1
|
Safina K, van Galen P. New frameworks for hematopoiesis derived from single-cell genomics. Blood 2024; 144:1039-1047. [PMID: 38985829 DOI: 10.1182/blood.2024024006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/21/2024] [Accepted: 06/22/2024] [Indexed: 07/12/2024] Open
Abstract
ABSTRACT Recent advancements in single-cell genomics have enriched our understanding of hematopoiesis, providing intricate details about hematopoietic stem cell biology, differentiation, and lineage commitment. Technological advancements have highlighted extensive heterogeneity of cell populations and continuity of differentiation routes. Nevertheless, intermediate "attractor" states signify structure in stem and progenitor populations that link state transition dynamics to fate potential. We discuss how innovative model systems quantify lineage bias and how stress accelerates differentiation, thereby reducing fate plasticity compared with native hematopoiesis. We conclude by offering our perspective on the current model of hematopoiesis and discuss how a more precise understanding can translate to strategies that extend healthy hematopoiesis and prevent disease.
Collapse
Affiliation(s)
- Ksenia Safina
- Division of Hematology, Brigham and Women's Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Ludwig Center at Harvard, Boston, MA
| | - Peter van Galen
- Division of Hematology, Brigham and Women's Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Ludwig Center at Harvard, Boston, MA
| |
Collapse
|
2
|
Schuetter J, Minard-Smith A, Hill B, Beare JL, Vornholt A, Burke TW, Murugan V, Smith AK, Chandrasekaran T, Shamma HJ, Kahaian SC, Fillinger KL, Amper MAS, Cheng WS, Ge Y, George MC, Guevara K, Lovette-Okwara N, Mahajan A, Marjanovic N, Mendelev N, Fowler VG, McClain MT, Miller CM, Mofsowitz S, Nair VD, Nudelman G, Evans TG, Castellino F, Ramos I, Rirak S, Ruf-Zamojski F, Seenarine N, Soares-Shanoski A, Vangeti S, Vasoya M, Yu X, Zaslavsky E, Ndhlovu LC, Corley MJ, Bowler S, Deeks SG, Letizia AG, Sealfon SC, Woods CW, Spurbeck RR. Integrated epigenomic exposure signature discovery. Epigenomics 2024; 16:1013-1029. [PMID: 39225561 DOI: 10.1080/17501911.2024.2375187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 06/28/2024] [Indexed: 09/04/2024] Open
Abstract
Aim: The epigenome influences gene regulation and phenotypes in response to exposures. Epigenome assessment can determine exposure history aiding in diagnosis.Materials & methods: Here we developed and implemented a machine learning algorithm, the exposure signature discovery algorithm (ESDA), to identify the most important features present in multiple epigenomic and transcriptomic datasets to produce an integrated exposure signature (ES).Results: Signatures were developed for seven exposures including Staphylococcus aureus, human immunodeficiency virus, SARS-CoV-2, influenza A (H3N2) virus and Bacillus anthracis vaccinations. ESs differed in the assays and features selected and predictive value.Conclusion: Integrated ESs can potentially be utilized for diagnosis or forensic attribution. The ESDA identifies the most distinguishing features enabling diagnostic panel development for future precision health deployment.
Collapse
Affiliation(s)
- Jared Schuetter
- Health Business Unit, Battelle Memorial Institute, Columbus, OH 43201, USA
| | | | | | - Jennifer L Beare
- Health Business Unit, Battelle Memorial Institute, Columbus, OH 43201, USA
| | | | - Thomas W Burke
- Division of Infectious Diseases, Duke University, Durham, NC 27710, USA
| | - Vel Murugan
- Center for Personalized Diagnostics, Biodesign Institute at Arizona State University, Tempe, AZ 85281, 85281USA
| | - Anthony K Smith
- Health Business Unit, Battelle Memorial Institute, Columbus, OH 43201, USA
| | - Thiruppavai Chandrasekaran
- Center for Personalized Diagnostics, Biodesign Institute at Arizona State University, Tempe, AZ 85281, 85281USA
| | - Hiba J Shamma
- Health Business Unit, Battelle Memorial Institute, Columbus, OH 43201, USA
| | - Sarah C Kahaian
- Health Business Unit, Battelle Memorial Institute, Columbus, OH 43201, USA
| | - Keegan L Fillinger
- Health Business Unit, Battelle Memorial Institute, Columbus, OH 43201, USA
| | - Mary Anne S Amper
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | - Wan-Sze Cheng
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | - Yongchao Ge
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | | | - Kristy Guevara
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | | | - Avinash Mahajan
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | - Nada Marjanovic
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | - Natalia Mendelev
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | - Vance G Fowler
- Division of Infectious Diseases, Duke University, Durham, NC 27710, USA
| | - Micah T McClain
- Division of Infectious Diseases, Duke University, Durham, NC 27710, USA
| | - Clare M Miller
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | - Sagie Mofsowitz
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | - Venugopalan D Nair
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | - German Nudelman
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | | | - Flora Castellino
- Biomedical Advanced Research & Development Authority-Administration for Strategic Preparedness & Response,Washington, DC 20201, USA
| | - Irene Ramos
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | - Stas Rirak
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | | | - Nitish Seenarine
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | | | - Sindhu Vangeti
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | - Mital Vasoya
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | - Xuechen Yu
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | - Elena Zaslavsky
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | - Lishomwa C Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Michael J Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Scott Bowler
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Steven G Deeks
- University of California San Francisco, San Francisco, CA 94143, 94143USA
| | | | - Stuart C Sealfon
- Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA
| | | | - Rachel R Spurbeck
- Health Business Unit, Battelle Memorial Institute, Columbus, OH 43201, USA
| |
Collapse
|
3
|
Sumida TS, Lincoln MR, He L, Park Y, Ota M, Oguchi A, Son R, Yi A, Stillwell HA, Leissa GA, Fujio K, Murakawa Y, Kulminski AM, Epstein CB, Bernstein BE, Kellis M, Hafler DA. An autoimmune transcriptional circuit drives FOXP3 + regulatory T cell dysfunction. Sci Transl Med 2024; 16:eadp1720. [PMID: 39196959 DOI: 10.1126/scitranslmed.adp1720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 08/02/2024] [Indexed: 08/30/2024]
Abstract
Autoimmune diseases, among the most common disorders of young adults, are mediated by genetic and environmental factors. Although CD4+FOXP3+ regulatory T cells (Tregs) play a central role in preventing autoimmunity, the molecular mechanism underlying their dysfunction is unknown. Here, we performed comprehensive transcriptomic and epigenomic profiling of Tregs in the autoimmune disease multiple sclerosis (MS) to identify critical transcriptional programs regulating human autoimmunity. We found that up-regulation of a primate-specific short isoform of PR domain zinc finger protein 1 (PRDM1-S) induces expression of serum and glucocorticoid-regulated kinase 1 (SGK1) independent from the evolutionarily conserved long PRDM1, which led to destabilization of forkhead box P3 (FOXP3) and Treg dysfunction. This aberrant PRDM1-S/SGK1 axis is shared among other autoimmune diseases. Furthermore, the chromatin landscape profiling in Tregs from individuals with MS revealed enriched activating protein-1 (AP-1)/interferon regulatory factor (IRF) transcription factor binding as candidate upstream regulators of PRDM1-S expression and Treg dysfunction. Our study uncovers a mechanistic model where the evolutionary emergence of PRDM1-S and epigenetic priming of AP-1/IRF may be key drivers of dysfunctional Tregs in autoimmune diseases.
Collapse
Affiliation(s)
- Tomokazu S Sumida
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew R Lincoln
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON M6R 1B5, Canada
- Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Toronto, ON M6R 1B5, Canada
| | - Liang He
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27705, USA
| | - Yongjin Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo 113-8655, Japan
| | - Akiko Oguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8303, Japan
| | - Raku Son
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8303, Japan
| | - Alice Yi
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Helen A Stillwell
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Greta A Leissa
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo 113-8655, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8303, Japan
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27705, USA
| | | | - Bradley E Bernstein
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| |
Collapse
|
4
|
Patra M, Klochendler A, Condiotti R, Kaffe B, Elgavish S, Drawshy Z, Avrahami D, Narita M, Hofree M, Drier Y, Meshorer E, Dor Y, Ben-Porath I. Senescence of human pancreatic beta cells enhances functional maturation through chromatin reorganization and promotes interferon responsiveness. Nucleic Acids Res 2024; 52:6298-6316. [PMID: 38682582 PMCID: PMC11194086 DOI: 10.1093/nar/gkae313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
Senescent cells can influence the function of tissues in which they reside, and their propensity for disease. A portion of adult human pancreatic beta cells express the senescence marker p16, yet it is unclear whether they are in a senescent state, and how this affects insulin secretion. We analyzed single-cell transcriptome datasets of adult human beta cells, and found that p16-positive cells express senescence gene signatures, as well as elevated levels of beta-cell maturation genes, consistent with enhanced functionality. Senescent human beta-like cells in culture undergo chromatin reorganization that leads to activation of enhancers regulating functional maturation genes and acquisition of glucose-stimulated insulin secretion capacity. Strikingly, Interferon-stimulated genes are elevated in senescent human beta cells, but genes encoding senescence-associated secretory phenotype (SASP) cytokines are not. Senescent beta cells in culture and in human tissue show elevated levels of cytoplasmic DNA, contributing to their increased interferon responsiveness. Human beta-cell senescence thus involves chromatin-driven upregulation of a functional-maturation program, and increased responsiveness of interferon-stimulated genes, changes that could increase both insulin secretion and immune reactivity.
Collapse
Affiliation(s)
- Milan Patra
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Agnes Klochendler
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Reba Condiotti
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Binyamin Kaffe
- Department of Genetics, the Institute of Life Sciences and the Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sharona Elgavish
- Info-CORE, Bioinformatics Unit of the I-CORE at the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zeina Drawshy
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dana Avrahami
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Matan Hofree
- The Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yotam Drier
- The Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eran Meshorer
- Department of Genetics, the Institute of Life Sciences and the Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ittai Ben-Porath
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|
5
|
Li J, Chin CR, Ying HY, Meydan C, Teater MR, Xia M, Farinha P, Takata K, Chu CS, Jiang Y, Eagles J, Passerini V, Tang Z, Rivas MA, Weigert O, Pugh TJ, Chadburn A, Steidl C, Scott DW, Roeder RG, Mason CE, Zappasodi R, Béguelin W, Melnick AM. Loss of CREBBP and KMT2D cooperate to accelerate lymphomagenesis and shape the lymphoma immune microenvironment. Nat Commun 2024; 15:2879. [PMID: 38570506 PMCID: PMC10991284 DOI: 10.1038/s41467-024-47012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 03/11/2024] [Indexed: 04/05/2024] Open
Abstract
Despite regulating overlapping gene enhancers and pathways, CREBBP and KMT2D mutations recurrently co-occur in germinal center (GC) B cell-derived lymphomas, suggesting potential oncogenic cooperation. Herein, we report that combined haploinsufficiency of Crebbp and Kmt2d induces a more severe mouse lymphoma phenotype (vs either allele alone) and unexpectedly confers an immune evasive microenvironment manifesting as CD8+ T-cell exhaustion and reduced infiltration. This is linked to profound repression of immune synapse genes that mediate crosstalk with T-cells, resulting in aberrant GC B cell fate decisions. From the epigenetic perspective, we observe interaction and mutually dependent binding and function of CREBBP and KMT2D on chromatin. Their combined deficiency preferentially impairs activation of immune synapse-responsive super-enhancers, pointing to a particular dependency for both co-activators at these specialized regulatory elements. Together, our data provide an example where chromatin modifier mutations cooperatively shape and induce an immune-evasive microenvironment to facilitate lymphomagenesis.
Collapse
Affiliation(s)
- Jie Li
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Christopher R Chin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Hsia-Yuan Ying
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew R Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Min Xia
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Pedro Farinha
- BC Cancer Centre for Lymphoid Cancer, Department of Pathology and Laboratorial Medicine, University of British Columbia, Vancouver, Canada
| | - Katsuyoshi Takata
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, Canada
| | - Chi-Shuen Chu
- The Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Yiyue Jiang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Jenna Eagles
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Verena Passerini
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians University (LMU) Hospital, Munich, Germany
| | - Zhanyun Tang
- The Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Martin A Rivas
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Oliver Weigert
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians University (LMU) Hospital, Munich, Germany
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, Canada
| | - David W Scott
- BC Cancer Centre for Lymphoid Cancer, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Robert G Roeder
- The Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Roberta Zappasodi
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Wendy Béguelin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
| |
Collapse
|
6
|
Lee HG, Rone JM, Li Z, Akl CF, Shin SW, Lee JH, Flausino LE, Pernin F, Chao CC, Kleemann KL, Srun L, Illouz T, Giovannoni F, Charabati M, Sanmarco LM, Kenison JE, Piester G, Zandee SEJ, Antel JP, Rothhammer V, Wheeler MA, Prat A, Clark IC, Quintana FJ. Disease-associated astrocyte epigenetic memory promotes CNS pathology. Nature 2024; 627:865-872. [PMID: 38509377 PMCID: PMC11016191 DOI: 10.1038/s41586-024-07187-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 02/09/2024] [Indexed: 03/22/2024]
Abstract
Disease-associated astrocyte subsets contribute to the pathology of neurologic diseases, including multiple sclerosis and experimental autoimmune encephalomyelitis1-8 (EAE), an experimental model for multiple sclerosis. However, little is known about the stability of these astrocyte subsets and their ability to integrate past stimulation events. Here we report the identification of an epigenetically controlled memory astrocyte subset that exhibits exacerbated pro-inflammatory responses upon rechallenge. Specifically, using a combination of single-cell RNA sequencing, assay for transposase-accessible chromatin with sequencing, chromatin immunoprecipitation with sequencing, focused interrogation of cells by nucleic acid detection and sequencing, and cell-specific in vivo CRISPR-Cas9-based genetic perturbation studies we established that astrocyte memory is controlled by the metabolic enzyme ATP-citrate lyase (ACLY), which produces acetyl coenzyme A (acetyl-CoA) that is used by histone acetyltransferase p300 to control chromatin accessibility. The number of ACLY+p300+ memory astrocytes is increased in acute and chronic EAE models, and their genetic inactivation ameliorated EAE. We also detected the pro-inflammatory memory phenotype in human astrocytes in vitro; single-cell RNA sequencing and immunohistochemistry studies detected increased numbers of ACLY+p300+ astrocytes in chronic multiple sclerosis lesions. In summary, these studies define an epigenetically controlled memory astrocyte subset that promotes CNS pathology in EAE and, potentially, multiple sclerosis. These findings may guide novel therapeutic approaches for multiple sclerosis and other neurologic diseases.
