1
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Tang G, Xia H, Huang Y, Guo Y, Chen Y, Ma Z, Liu W. Liquid-liquid phase separation of H3K27me3 reader BP1 regulates transcriptional repression. Genome Biol 2024; 25:67. [PMID: 38468348 PMCID: PMC10926671 DOI: 10.1186/s13059-024-03209-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 03/04/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Bromo-adjacent homology-plant homeodomain domain containing protein 1 (BP1) is a reader of histone post-translational modifications in fungi. BP1 recognizes trimethylation of lysine 27 in histone H3 (H3K27me3), an epigenetic hallmark of gene silencing. However, whether and how BP1 participates in transcriptional repression remains poorly understood. RESULTS We report that BP1 forms phase-separated liquid condensates to modulate its biological function in Fusarium graminearum. Deletion assays reveal that intrinsically disordered region 2 (IDR2) of BP1 mediates its liquid-liquid phase separation. The phase separation of BP1 is indispensable for its interaction with suppressor of Zeste 12, a component of polycomb repressive complex 2. Furthermore, IDR2 deletion abolishes BP1-H3K27me3 binding and alleviates the transcriptional repression of secondary metabolism-related genes, especially deoxynivalenol mycotoxin biosynthesis genes. CONCLUSIONS BP1 maintains transcriptional repression by forming liquid-liquid phase-separated condensates, expanding our understanding of the relationship between post-translational modifications and liquid-liquid phase separation.
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Affiliation(s)
- Guangfei Tang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Haoxue Xia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yufei Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuanwen Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yun Chen
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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2
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Diallo LH, Mariette J, Laugero N, Touriol C, Morfoisse F, Prats AC, Garmy-Susini B, Lacazette E. Specific Circular RNA Signature of Endothelial Cells: Potential Implications in Vascular Pathophysiology. Int J Mol Sci 2024; 25:680. [PMID: 38203852 PMCID: PMC10779679 DOI: 10.3390/ijms25010680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Circular RNAs (circRNAs) are a recently characterized family of gene transcripts forming a covalently closed loop of single-stranded RNA. The extent of their potential for fine-tuning gene expression is still being discovered. Several studies have implicated certain circular RNAs in pathophysiological processes within vascular endothelial cells and cancer cells independently. However, to date, no comparative study of circular RNA expression in different types of endothelial cells has been performed and analysed through the lens of their central role in vascular physiology and pathology. In this work, we analysed publicly available and original RNA sequencing datasets from arterial, veinous, and lymphatic endothelial cells to identify common and distinct circRNA expression profiles. We identified 4713 distinct circRNAs in the compared endothelial cell types, 95% of which originated from exons. Interestingly, the results show that the expression profile of circular RNAs is much more specific to each cell type than linear RNAs, and therefore appears to be more suitable for distinguishing between them. As a result, we have discovered a specific circRNA signature for each given endothelial cell type. Furthermore, we identified a specific endothelial cell circRNA signature that is composed four circRNAs: circCARD6, circPLXNA2, circCASC15 and circEPHB4. These circular RNAs are produced by genes that are related to endothelial cell migration pathways and cancer progression. More detailed studies of their functions could lead to a better understanding of the mechanisms involved in physiological and pathological (lymph)angiogenesis and might open new ways to tackle tumour spread through the vascular system.
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Affiliation(s)
- Leïla Halidou Diallo
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Jérôme Mariette
- MIAT, University of Toulouse, INRAE, 31326 Castanet-Tolosan, France;
| | - Nathalie Laugero
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Christian Touriol
- UMR1037 INSERM, University of Toulouse, 2 Avenue Hubert Curien, 31100 Toulouse, France;
| | - Florent Morfoisse
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Anne-Catherine Prats
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Barbara Garmy-Susini
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Eric Lacazette
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
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3
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Li N, Zhu Z, Deng Y, Tang R, Hui H, Kang Y, Rana TM. KIAA1429/VIRMA promotes breast cancer progression by m 6 A-dependent cytosolic HAS2 stabilization. EMBO Rep 2023; 24:e55506. [PMID: 37705505 PMCID: PMC10561361 DOI: 10.15252/embr.202255506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 08/14/2023] [Accepted: 08/24/2023] [Indexed: 09/15/2023] Open
Abstract
N6 -methyladenosine (m6 A), the most abundant internal modification in eukaryotic mRNA, plays important roles in many physiological and pathological processes, including the development and progression of cancer. RNA modification by m6 A is regulated by methyltransferases, demethylases, and m6 A-binding proteins that function in large part by regulating mRNA expression and function. Here, we investigate the expression of m6 A regulatory proteins in breast cancer. We find that expression of KIAA1429/VIRMA, a component of the m6 A methyltransferase complex, is upregulated in breast cancer tissue and correlates positively with poor survival. KIAA1429/VIRMA is mislocalized to the cytosol of breast cancer tissues and cell lines, and shRNA-mediated knockdown inhibits breast cancer cell proliferation, migration, and invasion. Mechanistically, KIAA1429/VIRMA is shown to bind to the m6 A-dependent RNA-binding protein insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3), leading to recruitment and stabilization of m6 A-modified hyaluronan synthase 2 (HAS2) mRNA. HAS2 mRNA and KIAA1429/VIRMA mRNA levels correlate positively in breast cancer tissues, suggesting that the KIAA1429/VIRMA-IGF2BP3-HAS2 axis promotes breast cancer growth and contributes to poor prognosis.
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Affiliation(s)
- Na Li
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology ProgramInstitute for Genomic MedicineLa JollaCAUSA
| | - Zhouting Zhu
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology ProgramInstitute for Genomic MedicineLa JollaCAUSA
| | - Yufei Deng
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology ProgramInstitute for Genomic MedicineLa JollaCAUSA
| | - Rachel Tang
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology ProgramInstitute for Genomic MedicineLa JollaCAUSA
| | - Hui Hui
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology ProgramInstitute for Genomic MedicineLa JollaCAUSA
| | - Yuqi Kang
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology ProgramInstitute for Genomic MedicineLa JollaCAUSA
| | - Tariq M Rana
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology ProgramInstitute for Genomic MedicineLa JollaCAUSA
- San Diego Center for Precision Immunotherapy, Moores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
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4
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Xiao M, Xu J, Wang W, Zhang B, Liu J, Li J, Xu H, Zhao Y, Yu X, Shi S. Functional significance of cholesterol metabolism in cancer: from threat to treatment. Exp Mol Med 2023; 55:1982-1995. [PMID: 37653037 PMCID: PMC10545798 DOI: 10.1038/s12276-023-01079-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 05/18/2023] [Accepted: 06/20/2023] [Indexed: 09/02/2023] Open
Abstract
Cholesterol is an essential structural component of membranes that contributes to membrane integrity and fluidity. Cholesterol homeostasis plays a critical role in the maintenance of cellular activities. Recently, increasing evidence has indicated that cholesterol is a major determinant by modulating cell signaling events governing the hallmarks of cancer. Numerous studies have shown the functional significance of cholesterol metabolism in tumorigenesis, cancer progression and metastasis through its regulatory effects on the immune response, ferroptosis, autophagy, cell stemness, and the DNA damage response. Here, we summarize recent literature describing cholesterol metabolism in cancer cells, including the cholesterol metabolism pathways and the mutual regulatory mechanisms involved in cancer progression and cholesterol metabolism. We also discuss various drugs targeting cholesterol metabolism to suggest new strategies for cancer treatment.
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Affiliation(s)
- Mingming Xiao
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Shanghai Pancreatic Center Institute, Shanghai, 200032, China
- Pancreatic Center Institute, Fudan University, Shanghai, 200032, China
| | - Jin Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Shanghai Pancreatic Center Institute, Shanghai, 200032, China
- Pancreatic Center Institute, Fudan University, Shanghai, 200032, China
| | - Wei Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Shanghai Pancreatic Center Institute, Shanghai, 200032, China
- Pancreatic Center Institute, Fudan University, Shanghai, 200032, China
| | - Bo Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Shanghai Pancreatic Center Institute, Shanghai, 200032, China
- Pancreatic Center Institute, Fudan University, Shanghai, 200032, China
| | - Jiang Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Shanghai Pancreatic Center Institute, Shanghai, 200032, China
- Pancreatic Center Institute, Fudan University, Shanghai, 200032, China
| | - Jialin Li
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Shanghai Pancreatic Center Institute, Shanghai, 200032, China
- Pancreatic Center Institute, Fudan University, Shanghai, 200032, China
| | - Hang Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Shanghai Pancreatic Center Institute, Shanghai, 200032, China
- Pancreatic Center Institute, Fudan University, Shanghai, 200032, China
| | - Yingjun Zhao
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
- Shanghai Pancreatic Center Institute, Shanghai, 200032, China.
- Pancreatic Center Institute, Fudan University, Shanghai, 200032, China.
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
- Shanghai Pancreatic Center Institute, Shanghai, 200032, China.
- Pancreatic Center Institute, Fudan University, Shanghai, 200032, China.
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5
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Li J, Lan Z, Liao W, Horner JW, Xu X, Liu J, Yoshihama Y, Jiang S, Shim HS, Slotnik M, LaBella KA, Wu CJ, Dunner K, Hsu WH, Lee R, Khanduri I, Terranova C, Akdemir K, Chakravarti D, Shang X, Spring DJ, Wang YA, DePinho RA. Histone demethylase KDM5D upregulation drives sex differences in colon cancer. Nature 2023; 619:632-639. [PMID: 37344599 PMCID: PMC10529424 DOI: 10.1038/s41586-023-06254-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/24/2023] [Indexed: 06/23/2023]
Abstract
Sex exerts a profound impact on cancer incidence, spectrum and outcomes, yet the molecular and genetic bases of such sex differences are ill-defined and presumptively ascribed to X-chromosome genes and sex hormones1. Such sex differences are particularly prominent in colorectal cancer (CRC) in which men experience higher metastases and mortality. A murine CRC model, engineered with an inducible transgene encoding oncogenic mutant KRASG12D and conditional null alleles of Apc and Trp53 tumour suppressors (designated iKAP)2, revealed higher metastases and worse outcomes specifically in males with oncogenic mutant KRAS (KRAS*) CRC. Integrated cross-species molecular and transcriptomic analyses identified Y-chromosome gene histone demethylase KDM5D as a transcriptionally upregulated gene driven by KRAS*-mediated activation of the STAT4 transcription factor. KDM5D-dependent chromatin mark and transcriptome changes showed repression of regulators of the epithelial cell tight junction and major histocompatibility complex class I complex components. Deletion of Kdm5d in iKAP cancer cells increased tight junction integrity, decreased cell invasiveness and enhanced cancer cell killing by CD8+ T cells. Conversely, iAP mice engineered with a Kdm5d transgene to provide constitutive Kdm5d expression specifically in iAP cancer cells showed an increased propensity for more invasive tumours in vivo. Thus, KRAS*-STAT4-mediated upregulation of Y chromosome KDM5D contributes substantially to the sex differences in KRAS* CRC by means of its disruption of cancer cell adhesion properties and tumour immunity, providing an actionable therapeutic strategy for metastasis risk reduction for men afflicted with KRAS* CRC.
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Affiliation(s)
- Jiexi Li
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhengdao Lan
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wenting Liao
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - James W Horner
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xueping Xu
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jielin Liu
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yohei Yoshihama
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shan Jiang
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hong Seok Shim
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Max Slotnik
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kyle A LaBella
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chang-Jiun Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kenneth Dunner
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wen-Hao Hsu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rumi Lee
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Isha Khanduri
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher Terranova
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kadir Akdemir
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Deepavali Chakravarti
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaoying Shang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Denise J Spring
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Y Alan Wang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Indiana University, Indianapolis, IN, USA
| | - Ronald A DePinho
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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6
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Binda O, Kimenyi Ishimwe AB, Galloy M, Jacquet K, Corpet A, Fradet-Turcotte A, Côté J, Lomonte P. The TUDOR domain of SMN is an H3K79 me1 histone mark reader. Life Sci Alliance 2023; 6:e202201752. [PMID: 36882285 PMCID: PMC9993015 DOI: 10.26508/lsa.202201752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
Spinal muscular atrophy is the leading genetic cause of infant mortality and results from depleted levels of functional survival of motor neuron (SMN) protein by either deletion or mutation of the SMN1 gene. SMN is characterized by a central TUDOR domain, which mediates the association of SMN with arginine methylated (Rme) partners, such as coilin, fibrillarin, and RNA pol II (RNA polymerase II). Herein, we biochemically demonstrate that SMN also associates with histone H3 monomethylated on lysine 79 (H3K79me1), defining SMN as not only the first protein known to associate with the H3K79me1 histone modification but also the first histone mark reader to recognize both methylated arginine and lysine residues. Mutational analyzes provide evidence that SMNTUDOR associates with H3 via an aromatic cage. Importantly, most SMNTUDOR mutants found in spinal muscular atrophy patients fail to associate with H3K79me1.
