1
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Chen H, Hou H, Wang X, Wang J, Yang Q, He G. Functional FOXC1 variants in familial and sporadic atrial septal defect with cellular and animal validation. Clin Transl Med 2024; 14:e1676. [PMID: 38924312 PMCID: PMC11199059 DOI: 10.1002/ctm2.1676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/10/2024] [Accepted: 04/14/2024] [Indexed: 06/28/2024] Open
Affiliation(s)
- Huan‐Xin Chen
- Department of Cardiac Surgery and The Institute of Cardiovascular DiseasesTEDA International Cardiovascular Hospital, Tianjin University and Chinese Academy of Medical ScienceTianjinChina
- Tianjin Key Laboratory of Molecular Regulation of Cardiovascular Diseases and Translational MedicineTianjinChina
| | - Hai‐Tao Hou
- Department of Cardiac Surgery and The Institute of Cardiovascular DiseasesTEDA International Cardiovascular Hospital, Tianjin University and Chinese Academy of Medical ScienceTianjinChina
- Tianjin Key Laboratory of Molecular Regulation of Cardiovascular Diseases and Translational MedicineTianjinChina
| | - Xiu‐Li Wang
- Department of Cardiac Surgery and The Institute of Cardiovascular DiseasesTEDA International Cardiovascular Hospital, Tianjin University and Chinese Academy of Medical ScienceTianjinChina
- Tianjin Key Laboratory of Molecular Regulation of Cardiovascular Diseases and Translational MedicineTianjinChina
| | - Jun Wang
- Department of Cardiac Surgery and The Institute of Cardiovascular DiseasesTEDA International Cardiovascular Hospital, Tianjin University and Chinese Academy of Medical ScienceTianjinChina
- Tianjin Key Laboratory of Molecular Regulation of Cardiovascular Diseases and Translational MedicineTianjinChina
| | - Qin Yang
- Department of Cardiac Surgery and The Institute of Cardiovascular DiseasesTEDA International Cardiovascular Hospital, Tianjin University and Chinese Academy of Medical ScienceTianjinChina
- Tianjin Key Laboratory of Molecular Regulation of Cardiovascular Diseases and Translational MedicineTianjinChina
| | - Guo‐Wei He
- Department of Cardiac Surgery and The Institute of Cardiovascular DiseasesTEDA International Cardiovascular Hospital, Tianjin University and Chinese Academy of Medical ScienceTianjinChina
- Tianjin Key Laboratory of Molecular Regulation of Cardiovascular Diseases and Translational MedicineTianjinChina
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2
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Sun C, Serra C, Kalicharan BH, Harding J, Rao M. Challenges and Considerations of Preclinical Development for iPSC-Based Myogenic Cell Therapy. Cells 2024; 13:596. [PMID: 38607035 PMCID: PMC11011706 DOI: 10.3390/cells13070596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Cell therapies derived from induced pluripotent stem cells (iPSCs) offer a promising avenue in the field of regenerative medicine due to iPSCs' expandability, immune compatibility, and pluripotent potential. An increasing number of preclinical and clinical trials have been carried out, exploring the application of iPSC-based therapies for challenging diseases, such as muscular dystrophies. The unique syncytial nature of skeletal muscle allows stem/progenitor cells to integrate, forming new myonuclei and restoring the expression of genes affected by myopathies. This characteristic makes genome-editing techniques especially attractive in these therapies. With genetic modification and iPSC lineage specification methodologies, immune-compatible healthy iPSC-derived muscle cells can be manufactured to reverse the progression of muscle diseases or facilitate tissue regeneration. Despite this exciting advancement, much of the development of iPSC-based therapies for muscle diseases and tissue regeneration is limited to academic settings, with no successful clinical translation reported. The unknown differentiation process in vivo, potential tumorigenicity, and epigenetic abnormality of transplanted cells are preventing their clinical application. In this review, we give an overview on preclinical development of iPSC-derived myogenic cell transplantation therapies including processes related to iPSC-derived myogenic cells such as differentiation, scaling-up, delivery, and cGMP compliance. And we discuss the potential challenges of each step of clinical translation. Additionally, preclinical model systems for testing myogenic cells intended for clinical applications are described.
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Affiliation(s)
- Congshan Sun
- Vita Therapeutics, Baltimore, MD 21043, USA (M.R.)
| | - Carlo Serra
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Mahendra Rao
- Vita Therapeutics, Baltimore, MD 21043, USA (M.R.)
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3
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Barral A, Zaret KS. Pioneer factors: roles and their regulation in development. Trends Genet 2024; 40:134-148. [PMID: 37940484 PMCID: PMC10873006 DOI: 10.1016/j.tig.2023.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Pioneer factors are a subclass of transcription factors that can bind and initiate opening of silent chromatin regions. Pioneer factors subsequently regulate lineage-specific genes and enhancers and, thus, activate the zygotic genome after fertilization, guide cell fate transitions during development, and promote various forms of human cancers. As such, pioneer factors are useful in directed cell reprogramming. In this review, we define the structural and functional characteristics of pioneer factors, how they bind and initiate opening of closed chromatin regions, and the consequences for chromatin dynamics and gene expression during cell differentiation. We also discuss emerging mechanisms that modulate pioneer factors during development.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA.
