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Han Y, Zhao H, Li G, Jia J, Guo H, Tan J, Sun X, Li S, Ran Q, Bai C, Gu Y, Li Z, Guan H, Gao S, Zhou PK. GCN5 mediates DNA-PKcs crotonylation for DNA double-strand break repair and determining cancer radiosensitivity. Br J Cancer 2024; 130:1621-1634. [PMID: 38575732 DOI: 10.1038/s41416-024-02636-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/18/2024] [Accepted: 02/21/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND DNA double-strand break (DSB) induction and repair are important events for determining cell survival and the outcome of cancer radiotherapy. The DNA-dependent protein kinase (DNA-PK) complex functions at the apex of DSBs repair, and its assembly and activity are strictly regulated by post-translation modifications (PTMs)-associated interactions. However, the PTMs of the catalytic subunit DNA-PKcs and how they affect DNA-PKcs's functions are not fully understood. METHODS Mass spectrometry analyses were performed to identify the crotonylation sites of DNA-PKcs in response to γ-ray irradiation. Co-immunoprecipitation (Co-IP), western blotting, in vitro crotonylation assays, laser microirradiation assays, in vitro DNA binding assays, in vitro DNA-PK assembly assays and IF assays were employed to confirm the crotonylation, identify the crotonylase and decrotonylase, and elucidate how crotonylation regulates the activity and function of DNA-PKcs. Subcutaneous xenografts of human HeLa GCN5 WT or HeLa GCN5 siRNA cells in BALB/c nude mice were generated and utilized to assess tumor proliferation in vivo after radiotherapy. RESULTS Here, we reveal that K525 is an important site of DNA-PKcs for crotonylation, and whose level is sharply increased by irradiation. The histone acetyltransferase GCN5 functions as the crotonylase for K525-Kcr, while HDAC3 serves as its dedicated decrotonylase. K525 crotonylation enhances DNA binding activity of DNA-PKcs, and facilitates assembly of the DNA-PK complex. Furthermore, GCN5-mediated K525 crotonylation is indispensable for DNA-PKcs autophosphorylation and the repair of double-strand breaks in the NHEJ pathway. GCN5 suppression significantly sensitizes xenograft tumors of mice to radiotherapy. CONCLUSIONS Our study defines K525 crotonylation of DNA-PKcs is important for the DNA-PK complex assembly and DSBs repair activity via NHEJ pathway. Targeting GCN5-mediated K525 Kcr of DNA-PKcs may be a promising therapeutic strategy for improving the outcome of cancer radiotherapy.
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Affiliation(s)
- Yang Han
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Hongling Zhao
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Gang Li
- School of Public Health, Institute for Environmental Medicine and Radiation Hygiene, University of South China, Hengyang, China
- Department of Hospital Infection Control, Shenzhen Luohu Peoples Hospital, Shenzhen, China
| | - Jin Jia
- School of Medicine, University of South China, Hengyang, China
| | - Hejiang Guo
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jinpeng Tan
- School of Medicine, University of South China, Hengyang, China
| | - Xingyao Sun
- School of Medicine, University of South China, Hengyang, China
| | - Saiyu Li
- School of life Sciences, Hebei University, Baoding, China
| | - Qian Ran
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China
| | - Chenjun Bai
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yongqing Gu
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - ZhongJun Li
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China.
| | - Hua Guan
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China.
| | - Shanshan Gao
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China.
| | - Ping-Kun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China.
- School of Public Health, Institute for Environmental Medicine and Radiation Hygiene, University of South China, Hengyang, China.
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Geng S, Liu SB, He W, Pan X, Sun Y, Xue T, Han S, Lou J, Chang Y, Zheng J, Shi X, Li Y, Song YH. Deletion of TECRL promotes skeletal muscle repair by up-regulating EGR2. Proc Natl Acad Sci U S A 2024; 121:e2317495121. [PMID: 38753506 PMCID: PMC11126978 DOI: 10.1073/pnas.2317495121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 04/10/2024] [Indexed: 05/18/2024] Open
Abstract
Myogenic regeneration relies on the proliferation and differentiation of satellite cells. TECRL (trans-2,3-enoyl-CoA reductase like) is an endoplasmic reticulum protein only expressed in cardiac and skeletal muscle. However, its role in myogenesis remains unknown. We show that TECRL expression is increased in response to injury. Satellite cell-specific deletion of TECRL enhances muscle repair by increasing the expression of EGR2 through the activation of the ERK1/2 signaling pathway, which in turn promotes the expression of PAX7. We further show that TECRL deletion led to the upregulation of the histone acetyltransferase general control nonderepressible 5, which enhances the transcription of EGR2 through acetylation. Importantly, we showed that AAV9-mediated TECRL silencing improved muscle repair in mice. These findings shed light on myogenic regeneration and muscle repair.
