1
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Sapoznikov A, Kozlovski S, Levi N, Feigelson SW, Regev O, Davidzohn N, Ben-Dor S, Haffner-Krausz R, Feldmesser E, Wigoda N, Petrovich-Kopitman E, Biton M, Alon R. Dendritic cell ICAM-1 strengthens synapses with CD8 T cells but is not required for their early differentiation. Cell Rep 2023; 42:112864. [PMID: 37494182 DOI: 10.1016/j.celrep.2023.112864] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 06/13/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023] [Imported: 07/30/2023] Open
Abstract
Lymphocyte priming in lymph nodes (LNs) was postulated to depend on the formation of stable T cell receptor (TCR)-specific immune synapses (ISs) with antigen (Ag)-presenting dendritic cells (DCs). The high-affinity LFA-1 ligand ICAM-1 was implicated in different ISs studied in vitro. We dissect the in vivo roles of endogenous DC ICAM-1 in Ag-stimulated T cell proliferation and differentiation and find that under type 1 polarizing conditions in vaccinated or vaccinia virus-infected skin-draining LNs, Ag-presenting DCs engage in ICAM-1-dependent stable conjugates with a subset of Ag-specific CD8 blasts. Nevertheless, in the absence of these conjugates, CD8 lymphocyte proliferation and differentiation into functional cytotoxic T cells (CTLs) and skin homing effector lymphocytes takes place normally. Our results suggest that although CD8 T cell blasts engage in tight ICAM-1-dependent DC-T ISs, firm ISs are dispensable for TCR-triggered proliferation and differentiation into productive effector lymphocytes.
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Affiliation(s)
- Anita Sapoznikov
- Deptartment of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Stav Kozlovski
- Deptartment of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nehora Levi
- Deptartment of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sara W Feigelson
- Deptartment of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ofer Regev
- Deptartment of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Natalia Davidzohn
- Deptartment of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | | | - Ester Feldmesser
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Wigoda
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | | | - Moshe Biton
- Deptartment of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Ronen Alon
- Deptartment of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
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2
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Weeks EM, Ulirsch JC, Cheng NY, Trippe BL, Fine RS, Miao J, Patwardhan TA, Kanai M, Nasser J, Fulco CP, Tashman KC, Aguet F, Li T, Ordovas-Montanes J, Smillie CS, Biton M, Shalek AK, Ananthakrishnan AN, Xavier RJ, Regev A, Gupta RM, Lage K, Ardlie KG, Hirschhorn JN, Lander ES, Engreitz JM, Finucane HK. Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases. Nat Genet 2023; 55:1267-1276. [PMID: 37443254 PMCID: PMC10836580 DOI: 10.1038/s41588-023-01443-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 06/09/2023] [Indexed: 07/15/2023]
Abstract
Genome-wide association studies (GWASs) are a valuable tool for understanding the biology of complex human traits and diseases, but associated variants rarely point directly to causal genes. In the present study, we introduce a new method, polygenic priority score (PoPS), that learns trait-relevant gene features, such as cell-type-specific expression, to prioritize genes at GWAS loci. Using a large evaluation set of genes with fine-mapped coding variants, we show that PoPS and the closest gene individually outperform other gene prioritization methods, but observe the best overall performance by combining PoPS with orthogonal methods. Using this combined approach, we prioritize 10,642 unique gene-trait pairs across 113 complex traits and diseases with high precision, finding not only well-established gene-trait relationships but nominating new genes at unresolved loci, such as LGR4 for estimated glomerular filtration rate and CCR7 for deep vein thrombosis. Overall, we demonstrate that PoPS provides a powerful addition to the gene prioritization toolbox.
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Affiliation(s)
- Elle M Weeks
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Jacob C Ulirsch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
- Artificial Intelligence Laboratory, Illumina, Inc., San Diego, CA, USA
| | | | - Brian L Trippe
- Program in Computational & Systems Biology, MIT, Cambridge, MA, USA
- Computer Science & Artificial Intelligence Lab, MIT, Cambridge, MA, USA
| | - Rebecca S Fine
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Vertex Pharmaceuticals Incorporated, Boston, MA, USA
| | - Jenkai Miao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
| | - Tejal A Patwardhan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - Masahiro Kanai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, MGH, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Joseph Nasser
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charles P Fulco
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Bristol Myers Squibb, Cambridge, MA, USA
| | | | | | - Taibo Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MD-PhD Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jose Ordovas-Montanes
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Program in Immunology, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Christopher S Smillie
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Computational & Systems Biology, MIT, Cambridge, MA, USA
| | - Moshe Biton
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, MGH, Boston, MA, USA
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Department of Chemistry, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Ragon Institute of MGH, MMIT, Cambridge, MA, USA
| | - Ashwin N Ananthakrishnan
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, MGH, Boston, MA, USA
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA, USA
- Genentech, San Francisco, CA, USA
| | - Rajat M Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Cardiovascular Medicine and Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kasper Lage
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, MGH, Boston, MA, USA
| | - Kristin G Ardlie
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Joel N Hirschhorn
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, MIT, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Jesse M Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, USA
| | - Hilary K Finucane
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, MGH, Boston, MA, USA.
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3
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Gur C, Wang SY, Sheban F, Zada M, Li B, Kharouf F, Peleg H, Aamar S, Yalin A, Kirschenbaum D, Braun-Moscovici Y, Jaitin DA, Meir-Salame T, Hagai E, Kragesteen BK, Avni B, Grisariu S, Bornstein C, Shlomi-Loubaton S, David E, Shreberk-Hassidim R, Molho-Pessach V, Amar D, Tzur T, Kuint R, Gross M, Barboy O, Moshe A, Fellus-Alyagor L, Hirsch D, Addadi Y, Erenfeld S, Biton M, Tzemach T, Elazary A, Naparstek Y, Tzemach R, Weiner A, Giladi A, Balbir-Gurman A, Amit I. LGR5 expressing skin fibroblasts define a major cellular hub perturbed in scleroderma. Cell 2022; 185:1373-1388.e20. [PMID: 35381199 PMCID: PMC7612792 DOI: 10.1016/j.cell.2022.03.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 12/26/2021] [Accepted: 03/09/2022] [Indexed: 11/28/2022] [Imported: 07/30/2023]
Abstract
Systemic sclerosis (scleroderma, SSc) is an incurable autoimmune disease with high morbidity and mortality rates. Here, we conducted a population-scale single-cell genomic analysis of skin and blood samples of 56 healthy controls and 97 SSc patients at different stages of the disease. We found immune compartment dysfunction only in a specific subtype of diffuse SSc patients but global dysregulation of the stromal compartment, particularly in a previously undefined subset of LGR5+-scleroderma-associated fibroblasts (ScAFs). ScAFs are perturbed morphologically and molecularly in SSc patients. Single-cell multiome profiling of stromal cells revealed ScAF-specific markers, pathways, regulatory elements, and transcription factors underlining disease development. Systematic analysis of these molecular features with clinical metadata associates specific ScAF targets with disease pathogenesis and SSc clinical traits. Our high-resolution atlas of the sclerodermatous skin spectrum will enable a paradigm shift in the understanding of SSc disease and facilitate the development of biomarkers and therapeutic strategies.
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Affiliation(s)
- Chamutal Gur
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel; Rheumatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Shuang-Yin Wang
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel.
| | - Fadi Sheban
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | - Mor Zada
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | - Baoguo Li
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | - Fadi Kharouf
- Rheumatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Hagit Peleg
- Rheumatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Suhail Aamar
- Rheumatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Adam Yalin
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | | | - Yolanda Braun-Moscovici
- Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion-Israeli Institute of Technology, Haifa, Israel
| | | | - Tomer Meir-Salame
- Flow Cytometry Unit, Department of Biological Services, Weizmann Institute, Rehovot, Israel
| | - Efrat Hagai
- Flow Cytometry Unit, Department of Biological Services, Weizmann Institute, Rehovot, Israel
| | | | - Batia Avni
- Department of Bone Marrow Transplantation, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Sigal Grisariu
- Department of Bone Marrow Transplantation, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | | | | | - Eyal David
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | - Rony Shreberk-Hassidim
- Dermatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Vered Molho-Pessach
- Dermatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Dalit Amar
- Plastic Surgery Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Tomer Tzur
- Plastic Surgery Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Rottem Kuint
- Institue of Pulmonology Medicine, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Moshe Gross
- Orthopedic Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Oren Barboy
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | - Adi Moshe
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | | | - Dana Hirsch
- The Department of Veterinary Resources, Weizmann Institute, Rehovot, Israel
| | - Yoseph Addadi
- Life Sciences Core Facilities, Weizmann Institute, Rehovot, Israel
| | - Shlomit Erenfeld
- Department of Bone Marrow Transplantation, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Moshe Biton
- Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
| | - Tehila Tzemach
- Rheumatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Anat Elazary
- Rheumatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Yaakov Naparstek
- Rheumatology Department, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Reut Tzemach
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel; Rheumatology Institute at the Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel
| | - Assaf Weiner
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | - Amir Giladi
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | - Alexandra Balbir-Gurman
- Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion-Israeli Institute of Technology, Haifa, Israel
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel.