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Affiliation(s)
- Olivier Binda
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
- University of Ottawa, Faculty of Medicine, Department of Cellular and Molecular Medicine, Ontario, Canada
| | - Aimé Boris Kimenyi Ishimwe
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
| | - Maxime Galloy
- Université Laval Cancer Research Center, Université Laval, Québec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, Canada; and Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, Canada
| | - Karine Jacquet
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
| | - Armelle Corpet
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
| | - Amélie Fradet-Turcotte
- Université Laval Cancer Research Center, Université Laval, Québec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, Canada; and Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, Canada
| | - Jocelyn Côté
- University of Ottawa, Faculty of Medicine, Department of Cellular and Molecular Medicine, Ontario, Canada
| | - Patrick Lomonte
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
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7
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Carney SV, Banerjee K, Mujeeb A, Zhu B, Haase S, Varela ML, Kadiyala P, Tronrud CE, Zhu Z, Mukherji D, Gorla P, Sun Y, Tagett R, Núñez FJ, Luo M, Luo W, Ljungman M, Liu Y, Xia Z, Schwendeman A, Qin T, Sartor MA, Costello JF, Cahill DP, Lowenstein PR, Castro MG. Zinc Finger MYND-Type Containing 8 (ZMYND8) Is Epigenetically Regulated in Mutant Isocitrate Dehydrogenase 1 (IDH1) Glioma to Promote Radioresistance. Clin Cancer Res 2023; 29:1763-1782. [PMID: 36692427 PMCID: PMC10159884 DOI: 10.1158/1078-0432.ccr-22-1896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/27/2022] [Accepted: 12/22/2022] [Indexed: 01/25/2023]
Abstract
PURPOSE Mutant isocitrate dehydrogenase 1 (mIDH1) alters the epigenetic regulation of chromatin, leading to a hypermethylation phenotype in adult glioma. This work focuses on identifying gene targets epigenetically dysregulated by mIDH1 to confer therapeutic resistance to ionizing radiation (IR). EXPERIMENTAL DESIGN We evaluated changes in the transcriptome and epigenome in a radioresistant mIDH1 patient-derived glioma cell culture (GCC) following treatment with an mIDH1-specific inhibitor, AGI-5198. We identified Zinc Finger MYND-Type Containing 8 (ZMYND8) as a potential target of mIDH1 reprogramming. We suppressed ZMYND8 expression by shRNA knockdown and genetic knockout (KO) in mIDH1 glioma cells and then assessed cellular viability to IR. We assessed the sensitivity of mIDH1 GCCS to pharmacologic inhibition of ZMYND8-interacting partners: HDAC, BRD4, and PARP. RESULTS Inhibition of mIDH1 leads to an upregulation of gene networks involved in replication stress. We found that the expression of ZMYND8, a regulator of DNA damage response, was decreased in three patient-derived mIDH1 GCCs after treatment with AGI-5198. Knockdown of ZMYND8 expression sensitized mIDH1 GCCs to radiotherapy marked by decreased cellular viability. Following IR, mIDH1 glioma cells with ZMYND8 KO exhibit significant phosphorylation of ATM and sustained γH2AX activation. ZMYND8 KO mIDH1 GCCs were further responsive to IR when treated with either BRD4 or HDAC inhibitors. PARP inhibition further enhanced the efficacy of radiotherapy in ZMYND8 KO mIDH1 glioma cells. CONCLUSIONS These findings indicate the impact of ZMYND8 in the maintenance of genomic integrity and repair of IR-induced DNA damage in mIDH1 glioma. See related commentary by Sachdev et al., p. 1648.
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Affiliation(s)
- Stephen V. Carney
- Cancer Biology Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kaushik Banerjee
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Anzar Mujeeb
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Brandon Zhu
- Graduate Program in Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, USA
| | - Santiago Haase
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria L. Varela
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Padma Kadiyala
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Claire E. Tronrud
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ziwen Zhu
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Devarshi Mukherji
- Neuroscience, University of Michigan College of Literature, Science, the Arts (LSA), Ann Arbor, MI 48109, USA
| | - Preethi Gorla
- Neuroscience, University of Michigan College of Literature, Science, the Arts (LSA), Ann Arbor, MI 48109, USA
| | - Yilun Sun
- Department of Radiation Oncology, University Hospitals/Case Western Reserve University, Cleveland, OH, USA
| | - Rebecca Tagett
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Felipe J. Núñez
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maowu Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas TX 75390, USA
| | - Weibo Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas TX 75390, USA
- Department of Pharmacology, UT Southwestern Medical Center, Dallas TX 75390, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Environmental Health Science, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yayuan Liu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ziyun Xia
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anna Schwendeman
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joseph F. Costello
- Department of Neurological Surgery, University of California, San Francisco, California, 94143 USA
| | - Daniel P. Cahill
- Department of Neurosurgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston Massachusetts, 02114, USA
| | - Pedro R. Lowenstein
- Cancer Biology Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Biosciences Initiative in Brain Cancer, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria G. Castro
- Cancer Biology Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Biosciences Initiative in Brain Cancer, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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8
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Black J, Kutateladze T. Atypical histone targets of PHD fingers. J Biol Chem 2023;:104601. [PMID: 36907441 DOI: 10.1016/j.jbc.2023.104601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023] Open
Abstract
Plant homeodomain (PHD) fingers are structurally conserved zinc fingers that selectively bind unmodified or methylated at lysine 4 histone H3 tails. This binding stabilizes transcription factors and chromatin-modifying proteins at specific genomic sites, which is required for vital cellular processes, including gene expression and DNA repair. Several PHD fingers have recently been shown to recognize other regions of H3 or histone H4. In this review, we detail molecular mechanisms and structural features of the non-canonical histone recognition, discuss biological implications of the atypical interactions, highlight therapeutic potential of PHD fingers, and compare inhibition strategies.
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9
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Pourasghariazar M, Zarredar H, Asadi M, Caner A, Akhgari A, Valizadeh H, Bornehdeli S, Hashemzadeh S, Raeisi M. Comparative evaluation of ZMYND-8 and RARβ2 genes promoters’ methylation changes in tumor and tumor margin tissues of patients with lung cancer. Egypt J Med Hum Genet 2023. [DOI: 10.1186/s43042-023-00399-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
Abstract
Abstract
Background
Lung cancer remains one of the most lethal carcinomas worldwide because of its late diagnosis. One of the DNA modifications is methylation, one of the primary alterations of tumor development, consisting of fascinating indicators for cancer diagnosis. This study investigated ZMYND-8 and RARβ2 gene methylation in NSCLC as a new epigenetic tool.
Methods
First, to find out the potential diagnostic capability of ZMYND-8 and RARβ2 genes methylation, we entirely surfed DNA methylation microarrays from the Cancer Genome Atlas (TCGA) data of NSCLC samples. Additionally, we took advantage of using q-MSP in several pieces comprising NSCLC tumors and neighboring normal tissues; ZMYND-8 and RARβ2 genes methylation grades were acquired.
Results
Our finding displayed significant hypomethylation of ZMYND-8 and hypermethylation of RARβ2 in NSCLC samples compared to neighboring standard specimens, which significantly correlated with the clinical stage of malignancy. In addition, the incredible precision of ZMYND-8 and RARβ2 methylations as reliable cancer diagnosis indicators in NSCLC was confirmed, drawing the ROC curve analysis with an AUC value of 0.751 and 0.8676, respectively, for ZMYND-8 and RARβ2. Additional studies of other dominant cancer entities in TCGA displayed that RARβ2’s higher methylation degree and ZMYND-8 lower methylation degree are prevalent changes in tumor evolution which could be possibly considered as a potential diagnostic biomarkers for lung cancer.
Conclusion
Based on this study, ZMYND-8 and RARβ2 methylation are reliable biomarkers for lung cancer.
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10
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Abou Khouzam R, Sharda M, Rao SP, Kyerewah-Kersi SM, Zeinelabdin NA, Mahmood AS, Nawafleh H, Khan MS, Venkatesh GH, Chouaib S. Chronic hypoxia is associated with transcriptomic reprogramming and increased genomic instability in cancer cells. Front Cell Dev Biol 2023; 11:1095419. [PMID: 36968212 PMCID: PMC10033758 DOI: 10.3389/fcell.2023.1095419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/23/2023] [Indexed: 03/29/2023] Open
Abstract
Hypoxia afflicts the microenvironment of solid tumors fueling malignancy. We investigated the impact of long hypoxia exposure on transcriptional remodeling, tumor mutational burden (TMB), and genomic instability of cancer cells that were grouped based on their inherent sensitivity or resistance to hypoxia. A hypoxia score was used as a metric to distinguish between the most hypoxia-sensitive (hypoxia high (HH)), and most resistant (hypoxia low (HL)) cancer cells. By applying whole exome sequencing and microarray analysis, we showed that the HH group was indeed more sensitive to hypoxia, having significantly higher TMB (p = 0.03) and copy number losses (p = 0.03), as well as a trend of higher transcriptional response. Globally cells adapted by decreasing expression of genes involved in metabolism, proliferation, and protein maturation, and increasing alternative splicing. They accumulated mutations, especially frameshift insertions, and harbored increased copy number alterations, indicating increased genomic instability. Cells showing highest TMB simultaneously experienced a significant downregulation of DNA replication and repair and chromosomal maintenance pathways. A sixteen-gene common response to chronic hypoxia was put forth, including genes regulating angiogenesis and proliferation. Our findings show that chronic hypoxia enables survival of tumor cells by metabolic reprogramming, modulating proliferation, and increasing genomic instability. They additionally highlight key adaptive pathways that can potentially be targeted to prevent cancer cells residing in chronically hypoxic tumor areas from thriving.
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Affiliation(s)
- Raefa Abou Khouzam
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Mohak Sharda
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
- School of Life Science, The University of Trans-Disciplinary Health Sciences & Technology (TDU), Bangalore, India
| | - Shyama Prasad Rao
- Center for Bioinformatics, NITTE deemed to be University, Mangaluru, India
| | | | - Nagwa Ahmed Zeinelabdin
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Ayda Shah Mahmood
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Husam Nawafleh
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Munazza Samar Khan
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Goutham Hassan Venkatesh
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Salem Chouaib
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates
- INSERM UMR 1186, Integrative Tumor Immunology and Cancer Immunotherapy, Gustave Roussy, EPHE, Faculty De médecine University Paris-Sud, University Paris-Saclay, Villejuif, France
- *Correspondence: Salem Chouaib, ,
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11
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Wen H, Shi X. Histone Readers and Their Roles in Cancer. Cancer Treat Res 2023; 190:245-272. [PMID: 38113004 DOI: 10.1007/978-3-031-45654-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Histone proteins in eukaryotic cells are subjected to a wide variety of post-translational modifications, which are known to play an important role in the partitioning of the genome into distinctive compartments and domains. One of the major functions of histone modifications is to recruit reader proteins, which recognize the epigenetic marks and transduce the molecular signals in chromatin to downstream effects. Histone readers are defined protein domains with well-organized three-dimensional structures. In this Chapter, we will outline major histone readers, delineate their biochemical and structural features in histone recognition, and describe how dysregulation of histone readout leads to human cancer.
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Affiliation(s)
- Hong Wen
- Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA
| | - Xiaobing Shi
- Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA.