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Affiliation(s)
- Sha Geng
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Song-Bai Liu
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, Suzhou215009, People’s Republic of China
| | - Wei He
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Xiangbin Pan
- Department of Structural Heart Disease, National Center for Cardiovascular Disease, China and Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100037, People’s Republic of China
| | - Yi Sun
- Department of Cardiovascular Surgery, Fuwai Yunnan Cardiovascular Hospital, Kunming650102, People’s Republic of China
| | - Ting Xue
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Shiyuan Han
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Jing Lou
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Ying Chang
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Jiqing Zheng
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Xinghong Shi
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Yangxin Li
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Yao-Hua Song
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
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Pina C. Contributions of transcriptional noise to leukaemia evolution: KAT2A as a case-study. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230052. [PMID: 38432321 PMCID: PMC10909511 DOI: 10.1098/rstb.2023.0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/04/2023] [Indexed: 03/05/2024] Open
Abstract
Transcriptional noise is proposed to participate in cell fate changes, but contributions to mammalian cell differentiation systems, including cancer, remain associative. Cancer evolution is driven by genetic variability, with modulatory or contributory participation of epigenetic variants. Accumulation of epigenetic variants enhances transcriptional noise, which can facilitate cancer cell fate transitions. Acute myeloid leukaemia (AML) is an aggressive cancer with strong epigenetic dependencies, characterized by blocked differentiation. It constitutes an attractive model to probe links between transcriptional noise and malignant cell fate regulation. Gcn5/KAT2A is a classical epigenetic transcriptional noise regulator. Its loss increases transcriptional noise and modifies cell fates in stem and AML cells. By reviewing the analysis of KAT2A-depleted pre-leukaemia and leukaemia models, I discuss that the net result of transcriptional noise is diversification of cell fates secondary to alternative transcriptional programmes. Cellular diversification can enable or hinder AML progression, respectively, by differentiation of cell types responsive to mutations, or by maladaptation of leukaemia stem cells. KAT2A-dependent noise-responsive genes participate in ribosome biogenesis and KAT2A loss destabilizes translational activity. I discuss putative contributions of perturbed translation to AML biology, and propose KAT2A loss as a model for mechanistic integration of transcriptional and translational control of noise and fate decisions. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Cristina Pina
- College of Health, Medicine and Life Sciences, Brunel University London, Kingston Lane, Uxbridge, London, UB8 3PH, United Kingdom
- CenGEM – Centre for Genome Engineering and Maintenance, Brunel University London, Kingston Lane, Uxbridge, London, UB8 3PH, United Kingdom
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4
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Kuang X, Salinger A, Benavides F, Muller WJ, Dent SYR, Koutelou E. USP22 overexpression fails to augment tumor formation in MMTV-ERBB2 mice but loss of function impacts MMTV promoter activity. PLoS One 2024; 19:e0290837. [PMID: 38236941 PMCID: PMC10796002 DOI: 10.1371/journal.pone.0290837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/15/2023] [Indexed: 01/22/2024] Open
Abstract
The Ubiquitin Specific Peptidase 22 (USP22), a component of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) histone modifying complex, is overexpressed in multiple human cancers, but how USP22 impacts tumorigenesis is not clear. We reported previously that Usp22 loss in mice impacts execution of several signaling pathways driven by growth factor receptors such as erythroblastic oncogene B b2 (ERBB2). To determine whether changes in USP22 expression affects ERBB2-driven tumorigenesis, we introduced conditional overexpression or deletion alleles of Usp22 into mice bearing the Mouse mammary tumor virus-Neu-Ires-Cre (MMTV-NIC) transgene, which drives both rat ERBB2/NEU expression and Cre recombinase activity from the MMTV promoter resulting in mammary tumor formation. We found that USP22 overexpression in mammary glands did not further enhance primary tumorigenesis in MMTV-NIC female mice, but increased lung metastases were observed. However, deletion of Usp22 significantly decreased tumor burden and increased survival of MMTV-NIC mice. These effects were associated with markedly decreased levels of both Erbb2 mRNA and protein, indicating Usp22 loss impacts MMTV promoter activity. Usp22 loss had no impact on ERBB2 expression in other settings, including MCF10A cells bearing a Cytomegalovirus (CMV)-driven ERBB2 transgene or in human epidermal growth factor receptor 2 (HER2)+ human SKBR3 and HCC1953 cells. Decreased activity of the MMTV promoter in MMTV-NIC mice correlated with decreased expression of known regulatory factors, including the glucocorticoid receptor (GR), the progesterone receptor (PR), and the chromatin remodeling factor Brahma-related gene-1 (BRG1). Together our findings indicate that increased expression of USP22 does not augment the activity of an activated ERBB2/NEU transgene but impacts of Usp22 loss on tumorigenesis cannot be assessed in this model due to unexpected effects on MMTV-driven Erbb2/Neu expression.
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Affiliation(s)
- Xianghong Kuang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Andrew Salinger
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Fernando Benavides
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - William J. Muller
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Canada
- Department of Biochemistry, McGill University, Montreal, Canada
- Faculty of Medicine, McGill University, Montreal, Canada
| | - Sharon Y. R. Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
- The University of Texas MD Anderson Cancer Center/UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, United States of America
| | - Evangelia Koutelou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
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5
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Xu M, Lin L, Ram BM, Shriwas O, Chuang KH, Dai S, Su KH, Tang Z, Dai C. Heat shock factor 1 (HSF1) specifically potentiates c-MYC-mediated transcription independently of the canonical heat shock response. Cell Rep 2023; 42:112557. [PMID: 37224019 PMCID: PMC10592515 DOI: 10.1016/j.celrep.2023.112557] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/27/2023] [Accepted: 05/08/2023] [Indexed: 05/26/2023] Open
Abstract
Despite its pivotal roles in biology, how the transcriptional activity of c-MYC is tuned quantitatively remains poorly defined. Here, we show that heat shock factor 1 (HSF1), the master transcriptional regulator of the heat shock response, acts as a prime modifier of the c-MYC-mediated transcription. HSF1 deficiency diminishes c-MYC DNA binding and dampens its transcriptional activity genome wide. Mechanistically, c-MYC, MAX, and HSF1 assemble into a transcription factor complex on genomic DNAs, and surprisingly, the DNA binding of HSF1 is dispensable. Instead, HSF1 physically recruits the histone acetyltransferase general control nonderepressible 5 (GCN5), promoting histone acetylation and augmenting c-MYC transcriptional activity. Thus, we find that HSF1 specifically potentiates the c-MYC-mediated transcription, discrete from its canonical role in countering proteotoxic stress. Importantly, this mechanism of action engenders two distinct c-MYC activation states, primary and advanced, which may be important to accommodate diverse physiological and pathological conditions.
