151
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Grillo G, Keshavarzian T, Linder S, Arlidge C, Mout L, Nand A, Teng M, Qamra A, Zhou S, Kron KJ, Murison A, Hawley JR, Fraser M, van der Kwast TH, Raj GV, He HH, Zwart W, Lupien M. Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer. Cancer Discov 2023; 13:2470-2487. [PMID: 37694973 PMCID: PMC10618745 DOI: 10.1158/2159-8290.cd-23-0331] [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: 03/21/2023] [Revised: 07/30/2023] [Accepted: 09/08/2023] [Indexed: 09/12/2023]
Abstract
Transposable elements hold regulatory functions that impact cell fate determination by controlling gene expression. However, little is known about the transcriptional machinery engaged at transposable elements in pluripotent and mature versus oncogenic cell states. Through positional analysis over repetitive DNA sequences of H3K27ac chromatin immunoprecipitation sequencing data from 32 normal cell states, we report pluripotent/stem and mature cell state-specific "regulatory transposable elements." Pluripotent/stem elements are binding sites for pluripotency factors (e.g., NANOG, SOX2, OCT4). Mature cell elements are docking sites for lineage-specific transcription factors, including AR and FOXA1 in prostate epithelium. Expanding the analysis to prostate tumors, we identify a subset of regulatory transposable elements shared with pluripotent/stem cells, including Tigger3a. Using chromatin editing technology, we show how such elements promote prostate cancer growth by regulating AR transcriptional activity. Collectively, our results suggest that oncogenesis arises from lineage-specific transcription factors hijacking pluripotent/stem cell regulatory transposable elements. SIGNIFICANCE We show that oncogenesis relies on co-opting transposable elements from pluripotent stem cells as regulatory elements altering the recruitment of lineage-specific transcription factors. We further discover how co-option is dependent on active chromatin states with important implications for developing treatment options against drivers of oncogenesis across the repetitive DNA. This article is featured in Selected Articles from This Issue, p. 2293.
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Affiliation(s)
- Giacomo Grillo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tina Keshavarzian
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Simon Linder
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Lisanne Mout
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ankita Nand
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mona Teng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Aditi Qamra
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ken J. Kron
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - James R. Hawley
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Theodorus H. van der Kwast
- Laboratory Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ganesh V. Raj
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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152
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Boers R, Boers J, Tan B, van Leeuwen ME, Wassenaar E, Sanchez EG, Sleddens E, Tenhagen Y, Mulugeta E, Laven J, Creyghton M, Baarends W, van IJcken WFJ, Gribnau J. Retrospective analysis of enhancer activity and transcriptome history. Nat Biotechnol 2023; 41:1582-1592. [PMID: 36823354 PMCID: PMC10635829 DOI: 10.1038/s41587-023-01683-1] [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: 07/01/2021] [Accepted: 01/20/2023] [Indexed: 02/25/2023]
Abstract
Cell state changes in development and disease are controlled by gene regulatory networks, the dynamics of which are difficult to track in real time. In this study, we used an inducible DCM-RNA polymerase subunit b fusion protein which labels active genes and enhancers with a bacterial methylation mark that does not affect gene transcription and is propagated in S-phase. This DCM-RNA polymerase fusion protein enables transcribed genes and active enhancers to be tagged and then examined at later stages of development or differentiation. We apply this DCM-time machine (DCM-TM) technology to study intestinal homeostasis, revealing rapid and coordinated activation of enhancers and nearby genes during enterocyte differentiation. We provide new insights in absorptive-secretory lineage decision-making in intestinal stem cell (ISC) differentiation and show that ISCs retain a unique chromatin landscape required to maintain ISC identity and delineate future expression of differentiation-associated genes. DCM-TM has wide applicability in tracking cell states, providing new insights in the regulatory networks underlying cell state changes.
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Affiliation(s)
- Ruben Boers
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Joachim Boers
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Beatrice Tan
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Marieke E van Leeuwen
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Evelyne Wassenaar
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Erlantz Gonzalez Sanchez
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Esther Sleddens
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Yasha Tenhagen
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Joop Laven
- Department of Obstetrics and Gynaecology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Menno Creyghton
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Willy Baarends
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.
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153
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Badia-I-Mompel P, Wessels L, Müller-Dott S, Trimbour R, Ramirez Flores RO, Argelaguet R, Saez-Rodriguez J. Gene regulatory network inference in the era of single-cell multi-omics. Nat Rev Genet 2023; 24:739-754. [PMID: 37365273 DOI: 10.1038/s41576-023-00618-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2023] [Indexed: 06/28/2023]
Abstract
The interplay between chromatin, transcription factors and genes generates complex regulatory circuits that can be represented as gene regulatory networks (GRNs). The study of GRNs is useful to understand how cellular identity is established, maintained and disrupted in disease. GRNs can be inferred from experimental data - historically, bulk omics data - and/or from the literature. The advent of single-cell multi-omics technologies has led to the development of novel computational methods that leverage genomic, transcriptomic and chromatin accessibility information to infer GRNs at an unprecedented resolution. Here, we review the key principles of inferring GRNs that encompass transcription factor-gene interactions from transcriptomics and chromatin accessibility data. We focus on the comparison and classification of methods that use single-cell multimodal data. We highlight challenges in GRN inference, in particular with respect to benchmarking, and potential further developments using additional data modalities.
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Affiliation(s)
- Pau Badia-I-Mompel
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Lorna Wessels
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience, Medical Faculty, MannHeim Heidelberg University, Mannheim, Germany
| | - Sophia Müller-Dott
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Rémi Trimbour
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Machine Learning for Integrative Genomics Group, Paris, France
| | - Ricardo O Ramirez Flores
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | | | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany.
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154
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Fiskin E, Eraslan G, Alora-Palli MB, Leyva-Castillo JM, Kim S, Choe H, Lareau CA, Lau H, Finan EP, Teixeira-Soldano I, LaBere B, Chu A, Woods B, Chou J, Slyper M, Waldman J, Islam S, Schneider L, Phipatanakul W, Platt C, Rozenblatt-Rosen O, Delorey TM, Deguine J, Smith GP, Geha R, Regev A, Xavier R. Multi-modal skin atlas identifies a multicellular immune-stromal community associated with altered cornification and specific T cell expansion in atopic dermatitis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.29.563503. [PMID: 37961084 PMCID: PMC10634929 DOI: 10.1101/2023.10.29.563503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In healthy skin, a cutaneous immune system maintains the balance between tolerance towards innocuous environmental antigens and immune responses against pathological agents. In atopic dermatitis (AD), barrier and immune dysfunction result in chronic tissue inflammation. Our understanding of the skin tissue ecosystem in AD remains incomplete with regard to the hallmarks of pathological barrier formation, and cellular state and clonal composition of disease-promoting cells. Here, we generated a multi-modal cell census of 310,691 cells spanning 86 cell subsets from whole skin tissue of 19 adult individuals, including non-lesional and lesional skin from 11 AD patients, and integrated it with 396,321 cells from four studies into a comprehensive human skin cell atlas in health and disease. Reconstruction of human keratinocyte differentiation from basal to cornified layers revealed a disrupted cornification trajectory in AD. This disrupted epithelial differentiation was associated with signals from a unique immune and stromal multicellular community comprised of MMP12 + dendritic cells (DCs), mature migratory DCs, cycling ILCs, NK cells, inflammatory CCL19 + IL4I1 + fibroblasts, and clonally expanded IL13 + IL22 + IL26 + T cells with overlapping type 2 and type 17 characteristics. Cell subsets within this immune and stromal multicellular community were connected by multiple inter-cellular positive feedback loops predicted to impact community assembly and maintenance. AD GWAS gene expression was enriched both in disrupted cornified keratinocytes and in cell subsets from the lesional immune and stromal multicellular community including IL13 + IL22 + IL26 + T cells and ILCs, suggesting that epithelial or immune dysfunction in the context of the observed cellular communication network can initiate and then converge towards AD. Our work highlights specific, disease-associated cell subsets and interactions as potential targets in progression and resolution of chronic inflammation.
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155
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Yang T, Barros-Martins J, Wang Z, Wencker M, Zhang J, Smout J, Gambhir P, Janssen A, Schimrock A, Georgiev H, León-Lara X, Weiss S, Huehn J, Prinz I, Krueger A, Foerster R, Walzer T, Ravens S. RORγt + c-Maf + Vγ4 + γδ T cells are generated in the adult thymus but do not reach the periphery. Cell Rep 2023; 42:113230. [PMID: 37815917 DOI: 10.1016/j.celrep.2023.113230] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/30/2023] [Accepted: 09/21/2023] [Indexed: 10/12/2023] Open
Abstract
T cell receptor (TCR) Vγ4-expressing γδ T cells comprise interferon γ (IFNγ)- and interleukin-17 (IL-17)-producing effector subsets, with a preference for IL-17 effector fate decisions during early ontogeny. The existence of adult-thymus-derived IL-17+ T cells (γδ17) remains controversial. Here, we use a mouse model in which T cells are generated exclusively in the adult thymus and employ single-cell chromatin state analysis to study their development. We identify adult-thymus-derived Vγ4 T cells that have all the molecular programs to become IL-17 producers. However, they have reduced IL-17 production capabilities and rarely reach the periphery. Moreover, this study provides high-resolution profiles of Vγ4 T cells in the adult thymus and lymph nodes and identifies Zeb1 as a potential γδ17 cell regulator. Together, this study provides valuable insights into the developmental traits of Vγ4 T cells during adulthood and supports the idea of age-specific signals required for thymic export and/or peripheral maturation of γδ17 cells.
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Affiliation(s)
- Tao Yang
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | | | - Ziqing Wang
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Melanie Wencker
- Centre International de Recherche en Infectiologie, INSERM U1111, École Normale Supérieure de Lyon, Claude Bernard University Lyon 1, CNRS, UMR 5308, 69365 Lyon, France
| | - Jiang Zhang
- Centre International de Recherche en Infectiologie, INSERM U1111, École Normale Supérieure de Lyon, Claude Bernard University Lyon 1, CNRS, UMR 5308, 69365 Lyon, France
| | - Justine Smout
- Experimental Immunology, Helmholtz Centre for Infection Research, 39124 Braunschweig, Germany
| | - Prerna Gambhir
- Molecular Immunology, Justus-Liebig-University, 35392 Gießen, Germany
| | - Anika Janssen
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Anja Schimrock
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Hristo Georgiev
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Ximena León-Lara
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Siegfried Weiss
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Jochen Huehn
- Experimental Immunology, Helmholtz Centre for Infection Research, 39124 Braunschweig, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Immo Prinz
- Institute of Systems Immunology, University Hamburg-Eppendorf, 20246 Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Andreas Krueger
- Molecular Immunology, Justus-Liebig-University, 35392 Gießen, Germany
| | - Reinhold Foerster
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Thierry Walzer
- Centre International de Recherche en Infectiologie, INSERM U1111, École Normale Supérieure de Lyon, Claude Bernard University Lyon 1, CNRS, UMR 5308, 69365 Lyon, France
| | - Sarina Ravens
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany.
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156
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Sin JH, Sucharov J, Kashyap S, Wang Y, Proekt I, Liu X, Parent AV, Gupta A, Kastner P, Chan S, Gardner JM, Ntranos V, Miller CN, Anderson MS, Schjerven H, Waterfield MR. Ikaros is a principal regulator of Aire + mTEC homeostasis, thymic mimetic cell diversity, and central tolerance. Sci Immunol 2023; 8:eabq3109. [PMID: 37889983 DOI: 10.1126/sciimmunol.abq3109] [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: 03/31/2022] [Accepted: 10/04/2023] [Indexed: 10/29/2023]
Abstract
Mutations in the gene encoding the zinc-finger transcription factor Ikaros (IKZF1) are found in patients with immunodeficiency, leukemia, and autoimmunity. Although Ikaros has a well-established function in modulating gene expression programs important for hematopoietic development, its role in other cell types is less well defined. Here, we uncover functions for Ikaros in thymic epithelial lineage development in mice and show that Ikzf1 expression in medullary thymic epithelial cells (mTECs) is required for both autoimmune regulator-positive (Aire+) mTEC development and tissue-specific antigen (TSA) gene expression. Accordingly, TEC-specific deletion of Ikzf1 in mice results in a profound decrease in Aire+ mTECs, a global loss of TSA gene expression, and the development of autoimmunity. Moreover, Ikaros shapes thymic mimetic cell diversity, and its deletion results in a marked expansion of thymic tuft cells and muscle-like mTECs and a loss of other Aire-dependent mimetic populations. Single-cell analysis reveals that Ikaros modulates core transcriptional programs in TECs that correlate with the observed cellular changes. Our findings highlight a previously undescribed role for Ikaros in regulating epithelial lineage development and function and suggest that failed thymic central tolerance could contribute to the autoimmunity seen in humans with IKZF1 mutations.
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Affiliation(s)
- Jun Hyung Sin
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Juliana Sucharov
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Sujit Kashyap
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Yi Wang
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- 10x Genomics, Pleasanton, CA, USA
| | - Irina Proekt
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Xian Liu
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Audrey V Parent
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Alexander Gupta
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Philippe Kastner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Susan Chan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - James M Gardner
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Vasilis Ntranos
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Corey N Miller
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Mark S Anderson
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hilde Schjerven
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael R Waterfield
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
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157
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Freie B, Carroll PA, Varnum-Finney BJ, Ramani V, Bernstein I, Eisenman RN. A Germline Point Mutation in the MYC-FBW7 Phosphodegron Initiates Hematopoietic Malignancies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563660. [PMID: 37961183 PMCID: PMC10634767 DOI: 10.1101/2023.10.23.563660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Oncogenic activation of MYC in cancers predominantly involves increased transcription rather than coding region mutations. However, MYC-dependent lymphomas frequently contain point mutations in the MYC phospho-degron, including at threonine-58 (T58), where phosphorylation permits binding by the FBW7 ubiquitin ligase triggering MYC degradation. To understand how T58 phosphorylation functions in normal cell physiology, we introduced an alanine mutation at T58 (T58A) into the endogenous c-Myc locus in the mouse germline. While MYC-T58A mice develop normally, lymphomas and myeloid leukemias emerge in ~60% of adult homozygous T58A mice. We find that primitive hematopoietic progenitor cells from MYC-T58A mice exhibit aberrant self-renewal normally associated with hematopoietic stem cells (HSCs) and upregulate a subset of Myc target genes important in maintaining stem/progenitor cell balance. Genomic occupancy by MYC-T58A was increased at all promoters, compared to WT MYC, while genes differentially expressed in a T58A-dependent manner were significantly more proximal to MYC-bound enhancers. MYC-T58A lymphocyte progenitors exhibited metabolic alterations and decreased activation of inflammatory and apoptotic pathways. Our data demonstrate that a single point mutation in Myc is sufficient to produce a profound gain of function in multipotential hematopoietic progenitors associated with self-renewal and initiation of lymphomas and leukemias.