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4
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Cordeiro-Spinetti E, Rothbart SB. Lysine methylation signaling in skeletal muscle biology: from myogenesis to clinical insights. Biochem J 2023; 480:1969-1986. [PMID: 38054592 DOI: 10.1042/bcj20230223] [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: 09/28/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023]
Abstract
Lysine methylation signaling is well studied for its key roles in the regulation of transcription states through modifications on histone proteins. While histone lysine methylation has been extensively studied, recent discoveries of lysine methylation on thousands of non-histone proteins has broadened our appreciation for this small chemical modification in the regulation of protein function. In this review, we highlight the significance of histone and non-histone lysine methylation signaling in skeletal muscle biology, spanning development, maintenance, regeneration, and disease progression. Furthermore, we discuss potential future implications for its roles in skeletal muscle biology as well as clinical applications for the treatment of skeletal muscle-related diseases.
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Affiliation(s)
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan 49503, U.S.A
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5
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Searcy MB, Larsen RK, Stevens BT, Zhang Y, Jin H, Drummond CJ, Langdon CG, Gadek KE, Vuong K, Reed KB, Garcia MR, Xu B, Kimbrough DW, Adkins GE, Djekidel N, Porter SN, Schreiner PA, Pruett-Miller SM, Abraham BJ, Rehg JE, Hatley ME. PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors. Nat Commun 2023; 14:7291. [PMID: 37968277 PMCID: PMC10651858 DOI: 10.1038/s41467-023-43044-1] [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: 12/12/2022] [Accepted: 10/27/2023] [Indexed: 11/17/2023] Open
Abstract
Fusion-positive rhabdomyosarcoma (FP-RMS) driven by the expression of the PAX3-FOXO1 (P3F) fusion oncoprotein is an aggressive subtype of pediatric rhabdomyosarcoma. FP-RMS histologically resembles developing muscle yet occurs throughout the body in areas devoid of skeletal muscle highlighting that FP-RMS is not derived from an exclusively myogenic cell of origin. Here we demonstrate that P3F reprograms mouse and human endothelial progenitors to FP-RMS. We show that P3F expression in aP2-Cre expressing cells reprograms endothelial progenitors to functional myogenic stem cells capable of regenerating injured muscle fibers. Further, we describe a FP-RMS mouse model driven by P3F expression and Cdkn2a loss in endothelial cells. Additionally, we show that P3F expression in TP53-null human iPSCs blocks endothelial-directed differentiation and guides cells to become myogenic cells that form FP-RMS tumors in immunocompromised mice. Together these findings demonstrate that FP-RMS can originate from aberrant development of non-myogenic cells driven by P3F.
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Affiliation(s)
- Madeline B Searcy
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Randolph K Larsen
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Bradley T Stevens
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Yang Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Catherine J Drummond
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Casey G Langdon
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Katherine E Gadek
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kyna Vuong
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kristin B Reed
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Matthew R Garcia
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Darden W Kimbrough
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Rhodes College, Memphis, TN, 38112, USA
| | - Grace E Adkins
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shaina N Porter
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Patrick A Schreiner
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Brian J Abraham
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jerold E Rehg
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mark E Hatley
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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6
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Wu HT, Wu Z, Hou YY, Fang ZX, Wu BX, Deng Y, Cui YK, Liu J. SIX4, a potential therapeutic target for estrogen receptor-positive breast cancer patients, is associated with low promoter methylation level. Epigenomics 2023; 15:911-925. [PMID: 37905439 DOI: 10.2217/epi-2023-0232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023] Open
Abstract
Aim: To investigate SIX4 in breast cancer. Methods: Publicly available online tools were used to analyze the expression, methylation and prognostic significance of SIX4 in breast cancer, as well as its immunohistochemistry. Results: High SIX4 levels were associated with low SIX4 promoter methylation, especially in estrogen receptor-positive breast cancer. Increased SIX4 was related to advanced stage and decreased immune infiltration. Gene set enrichment analysis found that the SIX4-correlated genes were enriched in transcriptional processing and immune response. Patients with high SIX4 expression tended to have poor survival, especially those with estrogen receptor-positive breast cancer. Conclusion: High SIX4 expression in breast cancer plays an oncogenic role, promoting the development of malignancies through suppressing the immune response, especially in luminal subtypes, and is associated with a low promoter methylation level.
