifold enabled ordering of regulatory pathways, principled classification of GIs (e.g., identifying suppressors), and mechanistic elucidation of synergistic interactions, including an unexpected synergy between CBL and CNN1 driving erythroid differentiation. Finally, we applied recommender system machine learning to predict interactions, facilitating exploration of vastly larger GI manifolds.
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Affiliation(s)
- Thomas M Norman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA
| | - Alex Y Ge
- Department of Urology, University of California, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Albert Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA
| | - Marco Jost
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA
| | - Luke A Gilbert
- Department of Urology, University of California, San Francisco, CA 94158, USA.
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA
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16
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Ryan KJ, White CC, Patel K, Xu J, Olah M, Replogle JM, Frangieh M, Cimpean M, Winn P, McHenry A, Kaskow BJ, Chan G, Cuerdon N, Bennett DA, Boyd JD, Imitola J, Elyaman W, De Jager PL, Bradshaw EM. A human microglia-like cellular model for assessing the effects of neurodegenerative disease gene variants. Sci Transl Med 2018; 9:9/421/eaai7635. [PMID: 29263232 DOI: 10.1126/scitranslmed.aai7635] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 04/12/2017] [Accepted: 08/18/2017] [Indexed: 12/25/2022]
Abstract
Microglia are emerging as a key cell type in neurodegenerative diseases, yet human microglia are challenging to study in vitro. We developed an in vitro cell model system composed of human monocyte-derived microglia-like (MDMi) cells that recapitulated key aspects of microglia phenotype and function. We then used this model system to perform an expression quantitative trait locus (eQTL) study examining 94 genes from loci associated with Alzheimer's disease, Parkinson's disease, and multiple sclerosis. We found six loci (CD33, PILRB, NUP160, LRRK2, RGS1, and METTL21B) in which the risk haplotype drives the association with both disease susceptibility and altered expression of a nearby gene (cis-eQTL). In the PILRB and LRRK2 loci, the cis-eQTL was found in the MDMi cells but not in human peripheral blood monocytes, suggesting that differentiation of monocytes into microglia-like cells led to the acquisition of a cellular state that could reveal the functional consequences of certain genetic variants. We further validated the effect of risk haplotypes at the protein level for PILRB and CD33, and we confirmed that the CD33 risk haplotype altered phagocytosis by the MDMi cells. We propose that increased LRRK2 gene expression by MDMi cells could be a functional outcome of rs76904798, a single-nucleotide polymorphism in the LRKK2 locus that is associated with Parkinson's disease.
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Affiliation(s)
- Katie J Ryan
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Charles C White
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Kruti Patel
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Jishu Xu
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Marta Olah
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.,Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Joseph M Replogle
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Michael Frangieh
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Maria Cimpean
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Phoebe Winn
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Allison McHenry
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Belinda J Kaskow
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Gail Chan
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Nicole Cuerdon
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Justin D Boyd
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Jaime Imitola
- Laboratory of Neural Stem Cells and Functional Neurogenetics, Departments of Neurology and Neuroscience, The Ohio State University College of Medicine, 333 West 10th Avenue, Columbus, OH 43210, USA
| | - Wassim Elyaman
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.,Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Philip L De Jager
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.,Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Elizabeth M Bradshaw
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA. .,Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168th Street, New York, NY 10032, USA
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17
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Raj T, Chibnik LB, McCabe C, Wong A, Replogle JM, Yu L, Gao S, Unverzagt FW, Stranger B, Murrell J, Barnes L, Hendrie HC, Foroud T, Krichevsky A, Bennett DA, Hall KS, Evans DA, De Jager PL. Genetic architecture of age-related cognitive decline in African Americans. Neurol Genet 2016; 3:e125. [PMID: 28078323 PMCID: PMC5206965 DOI: 10.1212/nxg.0000000000000125] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/09/2016] [Indexed: 11/23/2022]
Abstract
OBJECTIVE To identify genetic risk factors associated with susceptibility to age-related cognitive decline in African Americans (AAs). METHODS We performed a genome-wide association study (GWAS) and an admixture-mapping scan in 3,964 older AAs from 5 longitudinal cohorts; for each participant, we calculated a slope of an individual's global cognitive change from neuropsychological evaluations. We also performed a pathway-based analysis of the age-related cognitive decline GWAS. RESULTS We found no evidence to support the existence of a genomic region which has a strongly different contribution to age-related cognitive decline in African and European genomes. Known Alzheimer disease (AD) susceptibility variants in the ABCA7 and MS4A loci do influence this trait in AAs. Of interest, our pathway-based analyses returned statistically significant results highlighting a shared risk from lipid/metabolism and protein tyrosine signaling pathways between cognitive decline and AD, but the role of inflammatory pathways is polarized, being limited to AD susceptibility. CONCLUSIONS The genetic architecture of aging-related cognitive in AA individuals is largely similar to that of individuals of European descent. In both populations, we note a surprising lack of enrichment for immune pathways in the genetic risk for cognitive decline, despite strong enrichment of these pathways among genetic risk factors for AD.
