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Jin W, Dai Y, Chen L, Zhu H, Dong F, Zhu H, Meng G, Li J, Chen S, Chen Z, Fang H, Wang K. Cellular hierarchy insights reveal leukemic stem-like cells and early death risk in acute promyelocytic leukemia. Nat Commun 2024; 15:1423. [PMID: 38365836 PMCID: PMC10873341 DOI: 10.1038/s41467-024-45737-7] [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: 04/20/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
Acute promyelocytic leukemia (APL) represents a paradigm for targeted differentiation therapy, with a minority of patients experiencing treatment failure and even early death. We here report a comprehensive single-cell analysis of 16 APL patients, uncovering cellular compositions and their impact on all-trans retinoic acid (ATRA) response in vivo and early death. We unveil a cellular differentiation hierarchy within APL blasts, rooted in leukemic stem-like cells. The oncogenic PML/RARα fusion protein exerts branch-specific regulation in the APL trajectory, including stem-like cells. APL cohort analysis establishes an association of leukemic stemness with elevated white blood cell counts and FLT3-ITD mutations. Furthermore, we construct an APL-specific stemness score, which proves effective in assessing early death risk. Finally, we show that ATRA induces differentiation of primitive blasts and patients with early death exhibit distinct stemness-associated transcriptional programs. Our work provides a thorough survey of APL cellular hierarchies, offering insights into cellular dynamics during targeted therapy.
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Affiliation(s)
- Wen Jin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yuting Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Li Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Honghu Zhu
- Department of Hematology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Fangyi Dong
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hongming Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Guoyu Meng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Junmin Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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2
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Zhao F, Guo X, Li X, Liu F, Fu Y, Sun X, Yang Z, Zhang Z, Qin Z. Identification and Expressional Analysis of Putative PRDI-BF1 and RIZ Homology Domain-Containing Transcription Factors in Mulinia lateralis. BIOLOGY 2023; 12:1059. [PMID: 37626944 PMCID: PMC10451705 DOI: 10.3390/biology12081059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
Mollusca represents one of the ancient bilaterian groups with high morphological diversity, while the formation mechanisms of the precursors of all germ cells, primordial germ cells (PGCs), have not yet been clarified in mollusks. PRDI-BF1 and RIZ homology domain-containing proteins (PRDMs) are a group of transcriptional repressors, and PRDM1 (also known as BLIMP1) and PRDM14 have been reported to be essential for the formation of PGCs. In the present study, we performed a genome-wide retrieval in Mulinia lateralis and identified 11 putative PRDMs, all of which possessed an N-terminal PR domain. Expressional profiles revealed that all these prdm genes showed specifically high expression levels in the given stages, implying that all PRDMs played important roles during early development stages. Specifically, Ml-prdm1 was highly expressed at the gastrula stage, the key period when PGCs arise, and was specifically localized in the cytoplasm of two or three cells of blastula, gastrula, or trochophore larvae, matching the typical characteristics of PGCs. These results suggested that Ml-prdm1-positive cells may be PGCs and that Ml-prdm1 could be a candidate marker for tracing the formation of PGCs in M. lateralis. In addition, the expression profiles of Ml-prdm14 hinted that it may not be associated with PGCs of M. lateralis. The present study provides insights into the evolution of the PRDM family in mollusks and offers a better understanding of the formation of PGCs in mollusks.
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Affiliation(s)
- Feng Zhao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Xiaolin Guo
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Xixi Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Fang Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Yifan Fu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Xiaohan Sun
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Zujing Yang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Zhenkui Qin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
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3
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Atmakuru PS, Dhawan J. The cilium-centrosome axis in coupling cell cycle exit and cell fate. J Cell Sci 2023; 136:308872. [PMID: 37144419 DOI: 10.1242/jcs.260454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
The centrosome is an evolutionarily conserved, ancient organelle whose role in cell division was first described over a century ago. The structure and function of the centrosome as a microtubule-organizing center, and of its extracellular extension - the primary cilium - as a sensory antenna, have since been extensively studied, but the role of the cilium-centrosome axis in cell fate is still emerging. In this Opinion piece, we view cellular quiescence and tissue homeostasis from the vantage point of the cilium-centrosome axis. We focus on a less explored role in the choice between distinct forms of mitotic arrest - reversible quiescence and terminal differentiation, which play distinct roles in tissue homeostasis. We outline evidence implicating the centrosome-basal body switch in stem cell function, including how the cilium-centrosome complex regulates reversible versus irreversible arrest in adult skeletal muscle progenitors. We then highlight exciting new findings in other quiescent cell types that suggest signal-dependent coupling of nuclear and cytoplasmic events to the centrosome-basal body switch. Finally, we propose a framework for involvement of this axis in mitotically inactive cells and identify future avenues for understanding how the cilium-centrosome axis impacts central decisions in tissue homeostasis.
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Affiliation(s)
- Priti S Atmakuru
- CSIR Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
| | - Jyotsna Dhawan
- CSIR Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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4
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Rumman M, Dhawan J. PTPRU, a quiescence-induced receptor tyrosine phosphatase negatively regulates osteogenic differentiation of human mesenchymal stem cells. Biochem Biophys Res Commun 2022; 636:41-49. [DOI: 10.1016/j.bbrc.2022.10.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/18/2022] [Indexed: 11/02/2022]
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5
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Yao J, Ma F, Zhang L, Zhu C, Jumabay M, Yao Z, Wang L, Cai X, Zhang D, Qiao X, Shivkumar K, Pellegrini M, Yao Y, Wu X, Boström KI. Single-Cell RNA-Seq Identifies Dynamic Cardiac Transition Program from Adipose Derived Cells Induced by Leukemia Inhibitory Factor. Stem Cells 2022; 40:932-948. [PMID: 35896368 PMCID: PMC9585902 DOI: 10.1093/stmcls/sxac048] [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: 01/15/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022]
Abstract
Adipose-derived cells (ADCs) from white adipose tissue (WAT) are promising stem cell candidates because of their large regenerative reserves and the potential for cardiac regeneration. However, given the heterogeneity of ADC and its unsolved mechanisms of cardiac acquisition, ADC-cardiac transition efficiency remains low. In this study, we explored the heterogeneity of ADCs and the cellular kinetics of 39,432 single-cell transcriptomes along the leukemia inhibitory factor (LIF) induced ADC-cardiac transition. We identified distinct ADC subpopulations that reacted differentially to LIF when entering the cardiomyogenic program, further demonstrating that ADC-myogenesis is time-dependent and initiates from transient changes in nuclear factor erythroid 2-related factor 2 (Nrf2) signaling. At later stages, pseudotime analysis of ADCs navigated a trajectory with two branches corresponding to activated myofibroblast or cardiomyocyte-like cells. Our findings offer a high-resolution dissection of ADC heterogeneity and cell fate during ADC-cardiac transition, thus providing new insights into potential cardiac stem cells.