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12
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Voulgaridou GP, Theologidis V, Xanthis V, Papagiannaki E, Tsochantaridis I, Fadouloglou VE, Pappa A. Identification of a peptide ligand for human ALDH3A1 through peptide phage display: Prediction and characterization of protein interaction sites and inhibition of ALDH3A1 enzymatic activity. Front Mol Biosci 2023; 10:1161111. [PMID: 37021113 PMCID: PMC10067601 DOI: 10.3389/fmolb.2023.1161111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/07/2023] [Indexed: 04/07/2023] Open
Abstract
Aldehyde dehydrogenase 3A1 (ALDH3A1) by oxidizing medium chain aldehydes to their corresponding carboxylic acids, is involved in the detoxification of toxic byproducts and is considered to play an important role in antioxidant cellular defense. ALDH3A1 has been implicated in various other functions such as cell proliferation, cell cycle regulation, and DNA damage response. Recently, it has been identified as a putative biomarker of prostate, gastric, and lung cancer stem cell phenotype. Although ALDH3A1 has multifaceted functions in both normal and cancer homeostasis, its modes of action are currently unknown. To this end, we utilized a random 12-mer peptide phage display library to identify efficiently human ALDH3A1-interacting peptides. One prevailing peptide (P1) was systematically demonstrated to interact with the protein of interest, which was further validated in vitro by peptide ELISA. Bioinformatic analysis indicated two putative P1 binding sites on the protein surface implying biomedical potential and potent inhibitory activity of the P1 peptide on hALDH3A1 activity was demonstrated by enzymatic studies. Furthermore, in search of potential hALDH3A1 interacting players, a BLASTp search demonstrated that no protein in the database includes the full-length amino acid sequence of P1, but identified a list of proteins containing parts of the P1 sequence, which may prove potential hALDH3A1 interacting partners. Among them, Protein Kinase C Binding Protein 1 and General Transcription Factor II-I are candidates of high interest due to their cellular localization and function. To conclude, this study identifies a novel peptide with potential biomedical applications and further suggests a list of protein candidates be explored as possible hALDH3A1-interacting partners in future studies.
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Affiliation(s)
| | | | | | | | | | | | - Aglaia Pappa
- *Correspondence: Vasiliki E. Fadouloglou, ; Aglaia Pappa,
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13
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Xu C, Zhao S, Cai L. Epigenetic (De)regulation in Prostate Cancer. Cancer Treat Res 2023; 190:321-360. [PMID: 38113006 DOI: 10.1007/978-3-031-45654-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Prostate cancer (PCa) is a heterogeneous disease exhibiting both genetic and epigenetic deregulations. Epigenetic alterations are defined as changes not based on DNA sequence, which include those of DNA methylation, histone modification, and chromatin remodeling. Androgen receptor (AR) is the main driver for PCa and androgen deprivation therapy (ADT) remains a backbone treatment for patients with PCa; however, ADT resistance almost inevitably occurs and advanced diseases develop termed castration-resistant PCa (CRPC), due to both genetic and epigenetic changes. Due to the reversible nature of epigenetic modifications, inhibitors targeting epigenetic factors have become promising anti-cancer agents. In this chapter, we focus on recent studies about the dysregulation of epigenetic regulators crucially involved in the initiation, development, and progression of PCa and discuss the potential use of inhibitors targeting epigenetic modifiers for treatment of advanced PCa.
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Affiliation(s)
- Chenxi Xu
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Shuai Zhao
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Ling Cai
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
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Wu L, Huang J, Trivedi P, Sun X, Yu H, He Z, Zhang X. Zinc finger myeloid Nervy DEAF-1 type (ZMYND) domain containing proteins exert molecular interactions to implicate in carcinogenesis. Discov Oncol 2022; 13:139. [PMID: 36520265 PMCID: PMC9755447 DOI: 10.1007/s12672-022-00597-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Morphogenesis and organogenesis in the low organisms have been found to be modulated by a number of proteins, and one of such factor, deformed epidermal auto-regulatory factor-1 (DEAF-1) has been initially identified in Drosophila. The mammalian homologue of DEAF-1 and structurally related proteins have been identified, and they formed a family with over 20 members. The factors regulate gene expression through association with co-repressors, recognition of genomic marker, to exert histone modification by catalyze addition of some chemical groups to certain amino acid residues on histone and non-histone proteins, and degradation host proteins, so as to regulate cell cycle progression and execution of cell death. The formation of fused genes during chromosomal translocation, exemplified with myeloid transforming gene on chromosome 8 (MTG8)/eight-to-twenty one translocation (ETO) /ZMYND2, MTG receptor 1 (MTGR1)/ZMYND3, MTG on chromosome 16/MTGR2/ZMYND4 and BS69/ZMYND11 contributes to malignant transformation. Other anomaly like copy number variation (CNV) of BS69/ZMYND11 and promoter hyper methylation of BLU/ZMYND10 has been noted in malignancies. It has been reported that when fusing with Runt-related transcription factor 1 (RUNX1), the binding of MTG8/ZMYND2 with co-repressors is disturbed, and silencing of BLU/ZMYND10 abrogates its ability to inhibition of cell cycle and promotion of apoptotic death. Further characterization of the implication of ZMYND proteins in carcinogenesis would enhance understanding of the mechanisms of occurrence and early diagnosis of tumors, and effective antitumor efficacy.
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Affiliation(s)
- Longji Wu
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
- Institute of Modern Biology, Nanjing University, Nanjing, Jiangsu, China
| | - Jing Huang
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Pankaj Trivedi
- Department of Experimental Medicine, La Sapienza University, Rome, Italy
| | - Xuerong Sun
- Institute of Aging, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Hongbing Yu
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Zhiwei He
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Xiangning Zhang
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China.
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China.
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15
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Yi Q, Pu Y, Chao F, Bian P, Lv L. ACAP1 Deficiency Predicts Inferior Immunotherapy Response in Solid Tumors. Cancers (Basel) 2022; 14. [PMID: 36497434 DOI: 10.3390/cancers14235951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/20/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND ACAP1 plays a key role in endocytic recycling, which is essential for the normal function of lymphocytes. However, the expression and function of ACAP1 in lymphocytes have rarely been studied. METHODS Large-scale genomic data, including multiple bulk RNA-sequencing datasets, single-cell sequencing datasets, and immunotherapy cohorts, were exploited to comprehensively characterize ACAP1 expression, regulation, and function. Gene set enrichment analysis (GSEA) was used to uncover the pathways associated with ACAP1 expression. Eight algorithms, including TIMER, CIBERSORT, CIBERSORT-ABS, QUANTISEQ, xCELL, MCPCOUNTER, EPIC, and TIDE, were applied to estimate the infiltrating level of immune cells. Western blotting, qPCR, and ChIP-PCR were used to validate the findings from bioinformatic analyses. A T-cell co-culture killing assay was used to investigate the function of ACAP1 in lymphocytes. RESULTS ACAP1 was highly expressed in immune-related tissues and cells and minimally in other tissues. Moreover, single-cell sequencing analysis in tumor samples revealed that ACAP1 is expressed primarily in tumor-infiltrating lymphocytes (TILs), including T, B, and NK cells. ACAP1 expression is negatively regulated by promoter DNA methylation, with its promoter hypo-methylated in immune cells but hyper-methylated in other cells. Furthermore, SPI1 binds to the ACAP1 promoter and positively regulates its expression in immune cells. ACAP1 levels positively correlate with the infiltrating levels of TILs, especially CD8+ T cells, across a broad range of solid cancer types. ACAP1 deficiency is associated with poor prognosis and immunotherapeutic response in multiple cancer types treated with checkpoint blockade therapy (ICT). Functionally, the depletion of ACAP1 by RNA interference significantly impairs the T cell-mediated killing of tumor cells. CONCLUSIONS Our study demonstrates that ACAP1 is essential for the normal function of TILs, and its deficiency indicates an immunologically "cold" status of tumors that are resistant to ICT.
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Hussainy M, Korsching SI, Tresch A. Pseudotime analysis reveals novel regulatory factors for multigenic onset and monogenic transition of odorant receptor expression. Sci Rep 2022; 12:16183. [PMID: 36171231 PMCID: PMC9519747 DOI: 10.1038/s41598-022-20106-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 09/08/2022] [Indexed: 12/02/2022] Open
Abstract
During their maturation from horizontal basal stem cells, olfactory sensory neurons (OSNs) are known to select exactly one out of hundreds of olfactory receptors (ORs) and express it on their surface, a process called monogenic selection. Monogenic expression is preceded by a multigenic phase during which several OR genes are expressed in a single OSN. Here, we perform pseudotime analysis of a single cell RNA-Seq dataset of murine olfactory epithelium to precisely align the multigenic and monogenic expression phases with the cell types occurring during OSN differentiation. In combination with motif analysis of OR gene cluster-associated enhancer regions, we identify known and novel transcription (co-)factors (Ebf1, Lhx2, Ldb1, Fos and Ssbp2) and chromatin remodelers (Kdm1a, Eed and Zmynd8) associated with OR expression. The inferred temporal order of their activity suggests novel mechanisms contributing to multigenic OR expression and monogenic selection.
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Affiliation(s)
- Mohammad Hussainy
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany.,Institute of Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - Sigrun I Korsching
- Institute of Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - Achim Tresch
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany. .,Cologne Excellence Cluster On Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany. .,Center for Data and Simulation Science, University of Cologne, Cologne, Germany.
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17
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Reske JJ, Wilson MR, Armistead B, Harkins S, Perez C, Hrit J, Adams M, Rothbart SB, Missmer SA, Fazleabas AT, Chandler RL. ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers. BMC Biol 2022; 20:209. [PMID: 36153585 PMCID: PMC9509632 DOI: 10.1186/s12915-022-01407-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/12/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND SWI/SNF (BAF) chromatin remodeling complexes regulate lineage-specific enhancer activity by promoting accessibility for diverse DNA-binding factors and chromatin regulators. Additionally, they are known to modulate the function of the epigenome through regulation of histone post-translational modifications and nucleosome composition, although the way SWI/SNF complexes govern the epigenome remains poorly understood. Here, we investigate the function of ARID1A, a subunit of certain mammalian SWI/SNF chromatin remodeling complexes associated with malignancies and benign diseases originating from the uterine endometrium. RESULTS Through genome-wide analysis of human endometriotic epithelial cells, we show that more than half of ARID1A binding sites are marked by the variant histone H3.3, including active regulatory elements such as super-enhancers. ARID1A knockdown leads to H3.3 depletion and gain of canonical H3.1/3.2 at ARID1A-bound active regulatory elements, and a concomitant redistribution of H3.3 toward genic elements. ARID1A interactions with the repressive chromatin remodeler CHD4 (NuRD) are associated with H3.3, and ARID1A is required for CHD4 recruitment to H3.3. ZMYND8 interacts with CHD4 to suppress a subset of ARID1A, CHD4, and ZMYND8 co-bound, H3.3+ H4K16ac+ super-enhancers near genes governing extracellular matrix, motility, adhesion, and epithelial-to-mesenchymal transition. Moreover, these gene expression alterations are observed in human endometriomas. CONCLUSIONS These studies demonstrate that ARID1A-containing BAF complexes are required for maintenance of the histone variant H3.3 at active regulatory elements, such as super-enhancers, and this function is required for the physiologically relevant activities of alternative chromatin remodelers.
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Affiliation(s)
- Jake J. Reske
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA
| | - Mike R. Wilson
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA
| | - Brooke Armistead
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA
| | - Shannon Harkins
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA
| | - Cristina Perez
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA
| | - Joel Hrit
- grid.251017.00000 0004 0406 2057Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503 USA
| | - Marie Adams
- grid.251017.00000 0004 0406 2057Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503 USA
| | - Scott B. Rothbart
- grid.251017.00000 0004 0406 2057Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503 USA
| | - Stacey A. Missmer
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA ,grid.416230.20000 0004 0406 3236Department of Women’s Health, Spectrum Health System, Grand Rapids, MI 49341 USA
| | - Asgerally T. Fazleabas
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA ,grid.416230.20000 0004 0406 3236Department of Women’s Health, Spectrum Health System, Grand Rapids, MI 49341 USA
| | - Ronald L. Chandler
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA ,grid.251017.00000 0004 0406 2057Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503 USA ,grid.416230.20000 0004 0406 3236Department of Women’s Health, Spectrum Health System, Grand Rapids, MI 49341 USA
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Abstract
Packaging of eukaryotic genome into chromatin is a major obstacle to cells encountering DNA damage caused by external or internal agents. For maintaining genomic integrity, the double-strand breaks (DSB) must be efficiently repaired, as these are the most deleterious type of DNA damage. The DNA breaks have to be detected in chromatin context, the DNA damage response (DDR) pathways have to be activated to repair breaks either by non‐ homologous end joining and homologous recombination repair. It is becoming clearer now that chromatin is not a mere hindrance to DDR, it plays active role in sensing, detection and repair of DNA damage. The repair of DSB is governed by the reorganization of the pre-existing chromatin, leading to recruitment of specific machineries, chromatin remodelling complexes, histone modifiers to bring about dynamic alterations in histone composition, nucleosome positioning, histone modifications. In response to DNA break, modulation of chromatin occurs via various mechanisms including post-translational modification of histones. DNA breaks induce many types of histone modifications, such as phosphorylation, acetylation, methylation and ubiquitylation on specific histone residues which are signal and context dependent. DNA break induced histone modifications have been reported to function in sensing the breaks, activating processing of breaks by specific pathways, and repairing damaged DNA to ensure integrity of the genome. Favourable environment for DSB repair is created by generating open and relaxed chromatin structure. Histone acetylation mediate de-condensation of chromatin and recruitment of DSB repair proteins to their site of action at the DSB to facilitate repair. In this review, we will discuss the current understanding on the critical role of histone acetylation in inducing changes both in chromatin organization and promoting recruitment of DSB repair proteins to sites of DNA damage. It consists of an overview of function and regulation of the deacetylase enzymes which remove these marks and the function of histone acetylation and regulators of acetylation in genome surveillance.