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Affiliation(s)
- Towfique Raj
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Lori B Chibnik
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Cristin McCabe
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Andus Wong
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Joseph M Replogle
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Lei Yu
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Sujuan Gao
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Frederick W Unverzagt
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Barbara Stranger
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Jill Murrell
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Lisa Barnes
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Hugh C Hendrie
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Tatiana Foroud
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Anna Krichevsky
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - David A Bennett
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Kathleen S Hall
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Denis A Evans
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics (T.R., L.B.C., J.M.R., P.L.D.J.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Neurologic Disease (T.R., A.W., A.K., P.L.D.J.), Department of Neurology, and Division of Genetics (T.R., L.B.C., P.L.D.J.), Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (T.R., L.B.C., P.L.D.J.), Boston, MA; Program in Medical and Population genetics (T.R., L.B.C., C.M., J.M.R., P.L.D.J.), The Broad Institute, Cambridge, MA; Section of Genetic Medicine (B.S.), Department of Medicine, and Institute for Genomics and Systems Biology (B.S.), University of Chicago, IL; Indiana University Center for Aging Research (H.C.H.); Department of Psychiatry (F.W.U., H.C.H., K.S.H.), Department of Biostatistics (S.G.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (J.M., T.F.), Indiana University, Indianapolis; Rush Institute for Healthy Aging (D.A.V.), Department of Internal Medicine, Department of Neurology (L.B., D.A.B.), and Rush Alzheimer's Disease Center (L.Y., L.B., D.A.B.), Rush University Medical Center, Chicago, IL. T.R. is currently affiliated with Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York
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Chan G, White CC, Winn PA, Cimpean M, Replogle JM, Glick LR, Cuerdon NE, Ryan KJ, Johnson KA, Schneider JA, Bennett DA, Chibnik LB, Sperling RA, De Jager PL, Bradshaw EM. Trans-pQTL study identifies immune crosstalk between Parkinson and Alzheimer loci. Neurol Genet 2016; 2:e90. [PMID: 27504496 PMCID: PMC4962525 DOI: 10.1212/nxg.0000000000000090] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/15/2016] [Indexed: 01/26/2023]
Abstract
OBJECTIVE Given evidence from genetic studies, we hypothesized that there may be a shared component to the role of myeloid function in Parkinson and Alzheimer disease (PD and AD) and assessed whether PD susceptibility variants influenced protein expression of well-established AD-associated myeloid genes in human monocytes. METHODS We repurposed data in which AD-related myeloid proteins CD33, TREM1, TREM2, TREML2, TYROBP, and PTK2B were measured by flow cytometry in monocytes from 176 participants of the PhenoGenetic Project (PGP) and Harvard Aging Brain Study. Linear regression was used to identify associations between 24 PD risk variants and protein expression. The 2 cohorts were meta-analyzed in a discovery analysis, and the 4 most strongly suggestive results were validated in an independent cohort of 50 PGP participants. RESULTS We discovered and validated an association between the PD risk allele rs12456492(G) in the RIT2 locus and increased CD33 expression (p joint = 3.50 × 10(-5)) and found strongly suggestive evidence that rs11060180(A) in the CCDC62/HIP1R locus decreased PTK2B expression (p joint = 1.12 × 10(-4)). Furthermore, in older individuals, increased CD33 expression on peripheral monocytes was associated with a greater burden of parkinsonism (p = 0.047), particularly bradykinesia (p = 6.64 × 10(-3)). CONCLUSIONS We find that the rs12456492 PD risk variant affects expression of AD-associated protein CD33 in peripheral monocytes, which suggests that genetic factors for these 2 diseases may converge to influence overlapping innate immune-mediated mechanisms that contribute to neurodegeneration. Furthermore, the effect of the rs12456492(G) PD risk allele on increased CD33 suggests that the inhibition of certain myeloid functions may contribute to PD susceptibility, as is the case for AD.