Collapse
Affiliation(s)
- Hong-Gyun Lee
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joseph M Rone
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhaorong Li
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Camilo Faust Akl
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Seung Won Shin
- Department of Bioengineering, College of Engineering, California Institute for Quantitative Biosciences, QB3, University of California Berkeley, Berkeley, CA, USA
| | - Joon-Hyuk Lee
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lucas E Flausino
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Florian Pernin
- Neuroimmunology Unit, Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Chun-Cheih Chao
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Lena Srun
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Tomer Illouz
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Federico Giovannoni
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marc Charabati
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Liliana M Sanmarco
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jessica E Kenison
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gavin Piester
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Stephanie E J Zandee
- Neuroimmunology Research Lab, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Jack P Antel
- Neuroimmunology Unit, Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Veit Rothhammer
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, University Hospital, Friedrich-Alexander University Erlangen Nuremberg, Erlangen, Germany
| | - Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexandre Prat
- Neuroimmunology Research Lab, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Iain C Clark
- Department of Bioengineering, College of Engineering, California Institute for Quantitative Biosciences, QB3, University of California Berkeley, Berkeley, CA, USA
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Gene Lay Institute of Immunology and Inflammation, Boston, MA, USA.
| |
Collapse
|
7
|
Krause C, Bergmann E, Schmidt SV. Epigenetic modulation of myeloid cell functions in HIV and SARS-CoV-2 infection. Mol Biol Rep 2024; 51:342. [PMID: 38400997 PMCID: PMC10894183 DOI: 10.1007/s11033-024-09266-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/18/2024] [Indexed: 02/26/2024]
Abstract
Myeloid cells play a vital role in innate immune responses as they recognize and phagocytose pathogens like viruses, present antigens, produce cytokines, recruit other immune cells to combat infections, and contribute to the attenuation of immune responses to restore homeostasis. Signal integration by pathogen recognition receptors enables myeloid cells to adapt their functions by a network of transcription factors and chromatin remodelers. This review provides a brief overview of the subtypes of myeloid cells and the main epigenetic regulation mechanisms. Special focus is placed on the epigenomic alterations in viral nucleic acids of HIV and SARS-CoV-2 along with the epigenetic changes in the host's myeloid cell compartment. These changes are important as they lead to immune suppression and promote the progression of the disease. Finally, we highlight some promising examples of 'epidrugs' that modulate the epigenome of immune cells and could be used as therapeutics for viral infections.
Collapse
Affiliation(s)
- Carolyn Krause
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127, Bonn, Germany
- Department of Microbiology and Immunology, the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Eva Bergmann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127, Bonn, Germany
| | - Susanne Viktoria Schmidt
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127, Bonn, Germany.
| |
Collapse
|
8
|
Lee HG, Rone JM, Li Z, Akl CF, Shin SW, Lee JH, Flausino LE, Pernin F, Chao CC, Kleemann KL, Srun L, Illouz T, Giovannoni F, Charabati M, Sanmarco LM, Kenison JE, Piester G, Zandee SEJ, Antel J, Rothhammer V, Wheeler MA, Prat A, Clark IC, Quintana FJ. Disease-associated astrocyte epigenetic memory promotes CNS pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574196. [PMID: 38260616 PMCID: PMC10802318 DOI: 10.1101/2024.01.04.574196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Astrocytes play important roles in the central nervous system (CNS) physiology and pathology. Indeed, astrocyte subsets defined by specific transcriptional activation states contribute to the pathology of neurologic diseases, including multiple sclerosis (MS) and its pre-clinical model experimental autoimmune encephalomyelitis (EAE) 1-8 . However, little is known about the stability of these disease-associated astrocyte subsets, their regulation, and whether they integrate past stimulation events to respond to subsequent challenges. Here, we describe the identification of an epigenetically controlled memory astrocyte subset which exhibits exacerbated pro-inflammatory responses upon re-challenge. Specifically, using a combination of single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin with sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing (ChIP-seq), focused interrogation of cells by nucleic acid detection and sequencing (FIND-seq), and cell-specific in vivo CRISPR/Cas9-based genetic perturbation studies we established that astrocyte memory is controlled by the metabolic enzyme ATP citrate lyase (ACLY), which produces acetyl coenzyme A (acetyl-CoA) used by the histone acetyltransferase p300 to control chromatin accessibility. ACLY + p300 + memory astrocytes are increased in acute and chronic EAE models; the genetic targeting of ACLY + p300 + astrocytes using CRISPR/Cas9 ameliorated EAE. We also detected responses consistent with a pro-inflammatory memory phenotype in human astrocytes in vitro ; scRNA-seq and immunohistochemistry studies detected increased ACLY + p300 + astrocytes in chronic MS lesions. In summary, these studies define an epigenetically controlled memory astrocyte subset that promotes CNS pathology in EAE and, potentially, MS. These findings may guide novel therapeutic approaches for MS and other neurologic diseases.
Collapse
|
9
|
Ricke DO, Ng D, Michaleas A, Fremont-Smith P. Omics Analysis and Quality Control Pipelines in a High-Performance Computing Environment. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:519-525. [PMID: 37943668 DOI: 10.1089/omi.2023.0078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Data quality is often an overlooked feature in the analysis of omics data. This is particularly relevant in studies of chemical and pathogen exposures that can modify an individual's epigenome and transcriptome with persistence over time. Portable, quality control (QC) pipelines for multiple different omics datasets are therefore needed. To meet these goals, portable quality assurance (QA) metrics, metric acceptability criterion, and pipelines to compute these metrics were developed and consolidated into one framework for 12 different omics assays. Performance of these QA metrics and pipelines were evaluated on human data generated by the Defense Advanced Research Projects Agency (DARPA) Epigenetic CHaracterization and Observation (ECHO) program. Twelve analytical pipelines were developed leveraging standard tools when possible. These QC pipelines were containerized using Singularity to ensure portability and scalability. Datasets for these 12 omics assays were analyzed and results were summarized. The quality thresholds and metrics used were described. We found that these pipelines enabled early identification of lower quality datasets, datasets with insufficient reads for additional sequencing, and experimental protocols needing refinements. These omics data analysis and QC pipelines are available as open-source resources as reported and discussed in this article for the omics and life sciences communities.
Collapse
Affiliation(s)
- Darrell O Ricke
- Massachusetts Institute of Technology Lincoln Laboratory, Lexington, Massachusetts, USA
| | - Derek Ng
- Massachusetts Institute of Technology Lincoln Laboratory, Lexington, Massachusetts, USA
| | - Adam Michaleas
- Massachusetts Institute of Technology Lincoln Laboratory, Lexington, Massachusetts, USA
| | - Philip Fremont-Smith
- Massachusetts Institute of Technology Lincoln Laboratory, Lexington, Massachusetts, USA
| |
Collapse
|
10
|
Saha S, Jungas TT, Ohayon D, Audouard C, Ye T, Fawal MA, Davy A. Dihydrofolate reductase activity controls neurogenic transitions in the developing neocortex. Development 2023; 150:dev201696. [PMID: 37665322 DOI: 10.1242/dev.201696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 08/01/2023] [Indexed: 09/05/2023]
Abstract
One-carbon/folate (1C) metabolism supplies methyl groups required for DNA and histone methylation, and is involved in the maintenance of self-renewal in stem cells. Dihydrofolate reductase (DHFR), a key enzyme in 1C metabolism, is highly expressed in human and mouse neural progenitors at the early stages of neocortical development. Here, we have investigated the role of DHFR in the developing neocortex and report that reducing its activity in human neural organoids and mouse embryonic neocortex accelerates indirect neurogenesis, thereby affecting neuronal composition of the neocortex. Furthermore, we show that decreasing DHFR activity in neural progenitors leads to a reduction in one-carbon/folate metabolites and correlates with modifications of H3K4me3 levels. Our findings reveal an unanticipated role for DHFR in controlling specific steps of neocortex development and indicate that variations in 1C metabolic cues impact cell fate transitions.
Collapse
Affiliation(s)
- Sulov Saha
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Thomas T Jungas
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - David Ohayon
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Christophe Audouard
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS UMR7104, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Mohamad-Ali Fawal
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Alice Davy
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| |
Collapse
|
11
|
Yang Y, Gomez N, Infarinato N, Adam RC, Sribour M, Baek I, Laurin M, Fuchs E. The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates. Nat Cell Biol 2023; 25:1185-1195. [PMID: 37488435 PMCID: PMC10415178 DOI: 10.1038/s41556-023-01184-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 06/08/2023] [Indexed: 07/26/2023]
Abstract
During development, progenitors simultaneously activate one lineage while silencing another, a feature highly regulated in adult stem cells but derailed in cancers. Equipped to bind cognate motifs in closed chromatin, pioneer factors operate at these crossroads, but how they perform fate switching remains elusive. Here we tackle this question with SOX9, a master regulator that diverts embryonic epidermal stem cells (EpdSCs) into becoming hair follicle stem cells. By engineering mice to re-activate SOX9 in adult EpdSCs, we trigger fate switching. Combining epigenetic, proteomic and functional analyses, we interrogate the ensuing chromatin and transcriptional dynamics, slowed temporally by the mature EpdSC niche microenvironment. We show that as SOX9 binds and opens key hair follicle enhancers de novo in EpdSCs, it simultaneously recruits co-factors away from epidermal enhancers, which are silenced. Unhinged from its normal regulation, sustained SOX9 subsequently activates oncogenic transcriptional regulators that chart the path to cancers typified by constitutive SOX9 expression.
Collapse
Affiliation(s)
- Yihao Yang
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Nicholas Gomez
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Allen Institute for Cell Sciences, Seattle, WA, USA
| | - Nicole Infarinato
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- PRECISIONscientia, Yardley, PA, USA
| | - Rene C Adam
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Megan Sribour
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Inwha Baek
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Kyung Hee University, Seoul, South Korea
| | - Mélanie Laurin
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- CHU de Québec-Université Laval Research Center, Quebec City, Quebec, Canada
| | - Elaine Fuchs
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
12
|
Hitz BC, Lee JW, Jolanki O, Kagda MS, Graham K, Sud P, Gabdank I, Strattan JS, Sloan CA, Dreszer T, Rowe LD, Podduturi NR, Malladi VS, Chan ET, Davidson JM, Ho M, Miyasato S, Simison M, Tanaka F, Luo Y, Whaling I, Hong EL, Lee BT, Sandstrom R, Rynes E, Nelson J, Nishida A, Ingersoll A, Buckley M, Frerker M, Kim DS, Boley N, Trout D, Dobin A, Rahmanian S, Wyman D, Balderrama-Gutierrez G, Reese F, Durand NC, Dudchenko O, Weisz D, Rao SSP, Blackburn A, Gkountaroulis D, Sadr M, Olshansky M, Eliaz Y, Nguyen D, Bochkov I, Shamim MS, Mahajan R, Aiden E, Gingeras T, Heath S, Hirst M, Kent WJ, Kundaje A, Mortazavi A, Wold B, Cherry JM. The ENCODE Uniform Analysis Pipelines. RESEARCH SQUARE 2023:rs.3.rs-3111932. [PMID: 37503119 PMCID: PMC10371165 DOI: 10.21203/rs.3.rs-3111932/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses.
Collapse
Affiliation(s)
- Benjamin C Hitz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jin-Wook Lee
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Otto Jolanki
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meenakshi S Kagda
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Keenan Graham
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paul Sud
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Idan Gabdank
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - J Seth Strattan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cricket A Sloan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Timothy Dreszer
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laurence D Rowe
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nikhil R Podduturi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Venkat S Malladi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Esther T Chan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jean M Davidson
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marcus Ho
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stuart Miyasato
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matt Simison
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Forrest Tanaka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yunhai Luo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian Whaling
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eurie L Hong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian T Lee
- Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Richard Sandstrom
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Eric Rynes
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Andrew Nishida
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Alyssa Ingersoll
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Michael Buckley
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Mark Frerker
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Daniel S Kim
- Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Nathan Boley
- Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Diane Trout
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA
| | - Alex Dobin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sorena Rahmanian
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Dana Wyman
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Fairlie Reese
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Neva C Durand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Houston, TX 77030, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alyssa Blackburn
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Dimos Gkountaroulis
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Mahdi Sadr
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moshe Olshansky
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yossi Eliaz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dat Nguyen
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ivan Bochkov
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad Saad Shamim
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ragini Mahajan
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Erez Aiden
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Tom Gingeras
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Simon Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin Hirst
- Micheal Smith Laboratories, University of British Columbia, British Columbia, Canada
| | - W James Kent
- Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Anshul Kundaje
- Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Ali Mortazavi
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA
| | - J Michael Cherry
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
13
|
Benyoucef A, Haigh JJ, Brand M. Unveiling the complexity of transcription factor networks in hematopoietic stem cells: implications for cell therapy and hematological malignancies. Front Oncol 2023; 13:1151343. [PMID: 37441426 PMCID: PMC10333584 DOI: 10.3389/fonc.2023.1151343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
The functionality and longevity of hematopoietic tissue is ensured by a tightly controlled balance between self-renewal, quiescence, and differentiation of hematopoietic stem cells (HSCs) into the many different blood lineages. Cell fate determination in HSCs is influenced by signals from extrinsic factors (e.g., cytokines, irradiation, reactive oxygen species, O2 concentration) that are translated and integrated by intrinsic factors such as Transcription Factors (TFs) to establish specific gene regulatory programs. TFs also play a central role in the establishment and/or maintenance of hematological malignancies, highlighting the need to understand their functions in multiple contexts. TFs bind to specific DNA sequences and interact with each other to form transcriptional complexes that directly or indirectly control the expression of multiple genes. Over the past decades, significant research efforts have unraveled molecular programs that control HSC function. This, in turn, led to the identification of more than 50 TF proteins that influence HSC fate. However, much remains to be learned about how these proteins interact to form molecular networks in combination with cofactors (e.g. epigenetics factors) and how they control differentiation, expansion, and maintenance of cellular identity. Understanding these processes is critical for future applications particularly in the field of cell therapy, as this would allow for manipulation of cell fate and induction of expansion, differentiation, or reprogramming of HSCs using specific cocktails of TFs. Here, we review recent findings that have unraveled the complexity of molecular networks controlled by TFs in HSCs and point towards possible applications to obtain functional HSCs ex vivo for therapeutic purposes including hematological malignancies. Furthermore, we discuss the challenges and prospects for the derivation and expansion of functional adult HSCs in the near future.