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Affiliation(s)
- Hua-Tao Wu
- Department of General Surgery, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
- Laboratory for Diagnosis & Treatment of Breast Cancer, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Zheng Wu
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
- Department of Physiology/Changjiang Scholar's Laboratory, Shantou University Medical College, Shantou, 515041, China
| | - Yan-Yu Hou
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
- Department of Physiology/Changjiang Scholar's Laboratory, Shantou University Medical College, Shantou, 515041, China
| | - Ze-Xuan Fang
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
- Department of Physiology/Changjiang Scholar's Laboratory, Shantou University Medical College, Shantou, 515041, China
| | - Bing-Xuan Wu
- Department of General Surgery, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
- Laboratory for Diagnosis & Treatment of Breast Cancer, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Yu Deng
- Department of General Surgery, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
- Laboratory for Diagnosis & Treatment of Breast Cancer, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Yu-Kun Cui
- Laboratory for Diagnosis & Treatment of Breast Cancer, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Jing Liu
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
- Department of Physiology/Changjiang Scholar's Laboratory, Shantou University Medical College, Shantou, 515041, China
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7
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Fu X, Zhuang CL, Hu P. Regulation of muscle stem cell fate. CELL REGENERATION (LONDON, ENGLAND) 2022; 11:40. [PMID: 36456659 PMCID: PMC9715903 DOI: 10.1186/s13619-022-00142-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 09/29/2022] [Indexed: 12/03/2022]
Abstract
Skeletal muscle plays a critical role in human health. Muscle stem cells (MuSCs) serve as the major cell type contributing to muscle regeneration by directly differentiating to mature muscle cells. MuSCs usually remain quiescent with occasionally self-renewal and are activated to enter cell cycle for proliferation followed by differentiation upon muscle injury or under pathological conditions. The quiescence maintenance, activation, proliferation, and differentiation of MuSCs are tightly regulated. The MuSC cell-intrinsic regulatory network and the microenvironments work coordinately to orchestrate the fate transition of MuSCs. The heterogeneity of MuSCs further complicates the regulation of MuSCs. This review briefly summarizes the current progress on the heterogeneity of MuSCs and the microenvironments, epigenetic, and transcription regulations of MuSCs.
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Affiliation(s)
- Xin Fu
- grid.412987.10000 0004 0630 1330Spine Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Cheng-le Zhuang
- grid.412538.90000 0004 0527 0050Colorectal Cancer Center/Department of Gastrointestinal Surgery, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, 200072 China
| | - Ping Hu
- grid.412987.10000 0004 0630 1330Spine Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China ,grid.412538.90000 0004 0527 0050Colorectal Cancer Center/Department of Gastrointestinal Surgery, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, 200072 China ,Guangzhou Laboratory, Guanghzou International Bio Lsland, No. 9 XingDaoHuan Road, Guangzhou, 510005 China ,grid.9227.e0000000119573309Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101 China
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8
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Gosselin MRF, Mournetas V, Borczyk M, Verma S, Occhipinti A, Róg J, Bozycki L, Korostynski M, Robson SC, Angione C, Pinset C, Gorecki DC. Loss of full-length dystrophin expression results in major cell-autonomous abnormalities in proliferating myoblasts. eLife 2022; 11:e75521. [PMID: 36164827 PMCID: PMC9514850 DOI: 10.7554/elife.75521] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/02/2022] [Indexed: 12/05/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) affects myofibers and muscle stem cells, causing progressive muscle degeneration and repair defects. It was unknown whether dystrophic myoblasts-the effector cells of muscle growth and regeneration-are affected. Using transcriptomic, genome-scale metabolic modelling and functional analyses, we demonstrate, for the first time, convergent abnormalities in primary mouse and human dystrophic myoblasts. In Dmdmdx myoblasts lacking full-length dystrophin, the expression of 170 genes was significantly altered. Myod1 and key genes controlled by MyoD (Myog, Mymk, Mymx, epigenetic regulators, ECM interactors, calcium signalling and fibrosis genes) were significantly downregulated. Gene ontology analysis indicated enrichment in genes involved in muscle development and function. Functionally, we found increased myoblast proliferation, reduced chemotaxis and accelerated differentiation, which are all essential for myoregeneration. The defects were caused by the loss of expression of full-length dystrophin, as similar and not exacerbated alterations were observed in dystrophin-null Dmdmdx-βgeo myoblasts. Corresponding abnormalities were identified in human DMD primary myoblasts and a dystrophic mouse muscle cell line, confirming the cross-species and cell-autonomous nature of these defects. The genome-scale metabolic analysis in human DMD myoblasts showed alterations in the rate of glycolysis/gluconeogenesis, leukotriene metabolism, and mitochondrial beta-oxidation of various fatty acids. These results reveal the disease continuum: DMD defects in satellite cells, the myoblast dysfunction affecting muscle regeneration, which is insufficient to counteract muscle loss due to myofiber instability. Contrary to the established belief, our data demonstrate that DMD abnormalities occur in myoblasts, making these cells a novel therapeutic target for the treatment of this lethal disease.