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Affiliation(s)
- Meng Xu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Ling Lin
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Babul Moni Ram
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Omprakash Shriwas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Kun-Han Chuang
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Siyuan Dai
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Kuo-Hui Su
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Zijian Tang
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Chengkai Dai
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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6
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Navarro-Corcuera A, Sehrawat TS, Jalan-Sakrikar N, Gibbons HR, Pirius NE, Khanal S, Hamdan FH, Aseem SO, Cao S, Banales JM, Kang N, Faubion WA, LaRusso NF, Shah VH, Huebert RC. Long non-coding RNA ACTA2-AS1 promotes ductular reaction by interacting with the p300/ELK1 complex. J Hepatol 2022; 76:921-933. [PMID: 34953958 PMCID: PMC8934273 DOI: 10.1016/j.jhep.2021.12.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 11/01/2021] [Accepted: 12/03/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Biliary disease is associated with a proliferative/fibrogenic ductular reaction (DR). p300 is an epigenetic regulator that acetylates lysine 27 on histone 3 (H3K27ac) and is activated during fibrosis. Long non-coding RNAs (lncRNAs) are aberrantly expressed in cholangiopathies, but little is known about how they recruit epigenetic complexes and regulate DR. We investigated epigenetic complexes, including transcription factors (TFs) and lncRNAs, contributing to p300-mediated transcription during fibrosis. METHODS We evaluated p300 in vivo using tamoxifen-inducible, cholangiocyte-selective, p300 knockout (KO) coupled with bile duct ligation (BDL) and Mdr KO mice treated with SGC-CBP30. Primary cholangiocytes and liver tissue were analyzed for expression of Acta2-as1 lncRNA by qPCR and RNA in situ hybridization. In vitro, we performed RNA-sequencing in human cholangiocytes with a p300 inhibitor. Cholangiocytes were exposed to lipopolysaccharide (LPS) as an injury model. We confirmed formation of a p300/ELK1 complex by immunoprecipitation (IP). RNA IP was used to examine interactions between ACTA2-AS1 and p300. Chromatin IP assays were used to evaluate p300/ELK1 occupancy and p300-mediated H3K27ac. Organoids were generated from ACTA2-AS1-depleted cholangiocytes. RESULTS BDL-induced DR and fibrosis were reduced in Krt19-CreERT/p300fl/fl mice. Similarly, Mdr KO mice were protected from DR and fibrosis after SGC-CBP30 treatment. In vitro, depletion of ACTA2-AS1 reduced expression of proliferative/fibrogenic markers, reduced LPS-induced cholangiocyte proliferation, and impaired organoid formation. ACTA2-AS1 regulated transcription by facilitating p300/ELK1 binding to the PDGFB promoter after LPS exposure. Correspondingly, LPS-induced H3K27ac was mediated by p300/ELK1 and was reduced in ACTA2-AS1-depleted cholangiocytes. CONCLUSION Cholangiocyte-selective p300 KO or p300 inhibition attenuate DR/fibrosis in mice. ACTA2-AS1 influences recruitment of p300/ELK1 to specific promoters to drive H3K27ac and epigenetic activation of proliferative/fibrogenic genes. This suggests that cooperation between epigenetic co-activators and lncRNAs facilitates DR/fibrosis in biliary diseases. LAY SUMMARY We identified a three-part complex containing an RNA molecule, a transcription factor, and an epigenetic enzyme. The complex is active in injured bile duct cells and contributes to activation of genes involved in proliferation and fibrosis.
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Affiliation(s)
- Amaia Navarro-Corcuera
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Tejasav S Sehrawat
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Nidhi Jalan-Sakrikar
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Hunter R Gibbons
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Nicholas E Pirius
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States
| | - Shalil Khanal
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Feda H Hamdan
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Sayed Obaidullah Aseem
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Sheng Cao
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Jesus M Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, CIBERehd, Ikerbasque, San Sebastian, Spain
| | - Ningling Kang
- The Hormel Institute, University of Minnesota, Austin, MN, United States
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Nicholas F LaRusso
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States
| | - Vijay H Shah
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Robert C Huebert
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States.
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7
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Liu Y, Cheng W, Zhao Y, Gao L, Chang Y, Tong Z, Li H, Jing J. Cyclic Mechanical Strain Regulates Osteoblastic Differentiation of Mesenchymal Stem Cells on TiO 2 Nanotubes Through GCN5 and Wnt/β-Catenin. Front Bioeng Biotechnol 2021; 9:735949. [PMID: 34869255 PMCID: PMC8634263 DOI: 10.3389/fbioe.2021.735949] [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: 07/04/2021] [Accepted: 09/30/2021] [Indexed: 02/03/2023] Open
Abstract
Bone marrow mesenchymal stem cells (BMSCs) play a critical role in bone formation and are extremely sensitive to external mechanical stimuli. Mechanical signals can regulate the biological behavior of cells on the surface of titanium-related prostheses and inducing osteogenic differentiation of BMSCs, which provides the integration of host bone and prosthesis benefits. But the mechanism is still unclear. In this study, BMSCs planted on the surface of TiO2 nanotubes were subjected to cyclic mechanical stress, and the related mechanisms were explored. The results of alkaline phosphatase staining, real-time PCR, and Western blot showed that cyclic mechanical stress can regulate the expression level of osteogenic differentiation markers in BMSCs on the surface of TiO2 nanotubes through Wnt/β-catenin. As an important member of the histone acetyltransferase family, GCN5 exerted regulatory effects on receiving mechanical signals. The results of the ChIP assay indicated that GCN5 could activate the Wnt promoter region. Hence, we concluded that the osteogenic differentiation ability of BMSCs on the surface of TiO2 nanotubes was enhanced under the stimulation of cyclic mechanical stress, and GCN5 mediated this process through Wnt/β-catenin.