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Affiliation(s)
- Gail Chan
- Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL
| | - Charles C White
- Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL
| | - Phoebe A Winn
- Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL
| | - Maria Cimpean
- Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL
| | - Joseph M Replogle
- Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL
| | - Laura R Glick
- Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL
| | - Nicole E Cuerdon
- Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL
| | - Katie J Ryan
- Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL
| | - Keith A Johnson
- Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL
| | - Julie A Schneider
- Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL
| | - David A Bennett
- Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL
| | - Lori B Chibnik
- Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL
| | - Reisa A Sperling
- Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL
| | - Philip L De Jager
- Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL
| | - Elizabeth M Bradshaw
- Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL
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Horlbeck MA, Witkowsky LB, Guglielmi B, Replogle JM, Gilbert LA, Villalta JE, Torigoe SE, Tjian R, Weissman JS. Nucleosomes impede Cas9 access to DNA in vivo and in vitro. eLife 2016; 5. [PMID: 26987018 PMCID: PMC4861601 DOI: 10.7554/elife.12677] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [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: 10/29/2015] [Accepted: 03/16/2016] [Indexed: 12/23/2022] Open
Abstract
The prokaryotic CRISPR (clustered regularly interspaced palindromic repeats)-associated protein, Cas9, has been widely adopted as a tool for editing, imaging, and regulating eukaryotic genomes. However, our understanding of how to select single-guide RNAs (sgRNAs) that mediate efficient Cas9 activity is incomplete, as we lack insight into how chromatin impacts Cas9 targeting. To address this gap, we analyzed large-scale genetic screens performed in human cell lines using either nuclease-active or nuclease-dead Cas9 (dCas9). We observed that highly active sgRNAs for Cas9 and dCas9 were found almost exclusively in regions of low nucleosome occupancy. In vitro experiments demonstrated that nucleosomes in fact directly impede Cas9 binding and cleavage, while chromatin remodeling can restore Cas9 access. Our results reveal a critical role of eukaryotic chromatin in dictating the targeting specificity of this transplanted bacterial enzyme, and provide rules for selecting Cas9 target sites distinct from and complementary to those based on sequence properties. DOI:http://dx.doi.org/10.7554/eLife.12677.001 Many bacteria have a type of immune system known as CRISPR that can target and cut foreign DNA to protect it against viruses. Recently, the CRISPR system was adapted to allow scientists to easily manipulate the genome of humans and many other organisms. However, unlike the loosely organized DNA found in bacteria, the DNA that makes up the human genome is tightly packed and wrapped around complexes of proteins to form structures called nucleosomes. It was not clear whether the CRISPR system was able to effectively target the stretches of DNA in a nucleosome. In 2013, researchers developed a modified version of CRISPR, known as CRISPR interference, to block gene activity and in 2014 used it to systematically repress many of the genes in the human genome. Now, Horlbeck, Witkowsky et al. – who include several of the researchers from the 2014 work – have analyzed existing data for a specific type of human cell grown in the laboratory and found that CRISPR interference activity was strongest in certain areas around the start of