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Affiliation(s)
- Maxime RF Gosselin
- School of Pharmacy and Biomedical Sciences, University of PortsmouthPortsmouthUnited Kingdom
| | | | - Malgorzata Borczyk
- Laboratory of Pharmacogenomics, Maj Institute of Pharmacology PASKrakowPoland
| | - Suraj Verma
- School of Computing, Engineering and Digital Technologies, Teesside UniversityMiddlesbroughUnited Kingdom
| | - Annalisa Occhipinti
- School of Computing, Engineering and Digital Technologies, Teesside UniversityMiddlesbroughUnited Kingdom
| | - Justyna Róg
- School of Pharmacy and Biomedical Sciences, University of PortsmouthPortsmouthUnited Kingdom
- Laboratory of Cellular Metabolism, Nencki Institute of Experimental BiologyWarsawPoland
| | - Lukasz Bozycki
- School of Pharmacy and Biomedical Sciences, University of PortsmouthPortsmouthUnited Kingdom
- Laboratory of Cellular Metabolism, Nencki Institute of Experimental BiologyWarsawPoland
| | - Michal Korostynski
- Laboratory of Pharmacogenomics, Maj Institute of Pharmacology PASKrakowPoland
| | - Samuel C Robson
- School of Pharmacy and Biomedical Sciences, University of PortsmouthPortsmouthUnited Kingdom
- Centre for Enzyme Innovation, University of PortsmouthPortsmouthUnited Kingdom
| | - Claudio Angione
- School of Computing, Engineering and Digital Technologies, Teesside UniversityMiddlesbroughUnited Kingdom
| | | | - Dariusz C Gorecki
- School of Pharmacy and Biomedical Sciences, University of PortsmouthPortsmouthUnited Kingdom
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9
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Azzag K, Bosnakovski D, Tungtur S, Salama P, Kyba M, Perlingeiro RCR. Transplantation of PSC-derived myogenic progenitors counteracts disease phenotypes in FSHD mice. NPJ Regen Med 2022; 7:43. [PMID: 36056021 PMCID: PMC9440030 DOI: 10.1038/s41536-022-00249-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 08/08/2022] [Indexed: 12/02/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a genetically dominant progressive myopathy caused by improper silencing of the DUX4 gene, leading to fibrosis, muscle atrophy, and fatty replacement. Approaches focused on muscle regeneration through the delivery of stem cells represent an attractive therapeutic option for muscular dystrophies. To investigate the potential for cell transplantation in FSHD, we have used the doxycycline-regulated iDUX4pA-HSA mouse model in which low-level DUX4 can be induced in skeletal muscle. We find that mouse pluripotent stem cell (PSC)-derived myogenic progenitors engraft in muscle actively undergoing DUX4-mediated degeneration. Donor-derived muscle tissue displayed reduced fibrosis and importantly, engrafted muscles showed improved contractile specific force compared to non-transplanted controls. These data demonstrate the feasibility of replacement of diseased muscle with PSC-derived myogenic progenitors in a mouse model for FSHD, and highlight the potential for the clinical benefit of such a cell therapy approach.
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Affiliation(s)
- Karim Azzag
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Darko Bosnakovski
- Lillehei Heart Institute, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Sudheer Tungtur
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Peter Salama
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Michael Kyba
- Lillehei Heart Institute, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.,Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Rita C R Perlingeiro
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN, USA. .,Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA.
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10
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Khateb M, Perovanovic J, Ko KD, Jiang K, Feng X, Acevedo-Luna N, Chal J, Ciuffoli V, Genzor P, Simone J, Haase AD, Pourquié O, Dell'Orso S, Sartorelli V. Transcriptomics, regulatory syntax, and enhancer identification in mesoderm-induced ESCs at single-cell resolution. Cell Rep 2022; 40:111219. [PMID: 35977485 DOI: 10.1016/j.celrep.2022.111219] [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: 03/31/2022] [Revised: 06/11/2022] [Accepted: 07/25/2022] [Indexed: 11/03/2022] Open
Abstract
Embryonic stem cells (ESCs) can adopt lineage-specific gene-expression programs by stepwise exposure to defined factors, resulting in the generation of functional cell types. Bulk and single-cell-based assays were employed to catalog gene expression, histone modifications, chromatin conformation, and accessibility transitions in ESC populations and individual cells acquiring a presomitic mesoderm fate and undergoing further specification toward myogenic and neurogenic lineages. These assays identified cis-regulatory regions and transcription factors presiding over gene-expression programs occurring at defined ESC transitions and revealed the presence of heterogeneous cell populations within discrete ESC developmental stages. The datasets were employed to identify previously unappreciated genomic elements directing the initial activation of Pax7 and myogenic and neurogenic gene-expression programs. This study provides a resource for the discovery of genomic and transcriptional features of pluripotent, mesoderm-induced ESCs and ESC-derived cell lineages.
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Affiliation(s)
- Mamduh Khateb
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Jelena Perovanovic
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Kyung Dae Ko
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Kan Jiang
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD, USA
| | - Xuesong Feng
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Natalia Acevedo-Luna
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Jérome Chal
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Boston, MA, USA
| | - Veronica Ciuffoli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Pavol Genzor
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - James Simone
- FlowCytometry Section, NIAMS, NIH, Bethesda, MD, USA
| | - Astrid D Haase
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Boston, MA, USA
| | | | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA.