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Affiliation(s)
- Yanchang Liu
- Department of Orthopaedics, The Second Hospital of Anhui Medical University, Hefei, China
| | - Wendan Cheng
- Department of Orthopaedics, The Second Hospital of Anhui Medical University, Hefei, China
| | - Yao Zhao
- Department of Orthopaedics, The Second Hospital of Anhui Medical University, Hefei, China
| | - Liang Gao
- Sino Euro Orthopaedics Network, Berlin, Germany
| | - Yongyun Chang
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedics, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhicheng Tong
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedics, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Huiwu Li
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedics, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Juehua Jing
- Department of Orthopaedics, The Second Hospital of Anhui Medical University, Hefei, China
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8
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Fischer V, Plassard D, Ye T, Reina-San-Martin B, Stierle M, Tora L, Devys D. The related coactivator complexes SAGA and ATAC control embryonic stem cell self-renewal through acetyltransferase-independent mechanisms. Cell Rep 2021; 36:109598. [PMID: 34433046 PMCID: PMC8430043 DOI: 10.1016/j.celrep.2021.109598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/17/2021] [Accepted: 08/03/2021] [Indexed: 01/10/2023] Open
Abstract
SAGA (Spt-Ada-Gcn5 acetyltransferase) and ATAC (Ada-two-A-containing) are two related coactivator complexes, sharing the same histone acetyltransferase (HAT) subunit. The HAT activities of SAGA and ATAC are required for metazoan development, but the role of these complexes in RNA polymerase II transcription is less understood. To determine whether SAGA and ATAC have redundant or specific functions, we compare the effects of HAT inactivation in each complex with that of inactivation of either SAGA or ATAC core subunits in mouse embryonic stem cells (ESCs). We show that core subunits of SAGA or ATAC are required for complex assembly and mouse ESC growth and self-renewal. Surprisingly, depletion of HAT module subunits causes a global decrease in histone H3K9 acetylation, but does not result in significant phenotypic or transcriptional defects. Thus, our results indicate that SAGA and ATAC are differentially required for self-renewal of mouse ESCs by regulating transcription through different pathways in a HAT-independent manner.
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Affiliation(s)
- Veronique Fischer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Damien Plassard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France; Plateforme GenomEast, infrastructure France Génomique, Illkirch, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France; Plateforme GenomEast, infrastructure France Génomique, Illkirch, France
| | - Bernardo Reina-San-Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Matthieu Stierle
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Laszlo Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France.
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9
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Aseem SO, Jalan-Sakrikar N, Chi C, Navarro-Corcuera A, De Assuncao TM, Hamdan FH, Chowdhury S, Banales JM, Johnsen SA, Shah VH, Huebert RC. Epigenomic Evaluation of Cholangiocyte Transforming Growth Factor-β Signaling Identifies a Selective Role for Histone 3 Lysine 9 Acetylation in Biliary Fibrosis. Gastroenterology 2021; 160:889-905.e10. [PMID: 33058867 PMCID: PMC7878301 DOI: 10.1053/j.gastro.2020.10.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 09/14/2020] [Accepted: 10/02/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Transforming growth factor β (TGFβ) upregulates cholangiocyte-derived signals that activate myofibroblasts and promote fibrosis. Using epigenomic and transcriptomic approaches, we sought to distinguish the epigenetic activation mechanisms downstream of TGFβ that mediate transcription of fibrogenic signals. METHODS Chromatin immunoprecipitation (ChIP)-seq and RNA-seq were performed to assess histone modifications and transcriptional changes following TGFβ stimulation. Histone modifications and acetyltransferase occupancy were confirmed using ChIP assays. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was used to investigate changes in chromatin accessibility. Cholangiocyte cell lines and primary cholangiocytes were used for in vitro studies. Mdr2-/- and 3,5-diethoxycarboncyl-1,4-dihydrocollidine (DDC)-fed mice were used as animal models. RESULTS TGFβ stimulation caused widespread changes in histone 3 lysine 27 acetylation (H3K27ac), and was associated with global TGFβ-mediated transcription. In contrast, H3K9ac was gained in a smaller group of chromatin sites and was associated with fibrosis pathways. These pathways included overexpression of hepatic stellate cell (HSC) activators such as fibronectin 1 (FN1) and SERPINE1. The promoters of these genes showed H3K9ac enrichment following TGFβ. Of the acetyltransferases responsible for H3K9ac, cholangiocytes predominantly express Lysine Acetyltransferases 2A (KAT2A). Small interfering RNA knockdown of KAT2A or H3K9ac inhibition prevented the TGFβ-mediated increase in FN1 and SERPINE1. SMAD3 ChIP-seq and ATAC-seq suggested that TGFβ-mediated H3K9ac occurs through SMAD signaling, which was confirmed using colocalization and genetic knockdown studies. Pharmacologic inhibition or cholangiocyte-selective deletion of Kat2a was protective in mouse models of biliary fibrosis. CONCLUSIONS Cholangiocyte expression of HSC-activating signals occurs through SMAD-dependent, KAT2A-mediated, H3K9ac, and can be targeted to prevent biliary fibrosis.
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Affiliation(s)
- Sayed Obaidullah Aseem
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, Minnesota; Gastroenterology Research Unit, Mayo Clinic and Foundation, Rochester, Minnesota
| | - Nidhi Jalan-Sakrikar
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, Minnesota; Gastroenterology Research Unit, Mayo Clinic and Foundation, Rochester, Minnesota
| | - Cheng Chi
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, Minnesota; Gastroenterology Research Unit, Mayo Clinic and Foundation, Rochester, Minnesota
| | - Amaia Navarro-Corcuera
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, Minnesota; Gastroenterology Research Unit, Mayo Clinic and Foundation, Rochester, Minnesota
| | - Thiago M De Assuncao
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, Minnesota; Gastroenterology Research Unit, Mayo Clinic and Foundation, Rochester, Minnesota
| | - Feda H Hamdan
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, Minnesota; Gastroenterology Research Unit, Mayo Clinic and Foundation, Rochester, Minnesota
| | - Shiraj Chowdhury
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, Minnesota; Gastroenterology Research Unit, Mayo Clinic and Foundation, Rochester, Minnesota
| | - Jesus M Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, CIBERehd, Ikerbasque, San Sebastian, Spain
| | - Steven A Johnsen
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, Minnesota; Gastroenterology Research Unit, Mayo Clinic and Foundation, Rochester, Minnesota; Center for Cell Signaling in Gastroenterology Mayo Clinic and Foundation, Rochester, Minnesota
| | - Vijay H Shah
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, Minnesota; Gastroenterology Research Unit, Mayo Clinic and Foundation, Rochester, Minnesota; Center for Cell Signaling in Gastroenterology Mayo Clinic and Foundation, Rochester, Minnesota
| | - Robert C Huebert
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, Minnesota; Gastroenterology Research Unit, Mayo Clinic and Foundation, Rochester, Minnesota; Center for Cell Signaling in Gastroenterology Mayo Clinic and Foundation, Rochester, Minnesota.