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4
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Biram A, Liu J, Hezroni H, Davidzohn N, Schmiedel D, Khatib-Massalha E, Haddad M, Grenov A, Lebon S, Salame TM, Dezorella N, Hoffman D, Abou Karam P, Biton M, Lapidot T, Bemark M, Avraham R, Jung S, Shulman Z. Bacterial infection disrupts established germinal center reactions through monocyte recruitment and impaired metabolic adaptation. Immunity 2022; 55:442-458.e8. [PMID: 35182483 DOI: 10.1016/j.immuni.2022.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/11/2021] [Accepted: 01/18/2022] [Indexed: 02/07/2023] [Imported: 07/30/2023]
Abstract
Consecutive exposures to different pathogens are highly prevalent and often alter the host immune response. However, it remains unknown how a secondary bacterial infection affects an ongoing adaptive immune response elicited against primary invading pathogens. We demonstrated that recruitment of Sca-1+ monocytes into lymphoid organs during Salmonella Typhimurium (STm) infection disrupted pre-existing germinal center (GC) reactions. GC responses induced by influenza, plasmodium, or commensals deteriorated following STm infection. GC disruption was independent of the direct bacterial interactions with B cells and instead was induced through recruitment of CCR2-dependent Sca-1+ monocytes into the lymphoid organs. GC collapse was associated with impaired cellular respiration and was dependent on TNFα and IFNγ, the latter of which was essential for Sca-1+ monocyte differentiation. Monocyte recruitment and GC disruption also occurred during LPS-supplemented vaccination and Listeria monocytogenes infection. Thus, systemic activation of the innate immune response upon severe bacterial infection is induced at the expense of antibody-mediated immunity.
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Affiliation(s)
- Adi Biram
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Jingjing Liu
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hadas Hezroni
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Natalia Davidzohn
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dominik Schmiedel
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eman Khatib-Massalha
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Montaser Haddad
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amalie Grenov
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sacha Lebon
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tomer Meir Salame
- Department of Life Science Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nili Dezorella
- Electron Microscopy Unit, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dotan Hoffman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Paula Abou Karam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Moshe Biton
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tsvee Lapidot
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - Roi Avraham
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Steffen Jung
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ziv Shulman
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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5
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Beyaz S, Chung C, Mou H, Bauer-Rowe KE, Xifaras ME, Ergin I, Dohnalova L, Biton M, Shekhar K, Eskiocak O, Papciak K, Ozler K, Almeqdadi M, Yueh B, Fein M, Annamalai D, Valle-Encinas E, Erdemir A, Dogum K, Shah V, Alici-Garipcan A, Meyer HV, Özata DM, Elinav E, Kucukural A, Kumar P, McAleer JP, Fox JG, Thaiss CA, Regev A, Roper J, Orkin SH, Yilmaz ÖH. Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis. Cell Stem Cell 2021; 28:1922-1935.e5. [PMID: 34529935 DOI: 10.1016/j.stem.2021.08.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [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: 10/19/2020] [Revised: 05/25/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] [Imported: 07/30/2023]
Abstract
Little is known about how interactions of diet, intestinal stem cells (ISCs), and immune cells affect early-stage intestinal tumorigenesis. We show that a high-fat diet (HFD) reduces the expression of the major histocompatibility complex class II (MHC class II) genes in intestinal epithelial cells, including ISCs. This decline in epithelial MHC class II expression in a HFD correlates with reduced intestinal microbiome diversity. Microbial community transfer experiments suggest that epithelial MHC class II expression is regulated by intestinal flora. Mechanistically, pattern recognition receptor (PRR) and interferon-gamma (IFNγ) signaling regulates epithelial MHC class II expression. MHC class II-negative (MHC-II-) ISCs exhibit greater tumor-initiating capacity than their MHC class II-positive (MHC-II+) counterparts upon loss of the tumor suppressor Apc coupled with a HFD, suggesting a role for epithelial MHC class II-mediated immune surveillance in suppressing tumorigenesis. ISC-specific genetic ablation of MHC class II increases tumor burden cell autonomously. Thus, HFD perturbs a microbiome-stem cell-immune cell interaction that contributes to tumor initiation in the intestine.
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Affiliation(s)
- Semir Beyaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA.
| | - Charlie Chung
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Haiwei Mou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Khristian E Bauer-Rowe
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Michael E Xifaras
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Ilgin Ergin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Lenka Dohnalova
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Moshe Biton
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; The Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Karthik Shekhar
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemical and Biomolecular Engineering, Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720, USA
| | - Onur Eskiocak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Kadir Ozler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Mohammad Almeqdadi
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Brian Yueh
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Miriam Fein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Damodaran Annamalai
- Division of Comparative Medicine, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eider Valle-Encinas
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Aysegul Erdemir
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Karoline Dogum
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Vyom Shah
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Hannah V Meyer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Deniz M Özata
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alper Kucukural
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Pawan Kumar
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jeremy P McAleer
- Department of Pharmaceutical Science and Research, Marshall University School of Pharmacy, Huntington, WV 25701, USA
| | - James G Fox
- Division of Comparative Medicine, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christoph A Thaiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aviv Regev
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Jatin Roper
- Department of Medicine, Division of Gastroenterology, Duke University, Durham, NC 27710, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Ömer H Yilmaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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6
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Pelka K, Hofree M, Chen JH, Sarkizova S, Pirl JD, Jorgji V, Bejnood A, Dionne D, Ge WH, Xu KH, Chao SX, Zollinger DR, Lieb DJ, Reeves JW, Fuhrman CA, Hoang ML, Delorey T, Nguyen LT, Waldman J, Klapholz M, Wakiro I, Cohen O, Albers J, Smillie CS, Cuoco MS, Wu J, Su MJ, Yeung J, Vijaykumar B, Magnuson AM, Asinovski N, Moll T, Goder-Reiser MN, Applebaum AS, Brais LK, DelloStritto LK, Denning SL, Phillips ST, Hill EK, Meehan JK, Frederick DT, Sharova T, Kanodia A, Todres EZ, Jané-Valbuena J, Biton M, Izar B, Lambden CD, Clancy TE, Bleday R, Melnitchouk N, Irani J, Kunitake H, Berger DL, Srivastava A, Hornick JL, Ogino S, Rotem A, Vigneau S, Johnson BE, Corcoran RB, Sharpe AH, Kuchroo VK, Ng K, Giannakis M, Nieman LT, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N. Spatially organized multicellular immune hubs in human colorectal cancer. Cell 2021; 184:4734-4752.e20. [PMID: 34450029 PMCID: PMC8772395 DOI: 10.1016/j.cell.2021.08.003] [Citation(s) in RCA: 212] [Impact Index Per Article: 70.7] [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: 12/23/2020] [Revised: 05/28/2021] [Accepted: 08/03/2021] [Indexed: 12/11/2022] [Imported: 07/30/2023]
Abstract
Immune responses to cancer are highly variable, with mismatch repair-deficient (MMRd) tumors exhibiting more anti-tumor immunity than mismatch repair-proficient (MMRp) tumors. To understand the rules governing these varied responses, we transcriptionally profiled 371,223 cells from colorectal tumors and adjacent normal tissues of 28 MMRp and 34 MMRd individuals. Analysis of 88 cell subsets and their 204 associated gene expression programs revealed extensive transcriptional and spatial remodeling across tumors. To discover hubs of interacting malignant and immune cells, we identified expression programs in different cell types that co-varied across tumors from affected individuals and used spatial profiling to localize coordinated programs. We discovered a myeloid cell-attracting hub at the tumor-luminal interface associated with tissue damage and an MMRd-enriched immune hub within the tumor, with activated T cells together with malignant and myeloid cells expressing T cell-attracting chemokines. By identifying interacting cellular programs, we reveal the logic underlying spatially organized immune-malignant cell networks.