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11
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Gong W, Das S, Sierra-Pagan JE, Skie E, Dsouza N, Larson TA, Garry MG, Luzete-Monteiro E, Zaret KS, Garry DJ. ETV2 functions as a pioneer factor to regulate and reprogram the endothelial lineage. Nat Cell Biol 2022; 24:672-684. [PMID: 35550615 DOI: 10.1038/s41556-022-00901-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/17/2022] [Indexed: 12/14/2022]
Abstract
The vasculature is an essential organ for the delivery of blood and oxygen to all tissues of the body and is thus relevant to the treatment of ischaemic diseases, injury-induced regeneration and solid tumour growth. Previously, we demonstrated that ETV2 is an essential transcription factor for the development of cardiac, endothelial and haematopoietic lineages. Here we report that ETV2 functions as a pioneer factor that relaxes closed chromatin and regulates endothelial development. By comparing engineered embryonic stem cell differentiation and reprogramming models with multi-omics techniques, we demonstrated that ETV2 was able to bind nucleosomal DNA and recruit BRG1. BRG1 recruitment remodelled chromatin around endothelial genes and helped to maintain an open configuration, resulting in increased H3K27ac deposition. Collectively, these results will serve as a platform for the development of therapeutic initiatives directed towards cardiovascular diseases and solid tumours.
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Affiliation(s)
- Wuming Gong
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Satyabrata Das
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Javier E Sierra-Pagan
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Erik Skie
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Nikita Dsouza
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Thijs A Larson
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Mary G Garry
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, USA.,Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA.,Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, USA
| | - Edgar Luzete-Monteiro
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Daniel J Garry
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, USA. .,Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA. .,Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, USA.
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12
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Abstract
Transcription factors (TFs) are essential mediators of epigenetic regulation and modifiers of penetrance. Studies from the past decades have revealed a sub-class of TF that is capable of remodeling closed chromatin states through targeting nucleosomal motifs. This pioneer factor (PF) class of chromatin remodeler is ATP independent in its roles in epigenetic initiation, with nucleosome-motif recognition and association with repressive chromatin regions. Increasing evidence suggests that the fundamental properties of PFs can be coopted in human cancers. We explore the role of PFs in the larger context of tissue-specific epigenetic regulation. Moreover, we highlight an emerging class of chimeric PF derived from translocation partners in human disease and PFs associated with rare tumors. In the age of site-directed genome editing and targeted protein degradation, increasing our understanding of PFs will provide access to next-generation therapy for human disease driven from altered transcriptional circuitry.
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13
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Esteves de Lima J, Relaix F. Master regulators of skeletal muscle lineage development and pluripotent stem cells differentiation. CELL REGENERATION 2021; 10:31. [PMID: 34595600 PMCID: PMC8484369 DOI: 10.1186/s13619-021-00093-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/24/2021] [Indexed: 12/16/2022]
Abstract
In vertebrates, the skeletal muscles of the body and their associated stem cells originate from muscle progenitor cells, during development. The specification of the muscles of the trunk, head and limbs, relies on the activity of distinct genetic hierarchies. The major regulators of trunk and limb muscle specification are the paired-homeobox transcription factors PAX3 and PAX7. Distinct gene regulatory networks drive the formation of the different muscles of the head. Despite the redeployment of diverse upstream regulators of muscle progenitor differentiation, the commitment towards the myogenic fate requires the expression of the early myogenic regulatory factors MYF5, MRF4, MYOD and the late differentiation marker MYOG. The expression of these genes is activated by muscle progenitors throughout development, in several waves of myogenic differentiation, constituting the embryonic, fetal and postnatal phases of muscle growth. In order to achieve myogenic cell commitment while maintaining an undifferentiated pool of muscle progenitors, several signaling pathways regulate the switch between proliferation and differentiation of myoblasts. The identification of the gene regulatory networks operating during myogenesis is crucial for the development of in vitro protocols to differentiate pluripotent stem cells into myoblasts required for regenerative medicine.
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Affiliation(s)
| | - Frédéric Relaix
- Univ Paris Est Creteil, INSERM, EnvA, EFS, AP-HP, IMRB, 94010, Creteil, France.
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14
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Esteves de Lima J, Bou Akar R, Mansour M, Rocancourt D, Buckingham M, Relaix F. M-Cadherin Is a PAX3 Target During Myotome Patterning. Front Cell Dev Biol 2021; 9:652652. [PMID: 33869209 PMCID: PMC8047199 DOI: 10.3389/fcell.2021.652652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/12/2021] [Indexed: 11/13/2022] Open
Abstract
PAX3 belongs to the paired-homeobox family of transcription factors and plays a key role as an upstream regulator of muscle progenitor cells during embryonic development. Pax3-mutant embryos display impaired somite development, yet the consequences for myotome formation have not been characterized. The early myotome is formed by PAX3-expressing myogenic cells that delaminate from the dermomyotomal lips and migrate between the dermomyotome and sclerotome where they terminally differentiate. Here we show that in Pax3-mutant embryos, myotome formation is impaired, displays a defective basal lamina and the regionalization of the structural protein Desmin is lost. In addition, this phenotype is more severe in embryos combining Pax3-null and Pax3 dominant-negative alleles. We identify the adhesion molecule M-Cadherin as a PAX3 target gene, the expression of which is modulated in the myotome according to Pax3 gain- and loss-of-function alleles analyzed. Taken together, we identify M-Cadherin as a PAX3-target linked to the formation of the myotome.