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Affiliation(s)
- Jiayi Yao
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | - Feiyang Ma
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA.,Chongqing International Institute for Immunology, Chongqing 401338, China
| | - Li Zhang
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | - Ching Zhu
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | - Medet Jumabay
- Division of Allergy, Immunology Center for Immunity, Infection, and Inflammation Pediatrics, Dept of Medicine, University of California, San Diego, San Diego, CA
| | - Zehao Yao
- Peking Union Medical College, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Lumin Wang
- Institute of Precision Medicine, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xinjiang Cai
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | - Daoqin Zhang
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | - Xiaojing Qiao
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | | | - Matteo Pellegrini
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA.,Dept of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA
| | - Yucheng Yao
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | - Xiuju Wu
- Division of Cardiology, David Geffen School of Medicine at UCLA
| | - Kristina I Boström
- Division of Cardiology, David Geffen School of Medicine at UCLA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA
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Peng W, Tang W, Li JD, He RQ, Luo JY, Chen ZX, Zeng JH, Hu XH, Zhong JC, Li Y, Ma FC, Xie TY, Huang SN, Ge LY. Downregulation of the enhancer of zeste homolog 1 transcriptional factor predicts poor prognosis of triple-negative breast cancer patients. PeerJ 2022; 10:e13708. [PMID: 35846880 PMCID: PMC9285492 DOI: 10.7717/peerj.13708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/19/2022] [Indexed: 01/17/2023] Open
Abstract
Background Triple-negative breast cancer (TNBC) is the most malignant subtype of breast cancer and lacks effective biomarkers. This study seeks to unravel the expression status and the prospective transcriptional mechanisms of EZH1/EZH2 in TNBC tissue samples. Moreover, another objective of this study is to reveal the prognostic molecular signatures for risk stratification in TNBC patients. Methods To determine the expression status of EZH1/EZH2 in TNBC tissue samples, microarray analysis and immunohistochemistry were performed on in house breast cancer tissue samples. External mRNA expression matrices were used to verify its expression patterns. Furthermore, the prospective transcriptional mechanisms of EZH1/EZH2 in TNBC were explored by performing differential expression analysis, co-expression analysis, and chromatin immunoprecipitation sequencing analysis. Kaplan-Meier survival analysis and univariate Cox regression analysis were utilized to detect the prognostic molecular signatures in TNBC patients. Nomogram and time-dependent receiver operating characteristic curves were plotted to predict the risk stratification ability of the prognostic-signatures-based Cox model. Results In-house TMAs (66 TNBC vs. 106 non-TNBC) and external gene microarrays, as well as RNA-seq datasets (1,135 TNBC vs. 6,198 non-TNBC) results, confirmed the downregulation of EZH1 at both the protein and mRNA levels (SMD = -0.59 [-0.80, -0.37]), as is opposite to that of EZH2 (SMD = 0.74 [0.40, 1.08]). The upregulated transcriptional target genes of EZH1 were significantly aggregated in the cell cycle pathway, where CCNA2, CCNB1, MAD2L1, and PKMYT1 were determined as key transcriptional targets. Additionally, the downregulated transcriptional targets of EZH2 were enriched in response to the hormone, where ESR1 was identified as the hub gene. The six-signature-based prognostic model produced an impressive performance in this study, with a training AUC of 0.753, 0.981, and 0.977 at 3-, 5-, and 10-year survival probability, respectively. Conclusion EZH1 downregulation may be a key modulator in the progression of TNBC through negative transcriptional regulation by targeting CCNA2, CCNB1, MAD2L1, and PKMYT1.
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Affiliation(s)
- Wei Peng
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Wei Tang
- Department of Breast Surgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Jian-Di Li
- Department of Breast Surgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Rong-Quan He
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jia-Yuan Luo
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Zu-Xuan Chen
- Department of Medical Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jiang-Hui Zeng
- Department of Clinical Laboratory, The Third Affiliated Hospital of Guangxi Medical University/Nanning Second People’s Hospital, Nanning, Guangxi, China
| | - Xiao-Hua Hu
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jin-Cai Zhong
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yang Li
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Fu-Chao Ma
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Tian-Yi Xie
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Su-Ning Huang
- Department of Radiotherapy, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Lian-Ying Ge
- Department of Endoscopy, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
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7
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Gala HP, Saha D, Venugopal N, Aloysius A, Purohit G, Dhawan J. A transcriptionally repressed quiescence program is associated with paused RNAPII and is poised for cell cycle reentry. J Cell Sci 2022; 135:275901. [PMID: 35781573 DOI: 10.1242/jcs.259789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/27/2022] [Indexed: 11/20/2022] Open
Abstract
Adult stem cells persist in mammalian tissues by entering a state of reversible quiescence/ G0, associated with low transcription. Using cultured myoblasts and muscle stem cells, we report that in G0, global RNA content and synthesis are substantially repressed, correlating with decreased RNA Polymerase II (RNAPII) expression and activation. Integrating RNAPII occupancy and transcriptome profiling, we identify repressed networks and a role for promoter-proximal RNAPII pausing in G0. Strikingly, RNAPII shows enhanced pausing in G0 on repressed genes encoding regulators of RNA biogenesis (Nucleolin, Rps24, Ctdp1); release of pausing is associated with their increased expression in G1. Knockdown of these transcripts in proliferating cells leads to induction of G0 markers, confirming the importance of their repression in establishment of G0. A targeted screen of RNAPII regulators revealed that knockdown of Aff4 (positive regulator of elongation) unexpectedly enhances expression of G0-stalled genes and hastens S phase; NELF, a regulator of pausing appears to be dispensable. We propose that RNAPII pausing contributes to transcriptional control of a subset of G0-repressed genes to maintain quiescence and impacts the timing of the G0-G1 transition.
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Affiliation(s)
- Hardik P Gala
- Centre for Cellular and Molecular Biology, Hyderabad, 500007, India.,Institute for Stem Cell Science and Regenerative Medicine, Bangalore, 560065, India
| | - Debarya Saha
- Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Nisha Venugopal
- Centre for Cellular and Molecular Biology, Hyderabad, 500007, India.,Institute for Stem Cell Science and Regenerative Medicine, Bangalore, 560065, India
| | - Ajoy Aloysius
- Centre for Cellular and Molecular Biology, Hyderabad, 500007, India.,Institute for Stem Cell Science and Regenerative Medicine, Bangalore, 560065, India.,National Center for Biological Sciences, Bangalore, 560065, India
| | - Gunjan Purohit
- Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Jyotsna Dhawan
- Centre for Cellular and Molecular Biology, Hyderabad, 500007, India.,Institute for Stem Cell Science and Regenerative Medicine, Bangalore, 560065, India
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8
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Bonitto K, Sarathy K, Atai K, Mitra M, Coller HA. Is There a Histone Code for Cellular Quiescence? Front Cell Dev Biol 2021; 9:739780. [PMID: 34778253 PMCID: PMC8586460 DOI: 10.3389/fcell.2021.739780] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/17/2021] [Indexed: 12/14/2022] Open
Abstract
Many of the cells in our bodies are quiescent, that is, temporarily not dividing. Under certain physiological conditions such as during tissue repair and maintenance, quiescent cells receive the appropriate stimulus and are induced to enter the cell cycle. The ability of cells to successfully transition into and out of a quiescent state is crucial for many biological processes including wound healing, stem cell maintenance, and immunological responses. Across species and tissues, transcriptional, epigenetic, and chromosomal changes associated with the transition between proliferation and quiescence have been analyzed, and some consistent changes associated with quiescence have been identified. Histone modifications have been shown to play a role in chromatin packing and accessibility, nucleosome mobility, gene expression, and chromosome arrangement. In this review, we critically evaluate the role of different histone marks in these processes during quiescence entry and exit. We consider different model systems for quiescence, each of the most frequently monitored candidate histone marks, and the role of their writers, erasers and readers. We highlight data that support these marks contributing to the changes observed with quiescence. We specifically ask whether there is a quiescence histone “code,” a mechanism whereby the language encoded by specific combinations of histone marks is read and relayed downstream to modulate cell state and function. We conclude by highlighting emerging technologies that can be applied to gain greater insight into the role of a histone code for quiescence.