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Affiliation(s)
- Karin Pelka
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan H Chen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Pathology, MGH, Boston, MA, USA
| | - Siranush Sarkizova
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Joshua D Pirl
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Vjola Jorgji
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Pathology, MGH, Boston, MA, USA
| | - Alborz Bejnood
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William H Ge
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Katherine H Xu
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Sherry X Chao
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Biomedical Informatics, HMS, Boston, MA, USA
| | | | - David J Lieb
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | | | | | - Toni Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lan T Nguyen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Max Klapholz
- Evergrande Center for Immunologic Diseases, HMS and Brigham and Women's Hospital (BWH), Boston, MA, USA
| | - Isaac Wakiro
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Ofir Cohen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA; Department of Medical Oncology, DFCI, Boston, MA, USA
| | - Julian Albers
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | - Michael S Cuoco
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jingyi Wu
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Mei-Ju Su
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Jason Yeung
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | | | | | | | - Tabea Moll
- Clinical Research Center, MGH, Boston, MA, USA
| | | | | | | | - Laura K DelloStritto
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | | | | | - Emma K Hill
- Clinical Research Center, DFCI, Boston, MA, USA
| | | | | | | | - Abhay Kanodia
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Ellen Z Todres
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moshe Biton
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular Biology, MGH, Boston, MA, USA
| | - Benjamin Izar
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA; Department of Medical Oncology, DFCI, Boston, MA, USA
| | - Conner D Lambden
- Evergrande Center for Immunologic Diseases, HMS and Brigham and Women's Hospital (BWH), Boston, MA, USA
| | | | | | | | | | | | | | | | | | - Shuji Ogino
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Pathology, BWH, Boston, MA, USA
| | - Asaf Rotem
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Sébastien Vigneau
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Bruce E Johnson
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA; Department of Medical Oncology, DFCI, Boston, MA, USA
| | - Ryan B Corcoran
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Medicine, HMS, Boston, MA, USA
| | - Arlene H Sharpe
- Evergrande Center for Immunologic Diseases, HMS and Brigham and Women's Hospital (BWH), Boston, MA, USA; Department of Immunology, Blavatnik Institute, HMS, Boston, MA, USA
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, HMS and Brigham and Women's Hospital (BWH), Boston, MA, USA
| | - Kimmie Ng
- Department of Medical Oncology, DFCI, Boston, MA, USA
| | - Marios Giannakis
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Medical Oncology, DFCI, Boston, MA, USA
| | - Linda T Nieman
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Genevieve M Boland
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Surgery, MGH, Boston, MA, USA
| | - Andrew J Aguirre
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Medical Oncology, DFCI, Boston, MA, USA
| | - Ana C Anderson
- Evergrande Center for Immunologic Diseases, HMS and Brigham and Women's Hospital (BWH), Boston, MA, USA.
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA.
| | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Immunology, HMS, Boston, MA, USA.
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7
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Sullivan ZA, Khoury-Hanold W, Lim J, Smillie C, Biton M, Reis BS, Zwick RK, Pope SD, Israni-Winger K, Parsa R, Philip NH, Rashed S, Palm N, Wang A, Mucida D, Regev A, Medzhitov R. γδ T cells regulate the intestinal response to nutrient sensing. Science 2021; 371:eaba8310. [PMID: 33737460 DOI: 10.1126/science.aba8310] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 11/02/2020] [Accepted: 01/19/2021] [Indexed: 12/17/2022] [Imported: 07/30/2023]
Abstract
The intestine is a site of direct encounter with the external environment and must consequently balance barrier defense with nutrient uptake. To investigate how nutrient uptake is regulated in the small intestine, we tested the effect of diets with different macronutrient compositions on epithelial gene expression. We found that enzymes and transporters required for carbohydrate digestion and absorption were regulated by carbohydrate availability. The "on-demand" induction of this machinery required γδ T cells, which regulated this program through the suppression of interleukin-22 production by type 3 innate lymphoid cells. Nutrient availability altered the tissue localization and transcriptome of γδ T cells. Additionally, transcriptional responses to diet involved cellular remodeling of the epithelial compartment. Thus, this work identifies a role for γδ T cells in nutrient sensing.
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Affiliation(s)
- Zuri A Sullivan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Jaechul Lim
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Chris Smillie
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Moshe Biton
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Bernardo S Reis
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Rachel K Zwick
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, CA, USA
| | - Scott D Pope
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, New Haven, CT, USA
| | - Kavita Israni-Winger
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Roham Parsa
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Naomi H Philip
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Saleh Rashed
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Noah Palm
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew Wang
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Division of Rheumatology, Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Ruslan Medzhitov
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Howard Hughes Medical Institute, New Haven, CT, USA
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8
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Karthaus WR, Hofree M, Choi D, Linton EL, Turkekul M, Bejnood A, Carver B, Gopalan A, Abida W, Laudone V, Biton M, Chaudhary O, Xu T, Masilionis I, Manova K, Mazutis L, Pe'er D, Regev A, Sawyers CL. Regenerative potential of prostate luminal cells revealed by single-cell analysis. Science 2020; 368:497-505. [PMID: 32355025 DOI: 10.1126/science.aay0267] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 03/14/2020] [Indexed: 01/20/2023] [Imported: 07/30/2023]
Abstract
Androgen deprivation is the cornerstone of prostate cancer treatment. It results in involution of the normal gland to ~90% of its original size because of the loss of luminal cells. The prostate regenerates when androgen is restored, a process postulated to involve stem cells. Using single-cell RNA sequencing, we identified a rare luminal population in the mouse prostate that expresses stemlike genes (Sca1 + and Psca +) and a large population of differentiated cells (Nkx3.1 +, Pbsn +). In organoids and in mice, both populations contribute equally to prostate regeneration, partly through androgen-driven expression of growth factors (Nrg2, Rspo3) by mesenchymal cells acting in a paracrine fashion on luminal cells. Analysis of human prostate tissue revealed similar differentiated and stemlike luminal subpopulations that likewise acquire enhanced regenerative potential after androgen ablation. We propose that prostate regeneration is driven by nearly all persisting luminal cells, not just by rare stem cells.
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Affiliation(s)
- Wouter R Karthaus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Danielle Choi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Eliot L Linton
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mesruh Turkekul
- Molecular Cytology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alborz Bejnood
- Klarman Cell Observatory, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Brett Carver
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anuradha Gopalan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wassim Abida
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vincent Laudone
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Moshe Biton
- Klarman Cell Observatory, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Ojasvi Chaudhary
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tianhao Xu
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ignas Masilionis
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Katia Manova
- Molecular Cytology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Linas Mazutis
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dana Pe'er
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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9
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Smillie CS, Biton M, Ordovas-Montanes J, Sullivan KM, Burgin G, Graham DB, Herbst RH, Rogel N, Slyper M, Waldman J, Sud M, Andrews E, Velonias G, Haber AL, Jagadeesh K, Vickovic S, Yao J, Stevens C, Dionne D, Nguyen LT, Villani AC, Hofree M, Creasey EA, Huang H, Rozenblatt-Rosen O, Garber JJ, Khalili H, Desch AN, Daly MJ, Ananthakrishnan AN, Shalek AK, Xavier RJ, Regev A. Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis. Cell 2020; 178:714-730.e22. [PMID: 31348891 DOI: 10.1016/j.cell.2019.06.029] [Citation(s) in RCA: 623] [Impact Index Per Article: 155.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 03/25/2019] [Accepted: 06/18/2019] [Indexed: 11/29/2022] [Imported: 07/30/2023]
Abstract
Genome-wide association studies (GWAS) have revealed risk alleles for ulcerative colitis (UC). To understand their cell type specificities and pathways of action, we generate an atlas of 366,650 cells from the colon mucosa of 18 UC patients and 12 healthy individuals, revealing 51 epithelial, stromal, and immune cell subsets, including BEST4+ enterocytes, microfold-like cells, and IL13RA2+IL11+ inflammatory fibroblasts, which we associate with resistance to anti-TNF treatment. Inflammatory fibroblasts, inflammatory monocytes, microfold-like cells, and T cells that co-express CD8 and IL-17 expand with disease, forming intercellular interaction hubs. Many UC risk genes are cell type specific and co-regulated within relatively few gene modules, suggesting convergence onto limited sets of cell types and pathways. Using this observation, we nominate and infer functions for specific risk genes across GWAS loci. Our work provides a framework for interrogating complex human diseases and mapping risk variants to cell types and pathways.