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Affiliation(s)
- Joana Esteves de Lima
- Univ Paris Est Creteil, Institut National de la Santé et de la Recherche Médicale (INSERM), EnvA, Etablissement Français du Sang (EFS), Assistance Publique Hopitaux de Paris (AP-HP), Institut Mondor de Recherche Biomedicale (IMRB), Creteil, France
| | - Reem Bou Akar
- Univ Paris Est Creteil, Institut National de la Santé et de la Recherche Médicale (INSERM), EnvA, Etablissement Français du Sang (EFS), Assistance Publique Hopitaux de Paris (AP-HP), Institut Mondor de Recherche Biomedicale (IMRB), Creteil, France
| | - Myriam Mansour
- Univ Paris Est Creteil, Institut National de la Santé et de la Recherche Médicale (INSERM), EnvA, Etablissement Français du Sang (EFS), Assistance Publique Hopitaux de Paris (AP-HP), Institut Mondor de Recherche Biomedicale (IMRB), Creteil, France
| | - Didier Rocancourt
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Margaret Buckingham
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Frédéric Relaix
- Univ Paris Est Creteil, Institut National de la Santé et de la Recherche Médicale (INSERM), EnvA, Etablissement Français du Sang (EFS), Assistance Publique Hopitaux de Paris (AP-HP), Institut Mondor de Recherche Biomedicale (IMRB), Creteil, France
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15
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Zhang N, Mendieta-Esteban J, Magli A, Lilja KC, Perlingeiro RCR, Marti-Renom MA, Tsirigos A, Dynlacht BD. Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology. Nat Commun 2020; 11:6222. [PMID: 33277476 PMCID: PMC7718254 DOI: 10.1038/s41467-020-19999-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/03/2020] [Indexed: 12/31/2022] Open
Abstract
Using Hi-C, promoter-capture Hi-C (pCHi-C), and other genome-wide approaches in skeletal muscle progenitors that inducibly express a master transcription factor, Pax7, we systematically characterize at high-resolution the spatio-temporal re-organization of compartments and promoter-anchored interactions as a consequence of myogenic commitment and differentiation. We identify key promoter-enhancer interaction motifs, namely, cliques and networks, and interactions that are dependent on Pax7 binding. Remarkably, Pax7 binds to a majority of super-enhancers, and together with a cadre of interacting transcription factors, assembles feed-forward regulatory loops. During differentiation, epigenetic memory and persistent looping are maintained at a subset of Pax7 enhancers in the absence of Pax7. We also identify and functionally validate a previously uncharacterized Pax7-bound enhancer hub that regulates the essential myosin heavy chain cluster during skeletal muscle cell differentiation. Our studies lay the groundwork for understanding the role of Pax7 in orchestrating changes in the three-dimensional chromatin conformation in muscle progenitors.
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Affiliation(s)
- Nan Zhang
- Department of Pathology and Perlmutter Cancer Institute, New York University School of Medicine, New York, NY, 10016, USA
| | - Julen Mendieta-Esteban
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Alessandro Magli
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA.,Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Karin C Lilja
- Department of Pathology and Perlmutter Cancer Institute, New York University School of Medicine, New York, NY, 10016, USA
| | - Rita C R Perlingeiro
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA.,Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Aristotelis Tsirigos
- Department of Pathology and Perlmutter Cancer Institute, New York University School of Medicine, New York, NY, 10016, USA
| | - Brian David Dynlacht
- Department of Pathology and Perlmutter Cancer Institute, New York University School of Medicine, New York, NY, 10016, USA.
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16
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Azzag K, Ortiz-Cordero C, Oliveira NAJ, Magli A, Selvaraj S, Tungtur S, Upchurch W, Iaizzo PA, Lu QL, Perlingeiro RCR. Efficient engraftment of pluripotent stem cell-derived myogenic progenitors in a novel immunodeficient mouse model of limb girdle muscular dystrophy 2I. Skelet Muscle 2020; 10:10. [PMID: 32321586 PMCID: PMC7175515 DOI: 10.1186/s13395-020-00228-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/11/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Defects in α-dystroglycan (DG) glycosylation characterize a group of muscular dystrophies known as dystroglycanopathies. One of the key effectors in the α-DG glycosylation pathway is the glycosyltransferase fukutin-related protein (FKRP). Mutations in FKRP lead to a large spectrum of muscular dystrophies, including limb girdle muscular dystrophy 2I (LGMD2I). It remains unknown whether stem cell transplantation can promote muscle regeneration and ameliorate the muscle wasting phenotype associated with FKRP mutations. RESULTS Here we transplanted murine and human pluripotent stem cell-derived myogenic progenitors into a novel immunodeficient FKRP-mutant mouse model by intra-muscular injection. Upon both mouse and human cell transplantation, we observe the presence of donor-derived myofibers even in absence of pre-injury, and the rescue of α-DG functional glycosylation, as shown by IIH6 immunoreactivity. The presence of donor-derived cells expressing Pax7 under the basal lamina is indicative of satellite cell engraftment, and therefore, long-term repopulation potential. Functional assays performed in the mouse-to-mouse cohort revealed enhanced specific force in transplanted muscles compared to PBS-injected controls. CONCLUSIONS Altogether, our data demonstrate for the first time the suitability of a cell-based therapeutic approach to improve the muscle phenotype of dystrophic FKRP-mutant mice.