each gene. However, CRISPR interference was much weaker in other areas of genes that coincided well with stretches of DNA that are known to often be bound by nucleosomes. Nucleosomes also appeared to block CRISPR editing, although the effects were less pronounced. Horlbeck, Witkowsky et al. then directly tested whether nucleosomes could prevent the CRISPR system from binding or modifying the DNA. When the individual components were mixed in test tubes, the CRISPR system could readily target “naked” DNA. However, it could not access nucleosome-bound DNA, unless an enzyme that can move nucleosomes along the DNA in the human genome was also added to the mix. These findings suggest one way that CRISPR can manipulate much of the human genome despite the widespread presence of nucleosomes. Future work will now aim to develop computational methods that take the positions of nucleosomes into account when picking DNA sites to target with CRISPR. DOI:http://dx.doi.org/10.7554/eLife.12677.002
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Affiliation(s)
- Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Lea B Witkowsky
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Benjamin Guglielmi
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Jacqueline E Villalta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Sharon E Torigoe
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Robert Tjian
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
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20
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Orent W, Mchenry AR, Rao DA, White C, Klein HU, Bassil R, Srivastava G, Replogle JM, Raj T, Frangieh M, Cimpean M, Cuerdon N, Chibnik L, Khoury SJ, Karlson EW, Brenner MB, De Jager P, Bradshaw EM, Elyaman W. Rheumatoid arthritis-associated RBPJ polymorphism alters memory CD4+ T cells. Hum Mol Genet 2015; 25:404-17. [PMID: 26604133 DOI: 10.1093/hmg/ddv474] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 11/15/2015] [Indexed: 02/07/2023] Open
Abstract
Notch signaling has recently emerged as an important regulator of immune responses in autoimmune diseases. The recombination signal-binding protein for immunoglobulin kappa J region (RBPJ) is a transcriptional repressor, but converts into a transcriptional activator upon activation of the canonical Notch pathway. Genome-wide association studies of rheumatoid arthritis (RA) identified a susceptibility locus, rs874040(CC), which implicated the RBPJ gene. Here, chromatin state mapping generated using the chromHMM algorithm reveals strong enhancer regions containing DNase I hypersensitive sites overlapping the rs874040 linkage disequilibrium block in human memory, but not in naïve CD4(+) T cells. The rs874040 overlapping this chromatin state was associated with increased RBPJ expression in stimulated memory CD4(+) T cells from healthy subjects homozygous for the risk allele (CC) compared with memory CD4(+) T cells bearing the protective allele (GG). Transcriptomic analysis of rs874040(CC) memory T cells showed a repression of canonical Notch target genes IL (interleukin)-9, IL-17 and interferon (IFN)γ in the basal state. Interestingly, activation of the Notch pathway using soluble Notch ligand, Jagged2-Fc, induced IL-9 and IL-17A while delta-like 4Fc, another Notch ligand, induced higher IFNγ expression in the rs874040(CC) memory CD4(+) T cells compared with their rs874040(GG) counterparts. In RA, RBPJ expression is elevated in memory T cells from RA patients compared with control subjects, and this was associated with induced inflammatory cytokines IL-9, IL-17A and IFNγ in response to Notch ligation in vitro. These findings demonstrate that the rs874040(CC) allele skews memory T cells toward a pro-inflammatory phenotype involving Notch signaling, thus increasing the susceptibility to develop RA.