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Affiliation(s)
- Brian Freie
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA, USA
| | - Patrick A Carroll
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA, USA
| | | | - Vijay Ramani
- Gladstone Institute for Data Science and Biotechnology, University of California, San Francisco, San Francisco CA, USA
| | - Irwin Bernstein
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle WA, USA
| | - Robert N Eisenman
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA, USA
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158
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Carraro C, Bonaguro L, Srinivasa R, van Uelft M, Isakzai V, Schulte-Schrepping J, Gambhir P, Elmzzahi T, Montgomery JV, Hayer H, Li Y, Theis H, Kraut M, Mahbubani KT, Aschenbrenner AC, König I, Fava E, Fried HU, De Domenico E, Beyer M, Saglam A, Schultze JL. Chromatin accessibility profiling of targeted cell populations with laser capture microdissection coupled to ATAC-seq. CELL REPORTS METHODS 2023; 3:100598. [PMID: 37776856 PMCID: PMC10626193 DOI: 10.1016/j.crmeth.2023.100598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/04/2023] [Accepted: 09/05/2023] [Indexed: 10/02/2023]
Abstract
Spatially resolved omics technologies reveal context-dependent cellular regulatory networks in tissues of interest. Beyond transcriptome analysis, information on epigenetic traits and chromatin accessibility can provide further insights on gene regulation in health and disease. Nevertheless, compared to the enormous advancements in spatial transcriptomics technologies, the field of spatial epigenomics is much younger and still underexplored. In this study, we report laser capture microdissection coupled to ATAC-seq (LCM-ATAC-seq) applied to fresh frozen samples for the spatial characterization of chromatin accessibility. We first demonstrate the efficient use of LCM coupled to in situ tagmentation and evaluate its performance as a function of cell number, microdissected areas, and tissue type. Further, we demonstrate its use for the targeted chromatin accessibility analysis of discrete contiguous or scattered cell populations in tissues via single-nuclei capture based on immunostaining for specific cellular markers.
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Affiliation(s)
- Caterina Carraro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Rachana Srinivasa
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Martina van Uelft
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Victoria Isakzai
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Prerna Gambhir
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Tarek Elmzzahi
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Jessica V Montgomery
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Hannah Hayer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Yuanfang Li
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Heidi Theis
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Michael Kraut
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Ireen König
- Core Research Facilities and Services, Light Microscope Facility (LMF), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Eugenio Fava
- Core Research Facilities and Services, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Hans-Ulrich Fried
- Core Research Facilities and Services, Light Microscope Facility (LMF), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Elena De Domenico
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Marc Beyer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany; Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Adem Saglam
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany.
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
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159
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Angarola BL, Sharma S, Katiyar N, Gu Kang H, Nehar-Belaid D, Park S, Gott R, Eryilmaz GN, LaBarge MA, Palucka K, Chuang JH, Korstanje R, Ucar D, Anczukow O. Comprehensive single cell aging atlas of mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563147. [PMID: 37961129 PMCID: PMC10634680 DOI: 10.1101/2023.10.20.563147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Aging is the greatest risk factor for breast cancer; however, how age-related cellular and molecular events impact cancer initiation is unknown. We investigate how aging rewires transcriptomic and epigenomic programs of mouse mammary glands at single cell resolution, yielding a comprehensive resource for aging and cancer biology. Aged epithelial cells exhibit epigenetic and transcriptional changes in metabolic, pro-inflammatory, or cancer-associated genes. Aged stromal cells downregulate fibroblast marker genes and upregulate markers of senescence and cancer-associated fibroblasts. Among immune cells, distinct T cell subsets (Gzmk+, memory CD4+, γδ) and M2-like macrophages expand with age. Spatial transcriptomics reveal co-localization of aged immune and epithelial cells in situ. Lastly, transcriptional signatures of aging mammary cells are found in human breast tumors, suggesting mechanistic links between aging and cancer. Together, these data uncover that epithelial, immune, and stromal cells shift in proportions and cell identity, potentially impacting cell plasticity, aged microenvironment, and neoplasia risk.
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Affiliation(s)
| | | | - Neerja Katiyar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Hyeon Gu Kang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - SungHee Park
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Giray N Eryilmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mark A LaBarge
- Beckman Research Institute at City of Hope, Duarte, CA, USA
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Olga Anczukow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
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160
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Nair S, Ameen M, Sundaram L, Pampari A, Schreiber J, Balsubramani A, Wang YX, Burns D, Blau HM, Karakikes I, Wang KC, Kundaje A. Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.04.560808. [PMID: 37873116 PMCID: PMC10592962 DOI: 10.1101/2023.10.04.560808] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Ectopic expression of OCT4, SOX2, KLF4 and MYC (OSKM) transforms differentiated cells into induced pluripotent stem cells. To refine our mechanistic understanding of reprogramming, especially during the early stages, we profiled chromatin accessibility and gene expression at single-cell resolution across a densely sampled time course of human fibroblast reprogramming. Using neural networks that map DNA sequence to ATAC-seq profiles at base-resolution, we annotated cell-state-specific predictive transcription factor (TF) motif syntax in regulatory elements, inferred affinity- and concentration-dependent dynamics of Tn5-bias corrected TF footprints, linked peaks to putative target genes, and elucidated rewiring of TF-to-gene cis-regulatory networks. Our models reveal that early in reprogramming, OSK, at supraphysiological concentrations, rapidly open transient regulatory elements by occupying non-canonical low-affinity binding sites. As OSK concentration falls, the accessibility of these transient elements decays as a function of motif affinity. We find that these OSK-dependent transient elements sequester the somatic TF AP-1. This redistribution is strongly associated with the silencing of fibroblast-specific genes within individual nuclei. Together, our integrated single-cell resource and models reveal insights into the cis-regulatory code of reprogramming at unprecedented resolution, connect TF stoichiometry and motif syntax to diversification of cell fate trajectories, and provide new perspectives on the dynamics and role of transient regulatory elements in somatic silencing.
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Affiliation(s)
- Surag Nair
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Mohamed Ameen
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | | | - Anusri Pampari
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jacob Schreiber
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Yu Xin Wang
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, CA, USA
| | - David Burns
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, CA, USA
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Kevin C Wang
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
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161
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Lin H, Peng H, Sun Y, Si M, Wu J, Wang Y, Thomas SS, Sun Z, Hu Z. Reprogramming of cis-regulatory networks during skeletal muscle atrophy in male mice. Nat Commun 2023; 14:6581. [PMID: 37853001 PMCID: PMC10584982 DOI: 10.1038/s41467-023-42313-3] [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: 03/28/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023] Open
Abstract
A comprehensive atlas of cis-regulatory elements and their dynamic activity is necessary to understand the transcriptional basis of cellular structure maintenance, metabolism, and responses to the environment. Here we show, using matched single-nucleus chromatin accessibility and RNA-sequencing from juvenile male C57BL6 mice, an atlas of accessible chromatin regions in both normal and denervated skeletal muscles. We identified cell-type-specific cis-regulatory networks, highlighting the dynamic regulatory circuits mediating transitions between myonuclear types. Through comparison of normal and perturbed muscle, we delineated the reprogramming of cis-regulatory networks in response to denervation, described the interplay of promoters/enhancers and target genes. We further unveil a hierarchical structure of transcription factors that delineate a regulatory network in atrophic muscle, identifying ELK4 as a key atrophy-related transcription factor that instigates muscle atrophy through TGF-β1 regulation. This study furnishes a rich genomic resource, essential for decoding the regulatory dynamics of skeletal muscle in both physiological and pathological states.
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Affiliation(s)
- Hongchun Lin
- Nephrology Division, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hui Peng
- Nephrology Division, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Yuxiang Sun
- Nephrology Division, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Meijun Si
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangzhou, 510080, China
| | - Jiao Wu
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yanlin Wang
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Sandhya S Thomas
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zheng Sun
- Endocrinology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhaoyong Hu
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
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162
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Shi W, Ye J, Shi Z, Pan C, Zhang Q, Lin Y, Liang D, Liu Y, Lin X, Zheng Y. Single-cell chromatin accessibility and transcriptomic characterization of Behcet's disease. Commun Biol 2023; 6:1048. [PMID: 37848613 PMCID: PMC10582193 DOI: 10.1038/s42003-023-05420-x] [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: 04/06/2023] [Accepted: 10/04/2023] [Indexed: 10/19/2023] Open
Abstract
Behect's disease is a chronic vasculitis characterized by complex multi-organ immune aberrations. However, a comprehensive understanding of the gene-regulatory profile of peripheral autoimmunity and the diverse immune responses across distinct cell types in Behcet's disease (BD) is still lacking. Here, we present a multi-omic single-cell study of 424,817 cells in BD patients and non-BD individuals. This study maps chromatin accessibility and gene expression in the same biological samples, unraveling vast cellular heterogeneity. We identify widespread cell-type-specific, disease-associated active and pro-inflammatory immunity in both transcript and epigenomic aspects. Notably, integrative multi-omic analysis reveals putative TF regulators that might contribute to chromatin accessibility and gene expression in BD. Moreover, we predicted gene-regulatory networks within nominated TF activators, including AP-1, NF-kB, and ETS transcript factor families, which may regulate cellular interaction and govern inflammation. Our study illustrates the epigenetic and transcriptional landscape in BD peripheral blood and expands understanding of potential epigenomic immunopathology in this disease.
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Affiliation(s)
- Wen Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, 100085, Beijing, China
| | - Jinguo Ye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China
| | - Zhuoxing Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China
| | - Caineng Pan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China
| | - Qikai Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China
| | - Yuheng Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China
| | - Dan Liang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China.
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China.
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, 100085, Beijing, China.
| | - Xianchai Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China.
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, 100085, Beijing, China.
| | - Yingfeng Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China.
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, 100085, Beijing, China.
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163
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Braband KL, Nedwed AS, Helbich SS, Simon M, Beumer N, Brors B, Marini F, Delacher M. Using single-cell chromatin accessibility sequencing to characterize CD4+ T cells from murine tissues. Front Immunol 2023; 14:1232511. [PMID: 37908367 PMCID: PMC10613658 DOI: 10.3389/fimmu.2023.1232511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/29/2023] [Indexed: 11/02/2023] Open
Abstract
The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a cutting-edge technology that enables researchers to assess genome-wide chromatin accessibility and to characterize cell type specific gene-regulatory programs. Recent technological progress allows for using this technology also on the single-cell level. In this article, we describe the whole value chain from the isolation of T cells from murine tissues to a complete bioinformatic analysis workflow. We start with methods for isolating scATAC-seq-ready CD4+ T cells from murine tissues such as visceral adipose tissue, skin, colon, and secondary lymphoid tissues such as the spleen. We describe the preparation of nuclei and quality control parameters during library preparation. Based on publicly available sequencing data that was generated using these protocols, we describe a step-by-step bioinformatic analysis pipeline for data pre-processing and downstream analysis. Our analysis workflow will follow the R-based bioinformatics framework ArchR, which is currently well established for scATAC-seq datasets. All in all, this work serves as a one-stop shop for generating and analyzing chromatin accessibility landscapes in T cells.
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Affiliation(s)
- Kathrin Luise Braband
- Institute of Immunology, University Medical Center Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center Mainz, Mainz, Germany
| | - Annekathrin Silvia Nedwed
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, Mainz, Germany
| | - Sara Salome Helbich
- Institute of Immunology, University Medical Center Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center Mainz, Mainz, Germany
| | - Malte Simon
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Niklas Beumer
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- DKFZ-Hector Cancer Institute, University Medical Center Mannheim, Mannheim, Germany
- Division of Personalized Medical Oncology (A420), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Personalized Oncology, University Hospital Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Federico Marini
- Research Center for Immunotherapy (FZI), University Medical Center Mainz, Mainz, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, Mainz, Germany
| | - Michael Delacher
- Institute of Immunology, University Medical Center Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center Mainz, Mainz, Germany
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164
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Liu H, Caliz AD, Learnard H, Koupenova M, Keaney JF, Kant S, Zhu LJ, Vertii A. Inflammatory stress-mediated chromatin changes underlie dysfunction in endothelial cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.11.561959. [PMID: 37905100 PMCID: PMC10614786 DOI: 10.1101/2023.10.11.561959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Inflammatory stresses underlie endothelial dysfunction and contribute to the development of chronic cardiovascular disorders such as atherosclerosis and vascular fibrosis. The initial transcriptional response of endothelial cells to pro-inflammatory cytokines such as TNF-alpha is well established. However, very few studies uncover the effects of inflammatory stresses on chromatin architecture. We used integrative analysis of ATAC-seq and RNA-seq data to investigate chromatin alterations in human endothelial cells in response to TNF-alpha and febrile-range heat stress exposure. Multi-omics data analysis suggests a correlation between the transcription of stress-related genes and endothelial dysfunction drivers with chromatin regions exhibiting differential accessibility. Moreover, microscopy identified the dynamics in the nuclear organization, specifically, the changes in a subset of heterochromatic nucleoli-associated chromatin domains, the centromeres. Upon inflammatory stress exposure, the centromeres decreased association with nucleoli in a p38-dependent manner and increased the number of transcripts from pericentromeric regions. Overall, we provide two lines of evidence that suggest chromatin alterations in vascular endothelial cells during inflammatory stresses.