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Affiliation(s)
| | - Moshe Biton
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Department of Molecular Biology, MGH, Boston, MA, USA
| | - Jose Ordovas-Montanes
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA, USA; Department of Chemistry, MIT, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Division of Infectious Diseases and Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - Keri M Sullivan
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA
| | - Grace Burgin
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Daniel B Graham
- Department of Molecular Biology, MGH, Boston, MA, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA
| | - Rebecca H Herbst
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Noga Rogel
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Malika Sud
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Elizabeth Andrews
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA
| | - Gabriella Velonias
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA
| | - Adam L Haber
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | | | - Sanja Vickovic
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Junmei Yao
- Center for Computational and Integrative Biology, MGH, Boston, MA, USA
| | | | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Lan T Nguyen
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Alexandra-Chloé Villani
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, MGH, Boston, MA, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | | | - Hailiang Huang
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; Analytical and Translational Genetics Unit, MGH, Boston, MA, USA
| | | | - John J Garber
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA
| | - Hamed Khalili
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA
| | - A Nicole Desch
- Broad Institute, Cambridge, MA, USA; Center for Computational and Integrative Biology, MGH, Boston, MA, USA
| | - Mark J Daly
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; Analytical and Translational Genetics Unit, MGH, Boston, MA, USA; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Ashwin N Ananthakrishnan
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA.
| | - Alex K Shalek
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA, USA; Department of Chemistry, MIT, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
| | - Ramnik J Xavier
- Department of Molecular Biology, MGH, Boston, MA, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA; Center for Computational and Integrative Biology, MGH, Boston, MA, USA.
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA.
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10
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Bulvik R, Biton M, Berkman N, Breuer R, Wallach-Dayan SB. Forefront: MiR-34a-Knockout Mice with Wild Type Hematopoietic Cells, Retain Persistent Fibrosis Following Lung Injury. Int J Mol Sci 2020; 21:E2228. [PMID: 32210149 DOI: 10.3390/ijms21062228] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/15/2020] [Accepted: 03/19/2020] [Indexed: 12/19/2022] [Imported: 07/30/2023] Open
Abstract
MicroRNAs (miRs) are known to limit gene expression at the post-transcriptional level and have important roles in the pathogenesis of various conditions, including acute lung injury (ALI) and fibrotic diseases such as idiopathic pulmonary fibrosis (IPF). In this study, we found increased levels of miR-34 at times of fibrosis resolution following injury, in myofibroblasts from Bleomycin-treated mouse lungs, which correlates with susceptibility to cell death induced by immune cells. On the contrary, a substantial downregulation of miR-34 was detected at stages of evolution, when fibroblasts resist cell death. Concomitantly, we found an inverse correlation between miR-34 levels with that of the survival molecule FLICE-like inhibitory protein (FLIP) in lung myofibroblasts from humans with IPF and the experimental model. Forced upregulation of miR-34 with miR-34 mimic in human IPF fibrotic-lung myofibroblasts led to decreased cell survival through downregulation of FLIP. Using chimeric miR-34 knock-out (KO)-C57BL/6 mice with miR34KO myofibroblasts but wild-type (WT) hematopoietic cells, we found, in contrast to WT mice, increased and persistent FLIP levels with a more severe fibrosis and with no signs of resolution as detected in pathology and collagen accumulation. Moreover, a mimic of miR-34a decreased FLIP expression and susceptibility to cell death was regained in miR-34KO fibroblasts. Through this study, we show for the first time an inverse correlation between miR-34a and FLIP expression in myofibroblasts, which affects survival, and accumulation in lung fibrosis. Reprogramming fibrotic-lung myofibroblasts to regain susceptibility to cell-death by specifically increasing their miR34a and downregulating FLIP, may be a useful strategy, enabling tissue regeneration following lung injury.
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11
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Howitt MR, Cao YG, Gologorsky MB, Li JA, Haber AL, Biton M, Lang J, Michaud M, Regev A, Garrett WS. The Taste Receptor TAS1R3 Regulates Small Intestinal Tuft Cell Homeostasis. Immunohorizons 2020; 4:23-32. [PMID: 31980480 PMCID: PMC7197368 DOI: 10.4049/immunohorizons.1900099] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [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: 12/30/2019] [Accepted: 01/08/2020] [Indexed: 01/06/2023] Open
Abstract
Tuft cells are an epithelial cell type critical for initiating type 2 immune responses to parasites and protozoa in the small intestine. To respond to these stimuli, intestinal tuft cells use taste chemosensory signaling pathways, but the role of taste receptors in type 2 immunity is poorly understood. In this study, we show that the taste receptor TAS1R3, which detects sweet and umami in the tongue, also regulates tuft cell responses in the distal small intestine. BALB/c mice, which have an inactive form of TAS1R3, as well as Tas1r3-deficient C57BL6/J mice both have severely impaired responses to tuft cell–inducing signals in the ileum, including the protozoa Tritrichomonas muris and succinate. In contrast, TAS1R3 is not required to mount an immune response to the helminth Heligmosomoides polygyrus, which infects the proximal small intestine. Examination of uninfected Tas1r3−/− mice revealed a modest reduction in the number of tuft cells in the proximal small intestine but a severe decrease in the distal small intestine at homeostasis. Together, these results suggest that TAS1R3 influences intestinal immunity by shaping the epithelial cell landscape at steady-state. ImmunoHorizons, 2020, 4: 23–32.
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Affiliation(s)
- Michael R Howitt
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115; .,Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115.,Department of Pathology, Stanford University, Stanford, CA 94305
| | - Y Grace Cao
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115.,Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | | | - Jessica A Li
- Department of Pathology, Stanford University, Stanford, CA 94305
| | - Adam L Haber
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Moshe Biton
- Broad Institute of MIT and Harvard, Cambridge, MA 02142.,Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jessica Lang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115.,Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Monia Michaud
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115.,Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142; and
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115; .,Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115.,Broad Institute of MIT and Harvard, Cambridge, MA 02142.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
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12
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Khor B, Conway KL, Omar AS, Biton M, Haber AL, Rogel N, Baxt LA, Begun J, Kuballa P, Gagnon JD, Lassen KG, Regev A, Xavier RJ. Distinct Tissue-Specific Roles for the Disease-Associated Autophagy Genes ATG16L2 and ATG16L1. J Immunol 2019; 203:1820-1829. [PMID: 31451676 PMCID: PMC6761021 DOI: 10.4049/jimmunol.1800419] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/30/2019] [Indexed: 12/19/2022]
Abstract
The clear role of autophagy in human inflammatory diseases such as Crohn disease was first identified by genome-wide association studies and subsequently dissected in multiple mechanistic studies. ATG16L1 has been particularly well studied in knockout and hypomorph settings as well as models recapitulating the Crohn disease-associated T300A polymorphism. Interestingly, ATG16L1 has a single homolog, ATG16L2, which is independently implicated in diseases, including Crohn disease and systemic lupus erythematosus. However, the contribution of ATG16L2 to canonical autophagy pathways and other cellular functions is poorly understood. To better understand its role, we generated and analyzed the first, to our knowledge, ATG16L2 knockout mouse. Our results show that ATG16L1 and ATG16L2 contribute very distinctly to autophagy and cellular ontogeny in myeloid, lymphoid, and epithelial lineages. Dysregulation of any of these lineages could contribute to complex diseases like Crohn disease and systemic lupus erythematosus, highlighting the value of examining cell-specific effects. We also identify a novel genetic interaction between ATG16L2 and epithelial ATG16L1. These findings are discussed in the context of how these genes may contribute distinctly to human disease.