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Affiliation(s)
| | | | - Deepak A Rao
- Division of Rheumatology, Immunology and Allergy and
| | - Charles White
- Ann Romney Center for Neurologic Diseases, Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Broad Institute at Harvard University and MIT, NRB-641, 77 Avenue Louis Pasteur, Boston, MA 02115, USA and
| | - Hans-Ulrich Klein
- Ann Romney Center for Neurologic Diseases, Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Broad Institute at Harvard University and MIT, NRB-641, 77 Avenue Louis Pasteur, Boston, MA 02115, USA and
| | | | - Gyan Srivastava
- Ann Romney Center for Neurologic Diseases, Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Broad Institute at Harvard University and MIT, NRB-641, 77 Avenue Louis Pasteur, Boston, MA 02115, USA and
| | - Joseph M Replogle
- Ann Romney Center for Neurologic Diseases, Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Broad Institute at Harvard University and MIT, NRB-641, 77 Avenue Louis Pasteur, Boston, MA 02115, USA and
| | - Towfique Raj
- Ann Romney Center for Neurologic Diseases, Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Broad Institute at Harvard University and MIT, NRB-641, 77 Avenue Louis Pasteur, Boston, MA 02115, USA and
| | | | - Maria Cimpean
- Ann Romney Center for Neurologic Diseases, Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Broad Institute at Harvard University and MIT, NRB-641, 77 Avenue Louis Pasteur, Boston, MA 02115, USA and
| | - Nicole Cuerdon
- Ann Romney Center for Neurologic Diseases, Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Broad Institute at Harvard University and MIT, NRB-641, 77 Avenue Louis Pasteur, Boston, MA 02115, USA and
| | - Lori Chibnik
- Ann Romney Center for Neurologic Diseases, Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Broad Institute at Harvard University and MIT, NRB-641, 77 Avenue Louis Pasteur, Boston, MA 02115, USA and
| | - Samia J Khoury
- Ann Romney Center for Neurologic Diseases, Abu Haidar Neuroscience Institute, American University of Beirut Medical Center, Beirut, Lebanon
| | | | | | - Philip De Jager
- Ann Romney Center for Neurologic Diseases, Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Broad Institute at Harvard University and MIT, NRB-641, 77 Avenue Louis Pasteur, Boston, MA 02115, USA and
| | - Elizabeth M Bradshaw
- Ann Romney Center for Neurologic Diseases, Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Broad Institute at Harvard University and MIT, NRB-641, 77 Avenue Louis Pasteur, Boston, MA 02115, USA and
| | - Wassim Elyaman
- Ann Romney Center for Neurologic Diseases, Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Broad Institute at Harvard University and MIT, NRB-641, 77 Avenue Louis Pasteur, Boston, MA 02115, USA and
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21
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Chan G, White CC, Winn PA, Cimpean M, Replogle JM, Glick LR, Cuerdon NE, Ryan KJ, Johnson KA, Schneider JA, Bennett DA, Chibnik LB, Sperling RA, Bradshaw EM, De Jager PL. CD33 modulates TREM2: convergence of Alzheimer loci. Nat Neurosci 2015; 18:1556-8. [PMID: 26414614 PMCID: PMC4682915 DOI: 10.1038/nn.4126] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [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: 06/02/2015] [Accepted: 09/02/2015] [Indexed: 12/26/2022]
Abstract
Here, we report results from a protein quantitative trait analysis in monocytes from 226 individuals to evaluate cross-talk between Alzheimer loci. We find that the NME8 locus influences PTK2B and that the CD33 risk allele leads to greater TREM2 expression. Further, we observe (1) a decreased TREM1/TREM2 ratio with a TREM1 risk allele, (2) decreased TREM2 expression with CD33 suppression, and (3) elevated cortical TREM2 mRNA expression with amyloid pathology.