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Affiliation(s)
- Haibo Liu
- Molecular, Cell and Cancer Biology Department, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Amada D. Caliz
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Heather Learnard
- Cardiovascular Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Milka Koupenova
- Cardiovascular Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - John F. Keaney
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Shashi Kant
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lihua Julie Zhu
- Molecular, Cell and Cancer Biology Department, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Anastassiia Vertii
- Molecular, Cell and Cancer Biology Department, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Innate Immunity, University of Massachusetts Chan Medical School, Worcester, MA, USA
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165
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Gourisankar S, Wenderski W, Paulo JA, Kim SH, Roepke K, Ellis C, Gygi SP, Crabtree GR. Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562244. [PMID: 37873481 PMCID: PMC10592824 DOI: 10.1101/2023.10.13.562244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Genes encoding subunits of the SWI/SNF or BAF ATP-dependent chromatin remodeling complex are among the most enriched for deleterious de novo mutations in intellectual disabilities and autism spectrum disorder, but the causative molecular pathways are not fully known 1,2 . Synaptic activity in neurons is critical for learning and memory and proper neural development 3 . Neural activity prompts calcium influx and transcription within minutes, facilitated in the nucleus by various transcription factors (TFs) and chromatin modifiers 4 . While BAF is required for activity-dependent developmental processes such as dendritic outgrowth 5-7 , the immediate molecular consequences of neural activity on BAF complexes and their functions are unknown. Here we mapped minute-scale biochemical consequences of neural activity, modeled by membrane depolarization of embryonic mouse primary cortical neurons, on BAF complexes. We used acute chemical perturbations of BAF ATPase activity and kinase signaling to define the activity-dependent effects on BAF complexes and activity-dependent BAF functions. Our studies found that BAF complexes change in subunit composition and are selectively phosphorylated within 10 minutes of depolarization. Increased levels of the core PBAF subunit Baf200/ Arid2 , uniquely containing an RFX-like DNA-binding domain, are concurrent with ATPase-dependent opening of chromatin at RFX/X-box motifs. Changes in BAF composition and phosphorylation lead to the regulation of chromatin accessibility for critical neurogenesis TFs. These biochemical effects are a convergent phenomenon downstream of multiple growth factor signaling pathways in mouse neurons and fibroblasts suggesting that BAF integrates signaling information from the membrane. In support of such a membrane-to-nucleus signaling cascade, we also identified a BAF-interacting kinase, Dclk2, whose inhibition attenuates BAF phosphorylation selectively. Our findings support a direct role of BAF complexes in responding to synaptic activity to regulate TF binding and transcription.
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166
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Li YE, Preissl S, Miller M, Johnson ND, Wang Z, Jiao H, Zhu C, Wang Z, Xie Y, Poirion O, Kern C, Pinto-Duarte A, Tian W, Siletti K, Emerson N, Osteen J, Lucero J, Lin L, Yang Q, Zhu Q, Zemke N, Espinoza S, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Hodge RD, Linnarsson S, Bakken T, Levi B, Keene CD, Shang J, Lein E, Wang A, Behrens MM, Ecker JR, Ren B. A comparative atlas of single-cell chromatin accessibility in the human brain. Science 2023; 382:eadf7044. [PMID: 37824643 PMCID: PMC10852054 DOI: 10.1126/science.adf7044] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 09/14/2023] [Indexed: 10/14/2023]
Abstract
Recent advances in single-cell transcriptomics have illuminated the diverse neuronal and glial cell types within the human brain. However, the regulatory programs governing cell identity and function remain unclear. Using a single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq), we explored open chromatin landscapes across 1.1 million cells in 42 brain regions from three adults. Integrating this data unveiled 107 distinct cell types and their specific utilization of 544,735 candidate cis-regulatory DNA elements (cCREs) in the human genome. Nearly a third of the cCREs demonstrated conservation and chromatin accessibility in the mouse brain cells. We reveal strong links between specific brain cell types and neuropsychiatric disorders including schizophrenia, bipolar disorder, Alzheimer's disease (AD), and major depression, and have developed deep learning models to predict the regulatory roles of noncoding risk variants in these disorders.
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Affiliation(s)
- Yang Eric Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Michael Miller
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | | | - Zihan Wang
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Henry Jiao
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Chenxu Zhu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhaoning Wang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yang Xie
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Olivier Poirion
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Colin Kern
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | | | - Wei Tian
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kimberly Siletti
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Nora Emerson
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Julia Osteen
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jacinta Lucero
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Qian Yang
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Quan Zhu
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Nathan Zemke
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Sarah Espinoza
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Trygve Bakken
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98104, USA
| | - Jingbo Shang
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Allen Wang
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | | | - Joseph R Ecker
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
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167
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Wimmers F, Burrell AR, Feng Y, Zheng H, Arunachalam PS, Hu M, Spranger S, Nyhoff LE, Joshi D, Trisal M, Awasthi M, Bellusci L, Ashraf U, Kowli S, Konvinse KC, Yang E, Blanco M, Pellegrini K, Tharp G, Hagan T, Chinthrajah RS, Nguyen TT, Grifoni A, Sette A, Nadeau KC, Haslam DB, Bosinger SE, Wrammert J, Maecker HT, Utz PJ, Wang TT, Khurana S, Khatri P, Staat MA, Pulendran B. Multi-omics analysis of mucosal and systemic immunity to SARS-CoV-2 after birth. Cell 2023; 186:4632-4651.e23. [PMID: 37776858 PMCID: PMC10724861 DOI: 10.1016/j.cell.2023.08.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/18/2023] [Accepted: 08/31/2023] [Indexed: 10/02/2023]
Abstract
The dynamics of immunity to infection in infants remain obscure. Here, we used a multi-omics approach to perform a longitudinal analysis of immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in infants and young children by analyzing blood samples and weekly nasal swabs collected before, during, and after infection with Omicron and non-Omicron variants. Infection stimulated robust antibody titers that, unlike in adults, showed no sign of decay for up to 300 days. Infants mounted a robust mucosal immune response characterized by inflammatory cytokines, interferon (IFN) α, and T helper (Th) 17 and neutrophil markers (interleukin [IL]-17, IL-8, and CXCL1). The immune response in blood was characterized by upregulation of activation markers on innate cells, no inflammatory cytokines, but several chemokines and IFNα. The latter correlated with viral load and expression of interferon-stimulated genes (ISGs) in myeloid cells measured by single-cell multi-omics. Together, these data provide a snapshot of immunity to infection during the initial weeks and months of life.
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Affiliation(s)
- Florian Wimmers
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany; DFG Cluster of Excellence 2180 "Image-guided and Functional Instructed Tumor Therapy" (iFIT), University of Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany; German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Baden-Wuerttemberg, Germany
| | - Allison R Burrell
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Environmental and Public Health Sciences, Division of Epidemiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Mengyun Hu
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Sara Spranger
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lindsay E Nyhoff
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Devyani Joshi
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Meera Trisal
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Mayanka Awasthi
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Lorenza Bellusci
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Usama Ashraf
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
| | - Sangeeta Kowli
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Katherine C Konvinse
- Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Emily Yang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael Blanco
- Stanford Genomics Service Center, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Gregory Tharp
- Yerkes National Primate Research Center, Atlanta, GA 30024, USA
| | - Thomas Hagan
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - R Sharon Chinthrajah
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
| | - Tran T Nguyen
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kari C Nadeau
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
| | - David B Haslam
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Steven E Bosinger
- Yerkes National Primate Research Center, Atlanta, GA 30024, USA; Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Taia T Wang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mary A Staat
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
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168
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Shi Y, Guo Z, Liu F, Pan S, Gao D, Zhou S, Liu Z, Wang F, Liu D, Liu Z. Analysis of potential biomarkers for diabetic kidney disease based on single-cell RNA-sequencing integrated with a single-cell sequencing assay for transposase-accessible chromatin. Aging (Albany NY) 2023; 15:10681-10704. [PMID: 37827693 PMCID: PMC10599739 DOI: 10.18632/aging.205107] [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: 05/18/2023] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
Abstract
Diabetic kidney disease (DKD) is a renal microvascular disease caused by hyperglycemia that involves metabolic remodeling, oxidative stress, inflammation, and other factors. The mechanism is complex and not fully unraveled. We performed an integrated single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) and single-cell RNA-sequencing (scRNA-seq) analyses of kidneys from db/db and db/m mice to identify differential open chromatin regions and gene expression, particularly in genes related to proximal tubular reabsorption and secretion. We identified 9,776 differentially expressed genes (DEGs) and 884 cell type-specific transcription factors (TFs) across 15 cell types. Glucose and lipid transporters, and TFs related to the circadian rhythm in the proximal tubules had significantly higher expression in db/db mice than in db/m mice (P<0.01). Crosstalk between podocytes and tubular cells in the proximal tubules was enhanced, and renal inflammation, oxidative stress, and fibrosis pathways were activated in db/db mice. Western blotting and immunohistochemical staining results showed that Wfdc2 expression in the urine and kidneys of DKD patients was higher than that in non-diabetic kidney disease (NDKD) controls. The revealed landscape of chromatin accessibility and transcriptional profiles in db/db mice provide insights into the pathological mechanism of DKD.
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Affiliation(s)
- Yan Shi
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Zuishuang Guo
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Fengxun Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Shaokang Pan
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Dan Gao
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Sijie Zhou
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Zhenjie Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Feng Wang
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Department of Nephrology, Shanghai Eighth People’s Hospital, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai 200233, P.R. China
| | - Dongwei Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
| | - Zhangsuo Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, P.R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, P.R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P.R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou 450052, P.R. China
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169
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Rubenstein AB, Smith GR, Zhang Z, Chen X, Chambers TL, Ruf-Zamojski F, Mendelev N, Cheng WS, Zamojski M, Amper MAS, Nair VD, Marderstein AR, Montgomery SB, Troyanskaya OG, Zaslavsky E, Trappe T, Trappe S, Sealfon SC. Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.558914. [PMID: 37808658 PMCID: PMC10557702 DOI: 10.1101/2023.09.26.558914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Endurance exercise is an important health modifier. We studied cell-type specific adaptations of human skeletal muscle to acute endurance exercise using single-nucleus (sn) multiome sequencing in human vastus lateralis samples collected before and 3.5 hours after 40 min exercise at 70% VO2max in four subjects, as well as in matched time of day samples from two supine resting circadian controls. High quality same-cell RNA-seq and ATAC-seq data were obtained from 37,154 nuclei comprising 14 cell types. Among muscle fiber types, both shared and fiber-type specific regulatory programs were identified. Single-cell circuit analysis identified distinct adaptations in fast, slow and intermediate fibers as well as LUM-expressing FAP cells, involving a total of 328 transcription factors (TFs) acting at altered accessibility sites regulating 2,025 genes. These data and circuit mapping provide single-cell insight into the processes underlying tissue and metabolic remodeling responses to exercise.
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Affiliation(s)
- Aliza B. Rubenstein
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Gregory R. Smith
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Zidong Zhang
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Xi Chen
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Toby L. Chambers
- Human Performance Laboratory, Ball State University, Muncie, IN 47306, USA
| | - Frederique Ruf-Zamojski
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Natalia Mendelev
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Wan Sze Cheng
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Michel Zamojski
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mary Anne S. Amper
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Venugopalan D. Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Andrew R. Marderstein
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Stephen B. Montgomery
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Olga G. Troyanskaya
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Todd Trappe
- Human Performance Laboratory, Ball State University, Muncie, IN 47306, USA
| | - Scott Trappe
- Human Performance Laboratory, Ball State University, Muncie, IN 47306, USA
- Senior author
| | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
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170
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Xia L, Komissarova A, Jacover A, Shovman Y, Arcila-Barrera S, Tornovsky-Babeay S, Jaya Prakashan MM, Nasereddin A, Plaschkes I, Nevo Y, Shiff I, Yosefov-Levi O, Izhiman T, Medvedev E, Eilon E, Wilensky A, Yona S, Parnas O. Systematic identification of gene combinations to target in innate immune cells to enhance T cell activation. Nat Commun 2023; 14:6295. [PMID: 37813864 PMCID: PMC10562403 DOI: 10.1038/s41467-023-41792-8] [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: 07/06/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023] Open
Abstract
Genetic engineering of immune cells has opened new avenues for improving their functionality but it remains a challenge to pinpoint which genes or combination of genes are the most beneficial to target. Here, we conduct High Multiplicity of Perturbations and Cellular Indexing of Transcriptomes and Epitopes (HMPCITE-seq) to find combinations of genes whose joint targeting improves antigen-presenting cell activity and enhances their ability to activate T cells. Specifically, we perform two genome-wide CRISPR screens in bone marrow dendritic cells and identify negative regulators of CD86, that participate in the co-stimulation programs, including Chd4, Stat5b, Egr2, Med12, and positive regulators of PD-L1, that participate in the co-inhibitory programs, including Sptlc2, Nckap1l, and Pi4kb. To identify the genetic interactions between top-ranked genes and find superior combinations to target, we perform high-order Perturb-Seq experiments and we show that targeting both Cebpb and Med12 results in a better phenotype compared to the single perturbations or other combinations of perturbations.
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Affiliation(s)
- Lei Xia
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Anastasia Komissarova
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Arielle Jacover
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Yehuda Shovman
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel.
| | - Sebastian Arcila-Barrera
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Sharona Tornovsky-Babeay
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Milsee Mol Jaya Prakashan
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Abdelmajeed Nasereddin
- Core Research Facility, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Inbar Plaschkes
- I-CORE Bioinformatics Unit of the Hebrew University and Hadassah Medical Center, Jerusalem, 91120, Israel
| | - Yuval Nevo
- I-CORE Bioinformatics Unit of the Hebrew University and Hadassah Medical Center, Jerusalem, 91120, Israel
| | - Idit Shiff
- Core Research Facility, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Oshri Yosefov-Levi
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Tamara Izhiman
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Eleonora Medvedev
- Core Research Facility, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Elad Eilon
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Asaf Wilensky
- Department of Periodontology, Hadassah Medical Center, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Simon Yona
- The Institute of Biomedical and Oral Research, Hebrew University, Jerusalem, 91120, Israel
| | - Oren Parnas
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel.