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Affiliation(s)
- Bernard Khor
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; .,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114.,The Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142; and.,Pathology Service, Massachusetts General Hospital, Boston, MA 02114
| | - Kara L Conway
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Abdifatah S Omar
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Moshe Biton
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Adam L Haber
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Noga Rogel
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Leigh A Baxt
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Jakob Begun
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Petric Kuballa
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - John D Gagnon
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Kara G Lassen
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Aviv Regev
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; .,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114.,The Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142; and
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13
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Cheng CW, Biton M, Haber AL, Gunduz N, Eng G, Gaynor LT, Tripathi S, Calibasi-Kocal G, Rickelt S, Butty VL, Moreno M, Iqbal AM, Bauer-Rowe KE, Imada S, Ulutas MS, Mylonas C, Whary MT, Levine SS, Basbinar Y, Hynes RO, Mino-Kenudson M, Deshpande V, Boyer LA, Fox JG, Terranova C, Rai K, Piwnica-Worms H, Mihaylova MM, Regev A, Yilmaz ÖH. Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet. Cell 2019; 178:1115-1131.e15. [PMID: 31442404 PMCID: PMC6732196 DOI: 10.1016/j.cell.2019.07.048] [Citation(s) in RCA: 201] [Impact Index Per Article: 40.2] [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: 01/07/2019] [Revised: 06/03/2019] [Accepted: 07/25/2019] [Indexed: 01/18/2023] [Imported: 07/30/2023]
Abstract
Little is known about how metabolites couple tissue-specific stem cell function with physiology. Here we show that, in the mammalian small intestine, the expression of Hmgcs2 (3-hydroxy-3-methylglutaryl-CoA synthetase 2), the gene encoding the rate-limiting enzyme in the production of ketone bodies, including beta-hydroxybutyrate (βOHB), distinguishes self-renewing Lgr5+ stem cells (ISCs) from differentiated cell types. Hmgcs2 loss depletes βOHB levels in Lgr5+ ISCs and skews their differentiation toward secretory cell fates, which can be rescued by exogenous βOHB and class I histone deacetylase (HDAC) inhibitor treatment. Mechanistically, βOHB acts by inhibiting HDACs to reinforce Notch signaling, instructing ISC self-renewal and lineage decisions. Notably, although a high-fat ketogenic diet elevates ISC function and post-injury regeneration through βOHB-mediated Notch signaling, a glucose-supplemented diet has the opposite effects. These findings reveal how control of βOHB-activated signaling in ISCs by diet helps to fine-tune stem cell adaptation in homeostasis and injury.
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Affiliation(s)
- Chia-Wei Cheng
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Moshe Biton
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA,Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA,These authors contributed equally to this work
| | - Adam L. Haber
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA,These authors contributed equally to this work
| | - Nuray Gunduz
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, Turkey 06800
| | - George Eng
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Liam T. Gaynor
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston MA, 02215, USA
| | - Surya Tripathi
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Gizem Calibasi-Kocal
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Dokuz Eylul University, Institute of Oncology, Department of Translational Oncology, Izmir, Turkey
| | - Steffen Rickelt
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Vincent L. Butty
- BioMicro Center, at MIT, Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - Marta Moreno
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Ameena M Iqbal
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | | | - Shinya Imada
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University,1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Mehmet Sefa Ulutas
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Biology, Siirt University, Science and Arts Faculty, 56100 Siirt, Turkey
| | | | - Mark T. Whary
- Division of Comparative Medicine, Department of Biological Engineering, MIT, Cambridge, Massachusetts 02139, USA
| | - Stuart S. Levine
- BioMicro Center, at MIT, Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - Yasemin Basbinar
- Dokuz Eylul University, Institute of Oncology, Department of Translational Oncology, Izmir, Turkey
| | - Richard O. Hynes
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital Boston and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital Boston and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Laurie A. Boyer
- Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - James G. Fox
- Division of Comparative Medicine, Department of Biological Engineering, MIT, Cambridge, Massachusetts 02139, USA
| | - Christopher Terranova
- Genomic Medicine Department, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kunal Rai
- Genomic Medicine Department, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Helen Piwnica-Worms
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria M. Mihaylova
- The Ohio State Comprehensive Cancer Center, Department of Biological Chemistry and Pharmacology, Ohio State University, 308 Wiseman Hall, Columbus, OH 43210, USA
| | - Aviv Regev
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA,Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Ömer H. Yilmaz
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Biology, MIT, Cambridge, Massachusetts 02139, USA,Department of Pathology, Massachusetts General Hospital Boston and Harvard Medical School, Boston, Massachusetts 02114, USA,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA,Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA,Lead Contact,Correspondence: Ömer H. Yilmaz () (Ö.H.Y)
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14
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Biton M, Haber AL, Rogel N, Burgin G, Beyaz S, Schnell A, Ashenberg O, Su CW, Smillie C, Shekhar K, Chen Z, Wu C, Ordovas-Montanes J, Alvarez D, Herbst RH, Zhang M, Tirosh I, Dionne D, Nguyen LT, Xifaras ME, Shalek AK, von Andrian UH, Graham DB, Rozenblatt-Rosen O, Shi HN, Kuchroo V, Yilmaz OH, Regev A, Xavier RJ. T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation. Cell 2018; 175:1307-1320.e22. [PMID: 30392957 DOI: 10.1016/j.cell.2018.10.008] [Citation(s) in RCA: 324] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/13/2018] [Accepted: 10/01/2018] [Indexed: 01/15/2023] [Imported: 07/30/2023]
Abstract
In the small intestine, a niche of accessory cell types supports the generation of mature epithelial cell types from intestinal stem cells (ISCs). It is unclear, however, if and how immune cells in the niche affect ISC fate or the balance between self-renewal and differentiation. Here, we use single-cell RNA sequencing (scRNA-seq) to identify MHC class II (MHCII) machinery enrichment in two subsets of Lgr5+ ISCs. We show that MHCII+ Lgr5+ ISCs are non-conventional antigen-presenting cells in co-cultures with CD4+ T helper (Th) cells. Stimulation of intestinal organoids with key Th cytokines affects Lgr5+ ISC renewal and differentiation in opposing ways: pro-inflammatory signals promote differentiation, while regulatory cells and cytokines reduce it. In vivo genetic perturbation of Th cells or MHCII expression on Lgr5+ ISCs impacts epithelial cell differentiation and IEC fate during infection. These interactions between Th cells and Lgr5+ ISCs, thus, orchestrate tissue-wide responses to external signals.
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Affiliation(s)
- Moshe Biton
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Adam L Haber
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Noga Rogel
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Grace Burgin
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Semir Beyaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Alexandra Schnell
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Chien-Wen Su
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Christopher Smillie
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Karthik Shekhar
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Zuojia Chen
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chuan Wu
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jose Ordovas-Montanes
- Institute for Medical Engineering & Science (IMES) and Department of Chemistry, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA
| | - David Alvarez
- Department of Microbiology & Immunobiology and Center for Immune Imaging, Harvard Medical School, Boston, MA 02115, USA
| | - Rebecca H Herbst
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA
| | - Mei Zhang
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Itay Tirosh
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Lan T Nguyen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Michael E Xifaras
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Alex K Shalek
- Institute for Medical Engineering & Science (IMES) and Department of Chemistry, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA
| | - Ulrich H von Andrian
- Department of Microbiology & Immunobiology and Center for Immune Imaging, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel B Graham
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Hai Ning Shi
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Vijay Kuchroo
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Omer H Yilmaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.
| | - Ramnik J Xavier
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Microbiome informatics and Therapeutics, MIT, Cambridge, MA 02139, USA.