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Affiliation(s)
- Gail Chan
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Charles C White
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Phoebe A Winn
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Maria Cimpean
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Joseph M Replogle
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Laura R Glick
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Nicole E Cuerdon
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Katie J Ryan
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Keith A Johnson
- Harvard Medical School, Boston, Massachusetts, USA.,Center for Alzheimer's Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Lori B Chibnik
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Reisa A Sperling
- Harvard Medical School, Boston, Massachusetts, USA.,Center for Alzheimer's Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Elizabeth M Bradshaw
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Philip L De Jager
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
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22
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Affiliation(s)
- Joseph M Replogle
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, MA.,Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA.,Harvard Medical School, Boston, MA
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, MA.,Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA.,Harvard Medical School, Boston, MA
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23
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Esposito F, Sorosina M, Ottoboni L, Lim ET, Replogle JM, Raj T, Brambilla P, Liberatore G, Guaschino C, Romeo M, Pertel T, Stankiewicz JM, Martinelli V, Rodegher M, Weiner HL, Brassat D, Benoist C, Patsopoulos NA, Comi G, Elyaman W, Martinelli Boneschi F, De Jager PL. A pharmacogenetic study implicates SLC9a9 in multiple sclerosis disease activity. Ann Neurol 2015; 78:115-27. [PMID: 25914168 DOI: 10.1002/ana.24429] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/17/2015] [Accepted: 04/17/2015] [Indexed: 02/06/2023]
Abstract
OBJECTIVE A proportion of multiple sclerosis (MS) patients experience disease activity despite treatment. The early identification of the most effective drug is critical to impact long-term outcome and to move toward a personalized approach. The aim of the present study is to identify biomarkers for further clinical development and to yield insights into the pathophysiology of disease activity. METHODS We performed a genome-wide association study in interferon-β (IFNβ)-treated MS patients followed by validation in 3 independent cohorts. The role of the validated variant was examined in several RNA data sets, and the function of the presumed target gene was explored using an RNA interference approach in primary T cells in vitro. RESULTS We found an association between rs9828519(G) and nonresponse to IFNβ (pdiscovery = 4.43 × 10(-8)) and confirmed it in a meta-analysis across 3 replication data sets (preplication = 7.78 × 10(-4)). Only 1 gene is found in the linkage disequilibrium block containing rs9828519: SLC9A9. Exploring the function of this gene, we see that SLC9A9 mRNA expression is diminished in MS subjects who are more likely to have relapses. Moreover, SLC9A9 knockdown in T cells in vitro leads an increase in expression of IFNγ, which is a proinflammatory molecule. INTERPRETATION This study identifies and validates the role of rs9828519, an intronic variant in SLC9A9, in IFNβ-treated subjects, demonstrating a successful pharmacogenetic screen in MS. Functional characterization suggests that SLC9A9, an Na(+) -H(+) exchanger found in endosomes, appears to influence the differentiation of T cells to a proinflammatory fate and may have a broader role in MS disease activity, outside of IFNβ treatment.
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Affiliation(s)
- Federica Esposito
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy.,Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Melissa Sorosina
- Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Linda Ottoboni
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Elaine T Lim
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA
| | - Joseph M Replogle
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Program for Medical and Population Genetics, Broad Institute, Cambridge, MA.,Program in Translational Neuropsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Towfique Raj
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Program for Medical and Population Genetics, Broad Institute, Cambridge, MA.,Program in Translational Neuropsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Paola Brambilla
- Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Giuseppe Liberatore
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy.,Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Clara Guaschino
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy.,Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Marzia Romeo