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171
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Ibarra-Soria X, Thierion E, Mok GF, Münsterberg AE, Odom DT, Marioni JC. A transcriptional and regulatory map of mouse somite maturation. Dev Cell 2023; 58:1983-1995.e7. [PMID: 37499658 PMCID: PMC10563765 DOI: 10.1016/j.devcel.2023.07.003] [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: 01/25/2023] [Revised: 05/12/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023]
Abstract
The mammalian body plan is shaped by rhythmic segmentation of mesoderm into somites, which are transient embryonic structures that form down each side of the neural tube. We have analyzed the genome-wide transcriptional and chromatin dynamics occurring within nascent somites, from early inception of somitogenesis to the latest stages of body plan establishment. We created matched gene expression and open chromatin maps for the three leading pairs of somites at six time points during mouse embryonic development. We show that the rate of somite differentiation accelerates as development progresses. We identified a conserved maturation program followed by all somites, but somites from more developed embryos concomitantly switch on differentiation programs from derivative cell lineages soon after segmentation. Integrated analysis of the somitic transcriptional and chromatin activities identified opposing regulatory modules controlling the onset of differentiation. Our results provide a powerful, high-resolution view of the molecular genetics underlying somitic development in mammals.
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Affiliation(s)
- Ximena Ibarra-Soria
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
| | - Elodie Thierion
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Gi Fay Mok
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Andrea E Münsterberg
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; DKFZ, Division of Regulatory Genomics and Cancer Evolution B270, Im Neunheimer Feld 280, Heidelberg, 69120, Germany.
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
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172
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Yan KK, Condori J, Ma Z, Metais JY, Ju B, Ding L, Dhungana Y, Palmer LE, Langfitt DM, Ferrara F, Throm R, Shi H, Risch I, Bhatara S, Shaner B, Lockey TD, Talleur AC, Easton J, Meagher MM, Puck JM, Cowan MJ, Zhou S, Mamcarz E, Gottschalk S, Yu J. Integrome signatures of lentiviral gene therapy for SCID-X1 patients. SCIENCE ADVANCES 2023; 9:eadg9959. [PMID: 37801507 PMCID: PMC10558130 DOI: 10.1126/sciadv.adg9959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
Lentiviral vector (LV)-based gene therapy holds promise for a broad range of diseases. Analyzing more than 280,000 vector integration sites (VISs) in 273 samples from 10 patients with X-linked severe combined immunodeficiency (SCID-X1), we discovered shared LV integrome signatures in 9 of 10 patients in relation to the genomics, epigenomics, and 3D structure of the human genome. VISs were enriched in the nuclear subcompartment A1 and integrated into super-enhancers close to nuclear pore complexes. These signatures were validated in T cells transduced with an LV encoding a CD19-specific chimeric antigen receptor. Intriguingly, the one patient whose VISs deviated from the identified integrome signatures had a distinct clinical course. Comparison of LV and gamma retrovirus integromes regarding their 3D genome signatures identified differences that might explain the lower risk of insertional mutagenesis in LV-based gene therapy. Our findings suggest that LV integrome signatures, shaped by common features such as genome organization, may affect the efficacy of LV-based cellular therapies.
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Affiliation(s)
- Koon-Kiu Yan
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jose Condori
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zhijun Ma
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jean-Yves Metais
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Bensheng Ju
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Liang Ding
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yogesh Dhungana
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Lance E. Palmer
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Deanna M. Langfitt
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Francesca Ferrara
- Vector Development and Production Core, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robert Throm
- Vector Development and Production Core, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hao Shi
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Isabel Risch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sheetal Bhatara
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Bridget Shaner
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Timothy D. Lockey
- Department of Therapeutics Production and Quality, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Aimee C. Talleur
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Michael M. Meagher
- Department of Therapeutics Production and Quality, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jennifer M. Puck
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Bone Marrow Transplantation, University of California San Francisco Benioff Children’s Hospital, San Francisco, CA 94158, USA
| | - Morton J. Cowan
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Bone Marrow Transplantation, University of California San Francisco Benioff Children’s Hospital, San Francisco, CA 94158, USA
| | - Sheng Zhou
- Experimental Cellular Therapeutics Laboratory, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ewelina Mamcarz
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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173
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Harris AR, Panigrahi G, Liu H, Koparde VN, Bailey-Whyte M, Dorsey TH, Yates CC, Ambs S. Chromatin Accessibility Landscape of Human Triple-negative Breast Cancer Cell Lines Reveals Variation by Patient Donor Ancestry. CANCER RESEARCH COMMUNICATIONS 2023; 3:2014-2029. [PMID: 37732899 PMCID: PMC10552704 DOI: 10.1158/2767-9764.crc-23-0236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/01/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
African American (AA) women have an excessive risk of developing triple-negative breast cancer (TNBC). We employed Assay for Transposase-Accessible Chromatin using sequencing to characterize differences in chromatin accessibility between nine commonly used TNBC cell lines derived from patients of European and African ancestry. Principal component and chromosome mapping analyses of accessibility peaks with the most variance revealed separation of chromatin profiles by patient group. Motif enrichment and footprinting analyses of disparate open chromatin regions revealed differences in transcription factor activity, identifying 79 with ancestry-associated binding patterns (FDR < 0.01). AA TNBC cell lines exhibited increased accessibility for 62 transcription factors associated with epithelial-to-mesenchymal transition, cancer stemness/chemotherapeutic resistance, proliferation, and aberrant p53 regulation, as well as KAISO, which has been previously linked to aggressive tumor characteristics in AA patients with cancer. Differential Assay for Transposase-Accessible Chromatin signal analysis identified 1,596 genes located within promoters of differentially open chromatin regions in AA-derived TNBC, identifying DNA methyltransferase 1 as the top upregulated gene associated with African ancestry. Pathway analyses with these genes revealed enrichment in several pathways, including hypoxia. Culturing cells under hypoxia showed ancestry-specific stress responses that led to the identification of a core set of AA-associated transcription factors, which included members of the Kruppel-like factor and Sp subfamilies, as well as KAISO, and identified ZDHHC1, a gene previously implicated in immunity and STING activation, as the top upregulated AA-specific gene under hypoxia. Together, these data reveal a differential chromatin landscape in TNBC associated with donor ancestry. The open chromatin structure of AA TNBC may contribute to a more lethal disease. SIGNIFICANCE We identify an ancestry-associated open chromatin landscape and related transcription factors that may contribute to aggressive TNBC in AA women. Furthermore, this study advocates for the inclusion of diversely sourced cell lines in experimental in vitro studies to advance health equity at all levels of scientific research.
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Affiliation(s)
- Alexandra R. Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Gatikrushna Panigrahi
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Huaitian Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Vishal N. Koparde
- Center for Cancer Research Collaborative Bioinformatics Resource Frederick National Laboratory for Cancer Research, NCI, Frederick, Maryland
- Advanced Biomedical Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Maeve Bailey-Whyte
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- School of Medicine, University of Limerick, Limerick, Ireland
| | - Tiffany H. Dorsey
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Clayton C. Yates
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
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174
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Michelson DA, Zuo C, Verzi M, Benoist C, Mathis D. Hnf4 activates mimetic-cell enhancers to recapitulate gut and liver development within the thymus. J Exp Med 2023; 220:e20230461. [PMID: 37399024 PMCID: PMC10318407 DOI: 10.1084/jem.20230461] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/16/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023] Open
Abstract
Mimetic cells are medullary thymic epithelial cells (mTECs) that mimic extra-thymic cell types to tolerize T cells to self-antigens. Here, we dissected the biology of entero-hepato mTECs, mimetic cells expressing gut- and liver-associated transcripts. Entero-hepato mTECs conserved their thymic identity yet accessed wide swaths of enterocyte chromatin and transcriptional programs via the transcription factors Hnf4α and Hnf4γ. Deletion of Hnf4α and Hnf4γ in TECs ablated entero-hepato mTECs and downregulated numerous gut- and liver-associated transcripts, with a primary contribution from Hnf4γ. Loss of Hnf4 impaired enhancer activation and CTCF redistribution in mTECs but did not impact Polycomb-mediated repression or promoter-proximal histone marks. By single-cell RNA sequencing, Hnf4 loss produced three distinct effects on mimetic cell state, fate, and accumulation. Serendipitously, a requirement for Hnf4 in microfold mTECs was discovered, which exposed a requirement for Hnf4γ in gut microfold cells and the IgA response. Study of Hnf4 in entero-hepato mTECs thus revealed mechanisms of gene control in the thymus and periphery alike.
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Affiliation(s)
| | - Chong Zuo
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Michael Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | | | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA, USA
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175
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Fan AC, Nakauchi Y, Bai L, Azizi A, Nuno KA, Zhao F, Köhnke T, Karigane D, Cruz-Hernandez D, Reinisch A, Khatri P, Majeti R. RUNX1 loss renders hematopoietic and leukemic cells dependent on IL-3 and sensitive to JAK inhibition. J Clin Invest 2023; 133:e167053. [PMID: 37581927 PMCID: PMC10541186 DOI: 10.1172/jci167053] [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: 11/09/2022] [Accepted: 08/10/2023] [Indexed: 08/17/2023] Open
Abstract
Disease-initiating mutations in the transcription factor RUNX1 occur as germline and somatic events that cause leukemias with particularly poor prognosis. However, the role of RUNX1 in leukemogenesis is not fully understood, and effective therapies for RUNX1-mutant leukemias remain elusive. Here, we used primary patient samples and a RUNX1-KO model in primary human hematopoietic cells to investigate how RUNX1 loss contributes to leukemic progression and to identify targetable vulnerabilities. Surprisingly, we found that RUNX1 loss decreased proliferative capacity and stem cell function. However, RUNX1-deficient cells selectively upregulated the IL-3 receptor. Exposure to IL-3, but not other JAK/STAT cytokines, rescued RUNX1-KO proliferative and competitive defects. Further, we demonstrated that RUNX1 loss repressed JAK/STAT signaling and rendered RUNX1-deficient cells sensitive to JAK inhibitors. Our study identifies a dependency of RUNX1-mutant leukemias on IL-3/JAK/STAT signaling, which may enable targeting of these aggressive blood cancers with existing agents.
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Affiliation(s)
- Amy C. Fan
- Immunology Graduate Program
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | - Yusuke Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | | | - Armon Azizi
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
- University of California Irvine School of Medicine, Irvine, California, USA
| | - Kevin A. Nuno
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
- Cancer Biology Graduate Program, Stanford University School of Medicine, Stanford, California, USA
| | - Feifei Zhao
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | - Thomas Köhnke
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | - Daiki Karigane
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | - David Cruz-Hernandez
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
- Medical Research Council (MRC) Molecular Haematology Unit and Oxford Centre for Haematology, University of Oxford, Oxford, United Kingdom
| | - Andreas Reinisch
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
- Division of Hematology, Medical University of Graz, Graz, Austria
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, and
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
| | - Ravindra Majeti
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
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176
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Wartewig T, Daniels J, Schulz M, Hameister E, Joshi A, Park J, Morrish E, Venkatasubramani AV, Cernilogar FM, van Heijster FHA, Hundshammer C, Schneider H, Konstantinidis F, Gabler JV, Klement C, Kurniawan H, Law C, Lee Y, Choi S, Guitart J, Forne I, Giustinani J, Müschen M, Jain S, Weinstock DM, Rad R, Ortonne N, Schilling F, Schotta G, Imhof A, Brenner D, Choi J, Ruland J. PD-1 instructs a tumor-suppressive metabolic program that restricts glycolysis and restrains AP-1 activity in T cell lymphoma. NATURE CANCER 2023; 4:1508-1525. [PMID: 37723306 PMCID: PMC10597841 DOI: 10.1038/s43018-023-00635-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 08/15/2023] [Indexed: 09/20/2023]
Abstract
The PDCD1-encoded immune checkpoint receptor PD-1 is a key tumor suppressor in T cells that is recurrently inactivated in T cell non-Hodgkin lymphomas (T-NHLs). The highest frequencies of PDCD1 deletions are detected in advanced disease, predicting inferior prognosis. However, the tumor-suppressive mechanisms of PD-1 signaling remain unknown. Here, using tractable mouse models for T-NHL and primary patient samples, we demonstrate that PD-1 signaling suppresses T cell malignancy by restricting glycolytic energy and acetyl coenzyme A (CoA) production. In addition, PD-1 inactivation enforces ATP citrate lyase (ACLY) activity, which generates extramitochondrial acetyl-CoA for histone acetylation to enable hyperactivity of activating protein 1 (AP-1) transcription factors. Conversely, pharmacological ACLY inhibition impedes aberrant AP-1 signaling in PD-1-deficient T-NHLs and is toxic to these cancers. Our data uncover genotype-specific vulnerabilities in PDCD1-mutated T-NHL and identify PD-1 as regulator of AP-1 activity.
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Affiliation(s)
- Tim Wartewig
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- Center of Molecular and Cellular Oncology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Jay Daniels
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Miriam Schulz
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Erik Hameister
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Abhinav Joshi
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Joonhee Park
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Emma Morrish
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Anuroop V Venkatasubramani
- Protein Analysis Unit, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Martinsried, Germany
| | - Filippo M Cernilogar
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Martinsried, Germany
| | - Frits H A van Heijster
- Department of Nuclear Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christian Hundshammer
- Department of Nuclear Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - Heike Schneider
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Filippos Konstantinidis
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Judith V Gabler
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christine Klement
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Henry Kurniawan
- Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Immunology and Genetics, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Calvin Law
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Yujin Lee
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Sara Choi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Joan Guitart
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Ignasi Forne
- Protein Analysis Unit, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Martinsried, Germany
| | - Jérôme Giustinani
- Institut Mondor de Recherche Biomédicale, Inserm U955, Paris-Est Créteil University, Créteil, France
| | - Markus Müschen
- Center of Molecular and Cellular Oncology, Yale School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, Yale University, New Haven, CT, USA
| | - Salvia Jain
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - David M Weinstock
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Merck Research Laboratories, Boston, MA, USA
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Medicine II, School of Medicine, Technical University of Munich, Munich, Germany
| | - Nicolas Ortonne
- Institut Mondor de Recherche Biomédicale, Inserm U955, Paris-Est Créteil University, Créteil, France
- Pathology Department, AP-HP Inserm U955, Henri Mondor Hospital, Créteil, France
| | - Franz Schilling
- Department of Nuclear Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - Gunnar Schotta
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Martinsried, Germany
| | - Axel Imhof
- Protein Analysis Unit, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Martinsried, Germany
| | - Dirk Brenner
- Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Immunology and Genetics, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Jaehyuk Choi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
- Center for Genetic Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
- Center for Human Immunobiology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
| | - Jürgen Ruland
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany.