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Affiliation(s)
- Kenya Bonitto
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kirthana Sarathy
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kaiser Atai
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Mithun Mitra
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Hilary A Coller
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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9
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Roy N, Sundar S, Pillai M, Patell-Socha F, Ganesh S, Aloysius A, Rumman M, Gala H, Hughes SM, Zammit PS, Dhawan J. mRNP granule proteins Fmrp and Dcp1a differentially regulate mRNP complexes to contribute to control of muscle stem cell quiescence and activation. Skelet Muscle 2021; 11:18. [PMID: 34238354 PMCID: PMC8265057 DOI: 10.1186/s13395-021-00270-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 04/28/2021] [Indexed: 01/28/2023] Open
Abstract
Background During skeletal muscle regeneration, satellite stem cells use distinct pathways to repair damaged myofibers or to self-renew by returning to quiescence. Cellular/mitotic quiescence employs mechanisms that promote a poised or primed state, including altered RNA turnover and translational repression. Here, we investigate the role of mRNP granule proteins Fragile X Mental Retardation Protein (Fmrp) and Decapping protein 1a (Dcp1a) in muscle stem cell quiescence and differentiation. Methods Using isolated single muscle fibers from adult mice, we established differential enrichment of mRNP granule proteins including Fmrp and Dcp1a in muscle stem cells vs. myofibers. We investigated muscle tissue homeostasis in adult Fmr1-/- mice, analyzing myofiber cross-sectional area in vivo and satellite cell proliferation ex vivo. We explored the molecular mechanisms of Dcp1a and Fmrp function in quiescence, proliferation and differentiation in a C2C12 culture model. Here, we used polysome profiling, imaging and RNA/protein expression analysis to establish the abundance and assembly status of mRNP granule proteins in different cellular states, and the phenotype of knockdown cells. Results Quiescent muscle satellite cells are enriched for puncta containing the translational repressor Fmrp, but not the mRNA decay factor Dcp1a. MuSC isolated from Fmr1-/- mice exhibit defective proliferation, and mature myofibers show reduced cross-sectional area, suggesting a role for Fmrp in muscle homeostasis. Expression and organization of Fmrp and Dcp1a varies during primary MuSC activation on myofibers, with Fmrp puncta prominent in quiescence, but Dcp1a puncta appearing during activation/proliferation. This reciprocal expression of Fmrp and Dcp1a puncta is recapitulated in a C2C12 culture model of quiescence and activation: consistent with its role as a translational repressor, Fmrp is enriched in non-translating mRNP complexes abundant in quiescent myoblasts; Dcp1a puncta are lost in quiescence, suggesting stabilized and repressed transcripts. The function of each protein differs during proliferation; whereas Fmrp knockdown led to decreased proliferation and lower cyclin expression, Dcp1a knockdown led to increased cell proliferation and higher cyclin expression. However, knockdown of either Fmrp or Dcp1a led to compromised differentiation. We also observed cross-regulation of decay versus storage mRNP granules; knockdown of Fmrp enhances accumulation of Dcp1a puncta, whereas knockdown of Dcp1a leads to increased Fmrp in puncta. Conclusions Taken together, our results provide evidence that the balance of mRNA turnover versus utilization is specific for distinct cellular states. Supplementary Information The online version contains supplementary material available at 10.1186/s13395-021-00270-9.
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Affiliation(s)
- Nainita Roy
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Swetha Sundar
- Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Malini Pillai
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Farah Patell-Socha
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Sravya Ganesh
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Ajoy Aloysius
- National Center for Biological Sciences, Bangalore, India
| | - Mohammed Rumman
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Hardik Gala
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.,Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Simon M Hughes
- King's College London, Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, London, UK
| | - Peter S Zammit
- King's College London, Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, London, UK
| | - Jyotsna Dhawan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India. .,Centre for Cellular and Molecular Biology, Hyderabad, India.
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10
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Puri D, Swamy CVB, Dhawan J, Mishra RK. Comparative nuclear matrix proteome analysis of skeletal muscle cells in different cellular states. Cell Biol Int 2021; 45:580-598. [PMID: 33200434 DOI: 10.1002/cbin.11499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/01/2020] [Accepted: 11/11/2020] [Indexed: 12/20/2022]
Abstract
The nuclear matrix (NuMat) serves as the structural framework for organizing and maintaining nuclear architecture, however, the mechanisms by which this non-chromatin compartment is constructed and regulated are poorly understood. This study presents a proteomic analysis of the NuMat isolated from cultured skeletal muscle cells in three distinct cellular states- proliferating myoblasts (MBs), terminally differentiated myotubes (MTs), and mitotically quiescent (G0) myoblasts. About 40% of the proteins identified were found to be common in the NuMat proteome of these morphologically and functionally distinct cell states. These proteins, termed as the "core NuMat," define the stable, conserved, structural constituent of the nucleus, with functions such as RNA splicing, cytoskeletal organization, and chromatin modification, while the remaining NuMat proteins showed cell-state specificity, consistent with a more dynamic and potentially regulatory function. Specifically, myoblast NuMat was enriched in cell cycle, DNA replication and repair proteins, myotube NuMat in muscle differentiation and muscle function proteins, while G0 NuMat was enriched in metabolic, transcription, and transport proteins. These findings offer a new perspective for a cell-state-specific role of nuclear architecture and spatial organization, integrated with diverse cellular processes, and implicate NuMat proteins in the control of the cell cycle, lineage commitment, and differentiation.
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Affiliation(s)
- Deepika Puri
- Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Hyderabad, India
| | - Ch V B Swamy
- Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Hyderabad, India
| | - Jyotsna Dhawan
- Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Hyderabad, India
| | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Hyderabad, India
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11
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Emerging Roles of PRDM Factors in Stem Cells and Neuronal System: Cofactor Dependent Regulation of PRDM3/16 and FOG1/2 (Novel PRDM Factors). Cells 2020; 9:cells9122603. [PMID: 33291744 PMCID: PMC7761934 DOI: 10.3390/cells9122603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/13/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022] Open
Abstract
PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1) (PR) homologous domain containing (PRDM) transcription factors are expressed in neuronal and stem cell systems, and they exert multiple functions in a spatiotemporal manner. Therefore, it is believed that PRDM factors cooperate with a number of protein partners to regulate a critical set of genes required for maintenance of stem cell self-renewal and differentiation through genetic and epigenetic mechanisms. In this review, we summarize recent findings about the expression of PRDM factors and function in stem cell and neuronal systems with a focus on cofactor-dependent regulation of PRDM3/16 and FOG1/2. We put special attention on summarizing the effects of the PRDM proteins interaction with chromatin modulators (NuRD complex and CtBPs) on the stem cell characteristic and neuronal differentiation. Although PRDM factors are known to possess intrinsic enzyme activity, our literature analysis suggests that cofactor-dependent regulation of PRDM3/16 and FOG1/2 is also one of the important mechanisms to orchestrate bidirectional target gene regulation. Therefore, determining stem cell and neuronal-specific cofactors will help better understanding of PRDM3/16 and FOG1/2-controlled stem cell maintenance and neuronal differentiation. Finally, we discuss the clinical aspect of these PRDM factors in different diseases including cancer. Overall, this review will help further sharpen our knowledge of the function of the PRDM3/16 and FOG1/2 with hopes to open new research fields related to these factors in stem cell biology and neuroscience.
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Evans AM. On a Magical Mystery Tour with 8-Bromo-Cyclic ADP-Ribose: From All-or-None Block to Nanojunctions and the Cell-Wide Web. Molecules 2020; 25:E4768. [PMID: 33081414 PMCID: PMC7587525 DOI: 10.3390/molecules25204768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/08/2020] [Indexed: 11/16/2022] Open
Abstract
A plethora of cellular functions are controlled by calcium signals, that are greatly coordinated by calcium release from intracellular stores, the principal component of which is the sarco/endooplasmic reticulum (S/ER). In 1997 it was generally accepted that activation of various G protein-coupled receptors facilitated inositol-1,4,5-trisphosphate (IP3) production, activation of IP3 receptors and thus calcium release from S/ER. Adding to this, it was evident that S/ER resident ryanodine receptors (RyRs) could support two opposing cellular functions by delivering either highly localised calcium signals, such as calcium sparks, or by carrying propagating, global calcium waves. Coincidentally, it was reported that RyRs in mammalian cardiac myocytes might be regulated by a novel calcium mobilising messenger, cyclic adenosine diphosphate-ribose (cADPR), that had recently been discovered by HC Lee in sea urchin eggs. A reputedly selective and competitive cADPR antagonist, 8-bromo-cADPR, had been developed and was made available to us. We used 8-bromo-cADPR to further explore our observation that S/ER calcium release via RyRs could mediate two opposing functions, namely pulmonary artery dilation and constriction, in a manner seemingly independent of IP3Rs or calcium influx pathways. Importantly, the work of others had shown that, unlike skeletal and cardiac muscles, smooth muscles might express all three RyR subtypes. If this were the case in our experimental system and cADPR played a role, then 8-bromo-cADPR would surely block one of the opposing RyR-dependent functions identified, or the other, but certainly not both. The latter seemingly implausible scenario was confirmed. How could this be, do cells hold multiple, segregated SR stores that incorporate different RyR subtypes in receipt of spatially segregated signals carried by cADPR? The pharmacological profile of 8-bromo-cADPR action supported not only this, but also indicated that intracellular calcium signals were delivered across intracellular junctions formed by the S/ER. Not just one, at least two. This article retraces the steps along this journey, from the curious pharmacological profile of 8-bromo-cADPR to the discovery of the cell-wide web, a diverse network of cytoplasmic nanocourses demarcated by S/ER nanojunctions, which direct site-specific calcium flux and may thus coordinate the full panoply of cellular processes.