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10
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Farria AT, Plummer JB, Salinger AP, Shen J, Lin K, Lu Y, McBride KM, Koutelou E, Dent SYR. Transcriptional Activation of MYC-Induced Genes by GCN5 Promotes B-cell Lymphomagenesis. Cancer Res 2020; 80:5543-5553. [PMID: 33168647 DOI: 10.1158/0008-5472.can-20-2379] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/29/2020] [Accepted: 10/28/2020] [Indexed: 12/19/2022]
Abstract
Overexpression of the MYC oncoprotein is an initiating step in the formation of several cancers. MYC frequently recruits chromatin-modifying complexes to DNA to amplify the expression of cancer-promoting genes, including those regulating cell cycle, proliferation, and metabolism, yet the roles of specific modifiers in different cancer types are not well defined. Here, we show that GCN5 is an essential coactivator of cell-cycle gene expression driven by MYC overexpression and that deletion of Gcn5 delays or abrogates tumorigenesis in the Eμ-Myc mouse model of B-cell lymphoma. Our results demonstrate that Gcn5 loss impacts both expression and downstream functions of Myc. SIGNIFICANCE: Our results provide important proof of principle for Gcn5 functions in formation and progression of Myc-driven cancers, suggesting that GCN5 may be a viable target for development of new cancer therapies.
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Affiliation(s)
- Aimee T Farria
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas.,The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, Texas.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, Texas
| | - Joshua B Plummer
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - Andrew P Salinger
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, Texas
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - Kevin M McBride
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, Texas
| | - Evangelia Koutelou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas.,The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas. .,The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, Texas.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, Texas
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11
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Arede L, Pina C. Buffering noise: KAT2A modular contributions to stabilization of transcription and cell identity in cancer and development. Exp Hematol 2020; 93:25-37. [PMID: 33223444 DOI: 10.1016/j.exphem.2020.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023]
Abstract
KAT2A is a histone acetyltransferase recently identified as a vulnerability in at least some forms of Acute Myeloid Leukemia (AML). Its loss or inhibition prompts leukemia stem cells out of self-renewal and into differentiation with ultimate exhaustion of the leukemia pool. We have recently linked the Kat2a requirement in AML to control of transcriptional noise, reflecting an evolutionary-conserved role of Kat2a in promoting burst-like promoter activity and stabilizing gene expression. We suggest that through this role, Kat2a contributes to preservation of cell identity. KAT2A exerts its acetyltransferase activity in the context of two macromolecular complexes, Spt-Ada-Gcn5-Acetyltransferase (SAGA) and Ada-Two-A-Containing (ATAC), but the specific contribution of each complex to stabilization of gene expression is currently unknown. By reviewing specific gene targets and requirements of the two complexes in cancer and development, we suggest that SAGA regulates lineage-specific programs, and ATAC maintains biosynthetic activity through control of ribosomal protein and translation-associated genes, on which cells may be differentially dependent. While our data suggest that KAT2A-mediated regulation of transcriptional noise in AML may be exerted through ATAC, we discuss potential caveats and probe general vs. complex-specific contributions of KAT2A to transcriptional stability, with implications for control and perturbation of cell identity.
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Affiliation(s)
- Liliana Arede
- Departments of Haematology; Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Cristina Pina
- College of Health, Medicine and Life Sciences - Life Sciences, Division of Biosciences, Brunel University London, Uxbridge, UB8 3PH, United Kingdom.
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12
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Koutelou E, Farria AT, Dent SYR. Complex functions of Gcn5 and Pcaf in development and disease. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194609. [PMID: 32730897 DOI: 10.1016/j.bbagrm.2020.194609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022]
Abstract
A wealth of biochemical and cellular data, accumulated over several years by multiple groups, has provided a great degree of insight into the molecular mechanisms of actions of GCN5 and PCAF in gene activation. Studies of these lysine acetyltransferases (KATs) in vitro, in cultured cells, have revealed general mechanisms for their recruitment by sequence-specific binding factors and their molecular functions as transcriptional co-activators. Genetic studies indicate that GCN5 and PCAF are involved in multiple developmental processes in vertebrates, yet our understanding of their molecular functions in these contexts remains somewhat rudimentary. Understanding the functions of GCN5/PCAF in developmental processes provides clues to the roles of these KATs in disease states. Here we will review what is currently known about the developmental roles of GCN5 and PCAF, as well as emerging role of these KATs in oncogenesis.
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Affiliation(s)
- Evangelia Koutelou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, United States of America; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Aimee T Farria
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, United States of America; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, United States of America; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America.
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13
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Mustachio LM, Roszik J, Farria A, Dent SYR. Targeting the SAGA and ATAC Transcriptional Coactivator Complexes in MYC-Driven Cancers. Cancer Res 2020; 80:1905-1911. [PMID: 32094302 DOI: 10.1158/0008-5472.can-19-3652] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/28/2020] [Accepted: 02/19/2020] [Indexed: 12/26/2022]
Abstract
Targeting epigenetic regulators, such as histone-modifying enzymes, provides novel strategies for cancer therapy. The GCN5 lysine acetyltransferase (KAT) functions together with MYC both during normal development and in oncogenesis. As transcription factors, MYC family members are difficult to target with small-molecule inhibitors, but the acetyltransferase domain and the bromodomain in GCN5 might provide alternative targets for disruption of MYC-driven functions. GCN5 is part of two distinct multiprotein histone-modifying complexes, SAGA and ATAC. This review summarizes key findings on the roles of SAGA and ATAC in embryo development and in cancer to better understand the functional relationships of these complexes with MYC family members, as well as their future potential as therapeutic targets.