Collapse
Affiliation(s)
- Aissa Benyoucef
- Department of Pharmacology and Therapeutics, Rady Faulty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- CancerCare Manitoba Research Institute, Winnipeg, MB, Canada
| | - Jody J. Haigh
- Department of Pharmacology and Therapeutics, Rady Faulty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- CancerCare Manitoba Research Institute, Winnipeg, MB, Canada
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| |
Collapse
|
14
|
Tesfaye RA, Lavaud M, Charrier C, Brounais-Le Royer B, Cartron PF, Verrecchia F, Baud'huin M, Lamoureux F, Georges S, Ory B. Tracking Targets of Dynamic Super-Enhancers in Vitro to Better Characterize Osteoclastogenesis and to Evaluate the Effect of Diuron on the Maturation of Human Bone Cells. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:67007. [PMID: 37307168 DOI: 10.1289/ehp11690] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
BACKGROUND Osteoclasts are major actors in the maintenance of bone homeostasis. The full functional maturation of osteoclasts from monocyte lineage cells is essential for the degradation of old/damaged bone matrix. Diuron is one of the most frequently encountered herbicides, particularly in water sources. However, despite a reported delayed ossification in vivo, its impact on bone cells remains largely unknown. OBJECTIVES The objectives of this study were to first better characterize osteoclastogenesis by identifying genes that drive the differentiation of CD14+ monocyte progenitors into osteoclasts and to evaluate the toxicity of diuron on osteoblastic and osteoclastic differentiation in vitro. METHODS We performed chromatin immunoprecipitation (ChIP) against H3K27ac followed by ChIP-sequencing (ChIP-Seq) and RNA-sequencing (RNA-Seq) at different stages of differentiation of CD14+ monocytes into active osteoclasts. Differentially activated super-enhancers and their potential target genes were identified. Then to evaluate the toxicity of diuron on osteoblasts and osteoclasts, we performed RNA-Seq and functional tests during in vitro osteoblastic and osteoclastic differentiation by exposing cells to different concentrations of diuron. RESULTS The combinatorial study of the epigenetic and transcriptional remodeling taking place during differentiation has revealed a very dynamic epigenetic profile that supports the expression of genes vital for osteoclast differentiation and function. In total, we identified 122 genes induced by dynamic super-enhancers at late days. Our data suggest that high concentration of diuron (50μM) affects viability of mesenchymal stem cells (MSCs) in vitro associated with a decrease of bone mineralization. At a lower concentration (1μM), an inhibitory effect was observed in vitro on the number of osteoclasts derived from CD14+ monocytes without affecting cell viability. Among the diuron-affected genes, our analysis suggests a significant enrichment of genes targeted by pro-differentiation super-enhancers, with an odds ratio of 5.12 (ρ=2.59×10-5). DISCUSSION Exposure to high concentrations of diuron decreased the viability of MSCs and could therefore affect osteoblastic differentiation and bone mineralization. This pesticide also disrupted osteoclasts maturation by impairing the expression of cell-identity determining genes. Indeed, at sublethal concentrations, differences in the expression of these key genes were mild during the course of in vitro osteoclast differentiation. Taken together our results suggest that high exposure levels of diuron could have an effect on bone homeostasis. https://doi.org/10.1289/EHP11690.
Collapse
Affiliation(s)
- Robel A Tesfaye
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
- Cancéropole Grand-Ouest, réseau Epigénétique, Nantes, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
| | - Melanie Lavaud
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | - Céline Charrier
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | | | - Pierre-François Cartron
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
- LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Cancéropole Grand-Ouest, réseau Epigénétique, Nantes, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
| | - Franck Verrecchia
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | - Marc Baud'huin
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | - François Lamoureux
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | - Steven Georges
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | - Benjamin Ory
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
- Cancéropole Grand-Ouest, réseau Epigénétique, Nantes, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
| |
Collapse
|
15
|
Salma M, Andrieu-Soler C, Deleuze V, Soler E. High-throughput methods for the analysis of transcription factors and chromatin modifications: Low input, single cell and spatial genomic technologies. Blood Cells Mol Dis 2023; 101:102745. [PMID: 37121019 DOI: 10.1016/j.bcmd.2023.102745] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 05/02/2023]
Abstract
Genome-wide analysis of transcription factors and epigenomic features is instrumental to shed light on DNA-templated regulatory processes such as transcription, cellular differentiation or to monitor cellular responses to environmental cues. Two decades of technological developments have led to a rich set of approaches progressively pushing the limits of epigenetic profiling towards single cells. More recently, disruptive technologies using innovative biochemistry came into play. Assays such as CUT&RUN, CUT&Tag and variations thereof show considerable potential to survey multiple TFs or histone modifications in parallel from a single experiment and in native conditions. These are in the path to become the dominant assays for genome-wide analysis of TFs and chromatin modifications in bulk, single-cell, and spatial genomic applications. The principles together with pros and cons are discussed.
Collapse
Affiliation(s)
- Mohammad Salma
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France
| | - Charlotte Andrieu-Soler
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France
| | - Virginie Deleuze
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France
| | - Eric Soler
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France.
| |
Collapse
|
16
|
Hitz BC, Jin-Wook L, Jolanki O, Kagda MS, Graham K, Sud P, Gabdank I, Strattan JS, Sloan CA, Dreszer T, Rowe LD, Podduturi NR, Malladi VS, Chan ET, Davidson JM, Ho M, Miyasato S, Simison M, Tanaka F, Luo Y, Whaling I, Hong EL, Lee BT, Sandstrom R, Rynes E, Nelson J, Nishida A, Ingersoll A, Buckley M, Frerker M, Kim DS, Boley N, Trout D, Dobin A, Rahmanian S, Wyman D, Balderrama-Gutierrez G, Reese F, Durand NC, Dudchenko O, Weisz D, Rao SSP, Blackburn A, Gkountaroulis D, Sadr M, Olshansky M, Eliaz Y, Nguyen D, Bochkov I, Shamim MS, Mahajan R, Aiden E, Gingeras T, Heath S, Hirst M, Kent WJ, Kundaje A, Mortazavi A, Wold B, Cherry JM. The ENCODE Uniform Analysis Pipelines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.04.535623. [PMID: 37066421 PMCID: PMC10104020 DOI: 10.1101/2023.04.04.535623] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses.
Collapse
Affiliation(s)
- Benjamin C Hitz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lee Jin-Wook
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Otto Jolanki
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meenakshi S Kagda
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Keenan Graham
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paul Sud
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Idan Gabdank
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - J Seth Strattan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cricket A Sloan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Timothy Dreszer
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laurence D Rowe
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nikhil R Podduturi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Venkat S Malladi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Esther T Chan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jean M Davidson
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marcus Ho
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stuart Miyasato
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matt Simison
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Forrest Tanaka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yunhai Luo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian Whaling
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eurie L Hong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian T Lee
- Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Richard Sandstrom
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Eric Rynes
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Andrew Nishida
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Alyssa Ingersoll
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Michael Buckley
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Mark Frerker
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Daniel S Kim
- Dept. of Genetics, Dept. of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Nathan Boley
- Dept. of Genetics, Dept. of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Diane Trout
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA
| | - Alex Dobin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sorena Rahmanian
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Dana Wyman
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Fairlie Reese
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Neva C Durand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Houston, TX 77030, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alyssa Blackburn
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Dimos Gkountaroulis
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Mahdi Sadr
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moshe Olshansky
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yossi Eliaz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dat Nguyen
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ivan Bochkov
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad Saad Shamim
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ragini Mahajan
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Erez Aiden
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Tom Gingeras
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Simon Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin Hirst
- Micheal Smith Laboratories, University of British Columbia, British Columbia, Canada
| | - W James Kent
- Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Anshul Kundaje
- Dept. of Genetics, Dept. of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Ali Mortazavi
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA
| | - J Michael Cherry
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
17
|
Ford BR, Poholek AC. Regulation and Immunotherapeutic Targeting of the Epigenome in Exhausted CD8 T Cell Responses. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:869-879. [PMID: 36947818 PMCID: PMC10037537 DOI: 10.4049/jimmunol.2200681] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/04/2023] [Indexed: 03/24/2023]
Abstract
Exhaustion is a state of CD8 T cell differentiation that occurs in settings of chronic Ag such as tumors, chronic viral infection, and autoimmunity. Cellular differentiation is driven by a series of environmental signals that promote epigenetic landscapes that set transcriptomes needed for function. For CD8 T cells, the epigenome that underlies exhaustion is distinct from effector and memory cell differentiation, suggesting that signals early on set in motion a process where the epigenome is modified to promote a trajectory toward a dysfunctional state. Although we know many signals that promote exhaustion, putting this in the context of the epigenetic changes that occur during differentiation has been less clear. In this review, we aim to summarize the epigenetic changes associated with exhaustion in the context of signals that promote it, highlighting immunotherapeutic studies that support these observations or areas for future therapeutic opportunities.
Collapse
Affiliation(s)
- B Rhodes Ford
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA; and Department of Immunology, University of Pittsburgh, Pittsburgh, PA
| | - Amanda C Poholek
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA; and Department of Immunology, University of Pittsburgh, Pittsburgh, PA
| |
Collapse
|
18
|
Weigert R, Hetzel S, Bailly N, Haggerty C, Ilik IA, Yung PYK, Navarro C, Bolondi A, Kumar AS, Anania C, Brändl B, Meierhofer D, Lupiáñez DG, Müller FJ, Aktas T, Elsässer SJ, Kretzmer H, Smith ZD, Meissner A. Dynamic antagonism between key repressive pathways maintains the placental epigenome. Nat Cell Biol 2023; 25:579-591. [PMID: 37024684 PMCID: PMC10104784 DOI: 10.1038/s41556-023-01114-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 02/21/2023] [Indexed: 04/08/2023]
Abstract
DNA and Histone 3 Lysine 27 methylation typically function as repressive modifications and operate within distinct genomic compartments. In mammals, the majority of the genome is kept in a DNA methylated state, whereas the Polycomb repressive complexes regulate the unmethylated CpG-rich promoters of developmental genes. In contrast to this general framework, the extra-embryonic lineages display non-canonical, globally intermediate DNA methylation levels, including disruption of local Polycomb domains. Here, to better understand this unusual landscape's molecular properties, we genetically and chemically perturbed major epigenetic pathways in mouse trophoblast stem cells. We find that the extra-embryonic epigenome reflects ongoing and dynamic de novo methyltransferase recruitment, which is continuously antagonized by Polycomb to maintain intermediate, locally disordered methylation. Despite its disorganized molecular appearance, our data point to a highly controlled equilibrium between counteracting repressors within extra-embryonic cells, one that can seemingly persist indefinitely without bistable features typically seen for embryonic forms of epigenetic regulation.
Collapse
Affiliation(s)
- Raha Weigert
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Medical Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Sara Hetzel
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Nina Bailly
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Chuck Haggerty
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Ibrahim A Ilik
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Philip Yuk Kwong Yung
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Carmen Navarro
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Abhishek Sampath Kumar
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Chiara Anania
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Björn Brändl
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Universitätsklinikum Schleswig-Holstein Campus Kiel, Zentrum für Integrative Psychiatrie gGmbH, Kiel, Germany
| | - David Meierhofer
- Mass Spectrometry Joint Facilities Scientific Service, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Darío G Lupiáñez
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Franz-Josef Müller
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Universitätsklinikum Schleswig-Holstein Campus Kiel, Zentrum für Integrative Psychiatrie gGmbH, Kiel, Germany
| | - Tugce Aktas
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Zachary D Smith
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA.
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, US.
| |
Collapse
|
19
|
Cohen LRZ, Kaffe B, Deri E, Leibson C, Nissim-Rafinia M, Maman M, Harpaz N, Ron G, Shema E, Meshorer E. PRC2-independent actions of H3.3K27M in embryonic stem cell differentiation. Nucleic Acids Res 2023; 51:1662-1673. [PMID: 36156096 PMCID: PMC9976889 DOI: 10.1093/nar/gkac800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/28/2022] [Accepted: 09/06/2022] [Indexed: 01/11/2023] Open
Abstract
The histone H3 variant, H3.3, is localized at specific regions in the genome, especially promoters and active enhancers, and has been shown to play important roles in development. A lysine to methionine substitution in position 27 (H3.3K27M) is a main cause of Diffuse Intrinsic Pontine Glioma (specifically Diffuse Midline Glioma, K27M-mutant), a lethal type of pediatric cancer. H3.3K27M has a dominant-negative effect by inhibiting the Polycomb Repressor Complex 2 (PRC2) activity. Here, we studied the immediate, genome-wide, consequences of the H3.3K27M mutation independent of PRC2 activity. We developed Doxycycline (Dox)-inducible mouse embryonic stem cells (ESCs) carrying a single extra copy of WT-H3.3, H3.3K27M and H3.3K27L, all fused to HA. We performed RNA-Seq and ChIP-Seq at different times following Dox induction in undifferentiated and differentiated ESCs. We find increased binding of H3.3 around transcription start sites in cells expressing both H3.3K27M and H3.3K27L compared with WT, but not in cells treated with PRC2 inhibitors. Differentiated cells carrying either H3.3K27M or H3.3K27L retain expression of ESC-active genes, in expense of expression of genes related to neuronal differentiation. Taken together, our data suggest that a modifiable H3.3K27 is required for proper histone incorporation and cellular maturation, independent of PRC2 activity.
Collapse
Affiliation(s)
- Lea R Z Cohen
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Binyamin Kaffe
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Eden Deri
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Chen Leibson
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Malka Nissim-Rafinia
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Moria Maman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nofar Harpaz
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Guy Ron
- The Racah Institute of Physics, The Center for Nanoscience and Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| | - Efrat Shema
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| |
Collapse
|
20
|
Li J, Chin CR, Ying HY, Meydan C, Teater MR, Xia M, Farinha P, Takata K, Chu CS, Rivas MA, Chadburn A, Steidl C, Scott DW, Roeder RG, Mason CE, Béguelin W, Melnick AM. Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B cell fate decisions and yields T cell-depleted lymphomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528351. [PMID: 36824887 PMCID: PMC9949106 DOI: 10.1101/2023.02.13.528351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Mutations affecting enhancer chromatin regulators CREBBP and KMT2D are highly co-occurrent in germinal center (GC)-derived lymphomas and other tumors, even though regulating similar pathways. Herein, we report that combined haploinsufficiency of Crebbp and Kmt2d (C+K) indeed accelerated lymphomagenesis. C+K haploinsufficiency induced GC hyperplasia by altering cell fate decisions, skewing B cells away from memory and plasma cell differentiation. C+K deficiency particularly impaired enhancer activation for immune synapse genes involved in exiting the GC reaction. This effect was especially severe at super-enhancers for immunoregulatory and differentiation genes. Mechanistically, CREBBP and KMT2D formed a complex, were highly co-localized on chromatin, and were required for each-other's stable recruitment to enhancers. Notably, C+K lymphomas in mice and humans manifested significantly reduced CD8 + T-cell abundance. Hence, deficiency of C+K cooperatively induced an immune evasive phenotype due at least in part to failure to activate key immune synapse super-enhancers, associated with altered immune cell fate decisions. SIGNIFICANCE Although CREBBP and KMT2D have similar enhancer regulatory functions, they are paradoxically co-mutated in lymphomas. We show that their combined loss causes specific disruption of super-enhancers driving immune synapse genes. Importantly, this leads to reduction of CD8 cells in lymphomas, linking super-enhancer function to immune surveillance, with implications for immunotherapy resistance.