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Grants
- 01/A/S/07453 Biotechnology and Biological Sciences Research Council
- WT046374 , WT056423, WT070772, WT074434, WT081195AIA, WT212923, WT093147 Wellcome Trust
- PG/10/95/28657 British Heart Foundation
- FS/03/033/15432, FS/05/050, PG/05/128/19884, RG/12/14/29885, PG/10/95/28657 British Heart Foundation
- RG/12/14/29885 British Heart Foundation
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Affiliation(s)
- A Mark Evans
- Centre for Discovery Brain Sciences and Cardiovascular Science, Edinburgh Medical School, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
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13
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Wei D, Yiyuan C, Qian L, Jianhua L, Yazhuo Z, Hua G. The absence of PRDM2 involved the tumorigenesis of somatotroph adenomas through regulating c-Myc. Gene 2020; 737:144456. [PMID: 32044406 DOI: 10.1016/j.gene.2020.144456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 02/06/2020] [Indexed: 02/06/2023]
Abstract
Somatotroph adenoma is the main cause of acromegaly which have peripheral signs with growth of soft tissues and multiple comorbidities. Surgery and adjuvant therapy with somatostatin analogs (SSA) fail in more than 25% of patients. PRDM2, a tumor suppressor, plays an important role in cancer and obesity, including pituitary adenomas. In this study, we analyze the correlation of PRDM2 and oncogene c-Myc in 70 somatotroph adenomas according immunohistochemical staining, furthermore, we probed that whether PRDM2 participates in c-Myc signaling pathway in vitro experiment. 70 somatotroph adenomas patients were divided into low patients and high patients according to median of H-score of PRDM2 or c-Myc. Low PRDM2 patients had higher risk of invasive behavior, larger tumor volume and recurrence chance than high PRDM2 group (P = 0.015, P = 0.031, P = 0.017). High c-Myc patients had higher risk of invasive behavior, larger tumor volume and recurrence chance than low c-Myc group (P = 0.012, P = 0.002, P = 0.015). It was a negative correlation between H-score of PRDM2 and c-Myc (PRDM2 = -0.163 × c-Myc + 67.11, r = -0.407). The ability of cell proliferation was declined in a time dependent manner after overexpression of PRDM2 (PRDM2 group) compared to that in control GH3 cells (P < 0.05). Through flow cytometry assay, PRDM2 could induce the apoptosis and G2/M arrest in GH3 cell (both p < 0.05). Transwell experiment proved less trans-membrane cells in PRDM2 group than those in control group (415 ± 76 vs 145 ± 37, P < 0.01). RT-PCR and western blot both proved PRDM2 could inhibit the level c-Myc and elevate the levels of CDKN1A and CDKN1B. Combined with c-Myc inhibitor 10058-F4, PRDM2 further inhibited cell proliferation and induced more apoptosis in GH3 cell. Taken together, we found that PRDM2 negatively regulated the expression of c-Myc in somatotroph adenomas, and testified the synergism between PRDM2 gene therapy and c-Myc inhibitor in vitro experiment.
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Affiliation(s)
- Dong Wei
- Department of Neurosurgery, Tangshan People's Hospital, Tangshan, Hebei, China; Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Capital Medical University, 119# Southwest 4rd, Beijing 100050, China
| | - Chen Yiyuan
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Capital Medical University, 119# Southwest 4rd, Beijing 100050, China
| | - Liu Qian
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Capital Medical University, 119# Southwest 4rd, Beijing 100050, China
| | - Li Jianhua
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Capital Medical University, 119# Southwest 4rd, Beijing 100050, China; Department of Neurosurgery, Binzhou People's Hospital, Binzhou, Shandong 256610, China
| | - Zhang Yazhuo
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Capital Medical University, 119# Southwest 4rd, Beijing 100050, China
| | - Gao Hua
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Capital Medical University, 119# Southwest 4rd, Beijing 100050, China.
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14
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Zhang J, Si J, Gan L, Di C, Xie Y, Sun C, Li H, Guo M, Zhang H. Research progress on therapeutic targeting of quiescent cancer cells. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:2810-2820. [DOI: 10.1080/21691401.2019.1638793] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jinhua Zhang
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Si
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lu Gan
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cuixia Di
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yi Xie
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chao Sun
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hongyan Li
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Menghuan Guo
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Hong Zhang
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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15
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Pehlivan D, Bayram Y, Gunes N, Coban Akdemir Z, Shukla A, Bierhals T, Tabakci B, Sahin Y, Gezdirici A, Fatih JM, Gulec EY, Yesil G, Punetha J, Ocak Z, Grochowski CM, Karaca E, Albayrak HM, Radhakrishnan P, Erdem HB, Sahin I, Yildirim T, Bayhan IA, Bursali A, Elmas M, Yuksel Z, Ozdemir O, Silan F, Yildiz O, Yesilbas O, Isikay S, Balta B, Gu S, Jhangiani SN, Doddapaneni H, Hu J, Muzny DM, Boerwinkle E, Gibbs RA, Tsiakas K, Hempel M, Girisha KM, Gul D, Posey JE, Elcioglu NH, Tuysuz B, Lupski JR. The Genomics of Arthrogryposis, a Complex Trait: Candidate Genes and Further Evidence for Oligogenic Inheritance. Am J Hum Genet 2019; 105:132-150. [PMID: 31230720 PMCID: PMC6612529 DOI: 10.1016/j.ajhg.2019.05.015] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/21/2019] [Indexed: 01/29/2023] Open
Abstract
Arthrogryposis is a clinical finding that is present either as a feature of a neuromuscular condition or as part of a systemic disease in over 400 Mendelian conditions. The underlying molecular etiology remains largely unknown because of genetic and phenotypic heterogeneity. We applied exome sequencing (ES) in a cohort of 89 families with the clinical sign of arthrogryposis. Additional molecular techniques including array comparative genomic hybridization (aCGH) and Droplet Digital PCR (ddPCR) were performed on individuals who were found to have pathogenic copy number variants (CNVs) and mosaicism, respectively. A molecular diagnosis was established in 65.2% (58/89) of families. Eleven out of 58 families (19.0%) showed evidence for potential involvement of pathogenic variation at more than one locus, probably driven by absence of heterozygosity (AOH) burden due to identity-by-descent (IBD). RYR3, MYOM2, ERGIC1, SPTBN4, and ABCA7 represent genes, identified in two or more families, for which mutations are probably causative for arthrogryposis. We also provide evidence for the involvement of CNVs in the etiology of arthrogryposis and for the idea that both mono-allelic and bi-allelic variants in the same gene cause either similar or distinct syndromes. We were able to identify the molecular etiology in nine out of 20 families who underwent reanalysis. In summary, our data from family-based ES further delineate the molecular etiology of arthrogryposis, yielded several candidate disease-associated genes, and provide evidence for mutational burden in a biological pathway or network. Our study also highlights the importance of reanalysis of individuals with unsolved diagnoses in conjunction with sequencing extended family members.