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Adhikary S, Singh V, Choudhari R, Yang B, Adhikari S, Ramos EI, Chaudhuri S, Roy S, Gadad SS, Das C. ZMYND8 suppresses MAPT213 LncRNA transcription to promote neuronal differentiation. Cell Death Dis 2022; 13:766. [PMID: 36064715 PMCID: PMC9445031 DOI: 10.1038/s41419-022-05212-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/21/2022] [Accepted: 08/23/2022] [Indexed: 01/21/2023]
Abstract
Zinc Finger transcription factors are crucial in modulating various cellular processes, including differentiation. Chromatin reader Zinc Finger MYND (Myeloid, Nervy, and DEAF-1) type containing 8 (ZMYND8), an All-Trans Retinoic Acid (ATRA)-responsive gene, was previously shown to play a crucial role in promoting the expression of neuronal-lineage committed genes. Here, we report that ZMYND8 promotes neuronal differentiation by positively regulating canonical MAPT protein-coding gene isoform, a key player in the axonal development of neurons. Additionally, ZMYND8 modulates gene-isoform switching by epigenetically silencing key regulatory regions within the MAPT gene, thereby suppressing the expression of non-protein-coding isoforms such as MAPT213. Genetic deletion of ZMYND8 led to an increase in the MAPT213 that potentially suppressed the parental MAPT protein-coding transcript expression related to neuronal differentiation programs. In addition, ectopic expression of MAPT213 led to repression of MAPT protein-coding transcript. Similarly, ZMYND8-driven transcription regulation was also observed in other neuronal differentiation-promoting genes. Collectively our results elucidate a novel mechanism of ZMYND8-dependent transcription regulation of different neuronal lineage committing genes, including MAPT, to promote neural differentiation.
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Affiliation(s)
- Santanu Adhikary
- grid.473481.d0000 0001 0661 8707Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India ,grid.417635.20000 0001 2216 5074Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032 India
| | - Vipin Singh
- grid.473481.d0000 0001 0661 8707Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India ,grid.450257.10000 0004 1775 9822Homi Bhaba National Institute, Mumbai, 400094 India
| | - Ramesh Choudhari
- grid.449768.0Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, 5001 El Paso Drive, El Paso, TX 79905 USA
| | - Barbara Yang
- grid.449768.0Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, 5001 El Paso Drive, El Paso, TX 79905 USA
| | - Swagata Adhikari
- grid.473481.d0000 0001 0661 8707Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India ,grid.450257.10000 0004 1775 9822Homi Bhaba National Institute, Mumbai, 400094 India
| | - Enrique I. Ramos
- grid.449768.0Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, 5001 El Paso Drive, El Paso, TX 79905 USA
| | - Soumi Chaudhuri
- grid.473481.d0000 0001 0661 8707Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India
| | - Siddhartha Roy
- grid.417635.20000 0001 2216 5074Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032 India
| | - Shrikanth S. Gadad
- grid.449768.0Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, 5001 El Paso Drive, El Paso, TX 79905 USA ,grid.267309.90000 0001 0629 5880Mays Cancer Center, UT Health San Antonio MD Anderson Cancer Center, San Antonio, TX 78229 USA
| | - Chandrima Das
- grid.473481.d0000 0001 0661 8707Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India ,grid.450257.10000 0004 1775 9822Homi Bhaba National Institute, Mumbai, 400094 India
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20
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Bai Y, Yang Z, Xu X, Ding W, Qi J, Liu F, Wang X, Zhou B, Zhang W, Zhuang X, Li G, Zhao Y. Direct chemical induction of hepatocyte-like cells with capacity for liver repopulation. Hepatology 2022; 77:1550-1565. [PMID: 35881538 DOI: 10.1002/hep.32686] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 01/22/2023]
Abstract
BACKGROUND AND AIMS Cell fate can be directly reprogrammed from accessible cell types (e.g., fibroblasts) into functional cell types by exposure to small molecule stimuli. However, no chemical reprogramming method has been reported to date that successfully generates functional hepatocyte-like cells that can repopulate liver tissue, casting doubt over the feasibility of chemical reprogramming approaches to obtain desirable cell types for therapeutic applications. APPROACH AND RESULTS Here, through chemical induction of phenotypic plasticity, we provide a proof-of-concept demonstration of the direct chemical reprogramming of mouse fibroblasts into functional hepatocyte-like cells using exposure to small molecule cocktails in culture medium to successively stimulate endogenous expression of master transcription factors associated with hepatocyte development, such as hepatocyte nuclear factor 4a, nuclear receptor subfamily 1, group I, member 2, and nuclear receptor subfamily 1, group H, member 4. RNA sequencing analysis, metabolic assays, and in vivo physiological experiments show that chemically induced hepatocytes (CiHeps) exhibit comparable activity and function to primary hepatocytes, especially in liver repopulation to rescue liver failure in fumarylacetoacetate hydrolase-/- recombination activating gene 2-/- interleukin 2 receptor, gamma chain-/- mice in vivo. Single-cell RNA-seq further revealed that gastrointestinal-like and keratinocyte-like cells were induced along with CiHeps, resembling the activation of an intestinal program within hepatic reprogramming as described in transgenic approaches. CONCLUSIONS Our findings show that direct chemical reprogramming can generate hepatocyte-like cells with high-quality physiological properties, providing a paradigm for establishing hepatocyte identity in fibroblasts and demonstrating the potential for chemical reprogramming in organ/tissue repair and regeneration therapies.
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Affiliation(s)
- Yunfei Bai
- State Key Laboratory of Natural and Biomimetic Drugs, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Zhenghao Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | | | - Wanqiu Ding
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Juntian Qi
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Feng Liu
- National Clinical Research Center for Infectious Disease, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Peking University People's Hospital, Beijing, China
| | - Xiaoxiao Wang
- National Clinical Research Center for Infectious Disease, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Peking University People's Hospital, Beijing, China
| | - Bin Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Wenpeng Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Xiaomei Zhuang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Guanglu Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Yang Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
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21
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Luo M, Bao L, Chen Y, Xue Y, Wang Y, Zhang B, Wang C, Corley CD, McDonald JG, Kumar A, Xing C, Fang Y, Nelson ER, Wang JE, Wang Y, Luo W. ZMYND8 is a master regulator of 27-hydroxycholesterol that promotes tumorigenicity of breast cancer stem cells. Sci Adv 2022; 8:eabn5295. [PMID: 35857506 PMCID: PMC9286501 DOI: 10.1126/sciadv.abn5295] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
27-Hydroxycholesterol (27-HC) is the most abundant oxysterol that increases the risk of breast cancer progression. However, little is known about epigenetic regulation of 27-HC metabolism and its role in breast tumor initiation. Using genetic mouse mammary tumor and human breast cancer models, we showed here that the histone reader ZMYND8 was selectively expressed in breast cancer stem cells (BCSCs) and promoted epithelial-mesenchymal transition (EMT), BCSC maintenance and self-renewal, and oncogenic transformation through its epigenetic functions, leading to breast tumor initiation. Mechanistically, ZMYND8 was a master transcriptional regulator of 27-HC metabolism. It increased cholesterol biosynthesis and oxidation but blocked cholesterol efflux and 27-HC catabolism, leading to accumulation of 27-HC in BCSCs. Consequently, 27-HC promoted EMT, oncogenic transformation, and tumor initiation through activation of liver X receptor. These findings reveal that ZMYND8 is an epigenetic booster that drives breast tumor initiation through metabolic reprogramming.
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Affiliation(s)
- Maowu Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Lei Bao
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yan Chen
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yuanyuan Xue
- Children’s Medical Center Research Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yong Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Bo Zhang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chenliang Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chase D. Corley
- Center for Human Nutrition, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey G. McDonald
- Center for Human Nutrition, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yisheng Fang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Erik R. Nelson
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jennifer E. Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yingfei Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX, USA
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Weibo Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
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Abstract
Mammalian histone demethylases of the KDM5 family are mediators of gene expression dynamics during developmental, cellular differentiation, and other nuclear processes. They belong to the large group of JmjC domain containing, 2-oxoglutarate (2-OG) dependent oxygenases and target methylated lysine 4 of histone H3 (H3K4me1/2/3), an epigenetic mark associated with active transcription. In recent years, KDM5 demethylases have gained increasing attention due to their misregulation in many cancer entities and are intensively explored as therapeutic targets. Despite these implications, the molecular basis of KDM5 function has so far remained only poorly understood. Little is known about mechanisms of nucleosome recognition, the recruitment to genomic targets, as well as the local regulation of demethylase activity. Experimental evidence suggests close physical and functional interactions with epigenetic regulators such as histone deacetylase (HDAC) containing complexes, as well as the retinoblastoma protein (RB). To understand the regulation of KDM5 proteins in the context of chromatin, these interactions have to be taken into account. Here, we review the current state of knowledge on KDM5 function, with a particular emphasis on molecular interactions and their potential implications. We will discuss and outline open questions that need to be addressed to better understand histone demethylation and potential demethylation-independent functions of KDM5s. Addressing these questions will increase our understanding of histone demethylation and allow us to develop strategies to target individual KDM5 enzymes in specific biological and disease contexts.
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Affiliation(s)
- Egor Pavlenko
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Till Ruengeler
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Paulina Engel
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Simon Poepsel
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- *Correspondence: Simon Poepsel,
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23
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Ohguchi Y, Ohguchi H. Diverse Functions of KDM5 in Cancer: Transcriptional Repressor or Activator? Cancers (Basel) 2022; 14:3270. [PMID: 35805040 PMCID: PMC9265395 DOI: 10.3390/cancers14133270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 11/16/2022] Open
Abstract
Epigenetic modifications are crucial for chromatin remodeling and transcriptional regulation. Post-translational modifications of histones are epigenetic processes that are fine-tuned by writer and eraser enzymes, and the disorganization of these enzymes alters the cellular state, resulting in human diseases. The KDM5 family is an enzymatic family that removes di- and tri-methyl groups (me2 and me3) from lysine 4 of histone H3 (H3K4), and its dysregulation has been implicated in cancer. Although H3K4me3 is an active chromatin marker, KDM5 proteins serve as not only transcriptional repressors but also transcriptional activators in a demethylase-dependent or -independent manner in different contexts. Notably, KDM5 proteins regulate the H3K4 methylation cycle required for active transcription. Here, we review the recent findings regarding the mechanisms of transcriptional regulation mediated by KDM5 in various contexts, with a focus on cancer, and further shed light on the potential of targeting KDM5 for cancer therapy.
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24
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Alsagaby SA. Transcriptomics-Based Investigation of Molecular Mechanisms Underlying Apoptosis Induced by ZnO Nanoparticles in Human Diffuse Large B-Cell Lymphoma. Int J Nanomedicine 2022; 17:2261-2281. [PMID: 35611214 PMCID: PMC9124502 DOI: 10.2147/ijn.s355408] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/29/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction Zinc oxide nanoparticles (ZnO NPs) show anti-cancer activity. Diffuse Large B-cell Lymphoma (DLBCL) is a type of B-cell malignancies with unsatisfying treatment outcomes. This study was set to assess the potential of ZnO NPs to selectively induce apoptosis in human DLBCL cells (OCI-LY3), and to describe possible molecular mechanisms of action. Methods The impact of ZnO NPs on DLBCL cells and normal peripheral blood mononuclear cells (PBMCs) was studied using cytotoxicity assay and flow-cytometry. Transcriptomics analysis was conducted to identify ZnO NPs-dependent changes in the transcriptomic profiles of DLBCL cells. Results ZnO NPs selectively induced apoptosis in DLBCL cells, and caused changes in their transcriptomes. Deferential gene expression (DGE) with fold change (FC) ≥3 and p ≤ 0.008 with corrected p ≤ 0.05 was identified for 528 genes; 125 genes were over-expressed and 403 genes were under-expressed in ZnO NPs-treated DLBCL cells. The over-expressed genes involved in biological processes and pathways like stress response to metal ion, cellular response to zinc ion, metallothioneins bind metals, oxidative stress, and negative regulation of growth. In contrast, the under-expressed genes were implicated in DNA packaging complex, signaling by NOTCH, negative regulation of gene expression by epigenetic, signaling by WNT, M phase of cell cycle, and telomere maintenance. Setting the FC to ≥1.5 with p ≤ 0.05 and corrected p ≤ 0.1 showed ZnO NPs to induce over-expression of anti-oxidant genes and under-expression of oncogenes; target B-cell receptor (BCR) signaling pathway and NF-κB pathway; and promote apoptosis by intrinsic and extrinsic pathways. Discussion Overall, ZnO NPs selectively induced apoptosis in DLBCL cells, and possible molecular mechanisms of action were described.