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.
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177
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Li X, Li Y, Jin Y, Zhang Y, Wu J, Xu Z, Huang Y, Cai L, Gao S, Liu T, Zeng F, Wang Y, Wang W, Yuan TF, Tian H, Shu Y, Guo F, Lu W, Mao Y, Mei X, Rao Y, Peng B. Transcriptional and epigenetic decoding of the microglial aging process. NATURE AGING 2023; 3:1288-1311. [PMID: 37697166 PMCID: PMC10570141 DOI: 10.1038/s43587-023-00479-x] [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] [Received: 08/07/2022] [Accepted: 08/03/2023] [Indexed: 09/13/2023]
Abstract
As important immune cells, microglia undergo a series of alterations during aging that increase the susceptibility to brain dysfunctions. However, the longitudinal characteristics of microglia remain poorly understood. In this study, we mapped the transcriptional and epigenetic profiles of microglia from 3- to 24-month-old mice. We first discovered unexpected sex differences and identified age-dependent microglia (ADEM) genes during the aging process. We then compared the features of aging and reactivity in female microglia at single-cell resolution and epigenetic level. To dissect functions of aged microglia excluding the influence from other aged brain cells, we established an accelerated microglial turnover model without directly affecting other brain cells. By this model, we achieved aged-like microglia in non-aged brains and confirmed that aged-like microglia per se contribute to cognitive decline. Collectively, our work provides a comprehensive resource for decoding the aging process of microglia, shedding light on how microglia maintain brain functions.
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Affiliation(s)
- Xiaoyu Li
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Yuxin Li
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Yuxiao Jin
- Department of Neurology, Zhongshan Hospital, Department of Laboratory Animal Science, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Yuheng Zhang
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Jingchuan Wu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhen Xu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yubin Huang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lin Cai
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuai Gao
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Taohui Liu
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Fanzhuo Zeng
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
- Department of Orthopedics, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Yafei Wang
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Wenxu Wang
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Ti-Fei Yuan
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hengli Tian
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yousheng Shu
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Feifan Guo
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Wei Lu
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Xifan Mei
- Department of Orthopedics, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Yanxia Rao
- Department of Neurology, Zhongshan Hospital, Department of Laboratory Animal Science, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
| | - Bo Peng
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China.
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.
- Co-Innovation Center of Neurodegeneration, Nantong University, Nantong, China.
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178
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Givony T, Leshkowitz D, Del Castillo D, Nevo S, Kadouri N, Dassa B, Gruper Y, Khalaila R, Ben-Nun O, Gome T, Dobeš J, Ben-Dor S, Kedmi M, Keren-Shaul H, Heffner-Krausz R, Porat Z, Golani O, Addadi Y, Brenner O, Lo DD, Goldfarb Y, Abramson J. Thymic mimetic cells function beyond self-tolerance. Nature 2023; 622:164-172. [PMID: 37674082 DOI: 10.1038/s41586-023-06512-8] [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: 07/08/2022] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
Development of immunocompetent T cells in the thymus is required for effective defence against all types of pathogens, including viruses, bacteria and fungi. To this end, T cells undergo a very strict educational program in the thymus, during which both non-functional and self-reactive T cell clones are eliminated by means of positive and negative selection1.Thymic epithelial cells (TECs) have an indispensable role in these processes, and previous studies have shown the notable heterogeneity of these cells2-7. Here, using multiomic analysis, we provide further insights into the functional and developmental diversity of TECs in mice, and reveal a detailed atlas of the TEC compartment according to cell transcriptional states and chromatin landscapes. Our analysis highlights unconventional TEC subsets that are similar to functionally well-defined parenchymal populations, including endocrine cells, microfold cells and myocytes. By focusing on the endocrine and microfold TEC populations, we show that endocrine TECs require Insm1 for their development and are crucial to maintaining thymus cellularity in a ghrelin-dependent manner; by contrast, microfold TECs require Spib for their development and are essential for the generation of thymic IgA+ plasma cells. Collectively, our study reveals that medullary TECs have the potential to differentiate into various types of molecularly distinct and functionally defined cells, which not only contribute to the induction of central tolerance, but also regulate the homeostasis of other thymus-resident populations.
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Affiliation(s)
- Tal Givony
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dena Leshkowitz
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Diana Del Castillo
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Shir Nevo
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Kadouri
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Gruper
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Razi Khalaila
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Osher Ben-Nun
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tom Gome
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jan Dobeš
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Shifra Ben-Dor
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Kedmi
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Keren-Shaul
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, Israel
| | | | - Ziv Porat
- Flow Cytometry Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- MICC Cell Observatory, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Yoseph Addadi
- MICC Cell Observatory, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Brenner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - David D Lo
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Yael Goldfarb
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Jakub Abramson
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
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179
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Weatherbee BAT, Gantner CW, Iwamoto-Stohl LK, Daza RM, Hamazaki N, Shendure J, Zernicka-Goetz M. Pluripotent stem cell-derived model of the post-implantation human embryo. Nature 2023; 622:584-593. [PMID: 37369347 PMCID: PMC10584688 DOI: 10.1038/s41586-023-06368-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 06/23/2023] [Indexed: 06/29/2023]
Abstract
The human embryo undergoes morphogenetic transformations following implantation into the uterus, but our knowledge of this crucial stage is limited by the inability to observe the embryo in vivo. Models of the embryo derived from stem cells are important tools for interrogating developmental events and tissue-tissue crosstalk during these stages1. Here we establish a model of the human post-implantation embryo, a human embryoid, comprising embryonic and extraembryonic tissues. We combine two types of extraembryonic-like cell generated by overexpression of transcription factors with wild-type embryonic stem cells and promote their self-organization into structures that mimic several aspects of the post-implantation human embryo. These self-organized aggregates contain a pluripotent epiblast-like domain surrounded by extraembryonic-like tissues. Our functional studies demonstrate that the epiblast-like domain robustly differentiates into amnion, extraembryonic mesenchyme and primordial germ cell-like cells in response to bone morphogenetic protein cues. In addition, we identify an inhibitory role for SOX17 in the specification of anterior hypoblast-like cells2. Modulation of the subpopulations in the hypoblast-like compartment demonstrates that extraembryonic-like cells influence epiblast-like domain differentiation, highlighting functional tissue-tissue crosstalk. In conclusion, we present a modular, tractable, integrated3 model of the human embryo that will enable us to probe key questions of human post-implantation development, a critical window during which substantial numbers of pregnancies fail.
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Affiliation(s)
- Bailey A T Weatherbee
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Carlos W Gantner
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Lisa K Iwamoto-Stohl
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Riza M Daza
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Nobuhiko Hamazaki
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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180
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Takeuchi F, Liang YQ, Shimizu-Furusawa H, Isono M, Ang MY, Mori K, Mori T, Kakazu E, Yoshio S, Kato N. Gene-regulation modules in nonalcoholic fatty liver disease revealed by single-nucleus ATAC-seq. Life Sci Alliance 2023; 6:e202301988. [PMID: 37491046 PMCID: PMC10368228 DOI: 10.26508/lsa.202301988] [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: 02/13/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023] Open
Abstract
We investigated the progression of nonalcoholic fatty liver disease from fatty liver to steatohepatitis using single-nucleus and bulk ATAC-seq on the livers of rats fed a high-fat diet (HFD). Rats fed HFD for 4 wk developed fatty liver, and those fed HFD for 8 wk further progressed to steatohepatitis. We observed an increase in the proportion of inflammatory macrophages, consistent with the pathological progression. Utilizing machine learning, we divided global gene regulation into modules, wherein transcription factors within a module could regulate genes within the same module, reaffirming known regulatory relationships between transcription factors and biological processes. We identified core genes-central to co-expression and protein-protein interaction-for the biological processes discovered. Notably, a large part of the core genes overlapped with genes previously implicated in nonalcoholic fatty liver disease. Single-nucleus ATAC-seq, combined with data-driven statistical analysis, offers insight into in vivo global gene regulation as a combination of modules and assists in identifying core genes of relevant biological processes.
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Affiliation(s)
- Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Medical Genomics Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Systems Genomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Yi-Qiang Liang
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hana Shimizu-Furusawa
- Department of Hygiene and Public Health, School of Medicine, Teikyo University, Tokyo, Japan
| | - Masato Isono
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Mia Yang Ang
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Department of Clinical Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kotaro Mori
- Medical Genomics Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Taizo Mori
- Department of Liver Diseases, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan
| | - Eiji Kakazu
- Department of Liver Diseases, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan
| | - Sachiyo Yoshio
- Department of Liver Diseases, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Medical Genomics Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Department of Clinical Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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181
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Lu Z, Zhang M, Lee J, Sziraki A, Anderson S, Zhang Z, Xu Z, Jiang W, Ge S, Nelson PT, Zhou W, Cao J. Tracking cell-type-specific temporal dynamics in human and mouse brains. Cell 2023; 186:4345-4364.e24. [PMID: 37774676 PMCID: PMC10545416 DOI: 10.1016/j.cell.2023.08.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/28/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Progenitor cells are critical in preserving organismal homeostasis, yet their diversity and dynamics in the aged brain remain underexplored. We introduced TrackerSci, a single-cell genomic method that combines newborn cell labeling and combinatorial indexing to characterize the transcriptome and chromatin landscape of proliferating progenitor cells in vivo. Using TrackerSci, we investigated the dynamics of newborn cells in mouse brains across various ages and in a mouse model of Alzheimer's disease. Our dataset revealed diverse progenitor cell types in the brain and their epigenetic signatures. We further quantified aging-associated shifts in cell-type-specific proliferation and differentiation and deciphered the associated molecular programs. Extending our study to the progenitor cells in the aged human brain, we identified conserved genetic signatures across species and pinpointed region-specific cellular dynamics, such as the reduced oligodendrogenesis in the cerebellum. We anticipate that TrackerSci will be broadly applicable to unveil cell-type-specific temporal dynamics in diverse systems.
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Affiliation(s)
- Ziyu Lu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Melissa Zhang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Jasper Lee
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Andras Sziraki
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Sonya Anderson
- Department of Pathology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Zehao Zhang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Zihan Xu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Weirong Jiang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Shaoyu Ge
- Department of Neurobiology & Behavior, SUNY at Stony Brook, Stony Brook, NY, USA
| | - Peter T Nelson
- Department of Pathology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Wei Zhou
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
| | - Junyue Cao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
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182
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Chen D, Liu S, Chu X, Reiter J, Gao H, McGuire P, Yu X, Xuei X, Liu Y, Wan J, Fang F, Liu Y, Wang Y. Osteogenic Differentiation Potential of Mesenchymal Stem Cells Using Single Cell Multiomic Analysis. Genes (Basel) 2023; 14:1871. [PMID: 37895219 PMCID: PMC10606235 DOI: 10.3390/genes14101871] [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: 08/20/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Mesenchymal stem cells (MSC) are multipotent stem cells that can differentiate into multiple cell types, including osteoblasts, chondrocytes, and adipocytes. Osteoblast differentiation is reduced during osteoporosis development, resulting in reduced bone formation. Further, MSC isolated from different donors possess distinct osteogenic capacity. In this study, we used single-cell multiomic analysis to profile the transcriptome and epigenome of MSC from four healthy donors. Data were obtained from ~1300 to 1600 cells for each donor. These cells were clustered into four groups, indicating that MSC from different donors have distinct chromatin accessible regulatory elements for regulating gene expression. To investigate the mechanism by which MSC undergo osteogenic differentiation, we used the chromatin accessibility data from the single-cell multiome data to identify individual-specific enhancer-promoter pairs and evaluated the expression levels and activities of the transcriptional regulators. The MSC from four donors showed distinct differentiation potential into osteoblasts. MSC of donor 1 showed the largest average motif activities, indicating that MSC from donor 1 was most likely to differentiate into osteoblasts. The results of our validation experiments were consistent with the bioinformatics prediction. We also tested the enrichment of genome-wide association study (GWAS) signals of several musculoskeletal disease traits in the patient-specific chromatin accessible regions identified in the single-cell multiome data, including osteoporosis, osteopenia, and osteoarthritis. We found that osteoarthritis-associated variants were only enriched in the regions identified from donor 4. In contrast, osteoporosis and osteopenia variants were enriched in regions from donor 1 and least enriched in donor 4. Since osteoporosis and osteopenia are related to the density of bone cells, the enrichment of variants from these traits should be correlated with the osteogenic potential of MSC. In summary, this study provides large-scale data to link regulatory elements with their target genes to study the regulatory relationships during the differentiation of mesenchymal stem cells and provide a deeper insight into the gene regulatory mechanism.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Yue Wang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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183
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Travisano SI, Harrison MRM, Thornton ME, Grubbs BH, Quertermous T, Lien CL. Single-nuclei multiomic analyses identify human cardiac lymphatic endothelial cells associated with coronary arteries in the epicardium. Cell Rep 2023; 42:113106. [PMID: 37676760 DOI: 10.1016/j.celrep.2023.113106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/31/2023] [Accepted: 08/23/2023] [Indexed: 09/09/2023] Open
Abstract
Cardiac lymphatic vessels play important roles in fluid homeostasis, inflammation, disease, and regeneration of the heart. The developing cardiac lymphatics in human fetal hearts are closely associated with coronary arteries, similar to those in zebrafish hearts. We identify a population of cardiac lymphatic endothelial cells (LECs) that reside in the epicardium. Single-nuclei multiomic analysis of the human fetal heart reveals the plasticity and heterogeneity of the cardiac endothelium. Furthermore, we find that VEGFC is highly expressed in arterial endothelial cells and epicardium-derived cells, providing a molecular basis for the arterial association of cardiac lymphatic development. Using a cell-type-specific integrative analysis, we identify a population of cardiac lymphatic endothelial cells marked by the PROX1 and the lymphangiocrine RELN and enriched in binding motifs of erythroblast transformation specific (ETS) variant (ETV) transcription factors. We report the in vivo molecular characterization of human cardiac lymphatics and provide a valuable resource to understand fetal heart development.