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Affiliation(s)
- Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nilay Gunes
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa Medical Faculty, Istanbul 34096, Turkey
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg 20246, Germany
| | - Burcu Tabakci
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul 34854, Turkey
| | - Yavuz Sahin
- Department of Medical Genetics, Necip Fazıl City Hospital, Kahramanmaras 46050, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Gozde Yesil
- Department of Medical Genetics, Bezmi Alem Vakif University Faculty of Medicine, Istanbul 34093, Turkey
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Ocak
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | | | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hatice Mutlu Albayrak
- Department of Pediatrics, Division of Pediatric Genetics, Faculty of Medicine, Ondokuz Mayıs University, Samsun 55270, Turkey
| | - Periyasamy Radhakrishnan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Haktan Bagis Erdem
- Department of Medical Genetics, University of Health Sciences, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara 06110, Turkey
| | - Ibrahim Sahin
- Department of Medical Genetics, University of Erzurum, School of Medicine, Erzurum 25240, Turkey
| | - Timur Yildirim
- Department of Orthopedics and Traumatology, Baltalimani Bone Diseases Training and Research Hospital, Istanbul 34470, Turkey
| | - Ilhan A Bayhan
- Department of Orthopedics and Traumatology, Baltalimani Bone Diseases Training and Research Hospital, Istanbul 34470, Turkey
| | - Aysegul Bursali
- Department of Orthopedics and Traumatology, Baltalimani Bone Diseases Training and Research Hospital, Istanbul 34470, Turkey
| | - Muhsin Elmas
- Department of Medical Genetics, Afyon Kocatepe University, School of Medicine, Afyon 03218, Turkey
| | - Zafer Yuksel
- Medical Genetics Clinic, Mersin Women and Children Hospital, Mersin 33330, Turkey
| | - Ozturk Ozdemir
- Department of Medical Genetics, Faculty of Medicine, Onsekiz Mart University, Canakkale 17000, Turkey
| | - Fatma Silan
- Department of Medical Genetics, Faculty of Medicine, Onsekiz Mart University, Canakkale 17000, Turkey
| | - Onur Yildiz
- Department of Medical Genetics, Faculty of Medicine, Onsekiz Mart University, Canakkale 17000, Turkey
| | - Osman Yesilbas
- Division of Critical Care Medicine, Department of Pediatrics, University of Health Sciences, Van Training and Research Hospital, Van 65130, Turkey
| | - Sedat Isikay
- Department of Physiotherapy and Rehabilitation, Hasan Kalyoncu University, School of Health Sciences, Gaziantep 27000, Turkey
| | - Burhan Balta
- Department of Medical Genetics, Kayseri Training and Research Hospital, Kayseri 38080, Turkey
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genetics Center, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Konstantinos Tsiakas
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg 20246, Germany
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Davut Gul
- Department of Medical Genetics, Gulhane Military Medical School, Ankara 06010, Turkey
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nursel H Elcioglu
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul 34854, Turkey; Eastern Mediterranean University School of Medicine, Cyprus, Mersin 10, Turkey
| | - Beyhan Tuysuz
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa Medical Faculty, Istanbul 34096, Turkey
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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16
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DEK terminates diapause by activation of quiescent cells in the crustacean Artemia. Biochem J 2019; 476:1753-1769. [PMID: 31189566 DOI: 10.1042/bcj20190169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 12/24/2022]
Abstract
To cope with harsh environments, the Artemia shrimp produces gastrula embryos in diapause, a state of obligate dormancy, having cellular quiescence and suppressed metabolism. The mechanism behind these cellular events remains largely unknown. Here, we study the regulation of cell quiescence using diapause embryos of Artemia We found that Artemia DEK (Ar-DEK), a nuclear factor protein, was down-regulated in the quiescent cells of diapause embryos and enriched in the activated cells of post-diapause embryos. Knockdown of Ar-DEK induced the production of diapause embryos whereas the control Artemia released free-swimming nuaplii. Our results indicate that Ar-DEK correlated with the termination of cellular quiescence via the increase in euchromatin and decrease in heterochromatin. The phenomena of quiescence have many implications beyond shrimp ecology. In cancer cells, for example, knockdown of DEK also induced a short period of cellular quiescence and increased resistance to environmental stress in MCF-7 and MKN45 cancer cell lines. Analysis of RNA sequences in Artemia and in MCF-7 revealed that the Wnt and AURKA signaling pathways were all down-regulated and the p53 signaling pathway was up-regulated upon inhibition of DEK expression. Our results provide insight into the functions of Ar-DEK in the activation of cellular quiescence during diapause formation in Artemia.
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17
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Duan J, Navarro-Dorado J, Clark JH, Kinnear NP, Meinke P, Schirmer EC, Evans AM. The cell-wide web coordinates cellular processes by directing site-specific Ca 2+ flux across cytoplasmic nanocourses. Nat Commun 2019; 10:2299. [PMID: 31127110 PMCID: PMC6534574 DOI: 10.1038/s41467-019-10055-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 04/10/2019] [Indexed: 02/01/2023] Open
Abstract
Ca2+ coordinates diverse cellular processes, yet how function-specific signals arise is enigmatic. We describe a cell-wide network of distinct cytoplasmic nanocourses with the nucleus at its centre, demarcated by sarcoplasmic reticulum (SR) junctions (≤400 nm across) that restrict Ca2+ diffusion and by nanocourse-specific Ca2+-pumps that facilitate signal segregation. Ryanodine receptor subtype 1 (RyR1) supports relaxation of arterial myocytes by unloading Ca2+ into peripheral nanocourses delimited by plasmalemma-SR junctions, fed by sarco/endoplasmic reticulum Ca2+ ATPase 2b (SERCA2b). Conversely, stimulus-specified increases in Ca2+ flux through RyR2/3 clusters selects for rapid propagation of Ca2+ signals throughout deeper extraperinuclear nanocourses and thus myocyte contraction. Nuclear envelope invaginations incorporating SERCA1 in their outer nuclear membranes demarcate further diverse networks of cytoplasmic nanocourses that receive Ca2+ signals through discrete RyR1 clusters, impacting gene expression through epigenetic marks segregated by their associated invaginations. Critically, this circuit is not hardwired and remodels for different outputs during cell proliferation. Although calcium signals are known to be critical for many cellular processes, how signaling elicits specific functions remains unclear. In visually striking work, Duan et al. reveal that networks of cytoplasmic nanocourses orchestrate cell activity by directing site-specific calcium signals.
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Affiliation(s)
- Jingxian Duan
- Centres for Discovery Brain Sciences and Cardiovascular Sciences, College of Medicine and Veterinary Medicine, Hugh Robson Building, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Jorge Navarro-Dorado
- Centres for Discovery Brain Sciences and Cardiovascular Sciences, College of Medicine and Veterinary Medicine, Hugh Robson Building, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Jill H Clark
- Centres for Discovery Brain Sciences and Cardiovascular Sciences, College of Medicine and Veterinary Medicine, Hugh Robson Building, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Nicholas P Kinnear
- Centres for Discovery Brain Sciences and Cardiovascular Sciences, College of Medicine and Veterinary Medicine, Hugh Robson Building, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Peter Meinke
- Wellcome Centre for Cell Biology, Michael Swann Building, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Eric C Schirmer
- Wellcome Centre for Cell Biology, Michael Swann Building, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - A Mark Evans
- Centres for Discovery Brain Sciences and Cardiovascular Sciences, College of Medicine and Veterinary Medicine, Hugh Robson Building, University of Edinburgh, Edinburgh, EH8 9XD, UK.
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18
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Sahakian N, Castinetti F, Dufour H, Graillon T, Romanet P, Barlier A, Brue T, Cuny T. Clinical management of difficult to treat macroprolactinomas. Expert Rev Endocrinol Metab 2019; 14:179-192. [PMID: 30913932 DOI: 10.1080/17446651.2019.1596024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/13/2019] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Prolactinomas represent the most common pituitary adenomas encountered in the clinic. While a majority of these tumors will be successfully treated by dopamine agonist (DA) such as cabergoline, their management becomes problematic since a resistance to DA can occur and/or if the tumor displays features of aggressiveness, two conditions that are closely related. AREAS COVERED Epidemiology and medical treatment of prolactinomas; resistance to DA and molecular basis of DA-resistance; therapeutical alternatives in case of DA-resistant Prolactinomas and therapies in development; summarizing conclusions. EXPERT OPINION The management of DA-resistant prolactinomas requires a multidisciplinary approach by an expert team. Along with discussions about surgery with or without gamma knife radiosurgery, genetic screening for multiple endocrine neoplasia type 1 (MEN1) syndrome is actively discussed in a case-by-case approach. In case of surgery, a careful analysis of the tumor sample can provide information about its aggressivity potential according to recent criteria. Ultimately, temozolomide can be indicated if the tumor is rapidly growing and/or threatening for the patient.