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Affiliation(s)
- Suliman A Alsagaby
- Department of Medical Laboratories Sciences, College of Applied Medical Sciences, Majmaah University, AL-Majmaah, 11932, Saudi Arabia
- Correspondence: Suliman A Alsagaby, Email
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25
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Yang Z, Xu X, Gu C, Nielsen AV, Chen G, Guo F, Tang C, Zhao Y. Chemical Pretreatment Activated a Plastic State Amenable to Direct Lineage Reprogramming. Front Cell Dev Biol 2022; 10:865038. [PMID: 35399519 PMCID: PMC8990889 DOI: 10.3389/fcell.2022.865038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 02/21/2022] [Indexed: 11/21/2022] Open
Abstract
Somatic cells can be chemically reprogrammed into a pluripotent stem cell (CiPSC) state, mediated by an extraembryonic endoderm- (XEN-) like state. We found that the chemical cocktail applied in CiPSC generation initially activated a plastic state in mouse fibroblasts before transitioning into XEN-like cells. The plastic state was characterized by broadly activated expression of development-associated transcription factors (TFs), such as Sox17, Ascl1, Tbx3, and Nkx6-1, with a more accessible chromatin state indicating an enhanced capability of cell fate conversion. Intriguingly, introducing such a plastic state remarkably improved the efficiency of chemical reprogramming from fibroblasts to functional neuron-like cells with electrophysiological activity or beating skeletal muscles. Furthermore, the generation of chemically induced neuron-like cells or skeletal muscles from mouse fibroblasts was independent of the intermediate XEN-like state or the pluripotency state. In summary, our findings revealed a plastic chemically activated multi-lineage priming (CaMP) state at the onset of chemical reprogramming. This state enhanced the cells’ potential to adapt to other cell fates. It provides a general approach to empowering chemical reprogramming methods to obtain functional cell types bypassing inducing pluripotent stem cells.
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Affiliation(s)
- Zhenghao Yang
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xiaochan Xu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Chan Gu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | - Guokai Chen
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, China
| | - Fan Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chao Tang
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Center for Quantitative Biology, Peking University, Beijing, China
| | - Yang Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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26
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Hu M, Xing L, Zhang L, Liu F, Wang S, Xie Y, Wang J, Jiang H, Guo J, Li X, Wang J, Sui L, Li C, Liu D, Liu Z. NAP1L2 drives mesenchymal stem cell senescence and suppresses osteogenic differentiation. Aging Cell 2022; 21:e13551. [PMID: 35032339 PMCID: PMC8844120 DOI: 10.1111/acel.13551] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/08/2021] [Accepted: 12/31/2021] [Indexed: 12/19/2022] Open
Abstract
Senescence of bone marrow mesenchymal stem cells (BMSCs) impairs stemness and osteogenic differentiation, but the key regulators for senescence and the related osteogenesis are not well defined. Herein, we screened the gene expression profiles of human BMSCs from young and old donors and identified that elevation of the nucleosome assembly protein 1‐like 2 (NAP1L2) expression was correlated with BMSC senescence and impaired osteogenesis. Elevated NAP1L2 expression was observed in replicative cell senescence and induced cell senescence in vitro, and in age‐related senescent human and mouse BMSCs in vivo, concomitant with significantly augmented chromatin accessibility detected by ATAC‐seq. Loss‐ and gain‐of‐functions of NAP1L2 affected activation of NF‐κB pathway, status of histone 3 lysine 14 acetylation (H3K14ac), and chromatin accessibility on osteogenic genes in BMSCs. Mechanistic studies revealed that NAP1L2, a histone chaperone, recruited SIRT1 to deacetylate H3K14ac on promoters of osteogenic genes such as Runx2, Sp7, and Bglap and suppressed the osteogenic differentiation of BMSCs. Importantly, molecular docking analysis showed a possible bond between NAP1L2 and an anti‐aging reagent, the nicotinamide mononucleotide (NMN), and indeed, administration of NMN alleviated senescent phenotypes of BMSCs. In vivo and clinical evidence from aging mice and patients with senile osteoporosis also confirmed that elevation of NAP1L2 expression was associated with suppressed osteoblastogenesis. Taken together, our findings suggest that NAP1L2 is a regulator of both BMSC cell senescence and osteogenic differentiation, and provide a new theoretical basis for aging‐related disease.
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Affiliation(s)
- Meilin Hu
- Tianjin Medical University School of Stomatology Tianjin Medical University Tianjin China
| | - Liangyu Xing
- Tianjin Medical University School of Stomatology Tianjin Medical University Tianjin China
| | - Li Zhang
- Tianjin Medical University School of Stomatology Tianjin Medical University Tianjin China
| | - Fan Liu
- Tianjin Medical University School of Stomatology Tianjin Medical University Tianjin China
| | - Sheng Wang
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases Department of Physiology and Pathophysiology School of Basic Medical Science Tianjin Medical University Tianjin China
| | - Ying Xie
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases Department of Physiology and Pathophysiology School of Basic Medical Science Tianjin Medical University Tianjin China
| | - Jingjing Wang
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases Department of Physiology and Pathophysiology School of Basic Medical Science Tianjin Medical University Tianjin China
| | - Hongmei Jiang
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases Department of Physiology and Pathophysiology School of Basic Medical Science Tianjin Medical University Tianjin China
| | - Jing Guo
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases Department of Physiology and Pathophysiology School of Basic Medical Science Tianjin Medical University Tianjin China
| | - Xin Li
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases Department of Physiology and Pathophysiology School of Basic Medical Science Tianjin Medical University Tianjin China
| | - Jingya Wang
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases Department of Physiology and Pathophysiology School of Basic Medical Science Tianjin Medical University Tianjin China
| | - Lei Sui
- Tianjin Medical University School of Stomatology Tianjin Medical University Tianjin China
| | - Changyi Li
- Tianjin Medical University School of Stomatology Tianjin Medical University Tianjin China
| | - Dayong Liu
- Tianjin Medical University School of Stomatology Tianjin Medical University Tianjin China
| | - Zhiqiang Liu
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases Department of Physiology and Pathophysiology School of Basic Medical Science Tianjin Medical University Tianjin China
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27
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Li W, Li F, Zhang X, Lin HK, Xu C. Insights into the post-translational modification and its emerging role in shaping the tumor microenvironment. Signal Transduct Target Ther 2021; 6:422. [PMID: 34924561 PMCID: PMC8685280 DOI: 10.1038/s41392-021-00825-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 12/11/2022] Open
Abstract
More and more in-depth studies have revealed that the occurrence and development of tumors depend on gene mutation and tumor heterogeneity. The most important manifestation of tumor heterogeneity is the dynamic change of tumor microenvironment (TME) heterogeneity. This depends not only on the tumor cells themselves in the microenvironment where the infiltrating immune cells and matrix together forming an antitumor and/or pro-tumor network. TME has resulted in novel therapeutic interventions as a place beyond tumor beds. The malignant cancer cells, tumor infiltrate immune cells, angiogenic vascular cells, lymphatic endothelial cells, cancer-associated fibroblastic cells, and the released factors including intracellular metabolites, hormonal signals and inflammatory mediators all contribute actively to cancer progression. Protein post-translational modification (PTM) is often regarded as a degradative mechanism in protein destruction or turnover to maintain physiological homeostasis. Advances in quantitative transcriptomics, proteomics, and nuclease-based gene editing are now paving the global ways for exploring PTMs. In this review, we focus on recent developments in the PTM area and speculate on their importance as a critical functional readout for the regulation of TME. A wealth of information has been emerging to prove useful in the search for conventional therapies and the development of global therapeutic strategies.
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Affiliation(s)
- Wen Li
- grid.54549.390000 0004 0369 4060Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, 610042 Chengdu, P. R. China
| | - Feifei Li
- grid.54549.390000 0004 0369 4060Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, 610042 Chengdu, P. R. China ,grid.256607.00000 0004 1798 2653Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, 530021 Nanning, Guangxi China
| | - Xia Zhang
- grid.410570.70000 0004 1760 6682Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038 Chongqing, China
| | - Hui-Kuan Lin
- grid.241167.70000 0001 2185 3318Department of Cancer Biology, Wake Forest Baptist Medical Center, Wake Forest University, Winston Salem, NC 27101 USA
| | - Chuan Xu
- Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, 610042, Chengdu, P. R. China. .,Department of Cancer Biology, Wake Forest Baptist Medical Center, Wake Forest University, Winston Salem, NC, 27101, USA.
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28
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Morgan MAJ, Popova IK, Vaidya A, Burg JM, Marunde MR, Rendleman EJ, Dumar ZJ, Watson R, Meiners MJ, Howard SA, Khalatyan N, Vaughan RM, Rothbart SB, Keogh MC, Shilatifard A. A trivalent nucleosome interaction by PHIP/BRWD2 is disrupted in neurodevelopmental disorders and cancer. Genes Dev 2021; 35:1642-1656. [PMID: 34819353 PMCID: PMC8653789 DOI: 10.1101/gad.348766.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/09/2021] [Indexed: 11/24/2022]
Abstract
Mutations in the PHIP/BRWD2 chromatin regulator cause the human neurodevelopmental disorder Chung-Jansen syndrome, while alterations in PHIP expression are linked to cancer. Precisely how PHIP functions in these contexts is not fully understood. Here we demonstrate that PHIP is a chromatin-associated CRL4 ubiquitin ligase substrate receptor and is required for CRL4 recruitment to chromatin. PHIP binds to chromatin through a trivalent reader domain consisting of a H3K4-methyl binding Tudor domain and two bromodomains (BD1 and BD2). Using semisynthetic nucleosomes with defined histone post-translational modifications, we characterize PHIPs BD1 and BD2 as respective readers of H3K14ac and H4K12ac, and identify human disease-associated mutations in each domain and the intervening linker region that likely disrupt chromatin binding. These findings provide new insight into the biological function of this enigmatic chromatin protein and set the stage for the identification of both upstream chromatin modifiers and downstream targets of PHIP in human disease.
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Affiliation(s)
- Marc A J Morgan
- Simpson Querrey Center for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | - Anup Vaidya
- EpiCypher, Inc., Durham, North Carolina 27709, USA
| | | | | | - Emily J Rendleman
- Simpson Querrey Center for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Zachary J Dumar
- Simpson Querrey Center for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | | | | | - Natalia Khalatyan
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Robert M Vaughan
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, Minnesota 49503, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, Minnesota 49503, USA
| | | | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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29
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Jia P, Li X, Wang X, Yao L, Xu Y, Hu Y, Xu W, He Z, Zhao Q, Deng Y, Zang Y, Zhang M, Zhang Y, Qin J, Lu W. ZMYND8 mediated liquid condensates spatiotemporally decommission the latent super-enhancers during macrophage polarization. Nat Commun 2021; 12:6535. [PMID: 34764296 PMCID: PMC8586003 DOI: 10.1038/s41467-021-26864-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/27/2021] [Indexed: 12/31/2022] Open
Abstract
Super-enhancers (SEs) govern macrophage polarization and function. However, the mechanism underlying the signal-dependent latent SEs remodeling in macrophages remains largely undefined. Here we show that the epigenetic reader ZMYND8 forms liquid compartments with NF-κB/p65 to silence latent SEs and restrict macrophage-mediated inflammation. Mechanistically, the fusion of ZMYND8 and p65 liquid condensates is reinforced by signal-induced acetylation of p65. Then acetylated p65 guides the ZMYND8 redistribution onto latent SEs de novo generated in polarized macrophages, and consequently, recruit LSD1 to decommission latent SEs. The liquidity characteristic of ZMYND8 is critical for its regulatory effect since mutations coagulating ZMYND8 into solid compartments disable the translocation of ZMYND8 and its suppressive function. Thereby, ZMYND8 serves as a molecular rheostat to switch off latent SEs and control the magnitude of the immune response. Meanwhile, we propose a phase separation model by which the latent SEs are fine-tuned in a spatiotemporal manner. Macrophages employ epigenetic remodeling, especially the regulation of superenhancers (SEs), to promote classical polarization and function; whether liquid-liquid phase separation (LLPS) is involved is not known. Here, the authors show the epigenetic reader ZMYND8 forms condensates to deactivate latent SEs in a spatiotemporal manner and thereby restrict macrophage-mediated inflammation.