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy
| | - Thomas Pertel
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA
| | - James M Stankiewicz
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA
| | - Vittorio Martinelli
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy.,Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Mariaemma Rodegher
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy.,Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA
| | - David Brassat
- Department of Neurology, Purpan Hospital and Mixed Unit of Research 1043, University of Toulouse, Toulouse, France
| | - Christophe Benoist
- Harvard Medical School, Boston, MA.,Program for Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Nikolaos A Patsopoulos
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA.,Program for Medical and Population Genetics, Broad Institute, Cambridge, MA.,Program in Translational Neuropsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Giancarlo Comi
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy.,Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Wassim Elyaman
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA.,Program in Translational Neuropsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Filippo Martinelli Boneschi
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy.,Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Philip L De Jager
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA.,Program for Medical and Population Genetics, Broad Institute, Cambridge, MA.,Program in Translational Neuropsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, MA
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Replogle JM, Chan G, White CC, Raj T, Winn PA, Evans DA, Sperling RA, Chibnik LB, Bradshaw EM, Schneider JA, Bennett DA, De Jager PL. A TREM1 variant alters the accumulation of Alzheimer-related amyloid pathology. Ann Neurol 2015; 77:469-77. [PMID: 25545807 DOI: 10.1002/ana.24337] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 11/23/2014] [Accepted: 12/21/2014] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Genome-wide association studies have linked variants in TREM2 (triggering receptor expressed on myeloid cells 2) and TREML2 with Alzheimer disease (AD) and AD endophenotypes. Here, we pursue a targeted analysis of the TREM locus in relation to cognitive decline and pathological features of AD. METHODS Clinical, cognitive, and neuropathological phenotypes were collected in 3 prospective cohorts on aging (n = 3,421 subjects). Our primary analysis was an association with neuritic plaque pathology. To functionally characterize the associated variants, we used flow cytometry to measure TREM1 expression on monocytes. RESULTS We provide evidence that an intronic variant, rs6910730(G) , in TREM1, is associated with an increased burden of neuritic plaques (p = 3.7 × 10(-4) ), diffuse plaques (p = 4.1 × 10(-3) ), and Aβ density (p = 2.6 × 10(-3) ) as well as an increased rate of cognitive decline (p = 5.3 × 10(-3) ). A variant upstream of TREM2, rs7759295(C) , is independently associated with an increased tau tangle density (p = 4.9 × 10(-4) ), an increased burden of neurofibrillary tangles (p = 9.1 × 10(-3) ), and an increased rate of cognitive decline (p = 2.3 × 10(-3) ). Finally, a cytometric analysis shows that the TREM1 rs6910730(G) allele is associated with decreased TREM1 expression on the surface of myeloid cells (p = 1.7 × 10(-3) ). INTERPRETATION We provide evidence that 2 common variants within the TREM locus are associated with pathological features of AD and aging-related cognitive decline. Our evidence suggests that these variants are likely to be independent of known AD variants and that they may work through an alteration of myeloid cell function.
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Affiliation(s)
- Joseph M Replogle
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, MA; Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA; Harvard Medical School, Boston, MA
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Affiliation(s)
| | - Philip L De Jager
- Department of Neurology, Brigham and Women's Hospital, Boston, Mass.
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Raj T, Replogle JM, Ryan K, Chibnik L, Ye J, Mostafavi S, Lee M, Rothamel K, McCabe C, Von Korff A, Bradshaw EM, Evans D, Bennett D, Benoist C, Stranger B, De Jager P. O3‐04‐05: EXPRESSION QTL ANALYSIS FROM PRIMARY IMMUNE CELLS IDENTIFIES NOVEL REGULATORY EFFECTS UNDERLYING ALZHEIMER'S DISEASE SUSCEPTIBILITY. Alzheimers Dement 2014. [DOI: 10.1016/j.jalz.2014.04.290] [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: 11/28/2022]
Affiliation(s)
- Towfique Raj
- Brigham and Women's Hospital/Harvard Medical SchoolBostonMassachusettsUnited States
| | - Joseph M. Replogle
- Brigham and Women's Hospital, Broad InstituteBostonMassachusettsUnited States
| | - Katie Ryan
- Brigham and Women's HospitalBostonMassachusettsUnited States
| | - Lori Chibnik
- Brigham and Women's Hospital, Harvard Medical SchoolBostonIllinoisUnited States
| | - Jimmie Ye