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Affiliation(s)
- Nicolas Sahakian
- a Marseille Medical Genetics, Inserm U1251, Hôpital de la Conception, Service d'Endocrinologie , Aix Marseille Univ, APHM , Marseille , France
| | - Frederic Castinetti
- a Marseille Medical Genetics, Inserm U1251, Hôpital de la Conception, Service d'Endocrinologie , Aix Marseille Univ, APHM , Marseille , France
| | - Henry Dufour
- b Marseille Medical Genetics, Inserm U1251, Hôpital de la Timone, Service de Neurochirurgie , Aix Marseille Univ, APHM , Marseille , France
| | - Thomas Graillon
- b Marseille Medical Genetics, Inserm U1251, Hôpital de la Timone, Service de Neurochirurgie , Aix Marseille Univ, APHM , Marseille , France
| | - Pauline Romanet
- c Marseille Medical Genetics, Inserm U1251, Hôpital de la Conception, Laboratoire de Biologie Moléculaire et Biochimie , Aix Marseille Univ, APHM , Marseille , France
| | - Anne Barlier
- c Marseille Medical Genetics, Inserm U1251, Hôpital de la Conception, Laboratoire de Biologie Moléculaire et Biochimie , Aix Marseille Univ, APHM , Marseille , France
| | - Thierry Brue
- a Marseille Medical Genetics, Inserm U1251, Hôpital de la Conception, Service d'Endocrinologie , Aix Marseille Univ, APHM , Marseille , France
| | - Thomas Cuny
- a Marseille Medical Genetics, Inserm U1251, Hôpital de la Conception, Service d'Endocrinologie , Aix Marseille Univ, APHM , Marseille , France
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Puri D, Subramanyam D. Stress - (self) eating: Epigenetic regulation of autophagy in response to psychological stress. FEBS J 2019; 286:2447-2460. [PMID: 30927484 DOI: 10.1111/febs.14826] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/19/2019] [Accepted: 03/27/2019] [Indexed: 12/16/2022]
Abstract
Autophagy is a constitutive and cytoprotective catabolic process. Aberrations in autophagy lead to a multitude of degenerative disorders, with neurodegeneration being one of the most widely studied autophagy-related disorders. While the field has largely been focusing on the cytosolic constituents and processes of autophagy, recent studies are increasingly appreciating the role of chromatin modifications and epigenetic regulation in autophagy maintenance. Autophagy has been implicated in the regulation of neurogenesis, and disruption of neurogenesis in response to psychological stress is a proximal risk factor for development of neuropsychiatric disorders such as major depressive disorder (MDD). In this review, we will discuss the regulation of autophagy in normal neurogenesis as well as during chronic psychological stress, focusing on the epigenetic control of autophagy in these contexts, and also highlight the lacunae in our understanding of this process. The systematic study of these regulatory mechanisms will provide a novel therapeutic strategy, based on the use epigenetic regulators of autophagy to enhance neurogenesis and potentially alleviate stress-related behavioral disorders.
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Affiliation(s)
- Deepika Puri
- National Centre for Cell Science, Savitribai Phule Pune University, Pune, India
| | - Deepa Subramanyam
- National Centre for Cell Science, Savitribai Phule Pune University, Pune, India
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Gamage TKJB, Schierding W, Hurley D, Tsai P, Ludgate JL, Bhoothpur C, Chamley LW, Weeks RJ, Macaulay EC, James JL. The role of DNA methylation in human trophoblast differentiation. Epigenetics 2018; 13:1154-1173. [PMID: 30475094 DOI: 10.1080/15592294.2018.1549462] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The placenta is a vital fetal exchange organ connecting mother and baby. Specialised placental epithelial cells, called trophoblasts, are essential for adequate placental function. Trophoblasts transform the maternal vasculature to allow efficient blood flow to the placenta and facilitate adequate nutrient uptake. Placental development is in part regulated by epigenetic mechanisms. However, our understanding of how DNA methylation contributes to human trophoblast differentiation is limited. To better understand how genome-wide methylation differences affect trophoblast differentiation, reduced representation bisulfite sequencing (RRBS) was conducted on four matched sets of trophoblasts; side-population trophoblasts (a candidate human trophoblast stem cell population), cytotrophoblasts (an intermediate progenitor population), and extravillous trophoblasts (EVT, a terminally differentiated population) each isolated from the same first trimester placenta. Each trophoblast population had a distinct methylome. In line with their close differentiation relationship, the methylation profile of side-population trophoblasts was most similar to cytotrophoblasts, whilst EVT had the most distinct methylome. In comparison to mature trophoblast populations, side-population trophoblasts exhibited differential methylation of genes and miRNAs involved in cell cycle regulation, differentiation, and regulation of pluripotency. A combined methylomic and transcriptomic approach was taken to better understand cytotrophoblast differentiation to EVT. This revealed methylation of 41 genes involved in epithelial to mesenchymal transition and metastatic cancer pathways, which likely contributes to the acquisition of an invasive EVT phenotype. However, the methylation status of a gene did not always predict gene expression. Therefore, while CpG methylation plays a role in trophoblast differentiation, it is likely not the only regulatory mechanism involved in this process.
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Affiliation(s)
- Teena K J B Gamage
- a Department of Obstetrics and Gynaecology , The University of Auckland , Auckland , New Zealand
| | - William Schierding
- a Department of Obstetrics and Gynaecology , The University of Auckland , Auckland , New Zealand
| | - Daniel Hurley
- b Systems Biology Laboratory, Melbourne School of Engineering , University of Melbourne , Melbourne , Australia
| | - Peter Tsai
- a Department of Obstetrics and Gynaecology , The University of Auckland , Auckland , New Zealand
| | - Jackie L Ludgate
- c Department of Pathology, Dunedin School of Medicine , University of Otago , Dunedin , New Zealand
| | | | - Lawrence W Chamley
- a Department of Obstetrics and Gynaecology , The University of Auckland , Auckland , New Zealand
| | - Robert J Weeks
- c Department of Pathology, Dunedin School of Medicine , University of Otago , Dunedin , New Zealand
| | - Erin C Macaulay
- c Department of Pathology, Dunedin School of Medicine , University of Otago , Dunedin , New Zealand
| | - Joanna L James
- a Department of Obstetrics and Gynaecology , The University of Auckland , Auckland , New Zealand
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Aloysius A, DasGupta R, Dhawan J. The transcription factor Lef1 switches partners from β-catenin to Smad3 during muscle stem cell quiescence. Sci Signal 2018; 11:11/540/eaan3000. [PMID: 30042129 DOI: 10.1126/scisignal.aan3000] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Skeletal muscle stem cells (MuSCs), also known as satellite cells, persist in adult mammals by entering a state of quiescence (G0) during the early postnatal period. Quiescence is reversed during damage-induced regeneration and re-established after regeneration. Entry of cultured myoblasts into G0 is associated with a specific, reversible induction of Wnt target genes, thus implicating members of the Tcf and Lef1 (Tcf/Lef) transcription factor family, which mediate transcriptional responses to Wnt signaling, in the initiation of quiescence. We found that the canonical Wnt effector β-catenin, which cooperates with Tcf/Lef, was dispensable for myoblasts to enter quiescence. Using pharmacological and genetic approaches in cultured C2C12 myoblasts and in MuSCs, we demonstrated that Tcf/Lef activity during quiescence depended not on β-catenin but on the transforming growth factor-β (TGF-β) effector and transcriptional coactivator Smad3, which colocalized with Lef1 at canonical Wnt-responsive elements and directly interacted with Lef1 specifically in G0 Depletion of Smad3, but not β-catenin, reduced Lef1 occupancy at target promoters, Tcf/Lef target gene expression, and self-renewal of myoblasts. In vivo, MuSCs underwent a switch from β-catenin-Lef1 to Smad3-Lef1 interactions during the postnatal switch from proliferation to quiescence, with β-catenin-Lef1 interactions recurring during damage-induced reactivation. Our findings suggest that the interplay of Wnt-Tcf/Lef and TGF-β-Smad3 signaling activates canonical Wnt target promoters in a manner that depends on β-catenin during myoblast proliferation but is independent of β-catenin during MuSC quiescence.