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Affiliation(s)
- Pan Jia
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiang Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Xuelei Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liangjiao Yao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yingying Xu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu Hu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenwen Xu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhe He
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qifan Zhao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yicong Deng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yi Zang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Meiyu Zhang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yan Zhang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jun Qin
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
| | - Wei Lu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
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30
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Liu M, Gao N. KDM5D inhibits the transcriptional activation of FKBP4 by suppressing the expression of E2F1 in colorectal cancer in males. Biochem Pharmacol 2021; 194:114814. [PMID: 34688635 DOI: 10.1016/j.bcp.2021.114814] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 11/21/2022]
Abstract
Colorectal cancer (CRC) remains the most frequently diagnosed malignancy and also a major contributor to cancer-related death throughout the world. Here, we first revealed the role of histone lysine-specific demethylase 5D (KDM5D) in CRC in males. KDM5D expression in tumor and adjacent tissues of male CRC patients was investigated using immunohistochemistry and RT-qPCR, and the correlation between its expression and patients' prognosis was analyzed. Downregulation of KDM5D in CRC patients was associated with poor prognoses. Overexpression of KDM5D significantly inhibited the growth and metastasis of CRC in vitro and in vivo. The downstream mechanism of KDM5D in CRC was investigated using bioinformatics analysis, and the regulatory relationship was confirmed by ChIP-qPCR and luciferase reporter assays. KDM5D suppressed E2F1 expression by mediating H3K4me3 demethylation. E2F1, highly expressed in CRC, promoted the expression of FKBP4 at the transcriptional level by binding to the FKBP4 promoter. Finally, rescue experiments revealed that overexpression of FKBP4 significantly reversed the inhibitory effect of KDM5D on CRC growth and metastasis. Collectively, KDM5D exerted an anti-tumor and anti-metastatic in CRC through demethylation in E2F1 and suppression of FKBP4 transcription, which might represent a novel target in CRC treatment in male.
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31
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Yu B, Yu X, Xiong J, Ma M. Methylation Modification, Alternative Splicing, and Noncoding RNA Play a Role in Cancer Metastasis through Epigenetic Regulation. Biomed Res Int 2021; 2021:4061525. [PMID: 34660788 DOI: 10.1155/2021/4061525] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/15/2021] [Indexed: 12/15/2022]
Abstract
Metastasis is the leading cause of cancer-related deaths. Understanding the pathogenesis of metastasis at the molecular levels is of great significance for cancer research. However, the molecular diagnosis or treatment of cancer metastasis is limited. Accumulating and growing evidence shows that epigenetic changes are present in all human cancers, and epigenetic regulation is an indispensable factor to promote tumor metastasis. With the deepening of research and the advancement of technology, the function and mechanism of epigenetic regulation, including DNA methylation, histone/RNA modification, and precursor messenger RNA alternative splicing and noncoding RNAs, has become more increasingly clear. At present, the application of epigenetic therapies in tumor treatment is becoming a feasible therapeutic route. In this review, we looked for the key molecules in epigenetic regulation and discuss their relative regulating mechanisms in cancer metastasis. Furthermore, we highlight promising therapeutic strategies, including monitoring serum DNA for diagnostic purposes and early phase clinical trial therapies that target DNA and histone methylation. This may also be beneficial in finding new targets for further prognosis and diagnosis of cancer metastasis.
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32
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Qiu F, Jin Y, Pu J, Huang Y, Hou J, Zhao X, Lu Y. Aberrant FBXW7-mediated ubiquitination and degradation of ZMYND8 enhances tumor progression and stemness in bladder cancer. Exp Cell Res 2021; 407:112807. [PMID: 34487730 DOI: 10.1016/j.yexcr.2021.112807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/22/2021] [Accepted: 08/27/2021] [Indexed: 12/16/2022]
Abstract
ZMYND8, an epigenetic regulator, was identified as a common oncogene across various tumors. However, little was reported about the association between ZMYND8 and bladder cancer. Besides, aberrant mechanisms that contribute to abnormal ZMYND8 expressions still remain unclear. In the current study, we first found that ZMYND8 protein levels were significantly elevated in Bca samples versus normal tissues, but not the mRNA levels. We then utilized the Cell Counting Kit-8 (CCK-8) assay, clone formation assay and transwell analysis to confirm that ZMYND8 could remarkably promote the tumor progression in vitro, including growth capacity and migration. Bioinformatic predictive analysis revealed that E3 ubiquitin ligase FBXW7 interacts directly with ZMYND8 and degrades ZMYND8 in a polyubiquitination manner. Low FBXW7 was a hazard factor for promoting and depending on accumulated ZMYND8 proteins to promote Bca progression. Gene set enrichment analysis (GSEA) further indicated that ZMYND8 was notably associated with stemness process, which was well functionally validated. Lastly, ZMYND8 deficiency was observed to inhibit tumor growth of Bca in vivo, revealing a promising translational significance in Bca treatment. In conclusion, our study for the first time provided evidence for a novel mechanism of FBXW7/ZMYND8 axis in Bca, providing therapeutic vulnerability for individualized cancer treatment.
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Affiliation(s)
- Feng Qiu
- Department of Urology, The First Affiliated Hospital of Soochow University, China
| | - Yichen Jin
- Department of Urology, The First Affiliated Hospital of Soochow University, China
| | - Jinxian Pu
- Department of Urology, The First Affiliated Hospital of Soochow University, China
| | - Yuhua Huang
- Department of Urology, The First Affiliated Hospital of Soochow University, China
| | - Jianquan Hou
- Department of Urology, The First Affiliated Hospital of Soochow University, China
| | - Xiaojun Zhao
- Department of Urology, The First Affiliated Hospital of Soochow University, China
| | - Yong Lu
- Department of Urology, The First Affiliated Hospital of Soochow University, China.
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Abstract
The hereditary blueprint of a eukaryotic cell is encoded in its genomic DNA that is tightly compacted into chromatin together with histone proteins. The basic repeating units of chromatin fibers are nucleosomes, in which approximately 1.7 turns of DNA wrap around a proteinaceous octamer consisting of two copies of histones H2A, H2B, H3, and H4. Histones are extensively decorated by a variety of posttranslational modifications (PTMs, e.g., methylation, acetylation, ubiquitylation, phosphorylation, etc.), serving as one of the cellular mechanisms that regulates DNA-templated processes, including but not limited to gene transcription, DNA replication, and DNA damage repair. Most of the histone PTMs exist in dynamic fluctuations, and their on and off states are exquisitely regulated by enzymes known as "writers" and "erasers", respectively. When installed at certain sites, histone PTMs can change the local physicochemical environment and thereby directly influence the nucleosome and chromatin structures. Alternatively, histone PTMs can recruit effectors (or "readers") to signal the downstream events. A "histone code" hypothesis has been proposed in which the combinatory actions of different histone PTMs orchestrate the epigenetic landscape of cells, modulating the activity of the underlying DNA and maintaining the genome stability between generations. Accumulating evidence also suggests that malfunctions of histone PTMs are associated with the pathogenesis of human diseases, such as cancer. It is therefore important to fully decipher the histone code, namely, to dissect the regulatory mechanisms and biological functions of histone PTMs.Owing to the advances in state-of-the-art mass spectrometry, dozens of novel histone modifications have been archived during the past decade. However, most of these newly identified histone PTMs remain poorly explored. To unravel the roles played by these PTMs in histone code, key questions that have driven our study are (i) how to detect the novel histone PTMs; (ii) how to identify the enzymes that catalyze the addition (writers) and removal (erasers) of the histone PTMs along with the regulating mechanisms; (iii) what is the biological significance of the histone PTMs and how do they function, by affecting the nucleosome and chromatin dynamics or by recruiting readers; and (iv) how to develop chemical probes to interrogate the histone PTMs or even serve as potential leads for the drug discovery campaigns to treat diseases caused by abnormalities in the regulation of histone PTMs.This Account focuses on our efforts in developing and applying chemical tools and methods to answer the above questions. Specifically, we review the detection of negatively charged histone acylations by developing and applying chemical reporters; preparing homogeneous nucleosomes carrying negatively charged acylations by protein chemistry approaches and the in vitro biophysical analyses of the effects of the acylations on nucleosome structures; investigating the negatively charged acylations' influence on chromatin dynamics in vivo using yeast genetic approaches; identifying and characterizing protein-protein interactions (PPIs) mediated by histone PTMs in different biological contexts (i.e., to identify the readers and erasers) by establishing a chemical proteomics platform that is enabled by photo-cross-linking chemistry and quantitative proteomics strategies; and manipulating PTM-mediated PPIs by the structure-guided design of inhibitors. We also discuss possible future directions in our journey to fully decipher the histone code.
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Affiliation(s)
- Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, 999077 China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, 999077 China
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Yu H, He J, Liu W, Feng S, Gao L, Xu Y, Zhang Y, Hou X, Zhou Y, Yang L, Wang X. The Transcriptional Coactivator, ALL1-Fused Gene From Chromosome 9, Simultaneously Sustains Hypoxia Tolerance and Metabolic Advantages in Liver Cancer. Hepatology 2021; 74:1952-1970. [PMID: 33928666 DOI: 10.1002/hep.31870] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/21/2021] [Accepted: 04/09/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND AND AIMS Proteins that recognize epigenetic modifications function as mediators to interpret epigenetic codes. Hypoxia response and metabolic rewiring are two major events during cancer progression. However, whether and how the epigenetic regulator integrates hypoxia response and metabolism together remain open for study. APPROACH AND RESULTS We data mined the clinical association of 33 histone lysine acetylation reader proteins with liver cancer and found that ALL1-fused gene from chromosome 9 (AF9) is up-regulated in cancer and correlates with tumor stage and poor prognosis. Conditional deletion of Af9 in mouse liver resulted in decreased tumor formation induced by c-MET proto-oncogene/β-catenin. Loss of AF9 heavily impaired cell proliferation and completely blocked solid tumor formation. We further discovered that AF9 formed a positive feedback circuit with hypoxia-inducible factor 1 alpha (HIF1α) and also stabilized MYC proto-oncogene (cMyc). Mechanically, AF9 interacted with HIF1α and targeted HIF1A promoter whereas AF9 recognized cMyc acetylation at K148, protected cMyc phosphorylation at S62, and then stabilized cMyc, which, in turn, up-regulates phosphofructokinase, platelet expression. Otherwise, knockout of Af9 in mouse hepatocytes increased the infiltration of CD8+ T cells, which is linked to the down-regulation of lactate dehydrogenase A. CONCLUSIONS AF9 is up-regulated to promote gene expression of hypoxia tolerance and glycolysis by simultaneously forming a complex with HIF1α and recognizing acetylated cMyc. Our results establish the oncogenic role of AF9 in human liver cancer, which could be a potential target for designing drugs against liver cancer.
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Affiliation(s)
- Hua Yu
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China.,CAS Key Laboratory of Tissue Microenvironment and Tumor, Institute of Nutrition and Health Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jun He
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Wei Liu
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shuya Feng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Institute of Nutrition and Health Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Li Gao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Institute of Nutrition and Health Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yingying Xu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Institute of Nutrition and Health Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yawei Zhang
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Xuyang Hou
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Yan Zhou
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Leping Yang
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Xiongjun Wang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China.,CAS Key Laboratory of Tissue Microenvironment and Tumor, Institute of Nutrition and Health Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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Chen JF, Yan Q. The roles of epigenetics in cancer progression and metastasis. Biochem J 2021; 478:3373-93. [PMID: 34520519 DOI: 10.1042/BCJ20210084] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 01/12/2023]
Abstract
Cancer metastasis remains a major clinical challenge for cancer treatment. It is therefore crucial to understand how cancer cells establish and maintain their metastatic traits. However, metastasis-specific genetic mutations have not been identified in most exome or genome sequencing studies. Emerging evidence suggests that key steps of metastasis are controlled by reversible epigenetic mechanisms, which can be targeted to prevent and treat the metastatic disease. A variety of epigenetic mechanisms were identified to regulate metastasis, including the well-studied DNA methylation and histone modifications. In the past few years, large scale chromatin structure alterations including reprogramming of the enhancers and chromatin accessibility to the transcription factors were shown to be potential driving force of cancer metastasis. To dissect the molecular mechanisms and functional output of these epigenetic changes, it is critical to use advanced techniques and alternative animal models for interdisciplinary and translational research on this topic. Here we summarize our current understanding of epigenetic aberrations in cancer progression and metastasis, and their implications in developing new effective metastasis-specific therapies.