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15
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Montoro DT, Haber AL, Biton M, Vinarsky V, Lin B, Birket SE, Yuan F, Chen S, Leung HM, Villoria J, Rogel N, Burgin G, Tsankov AM, Waghray A, Slyper M, Waldman J, Nguyen L, Dionne D, Rozenblatt-Rosen O, Tata PR, Mou H, Shivaraju M, Bihler H, Mense M, Tearney GJ, Rowe SM, Engelhardt JF, Regev A, Rajagopal J. A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. Nature 2018; 560:319-324. [PMID: 30069044 PMCID: PMC6295155 DOI: 10.1038/s41586-018-0393-7] [Citation(s) in RCA: 684] [Impact Index Per Article: 114.0] [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: 07/31/2017] [Accepted: 06/21/2018] [Indexed: 12/16/2022]
Abstract
The airways of the lung are the primary sites of disease in asthma and cystic fibrosis. Here we study the cellular composition and hierarchy of the mouse tracheal epithelium by single-cell RNA-sequencing (scRNA-seq) and in vivo lineage tracing. We identify a rare cell type, the Foxi1+ pulmonary ionocyte; functional variations in club cells based on their location; a distinct cell type in high turnover squamous epithelial structures that we term 'hillocks'; and disease-relevant subsets of tuft and goblet cells. We developed 'pulse-seq', combining scRNA-seq and lineage tracing, to show that tuft, neuroendocrine and ionocyte cells are continually and directly replenished by basal progenitor cells. Ionocytes are the major source of transcripts of the cystic fibrosis transmembrane conductance regulator in both mouse (Cftr) and human (CFTR). Knockout of Foxi1 in mouse ionocytes causes loss of Cftr expression and disrupts airway fluid and mucus physiology, phenotypes that are characteristic of cystic fibrosis. By associating cell-type-specific expression programs with key disease genes, we establish a new cellular narrative for airways disease.
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Affiliation(s)
- Daniel T Montoro
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam L Haber
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moshe Biton
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Vladimir Vinarsky
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Brian Lin
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Susan E Birket
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Gregory Fleming James Cystic Fibrosis Research Center, Birmingham, AL, USA
| | - Feng Yuan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Sijia Chen
- Department of Experimental Immunology, Academic Medical Center/University of Amsterdam, Amsterdam, The Netherlands
| | - Hui Min Leung
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jorge Villoria
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Noga Rogel
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace Burgin
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander M Tsankov
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Avinash Waghray
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lan Nguyen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Purushothama Rao Tata
- Department of Cell Biology, Duke University, Durham, NC, USA
- Duke Cancer Institute, Duke University, Durham, NC, USA
- Division of Pulmonary Critical Care, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Regeneration Next, Duke University, Durham, NC, USA
| | - Hongmei Mou
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Manjunatha Shivaraju
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Hermann Bihler
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Martin Mense
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Guillermo J Tearney
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steven M Rowe
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Gregory Fleming James Cystic Fibrosis Research Center, Birmingham, AL, USA
| | - John F Engelhardt
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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16
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Kfir-Erenfeld S, Haggiag N, Biton M, Stepensky P, Assayag-Asherie N, Yefenof E. miR-103 inhibits proliferation and sensitizes hemopoietic tumor cells for glucocorticoid-induced apoptosis. Oncotarget 2017; 8:472-89. [PMID: 27888798 DOI: 10.18632/oncotarget.13447] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 11/12/2016] [Indexed: 11/25/2022] [Imported: 07/30/2023] Open
Abstract
Glucocorticoid (GC) hormones are an important ingredient of leukemia therapy since they are potent inducers of lymphoid cell apoptosis. However, the development of GC resistance remains an obstacle in GC-based treatment. In the present investigation we found that miR-103 is upregulated in GC-sensitive leukemia cells treated by the hormone. Transfection of GC resistant cells with miR-103 sensitized them to GC induced apoptosis (GCIA), while miR-103 sponging of GC sensitive cells rendered them partially resistant. miR-103 reduced the expression of cyclin dependent kinase (CDK2) and its cyclin E1 target, thereby leading to inhibition of cellular proliferation. miR-103 is encoded within the fifth intron of PANK3 gene. We demonstrate that the GC receptor (GR) upregulates miR-103 by direct interaction with GC response element (GRE) in the PANK3 enhancer. Consequently, miR-103 targets the c-Myc activators c-Myb and DVL1, thereby reducing c-Myc expression. Since c-Myc is a transcription factor of the miR-17~92a poly-cistron, all six miRNAs of the latter are also downregulated. Of these, miR-18a and miR-20a are involved in GCIA, as they target GR and BIM, respectively. Consequently, GR and BIM expression are elevated, thus advancing GCIA. Altogether, this study highlights miR-103 as a useful prognostic biomarker and drug for leukemia management in the future.
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17
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Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C, Burgin G, Delorey TM, Howitt MR, Katz Y, Tirosh I, Beyaz S, Dionne D, Zhang M, Raychowdhury R, Garrett WS, Rozenblatt-Rosen O, Shi HN, Yilmaz O, Xavier RJ, Regev A. A single-cell survey of the small intestinal epithelium. Nature. 2017;551:333-339. [PMID: 29144463 PMCID: PMC6022292 DOI: 10.1038/nature24489] [Citation(s) in RCA: 956] [Impact Index Per Article: 136.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 10/03/2017] [Indexed: 12/17/2022] [Imported: 07/30/2023]
Abstract
Intestinal epithelial cells (IECs) absorb nutrients, respond to microbes, provide barrier function and help coordinate immune responses. We profiled 53,193 individual epithelial cells from mouse small intestine and organoids, and characterized novel subtypes and their gene signatures. We showed unexpected diversity of hormone-secreting enteroendocrine cells and constructed their novel taxonomy. We distinguished between two tuft cell subtypes, one of which expresses the epithelial cytokine TSLP and CD45 (Ptprc), the pan-immune marker not previously associated with non-hematopoietic cells. We also characterized how cell-intrinsic states and cell proportions respond to bacterial and helminth infections. Salmonella infection caused an increase in Paneth cells and enterocytes abundance, and broad activation of an antimicrobial program. In contrast, Heligmosomoides polygyrus caused an expansion of goblet and tuft cell populations. Our survey highlights new markers and programs, associates sensory molecules to cell types, and uncovers principles of gut homeostasis and response to pathogens.
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Aran D, Lasry A, Zinger A, Biton M, Pikarsky E, Hellman A, Butte AJ, Ben-Neriah Y. Widespread parainflammation in human cancer. Genome Biol 2016; 17:145. [PMID: 27386949 PMCID: PMC4937599 DOI: 10.1186/s13059-016-0995-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/02/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Chronic inflammation has been recognized as one of the hallmarks of cancer. We recently showed that parainflammation, a unique variant of inflammation between homeostasis and chronic inflammation, strongly promotes mouse gut tumorigenesis upon p53 loss. Here we explore the prevalence of parainflammation in human cancer and determine its relationship to certain molecular and clinical parameters affecting treatment and prognosis. RESULTS We generated a transcriptome signature to identify parainflammation in many primary human tumors and carcinoma cell lines as distinct from their normal tissue counterparts and the tumor microenvironment and show that parainflammation-positive tumors are enriched for p53 mutations and associated with poor prognosis. Non-steroidal anti-inflammatory drug (NSAID) treatment suppresses parainflammation in both murine and human cancers, possibly explaining a protective effect of NSAIDs against cancer. CONCLUSIONS We conclude that parainflammation, a low-grade form of inflammation, is widely prevalent in human cancer, particularly in cancer types commonly harboring p53 mutations. Our data suggest that parainflammation may be a driver for p53 mutagenesis and a guide for cancer prevention by NSAID treatment.
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Affiliation(s)
- Dvir Aran
- Institute for Computational Health Sciences, University of California, San Francisco, California, 94158, USA
| | - Audrey Lasry
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Adar Zinger
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Moshe Biton
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Eli Pikarsky
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Asaf Hellman
- Developmental Biology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Atul J Butte
- Institute for Computational Health Sciences, University of California, San Francisco, California, 94158, USA.
| | - Yinon Ben-Neriah
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel.