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Affiliation(s)
- Lisa Maria Mustachio
- Departments of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason Roszik
- Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aimee Farria
- Departments of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sharon Y R Dent
- Departments of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
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14
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Domingues AF, Kulkarni R, Giotopoulos G, Gupta S, Vinnenberg L, Arede L, Foerner E, Khalili M, Adao RR, Johns A, Tan S, Zeka K, Huntly BJ, Prabakaran S, Pina C. Loss of Kat2a enhances transcriptional noise and depletes acute myeloid leukemia stem-like cells. eLife 2020; 9:e51754. [PMID: 31985402 PMCID: PMC7039681 DOI: 10.7554/elife.51754] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/24/2020] [Indexed: 12/21/2022] Open
Abstract
Acute Myeloid Leukemia (AML) is an aggressive hematological malignancy with abnormal progenitor self-renewal and defective white blood cell differentiation. Its pathogenesis comprises subversion of transcriptional regulation, through mutation and by hijacking normal chromatin regulation. Kat2a is a histone acetyltransferase central to promoter activity, that we recently associated with stability of pluripotency networks, and identified as a genetic vulnerability in AML. Through combined chromatin profiling and single-cell transcriptomics of a conditional knockout mouse, we demonstrate that Kat2a contributes to leukemia propagation through preservation of leukemia stem-like cells. Kat2a loss impacts transcription factor binding and reduces transcriptional burst frequency in a subset of gene promoters, generating enhanced variability of transcript levels. Destabilization of target programs shifts leukemia cell fate out of self-renewal into differentiation. We propose that control of transcriptional variability is central to leukemia stem-like cell propagation, and establish a paradigm exploitable in different tumors and distinct stages of cancer evolution.
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Affiliation(s)
- Ana Filipa Domingues
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
| | - Rashmi Kulkarni
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
| | - George Giotopoulos
- Department of HaematologyUniversity of Cambridge, Cambridge Institute for Medical ResearchCambridgeUnited Kingdom
- Wellcome Trust-Medical Research Council Cambridge Stem Cell InstituteCambridgeUnited Kingdom
| | - Shikha Gupta
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Laura Vinnenberg
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
| | - Liliana Arede
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Elena Foerner
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
| | - Mitra Khalili
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
- Department of Medical Genetics and Molecular Medicine, School of MedicineZanjan University of Medical Sciences (ZUMS)ZanjanIslamic Republic of Iran
| | - Rita Romano Adao
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
| | - Ayona Johns
- Division of Biosciences, College of Health and Life SciencesBrunel University LondonUxbridgeUnited Kingdom
| | - Shengjiang Tan
- Department of HaematologyUniversity of Cambridge, Cambridge Institute for Medical ResearchCambridgeUnited Kingdom
| | - Keti Zeka
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Brian J Huntly
- Department of HaematologyUniversity of Cambridge, Cambridge Institute for Medical ResearchCambridgeUnited Kingdom
- Wellcome Trust-Medical Research Council Cambridge Stem Cell InstituteCambridgeUnited Kingdom
| | - Sudhakaran Prabakaran
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
- Department of BiologyIISERPuneIndia
| | - Cristina Pina
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
- Division of Biosciences, College of Health and Life SciencesBrunel University LondonUxbridgeUnited Kingdom
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15
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GCN5 HAT inhibition reduces human Burkitt lymphoma cell survival through reduction of MYC target gene expression and impeding BCR signaling pathways. Oncotarget 2019; 10:5847-5858. [PMID: 31645904 PMCID: PMC6791378 DOI: 10.18632/oncotarget.27226] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/10/2019] [Indexed: 12/14/2022] Open
Abstract
GCN5, the catalytic subunit in the acetyltransferase modules of SAGA and ATAC, functions as a coactivator of gene transcription. The SAGA complex is recruited to chromatin by transcription factors such as MYC and E2F1 to facilitate acetylation of histones, especially H3 at lysine 9 (H3K9). Burkitt lymphoma is an aggressive subtype of Non-Hodgkin lymphoma driven by the overexpression of MYC. Comparison of GCN5 expression in normal human B cells versus human Burkitt Lymphoma cell lines indicates overexpression of GCN5 in lymphoma. Treatment of Burkitt lymphoma cell lines with a specific inhibitor indicates that decreased GCN5 HAT activity reduces viability and proliferation of these cells. Inhibition of GCN5 HAT activity also induces apoptosis in lymphoma cells. Expression of MYC target genes as well as genes associated with B cell receptor signaling are significantly downregulated upon inhibition of GCN5 enzymatic activity. This downregulation leads to diminished PI3K signaling, a critical pathway in lymphomagenesis. Our data indicate that inhibition of GCN5 HAT activity reduces the tumorigenic properties of human Burkitt lymphoma cells by attenuating BCR signaling and that GCN5 may be a viable target for lymphoma drug therapy.
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16
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Wurm AA, Pina C. Long Non-coding RNAs as Functional and Structural Chromatin Modulators in Acute Myeloid Leukemia. Front Oncol 2019; 9:899. [PMID: 31572684 PMCID: PMC6749032 DOI: 10.3389/fonc.2019.00899] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/29/2019] [Indexed: 01/17/2023] Open
Abstract
Acute myeloid leukemia is a hematopoietic neoplasm of dismal prognosis that results from the accumulation of immature myeloid blasts in the bone marrow and the peripheral blood. It is strongly dependent on epigenetic regulation for disease onset, maintenance and in response to treatment. Epigenetic regulation refers to the multiple chemical modifications of DNA or DNA-associated proteins that alter chromatin structure and DNA accessibility in a heritable manner, without changing DNA sequence. Unlike sequence-specific transcription factors, epigenetic regulators do not necessarily bind DNA at consensus sequences, but still achieve reproducible target binding in a manner that is cell and maturation-type specific. A growing body of evidence indicates that epigenetic regulators rely, amongst other factors, on their interaction with untranslated RNA molecules for guidance to particular targets on DNA. Non (protein)-coding RNAs are the most abundant transcriptional products of the coding genome, and comprise several different classes of molecules with unique lengths, conformations and targets. Amongst these, long non-coding RNAs (lncRNAs) are species of 200 bp to >100 K bp in length, that recognize, and bind unique and largely uncharacterized DNA conformations. Some have been shown to bind epigenetic regulators, and thus constitute attractive candidates to mediate epigenetic target specificity. Herein, we postulate that lncRNAs are central players in the unique epigenetic programming of AML and review recent evidence in support of this view. We discuss the value of lncRNAs as putative diagnostic, prognostic and therapeutic targets in myeloid leukemias and indicate novel directions in this exciting research field.