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36
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Lan W, Li Z, Jiao F, Wang C, Guo R, Cao C. Structural Basis of
RACK7 PHD
Domain to Read a Pediatric
Glioblastoma‐Associated
Histone Mutation
H3
.
3G34R. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Wenxian Lan
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road Shanghai 200032 China
| | - Ze Li
- Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics Shanghai Medical College of Fudan University Shanghai 200032 China
| | - Fangfang Jiao
- Center for Medical Research and Innovation, Shanghai Pudong Hospital Fudan University Pudong Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University Shanghai 200032 China
| | - Chunxi Wang
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road Shanghai 200032 China
| | - Rui Guo
- Center for Medical Research and Innovation, Shanghai Pudong Hospital Fudan University Pudong Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University Shanghai 200032 China
| | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road Shanghai 200032 China
- University of Chinese Academy of Science No. 19A, Yuquan Road, Shijingshan District Beijing 100049 China
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Choi S, Lee KW, Koh HH, Park S, Yeo SY, Joh JW, Choi MS, Kim SH, Park CK, Ha SY. Validation of ZMYND8 as a new treatment target in hepatocellular carcinoma. J Cancer Res Clin Oncol 2021; 147:3517-34. [PMID: 34462784 DOI: 10.1007/s00432-021-03768-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/14/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND ZMYND8 (Zinc finger MYND (Myeloid, Nervy and DEAF-1)-type containing 8) has been known to play an important role in tumor regulation in various types of cancer. However, the results of ZMYND8 expression and their clinical significance in hepatocellular carcinoma (HCC) have not yet been published. In the present study, we investigate the expression of ZMYND8 protein and mRNA in HCC and elucidate its prognostic significance. METHODS ZMYND8 protein and mRNA expression in 283 and 234 HCCs were investigated using immunohistochemistry and microarray gene expression profiling data. The relationships between ZMYND8 expression with clinicopathologic features and prognosis of HCC patients were evaluated. Furthermore, we performed the invasion, migration, apoptosis, soft agar formation assay and sphere formation assay in HCC cell lines, and evaluated tumorigenicity in a nude mouse model, after ZMYND8 knockdown. RESULTS Overexpression of ZMYND8 protein and mRNA was observed in 20.5% and 26.9% of HCC cases, respectively. High ZMYND8 expression showed significant correlations with microvascular invasion, high Edmondson grade, advanced American Joint Committee on Cancer, and increased alpha-fetoprotein level. ZMYND8 mRNA overexpression was an independent prognostic factor for predicting early recurrence as well as short recurrence-free survival (RFS). Downregulation of ZMYND8 reduced migration and invasion of HCC cells, and promoted apoptosis of HCC cells in an in vitro model. In a xenograft nude mouse model, knockdown of ZMYND8 significantly reduced tumor growth. CONCLUSION ZMYND8 mRNA overexpression could be a prognostic marker of shorter RFS in HCC patients after curative resection. ZMYND8 might play an important role in the proliferation and progression of HCC and could be a promising candidate for targeted therapy.
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Peña-Hernández R, Aprigliano R, Carina Frommel S, Pietrzak K, Steiger S, Roganowicz M, Lerra L, Bizzarro J, Santoro R. BAZ2A-mediated repression via H3K14ac-marked enhancers promotes prostate cancer stem cells. EMBO Rep 2021; 22:e53014. [PMID: 34403195 PMCID: PMC8567280 DOI: 10.15252/embr.202153014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 12/09/2022] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent cancers in men. Cancer stem cells are thought to be associated with PCa relapse. Here, we show that BAZ2A is required for PCa cells with a cancer stem‐like state. BAZ2A genomic occupancy in PCa cells coincides with H3K14ac‐enriched chromatin regions. This association is mediated by BAZ2A‐bromodomain (BAZ2A‐BRD) that specifically binds H3K14ac. BAZ2A associates with inactive enhancers marked by H3K14ac and repressing transcription of genes frequently silenced in aggressive and poorly differentiated PCa. BAZ2A‐mediated repression is also linked to EP300 that acetylates H3K14ac. BAZ2A‐BRD mutations or treatment with inhibitors abrogating BAZ2A‐BRD/H3K14ac interaction impair PCa stem cells. Furthermore, pharmacological inactivation of BAZ2A‐BRD impairs Pten‐loss oncogenic transformation of prostate organoids. Our findings indicate a role of BAZ2A‐BRD in PCa stem cell features and suggest potential epigenetic‐reader therapeutic strategies to target BAZ2A in aggressive PCa.
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Affiliation(s)
- Rodrigo Peña-Hernández
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland.,Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Rossana Aprigliano
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
| | - Sandra Carina Frommel
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
| | - Karolina Pietrzak
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland.,Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Seraina Steiger
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
| | - Marcin Roganowicz
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland.,RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Luigi Lerra
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland.,RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Juliana Bizzarro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
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Tang B, Sun R, Wang D, Sheng H, Wei T, Wang L, Zhang J, Ho TH, Yang L, Wei Q, Huang H. ZMYND8 preferentially binds phosphorylated EZH2 to promote a PRC2-dependent to -independent function switch in hypoxia-inducible factor-activated cancer. Proc Natl Acad Sci U S A 2021; 118:e2019052118. [PMID: 33593912 DOI: 10.1073/pnas.2019052118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Both gene repressor (Polycomb-dependent) and activator (Polycomb-independent) functions of the Polycomb protein enhancer of zeste homolog 2 (EZH2) are implicated in cancer progression. EZH2 protein can be phosphorylated at various residues, such as threonine 487 (T487), by CDK1 kinase, and such phosphorylation acts as a Polycomb repressive complex 2 (PRC2) suppression "code" to mediate the gene repressor-to-activator switch of EZH2 functions. Here we demonstrate that the histone reader protein ZMYND8 is overexpressed in human clear cell renal cell carcinoma (ccRCC). ZMYND8 binds to EZH2, and their interaction is largely enhanced by CDK1 phosphorylation of EZH2 at T487. ZMYND8 depletion not only enhances Polycomb-dependent function of EZH2 in hypoxia-exposed breast cancer cells or von Hippel-Lindau (VHL)-deficient ccRCC cells, but also suppresses the FOXM1 transcription program. We further show that ZMYND8 is required for EZH2-FOXM1 interaction and is important for FOXM1-dependent matrix metalloproteinase (MMP) gene expression and EZH2-mediated migration and invasion of VHL-deficient ccRCC cells. Our results identify a previously uncharacterized role of the chromatin reader ZMYND8 in recognizing the PRC2-inhibitory phosphorylation "code" essential for the Polycomb-dependent to -independent switch of EZH2 functions. They also reveal an oncogenic pathway driving cell migration and invasion in hypoxia-inducible factor-activated (hypoxia or VHL-deficient) cancer.
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Cao Z, Budinich KA, Huang H, Ren D, Lu B, Zhang Z, Chen Q, Zhou Y, Huang YH, Alikarami F, Kingsley MC, Lenard AK, Wakabayashi A, Khandros E, Bailis W, Qi J, Carroll MP, Blobel GA, Faryabi RB, Bernt KM, Berger SL, Shi J. ZMYND8-regulated IRF8 transcription axis is an acute myeloid leukemia dependency. Mol Cell 2021:S1097-2765(21)00587-6. [PMID: 34358447 DOI: 10.1016/j.molcel.2021.07.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 02/06/2023]
Abstract
The transformed state in acute leukemia requires gene regulatory programs involving transcription factors and chromatin modulators. Here, we uncover an IRF8-MEF2D transcriptional circuit as an acute myeloid leukemia (AML)-biased dependency. We discover and characterize the mechanism by which the chromatin "reader" ZMYND8 directly activates IRF8 in parallel with the MYC proto-oncogene through their lineage-specific enhancers. ZMYND8 is essential for AML proliferation in vitro and in vivo and associates with MYC and IRF8 enhancer elements that we define in cell lines and in patient samples. ZMYND8 occupancy at IRF8 and MYC enhancers requires BRD4, a transcription coactivator also necessary for AML proliferation. We show that ZMYND8 binds to the ET domain of BRD4 via its chromatin reader cassette, which in turn is required for proper chromatin occupancy and maintenance of leukemic growth in vivo. Our results rationalize ZMYND8 as a potential therapeutic target for modulating essential transcriptional programs in AML.
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Boyson SP, Gao C, Quinn K, Boyd J, Paculova H, Frietze S, Glass KC. Functional Roles of Bromodomain Proteins in Cancer. Cancers (Basel) 2021; 13:3606. [PMID: 34298819 PMCID: PMC8303718 DOI: 10.3390/cancers13143606] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/31/2022] Open
Abstract
Histone acetylation is generally associated with an open chromatin configuration that facilitates many cellular processes including gene transcription, DNA repair, and DNA replication. Aberrant levels of histone lysine acetylation are associated with the development of cancer. Bromodomains represent a family of structurally well-characterized effector domains that recognize acetylated lysines in chromatin. As part of their fundamental reader activity, bromodomain-containing proteins play versatile roles in epigenetic regulation, and additional functional modules are often present in the same protein, or through the assembly of larger enzymatic complexes. Dysregulated gene expression, chromosomal translocations, and/or mutations in bromodomain-containing proteins have been correlated with poor patient outcomes in cancer. Thus, bromodomains have emerged as a highly tractable class of epigenetic targets due to their well-defined structural domains, and the increasing ease of designing or screening for molecules that modulate the reading process. Recent developments in pharmacological agents that target specific bromodomains has helped to understand the diverse mechanisms that bromodomains play with their interaction partners in a variety of chromatin processes, and provide the promise of applying bromodomain inhibitors into the clinical field of cancer treatment. In this review, we explore the expression and protein interactome profiles of bromodomain-containing proteins and discuss them in terms of functional groups. Furthermore, we highlight our current understanding of the roles of bromodomain-containing proteins in cancer, as well as emerging strategies to specifically target bromodomains, including combination therapies using bromodomain inhibitors alongside traditional therapeutic approaches designed to re-program tumorigenesis and metastasis.
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Affiliation(s)
- Samuel P. Boyson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
| | - Cong Gao
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Kathleen Quinn
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Joseph Boyd
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Hana Paculova
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
- University of Vermont Cancer Center, Burlington, VT 05405, USA
| | - Karen C. Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- University of Vermont Cancer Center, Burlington, VT 05405, USA
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Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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Abstract
The genetic information of human cells is stored in the context of chromatin, which is subjected to DNA methylation and various histone modifications. Such a 'language' of chromatin modification constitutes a fundamental means of gene and (epi)genome regulation, underlying a myriad of cellular and developmental processes. In recent years, mounting evidence has demonstrated that miswriting, misreading or mis-erasing of the modification language embedded in chromatin represents a common, sometimes early and pivotal, event across a wide range of human cancers, contributing to oncogenesis through the induction of epigenetic, transcriptomic and phenotypic alterations. It is increasingly clear that cancer-related metabolic perturbations and oncohistone mutations also directly impact chromatin modification, thereby promoting cancerous transformation. Phase separation-based deregulation of chromatin modulators and chromatin structure is also emerging to be an important underpinning of tumorigenesis. Understanding the various molecular pathways that underscore a misregulated chromatin language in cancer, together with discovery and development of more effective drugs to target these chromatin-related vulnerabilities, will enhance treatment of human malignancies.