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19
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Patursky-Polischuk I, Kasir J, Miloslavski R, Hayouka Z, Hausner-Hanochi M, Stolovich-Rain M, Tsukerman P, Biton M, Mudhasani R, Jones SN, Meyuhas O. Reassessment of the role of TSC, mTORC1 and microRNAs in amino acids-meditated translational control of TOP mRNAs. PLoS One 2014; 9:e109410. [PMID: 25338081 PMCID: PMC4206288 DOI: 10.1371/journal.pone.0109410] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 08/30/2014] [Indexed: 01/02/2023] Open
Abstract
TOP mRNAs encode components of the translational apparatus, and repression of their translation comprises one mechanism, by which cells encountering amino acid deprivation downregulate the biosynthesis of the protein synthesis machinery. This mode of regulation involves TSC as knockout of TSC1 or TSC2 rescued TOP mRNAs translation in amino acid-starved cells. The involvement of mTOR in translational control of TOP mRNAs is demonstrated by the ability of constitutively active mTOR to relieve the translational repression of TOP mRNA upon amino acid deprivation. Consistently, knockdown of this kinase as well as its inhibition by pharmacological means blocked amino acid-induced translational activation of these mRNAs. The signaling of amino acids to TOP mRNAs involves RagB, as overexpression of active RagB derepressed the translation of these mRNAs in amino acid-starved cells. Nonetheless, knockdown of raptor or rictor failed to suppress translational activation of TOP mRNAs by amino acids, suggesting that mTORC1 or mTORC2 plays a minor, if any, role in this mode of regulation. Finally, miR10a has previously been suggested to positively regulate the translation of TOP mRNAs. However, we show here that titration of this microRNA failed to downregulate the basal translation efficiency of TOP mRNAs. Moreover, Drosha knockdown or Dicer knockout, which carries out the first and second processing steps in microRNAs biosynthesis, respectively, failed to block the translational activation of TOP mRNAs by amino acid or serum stimulation. Evidently, these results are questioning the positive role of microRNAs in this mode of regulation.
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Affiliation(s)
- Ilona Patursky-Polischuk
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research – Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Judith Kasir
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research – Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Rachel Miloslavski
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research – Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Zvi Hayouka
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research – Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Mirit Hausner-Hanochi
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research – Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Miri Stolovich-Rain
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research – Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Pinchas Tsukerman
- Lautenberg Center for General and Tumor Immunology, The Institute for Medical Research – Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Moshe Biton
- Lautenberg Center for General and Tumor Immunology, The Institute for Medical Research – Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Rajini Mudhasani
- Department of Cell Biology, University of Massachusetts Medical School, North Worcester, Massachusetts, United States of America
| | - Stephen N. Jones
- Department of Cell Biology, University of Massachusetts Medical School, North Worcester, Massachusetts, United States of America
| | - Oded Meyuhas
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research – Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- * E-mail:
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20
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Kanterman J, Sade-Feldman M, Biton M, Ish-Shalom E, Lasry A, Goldshtein A, Hubert A, Baniyash M. Adverse immunoregulatory effects of 5FU and CPT11 chemotherapy on myeloid-derived suppressor cells and colorectal cancer outcomes. Cancer Res 2014; 74:6022-35. [PMID: 25209187 DOI: 10.1158/0008-5472.can-14-0657] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Colorectal cancer is associated with chronic inflammation and immunosuppression mediated by myeloid-derived suppressor cells (MDSC). Although chemotherapy reduces tumor burden at early stages, it tends to have limited effect on a progressive disease, possibly due to adverse effects on the immune system in dictating disease outcome. Here, we show that patients with advanced colorectal cancer display enhanced MDSC levels and reduced CD247 expression and that some conventional colorectal cancer chemotherapy supports the immunosuppressive tumor microenvironment. A FOLFOX combined therapy reduced immunosuppression, whereas a FOLFIRI combined therapy enhanced immunosuppression. Mechanistic studies in a colorectal cancer mouse model revealed that FOLFIRI-like therapy including the drugs CPT11 and 5-fluorouracil (5FU) damaged host immunocompetence in a manner that limits treatment outcomes. CPT11 blocked MDSC apoptosis and myeloid cell differentiation, increasing MDSC immunosuppressive features and mouse mortality. In contrast, 5FU promoted immune recovery and tumor regression. Thus, CPT11 exhibited detrimental immunoregulatory effects that offset 5FU benefits when administered in combination. Our results highlight the importance of developing therapeutic regimens that can target both the immune system and tumor towards improved personalized treatments for colorectal cancer.
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Affiliation(s)
- Julia Kanterman
- The Lautenberg Center for General and Tumor Immunology, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Moshe Sade-Feldman
- The Lautenberg Center for General and Tumor Immunology, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Moshe Biton
- The Lautenberg Center for General and Tumor Immunology, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Eliran Ish-Shalom
- The Lautenberg Center for General and Tumor Immunology, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Audrey Lasry
- The Lautenberg Center for General and Tumor Immunology, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Aviya Goldshtein
- The Lautenberg Center for General and Tumor Immunology, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Ayala Hubert
- Sharett Institute of Oncology, Hadassah University Medical Center Ein Kerem, Jerusalem, Israel
| | - Michal Baniyash
- The Lautenberg Center for General and Tumor Immunology, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, Jerusalem, Israel.
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21
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Pribluda A, Elyada E, Wiener Z, Hamza H, Goldstein RE, Biton M, Burstain I, Morgenstern Y, Brachya G, Billauer H, Biton S, Snir-Alkalay I, Vucic D, Schlereth K, Mernberger M, Stiewe T, Oren M, Alitalo K, Pikarsky E, Ben-Neriah Y. A senescence-inflammatory switch from cancer-inhibitory to cancer-promoting mechanism. Cancer Cell 2013; 24:242-56. [PMID: 23890787 DOI: 10.1016/j.ccr.2013.06.005] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 04/19/2013] [Accepted: 06/17/2013] [Indexed: 01/07/2023]
Abstract
Senescence, perceived as a cancer barrier, is paradoxically associated with inflammation, which promotes tumorigenesis. Here, we characterize a distinct low-grade inflammatory process in stressed epithelium that is related to para-inflammation; this process either represses or promotes tumorigenesis, depending on p53 activity. Csnk1a1 (CKIα) downregulation induces a senescence-associated inflammatory response (SIR) with growth arrest in colorectal tumors, which loses its growth control capacity in the absence of p53 and instead, accelerates growth and invasiveness. Corresponding processes occur in CKIα-deleted intestinal organoids, assuming tumorigenic transformation properties ex vivo, upon p53 loss. Treatment of organoids and mice with anti-inflammatory agents suppresses the SIR and prevents p53-deficient organoid transformation and mouse carcinogenesis. SIR/para-inflammation suppression may therefore constitute a key mechanism in the anticarcinogenic effects of nonsteroidal anti-inflammatory drugs.
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Affiliation(s)
- Ariel Pribluda
- The Lautenberg Center for Immunology, Institute of Medical Research, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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22
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Biton M, Levin A, Slyper M, Alkalay I, Horwitz E, Mor H, Kredo-Russo S, Avnit-Sagi T, Cojocaru G, Zreik F. Epithelial microRNAs regulate gut mucosal immunity via epithelium-T cell crosstalk. Nat Immunol. 2011;12:239-246. [PMID: 21278735 DOI: 10.1038/ni.1994] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 01/10/2011] [Indexed: 12/12/2022] [Imported: 07/30/2023]
Abstract
Colonic homeostasis entails epithelium-lymphocyte cooperation, yet many participants in this process are unknown. We show here that epithelial microRNAs mediate the mucosa-immune system crosstalk necessary for mounting protective T helper type 2 (T(H)2) responses. Abolishing the induction of microRNA by gut-specific deletion of Dicer1 (Dicer1(Δgut)), which encodes an enzyme involved in microRNA biogenesis, deprived goblet cells of RELMβ, a key T(H)2 antiparasitic cytokine; this predisposed the host to parasite infection. Infection of Dicer1(Δgut) mice with helminths favored a futile T(H)1 response with hallmarks of inflammatory bowel disease. Interleukin 13 (IL-13) induced the microRNA miR-375, which regulates the expression of TSLP, a T(H)2-facilitating epithelial cytokine; this indicated a T(H)2-amplification loop. We found that miR-375 was required for RELMβ expression in vivo; miR-375-deficient mice had significantly less intestinal RELMβ, which possibly explains the greater susceptibility of Dicer1(Δgut) mice to parasites. Our findings indicate that epithelial microRNAs are key regulators of gut homeostasis and mucosal immunity.