Collapse
|
21
|
Godfrey LC, Rodriguez-Meira A. Viewing AML through a New Lens: Technological Advances in the Study of Epigenetic Regulation. Cancers (Basel) 2022; 14:cancers14235989. [PMID: 36497471 PMCID: PMC9740143 DOI: 10.3390/cancers14235989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Epigenetic modifications, such as histone modifications and DNA methylation, are essential for ensuring the dynamic control of gene regulation in every cell type. These modifications are associated with gene activation or repression, depending on the genomic context and specific type of modification. In both cases, they are deposited and removed by epigenetic modifier proteins. In acute myeloid leukemia (AML), the function of these proteins is perturbed through genetic mutations (i.e., in the DNA methylation machinery) or translocations (i.e., MLL-rearrangements) arising during leukemogenesis. This can lead to an imbalance in the epigenomic landscape, which drives aberrant gene expression patterns. New technological advances, such as CRISPR editing, are now being used to precisely model genetic mutations and chromosomal translocations. In addition, high-precision epigenomic editing using dCas9 or CRISPR base editing are being used to investigate the function of epigenetic mechanisms in gene regulation. To interrogate these mechanisms at higher resolution, advances in single-cell techniques have begun to highlight the heterogeneity of epigenomic landscapes and how these impact on gene expression within different AML populations in individual cells. Combined, these technologies provide a new lens through which to study the role of epigenetic modifications in normal hematopoiesis and how the underlying mechanisms can be hijacked in the context of malignancies such as AML.
Collapse
Affiliation(s)
- Laura C. Godfrey
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02215, USA
- Correspondence: (L.C.G.); (A.R.-M.)
| | - Alba Rodriguez-Meira
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Haematology, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
- Correspondence: (L.C.G.); (A.R.-M.)
| |
Collapse
|
22
|
Paolicelli RC, Sierra A, Stevens B, Tremblay ME, Aguzzi A, Ajami B, Amit I, Audinat E, Bechmann I, Bennett M, Bennett F, Bessis A, Biber K, Bilbo S, Blurton-Jones M, Boddeke E, Brites D, Brône B, Brown GC, Butovsky O, Carson MJ, Castellano B, Colonna M, Cowley SA, Cunningham C, Davalos D, De Jager PL, de Strooper B, Denes A, Eggen BJL, Eyo U, Galea E, Garel S, Ginhoux F, Glass CK, Gokce O, Gomez-Nicola D, González B, Gordon S, Graeber MB, Greenhalgh AD, Gressens P, Greter M, Gutmann DH, Haass C, Heneka MT, Heppner FL, Hong S, Hume DA, Jung S, Kettenmann H, Kipnis J, Koyama R, Lemke G, Lynch M, Majewska A, Malcangio M, Malm T, Mancuso R, Masuda T, Matteoli M, McColl BW, Miron VE, Molofsky AV, Monje M, Mracsko E, Nadjar A, Neher JJ, Neniskyte U, Neumann H, Noda M, Peng B, Peri F, Perry VH, Popovich PG, Pridans C, Priller J, Prinz M, Ragozzino D, Ransohoff RM, Salter MW, Schaefer A, Schafer DP, Schwartz M, Simons M, Smith CJ, Streit WJ, Tay TL, Tsai LH, Verkhratsky A, von Bernhardi R, Wake H, Wittamer V, Wolf SA, Wu LJ, Wyss-Coray T. Microglia states and nomenclature: A field at its crossroads. Neuron 2022; 110:3458-3483. [PMID: 36327895 PMCID: PMC9999291 DOI: 10.1016/j.neuron.2022.10.020] [Citation(s) in RCA: 566] [Impact Index Per Article: 283.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/06/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
Microglial research has advanced considerably in recent decades yet has been constrained by a rolling series of dichotomies such as "resting versus activated" and "M1 versus M2." This dualistic classification of good or bad microglia is inconsistent with the wide repertoire of microglial states and functions in development, plasticity, aging, and diseases that were elucidated in recent years. New designations continuously arising in an attempt to describe the different microglial states, notably defined using transcriptomics and proteomics, may easily lead to a misleading, although unintentional, coupling of categories and functions. To address these issues, we assembled a group of multidisciplinary experts to discuss our current understanding of microglial states as a dynamic concept and the importance of addressing microglial function. Here, we provide a conceptual framework and recommendations on the use of microglial nomenclature for researchers, reviewers, and editors, which will serve as the foundations for a future white paper.
Collapse
Affiliation(s)
- Rosa C Paolicelli
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
| | - Amanda Sierra
- Achucarro Basque Center for Neuroscience, Glial Cell Biology Lab, Leioa, Spain; Department of Neuroscience, University of the Basque Country EHU/UPV, Leioa, Spain; Ikerbasque Foundation, Bilbao, Spain.
| | - Beth Stevens
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, (HHMI), MD, USA; Boston Children's Hospital, Boston, MA, USA.
| | - Marie-Eve Tremblay
- Centre de recherche du CHU de Québec-Université Laval, Québec City, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada; Division of Medical Sciences, University of Victoria, Victoria, BC, Canada; Center for Advanced Materials and Related Technology (CAMTEC), University of Victoria, Victoria, BC, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Bahareh Ajami
- Department of Molecular Microbiology & Immunology, Department of Behavioral and Systems Neuroscience, Oregon Health & Science University School of Medicine, Portland, OR, USA
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Etienne Audinat
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Ingo Bechmann
- Institute of Anatomy, University of Leipzig, Leipzig, Germany
| | - Mariko Bennett
- Children's Hospital of Philadelphia, Department of Psychiatry, Department of Pediatrics, Division of Child Neurology, Philadelphia, PA, USA
| | - Frederick Bennett
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Alain Bessis
- École Normale Supérieure, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Paris Sciences et Lettres Research University, Paris, France
| | - Knut Biber
- Neuroscience Discovery, AbbVie Deutschland GmbH, Ludwigshafen, Germany
| | - Staci Bilbo
- Departments of Psychology & Neuroscience, Neurobiology, and Cell Biology, Duke University, Durham, NC, USA
| | - Mathew Blurton-Jones
- Center for the Neurobiology of Learning and Memory, UCI MIND, University of California, Irvine, CA, USA
| | - Erik Boddeke
- Department Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center, Groningen, the Netherlands
| | - Dora Brites
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Bert Brône
- BIOMED Research Institute, University of Hasselt, Hasselt, Belgium
| | - Guy C Brown
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Oleg Butovsky
- Ann Romney Center for Neurologic Diseases, Department Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Monica J Carson
- Center for Glial-Neuronal Interactions, Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Bernardo Castellano
- Unidad de Histología Medica, Depto. Biología Celular, Fisiología e Inmunología, Barcelona, Spain; Instituto de Neurociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Sally A Cowley
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Colm Cunningham
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College, Dublin, Republic of Ireland; Trinity College Institute of Neuroscience, Trinity College, Dublin, Republic of Ireland
| | - Dimitrios Davalos
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Bart de Strooper
- UK Dementia Research Institute at University College London, London, UK; Vlaams Instituut voor Biotechnologie at Katholieke Universiteit Leuven, Leuven, Belgium
| | - Adam Denes
- "Momentum" Laboratory of Neuroimmunology, Institute of Experimental Medicine, Budapest, Hungary
| | - Bart J L Eggen
- Department of Biomedical Sciences of Cells & Systems, section Molecular Neurobiology, University of Groningen, Groningen, the Netherlands; University Medical Center Groningen, Groningen, the Netherlands
| | - Ukpong Eyo
- Department of Neuroscience, Center for Brain Immunology and Glia, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Elena Galea
- Institut de Neurociències and Departament de Bioquímica, Unitat de Bioquímica, Universitat Autònoma de Barcelona, Barcelona, Spain; ICREA, Barcelona, Spain
| | - Sonia Garel
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Paris, France; College de France, Paris, France
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore, Singapore
| | | | - Ozgun Gokce
- Institute for Stroke and Dementia Research, Ludwig Maximillian's University of Munich, Munich, Germany
| | - Diego Gomez-Nicola
- School of Biological Sciences, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Berta González
- Unidad de Histología Medica, Depto. Biología Celular, Fisiología e Inmunología and Instituto de Neurociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Siamon Gordon
- Chang Gung University, Taoyuan City, Taiwan (ROC); Sir William Dunn School of Pathology, Oxford, UK
| | - Manuel B Graeber
- Ken Parker Brain Tumour Research Laboratories, Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Andrew D Greenhalgh
- Lydia Becker Institute of Immunology and Inflammation, Geoffrey Jefferson Brain Research Centre, Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Pierre Gressens
- Université Paris Cité, Inserm, NeuroDiderot, 75019 Paris, France
| | - Melanie Greter
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - David H Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Christian Haass
- Division of Metabolic Biochemistry, Faculty of Medicine, Biomedical Center (BMC), Ludwig-Maximilians-Universität Munchen, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Munich Cluster for Systems Neurology (SyNergy); Munich, Germany
| | - Michael T Heneka
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Frank L Heppner
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Soyon Hong
- UK Dementia Research Institute at University College London, London, UK
| | - David A Hume
- Mater Research Institute-University of Queensland, Brisbane, QLD, Australia
| | - Steffen Jung
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Helmut Kettenmann
- Max-Delbrück Center for Molecular Medicine, Berlin, Germany; Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jonathan Kipnis
- Center for Brain Immunology and Glia (BIG), Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Ryuta Koyama
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Greg Lemke
- MNL-L, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Marina Lynch
- Trinity College Institute of Neuroscience, Trinity College, Dublin, Republic of Ireland
| | - Ania Majewska
- Department of Neuroscience, University of Rochester, Rochester, NY, USA
| | - Marzia Malcangio
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Tarja Malm
- University of Eastern Finland, Kuopio, Finland
| | - Renzo Mancuso
- Microglia and Inflammation in Neurological Disorders (MIND) Lab, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Takahiro Masuda
- Department of Molecular and System Pharmacology, Graduate School of Pharmaceutical Sciences, Kyushu University, Japan
| | - Michela Matteoli
- Humanitas University, Department of Biomedical Sciences, Milan, Italy
| | - Barry W McColl
- UK Dementia Research Institute, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, UK
| | - Veronique E Miron
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute, Edinburgh BioQuarter, Edinburgh, UK; UK Dementia Research Institute at the University of Edinburgh, Edinburgh BioQuarter, Edinburgh, UK
| | | | - Michelle Monje
- Howard Hughes Medical Institute, (HHMI), MD, USA; Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Agnes Nadjar
- Neurocentre Magendie, University of Bordeaux, Bordeaux, France; Institut Universitaire de France (IUF), Paris, France
| | - Jonas J Neher
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany; Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Urte Neniskyte
- VU LSC-EMBL Partnership for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania; Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Harald Neumann
- Institute of Reconstructive Neurobiology, Medical Faculty and University Hospital of Bonn, University of Bonn, Bonn, Germany
| | - Mami Noda
- Laboratory of Pathophysiology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan; Institute of Mitochondrial Biology and Medicine of Xi'an Jiaotong University School of Life Science and Technology, Xi'an, China
| | - Bo Peng
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Francesca Peri
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - V Hugh Perry
- UK Dementia Research Institute, University College London, London, UK; School of Biological Sciences, University of Southampton, Southampton, UK
| | - Phillip G Popovich
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Clare Pridans
- University of Edinburgh, Centre for Inflammation Research, Edinburgh, UK
| | - Josef Priller
- Department of Psychiatry & Psychotherapy, School of Medicine, Technical University of Munich, Munich, Germany; Charité - Universitätsmedizin Berlin and DZNE, Berlin, Germany; University of Edinburgh and UK DRI, Edinburgh, UK
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Davide Ragozzino
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy; Santa Lucia Foundation (IRCCS Fondazione Santa Lucia), Rome, Italy
| | | | - Michael W Salter
- Hospital for Sick Children, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - Anne Schaefer
- Nash Family Department of Neuroscience, Center for Glial Biology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Max Planck Institute for Biology of Ageing, Koeln, Germany
| | - Dorothy P Schafer
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Michal Schwartz
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Mikael Simons
- Institute of Neuronal Cell Biology, Technical University Munich, German Center for Neurodegenerative Diseases, Munich, Germany
| | - Cody J Smith
- Galvin Life Science Center, University of Notre Dame, Indianapolis, IN, USA
| | - Wolfgang J Streit
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | - Tuan Leng Tay
- Faculty of Biology, University of Freiburg, Freiburg, Germany; BrainLinks-BrainTools Centre, University of Freiburg, Freiburg, Germany; Freiburg Institute of Advanced Studies, University of Freiburg, Freiburg, Germany; Department of Biology, Boston University, Boston, MA, USA; Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA, USA
| | - Li-Huei Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexei Verkhratsky
- Achucarro Basque Center for Neuroscience, Glial Cell Biology Lab, Leioa, Spain; Department of Neuroscience, University of the Basque Country EHU/UPV, Leioa, Spain; Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | | | - Hiroaki Wake
- Department of Anatomy and Molecular Cell Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Valérie Wittamer
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium; ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Susanne A Wolf
- Charité Universitätsmedizin, Experimental Ophthalmology and Neuroimmunology, Berlin, Germany
| | - Long-Jun Wu
- Department of Neurology and Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| |
Collapse
|
23
|
Amatullah H, Fraschilla I, Digumarthi S, Huang J, Adiliaghdam F, Bonilla G, Wong LP, Rivard ME, Beauchamp C, Mercier V, Goyette P, Sadreyev RI, Anthony RM, Rioux JD, Jeffrey KL. Epigenetic reader SP140 loss of function drives Crohn's disease due to uncontrolled macrophage topoisomerases. Cell 2022; 185:3232-3247.e18. [PMID: 35952671 PMCID: PMC9442451 DOI: 10.1016/j.cell.2022.06.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 03/07/2022] [Accepted: 06/27/2022] [Indexed: 01/19/2023]
Abstract
How mis-regulated chromatin directly impacts human immune disorders is poorly understood. Speckled Protein 140 (SP140) is an immune-restricted PHD and bromodomain-containing epigenetic "reader," and SP140 loss-of-function mutations associate with Crohn's disease (CD), multiple sclerosis (MS), and chronic lymphocytic leukemia (CLL). However, the relevance of these mutations and mechanisms underlying SP140-driven pathogenicity remains unexplored. Using a global proteomic strategy, we identified SP140 as a repressor of topoisomerases (TOPs) that maintains heterochromatin and macrophage fate. In humans and mice, SP140 loss resulted in unleashed TOP activity, de-repression of developmentally silenced genes, and ultimately defective microbe-inducible macrophage transcriptional programs and bacterial killing that drive intestinal pathology. Pharmacological inhibition of TOP1/2 rescued these defects. Furthermore, exacerbated colitis was restored with TOP1/2 inhibitors in Sp140-/- mice, but not wild-type mice, in vivo. Collectively, we identify SP140 as a TOP repressor and reveal repurposing of TOP inhibition to reverse immune diseases driven by SP140 loss.