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Affiliation(s)
| | - Michael R M Harrison
- The Saban Research Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Cardiovascular Research Institute, Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Matthew E Thornton
- Maternal-Fetal Medicine Division, Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Brendan H Grubbs
- Maternal-Fetal Medicine Division, Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Thomas Quertermous
- Division of Cardiovascular Medicine and the Cardiovascular Institute, School of Medicine, Stanford University, Falk CVRC, Stanford, CA 94305, USA
| | - Ching-Ling Lien
- The Saban Research Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Departments of Surgery, Biochemistry, and Molecular Medicine, Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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184
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Laddach A, Chng SH, Lasrado R, Progatzky F, Shapiro M, Erickson A, Sampedro Castaneda M, Artemov AV, Bon-Frauches AC, Amaniti EM, Kleinjung J, Boeing S, Ultanir S, Adameyko I, Pachnis V. A branching model of lineage differentiation underpinning the neurogenic potential of enteric glia. Nat Commun 2023; 14:5904. [PMID: 37737269 PMCID: PMC10516949 DOI: 10.1038/s41467-023-41492-3] [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: 03/08/2023] [Accepted: 09/06/2023] [Indexed: 09/23/2023] Open
Abstract
Glial cells have been proposed as a source of neural progenitors, but the mechanisms underpinning the neurogenic potential of adult glia are not known. Using single cell transcriptomic profiling, we show that enteric glial cells represent a cell state attained by autonomic neural crest cells as they transition along a linear differentiation trajectory that allows them to retain neurogenic potential while acquiring mature glial functions. Key neurogenic loci in early enteric nervous system progenitors remain in open chromatin configuration in mature enteric glia, thus facilitating neuronal differentiation under appropriate conditions. Molecular profiling and gene targeting of enteric glial cells in a cell culture model of enteric neurogenesis and a gut injury model demonstrate that neuronal differentiation of glia is driven by transcriptional programs employed in vivo by early progenitors. Our work provides mechanistic insight into the regulatory landscape underpinning the development of intestinal neural circuits and generates a platform for advancing glial cells as therapeutic agents for the treatment of neural deficits.
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Affiliation(s)
- Anna Laddach
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Song Hui Chng
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Experimental Drug Development Centre A*STAR 10 Biopolis Road, Chromos, 138670, Singapore
| | - Reena Lasrado
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- COMPASS Pathways PLC, Fora, 33 Broadwick St, London, W1F 0DQ, UK
| | - Fränze Progatzky
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Michael Shapiro
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alek Erickson
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Marisol Sampedro Castaneda
- Kinases and Brain Development Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Artem V Artemov
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Bienna, 1090, Austria
- Boehringer Ingelheim RCV, Vienna, Austria
| | - Ana Carina Bon-Frauches
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Eleni-Maria Amaniti
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Sainsbury Wellcome Centre, London, UK
| | - Jens Kleinjung
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Stefan Boeing
- Bioinformatics and Biostatistics Science Technology Platform, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sila Ultanir
- Kinases and Brain Development Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, 17165, Sweden
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Bienna, 1090, Austria
| | - Vassilis Pachnis
- Nervous System Development and Homeostasis Laboratory, the Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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185
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Hu H, Ho D, Tan DS, MacCarthy C, Yu CH, Weng M, Schöler H, Jauch R. Evaluation of the determinants for improved pluripotency induction and maintenance by engineered SOX17. Nucleic Acids Res 2023; 51:8934-8956. [PMID: 37607832 PMCID: PMC10516664 DOI: 10.1093/nar/gkad597] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 08/24/2023] Open
Abstract
An engineered SOX17 variant with point mutations within its DNA binding domain termed SOX17FNV is a more potent pluripotency inducer than SOX2, yet the underlying mechanism remains unclear. Although wild-type SOX17 was incapable of inducing pluripotency, SOX17FNV outperformed SOX2 in mouse and human pluripotency reprogramming. In embryonic stem cells, SOX17FNV could replace SOX2 to maintain pluripotency despite considerable sequence differences and upregulated genes expressed in cleavage-stage embryos. Mechanistically, SOX17FNV co-bound OCT4 more cooperatively than SOX2 in the context of the canonical SoxOct DNA element. SOX2, SOX17, and SOX17FNV were all able to bind nucleosome core particles in vitro, which is a prerequisite for pioneer transcription factors. Experiments using purified proteins and in cellular contexts showed that SOX17 variants phase-separated more efficiently than SOX2, suggesting an enhanced ability to self-organise. Systematic deletion analyses showed that the N-terminus of SOX17FNV was dispensable for its reprogramming activity. However, the C-terminus encodes essential domains indicating multivalent interactions that drive transactivation and reprogramming. We defined a minimal SOX17FNV (miniSOX) that can support reprogramming with high activity, reducing the payload of reprogramming cassettes. This study uncovers the mechanisms behind SOX17FNV-induced pluripotency and establishes engineered SOX factors as powerful cell engineering tools.
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Affiliation(s)
- Haoqing Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Derek Hoi Hang Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Translational Stem Cell Biology, Hong Kong
| | - Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | | | - Cheng-han Yu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mingxi Weng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Translational Stem Cell Biology, Hong Kong
| | | | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Translational Stem Cell Biology, Hong Kong
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186
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Yi D, Nam JW, Jeong H. Toward the functional interpretation of somatic structural variations: bulk- and single-cell approaches. Brief Bioinform 2023; 24:bbad297. [PMID: 37587831 PMCID: PMC10516374 DOI: 10.1093/bib/bbad297] [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: 05/10/2023] [Revised: 07/05/2023] [Accepted: 07/23/2023] [Indexed: 08/18/2023] Open
Abstract
Structural variants (SVs) are genomic rearrangements that can take many different forms such as copy number alterations, inversions and translocations. During cell development and aging, somatic SVs accumulate in the genome with potentially neutral, deleterious or pathological effects. Generation of somatic SVs is a key mutational process in cancer development and progression. Despite their importance, the detection of somatic SVs is challenging, making them less studied than somatic single-nucleotide variants. In this review, we summarize recent advances in whole-genome sequencing (WGS)-based approaches for detecting somatic SVs at the tissue and single-cell levels and discuss their advantages and limitations. First, we describe the state-of-the-art computational algorithms for somatic SV calling using bulk WGS data and compare the performance of somatic SV detectors in the presence or absence of a matched-normal control. We then discuss the unique features of cutting-edge single-cell-based techniques for analyzing somatic SVs. The advantages and disadvantages of bulk and single-cell approaches are highlighted, along with a discussion of their sensitivity to copy-neutral SVs, usefulness for functional inferences and experimental and computational costs. Finally, computational approaches for linking somatic SVs to their functional readouts, such as those obtained from single-cell transcriptome and epigenome analyses, are illustrated, with a discussion of the promise of these approaches in health and diseases.
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Affiliation(s)
- Dohun Yi
- Department of Life Science, College of Natural Sciences, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
- Bio-BigData Center, Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
- Hanyang Institute of Advanced BioConvergence, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Hyobin Jeong
- Department of Life Science, College of Natural Sciences, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
- Bio-BigData Center, Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
- Hanyang Institute of Advanced BioConvergence, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
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187
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Chakraborty A, Li Y, Zhang C, Li Y, Rebello KR, Li S, Xu S, Vasquez HG, Zhang L, Luo W, Wang G, Chen K, Coselli JS, LeMaire SA, Shen YH. Epigenetic Induction of Smooth Muscle Cell Phenotypic Alterations in Aortic Aneurysms and Dissections. Circulation 2023; 148:959-977. [PMID: 37555319 PMCID: PMC10529114 DOI: 10.1161/circulationaha.123.063332] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/17/2023] [Indexed: 08/10/2023]
Abstract
BACKGROUND Smooth muscle cell (SMC) phenotypic switching has been increasingly detected in aortic aneurysm and dissection (AAD) tissues. However, the diverse SMC phenotypes in AAD tissues and the mechanisms driving SMC phenotypic alterations remain to be identified. METHODS We examined the transcriptomic and epigenomic dynamics of aortic SMC phenotypic changes in mice with angiotensin II-induced AAD by using single-cell RNA sequencing and single-cell sequencing assay for transposase-accessible chromatin. SMC phenotypic alteration in aortas from patients with ascending thoracic AAD was examined by using single-cell RNA sequencing analysis. RESULTS Single-cell RNA sequencing analysis revealed that aortic stress induced the transition of SMCs from a primary contractile phenotype to proliferative, extracellular matrix-producing, and inflammatory phenotypes. Lineage tracing showed the complete transformation of SMCs to fibroblasts and macrophages. Single-cell sequencing assay for transposase-accessible chromatin analysis indicated that these phenotypic alterations were controlled by chromatin remodeling marked by the reduced chromatin accessibility of contractile genes and the induced chromatin accessibility of genes involved in proliferation, extracellular matrix, and inflammation. IRF3 (interferon regulatory factor 3), a proinflammatory transcription factor activated by cytosolic DNA, was identified as a key driver of the transition of aortic SMCs from a contractile phenotype to an inflammatory phenotype. In cultured SMCs, cytosolic DNA signaled through its sensor STING (stimulator of interferon genes)-TBK1 (tank-binding kinase 1) to activate IRF3, which bound and recruited EZH2 (enhancer of zeste homolog 2) to contractile genes to induce repressive H3K27me3 modification and gene suppression. In contrast, double-stranded DNA-STING-IRF3 signaling induced inflammatory gene expression in SMCs. In Sting-/- mice, the aortic stress-induced transition of SMCs into an inflammatory phenotype was prevented, and SMC populations were preserved. Finally, profound SMC phenotypic alterations toward diverse directions were detected in human ascending thoracic AAD tissues. CONCLUSIONS Our study reveals the dynamic epigenetic induction of SMC phenotypic alterations in AAD. DNA damage and cytosolic leakage drive SMCs from a contractile phenotype to an inflammatory phenotype.
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Affiliation(s)
- Abhijit Chakraborty
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery (A.C., Y.L., C.Z., K.R.R., Y.L., S.X., W.L., H.G.V., L.Z., J.S.C., S.A.L., Y.H.S.), Baylor College of Medicine, Houston, TX
- Department of Cardiovascular Surgery, The Texas Heart Institute, Houston (A.C., Y.L., C.Z., K.R.R., Y.L., W.L., H.G.V., L.Z., J.S.C., S.A.L.)
| | - Yanming Li
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery (A.C., Y.L., C.Z., K.R.R., Y.L., S.X., W.L., H.G.V., L.Z., J.S.C., S.A.L., Y.H.S.), Baylor College of Medicine, Houston, TX
- Department of Cardiovascular Surgery, The Texas Heart Institute, Houston (A.C., Y.L., C.Z., K.R.R., Y.L., W.L., H.G.V., L.Z., J.S.C., S.A.L.)
| | - Chen Zhang
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery (A.C., Y.L., C.Z., K.R.R., Y.L., S.X., W.L., H.G.V., L.Z., J.S.C., S.A.L., Y.H.S.), Baylor College of Medicine, Houston, TX
- Department of Cardiovascular Surgery, The Texas Heart Institute, Houston (A.C., Y.L., C.Z., K.R.R., Y.L., W.L., H.G.V., L.Z., J.S.C., S.A.L.)
| | - Yang Li
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery (A.C., Y.L., C.Z., K.R.R., Y.L., S.X., W.L., H.G.V., L.Z., J.S.C., S.A.L., Y.H.S.), Baylor College of Medicine, Houston, TX
- Department of Cardiovascular Surgery, The Texas Heart Institute, Houston (A.C., Y.L., C.Z., K.R.R., Y.L., W.L., H.G.V., L.Z., J.S.C., S.A.L.)
| | - Kimberly R Rebello
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery (A.C., Y.L., C.Z., K.R.R., Y.L., S.X., W.L., H.G.V., L.Z., J.S.C., S.A.L., Y.H.S.), Baylor College of Medicine, Houston, TX
- Department of Cardiovascular Surgery, The Texas Heart Institute, Houston (A.C., Y.L., C.Z., K.R.R., Y.L., W.L., H.G.V., L.Z., J.S.C., S.A.L.)
| | - Shengyu Li
- Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, TX (S.L., G.W.)
| | - Samantha Xu
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery (A.C., Y.L., C.Z., K.R.R., Y.L., S.X., W.L., H.G.V., L.Z., J.S.C., S.A.L., Y.H.S.), Baylor College of Medicine, Houston, TX
| | - Hernan G Vasquez
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery (A.C., Y.L., C.Z., K.R.R., Y.L., S.X., W.L., H.G.V., L.Z., J.S.C., S.A.L., Y.H.S.), Baylor College of Medicine, Houston, TX
- Department of Cardiovascular Surgery, The Texas Heart Institute, Houston (A.C., Y.L., C.Z., K.R.R., Y.L., W.L., H.G.V., L.Z., J.S.C., S.A.L.)
| | - Lin Zhang
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery (A.C., Y.L., C.Z., K.R.R., Y.L., S.X., W.L., H.G.V., L.Z., J.S.C., S.A.L., Y.H.S.), Baylor College of Medicine, Houston, TX
- Department of Cardiovascular Surgery, The Texas Heart Institute, Houston (A.C., Y.L., C.Z., K.R.R., Y.L., W.L., H.G.V., L.Z., J.S.C., S.A.L.)
| | - Wei Luo
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery (A.C., Y.L., C.Z., K.R.R., Y.L., S.X., W.L., H.G.V., L.Z., J.S.C., S.A.L., Y.H.S.), Baylor College of Medicine, Houston, TX
- Department of Cardiovascular Surgery, The Texas Heart Institute, Houston (A.C., Y.L., C.Z., K.R.R., Y.L., W.L., H.G.V., L.Z., J.S.C., S.A.L.)
| | - Guangyu Wang
- Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, TX (S.L., G.W.)
| | - Kaifu Chen
- Department of Pediatrics, Harvard Medical School, Boston, MA (K.C.)