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23
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Stern-Ginossar N, Gur C, Biton M, Horwitz E, Elboim M, Stanietsky N, Mandelboim M, Mandelboim O. Human microRNAs regulate stress-induced immune responses mediated by the receptor NKG2D. Nat Immunol 2008; 9:1065-73. [PMID: 18677316 DOI: 10.1038/ni.1642] [Citation(s) in RCA: 245] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 07/08/2008] [Indexed: 01/07/2023] [Imported: 07/30/2023]
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24
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Stern-Ginossar N, Elefant N, Zimmermann A, Wolf DG, Saleh N, Biton M, Horwitz E, Prokocimer Z, Prichard M, Hahn G, Goldman-Wohl D, Greenfield C, Yagel S, Hengel H, Altuvia Y, Margalit H, Mandelboim1 O. Host immune system gene targeting by a viral miRNA. Science 2007; 317:376-81. [PMID: 17641203 PMCID: PMC4283197 DOI: 10.1126/science.1140956] [Citation(s) in RCA: 530] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Virally encoded microRNAs (miRNAs) have recently been discovered in herpesviruses. However, their biological roles are mostly unknown. We developed an algorithm for the prediction of miRNA targets and applied it to human cytomegalovirus miRNAs, resulting in the identification of the major histocompatibility complex class I-related chain B (MICB) gene as a top candidate target of hcmv-miR-UL112. MICB is a stress-induced ligand of the natural killer (NK) cell activating receptor NKG2D and is critical for the NK cell killing of virus-infected cells and tumor cells. We show that hcmv-miR-UL112 specifically down-regulates MICB expression during viral infection, leading to decreased binding of NKG2D and reduced killing by NK cells. Our results reveal a miRNA-based immunoevasion mechanism that appears to be exploited by human cytomegalovirus.
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Affiliation(s)
- Noam Stern-Ginossar
- Lautenberg Center for General and Tumor Immunology, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Naama Elefant
- Department of Molecular Genetics and Biotechnology, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Albert Zimmermann
- Institute for Virology, Heinrich Heine University, D40225 Düsseldorf, Germany
| | - Dana G. Wolf
- Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem, Israel
| | - Nivin Saleh
- Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem, Israel
| | - Moshe Biton
- Lautenberg Center for General and Tumor Immunology, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Elad Horwitz
- Lautenberg Center for General and Tumor Immunology, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Zafnat Prokocimer
- Lautenberg Center for General and Tumor Immunology, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Mark Prichard
- Department of Pediatrics, University of Alabama, Birmingham, AL 35233, USA
| | - Gabriele Hahn
- Max von Pettenkofer Institut, Department of Virology, D80336 Munich, Germany
| | - Debra Goldman-Wohl
- Department of Obstetrics and Gynecology, Hadassah Hebrew University Hospital Mount Scopus, Jerusalem, Israel
| | - Caryn Greenfield
- Department of Obstetrics and Gynecology, Hadassah Hebrew University Hospital Mount Scopus, Jerusalem, Israel
| | - Simcha Yagel
- Department of Obstetrics and Gynecology, Hadassah Hebrew University Hospital Mount Scopus, Jerusalem, Israel
| | - Hartmut Hengel
- Institute for Virology, Heinrich Heine University, D40225 Düsseldorf, Germany
| | - Yael Altuvia
- Department of Molecular Genetics and Biotechnology, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Hanah Margalit
- Department of Molecular Genetics and Biotechnology, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Ofer Mandelboim1
- To whom correspondence should be addressed. (Y.A.); (H.M.); (O.M.)
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25
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Tkacz ID, Lustig Y, Stern MZ, Biton M, Salmon-Divon M, Das A, Bellofatto V, Michaeli S. Identification of novel snRNA-specific Sm proteins that bind selectively to U2 and U4 snRNAs in Trypanosoma brucei. RNA 2007; 13:30-43. [PMID: 17105994 PMCID: PMC1705756 DOI: 10.1261/rna.174307] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In eukaryotes the seven Sm core proteins bind to U1, U2, U4, and U5 snRNAs. In Trypanosoma brucei, Sm proteins have been implicated in binding both spliced leader (SL) and U snRNAs. In this study, we examined the function of these Sm proteins using RNAi silencing and protein purification. RNAi silencing of each of the seven Sm genes resulted in accumulation of SL RNA as well as reduction of several U snRNAs. Interestingly, U2 was unaffected by the loss of SmB, and both U2 and U4 snRNAs were unaffected by the loss of SmD3, suggesting that these snRNAs are not bound by the heptameric Sm complex that binds to U1, U5, and SL RNA. RNAi silencing and protein purification showed that U2 and U4 snRNAs were bound by a unique set of Sm proteins that we termed SSm (specific spliceosomal Sm proteins). This is the first study that identifies specific core Sm proteins that bind only to a subset of spliceosomal snRNAs.
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Affiliation(s)
- Itai Dov Tkacz
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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26
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Biton M, Mandelboim M, Arvatz G, Michaeli S. RNAi interference of XPO1 and Sm genes and their effect on the spliced leader RNA in Trypanosoma brucei. Mol Biochem Parasitol 2006; 150:132-43. [PMID: 16916550 DOI: 10.1016/j.molbiopara.2006.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2006] [Revised: 07/03/2006] [Accepted: 07/11/2006] [Indexed: 12/30/2022]
Abstract
In trypanosomes, trans-splicing is a major essential RNA-processing mechanism that involves the addition of a spliced leader sequence to all mRNAs from a small RNA species, known as the spliced leader RNA (SL RNA). SL RNA maturation is poorly understood and it is not clear where assembly with Sm proteins takes place. In this study, we followed the localization of the SL RNA during knockdown of Sm proteins and XPO1, which in metazoa functions in transport of mRNA and U snRNAs from the nucleus to the cytoplasm. We found that XPO1 has no role in SL RNA biogenesis in wild-type cells, or when the cells are depleted of Sm proteins. During Sm depletion, 'defective' SL RNA lacking cap modification at position +4 first accumulates in the nucleus, suggesting that Sm assembly on SL RNA most probably takes place in this compartment. Only after massive nuclear accumulation is the 'defective' SL RNA exported to the cytoplasm to form SL RNP-C, which may be a route to dispose of SL RNA when its normal biogenesis is blocked.
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MESH Headings
- Active Transport, Cell Nucleus
- Animals
- Autoantigens/genetics
- Autoantigens/physiology
- Cell Nucleus/chemistry
- Cell Nucleus/metabolism
- Cytoplasm/metabolism
- Fatty Acids, Unsaturated/pharmacology
- Karyopherins/genetics
- Karyopherins/physiology
- Kinetics
- Protozoan Proteins/genetics
- Protozoan Proteins/physiology
- RNA Interference
- RNA Processing, Post-Transcriptional/physiology
- RNA, Protozoan/analysis
- RNA, Protozoan/metabolism
- RNA, Spliced Leader/analysis
- RNA, Spliced Leader/metabolism
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/physiology
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/physiology
- Trans-Splicing
- Trypanosoma brucei brucei/genetics
- Trypanosoma brucei brucei/physiology
- snRNP Core Proteins
- Exportin 1 Protein
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Affiliation(s)
- Moshe Biton
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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27
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Mandelboim M, Barth S, Biton M, Liang XH, Michaeli S. Silencing of Sm proteins in Trypanosoma brucei by RNA interference captured a novel cytoplasmic intermediate in spliced leader RNA biogenesis. J Biol Chem 2003; 278:51469-78. [PMID: 14532264 DOI: 10.1074/jbc.m308997200] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Trypanosoma brucei the small nuclear (sn) RNAs U1, U2, U4, and U5, as well as the spliced leader (SL) RNA, bind the seven Sm canonical proteins carrying the consensus Sm motif. To determine the function of these proteins in snRNA and SL RNA biogenesis, two of the Sm core proteins, SmE and SmD1, were silenced by RNAi. Surprisingly, whereas the level of all snRNAs, including U1, U2, U4, and U5 was reduced during silencing, the level of SL RNA was dramatically elevated, but the levels of U6 and spliced leader-associated RNA (SLA1) remained unchanged. The SL RNA that had accumulated in silenced cells lacked modification at the cap4 nucleotide but harbored modifications at the cap1 and cap2 nucleotides and carried the characteristic psi. This SL RNA possessed a longer tail and had accumulated in the cytoplasm in 10 and 50 S particles that were found by in situ hybridization to be present in "speckles." We propose a model for SL RNA biogenesis involving a cytoplasmic phase and suggest that the trypanosome-specific "cap4" nucleotides function as a signal for export and import of SL RNA out and into the nucleus. The SL RNA biogenesis pathway differs from that of U sn ribonucleoproteins (RNPs) in that it is the only RNA that binds Sm proteins that were stabilized under Sm depletion in a novel RNP, which we termed SL RNP-C.
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Affiliation(s)
- Michal Mandelboim
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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