- Broad InstituteCambridgeMassachusettsUnited States
| | | | - Mark Lee
- Harvard Medical SchoolBostonMassachusettsUnited States
| | | | | | - Alina Von Korff
- Brigham and Women's HospitalBostonMassachusettsUnited States
| | | | - Denis Evans
- Rush University Medical CenterChicagoIllinoisUnited States
| | - David Bennett
- Rush University Medical CenterChicagoIllinoisUnited States
| | | | | | - Philip De Jager
- Brigham and Women's HospitalBostonMassachusettsUnited States
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Replogle JM, Raj T, Chan G, White C, Evans D, Chibnik L, Schneider J, Bennett D, De Jager PL. P1‐034: AN INTRONIC TREM1 VARIANT INFLUENCES THE ACCUMULATION OF ALZHEIMER'S DISEASE‐RELATED AMYLOID PATHOLOGY. Alzheimers Dement 2014. [DOI: 10.1016/j.jalz.2014.05.269] [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: 11/28/2022]
Affiliation(s)
| | - Towfique Raj
- Brigham and Women's Hospital/Harvard Medical SchoolBostonMassachusettsUnited States
| | - Gail Chan
- Brigham and Women's HospitalBostonMassachusettsUnited States
| | - Charles White
- Brigham and Women's HospitalBostonMassachusettsUnited States
| | - Denis Evans
- Rush University Medical CenterChicagoIllinoisUnited States
| | - Lori Chibnik
- Brigham & Women's Hospital, Harvard Medical SchoolBostonMassachusettsUnited States
| | - Julie Schneider
- Rush University Medical Center, Rush Alzheimer's Disease CenterChicagoIllinoisUnited States
| | - David Bennett
- Rush University Medical CenterChicagoIllinoisUnited States
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Raj T, Rothamel K, Mostafavi S, Ye C, Lee MN, Replogle JM, Feng T, Lee M, Asinovski N, Frohlich I, Imboywa S, Von Korff A, Okada Y, Patsopoulos NA, Davis S, McCabe C, Paik HI, Srivastava GP, Raychaudhuri S, Hafler DA, Koller D, Regev A, Hacohen N, Mathis D, Benoist C, Stranger BE, De Jager PL. Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science 2014; 344:519-23. [PMID: 24786080 DOI: 10.1126/science.1249547] [Citation(s) in RCA: 364] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To extend our understanding of the genetic basis of human immune function and dysfunction, we performed an expression quantitative trait locus (eQTL) study of purified CD4(+) T cells and monocytes, representing adaptive and innate immunity, in a multi-ethnic cohort of 461 healthy individuals. Context-specific cis- and trans-eQTLs were identified, and cross-population mapping allowed, in some cases, putative functional assignment of candidate causal regulatory variants for disease-associated loci. We note an over-representation of T cell-specific eQTLs among susceptibility alleles for autoimmune diseases and of monocyte-specific eQTLs among Alzheimer's and Parkinson's disease variants. This polarization implicates specific immune cell types in these diseases and points to the need to identify the cell-autonomous effects of disease susceptibility variants.
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Affiliation(s)
- Towfique Raj
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, MA 02115, USA
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Raj T, Ryan KJ, Replogle JM, Chibnik LB, Rosenkrantz L, Tang A, Rothamel K, Stranger BE, Bennett DA, Evans DA, De Jager PL, Bradshaw EM. CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer's disease susceptibility. Hum Mol Genet 2013; 23:2729-36. [PMID: 24381305 DOI: 10.1093/hmg/ddt666] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We previously demonstrated that the Alzheimer's disease (AD) associated risk allele, rs3865444(C), results in a higher surface density of CD33 on monocytes. Here, we find alternative splicing of exon 2 to be the primary mechanism of the genetically driven differential expression of CD33 protein. We report that the risk allele, rs3865444(C), is associated with greater cell surface expression of CD33 in both subjects of European and African-American ancestry and that there is a single haplotype influencing CD33 surface expression. A meta-analysis of the two populations narrowed the number of significant SNPs in high linkage disequilibrium (LD) (r(2) > 0.8) with rs3865444 to just five putative causal variants associated with increased protein expression. Using gene expression data from flow-sorted CD14(+)CD16(-) monocytes from 398 healthy subjects of three populations, we show that the rs3865444(C) risk allele is strongly associated with greater expression of CD33 exon 2 (pMETA = 2.36 × 10(-60)). Western blotting confirms increased protein expression of the full-length CD33 isoform containing exon 2 relative to the rs3865444(C) allele (P < 0.0001). Of the variants in strong LD with rs3865444, rs12459419, which is located in a putative SRSF2 splice site of exon 2, is the most likely candidate to mediate the altered alternative splicing of CD33's Immunoglobulin V-set domain 2 and ultimately influence AD susceptibility.
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Affiliation(s)
- Towfique Raj
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, MA 02115, USA
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