| | - Joseph S Coselli
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery (A.C., Y.L., C.Z., K.R.R., Y.L., S.X., W.L., H.G.V., L.Z., J.S.C., S.A.L., Y.H.S.), Baylor College of Medicine, Houston, TX
- Cardiovascular Research Institute (J.S.C., S.A.L., Y.H.S.), Baylor College of Medicine, Houston, TX
- Department of Cardiovascular Surgery, The Texas Heart Institute, Houston (A.C., Y.L., C.Z., K.R.R., Y.L., W.L., H.G.V., L.Z., J.S.C., S.A.L.)
| | - Scott A LeMaire
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery (A.C., Y.L., C.Z., K.R.R., Y.L., S.X., W.L., H.G.V., L.Z., J.S.C., S.A.L., Y.H.S.), Baylor College of Medicine, Houston, TX
- Cardiovascular Research Institute (J.S.C., S.A.L., Y.H.S.), Baylor College of Medicine, Houston, TX
- Department of Cardiovascular Surgery, The Texas Heart Institute, Houston (A.C., Y.L., C.Z., K.R.R., Y.L., W.L., H.G.V., L.Z., J.S.C., S.A.L.)
| | - Ying H Shen
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery (A.C., Y.L., C.Z., K.R.R., Y.L., S.X., W.L., H.G.V., L.Z., J.S.C., S.A.L., Y.H.S.), Baylor College of Medicine, Houston, TX
- Cardiovascular Research Institute (J.S.C., S.A.L., Y.H.S.), Baylor College of Medicine, Houston, TX
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188
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Blackshaw S, Lyu P, Zhai Y, Qian J, Iribarne M, Serjanov D, Campbell L, Boyd P, Hyde D, Palazzo I, Hoang T, Nagashima M, Silva N, Hitchcock P. Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina. RESEARCH SQUARE 2023:rs.3.rs-3294233. [PMID: 37790324 PMCID: PMC10543505 DOI: 10.21203/rs.3.rs-3294233/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Following acute retinal damage, zebrafish possess the ability to regenerate all neuronal subtypes. This regeneration requires Müller glia (MG) to reprogram and divide asymmetrically to produce a multipotent Müller glia-derived neuronal progenitor cell (MGPC). This raises three key questions. First, does loss of different retinal cell subtypes induce unique MG regeneration responses? Second, do MG reprogram to a developmental retinal progenitor cell state? And finally, to what extent does regeneration recapitulate retinal development? We examined these questions by performing single-nuclear and single-cell RNA-Seq and ATAC-Seq in both developing and regenerating retinas. While MG reprogram to a state similar to late-stage retinal progenitors in developing retinas, there are transcriptional differences between reprogrammed MG/MGPCs and late progenitors, as well as reprogrammed MG in outer and inner retinal damage models. Validation of candidate genes confirmed that loss of different subtypes induces differences in transcription factor gene expression and regeneration outcomes. This work identifies major differences between gene regulatory networks activated following the selective loss of different subtypes of retina neurons, as well as between retinal regeneration and development.
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Affiliation(s)
| | | | - Yijie Zhai
- Johns Hopkins University School of Medicine
| | - Jiang Qian
- Johns Hopkins University School of Medicine
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189
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Li J, Jaiswal MK, Chien JF, Kozlenkov A, Jung J, Zhou P, Gardashli M, Pregent LJ, Engelberg-Cook E, Dickson DW, Belzil VV, Mukamel EA, Dracheva S. Divergent single cell transcriptome and epigenome alterations in ALS and FTD patients with C9orf72 mutation. Nat Commun 2023; 14:5714. [PMID: 37714849 PMCID: PMC10504300 DOI: 10.1038/s41467-023-41033-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 08/21/2023] [Indexed: 09/17/2023] Open
Abstract
A repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here we investigate single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem motor and frontal cortices from C9-ALS, C9-FTD, and control donors. C9-ALS donors present pervasive alterations of gene expression with concordant changes in chromatin accessibility and histone modifications. The greatest alterations occur in upper and deep layer excitatory neurons, as well as in astrocytes. In neurons, the changes imply an increase in proteostasis, metabolism, and protein expression pathways, alongside a decrease in neuronal function. In astrocytes, the alterations suggest activation and structural remodeling. Conversely, C9-FTD donors have fewer high-quality neuronal nuclei in the frontal cortex and numerous gene expression changes in glial cells. These findings highlight a context-dependent molecular disruption in C9-ALS and C9-FTD, indicating unique effects across cell types, brain regions, and diseases.
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Affiliation(s)
- Junhao Li
- Department of Cognitive Science, University of California San Diego, La Jolla, CA, 92037, US
| | - Manoj K Jaiswal
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, US
| | - Jo-Fan Chien
- Department of Physics, University of California San Diego, La Jolla, CA, 92037, US
| | - Alexey Kozlenkov
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, US
| | - Jinyoung Jung
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, US
| | - Ping Zhou
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, US
| | | | - Luc J Pregent
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, US
| | | | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, US
| | | | - Eran A Mukamel
- Department of Cognitive Science, University of California San Diego, La Jolla, CA, 92037, US.
| | - Stella Dracheva
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, US.
- Research & Development and VISN2 MIREC, James J, Peters VA Medical Center, Bronx, NY, 10468, US.
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190
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Falquet M, Su Z, Wyss T, Ercolano G, Trabanelli S, Jandus C. Dynamic single-cell regulomes characterize human peripheral blood innate lymphoid cell subpopulations. iScience 2023; 26:107728. [PMID: 37694139 PMCID: PMC10483052 DOI: 10.1016/j.isci.2023.107728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/25/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
Innate lymphoid cells (ILCs) are plastic immune cells divided into 3 main subsets, characterized by distinct phenotypic and functional profiles. Using single cell approaches, heightened heterogeneity of mouse ILCs has been appreciated, imprinted by tissue signals that shape their transcriptome and epigenome. Intra-subset diversity has also been observed in human ILCs. However, combined transcriptomic and epigenetic analyses of single ILCs in humans are lacking. Here, we show high transcriptional and epigenetic heterogeneity among human circulating ILCs in healthy individuals. We describe phenotypically distinct subclusters and diverse chromatin accessibility within main ILC populations, compatible with differentially poised states. We validate the use of this healthy donor-based analysis as resource dataset to help inferring ILC changes occurring in disease conditions. Overall, our work provides insights in the complex human ILC biology. We anticipate it to facilitate hypothesis-driven studies in patients, without the need to perform single cell OMICs using precious patients' material.
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Affiliation(s)
- Maryline Falquet
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Geneva Center for Inflammation Research, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ziyang Su
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Geneva Center for Inflammation Research, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Tania Wyss
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Geneva Center for Inflammation Research, Geneva, Switzerland
- Translational Data Science Facility, AGORA Cancer Research Center, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Giuseppe Ercolano
- Department of Experimental Pharmacology, University of Naples Federico II, Naples, Italy
| | - Sara Trabanelli
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Geneva Center for Inflammation Research, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Camilla Jandus
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Geneva Center for Inflammation Research, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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191
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Han CZ, Li RZ, Hansen E, Trescott S, Fixsen BR, Nguyen CT, Mora CM, Spann NJ, Bennett HR, Poirion O, Buchanan J, Warden AS, Xia B, Schlachetzki JCM, Pasillas MP, Preissl S, Wang A, O'Connor C, Shriram S, Kim R, Schafer D, Ramirez G, Challacombe J, Anavim SA, Johnson A, Gupta M, Glass IA, Levy ML, Haim SB, Gonda DD, Laurent L, Hughes JF, Page DC, Blurton-Jones M, Glass CK, Coufal NG. Human microglia maturation is underpinned by specific gene regulatory networks. Immunity 2023; 56:2152-2171.e13. [PMID: 37582369 PMCID: PMC10529991 DOI: 10.1016/j.immuni.2023.07.016] [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: 09/13/2022] [Revised: 04/11/2023] [Accepted: 07/21/2023] [Indexed: 08/17/2023]
Abstract
Microglia phenotypes are highly regulated by the brain environment, but the transcriptional networks that specify the maturation of human microglia are poorly understood. Here, we characterized stage-specific transcriptomes and epigenetic landscapes of fetal and postnatal human microglia and acquired corresponding data in induced pluripotent stem cell (iPSC)-derived microglia, in cerebral organoids, and following engraftment into humanized mice. Parallel development of computational approaches that considered transcription factor (TF) co-occurrence and enhancer activity allowed prediction of shared and state-specific gene regulatory networks associated with fetal and postnatal microglia. Additionally, many features of the human fetal-to-postnatal transition were recapitulated in a time-dependent manner following the engraftment of iPSC cells into humanized mice. These data and accompanying computational approaches will facilitate further efforts to elucidate mechanisms by which human microglia acquire stage- and disease-specific phenotypes.
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Affiliation(s)
- Claudia Z Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rick Z Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emily Hansen
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Samantha Trescott
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Bethany R Fixsen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Celina T Nguyen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Cristina M Mora
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hunter R Bennett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Olivier Poirion
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Justin Buchanan
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anna S Warden
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Bing Xia
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Martina P Pasillas
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sebastian Preissl
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Allen Wang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Shreya Shriram
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Roy Kim
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Danielle Schafer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Gabriela Ramirez
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Jean Challacombe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samuel A Anavim
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Avalon Johnson
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Mihir Gupta
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ian A Glass
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, USA
| | - Michael L Levy
- Department of Neurosurgery, University of California, San Diego-Rady Children's Hospital, San Diego, CA 92123, USA
| | - Sharona Ben Haim
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
| | - David D Gonda
- Department of Neurosurgery, University of California, San Diego-Rady Children's Hospital, San Diego, CA 92123, USA
| | - Louise Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Mathew Blurton-Jones
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92696, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Nicole G Coufal
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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192
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Chen S, Zhu B, Huang S, Hickey JW, Lin KZ, Snyder M, Greenleaf WJ, Nolan GP, Zhang NR, Ma Z. Integration of spatial and single-cell data across modalities with weakly linked features. Nat Biotechnol 2023:10.1038/s41587-023-01935-0. [PMID: 37679544 DOI: 10.1038/s41587-023-01935-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/02/2023] [Indexed: 09/09/2023]
Abstract
Although single-cell and spatial sequencing methods enable simultaneous measurement of more than one biological modality, no technology can capture all modalities within the same cell. For current data integration methods, the feasibility of cross-modal integration relies on the existence of highly correlated, a priori 'linked' features. We describe matching X-modality via fuzzy smoothed embedding (MaxFuse), a cross-modal data integration method that, through iterative coembedding, data smoothing and cell matching, uses all information in each modality to obtain high-quality integration even when features are weakly linked. MaxFuse is modality-agnostic and demonstrates high robustness and accuracy in the weak linkage scenario, achieving 20~70% relative improvement over existing methods under key evaluation metrics on benchmarking datasets. A prototypical example of weak linkage is the integration of spatial proteomic data with single-cell sequencing data. On two example analyses of this type, MaxFuse enabled the spatial consolidation of proteomic, transcriptomic and epigenomic information at single-cell resolution on the same tissue section.
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Affiliation(s)
- Shuxiao Chen
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Bokai Zhu
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sijia Huang
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - John W Hickey
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kevin Z Lin
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Nancy R Zhang
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA.
| | - Zongming Ma
- Department of Statistics and Data Science, Yale University, New Haven, CT, USA.
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193
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Weng C, Gu A, Zhang S, Lu L, Ke L, Gao P, Liu X, Wang Y, Hu P, Plummer D, MacDonald E, Zhang S, Xi J, Lai S, Leskov K, Yuan K, Jin F, Li Y. Single cell multiomic analysis reveals diabetes-associated β-cell heterogeneity driven by HNF1A. Nat Commun 2023; 14:5400. [PMID: 37669939 PMCID: PMC10480445 DOI: 10.1038/s41467-023-41228-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
Broad heterogeneity in pancreatic β-cell function and morphology has been widely reported. However, determining which components of this cellular heterogeneity serve a diabetes-relevant function remains challenging. Here, we integrate single-cell transcriptome, single-nuclei chromatin accessibility, and cell-type specific 3D genome profiles from human islets and identify Type II Diabetes (T2D)-associated β-cell heterogeneity at both transcriptomic and epigenomic levels. We develop a computational method to explicitly dissect the intra-donor and inter-donor heterogeneity between single β-cells, which reflect distinct mechanisms of T2D pathogenesis. Integrative transcriptomic and epigenomic analysis identifies HNF1A as a principal driver of intra-donor heterogeneity between β-cells from the same donors; HNF1A expression is also reduced in β-cells from T2D donors. Interestingly, HNF1A activity in single β-cells is significantly associated with lower Na+ currents and we nominate a HNF1A target, FXYD2, as the primary mitigator. Our study demonstrates the value of investigating disease-associated single-cell heterogeneity and provides new insights into the pathogenesis of T2D.
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Affiliation(s)
- Chen Weng
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Anniya Gu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Medical Scientist Training Program (MSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Shanshan Zhang
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Leina Lu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Luxin Ke
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Peidong Gao
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Xiaoxiao Liu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Yuntong Wang
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Peinan Hu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Dylan Plummer
- Department of Computer and Data Sciences, School of Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Elise MacDonald
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Saixian Zhang
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jiajia Xi
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Sisi Lai
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Konstantin Leskov
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kyle Yuan
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Fulai Jin
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Department of Computer and Data Sciences, School of Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Yan Li
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
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194
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Ma Z, Zhang X, Zhong W, Yi H, Chen X, Zhao Y, Ma Y, Song E, Xu T. Deciphering early human pancreas development at the single-cell level. Nat Commun 2023; 14:5354. [PMID: 37660175 PMCID: PMC10475098 DOI: 10.1038/s41467-023-40893-8] [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: 11/13/2022] [Accepted: 08/15/2023] [Indexed: 09/04/2023] Open
Abstract
Understanding pancreas development can provide clues for better treatments of pancreatic diseases. However, the molecular heterogeneity and developmental trajectory of the early human pancreas are poorly explored. Here, we performed large-scale single-cell RNA sequencing and single-cell assay for transposase accessible chromatin sequencing of human embryonic pancreas tissue obtained from first-trimester embryos. We unraveled the molecular heterogeneity, developmental trajectories and regulatory networks of the major cell types. The results reveal that dorsal pancreatic multipotent cells in humans exhibit different gene expression patterns than ventral multipotent cells. Pancreato-biliary progenitors that generate ventral multipotent cells in humans were identified. Notch and MAPK signals from mesenchymal cells regulate the differentiation of multipotent cells into trunk and duct cells. Notably, we identified endocrine progenitor subclusters with different differentiation potentials. Although the developmental trajectories are largely conserved between humans and mice, some distinct gene expression patterns have also been identified. Overall, we provide a comprehensive landscape of early human pancreas development to understand its lineage transitions and molecular complexity.