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Affiliation(s)
- Alexander A Wurm
- Department of Medical Translational Oncology, National Center for Tumor Diseases (NCT) Dresden, Dresden, Germany
| | - Cristina Pina
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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17
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Mustachio LM, Roszik J, Farria AT, Guerra K, Dent SYR. Repression of GCN5 expression or activity attenuates c-MYC expression in non-small cell lung cancer. Am J Cancer Res 2019; 9:1830-1845. [PMID: 31497362 PMCID: PMC6726999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023] Open
Abstract
Lung cancer causes the highest mortality in cancer-related deaths. As these cancers often become resistant to existing therapies, definition of novel molecular targets is needed. Epigenetic modifiers may provide such targets. Recent reports suggest that the histone acetyltransferase (HAT) module within the transcriptional coactivator SAGA complex plays a role in cancer, creating a new link between epigenetic regulators and this disease. GCN5 serves as a coactivator for MYC target genes, and here we investigate links between GCN5 and c-MYC in non-small cell lung cancer (NSCLC). Our data indicate that both GCN5 and c-MYC proteins are upregulated in mouse and human NSCLC cells compared to normal lung epithelial cells. This trend is observable only at the protein level, indicating that this upregulation occurs post-transcriptionally. Human NSCLC tissue data provided by The Cancer Genome Atlas (TCGA) indicates that GCN5 and c-MYC expression are positively associated with one another and with the expression of c-MYC target genes. Depletion of GCN5 in NSCLC cells reduces c-MYC expression, cell proliferation, and increases the population of necrotic cells. Similarly, inhibition of the GCN5 catalytic site using a commercially available probe reduces c-MYC expression, cell proliferation, and increases the percentage of cells undergoing apoptosis. Our findings suggest that GCN5 might provide a novel target for inhibition of NSCLC growth and progression.
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Affiliation(s)
- Lisa Maria Mustachio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
- Department of Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
| | - Aimee T Farria
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
- Department of Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
- Department of Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
| | - Karla Guerra
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
| | - Sharon YR Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
- Department of Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
- Department of Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
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18
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Koutelou E, Wang L, Schibler AC, Chao HP, Kuang X, Lin K, Lu Y, Shen J, Jeter CR, Salinger A, Wilson M, Chen YC, Atanassov BS, Tang DG, Dent SYR. USP22 controls multiple signaling pathways that are essential for vasculature formation in the mouse placenta. Development 2019; 146:dev.174037. [PMID: 30718289 DOI: 10.1242/dev.174037] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/24/2019] [Indexed: 12/14/2022]
Abstract
USP22, a component of the SAGA complex, is overexpressed in highly aggressive cancers, but the normal functions of this deubiquitinase are not well defined. We determined that loss of USP22 in mice results in embryonic lethality due to defects in extra-embryonic placental tissues and failure to establish proper vascular interactions with the maternal circulatory system. These phenotypes arise from abnormal gene expression patterns that reflect defective kinase signaling, including TGFβ and several receptor tyrosine kinase pathways. USP22 deletion in endothelial cells and pericytes that are induced from embryonic stem cells also hinders these signaling cascades, with detrimental effects on cell survival and differentiation as well as on the ability to form vessels. Our findings provide new insights into the functions of USP22 during development that may offer clues to its role in disease states.
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Affiliation(s)
- Evangelia Koutelou
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA .,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Li Wang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,MD Anderson UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, TX 77030, USA
| | - Andria C Schibler
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,MD Anderson UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, TX 77030, USA.,Program in Genes and Development, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hsueh-Ping Chao
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,MD Anderson UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, TX 77030, USA
| | - Xianghong Kuang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,MD Anderson UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, TX 77030, USA
| | - Collene R Jeter
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Andrew Salinger
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Marenda Wilson
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yi Chun Chen
- MD Anderson UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, TX 77030, USA.,Program in Genes and Development, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Boyko S Atanassov
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Dean G Tang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA .,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,MD Anderson UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, TX 77030, USA
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19
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Moris N, Edri S, Seyres D, Kulkarni R, Domingues AF, Balayo T, Frontini M, Pina C. Histone Acetyltransferase KAT2A Stabilizes Pluripotency with Control of Transcriptional Heterogeneity. Stem Cells 2018; 36:1828-1838. [PMID: 30270482 PMCID: PMC6334525 DOI: 10.1002/stem.2919] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/19/2018] [Accepted: 09/01/2018] [Indexed: 12/20/2022]
Abstract
Cell fate transitions in mammalian stem cell systems have often been associated with transcriptional heterogeneity; however, existing data have failed to establish a functional or mechanistic link between the two phenomena. Experiments in unicellular organisms support the notion that transcriptional heterogeneity can be used to facilitate adaptability to environmental changes and have identified conserved chromatin‐associated factors that modulate levels of transcriptional noise. Herein, we show destabilization of pluripotency‐associated gene regulatory networks through increased transcriptional heterogeneity of mouse embryonic stem cells in which paradigmatic histone acetyl‐transferase, and candidate noise modulator, Kat2a (yeast orthologue Gcn5), have been inhibited. Functionally, network destabilization associates with reduced pluripotency and accelerated mesendodermal differentiation, with increased probability of transitions into lineage commitment. Thus, we show evidence of a relationship between transcriptional heterogeneity and cell fate transitions through manipulation of the histone acetylation landscape of mouse embryonic stem cells, suggesting a general principle that could be exploited in other normal and malignant stem cell fate transitions. stem cells2018;36:1828–11