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Affiliation(s)
- Karim Azzag
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, 4-128 CCRB, 2231 6th St. SE, Minneapolis, MN, 55455, USA
| | - Carolina Ortiz-Cordero
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, 4-128 CCRB, 2231 6th St. SE, Minneapolis, MN, 55455, USA
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - Nelio A J Oliveira
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, 4-128 CCRB, 2231 6th St. SE, Minneapolis, MN, 55455, USA
| | - Alessandro Magli
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, 4-128 CCRB, 2231 6th St. SE, Minneapolis, MN, 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Sridhar Selvaraj
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, 4-128 CCRB, 2231 6th St. SE, Minneapolis, MN, 55455, USA
| | - Sudheer Tungtur
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, 4-128 CCRB, 2231 6th St. SE, Minneapolis, MN, 55455, USA
| | - Weston Upchurch
- Visible Heart Laboratories, Department of Surgery, University of Minnesota, Minneapolis, MN, USA
| | - Paul A Iaizzo
- Visible Heart Laboratories, Department of Surgery, University of Minnesota, Minneapolis, MN, USA
| | - Qi Long Lu
- McColl-Lockwood Laboratory for Muscular Dystrophy Research, Cannon Research Center, Carolinas Medical Center, Atrium Health, Charlotte, North Carolina, NC, USA
| | - Rita C R Perlingeiro
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, 4-128 CCRB, 2231 6th St. SE, Minneapolis, MN, 55455, USA.
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA.
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17
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Maire P, Dos Santos M, Madani R, Sakakibara I, Viaut C, Wurmser M. Myogenesis control by SIX transcriptional complexes. Semin Cell Dev Biol 2020; 104:51-64. [PMID: 32247726 DOI: 10.1016/j.semcdb.2020.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 02/07/2023]
Abstract
SIX homeoproteins were first described in Drosophila, where they participate in the Pax-Six-Eya-Dach (PSED) network with eyeless, eyes absent and dachsund to drive synergistically eye development through genetic and biochemical interactions. The role of the PSED network and SIX proteins in muscle formation in vertebrates was subsequently identified. Evolutionary conserved interactions with EYA and DACH proteins underlie the activity of SIX transcriptional complexes (STC) both during embryogenesis and in adult myofibers. Six genes are expressed throughout muscle development, in embryonic and adult proliferating myogenic stem cells and in fetal and adult post-mitotic myofibers, where SIX proteins regulate the expression of various categories of genes. In vivo, SIX proteins control many steps of muscle development, acting through feedforward mechanisms: in the embryo for myogenic fate acquisition through the direct control of Myogenic Regulatory Factors; in adult myofibers for their contraction/relaxation and fatigability properties through the control of genes involved in metabolism, sarcomeric organization and calcium homeostasis. Furthermore, during development and in the adult, SIX homeoproteins participate in the genesis and the maintenance of myofibers diversity.
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Affiliation(s)
- Pascal Maire
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France.
| | | | - Rouba Madani
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - Iori Sakakibara
- Research Center for Advanced Science and Technology, The University of Tokyo, Japan
| | - Camille Viaut
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - Maud Wurmser
- Department of Integrative Medical Biology (IMB), Umeå universitet, Sweden
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18
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Takematsu E, Spencer A, Auster J, Chen PC, Graham A, Martin P, Baker AB. Genome wide analysis of gene expression changes in skin from patients with type 2 diabetes. PLoS One 2020; 15:e0225267. [PMID: 32084158 PMCID: PMC7034863 DOI: 10.1371/journal.pone.0225267] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 10/31/2019] [Indexed: 12/15/2022] Open
Abstract
Non-healing chronic ulcers are a serious complication of diabetes and are a major healthcare problem. While a host of treatments have been explored to heal or prevent these ulcers from forming, these treatments have not been found to be consistently effective in clinical trials. An understanding of the changes in gene expression in the skin of diabetic patients may provide insight into the processes and mechanisms that precede the formation of non-healing ulcers. In this study, we investigated genome wide changes in gene expression in skin between patients with type 2 diabetes and non-diabetic patients using next generation sequencing. We compared the gene expression in skin samples taken from 27 patients (13 with type 2 diabetes and 14 non-diabetic). This information may be useful in identifying the causal factors and potential therapeutic targets for the prevention and treatment of diabetic related diseases.