Collapse
Affiliation(s)
- Hajera Amatullah
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Isabella Fraschilla
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Sreehaas Digumarthi
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA
| | - Julie Huang
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA
| | - Fatemeh Adiliaghdam
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Gracia Bonilla
- Department of Molecular Biology, Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lai Ping Wong
- Department of Molecular Biology, Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | | | | | | | | | - Ruslan I Sadreyev
- Department of Molecular Biology, Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Robert M Anthony
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - John D Rioux
- Montreal Heart Institute, Montreal, QC H1T 1C8, Canada
| | - Kate L Jeffrey
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
24
|
Kumar B, Navarro C, Winblad N, Schell JP, Zhao C, Weltner J, Baqué-Vidal L, Salazar Mantero A, Petropoulos S, Lanner F, Elsässer SJ. Polycomb repressive complex 2 shields naïve human pluripotent cells from trophectoderm differentiation. Nat Cell Biol 2022; 24:845-857. [PMID: 35637409 PMCID: PMC9203276 DOI: 10.1038/s41556-022-00916-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 04/13/2022] [Indexed: 12/12/2022]
Abstract
The first lineage choice in human embryo development separates trophectoderm from the inner cell mass. Naïve human embryonic stem cells are derived from the inner cell mass and offer possibilities to explore how lineage integrity is maintained. Here, we discover that polycomb repressive complex 2 (PRC2) maintains naïve pluripotency and restricts differentiation to trophectoderm and mesoderm lineages. Through quantitative epigenome profiling, we found that a broad gain of histone H3 lysine 27 trimethylation (H3K27me3) is a distinct feature of naïve pluripotency. We define shared and naïve-specific bivalent promoters featuring PRC2-mediated H3K27me3 concomitant with H3K4me3. Naïve bivalency maintains key trophectoderm and mesoderm transcription factors in a transcriptionally poised state. Inhibition of PRC2 forces naïve human embryonic stem cells into an 'activated' state, characterized by co-expression of pluripotency and lineage-specific transcription factors, followed by differentiation into either trophectoderm or mesoderm lineages. In summary, PRC2-mediated repression provides a highly adaptive mechanism to restrict lineage potential during early human development.
Collapse
Affiliation(s)
- Banushree Kumar
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Carmen Navarro
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Nerges Winblad
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - John P Schell
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Cheng Zhao
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Jere Weltner
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Laura Baqué-Vidal
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Angelo Salazar Mantero
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Sophie Petropoulos
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
- Département de Médecine, Université de Montréal, Montreal, Canada
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, Montreal, Canada
| | - Fredrik Lanner
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden.
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden.
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
25
|
Fraschilla I, Amatullah H, Jeffrey KL. One genome, many cell states: epigenetic control of innate immunity. Curr Opin Immunol 2022; 75:102173. [PMID: 35405493 PMCID: PMC9081230 DOI: 10.1016/j.coi.2022.102173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/23/2022] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
A hallmark of the innate immune system is its ability to rapidly initiate short-lived or sustained transcriptional programs in a cell-specific and pathogen-specific manner that is dependent on dynamic chromatin states. Much of the epigenetic landscape is set during cellular differentiation; however, pathogens and other environmental cues also induce changes in chromatin that can either promote tolerance or 'train' innate immune cells for amplified secondary responses. We review chromatin processes that enable innate immune cell differentiation and functional transcriptional responses in naive or experienced cells, in concert with signal transduction and cellular metabolic shifts. We discuss how immune chromatin mechanisms are maladapted in disease and novel therapeutic approaches for cellular reprogramming.
Collapse
Affiliation(s)
- Isabella Fraschilla
- Division of Gastroenterology and Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Hajera Amatullah
- Division of Gastroenterology and Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Kate L Jeffrey
- Division of Gastroenterology and Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
26
|
Marsolier J, Prompsy P, Durand A, Lyne AM, Landragin C, Trouchet A, Bento ST, Eisele A, Foulon S, Baudre L, Grosselin K, Bohec M, Baulande S, Dahmani A, Sourd L, Letouzé E, Salomon AV, Marangoni E, Perié L, Vallot C. H3K27me3 conditions chemotolerance in triple-negative breast cancer. Nat Genet 2022; 54:459-468. [PMID: 35410383 PMCID: PMC7612638 DOI: 10.1038/s41588-022-01047-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/04/2022] [Indexed: 12/11/2022]
Abstract
The persistence of cancer cells resistant to therapy remains a major clinical challenge. In triple-negative breast cancer, resistance to chemotherapy results in the highest recurrence risk among breast cancer subtypes. The drug-tolerant state seems largely defined by nongenetic features, but the underlying mechanisms are poorly understood. Here, by monitoring epigenomes, transcriptomes and lineages with single-cell resolution, we show that the repressive histone mark H3K27me3 (trimethylation of histone H3 at lysine 27) regulates cell fate at the onset of chemotherapy. We report that a persister expression program is primed with both H3K4me3 (trimethylation of histone H3 at lysine 4) and H3K27me3 in unchallenged cells, with H3K27me3 being the lock to its transcriptional activation. We further demonstrate that depleting H3K27me3 enhances the potential of cancer cells to tolerate chemotherapy. Conversely, preventing H3K27me3 demethylation simultaneously to chemotherapy inhibits the transition to a drug-tolerant state, and delays tumor recurrence in vivo. Our results highlight how chromatin landscapes shape the potential of cancer cells to respond to initial therapy.
Collapse
Affiliation(s)
- Justine Marsolier
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Pacôme Prompsy
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Adeline Durand
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Anne-Marie Lyne
- CNRS UMR168, Institut Curie, PSL University, Sorbonne University, Paris, France
| | - Camille Landragin
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Amandine Trouchet
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Single Cell Initiative, Institut Curie, PSL University, Paris, France
| | | | - Almut Eisele
- CNRS UMR168, Institut Curie, PSL University, Sorbonne University, Paris, France
| | - Sophie Foulon
- CNRS UMR8231, ESPCI Paris, PSL University, Paris, France
| | - Léa Baudre
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Kevin Grosselin
- CNRS UMR8231, ESPCI Paris, PSL University, Paris, France,HiFiBio SAS, Paris, France,Current Affiliation: Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Mylène Bohec
- Single Cell Initiative, Institut Curie, PSL University, Paris, France,Genomics of Excellence (ICGex) Platform, Institut Curie, PSL University, Paris, France
| | - Sylvain Baulande
- Single Cell Initiative, Institut Curie, PSL University, Paris, France,Genomics of Excellence (ICGex) Platform, Institut Curie, PSL University, Paris, France
| | - Ahmed Dahmani
- Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Laura Sourd
- Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Eric Letouzé
- Functional Genomics of Solid Tumors laboratory, Centre de Recherche des Cordeliers, Sorbonne University, Inserm, USPC, Paris Descartes University, Paris Diderot University, Paris, France
| | - Anne-Vincent Salomon
- Pathology-Genetics-Immunology Department, Institut Curie, PSL Research University, Paris, France,INSERM U934, Institut Curie, PSL Research University, Paris, France
| | - Elisabetta Marangoni
- Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Leïla Perié
- CNRS UMR168, Institut Curie, PSL University, Sorbonne University, Paris, France
| | - Céline Vallot
- CNRS UMR3244, Institut Curie, PSL University, Paris, France. .,Translational Research Department, Institut Curie, PSL University, Paris, France.
| |
Collapse
|
27
|
Mines RC, Lipniacki T, Shen X. Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts. PLoS Comput Biol 2022; 18:e1009811. [PMID: 35143483 PMCID: PMC8865691 DOI: 10.1371/journal.pcbi.1009811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 02/23/2022] [Accepted: 01/06/2022] [Indexed: 11/19/2022] Open
Abstract
Nucleosomes are recognized as key regulators of transcription. However, the relationship between slow nucleosome unwrapping dynamics and bulk transcriptional properties has not been thoroughly explored. Here, an agent-based model that we call the dynamic defect Totally Asymmetric Simple Exclusion Process (ddTASEP) was constructed to investigate the effects of nucleosome-induced pausing on transcriptional dynamics. Pausing due to slow nucleosome dynamics induced RNAPII convoy formation, which would cooperatively prevent nucleosome rebinding leading to bursts of transcription. The mean first passage time (MFPT) and the variance of first passage time (VFPT) were analytically expressed in terms of the nucleosome rate constants, allowing for the direct quantification of the effects of nucleosome-induced pausing on pioneering polymerase dynamics. The mean first passage elongation rate γ(hc, ho) is inversely proportional to the MFPT and can be considered to be a new axis of the ddTASEP phase diagram, orthogonal to the classical αβ-plane (where α and β are the initiation and termination rates). Subsequently, we showed that, for β = 1, there is a novel jamming transition in the αγ-plane that separates the ddTASEP dynamics into initiation-limited and nucleosome pausing-limited regions. We propose analytical estimates for the RNAPII density ρ, average elongation rate v, and transcription flux J and verified them numerically. We demonstrate that the intra-burst RNAPII waiting times tin follow the time-headway distribution of a max flux TASEP and that the average inter-burst interval tIBI¯ correlates with the index of dispersion De. In the limit γ→0, the average burst size reaches a maximum set by the closing rate hc. When α≪1, the burst sizes are geometrically distributed, allowing large bursts even while the average burst size NB¯ is small. Last, preliminary results on the relative effects of static and dynamic defects are presented to show that dynamic defects can induce equal or greater pausing than static bottle necks. To perform specific functions, cells must express specific genes by copying the information in DNA into RNA via transcription. Structural proteins called nucleosomes are spaced every 200 base pairs along the length of a strand of DNA and play a crucial function in the regulation of gene activity by tightly binding DNA strands and condensing them into heterochromatin, preventing transcription by RNA polymerase II (RNAPII). Even on active genes where nucleosomes are loosely attached to DNA strands, the wrapping and unwrapping of nucleosomes pause transcription as RNAPII passes by. Previous mathematical models of transcription have compared this biological process to traffic on a one lane highway without obstructions. In contrast, our proposed model simulates transcription like traffic in a grid system where nucleosomes can be thought of as pedestrians or other vehicles crossing the road at regularly spaced intersections. Just as side street traffic and pedestrian crossings can cause cars to form convoys and cause jams limiting the max speed in an area, nucleosomes can cause RNAPII to form convoys that lead to bursts of mRNA production and limit the average polymerase flux through the gene.
Collapse
Affiliation(s)
- Robert C. Mines
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Tomasz Lipniacki
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
- * E-mail: (TL); (XS)
| | - Xiling Shen
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
- Woo Center for Big Data and Precision Health, Duke University, Durham, North Carolina, United States of America
- * E-mail: (TL); (XS)
| |
Collapse
|
28
|
Kadur Lakshminarasimha Murthy P, Xi R, Arguijo D, Everitt JI, Kocak DD, Kobayashi Y, Bozec A, Vicent S, Ding S, Crawford GE, Hsu D, Tata PR, Reddy T, Shen X. Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity. Dev Cell 2022; 57:310-328.e9. [PMID: 35134344 PMCID: PMC8938988 DOI: 10.1016/j.devcel.2022.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 09/15/2021] [Accepted: 01/06/2022] [Indexed: 12/13/2022]
Abstract
Oncogenic Kras induces a hyper-proliferative state that permits cells to progress to neoplasms in diverse epithelial tissues. Depending on the cell of origin, this also involves lineage transformation. Although a multitude of downstream factors have been implicated in these processes, the precise chronology of molecular events controlling them remains elusive. Using mouse models, primary human tissues, and cell lines, we show that, in Kras-mutant alveolar type II cells (AEC2), FOSL1-based AP-1 factor guides the mSWI/SNF complex to increase chromatin accessibility at genomic loci controlling the expression of genes necessary for neoplastic transformation. We identified two orthogonal processes in Kras-mutant distal airway club cells. The first promoted their transdifferentiation into an AEC2-like state through NKX2.1, and the second controlled oncogenic transformation through the AP-1 complex. Our results suggest that neoplasms retain an epigenetic memory of their cell of origin through cell-type-specific transcription factors. Our analysis showed that a cross-tissue-conserved AP-1-dependent chromatin remodeling program regulates carcinogenesis.