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Affiliation(s)
- Zhuo Ma
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofei Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 570102, China
| | - Wen Zhong
- Science for Life Laboratory, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, 581 83, Sweden
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Hongyan Yi
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 570102, China
| | - Xiaowei Chen
- Center for High Throughput Sequencing, Core Facility for Protein Research, Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yinsuo Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanlin Ma
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 570102, China.
| | - Eli Song
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Tao Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Guangzhou Laboratory, Guangzhou, 510005, China.
- Central Hospital Affiliated to Shandong First Medical University, Jinan, 250013, China.
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China.
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195
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Zhong J, Qiu M, Meng Y, Wang P, Chen S, Wang L. Single-cell multi-omics sequencing reveals the immunological disturbance underlying STAT3-V637M Hyper-IgE syndrome. Int Immunopharmacol 2023; 122:110624. [PMID: 37480751 DOI: 10.1016/j.intimp.2023.110624] [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: 03/23/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/24/2023]
Abstract
Hyper-IgE syndrome (HIES) is a primary immunodeficiency characterized by, among others, the excessive production of IgE and repetitive bacterial/fungal infections. Mutations in STAT3, a transcription factor that orchestrates immune responses, may cause HIES, but the underlying mechanisms are not fully understood. Here, we used multi-omic approaches to comprehensively decipher the immune disturbance in a male HIES patient harboring STAT3-V637M. In his peripheral blood mononuclear cell (PBMC) we found significant clonal expansion of CD8 T cells (with increased CD8 subunits expression, potentially enhancing responsiveness to MHC I molecules), but not in his CD4 T cells and B cells. Although his B cells exhibited a higher potential in producing immunoglobulin, elevated SPIC binding might bias the products toward IgE isotype. Immune checkpoint inhibitors, including CTLA4, LAG3, were overexpressed in his PBMC-CD4 T cells, accompanied by reduced CD28 and IL6ST (gp130) expression. In his CD4 T cells, integrative analyses predicted upstream transcription factors (including ETV6, KLF13, and RORA) for LAG3, IL6ST, and CD28, respectively. The down-regulation of phagocytosis and nitric oxide synthesis-related genes in his PBMC-monocytes seem to be the culprit of his disseminated bacterial/fungal infection. Counterintuitively, in his PBMC we predicted increased STAT3 binding in both naïve and mature CD4 compartments, although this was not observed in most of his PBMC. In his bronchoalveolar lavage fluid (BALF), we found two macrophage subtypes with anti-bacterial properties, which were identified by CXCL8/S100A8/S100A9, or SOD2, respectively. Together, we described how the immune cell landscape was disturbed in STAT3-V637M HIES, providing a resource for further studies.
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Affiliation(s)
- Jiacheng Zhong
- Shenzhen Institute of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Shenzhen People's Hospital, Shenzhen 518055, Guangdong, China; Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518055, Guangdong, China
| | - Minzhi Qiu
- Health Management Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Yu Meng
- Department of Quality Control, Shenzhen People's Hospital, Shenzhen 518055, Guangdong, China
| | - Peizhong Wang
- Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Shanze Chen
- Shenzhen Institute of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Shenzhen People's Hospital, Shenzhen 518055, Guangdong, China; Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518055, Guangdong, China.
| | - Lingwei Wang
- Shenzhen Institute of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Shenzhen People's Hospital, Shenzhen 518055, Guangdong, China; Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518055, Guangdong, China.
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196
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Li S, Yang M, Teng S, Lin K, Wang Y, Zhang Y, Guo W, Wang D. Chromatin accessibility dynamics in colorectal cancer liver metastasis: Uncovering the liver tropism at single cell resolution. Pharmacol Res 2023; 195:106896. [PMID: 37633511 DOI: 10.1016/j.phrs.2023.106896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
Tumor metastasis causes over 90% of cancer related death and no currently available therapies target it. However, there is limited understanding regarding the epigenetic regulation of genes during this complex process. Here by integrating single-cell ATAC-seq (scATAC-seq), single-cell RNA-seq (scRNA-seq), microarray, bulk RNA-seq, immunohistochemistry (IHC) staining, as well as proteomics datasets from paired primary and liver metastatic colorectal cancer (CRC) patient-derived xenograft (PDX) model and patients, we discovered that liver metastatic CRC cells lose their colon-specific chromatin accessible sites yet gain liver-specific ones. Importantly, we observed elevated accessibility of HNF4A, a liver-specific transcription factor, in liver metastatic CRC cells. Subsequently, we performed clustering analysis of liver metastatic CRC cells together with cells involved in liver development, revealing significant heterogeneity among the liver metastatic CRC cells. Over 50% of the liver metastatic CRC cells exhibited characteristics similar to those of erythroid progenitors and hepatocytes, showing increased expression of genes involved in oxidative phosphorylation and glycolysis. Moreover, our discovery further revealed that the MHC and IFN response genes in these cells exhibit moderate epigenetic activity, which is significantly associated with the low objective response rates in checkpoint blockade immunotherapy. Our findings uncovered the critical roles of HNF4A and the cell populations within liver metastatic CRC cells might serve as crucial therapeutic targets for addressing liver metastasis and improving the immunotherapy response in patients with CRC.
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Affiliation(s)
- Shasha Li
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology & Guangzhou Municipal Key Laboratory of Mechanistic and Translational Obesity Research, Medical Center for Comprehensive Weight Control, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China.
| | - Ming Yang
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shuaishuai Teng
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Kequan Lin
- Department of Cardiology of The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Yumei Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yanmei Zhang
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, China
| | - Wei Guo
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Haining 314400, China; Institute of Hematology, the First Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Dong Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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197
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Lee JD, Menasche BL, Mavrikaki M, Uyemura MM, Hong SM, Kozlova N, Wei J, Alfajaro MM, Filler RB, Müller A, Saxena T, Posey RR, Cheung P, Muranen T, Heng YJ, Paulo JA, Wilen CB, Slack FJ. Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555625. [PMID: 37693555 PMCID: PMC10491142 DOI: 10.1101/2023.08.31.555625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
COVID-19 remains a significant public health threat due to the ability of SARS-CoV-2 variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and MERS-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here we used our recently developed integrative DNA And Protein Tagging (iDAPT) methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. SARS-CoV-2 infection induces TP53 stabilization on chromatin, which contributes to its host cytopathic effect. We mapped this TP53 stabilization to the SARS-CoV-2 spike and its propensity to form syncytia, a consequence of cell-cell fusion. Differences in SARS-CoV-2 spike variant-induced syncytia formation modify chromatin accessibility, cellular senescence, and inflammatory cytokine release via TP53. Our findings suggest that differences in syncytia formation alter senescence-associated inflammation, which varies among SARS-CoV-2 variants.
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198
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You M, Gao Y, Fu J, Xie R, Zhu Z, Hong Z, Meng L, Du S, Liu J, Wang FS, Yang P, Chen L. Epigenetic regulation of HBV-specific tumor-infiltrating T cells in HBV-related HCC. Hepatology 2023; 78:943-958. [PMID: 36999652 PMCID: PMC10442105 DOI: 10.1097/hep.0000000000000369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 04/01/2023]
Abstract
BACKGROUND AND AIMS HBV shapes the T-cell immune responses in HBV-related HCC. T cells can be recruited to the nidus, but limited T cells participate specifically in response to the HBV-related tumor microenvironment and HBV antigens. How epigenomic programs regulate T-cell compartments in virus-specific immune processes is unclear. APPROACH AND RESULTS We developed Ti-ATAC-seq. 2 to map the T-cell receptor repertoire, epigenomic, and transcriptomic landscape of αβ T cells at both the bulk-cell and single-cell levels in 54 patients with HCC. We deeply investigated HBV-specific T cells and HBV-related T-cell subsets that specifically responded to HBV antigens and the HBV + tumor microenvironment, respectively, characterizing their T-cell receptor clonality and specificity and performing epigenomic profiling. A shared program comprising NFKB1/2-, Proto-Oncogene, NF-KB Sub unit, NFATC2-, and NR4A1-associated unique T-cell receptor-downstream core epigenomic and transcriptomic regulome commonly regulated the differentiation of HBV-specific regulatory T-cell (Treg) cells and CD8 + exhausted T cells; this program was also selectively enriched in the HBV-related Treg-CTLA4 and CD8-exhausted T cell-thymocyte selection associated high mobility subsets and drove greater clonal expansion in HBV-related Treg-CTLA4 subset. Overall, 54% of the effector and memory HBV-specific T cells are governed by transcription factor motifs of activator protein 1, NFE2, and BACH1/2, which have been reported to be associated with prolonged patient relapse-free survival. Moreover, HBV-related tumor-infiltrating Tregs correlated with both increased viral titer and poor prognosis in patients. CONCLUSIONS This study provides insight into the cellular and molecular basis of the epigenomic programs that regulate the differentiation and generation of HBV-related T cells from viral infection and HBV + HCC unique immune exhaustion.
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Affiliation(s)
- Maojun You
- Chongqing International Institute for Immunology, Chongqing, China
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Gao
- Chongqing International Institute for Immunology, Chongqing, China
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Junliang Fu
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Runze Xie
- Chongqing International Institute for Immunology, Chongqing, China
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhenyu Zhu
- Senior Department of Hepatobiliary Surgery, The Fifth Medical Center of Chinese PLA Centeral Hospital, Beijing, China
| | - Zhixian Hong
- Senior Department of Hepatobiliary Surgery, The Fifth Medical Center of Chinese PLA Centeral Hospital, Beijing, China
| | - Lingzhan Meng
- Senior Department of Hepatobiliary Surgery, The Fifth Medical Center of Chinese PLA Centeral Hospital, Beijing, China
| | - Shunda Du
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Science and PUMC, Beijing, China
| | - Junliang Liu
- Chongqing International Institute for Immunology, Chongqing, China
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fu-Sheng Wang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Pengyuan Yang
- Chongqing International Institute for Immunology, Chongqing, China
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang Chen
- School of Medicine, Shanghai University, Shanghai, China
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199
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Rudloff MW, Zumbo P, Favret NR, Roetman JJ, Detrés Román CR, Erwin MM, Murray KA, Jonnakuti ST, Dündar F, Betel D, Philip M. Hallmarks of CD8 + T cell dysfunction are established within hours of tumor antigen encounter before cell division. Nat Immunol 2023; 24:1527-1539. [PMID: 37537361 PMCID: PMC10878719 DOI: 10.1038/s41590-023-01578-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 07/07/2023] [Indexed: 08/05/2023]
Abstract
Tumor-specific CD8+ T cells (TST) in patients with cancer are dysfunctional and unable to halt cancer progression. TST dysfunction, also known as exhaustion, is thought to be driven by chronic T cell antigen receptor (TCR) stimulation over days to weeks. However, we know little about the interplay between CD8+ T cell function, cell division and epigenetic remodeling within hours of activation. Here, we assessed early CD8+ T cell differentiation, cell division, chromatin accessibility and transcription in tumor-bearing mice and acutely infected mice. Surprisingly, despite robust activation and proliferation, TST had near complete effector function impairment even before undergoing cell division and had acquired hallmark chromatin accessibility features previously associated with later dysfunction/exhaustion. Moreover, continued tumor/antigen exposure drove progressive epigenetic remodeling, 'imprinting' the dysfunctional state. Our study reveals the rapid divergence of T cell fate choice before cell division in the context of tumors versus infection.
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Affiliation(s)
- Michael W Rudloff
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Natalie R Favret
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Jessica J Roetman
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Carlos R Detrés Román
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Megan M Erwin
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Kristen A Murray
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Sriya T Jonnakuti
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Friederike Dündar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Doron Betel
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mary Philip
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA.
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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200
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Preiss NK, Kamal Y, Wilkins OM, Li C, Kolling FW, Trask HW, Usherwood YK, Cheng C, Frost HR, Usherwood EJ. Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20. Life Sci Alliance 2023; 6:e202201683. [PMID: 37414528 PMCID: PMC10326419 DOI: 10.26508/lsa.202201683] [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: 08/19/2022] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023] Open
Abstract
Members of the BTB-ZF transcription factor family regulate the immune system. Our laboratory identified that family member Zbtb20 contributes to the differentiation, recall responses, and metabolism of CD8 T cells. Here, we report a characterization of the transcriptional and epigenetic signatures controlled by Zbtb20 at single-cell resolution during the effector and memory phases of the CD8 T cell response. Without Zbtb20, transcriptional programs associated with memory CD8 T cell formation were up-regulated throughout the CD8 T response. A signature of open chromatin was associated with genes controlling T cell activation, consistent with the known impact on differentiation. In addition, memory CD8 T cells lacking Zbtb20 were characterized by open chromatin regions with overrepresentation of AP-1 transcription factor motifs and elevated RNA- and protein-level expressions of the corresponding AP-1 components. Finally, we describe motifs and genomic annotations from the DNA targets of Zbtb20 in CD8 T cells identified by cleavage under targets and release under nuclease (CUT&RUN). Together, these data establish the transcriptional and epigenetic networks contributing to the control of CD8 T cell responses by Zbtb20.
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Affiliation(s)
- Nicholas K Preiss
- Microbiology and Immunology Department, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Yasmin Kamal
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Owen M Wilkins
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
- Genomics and Molecular Biology Shared Resource, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, NH, USA
| | - Chenyang Li
- Genomic Medicine Department, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth Houston, Houston, TX, USA
| | - Fred W Kolling
- Genomics and Molecular Biology Shared Resource, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, NH, USA
| | - Heidi W Trask
- Genomics and Molecular Biology Shared Resource, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, NH, USA
| | - Young-Kwang Usherwood
- Microbiology and Immunology Department, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- The Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Hildreth R Frost
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Edward J Usherwood
- Microbiology and Immunology Department, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
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