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Affiliation(s)
- Ajoy Aloysius
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India.,Centre for Cellular and Molecular Biology, Hyderabad 500007, India.,Institute for Stem Cell Biology and Regenerative Medicine, Bangalore 560065, India
| | | | - Jyotsna Dhawan
- Centre for Cellular and Molecular Biology, Hyderabad 500007, India. .,Institute for Stem Cell Biology and Regenerative Medicine, Bangalore 560065, India
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22
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Guarnieri V, Muscarella LA, Verdelli C, Corbetta S. Alterations of DNA methylation in parathyroid tumors. Mol Cell Endocrinol 2018; 469:60-69. [PMID: 28501573 DOI: 10.1016/j.mce.2017.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 05/01/2017] [Accepted: 05/07/2017] [Indexed: 12/11/2022]
Abstract
Parathyroid tumors are common endocrine neoplasias associated with primary hyperparathyroidism, a metabolic disorder characterized by parathormone hypersecretion. Parathyroid neoplasia are frequently benign adenomas or multiple glands hyperplasia, while malignancies are rare. The epigenetic scenario in parathyroid tumors has just begun to be decoded: DNA methylation, histones and chromatin modifiers expression have been investigated so far. The main findings suggest that DNA methylation and chromatin remodeling are active and deregulated in parathyroid tumors, cooperating with genetic alterations to drive the tumor phenotype: the tumor suppressors menin and parafibromin, involved in parathyroid tumorigenesis, interact with chromatin modifiers, defining distinct epigenetic derangements. Many epigenetic alterations identified in parathyroid tumors are common to those in human cancers; moreover, some aspects of the epigenetic profile resemble epigenetic features of embryonic stem cells. Epigenetic profile may contribute to define the heterogeneity of parathyroid tumors and to provide targets for new therapeutic approaches.
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Affiliation(s)
- Vito Guarnieri
- Genetic Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Lucia Anna Muscarella
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Chiara Verdelli
- Laboratory of Experimental Endocrinology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Sabrina Corbetta
- Endocrinology Service, Department of Biomedical Sciences for Health, University of Milan, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy.
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23
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Induction of quiescence (G0) in bone marrow stromal stem cells enhances their stem cell characteristics. Stem Cell Res 2018; 30:69-80. [DOI: 10.1016/j.scr.2018.05.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 04/22/2018] [Accepted: 05/16/2018] [Indexed: 12/14/2022] Open
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24
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Sorrentino A, Rienzo M, Ciccodicola A, Casamassimi A, Abbondanza C. Human PRDM2: Structure, function and pathophysiology. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:S1874-9399(18)30071-3. [PMID: 29883756 DOI: 10.1016/j.bbagrm.2018.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 12/22/2022]
Abstract
PRDM2/RIZ is a member of a superfamily of histone/protein methyltransferases (PRDMs), which are characterized by the conserved N-terminal PR domain, with methyltransferase activity and zinc finger arrays at the C-terminus. Similar to other family members, two main protein types, known as RIZ1 and RIZ2, are produced from the PRDM2 locus differing by the presence or absence of the PR domain. The imbalance in their respective amounts may be an important cause of malignancy, with the PR-positive isoform commonly lost or downregulated and the PR-negative isoform always being present at higher levels in cancer cells. Interestingly, the RIZ1 isoform also represents an important target of estradiol action downstream of the interaction with hormone receptor. Furthermore, the imbalance between the two products could also be a molecular basis for other human diseases. Thus, understanding the molecular mechanisms underlying PRDM2 function could be useful in the pathophysiological context, with a potential to exploit this information in clinical practice.
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Affiliation(s)
- A Sorrentino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy; Department of Science and Technology, University of Naples "Parthenope", Naples, Italy
| | - M Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - A Ciccodicola
- Department of Science and Technology, University of Naples "Parthenope", Naples, Italy; Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy
| | - A Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - C Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
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Distinguishing States of Arrest: Genome-Wide Descriptions of Cellular Quiescence Using ChIP-Seq and RNA-Seq Analysis. Methods Mol Biol 2018; 1686:215-239. [PMID: 29030824 DOI: 10.1007/978-1-4939-7371-2_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Regenerative potential in adult stem cells is closely associated with the establishment of-and exit from-a temporary state of quiescence. Emerging evidence not only provides a rationale for the link between lineage determination programs and cell cycle regulation but also highlights the understanding of quiescence as an actively maintained cellular program, encompassing networks and mechanisms beyond mitotic inactivity or metabolic restriction. Interrogating the quiescent genome and transcriptome using deep-sequencing technologies offers an unprecedented view of the global mechanisms governing this reversibly arrested cellular state and its importance for cell identity. While many efforts have identified and isolated pure target stem cell populations from a variety of adult tissues, there is a growing appreciation that their isolation from the stem cell niche in vivo leads to activation and loss of hallmarks of quiescence. Thus, in vitro models that recapitulate the dynamic reversibly arrested stem cell state in culture and lend themselves to comparison with the activated or differentiated state are useful templates for genome-wide analysis of the quiescence network.In this chapter, we describe the methods that can be adopted for whole genome epigenomic and transcriptomic analysis of cells derived from one such established culture model where mouse myoblasts are triggered to enter or exit quiescence as homogeneous populations. The ability to synchronize myoblasts in G0 permits insights into the genome in "deep quiescence." The culture methods for generating large populations of quiescent myoblasts in either 2D or 3D culture formats are described in detail in a previous chapter in this series (Arora et al. Methods Mol Biol 1556:283-302, 2017). Among the attractive features of this model are that genes isolated from quiescent myoblasts in culture mark satellite cells in vivo (Sachidanandan et al., J Cell Sci 115:2701-2712, 2002) providing a validation of its approximation of the molecular state of true stem cells. Here, we provide our working protocols for ChIP-seq and RNA-seq analysis, focusing on those experimental elements that require standardization for optimal analysis of chromatin and RNA from quiescent myoblasts, and permitting useful and revealing comparisons with proliferating myoblasts or differentiated myotubes.
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27
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Dependence-induced increase of alcohol self-administration and compulsive drinking mediated by the histone methyltransferase PRDM2. Mol Psychiatry 2017; 22:1746-1758. [PMID: 27573876 PMCID: PMC5677579 DOI: 10.1038/mp.2016.131] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 05/20/2016] [Accepted: 06/01/2016] [Indexed: 12/20/2022]
Abstract
Epigenetic processes have been implicated in the pathophysiology of alcohol dependence, but the specific molecular mechanisms mediating dependence-induced neuroadaptations remain largely unknown. Here, we found that a history of alcohol dependence persistently decreased the expression of Prdm2, a histone methyltransferase that monomethylates histone 3 at the lysine 9 residue (H3K9me1), in the rat dorsomedial prefrontal cortex (dmPFC). Downregulation of Prdm2 was associated with decreased H3K9me1, supporting that changes in Prdm2 mRNA levels affected its activity. Chromatin immunoprecipitation followed by massively parallel DNA sequencing showed that genes involved in synaptic communication are epigenetically regulated by H3K9me1 in dependent rats. In non-dependent rats, viral-vector-mediated knockdown of Prdm2 in the dmPFC resulted in expression changes similar to those observed following a history of alcohol dependence. Prdm2 knockdown resulted in increased alcohol self-administration, increased aversion-resistant alcohol intake and enhanced stress-induced relapse to alcohol seeking, a phenocopy of postdependent rats. Collectively, these results identify a novel epigenetic mechanism that contributes to the development of alcohol-seeking behavior following a history of dependence.
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28
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Xue Y, Chen R, Du W, Yang F, Wei X. RIZ1 and histone methylation status in pituitary adenomas. Tumour Biol 2017; 39:1010428317711794. [PMID: 28718376 DOI: 10.1177/1010428317711794] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
RIZ1 displays strong tumor-suppressive activities, which has a potential histone methyltransferase activity. The objective of the study was to evaluate the level and the methylation status of RIZ1 and analyze its association with clinicopathological features and the histone in the pituitary adenomas. We found that RIZ1-positive cases were 11/50 and H-Scores 22.75 ± 11.83 in invasive pituitary adenomas and 26/53 and 66.3 ± 21.7 in non-invasive pituitary adenomas (χ2 = 8.182, p = 0.004). RIZ1 and C-myc showed the opposite trend in these cases. The methylation levels of RIZ1 were more than 50% in 30.4% (7/23) CpG sites through MALDI-TOF Mass array. There was significant difference (p < 0.01) in 4 CpG sites between invasive pituitary adenoma group and non-invasive pituitary adenoma group; furthermore, the relieved methylation levels of H3K4/H3K9 and enhanced methylation levels of H3K27 in the patients' serum were found. Furthermore, there was statistic difference of H3K4 and H3K27 methylation between invasive pituitary adenoma and non-invasive pituitary adenoma group (p < 0.01). The average progression-free survival in high RIZ1 group was 52.63 ± 7.62 months and 26.06 ± 4.23 months in low RIZ1 group (p < 0.05). Promoter region methylation of RIZ1 may play an important role in the epigenetic silencing of RIZ1 expression in pituitary adenomas, which may translate into important diagnostic and therapeutic applications.