Collapse
Affiliation(s)
- Preetish Kadur Lakshminarasimha Murthy
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14853, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA. :
| | - Rui Xi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Diana Arguijo
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Jeffrey I Everitt
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Dewran D Kocak
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Yoshihiko Kobayashi
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Aline Bozec
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Internal Medicine 3 - Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Silvestre Vicent
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain; University of Navarra, Department of Pathology, Anatomy and Physiology, Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Shengli Ding
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Gregory E Crawford
- Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27710, USA
| | - David Hsu
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Timothy Reddy
- Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA.
| |
Collapse
|
29
|
Fishman H, Madiwale S, Geron I, Bari V, Van Loocke W, Kirschenbaum Y, Ganmore I, Kugler E, Rein-Gil A, Friedlander G, Schiby G, Birger Y, Strehl S, Soulier J, Knoechel B, Ferrando A, Noy-Lotan S, Nagler A, Mulloy JC, Van Vlierberghe P, Izraeli S. ETV6-NCOA2 fusion induces T/myeloid mixed-phenotype leukemia through transformation of nonthymic hematopoietic progenitor cells. Blood 2022; 139:399-412. [PMID: 34624096 PMCID: PMC9906988 DOI: 10.1182/blood.2020010405] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 09/26/2021] [Indexed: 01/05/2023] Open
Abstract
Mixed-phenotype acute leukemia is a rare subtype of leukemia in which both myeloid and lymphoid markers are co-expressed on the same malignant cells. The pathogenesis is largely unknown, and the treatment is challenging. We previously reported the specific association of the recurrent t(8;12)(q13;p13) chromosomal translocation that creates the ETV6-NCOA2 fusion with T/myeloid leukemias. Here we report that ETV6-NCOA2 initiates T/myeloid leukemia in preclinical models; ectopic expression of ETV6-NCOA2 in mouse bone marrow hematopoietic progenitors induced T/myeloid lymphoma accompanied by spontaneous Notch1-activating mutations. Similarly, cotransduction of human cord blood CD34+ progenitors with ETV6-NCOA2 and a nontransforming NOTCH1 mutant induced T/myeloid leukemia in immunodeficient mice; the immunophenotype and gene expression pattern were similar to those of patient-derived ETV6-NCOA2 leukemias. Mechanistically, we show that ETV6-NCOA2 forms a transcriptional complex with ETV6 and the histone acetyltransferase p300, leading to derepression of ETV6 target genes. The expression of ETV6-NCOA2 in human and mouse nonthymic hematopoietic progenitor cells induces transcriptional dysregulation, which activates a lymphoid program while failing to repress the expression of myeloid genes such as CSF1 and MEF2C. The ETV6-NCOA2 induced arrest at an early immature T-cell developmental stage. The additional acquisition of activating NOTCH1 mutations transforms the early immature ETV6-NCOA2 cells into T/myeloid leukemias. Here, we describe the first preclinical model to depict the initiation of T/myeloid leukemia by a specific somatic genetic aberration.
Collapse
Affiliation(s)
- Hila Fishman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Shreyas Madiwale
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Ifat Geron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Vase Bari
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital, Cincinnati, OH
| | - Wouter Van Loocke
- Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - Yael Kirschenbaum
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Cancer Research Center, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - Itamar Ganmore
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Cancer Research Center, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - Eitan Kugler
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Avigail Rein-Gil
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Gilgi Friedlander
- The Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Ginette Schiby
- Institute for Pathology Laboratory, Hematology Institute, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - Yehudit Birger
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Sabine Strehl
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Jean Soulier
- Genomes and Cell Biology of Disease, Hôpital Saint-Louis, Paris, France
| | - Birgit Knoechel
- Dana-Farber Cancer Institute, Boston Children's Hospital, Boston, MA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Sharon Noy-Lotan
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Arnon Nagler
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Hematology Division Bone Marrow Transplants and Cord-Blood Bank, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - James C. Mulloy
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital, Cincinnati, OH
| | | | - Shai Izraeli
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
- Department of System Biology, City of Hope, Duarte, CA
| |
Collapse
|
30
|
Brind'Amour J, Lorincz MC. Profiling Histone Methylation in Low Numbers of Cells. Methods Mol Biol 2022; 2529:229-251. [PMID: 35733018 DOI: 10.1007/978-1-0716-2481-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Chromatin immunoprecipitation (ChIP) enables the study of DNA-protein interactions. When coupled with high-throughput sequencing (ChIP-seq), this method allows the generation of genome-wide profiles of the distribution of specific proteins in a given cellular context. Typical ChIP-seq experiments require millions of cells as input material and thus are not ideal to study many in vivo cell populations. Here, we describe an ultra-low-input native ChIP-seq method, ULI-NChIP-seq, to profile histone modification patterns in as low as 150 cells.
Collapse
Affiliation(s)
- Julie Brind'Amour
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Département de Biomédecine Vétérinaire, Université de Montréal, Montréal, QC, Canada
| | - Matthew C Lorincz
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
31
|
Bartlett DA, Dileep V, Handa T, Ohkawa Y, Kimura H, Henikoff S, Gilbert DM. High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq). J Cell Biol 2021; 220:e202103078. [PMID: 34783858 PMCID: PMC8600797 DOI: 10.1083/jcb.202103078] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 09/15/2021] [Accepted: 10/27/2021] [Indexed: 12/16/2022] Open
Abstract
Chromatin profiling in single cells has been extremely challenging and almost exclusively limited to histone proteins. In cases where single-cell methods have shown promise, many require highly specialized equipment or cell type-specific protocols and are relatively low throughput. Here, we combine the advantages of tagmentation, linear amplification, and combinatorial indexing to produce a high-throughput single-cell DNA binding site mapping method that is simple, inexpensive, and capable of multiplexing several independent samples per experiment. Targeted insertion of promoters sequencing (TIP-seq) uses Tn5 fused to proteinA to insert a T7 RNA polymerase promoter adjacent to a chromatin protein of interest. Linear amplification of flanking DNA with T7 polymerase before sequencing library preparation provides ∼10-fold higher unique reads per single cell compared with other methods. We applied TIP-seq to map histone modifications, RNA polymerase II (RNAPII), and transcription factor CTCF binding sites in single human and mouse cells.
Collapse
Affiliation(s)
- Daniel A. Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL
- San Diego Biomedical Research Institute, La Jolla, CA
| | - Vishnu Dileep
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Tetsuya Handa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Steven Henikoff
- Basic Sciences Division and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - David M. Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL
- San Diego Biomedical Research Institute, La Jolla, CA
| |
Collapse
|
32
|
Zhao L, Xing P, Polavarapu VK, Zhao M, Valero-Martínez B, Dang Y, Maturi N, Mathot L, Neves I, Yildirim I, Swartling FJ, Sjöblom T, Uhrbom L, Chen X. FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers. Nucleic Acids Res 2021; 49:e125. [PMID: 34534335 PMCID: PMC8643707 DOI: 10.1093/nar/gkab813] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/16/2021] [Accepted: 09/06/2021] [Indexed: 01/05/2023] Open
Abstract
The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. The required input for current genome-wide histone modification profiling studies from FFPE samples is either 10-20 tissue sections or whole tissue blocks, which prevents better resolved analyses. But it is desirable to consume a minimal amount of FFPE tissue sections in the analysis as clinical tissues of interest are limited. Here, we present FFPE tissue with antibody-guided chromatin tagmentation with sequencing (FACT-seq), the first highly sensitive method to efficiently profile histone modifications in FFPE tissues by combining a novel fusion protein of hyperactive Tn5 transposase and protein A (T7-pA-Tn5) transposition and T7 in vitro transcription. FACT-seq generates high-quality chromatin profiles from different histone modifications with low number of FFPE nuclei. We proved a very small piece of FFPE tissue section containing ∼4000 nuclei is sufficient to decode H3K27ac modifications with FACT-seq. H3K27ac FACT-seq revealed disease-specific super enhancers in the archived FFPE human colorectal and human glioblastoma cancer tissue. In summary, FACT-seq allows decoding the histone modifications in archival FFPE tissues with high sensitivity and help researchers to better understand epigenetic regulation in cancer and human disease.
Collapse
Affiliation(s)
- Linxuan Zhao
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
| | - Pengwei Xing
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
| | | | - Miao Zhao
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
| | - Blanca Valero-Martínez
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
| | - Yonglong Dang
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
| | - Nagaprathyusha Maturi
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Rudbeck Laboratory, SE-75185 Uppsala, Sweden
| | - Lucy Mathot
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
| | - Inês Neves
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Rudbeck Laboratory, SE-75185 Uppsala, Sweden
| | - Irem Yildirim
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Rudbeck Laboratory, SE-75185 Uppsala, Sweden
| | | | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
| | - Lene Uhrbom
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Rudbeck Laboratory, SE-75185 Uppsala, Sweden
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
- Beijer Laboratories, Uppsala University, Uppsala, Sweden
| |
Collapse
|
33
|
Larsen SB, Cowley CJ, Sajjath SM, Barrows D, Yang Y, Carroll TS, Fuchs E. Establishment, maintenance, and recall of inflammatory memory. Cell Stem Cell 2021; 28:1758-1774.e8. [PMID: 34320411 PMCID: PMC8500942 DOI: 10.1016/j.stem.2021.07.001] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/21/2021] [Accepted: 07/01/2021] [Indexed: 01/12/2023]
Abstract
Known for nearly a century but through mechanisms that remain elusive, cells retain a memory of inflammation that equips them to react quickly and broadly to diverse secondary stimuli. Using murine epidermal stem cells as a model, we elucidate how cells establish, maintain, and recall inflammatory memory. Specifically, we landscape and functionally interrogate temporal, dynamic changes to chromatin accessibility, histone modifications, and transcription factor binding that occur during inflammation, post-resolution, and in memory recall following injury. We unearth an essential, unifying role for the general stress-responsive transcription factor FOS, which partners with JUN and cooperates with stimulus-specific STAT3 to establish memory; JUN then remains with other homeostatic factors on memory domains, facilitating rapid FOS re-recruitment and gene re-activation upon diverse secondary challenges. Extending our findings, we offer a comprehensive, potentially universal mechanism behind inflammatory memory and less discriminate recall phenomena with profound implications for tissue fitness in health and disease.
Collapse
Affiliation(s)
- Samantha B. Larsen
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA,New York University School of Medicine, Neuroscience Institute, New York, NY 10016, USA
| | - Christopher J. Cowley
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Sairaj M. Sajjath
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Douglas Barrows
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Yihao Yang
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Thomas S. Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Elaine Fuchs
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA,Lead Contact to whom correspondence should be addressed during the review process:
| |
Collapse
|
34
|
Wang L, Wang E, Prado Balcazar J, Wu Z, Xiang K, Wang Y, Huang Q, Negrete M, Chen K, Li W, Fu Y, Dohlman A, Mines R, Zhang L, Kobayashi Y, Chen T, Shi G, Shen JP, Kopetz S, Tata PR, Moreno V, Gersbach C, Crawford G, Hsu D, Huang E, Bu P, Shen X. Chromatin Remodeling of Colorectal Cancer Liver Metastasis is Mediated by an HGF-PU.1-DPP4 Axis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2004673. [PMID: 34378358 PMCID: PMC8498885 DOI: 10.1002/advs.202004673] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 06/09/2021] [Indexed: 06/13/2023]
Abstract
Colorectal cancer (CRC) metastasizes mainly to the liver, which accounts for the majority of CRC-related deaths. Here it is shown that metastatic cells undergo specific chromatin remodeling in the liver. Hepatic growth factor (HGF) induces phosphorylation of PU.1, a pioneer factor, which in turn binds and opens chromatin regions of downstream effector genes. PU.1 increases histone acetylation at the DPP4 locus. Precise epigenetic silencing by CRISPR/dCas9KRAB or CRISPR/dCas9HDAC revealed that individual PU.1-remodeled regulatory elements collectively modulate DPP4 expression and liver metastasis growth. Genetic silencing or pharmacological inhibition of each factor along this chromatin remodeling axis strongly suppressed liver metastasis. Therefore, microenvironment-induced epimutation is an important mechanism for metastatic tumor cells to grow in their new niche. This study presents a potential strategy to target chromatin remodeling in metastatic cancer and the promise of repurposing drugs to treat metastasis.
Collapse
Affiliation(s)
- Lihua Wang
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Ergang Wang
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | | | - Zhenzhen Wu
- Key Laboratory of RNA BiologyKey Laboratory of Protein and Peptide PharmaceuticalInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Kun Xiang
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Yi Wang
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Qiang Huang
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Marcos Negrete
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Kai‐Yuan Chen
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Wei Li
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Yujie Fu
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Anders Dohlman
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Robert Mines
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Liwen Zhang
- Key Laboratory of RNA BiologyKey Laboratory of Protein and Peptide PharmaceuticalInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yoshihiko Kobayashi
- Department of Cell BiologyRegeneration NextDuke University School of MedicineDurhamNC27710USA
| | - Tianyi Chen
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Guizhi Shi
- Laboratory Animal Research CenterInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
| | - John Paul Shen
- Department of Gastrointestinal Medical OncologyMD AndersonDurhamNC77030USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical OncologyMD AndersonDurhamNC77030USA
| | - Purushothama Rao Tata
- Department of Cell BiologyRegeneration NextDuke University School of MedicineDurhamNC27710USA
| | - Victor Moreno
- Department of Clinical SciencesUniversity of BarcelonaBarcelona08193Spain
- Prevention and Control ProgramCatalan Institute of Oncology‐IDIBELLCIBERESPBarcelonaE08907Spain
| | - Charles Gersbach
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Gregory Crawford
- Department of PediatricsDuke University School of MedicineDurhamNC27710USA
| | - David Hsu
- Department of MedicineDuke University School of MedicineDurhamNC27710USA
| | - Emina Huang
- Department of Cancer Biology and Colorectal SurgeryLerner Research Institute, Cleveland ClinicClevelandOH44195USA
| | - Pengcheng Bu
- Key Laboratory of RNA BiologyKey Laboratory of Protein and Peptide PharmaceuticalInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
- Center for Excellence in BiomacromoleculesChinese Academy of SciencesBeijing100101China
| | - Xiling Shen
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| |
Collapse
|
35
|
Harada A, Kimura H, Ohkawa Y. Recent advance in single-cell epigenomics. Curr Opin Struct Biol 2021; 71:116-122. [PMID: 34303078 DOI: 10.1016/j.sbi.2021.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/13/2021] [Accepted: 06/13/2021] [Indexed: 12/13/2022]
Abstract
The analysis of gene expression regulation, or the epigenome analysis, at the single-cell level is at the forefront of genomics research. To elucidate the mechanisms that regulate gene expression, chromatin immunoprecipitation has been conventionally used for determining the binding sites of DNA-binding proteins, such as histones and transcription factors. Now several new approaches have been emerged to reveal epigenome states at the single-cell level. Instead of using immunoprecipitation of fragmented chromatin, in situ reactions using cells or nuclei, combining with transposase tagging and other methods, have enabled single-cell analysis. Furthermore, single-cell multiomics techniques to simultaneously profiling transcriptome and open chromatin or histone modification have been developed. These single-cell analyses have the potential to identify different cell types in a cell population and reveal the dynamic changes of gene regulation, although those technologies have not yet reached a level for general application.
Collapse
Affiliation(s)
- Akihito Harada
- Division of Transcriptomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-0054, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-Ku, Yokohama, 226-8503, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-0054, Japan.
| |
Collapse
|
36
|
Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity. Nature 2021; 595:309-314. [PMID: 33953401 PMCID: PMC9166167 DOI: 10.1038/s41586-021-03520-4] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 04/07/2021] [Indexed: 02/03/2023]
Abstract
Epigenetic dysregulation is a defining feature of tumorigenesis that is implicated in immune escape1,2. Here, to identify factors that modulate the immune sensitivity of cancer cells, we performed in vivo CRISPR-Cas9 screens targeting 936 chromatin regulators in mouse tumour models treated with immune checkpoint blockade. We identified the H3K9 methyltransferase SETDB1 and other members of the HUSH and KAP1 complexes as mediators of immune escape3-5. We also found that amplification of SETDB1 (1q21.3) in human tumours is associated with immune exclusion and resistance to immune checkpoint blockade. SETDB1 represses broad domains, primarily within the open genome compartment. These domains are enriched for transposable elements (TEs) and immune clusters associated with segmental duplication events, a central mechanism of genome evolution6. SETDB1 loss derepresses latent TE-derived regulatory elements, immunostimulatory genes, and TE-encoded retroviral antigens in these regions, and triggers TE-specific cytotoxic T cell responses in vivo. Our study establishes SETDB1 as an epigenetic checkpoint that suppresses tumour-intrinsic immunogenicity, and thus represents a candidate target for immunotherapy.