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Affiliation(s)
- Shuai Zhao
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics and Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics and Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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Shen H, Zhang W, Huang Y, He Y, Hu G, Wang L, Peng B, Yi J, Li T, Rong R, Chen X, Liu J, Li W, Ohgi K, Li S, Rosenfeld MG, Liu W. The Dual Function of KDM5C in Both Gene Transcriptional Activation and Repression Promotes Breast Cancer Cell Growth and Tumorigenesis. Adv Sci (Weinh) 2021; 8:2004635. [PMID: 33977073 PMCID: PMC8097366 DOI: 10.1002/advs.202004635] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/25/2020] [Indexed: 06/01/2023]
Abstract
Emerging evidence suggested that epigenetic regulators can exhibit both activator and repressor activities in gene transcriptional regulation and disease development, such as cancer. However, how these dual activities are regulated and coordinated in specific cellular contexts remains elusive. Here, it is reported that KDM5C, a repressive histone demethylase, unexpectedly activates estrogen receptor alpha (ERα)-target genes, and meanwhile suppresses type I interferons (IFNs) and IFN-stimulated genes (ISGs) to promote ERα-positive breast cancer cell growth and tumorigenesis. KDM5C-interacting protein, ZMYND8, is found to be involved in both processes. Mechanistically, KDM5C binds to active enhancers and recruits the P-TEFb complex to activate ERα-target genes, while inhibits TBK1 phosphorylation in the cytosol to repress type I IFNs and ISGs. Pharmacological inhibition of both ERα and KDM5C is effective in inhibiting cell growth and tumorigenesis. Taken together, it is revealed that the dual activator and repressor nature of an epigenetic regulator together contributes to cancer development.
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Affiliation(s)
- Hai‐feng Shen
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Wen‐juan Zhang
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Ying Huang
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Yao‐hui He
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Guo‐sheng Hu
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Lei Wang
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Bing‐ling Peng
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Jia Yi
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Ting‐ting Li
- State Key Laboratory of Molecular Vaccinology and Molecular DiagnosticsXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Rui Rong
- State Key Laboratory of Molecular Vaccinology and Molecular DiagnosticsXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Xiao‐yan Chen
- School of Life SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Jun‐yi Liu
- State Key Laboratory of Molecular Vaccinology and Molecular DiagnosticsXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Wen‐juan Li
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Kenny Ohgi
- Howard Hughes Medical InstituteDepartment of MedicineUniversity of California9500 Gilman Drive La JollaSan DiegoCA92093USA
| | - Shao‐Wei Li
- State Key Laboratory of Molecular Vaccinology and Molecular DiagnosticsXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Michael G. Rosenfeld
- Howard Hughes Medical InstituteDepartment of MedicineUniversity of California9500 Gilman Drive La JollaSan DiegoCA92093USA
| | - Wen Liu
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
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Pan Q, Zhong S, Wang H, Wang X, Li N, Li Y, Zhang G, Yuan H, Lian Y, Chen Q, Han Y, Guo J, Liu Q, Qiu T, Jiang J, Li Q, Tan M, Yin H, Peng J, Xiao Y, Qin J. The ZMYND8-regulated mevalonate pathway endows YAP-high intestinal cancer with metabolic vulnerability. Mol Cell 2021; 81:2736-2751.e8. [PMID: 33932349 DOI: 10.1016/j.molcel.2021.04.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 01/18/2021] [Accepted: 04/08/2021] [Indexed: 12/14/2022]
Abstract
Cholesterol metabolism is tightly associated with colorectal cancer (CRC). Nevertheless, the clinical benefit of statins, the inhibitor of cholesterol biogenesis mevalonate (MVA) pathway, is inconclusive, possibly because of a lack of patient stratification criteria. Here, we describe that YAP-mediated zinc finger MYND-type containing 8 (ZMYND8) expression sensitizes intestinal tumors to the inhibition of the MVA pathway. We show that the oncogenic activity of YAP relies largely on ZMYND8 to enhance intracellular de novo cholesterol biogenesis. Disruption of the ZMYND8-dependent MVA pathway greatly restricts the self-renewal capacity of Lgr5+ intestinal stem cells (ISCs) and intestinal tumorigenesis. Mechanistically, ZMYND8 and SREBP2 drive the enhancer-promoter interaction to facilitate the recruitment of Mediator complex, thus upregulating MVA pathway genes. Together, our results establish that the epigenetic reader ZMYND8 endows YAP-high intestinal cancer with metabolic vulnerability.
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Affiliation(s)
- Qiang Pan
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Shanshan Zhong
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Hanling Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Xuege Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Ni Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yaqi Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Guoying Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Huairui Yuan
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yannan Lian
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Qilong Chen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Ying Han
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Jiacheng Guo
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Qiuli Liu
- Department of Urology, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Tong Qiu
- Department of Obstetrics, Gynecology and Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, 20 Renmin South Road, Chengdu 610041, China
| | - Jun Jiang
- Department of Urology, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Qintong Li
- Department of Obstetrics, Gynecology and Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, 20 Renmin South Road, Chengdu 610041, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Huiyong Yin
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Junjie Peng
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Yichuan Xiao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
| | - Jun Qin
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
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Lin J, Bao X, Li XD. A tri-functional amino acid enables mapping of binding sites for posttranslational-modification-mediated protein-protein interactions. Mol Cell 2021; 81:2669-2681.e9. [PMID: 33894155 DOI: 10.1016/j.molcel.2021.04.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/01/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022]
Abstract
Posttranslational modification (PTM), through the recruitment of effector proteins (i.e., "readers") that signal downstream events, plays key roles in regulating a variety of cellular processes. To understand how a PTM is recognized, it is necessary to find its readers and, importantly, the location of the binding pockets responsible for PTM recognition. Although various methods have been developed to identify PTM readers, it remains a challenge to directly map the PTM-binding regions, especially for intrinsically disordered domains. Here, we demonstrate a photo-crosslinkable, clickable, and cleavable tri-functional amino acid, ADdis-Cys, that when coupled with mass spectrometry (ADdis-Cys-MS) can not only identify PTM readers from complex proteomes but also simultaneously map their PTM-recognition modules. Using ADdis-Cys-MS, we successfully identify the binding sites of several reader-PTM interactions, among which we discover human C1QBP as a histone chaperone. This robust method should find wide applications in examining other histone or non-histone PTM-mediated protein-protein interactions.
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Abstract
Zinc finger myeloid, nervy, and deformed epidermal autoregulatory factor 1-type containing 8 (Zinc finger MYND-type containing 8, ZMYND8) is a transcription factor, a histone H3-interacting protein, and a putative chromatin reader/effector that plays an essential role in regulating transcription during normal cellular growth. Mutations and altered expression of ZMYND8 are associated with the development and progression of cancer. Increased expression of ZMYND8 is linked to breast, prostate, colorectal, and cervical cancers. It exerts pro-oncogenic effects in breast and prostate cancers, and it promotes angiogenesis in zebrafish, as well as in breast and prostate cancers. In contrast, downregulation of ZMYND8 is also reported in breast, prostate, and nasopharyngeal cancers. ZMYND8 acts as a tumor suppressor in breast and prostate cancers, and it inhibits tumor growth by promoting differentiation; inhibiting proliferation, cell-cycle progression, invasiveness, and metastasis; and maintaining the epithelial phenotype in various types of cancers. These data together suggest that ZMYND8 is important in tumorigenesis; however, the existing data are contradictory. More studies are necessary to clarify the exact role of ZMYND8 in tumorigenesis. In the future, regulation of expression/activity of ZMYND8 and/or its binding partners may become useful in treating cancer.
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48
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Taylor BC, Young NL. Combinations of histone post-translational modifications. Biochem J 2021; 478:511-32. [DOI: 10.1042/bcj20200170] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 01/13/2021] [Accepted: 01/18/2021] [Indexed: 12/20/2022]
Abstract
Histones are essential proteins that package the eukaryotic genome into its physiological state of nucleosomes, chromatin, and chromosomes. Post-translational modifications (PTMs) of histones are crucial to both the dynamic and persistent regulation of the genome. Histone PTMs store and convey complex signals about the state of the genome. This is often achieved by multiple variable PTM sites, occupied or unoccupied, on the same histone molecule or nucleosome functioning in concert. These mechanisms are supported by the structures of ‘readers’ that transduce the signal from the presence or absence of PTMs in specific cellular contexts. We provide background on PTMs and their complexes, review the known combinatorial function of PTMs, and assess the value and limitations of common approaches to measure combinatorial PTMs. This review serves as both a reference and a path forward to investigate combinatorial PTM functions, discover new synergies, and gather additional evidence supporting that combinations of histone PTMs are the central currency of chromatin-mediated regulation of the genome.
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Funamoto M, Sunagawa Y, Katanasaka Y, Shimizu K, Miyazaki Y, Sari N, Shimizu S, Mori K, Wada H, Hasegawa K, Morimoto T. Histone Acetylation Domains Are Differentially Induced during Development of Heart Failure in Dahl Salt-Sensitive Rats. Int J Mol Sci 2021; 22:1771. [PMID: 33578969 PMCID: PMC7916721 DOI: 10.3390/ijms22041771] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/06/2021] [Accepted: 02/07/2021] [Indexed: 12/21/2022] Open
Abstract
Histone acetylation by epigenetic regulators has been shown to activate the transcription of hypertrophic response genes, which subsequently leads to the development and progression of heart failure. However, nothing is known about the acetylation of the histone tail and globular domains in left ventricular hypertrophy or in heart failure. The acetylation of H3K9 on the promoter of the hypertrophic response gene was significantly increased in the left ventricular hypertrophy stage, whereas the acetylation of H3K122 did not increase in the left ventricular hypertrophy stage but did significantly increase in the heart failure stage. Interestingly, the interaction between the chromatin remodeling factor BRG1 and p300 was significantly increased in the heart failure stage, but not in the left ventricular hypertrophy stage. This study demonstrates that stage-specific acetylation of the histone tail and globular domains occurs during the development and progression of heart failure, providing novel insights into the epigenetic regulatory mechanism governing transcriptional activity in these processes.
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Affiliation(s)
- Masafumi Funamoto
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
| | - Yoichi Sunagawa
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
- Shizuoka General Hospital, 4-27-1 Kitaando, Aoi-ku, Shizuoka 420-8527, Japan;
| | - Yasufumi Katanasaka
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
- Shizuoka General Hospital, 4-27-1 Kitaando, Aoi-ku, Shizuoka 420-8527, Japan;
| | - Kana Shimizu
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
| | - Yusuke Miyazaki
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
- Shizuoka General Hospital, 4-27-1 Kitaando, Aoi-ku, Shizuoka 420-8527, Japan;
| | - Nurmila Sari
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
| | - Satoshi Shimizu
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
| | - Kiyoshi Mori
- Shizuoka General Hospital, 4-27-1 Kitaando, Aoi-ku, Shizuoka 420-8527, Japan;
| | - Hiromichi Wada
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
| | - Koji Hasegawa
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
| | - Tatsuya Morimoto
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
- Shizuoka General Hospital, 4-27-1 Kitaando, Aoi-ku, Shizuoka 420-8527, Japan;
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Abstract
NUT carcinoma (NC) is an extremely aggressive squamous cancer with no effective therapy. NC is driven, most commonly, by the BRD4-NUT fusion oncoprotein. BRD4-NUT combines the chromatin-binding bromo- and extraterminal domain-containing (BET) protein, BRD4, with an unstructured, poorly understood protein, NUT, which recruits and activates the histone acetyltransferase p300. Recruitment of p300 to chromatin by BRD4 is believed to lead to the formation of hyperacetylated nuclear foci, as seen by immunofluorescence. BRD4-NUT nuclear foci correspond with massive contiguous regions of chromatin co-enriched with BRD4-NUT, p300, and acetylated histones, termed "megadomains" (MD). Megadomains stretch for as long as 2 MB. Proteomics has defined a BRD4-NUT chromatin complex in which members that associate with BRD4 also exist as rare NUT-fusion partners. This suggests that the common pathogenic denominator is the presence of both BRD4 and NUT, and that the function of BRD4-NUT may mimic that of wild-type BRD4. If so, then MDs may function as massive super-enhancers, activating transcription in a BET-dependent manner. Common targets of MDs across multiple NCs and tissues are three stem cell-related transcription factors frequently implicated in cancer: MYC, SOX2, and TP63. Recently, MDs were found to form a novel nuclear sub-compartment, called subcompartment M (subM), where MD-MD interactions occur both intra- and inter-chromosomally. Included in subM are MYC, SOX2, and TP63. Here we explore the possibility that if MDs are simply large super-enhancers, subM may exist in other cell systems, with broad implications for how 3D organization of the genome may function in gene regulation and maintenance of cell identity. Finally, we discuss how our knowledge of BRD4-NUT function has been leveraged for the therapeutic development of first-in-class BET inhibitors and other targeted strategies.
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