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Santarelli P, Rosti V, Vivo M, Lanzuolo C. Chromatin organization of muscle stem cell. Curr Top Dev Biol 2024; 158:375-406. [PMID: 38670713 DOI: 10.1016/bs.ctdb.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
The proper functioning of skeletal muscles is essential throughout life. A crucial crosstalk between the environment and several cellular mechanisms allows striated muscles to perform successfully. Notably, the skeletal muscle tissue reacts to an injury producing a completely functioning tissue. The muscle's robust regenerative capacity relies on the fine coordination between muscle stem cells (MuSCs or "satellite cells") and their specific microenvironment that dictates stem cells' activation, differentiation, and self-renewal. Critical for the muscle stem cell pool is a fine regulation of chromatin organization and gene expression. Acquiring a lineage-specific 3D genome architecture constitutes a crucial modulator of muscle stem cell function during development, in the adult stage, in physiological and pathological conditions. The context-dependent relationship between genome structure, such as accessibility and chromatin compartmentalization, and their functional effects will be analysed considering the improved 3D epigenome knowledge, underlining the intimate liaison between environmental encounters and epigenetics.
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Affiliation(s)
- Philina Santarelli
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Valentina Rosti
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy; CNR Institute of Biomedical Technologies, Milan, Italy
| | - Maria Vivo
- Università degli studi di Salerno, Fisciano, Italy.
| | - Chiara Lanzuolo
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy; CNR Institute of Biomedical Technologies, Milan, Italy.
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Choi AS, Jenkins-Lane LM, Barton W, Kumari A, Lancaster C, Raulerson C, Ji H, Altomare D, Starr MD, Whitaker R, Phaeton R, Arend R, Shtutman M, Nixon AB, Hempel N, Lee NY, Mythreye K. Glycosaminoglycan modifications of betaglycan regulate ectodomain shedding to fine-tune TGF-β signaling responses in ovarian cancer. Cell Commun Signal 2024; 22:128. [PMID: 38360757 PMCID: PMC10870443 DOI: 10.1186/s12964-024-01496-y] [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: 09/14/2023] [Accepted: 01/21/2024] [Indexed: 02/17/2024] Open
Abstract
In pathologies including cancer, aberrant Transforming Growth Factor-β (TGF-β) signaling exerts profound tumor intrinsic and extrinsic consequences. Intense clinical endeavors are underway to target this pathway. Central to the success of these interventions is pinpointing factors that decisively modulate the TGF-β responses. Betaglycan/type III TGF-β receptor (TβRIII), is an established co-receptor for the TGF-β superfamily known to bind directly to TGF-βs 1-3 and inhibin A/B. Betaglycan can be membrane-bound and also undergo ectodomain cleavage to produce soluble-betaglycan that can sequester its ligands. Its extracellular domain undergoes heparan sulfate and chondroitin sulfate glycosaminoglycan modifications, transforming betaglycan into a proteoglycan. We report the unexpected discovery that the heparan sulfate glycosaminoglycan chains on betaglycan are critical for the ectodomain shedding. In the absence of such glycosaminoglycan chains betaglycan is not shed, a feature indispensable for the ability of betaglycan to suppress TGF-β signaling and the cells' responses to exogenous TGF-β ligands. Using unbiased transcriptomics, we identified TIMP3 as a key inhibitor of betaglycan shedding thereby influencing TGF-β signaling. Our results bear significant clinical relevance as modified betaglycan is present in the ascites of patients with ovarian cancer and can serve as a marker for predicting patient outcomes and TGF-β signaling responses. These studies are the first to demonstrate a unique reliance on the glycosaminoglycan chains of betaglycan for shedding and influence on TGF-β signaling responses. Dysregulated shedding of TGF-β receptors plays a vital role in determining the response and availability of TGF-βs', which is crucial for prognostic predictions and understanding of TGF-β signaling dynamics.
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Affiliation(s)
- Alex S Choi
- Department of Pathology and O'Neal Comprehensive Cancer Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Laura M Jenkins-Lane
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Wade Barton
- Department of Gynecology Oncology, Heersink School of Medicine, University of Alabama School of Medicine, Birmingham, AL, 35233, USA
| | - Asha Kumari
- Department of Pathology and O'Neal Comprehensive Cancer Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Carly Lancaster
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Calen Raulerson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Hao Ji
- Department of Drug Discovery & Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, 29208, USA
| | - Diego Altomare
- Department of Drug Discovery & Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, 29208, USA
| | - Mark D Starr
- Department of Medicine and Duke Cancer Institute, Duke University Medical Center, Durham, NC, 27710, USA
| | - Regina Whitaker
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Rebecca Phaeton
- Department of Obstetrics and Gynecology, and Microbiology and Immunology, College of Medicine, Pennsylvania State University, Hershey, PA, 17033, USA
| | - Rebecca Arend
- Department of Gynecology Oncology, Heersink School of Medicine, University of Alabama School of Medicine, Birmingham, AL, 35233, USA
| | - Michael Shtutman
- Department of Drug Discovery & Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, 29208, USA
| | - Andrew B Nixon
- Department of Medicine and Duke Cancer Institute, Duke University Medical Center, Durham, NC, 27710, USA
| | - Nadine Hempel
- Department of Medicine, Division of Hematology-Oncology, Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Nam Y Lee
- Division of Pharmacology, Chemistry and Biochemistry, College of Medicine, University of Arizona, Tucson, AZ, 85721, USA
| | - Karthikeyan Mythreye
- Department of Pathology and O'Neal Comprehensive Cancer Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA.