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Affiliation(s)
- Yake Xue
- Department of Neurosurgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Ruokun Chen
- Department of Neurosurgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Wei Du
- Department of Neurosurgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Fengdong Yang
- Department of Neurosurgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Xinting Wei
- Department of Neurosurgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
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29
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Arora R, Rumman M, Venugopal N, Gala H, Dhawan J. Mimicking Muscle Stem Cell Quiescence in Culture: Methods for Synchronization in Reversible Arrest. Methods Mol Biol 2017; 1556:283-302. [PMID: 28247356 DOI: 10.1007/978-1-4939-6771-1_15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Growing evidence supports the view that in adult stem cells, the defining stem cell features of potency and self-renewal are associated with the quiescent state. Thus, uncovering the molecular logic of this reversibly arrested state underlies not only a fundamental understanding of adult tissue dynamics but also hopes for therapeutic regeneration and rejuvenation of damaged or aging tissue. A key question concerns how adult stem cells use quiescence to establish or reinforce the property of self-renewal. Since self-renewal is largely studied by assays that measure proliferation, the concept of self-renewal programs imposed during non-proliferating conditions is counterintuitive. However, there is increasing evidence generated by deconstructing the quiescent state that highlights how programs characteristic of this particular cell cycle exit may enhance stem cell capabilities, through both cell-intrinsic and extrinsic programs.Toward this end, culture models that recapitulate key aspects of stem cell quiescence are useful for molecular analysis to explore attributes and regulation of the quiescent state. In this chapter, we review the different methods used to generate homogeneous populations of quiescent muscle cells, largely by manipulating culture conditions that feed into core signaling programs that regulate the cell cycle. We also provide detailed protocols developed or refined in our lab over the past two decades.
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Affiliation(s)
- Reety Arora
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India
- National Centre for Biological Sciences, Bangalore, India
| | - Mohammed Rumman
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India
- Manipal University, Manipal, India
| | - Nisha Venugopal
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Hardik Gala
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Jyotsna Dhawan
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India.
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
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30
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Segalés J, Perdiguero E, Muñoz-Cánoves P. Regulation of Muscle Stem Cell Functions: A Focus on the p38 MAPK Signaling Pathway. Front Cell Dev Biol 2016; 4:91. [PMID: 27626031 PMCID: PMC5003838 DOI: 10.3389/fcell.2016.00091] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/17/2016] [Indexed: 12/17/2022] Open
Abstract
Formation of skeletal muscle fibers (myogenesis) during development and after tissue injury in the adult constitutes an excellent paradigm to investigate the mechanisms whereby environmental cues control gene expression programs in muscle stem cells (satellite cells) by acting on transcriptional and epigenetic effectors. Here we will review the molecular mechanisms implicated in the transition of satellite cells throughout the distinct myogenic stages (i.e., activation from quiescence, proliferation, differentiation, and self-renewal). We will also discuss recent findings on the causes underlying satellite cell functional decline with aging. In particular, our review will focus on the epigenetic changes underlying fate decisions and on how the p38 MAPK signaling pathway integrates the environmental signals at the chromatin to build up satellite cell adaptive responses during the process of muscle regeneration, and how these responses are altered in aging. A better comprehension of the signaling pathways connecting external and intrinsic factors will illuminate the path for improving muscle regeneration in the aged.
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Affiliation(s)
- Jessica Segalés
- Cell Biology Group, Department of Experimental and Health Sciences, CIBER on Neurodegenerative diseases (CIBERNED), Pompeu Fabra University Barcelona, Spain
| | - Eusebio Perdiguero
- Cell Biology Group, Department of Experimental and Health Sciences, CIBER on Neurodegenerative diseases (CIBERNED), Pompeu Fabra University Barcelona, Spain
| | - Pura Muñoz-Cánoves
- Cell Biology Group, Department of Experimental and Health Sciences, CIBER on Neurodegenerative diseases (CIBERNED), Pompeu Fabra UniversityBarcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA)Barcelona, Spain; Tissue Regeneration Laboratory, Centro Nacional de Investigaciones CardiovascularesMadrid, Spain
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31
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Rao VK, Ow JR, Shankar SR, Bharathy N, Manikandan J, Wang Y, Taneja R. G9a promotes proliferation and inhibits cell cycle exit during myogenic differentiation. Nucleic Acids Res 2016; 44:8129-43. [PMID: 27229136 PMCID: PMC5041453 DOI: 10.1093/nar/gkw483] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/19/2016] [Indexed: 11/12/2022] Open
Abstract
Differentiation of skeletal muscle cells, like most other cell types, requires a permanent exit from the cell cycle. The epigenetic programming underlying these distinct cellular states is not fully understood. In this study, we provide evidence that the lysine methyltransferase G9a functions as a central axis to regulate proliferation and differentiation of skeletal muscle cells. Transcriptome analysis of G9a knockdown cells revealed deregulation of many cell cycle regulatory genes. We demonstrate that G9a enhances cellular proliferation by two distinct mechanisms. G9a blocks cell cycle exit via methylation-dependent transcriptional repression of the MyoD target genes p21(Cip/Waf1) and Rb1. In addition, it activates E2F1-target genes in a methyltransferase activity-independent manner. We show that G9a is present in the E2F1/PCAF complex, and enhances PCAF occupancy and histone acetylation marks at E2F1-target promoters. Interestingly, G9a preferentially associates with E2F1 at the G1/S phase and with MyoD at the G2/M phase. Our results provide evidence that G9a functions both as a co-activator and a co-repressor to enhance cellular proliferation and inhibit myogenic differentiation.
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Affiliation(s)
- Vinay Kumar Rao
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Jin Rong Ow
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Shilpa Rani Shankar
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Narendra Bharathy
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Jayapal Manikandan
- NanoString Technologies, 530 Fairview Ave N, Suite 2000 Seattle, WA, USA
| | - Yaju Wang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
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32
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Cheedipudi S, Gala HP, Puri D, Dhawan J. Identification of PRDM2 regulated genes in quiescent C2C12 myoblasts. GENOMICS DATA 2015; 6:264-6. [PMID: 26697392 PMCID: PMC4664777 DOI: 10.1016/j.gdata.2015.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 10/10/2015] [Accepted: 10/13/2015] [Indexed: 12/03/2022]
Abstract
Quiescent stem cells contribute to tissue homeostasis and repair in adult mammals. We identified a tumor suppressor PRDM2, as an epigenetic regulator induced in quiescent muscle stem cells as well as in cultured quiescent myoblasts. To delineate the functions of PRDM2 in muscle cells, we compared the gene expression profiles of control and PRDM2 knockdown myoblasts in growing, differentiating and quiescent conditions (GEO accession number: GSE 58676). To identify the direct targets of PRDM2 and the promoters co-associated with H3K9me2 (mark catalyzed by PRDM2), ChIP-Chip analysis was performed (GSE58748). In this report we discuss in detail the methodology used to identify PRDM2 regulated genes and classify them into potential direct and indirect targets.
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Affiliation(s)
- Sirisha Cheedipudi
- Institute for Stem Cell Biology and Regenerative Medicine, National Center for Biological Sciences, GKVK Post, Bellary Road, Bangalore 560065, India ; Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
| | - Hardik P Gala
- Institute for Stem Cell Biology and Regenerative Medicine, National Center for Biological Sciences, GKVK Post, Bellary Road, Bangalore 560065, India ; Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
| | - Deepika Puri
- Institute for Stem Cell Biology and Regenerative Medicine, National Center for Biological Sciences, GKVK Post, Bellary Road, Bangalore 560065, India
| | - Jyotsna Dhawan
- Institute for Stem Cell Biology and Regenerative Medicine, National Center for Biological Sciences, GKVK Post, Bellary Road, Bangalore 560065, India ; Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
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