Collapse
|
37
|
Patty BJ, Hainer SJ. Transcription factor chromatin profiling genome-wide using uliCUT&RUN in single cells and individual blastocysts. Nat Protoc 2021; 16:2633-2666. [PMID: 33911257 PMCID: PMC8177051 DOI: 10.1038/s41596-021-00516-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/04/2021] [Indexed: 02/02/2023]
Abstract
Determining chromatin-associated protein localization across the genome has provided insight into the functions of DNA-binding proteins and their connections to disease. However, established protocols requiring large quantities of cell or tissue samples currently limit applications for clinical and biomedical research in this field. Furthermore, most technologies have been optimized to assess abundant histone protein localization, prohibiting the investigation of nonhistone protein localization in low cell numbers. We recently described a protocol to profile chromatin-associated protein localization in as low as one cell: ultra-low-input cleavage under targets and release using nuclease (uliCUT&RUN). Optimized from chromatin immunocleavage and CUT&RUN, uliCUT&RUN is a tethered enzyme-based protocol that utilizes a combination of recombinant protein, antibody recognition and stringent purification to selectively target proteins of interest and isolate the associated DNA. Performed in native conditions, uliCUT&RUN profiles protein localization to chromatin with low input and high precision. Compared with other profiling technologies, uliCUT&RUN can determine nonhistone protein chromatin occupancies in low cell numbers, permitting the investigation into the molecular functions of a range of DNA-binding proteins within rare samples. From sample preparation to sequencing library submission, the uliCUT&RUN protocol takes <2 d to perform, with the accompanying data analysis timeline dependent on experience level.
Collapse
Affiliation(s)
- Benjamin J Patty
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
38
|
Dirks RAM, Thomas PC, Wu H, Jones RC, Stunnenberg HG, Marks H. A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation. Genome Res 2021; 31:919-933. [PMID: 33707229 PMCID: PMC8092002 DOI: 10.1101/gr.260745.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/22/2021] [Indexed: 11/24/2022]
Abstract
Epigenetic profiling by chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become a powerful tool for genome-wide identification of regulatory elements, for defining transcriptional regulatory networks, and for screening for biomarkers. However, the ChIP-seq protocol for low-input samples is laborious and time-consuming and suffers from experimental variation, resulting in poor reproducibility and low throughput. Although prototypic microfluidic ChIP-seq platforms have been developed, these are poorly transferable as they require sophisticated custom-made equipment and in-depth microfluidic and ChIP expertise, while lacking parallelization. To enable standardized, automated ChIP-seq profiling of low-input samples, we constructed microfluidic PDMS-based plates capable of performing 24 sensitive ChIP reactions within 30 min of hands-on time and 4.5 h of machine-running time. These disposable plates can be conveniently loaded into a widely available controller for pneumatics and thermocycling. In light of the plug and play (PnP) ChIP plates and workflow, we named our procedure PnP-ChIP-seq. We show high-quality ChIP-seq on hundreds to a few thousand of cells for all six post-translational histone modifications that are included in the International Human Epigenome Consortium set of reference epigenomes. PnP-ChIP-seq robustly detects epigenetic differences on promoters and enhancers between naive and more primed mouse embryonic stem cells (mESCs). Furthermore, we used our platform to generate epigenetic profiles of rare subpopulations of mESCs that resemble the two-cell stage of embryonic development. PnP-ChIP-seq allows nonexpert laboratories worldwide to conveniently run robust, standardized ChIP-seq, whereas its high throughput, consistency, and sensitivity pave the way toward large-scale profiling of precious sample types such as rare subpopulations of cells or biopsies.
Collapse
Affiliation(s)
- René A M Dirks
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Peter C Thomas
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | - Haoyu Wu
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Robert C Jones
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| |
Collapse
|
39
|
Rivas MA, Meydan C, Chin CR, Challman MF, Kim D, Bhinder B, Kloetgen A, Viny AD, Teater MR, McNally DR, Doane AS, Béguelin W, Fernández MTC, Shen H, Wang X, Levine RL, Chen Z, Tsirigos A, Elemento O, Mason CE, Melnick AM. Smc3 dosage regulates B cell transit through germinal centers and restricts their malignant transformation. Nat Immunol 2021; 22:240-253. [PMID: 33432228 PMCID: PMC7855695 DOI: 10.1038/s41590-020-00827-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 10/25/2020] [Indexed: 01/28/2023]
Abstract
During the germinal center (GC) reaction, B cells undergo extensive redistribution of cohesin complex and three-dimensional reorganization of their genomes. Yet, the significance of cohesin and architectural programming in the humoral immune response is unknown. Herein we report that homozygous deletion of Smc3, encoding the cohesin ATPase subunit, abrogated GC formation, while, in marked contrast, Smc3 haploinsufficiency resulted in GC hyperplasia, skewing of GC polarity and impaired plasma cell (PC) differentiation. Genome-wide chromosomal conformation and transcriptional profiling revealed defects in GC B cell terminal differentiation programs controlled by the lymphoma epigenetic tumor suppressors Tet2 and Kmt2d and failure of Smc3-haploinsufficient GC B cells to switch from B cell- to PC-defining transcription factors. Smc3 haploinsufficiency preferentially impaired the connectivity of enhancer elements controlling various lymphoma tumor suppressor genes, and, accordingly, Smc3 haploinsufficiency accelerated lymphomagenesis in mice with constitutive Bcl6 expression. Collectively, our data indicate a dose-dependent function for cohesin in humoral immunity to facilitate the B cell to PC phenotypic switch while restricting malignant transformation.
Collapse
MESH Headings
- Animals
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Cell Cycle Proteins/deficiency
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Differentiation
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Cells, Cultured
- Chondroitin Sulfate Proteoglycans/deficiency
- Chondroitin Sulfate Proteoglycans/genetics
- Chondroitin Sulfate Proteoglycans/metabolism
- Chromosomal Proteins, Non-Histone/deficiency
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Dioxygenases
- Gene Deletion
- Gene Dosage
- Gene Expression Regulation, Neoplastic
- Germinal Center/immunology
- Germinal Center/metabolism
- Germinal Center/pathology
- Haploinsufficiency
- Histone-Lysine N-Methyltransferase/genetics
- Histone-Lysine N-Methyltransferase/metabolism
- Humans
- Immunity, Humoral
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/metabolism
- Lymphoma, B-Cell/pathology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/pathology
- Mice, Inbred C57BL
- Mice, Knockout
- Myeloid-Lymphoid Leukemia Protein/genetics
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Signal Transduction
- Cohesins
- Mice
Collapse
Affiliation(s)
- Martín A Rivas
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher R Chin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matt F Challman
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Daleum Kim
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Bhavneet Bhinder
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Aaron D Viny
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matt R Teater
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dylan R McNally
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ashley S Doane
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Wendy Béguelin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Hao Shen
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xiang Wang
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ross L Levine
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhengming Chen
- Division of Biostatistics and Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Institute for Computational Medicine, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ari M Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
40
|
Saint Fleur-Lominy S, Evensen NA, Bhatla T, Sethia G, Narang S, Choi JH, Ma X, Yang JJ, Kelly S, Raetz E, Harvey RC, Willman C, Loh ML, Hunger SP, Brown PA, Getz KM, Meydan C, Mason CE, Tsirigos A, Carroll WL. Evolution of the Epigenetic Landscape in Childhood B Acute Lymphoblastic Leukemia and Its Role in Drug Resistance. Cancer Res 2020; 80:5189-5202. [PMID: 33067268 DOI: 10.1158/0008-5472.can-20-1145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 08/13/2020] [Accepted: 10/12/2020] [Indexed: 11/16/2022]
Abstract
Although B-cell acute lymphoblastic leukemia (B-ALL) is the most common malignancy in children and while highly curable, it remains a leading cause of cancer-related mortality. The outgrowth of tumor subclones carrying mutations in genes responsible for resistance to therapy has led to a Darwinian model of clonal selection. Previous work has indicated that alterations in the epigenome might contribute to clonal selection, yet the extent to which the chromatin state is altered under the selective pressures of therapy is unknown. To address this, we performed chromatin immunoprecipitation, gene expression analysis, and enhanced reduced representation bisulfite sequencing on a cohort of paired diagnosis and relapse samples from individual patients who all but one relapsed within 36 months of initial diagnosis. The chromatin state at diagnosis varied widely among patients, while the majority of peaks remained stable between diagnosis and relapse. Yet a significant fraction was either lost or newly gained, with some patients showing few differences and others showing massive changes of the epigenetic state. Evolution of the epigenome was associated with pathways previously linked to therapy resistance as well as novel candidate pathways through alterations in pyrimidine biosynthesis and downregulation of polycomb repressive complex 2 targets. Three novel, relapse-specific superenhancers were shared by a majority of patients including one associated with S100A8, the top upregulated gene seen at relapse in childhood B-ALL. Overall, our results support a role of the epigenome in clonal evolution and uncover new candidate pathways associated with relapse. SIGNIFICANCE: This study suggests a major role for epigenetic mechanisms in driving clonal evolution in B-ALL and identifies novel pathways associated with drug resistance.
Collapse
Affiliation(s)
- Shella Saint Fleur-Lominy
- Perlmutter Cancer Center, NYU Langone Health, New York, New York.,Department of Medicine, NYU Langone Health, New York, New York
| | - Nikki A Evensen
- Perlmutter Cancer Center, NYU Langone Health, New York, New York
| | - Teena Bhatla
- Department of Pediatrics, Children's Hospital of New Jersey at NBI, RWJBarnabas Health, Newark, New Jersey
| | - Gunjan Sethia
- Perlmutter Cancer Center, NYU Langone Health, New York, New York
| | - Sonali Narang
- Perlmutter Cancer Center, NYU Langone Health, New York, New York
| | - Jun H Choi
- Department of Medicine, NYU Langone Health, New York, New York
| | - Xiaotu Ma
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stephen Kelly
- Perlmutter Cancer Center, NYU Langone Health, New York, New York
| | - Elizabeth Raetz
- Perlmutter Cancer Center, NYU Langone Health, New York, New York.,Department of Pediatrics, NYU Health, New York, New York
| | - Richard C Harvey
- University of New Mexico Comprehensive Cancer Center, Department of Pathology, University of New Mexico School of Medicine and Health Sciences Center, Albuquerque, New Mexico
| | - Cheryl Willman
- University of New Mexico Comprehensive Cancer Center, Department of Pathology, University of New Mexico School of Medicine and Health Sciences Center, Albuquerque, New Mexico
| | - Mignon L Loh
- Department of Pediatrics, UCSF Benioff Children's Hospital, San Francisco, California
| | - Stephen P Hunger
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia and The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Patrick A Brown
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kylie M Getz
- Department of Physiology and Biophysics and Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Cem Meydan
- Department of Physiology and Biophysics and Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Christopher E Mason
- Department of Physiology and Biophysics and Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Aristotelis Tsirigos
- Perlmutter Cancer Center, NYU Langone Health, New York, New York. .,Department of Pathology, NYU Langone Health, New York, New York
| | - William L Carroll
- Perlmutter Cancer Center, NYU Langone Health, New York, New York. .,Department of Pediatrics, NYU Health, New York, New York.,Department of Pathology, NYU Langone Health, New York, New York
| |
Collapse
|
41
|
Ferrari F, Arrigoni L, Franz H, Izzo A, Butenko L, Trompouki E, Vogel T, Manke T. DOT1L-mediated murine neuronal differentiation associates with H3K79me2 accumulation and preserves SOX2-enhancer accessibility. Nat Commun 2020; 11:5200. [PMID: 33060580 PMCID: PMC7562744 DOI: 10.1038/s41467-020-19001-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 09/21/2020] [Indexed: 01/27/2023] Open
Abstract
During neuronal differentiation, the transcriptional profile and the epigenetic context of neural committed cells is subject to significant rearrangements, but a systematic quantification of global histone modification changes is still missing. Here, we show that H3K79me2 increases and H3K27ac decreases globally during in-vitro neuronal differentiation of murine embryonic stem cells. DOT1L mediates all three degrees of methylation of H3K79 and its enzymatic activity is critical to modulate cellular differentiation and reprogramming. In this context, we find that inhibition of DOT1L in neural progenitor cells biases the transcriptional state towards neuronal differentiation, resulting in transcriptional upregulation of genes marked with H3K27me3 on the promoter region. We further show that DOT1L inhibition affects accessibility of SOX2-bound enhancers and impairs SOX2 binding in neural progenitors. Our work provides evidence that DOT1L activity gates differentiation of progenitors by allowing SOX2-dependent transcription of stemness programs.
Collapse
Affiliation(s)
- Francesco Ferrari
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Henriette Franz
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Annalisa Izzo
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ludmila Butenko
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eirini Trompouki
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Tanja Vogel
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Center for Basics in NeuroModulation (NeuroModul Basics), Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| |
Collapse
|
42
|
Liu S, Yin P, Xu J, Dotts AJ, Kujawa SA, Coon V JS, Zhao H, Shilatifard A, Dai Y, Bulun SE. Targeting DNA Methylation Depletes Uterine Leiomyoma Stem Cell-enriched Population by Stimulating Their Differentiation. Endocrinology 2020; 161:5894164. [PMID: 32812024 PMCID: PMC7497820 DOI: 10.1210/endocr/bqaa143] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/11/2020] [Indexed: 01/01/2023]
Abstract
Uterine leiomyoma (LM) is the most common tumor in women and can cause severe morbidity. Leiomyoma growth requires the maintenance and proliferation of a stem cell population. Dysregulated deoxyribonucleic acid (DNA) methylation has been reported in LM, but its role in LM stem cell regulation remains unclear. Here, we fluorescence-activated cell sorting (FACS)-sorted cells from human LM tissues into 3 populations: LM stem cell-like cells (LSC, 5%), LM intermediate cells (LIC, 7%), and differentiated LM cells (LDC, 88%), and we analyzed the transcriptome and epigenetic landscape of LM cells at different differentiation stages. Leiomyoma stem cell-like cells harbored a unique methylome, with 8862 differentially methylated regions compared to LIC and 9444 compared to LDC, most of which were hypermethylated. Consistent with global hypermethylation, transcript levels of TET1 and TET3 methylcytosine dioxygenases were lower in LSC. Integrative analyses revealed an inverse relationship between methylation and gene expression changes during LSC differentiation. In LSC, hypermethylation suppressed the genes important for myometrium- and LM-associated functions, including muscle contraction and hormone action, to maintain stemness. The hypomethylating drug, 5'-Aza, stimulated LSC differentiation, depleting the stem cell population and inhibiting tumor initiation. Our data suggest that DNA methylation maintains the pool of LSC, which is critical for the regeneration of LM tumors.