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Affiliation(s)
- Eri Takematsu
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX
| | - Adrianne Spencer
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX
| | - Jeff Auster
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX
| | - Po-Chih Chen
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX
| | - Annette Graham
- Department of Biological and Biomedical Sciences, School of Health and Life Sciences, Glasgow Caledonian University, Scotland, United Kingdom
| | - Patricia Martin
- Department of Biological and Biomedical Sciences, School of Health and Life Sciences, Glasgow Caledonian University, Scotland, United Kingdom
| | - Aaron B. Baker
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX
- The Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX
- Institute for Biomaterials, Drug Delivery and Regenerative Medicine, University of Texas at Austin, Austin, TX
- * E-mail:
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19
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Master control: transcriptional regulation of mammalian Myod. J Muscle Res Cell Motil 2019; 40:211-226. [PMID: 31301002 PMCID: PMC6726840 DOI: 10.1007/s10974-019-09538-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/03/2019] [Indexed: 12/22/2022]
Abstract
MYOD is a master regulator of the skeletal myogenic program. But what regulates expression of Myod? More than 20 years ago, studies established that Myod expression is largely controlled by just two enhancer regions located within a region 24 kb upstream of the transcription start site in mammals, which regulate Myod expression in the embryo, fetus and adult. Despite this apparently simple arrangement, Myod regulation is complex, with different combinations of transcription factors acting on these enhancers in different muscle progenitor cells and phases of differentiation. A range of epigenetic modifications in the Myod upstream region also play a part in activating and repressing Myod expression during development and regeneration. Here the evidence for this binding at Myod control regions is summarized, giving an overview of our current understanding of Myod expression regulation in mammals.
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20
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Magli A, Baik J, Pota P, Cordero CO, Kwak IY, Garry DJ, Love PE, Dynlacht BD, Perlingeiro RCR. Pax3 cooperates with Ldb1 to direct local chromosome architecture during myogenic lineage specification. Nat Commun 2019; 10:2316. [PMID: 31127120 PMCID: PMC6534668 DOI: 10.1038/s41467-019-10318-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 04/26/2019] [Indexed: 12/12/2022] Open
Abstract
Chromatin looping allows enhancer-bound regulatory factors to influence transcription. Large domains, referred to as topologically associated domains, participate in genome organization. However, the mechanisms underlining interactions within these domains, which control gene expression, are not fully understood. Here we report that activation of embryonic myogenesis is associated with establishment of long-range chromatin interactions centered on Pax3-bound loci. Using mass spectrometry and genomic studies, we identify the ubiquitously expressed LIM-domain binding protein 1 (Ldb1) as the mediator of looping interactions at a subset of Pax3 binding sites. Ldb1 is recruited to Pax3-bound elements independently of CTCF-Cohesin, and is necessary for efficient deposition of H3K4me1 at these sites and chromatin looping. When Ldb1 is deleted in Pax3-expressing cells in vivo, specification of migratory myogenic progenitors is severely impaired. These results highlight Ldb1 requirement for Pax3 myogenic activity and demonstrate how transcription factors can promote formation of sub-topologically associated domain interactions involved in lineage specification.
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Affiliation(s)
- Alessandro Magli
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - June Baik
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Pruthvi Pota
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Carolina Ortiz Cordero
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Il-Youp Kwak
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Daniel J Garry
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Paul E Love
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Brian D Dynlacht
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, 10016, USA
| | - Rita C R Perlingeiro
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
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21
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Gohl DM, Magli A, Garbe J, Becker A, Johnson DM, Anderson S, Auch B, Billstein B, Froehling E, McDevitt SL, Beckman KB. Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification. Genome Biol 2019; 20:85. [PMID: 31036053 PMCID: PMC6489363 DOI: 10.1186/s13059-019-1691-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/09/2019] [Indexed: 01/15/2023] Open
Abstract
Quantification of DNA sequence tags from engineered constructs such as plasmids, transposons, or other transgenes underlies many functional genomics measurements. Typically, such measurements rely on PCR followed by next-generation sequencing. However, PCR amplification can introduce significant quantitative error. We describe REcount, a novel PCR-free direct counting method. Comparing measurements of defined plasmid pools to droplet digital PCR data demonstrates that REcount is highly accurate and reproducible. We use REcount to provide new insights into clustering biases due to molecule length across different Illumina sequencers and illustrate the impacts on interpretation of next-generation sequencing data and the economics of data generation.
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Affiliation(s)
- Daryl M. Gohl
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 USA
| | - Alessandro Magli
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455 USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455 USA
| | - John Garbe
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
| | - Aaron Becker
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
| | | | - Shea Anderson
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
| | - Benjamin Auch
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
| | - Bradley Billstein
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
- Present Address: Illumina, Inc, San Diego, CA 92122 USA
| | - Elyse Froehling
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
| | - Shana L. McDevitt
- Vincent J. Coates Genomics Sequencing Laboratory, University of California, Berkeley, CA 94720 USA
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