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Southerland KW, Xu Y, Peters DT, Lin X, Wei X, Xiang Y, Fei K, Olivere LA, Morowitz JM, Otto J, Dai Q, Kontos CD, Diao Y. Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells. Genome Med 2023; 15:95. [PMID: 37950327 PMCID: PMC10636829 DOI: 10.1186/s13073-023-01250-y] [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: 04/11/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Chronic limb-threatening ischemia (CLTI), a severe manifestation of peripheral arterial disease (PAD), is associated with a 1-year limb amputation rate of approximately 15-20% and substantial mortality. A key feature of CLTI is the compromised regenerative ability of skeletal muscle; however, the mechanisms responsible for this impairment are not yet fully understood. In this study, we aim to delineate pathological changes at both the cellular and transcriptomic levels, as well as in cell-cell signaling pathways, associated with compromised muscle regeneration in limb ischemia in both human tissue samples and murine models of CLTI. METHODS We performed single-cell transcriptome analysis of ischemic and non-ischemic muscle from the same CLTI patients and from a murine model of CLTI. In both datasets, we analyzed gene expression changes in macrophage and muscle satellite cell (MuSC) populations as well as differential cell-cell signaling interactions and differentiation trajectories. RESULTS Single-cell transcriptomic profiling and immunofluorescence analysis of CLTI patient skeletal muscle demonstrated that ischemic-damaged tissue displays a pro-inflammatory macrophage signature. Comparable results were observed in a murine CLTI model. Moreover, integrated analyses of both human and murine datasets revealed premature differentiation of MuSCs to be a key feature of failed muscle regeneration in the ischemic limb. Furthermore, in silico inferences of intercellular communication and in vitro assays highlight the importance of macrophage-MuSC signaling in ischemia induced muscle injuries. CONCLUSIONS Collectively, our research provides the first single-cell transcriptome atlases of skeletal muscle from CLTI patients and a murine CLTI model, emphasizing the crucial role of macrophages and inflammation in regulating muscle regeneration in CLTI through interactions with MuSCs.
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Affiliation(s)
- Kevin W Southerland
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Yueyuan Xu
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA
| | - Derek T Peters
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA
| | - Xin Lin
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA
| | - Xiaolin Wei
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA
| | - Yu Xiang
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA
| | - Kaileen Fei
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke University School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Lindsey A Olivere
- Division of Vascular Surgery, Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, 15217, USA
| | - Jeremy M Morowitz
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Development and Stem Cell Biology Program, Duke University, Durham, NC, 27710, USA
| | - James Otto
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
| | - Qunsheng Dai
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
| | - Christopher D Kontos
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Yarui Diao
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA.
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA.
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA.
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.
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den Berge KV, Chou HJ, Kunda D, Risso D, Street K, Purdom E, Dudoit S, Ngai J, Heavner W. A Latent Activated Olfactory Stem Cell State Revealed by Single Cell Transcriptomic and Epigenomic Profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564041. [PMID: 37961539 PMCID: PMC10634988 DOI: 10.1101/2023.10.26.564041] [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
The olfactory epithelium is one of the few regions of the nervous system that sustains neurogenesis throughout life. Its experimental accessibility makes it especially tractable for studying molecular mechanisms that drive neural regeneration after injury-induced cell death. In this study, we used single cell sequencing to identify major regulatory players in determining olfactory epithelial stem cell fate after acute injury. We combined gene expression and accessible chromatin profiles of individual lineage traced olfactory stem cells to predict transcription factor activity specific to different lineages and stages of recovery. We further identified a discrete stem cell state that appears poised for activation, characterized by accessible chromatin around wound response and lineage specific genes prior to their later expression in response to injury. Together these results provide evidence that a subset of quiescent olfactory epithelial stem cells are epigenetically primed to support injury-induced regeneration.
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Affiliation(s)
| | - Hsin-Jung Chou
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
| | - Divya Kunda
- Molecular Neurobiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, Padova, Italy
| | - Kelly Street
- Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, CA
| | - Sandrine Dudoit
- Department of Statistics, University of California, Berkeley, CA
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA
| | - John Ngai
- Molecular Neurobiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Whitney Heavner
- Molecular Neurobiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
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