Collapse
Affiliation(s)
- Shimeng Liu
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ping Yin
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jingting Xu
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois
| | - Ariel J Dotts
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Stacy A Kujawa
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - John S Coon V
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Hong Zhao
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
| | - Yang Dai
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois
| | - Serdar E Bulun
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Correspondence: Serdar E Bulun, MD, Prentice Women’s Hospital, 250 E. Superior Street, Chicago, IL 60611, USA.
| |
Collapse
|
43
|
Handa T, Harada A, Maehara K, Sato S, Nakao M, Goto N, Kurumizaka H, Ohkawa Y, Kimura H. Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input. Nat Protoc 2020; 15:3334-3360. [PMID: 32807906 DOI: 10.1038/s41596-020-0375-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 05/29/2020] [Indexed: 12/21/2022]
Abstract
Cell identity is determined by the selective activation or silencing of specific genes via transcription factor binding and epigenetic modifications on the genome. Chromatin immunoprecipitation (ChIP) has been the standard technique for mapping the sites of transcription factor binding and histone modification. Recently, alternative methods to ChIP have been developed for addressing the increasing demands for low-input epigenomic profiling. Chromatin integration labeling (ChIL) followed by sequencing (ChIL-seq) has been demonstrated to be particularly useful for epigenomic profiling of low-input samples or even single cells because the technique amplifies the target genomic sequence before cell lysis. After labeling the target protein or modification in situ with an oligonucleotide-conjugated antibody (ChIL probe), the nearby genome sequence is amplified by Tn5 transposase-mediated transposition followed by T7 RNA polymerase-mediated transcription. ChIL-seq enables the detection of the antibody target localization under a fluorescence microscope and at the genomic level. Here we describe the detailed protocol of ChIL-seq with assessment methods for the key steps, including ChIL probe reaction, transposition, in situ transcription and sequencing library preparation. The protocol usually takes 3 d to prepare the sequencing library, including overnight incubations for the ChIL probe reaction and in situ transcription. The ChIL probe can be separately prepared and stored for several months, and its preparation and evaluation protocols are also documented in detail. An optional analysis for multiple targets (multitarget ChIL-seq) is also described. We anticipate that the protocol presented here will make the ChIL technique more widely accessible for analyzing precious samples and facilitate further applications.
Collapse
Affiliation(s)
- Tetsuya Handa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Japan
| | - Shoko Sato
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Masaru Nakao
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Japan
| | - Naoki Goto
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Japan.
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Japan.
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Japan.
| |
Collapse
|
44
|
Dickson BM, Tiedemann RL, Chomiak AA, Cornett EM, Vaughan RM, Rothbart SB. A physical basis for quantitative ChIP-sequencing. J Biol Chem 2020; 295:15826-15837. [PMID: 32994221 PMCID: PMC7681007 DOI: 10.1074/jbc.ra120.015353] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/09/2020] [Indexed: 01/28/2023] Open
Abstract
ChIP followed by next-generation sequencing (ChIP-Seq) is a key technique for mapping the distribution of histone posttranslational modifications (PTMs) and chromatin-associated factors across genomes. There is a perceived challenge to define a quantitative scale for ChIP-Seq data, and as such, several approaches making use of exogenous additives, or "spike-ins," have recently been developed. Herein, we report on the development of a quantitative, physical model defining ChIP-Seq. The quantitative scale on which ChIP-Seq results should be compared emerges from the model. To test the model and demonstrate the quantitative scale, we examine the impacts of an EZH2 inhibitor through the lens of ChIP-Seq. We report a significant increase in immunoprecipitation of presumed off-target histone PTMs after inhibitor treatment, a trend predicted by the model but contrary to spike-in-based indications. Our work also identifies a sensitivity issue in spike-in normalization that has not been considered in the literature, placing limitations on its utility and trustworthiness. We call our new approach the sans-spike-in method for quantitative ChIP-sequencing (siQ-ChIP). A number of changes in community practice of ChIP-Seq, data reporting, and analysis are motivated by this work.
Collapse
Affiliation(s)
- Bradley M Dickson
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA.
| | - Rochelle L Tiedemann
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Alison A Chomiak
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Evan M Cornett
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Robert M Vaughan
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA
| |
Collapse
|
45
|
Lincoln MR, Axisa PP, Hafler DA. Epigenetic fine-mapping: identification of causal mechanisms for autoimmunity. Curr Opin Immunol 2020; 67:50-56. [PMID: 32977183 DOI: 10.1016/j.coi.2020.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/28/2020] [Accepted: 09/07/2020] [Indexed: 11/25/2022]
Abstract
Genome-wide association studies (GWAS) have identified genetic susceptibility loci for a variety of autoimmune and inflammatory diseases. These studies confirm the fundamental genetic basis of individual autoimmune diseases, and also point to shared etiological mechanisms across the spectrum of autoimmunity. While hundreds of genetic loci have been implicated in autoimmune diseases, the translation of individual susceptibility loci into specific molecular mechanisms for individual diseases remains difficult. This review highlights recent advances in the genetics of autoimmune disease, and the emerging use of epigenetic techniques to identify pathogenic cell types and causal molecular mechanisms of autoimmunity.
Collapse
Affiliation(s)
- Matthew R Lincoln
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Pierre-Paul Axisa
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA.
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| |
Collapse
|
46
|
Kobayashi Y, Tata A, Konkimalla A, Katsura H, Lee RF, Ou J, Banovich NE, Kropski JA, Tata PR. Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis. Nat Cell Biol 2020; 22:934-946. [PMID: 32661339 PMCID: PMC7461628 DOI: 10.1038/s41556-020-0542-8] [Citation(s) in RCA: 274] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 06/08/2020] [Indexed: 12/21/2022]
Abstract
Stem cells undergo dynamic changes in response to injury to regenerate lost cells. However, the identity of transitional states and the mechanisms that drive their trajectories remain understudied. Using lung organoids, multiple in vivo repair models, single-cell transcriptomics and lineage tracing, we find that alveolar type-2 epithelial cells undergoing differentiation into type-1 cells acquire pre-alveolar type-1 transitional cell state (PATS) en route to terminal maturation. Transitional cells undergo extensive stretching during differentiation, making them vulnerable to DNA damage. Cells in the PATS show an enrichment of TP53, TGFβ, DNA-damage-response signalling and cellular senescence. Gain and loss of function as well as genomic binding assays revealed a direct transcriptional control of PATS by TP53 signalling. Notably, accumulation of PATS-like cells in human fibrotic lungs was observed, suggesting persistence of the transitional state in fibrosis. Our study thus implicates a transient state associated with senescence in normal epithelial tissue repair and its abnormal persistence in disease conditions.
Collapse
Affiliation(s)
- Yoshihiko Kobayashi
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Aleksandra Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Arvind Konkimalla
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Medical Scientist Training Program, Duke University School of Medicine, Durham, NC, USA
| | - Hiroaki Katsura
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Rebecca F Lee
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Jianhong Ou
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Regeneration Next, Duke University, Durham, NC, USA
| | | | - Jonathan A Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA.
- Regeneration Next, Duke University, Durham, NC, USA.
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA.
| |
Collapse
|
47
|
Arrigoni L, Ferrari F, Weller J, Bella C, Bönisch U, Manke T. AutoRELACS: automated generation and analysis of ultra-parallel ChIP-seq. Sci Rep 2020; 10:12400. [PMID: 32709929 PMCID: PMC7381599 DOI: 10.1038/s41598-020-69443-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/07/2020] [Indexed: 11/09/2022] Open
Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to profile protein-DNA interactions genome-wide. Restriction Enzyme-based Labeling of Chromatin in Situ (RELACS) is a recently developed ChIP-seq protocol that deploys a chromatin barcoding strategy to enable standardized and high-throughput generation of ChIP-seq data. The manual implementation of RELACS is constrained by human processivity in both data generation and data analysis. To overcome these limitations, we have developed AutoRELACS, an automated implementation of the RELACS protocol using the liquid handler Biomek i7 workstation. We match the unprecedented processivity in data generation allowed by AutoRELACS with the automated computation pipelines offered by snakePipes. In doing so, we build a continuous workflow that streamlines epigenetic profiling, from sample collection to biological interpretation. Here, we show that AutoRELACS successfully automates chromatin barcode integration, and is able to generate high-quality ChIP-seq data comparable with the standards of the manual protocol, also for limited amounts of biological samples.
Collapse
Affiliation(s)
- L Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - F Ferrari
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - J Weller
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - C Bella
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - U Bönisch
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - T Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| |
Collapse
|
48
|
A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors. Proc Natl Acad Sci U S A 2020; 117:13828-13838. [PMID: 32461370 DOI: 10.1073/pnas.1913261117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Despite its popularity, chromatin immunoprecipitation followed by sequencing (ChIP-seq) remains a tedious (>2 d), manually intensive, low-sensitivity and low-throughput approach. Here, we combine principles of microengineering, surface chemistry, and molecular biology to address the major limitations of standard ChIP-seq. The resulting technology, FloChIP, automates and miniaturizes ChIP in a beadless fashion while facilitating the downstream library preparation process through on-chip chromatin tagmentation. FloChIP is fast (<2 h), has a wide dynamic range (from 106 to 500 cells), is scalable and parallelized, and supports antibody- or sample-multiplexed ChIP on both histone marks and transcription factors. In addition, FloChIP's interconnected design allows for straightforward chromatin reimmunoprecipitation, which allows this technology to also act as a microfluidic sequential ChIP-seq system. Finally, we ran FloChIP for the transcription factor MEF2A in 32 distinct human lymphoblastoid cell lines, providing insights into the main factors driving collaborative DNA binding of MEF2A and into its role in B cell-specific gene regulation. Together, our results validate FloChIP as a flexible and reproducible automated solution for individual or sequential ChIP-seq.
Collapse
|
49
|
Zhang T, Pilko A, Wollman R. Loci specific epigenetic drug sensitivity. Nucleic Acids Res 2020; 48:4797-4810. [PMID: 32246716 PMCID: PMC7229858 DOI: 10.1093/nar/gkaa210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 02/10/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022] Open
Abstract
Therapeutic targeting of epigenetic modulators offers a novel approach to the treatment of multiple diseases. The cellular consequences of chemical compounds that target epigenetic regulators (epi-drugs) are complex. Epi-drugs affect global cellular phenotypes and cause local changes to gene expression due to alteration of a gene chromatin environment. Despite increasing use in the clinic, the mechanisms responsible for cellular changes are unclear. Specifically, to what degree the effects are a result of cell-wide changes or disease related locus specific effects is unknown. Here we developed a platform to systematically and simultaneously investigate the sensitivity of epi-drugs at hundreds of genomic locations by combining DNA barcoding, unique split-pool encoding, and single cell expression measurements. Internal controls are used to isolate locus specific effects separately from any global consequences these drugs have. Using this platform we discovered wide-spread loci specific sensitivities to epi-drugs for three distinct epi-drugs that target histone deacetylase, DNA methylation and bromodomain proteins. By leveraging ENCODE data on chromatin modification, we identified features of chromatin environments that are most likely to be affected by epi-drugs. The measurements of loci specific epi-drugs sensitivities will pave the way to the development of targeted therapy for personalized medicine.
Collapse
Affiliation(s)
- Thanutra Zhang
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA
| | - Anna Pilko
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA
- Departments of Integrative Biology and Physiology and Chemistry and Biochemistry, University of California UCLA, CA, USA
| | - Roy Wollman
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA
- Departments of Integrative Biology and Physiology and Chemistry and Biochemistry, University of California UCLA, CA, USA
| |
Collapse
|
50
|
Koth ML, Garcia-Moreno SA, Novak A, Holthusen KA, Kothandapani A, Jiang K, Taketo MM, Nicol B, Yao HHC, Futtner CR, Maatouk DM, Jorgensen JS. Canonical Wnt/β-catenin activity and differential epigenetic marks direct sexually dimorphic regulation of Irx3 and Irx5 in developing mouse gonads. Development 2020; 147:dev183814. [PMID: 32108023 PMCID: PMC7132837 DOI: 10.1242/dev.183814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 02/14/2020] [Indexed: 11/20/2022]
Abstract
Members of the Iroquois B (IrxB) homeodomain cluster genes, specifically Irx3 and Irx5, are crucial for heart, limb and bone development. Recently, we reported their importance for oocyte and follicle survival within the developing ovary. Irx3 and Irx5 expression begins after sex determination in the ovary but remains absent in the fetal testis. Mutually antagonistic molecular signals ensure ovary versus testis differentiation with canonical Wnt/β-catenin signals paramount for promoting the ovary pathway. Notably, few direct downstream targets have been identified. We report that Wnt/β-catenin signaling directly stimulates Irx3 and Irx5 transcription in the developing ovary. Using in silico analysis of ATAC- and ChIP-Seq databases in conjunction with mouse gonad explant transfection assays, we identified TCF/LEF-binding sequences within two distal enhancers of the IrxB locus that promote β-catenin-responsive ovary expression. Meanwhile, Irx3 and Irx5 transcription is suppressed within the developing testis by the presence of H3K27me3 on these same sites. Thus, we resolved sexually dimorphic regulation of Irx3 and Irx5 via epigenetic and β-catenin transcriptional control where their ovarian presence promotes oocyte and follicle survival vital for future ovarian health.
Collapse
Affiliation(s)
- Megan L Koth
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA
| | | | - Annie Novak
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Kirsten A Holthusen
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA
| | - Anbarasi Kothandapani
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Keer Jiang
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Makoto Mark Taketo
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Barbara Nicol
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Humphrey H-C Yao
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Christopher R Futtner
- Department of Obstetrics and Gynecology, Northwestern University, Chicago, IL 60611, USA
| | - Danielle M Maatouk
- Department of Obstetrics and Gynecology, Northwestern University, Chicago, IL 60611, USA
| | - Joan S Jorgensen
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA
| |
Collapse
|