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Affiliation(s)
- Naomi Moris
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Shlomit Edri
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Denis Seyres
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom.,National Health Service Blood and Transplant, University of Cambridge, Cambridge, United Kingdom.,NIHR BioResource-Rare Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Rashmi Kulkarni
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | | | - Tina Balayo
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom.,National Health Service Blood and Transplant, University of Cambridge, Cambridge, United Kingdom.,BHF Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Cristina Pina
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
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20
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Validation of Housekeeping Genes as Reference for Reverse-Transcription-qPCR Analysis in Busulfan-Injured Microvascular Endothelial Cells. BIOMED RESEARCH INTERNATIONAL 2018; 2018:4953806. [PMID: 30386793 PMCID: PMC6189687 DOI: 10.1155/2018/4953806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/10/2018] [Accepted: 09/17/2018] [Indexed: 12/17/2022]
Abstract
Endothelial cells (ECs) could express some important cytokines and signal molecules which play a key role in normal hematopoiesis and repopulation. Busulfan-induced vascular endothelial injury is an important feature after hematopoietic stem cell transplantation (HSCT). But the molecular mechanism of how the injured ECs affect hematopoietic reconstruction is still unknown. It is possibly through modulation of the change of some gene expression. RT-qPCR is one of the most popular methods used to accurately determine gene expression levels, based on stable reference gene (RG) selection from housekeeping genes. So our aim is to select stable RGs for more accurate measures of mRNA levels during Busulfan-induced vascular endothelial injury. In this study, 14 RGs were selected to investigate their expression stability in ECs during 72 hours of EC injury treated with Busulfan. Our results revealed extreme variation in RG stability compared by five statistical algorithms. ywhaz and alas1 were recognized as the two idlest RGs on account of the final ranking, while the two most usually used RGs (gapdh and actb) were not the most stable RGs. Next, these data were verified by testing signalling pathway genes ctnnb1, robo4, and notch1 based on the above four genes ywha, alas1, gapdh, and actb. It shows that the normalization of mRNA expression data using unstable RGs greatly affects gene fold change, which means the reliability of the biological conclusions is questionable. Based on the best RGs used, we also found that robo4 is significantly overexpressed in Busulfan-impaired ECs. In conclusion, our data reaffirms the importance of RGs selection for the valid analysis of gene expression in Busulfan-impaired ECs. And it also provides very useful guidance and basis for more accurate differential expression gene screening and future expanding biomolecule study of different drugs such as cyclophosphamide and fludarabine-injured ECs.
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21
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García-Molinero V, García-Martínez J, Reja R, Furió-Tarí P, Antúnez O, Vinayachandran V, Conesa A, Pugh BF, Pérez-Ortín JE, Rodríguez-Navarro S. The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally. Epigenetics Chromatin 2018; 11:13. [PMID: 29598828 PMCID: PMC5875001 DOI: 10.1186/s13072-018-0184-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/23/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Eukaryotic transcription is regulated through two complexes, the general transcription factor IID (TFIID) and the coactivator Spt-Ada-Gcn5 acetyltransferase (SAGA). Recent findings confirm that both TFIID and SAGA contribute to the synthesis of nearly all transcripts and are recruited genome-wide in yeast. However, how this broad recruitment confers selectivity under specific conditions remains an open question. RESULTS Here we find that the SAGA/TREX-2 subunit Sus1 associates with upstream regulatory regions of many yeast genes and that heat shock drastically changes Sus1 binding. While Sus1 binding to TFIID-dominated genes is not affected by temperature, its recruitment to SAGA-dominated genes and RP genes is significantly disturbed under heat shock, with Sus1 relocated to environmental stress-responsive genes in these conditions. Moreover, in contrast to recent results showing that SAGA deubiquitinating enzyme Ubp8 is dispensable for RNA synthesis, genomic run-on experiments demonstrate that Sus1 contributes to synthesis and stability of a wide range of transcripts. CONCLUSIONS Our study provides support for a model in which SAGA/TREX-2 factor Sus1 acts as a global transcriptional regulator in yeast but has differential activity at yeast genes as a function of their transcription rate or during stress conditions.
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Affiliation(s)
- Varinia García-Molinero
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Eduardo Primo Yúfera 3, 46012, Valencia, Spain.,Inserm Avenir: 'Biology of Repetitive Sequences'-Institute of Human Genetics, CNRS UPR1142, Montpellier, France
| | - José García-Martínez
- Departamento de Genética and E.R.I. Biotecmed, Facultad de Biología, Universitat de València, C/Dr. Moliner 50, 46100, Burjassot, Spain
| | - Rohit Reja
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, Pennsylvania, PA, 16802, USA.,Genentech Inc., South San Francisco, CA, USA
| | - Pedro Furió-Tarí
- Genomics of Gene Expression Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Eduardo Primo Yúfera 3, 46012, Valencia, Spain
| | - Oreto Antúnez
- Departamento de Bioquímica y Biología Molecular and E.R.I. Biotecmed, Facultad de Biología, Universitat de València, C/Dr. Moliner 50, 46100, Burjassot, Spain
| | - Vinesh Vinayachandran
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, Pennsylvania, PA, 16802, USA
| | - Ana Conesa
- Genomics of Gene Expression Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Eduardo Primo Yúfera 3, 46012, Valencia, Spain.,Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, P.O. Box 110700, Gainesville, FL, 32611-0700, USA.,Genetics Institute, University of Florida, 2033 Mowry Road, Gainesville, FL, 32610, USA
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, Pennsylvania, PA, 16802, USA
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular and E.R.I. Biotecmed, Facultad de Biología, Universitat de València, C/Dr. Moliner 50, 46100, Burjassot, Spain
| | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), Jaime Roig 11, 46010, Valencia, Spain. .,Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Eduardo Primo Yúfera 3, 46012, Valencia, Spain.
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