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Chen X, Huang MF, Fan DM, He YH, Zhang WJ, Ding JC, Peng BL, Pan X, Liu Y, Du J, Li Y, Liu ZY, Xie BL, Kuang ZJ, Yi J, Liu W. CARM1 hypermethylates the NuRD chromatin remodeling complex to promote cell cycle gene expression and breast cancer development. Nucleic Acids Res 2024; 52:6811-6829. [PMID: 38676947 PMCID: PMC11229315 DOI: 10.1093/nar/gkae329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/25/2024] [Accepted: 04/15/2024] [Indexed: 04/29/2024] Open
Abstract
Protein arginine methyltransferase CARM1 has been shown to methylate a large number of non-histone proteins, and play important roles in gene transcriptional activation, cell cycle progress, and tumorigenesis. However, the critical substrates through which CARM1 exerts its functions remain to be fully characterized. Here, we reported that CARM1 directly interacts with the GATAD2A/2B subunit in the nucleosome remodeling and deacetylase (NuRD) complex, expanding the activities of NuRD to include protein arginine methylation. CARM1 and NuRD bind and activate a large cohort of genes with implications in cell cycle control to facilitate the G1 to S phase transition. This gene activation process requires CARM1 to hypermethylate GATAD2A/2B at a cluster of arginines, which is critical for the recruitment of the NuRD complex. The clinical significance of this gene activation mechanism is underscored by the high expression of CARM1 and NuRD in breast cancers, and the fact that knockdown CARM1 and NuRD inhibits cancer cell growth in vitro and tumorigenesis in vivo. Targeting CARM1-mediated GATAD2A/2B methylation with CARM1 specific inhibitors potently inhibit breast cancer cell growth in vitro and tumorigenesis in vivo. These findings reveal a gene activation program that requires arginine methylation established by CARM1 on a key chromatin remodeler, and targeting such methylation might represent a promising therapeutic avenue in the clinic.
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Affiliation(s)
- Xue Chen
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Ming-feng Huang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Da-meng Fan
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Yao-hui He
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Wen-juan Zhang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, No. 23, Qingnian Road, Ganzhou, Jiangxi 341000, China
| | - Jian-cheng Ding
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Bing-ling Peng
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Xu Pan
- Xiamen University-Amogene Joint R&D Center for Genetic Diagnostics, School of Pharmaceutical Sciences, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Ya Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Jun Du
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Ying Li
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Zhi-ying Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Bing-lan Xie
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Zhi-jian Kuang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Jia Yi
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Wen Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
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Asmamaw MD, He A, Zhang LR, Liu HM, Gao Y. Histone deacetylase complexes: Structure, regulation and function. Biochim Biophys Acta Rev Cancer 2024; 1879:189150. [PMID: 38971208 DOI: 10.1016/j.bbcan.2024.189150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 06/07/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
Histone deacetylases (HDACs) are key epigenetic regulators, and transcriptional complexes with deacetylase function are among the epigenetic corepressor complexes in the nucleus that target the epigenome. HDAC-bearing corepressor complexes such as the Sin3 complex, NuRD complex, CoREST complex, and SMRT/NCoR complex are common in biological systems. These complexes activate the otherwise inactive HDACs in a solitary state. HDAC complexes play vital roles in the regulation of key biological processes such as transcription, replication, and DNA repair. Moreover, deregulated HDAC complex function is implicated in human diseases including cancer. Therapeutic strategies targeting HDAC complexes are being sought actively. Thus, illustration of the nature and composition of HDAC complexes is vital to understanding the molecular basis of their functions under physiologic and pathologic conditions, and for designing targeted therapies. This review presents key aspects of large multiprotein HDAC-bearing complexes including their structure, function, regulatory mechanisms, implication in disease development, and role in therapeutics.
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Affiliation(s)
- Moges Dessale Asmamaw
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory for Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Ang He
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Li-Rong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory for Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan Province 450001, China.
| | - Hong-Min Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China.
| | - Ya Gao
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China.
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3
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Liu Z, Ajit K, Wu Y, Zhu WG, Gullerova M. The GATAD2B-NuRD complex drives DNA:RNA hybrid-dependent chromatin boundary formation upon DNA damage. EMBO J 2024; 43:2453-2485. [PMID: 38719994 PMCID: PMC11183058 DOI: 10.1038/s44318-024-00111-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/19/2024] Open
Abstract
Double-strand breaks (DSBs) are the most lethal form of DNA damage. Transcriptional activity at DSBs, as well as transcriptional repression around DSBs, are both required for efficient DNA repair. The chromatin landscape defines and coordinates these two opposing events. However, how the open and condensed chromatin architecture is regulated remains unclear. Here, we show that the GATAD2B-NuRD complex associates with DSBs in a transcription- and DNA:RNA hybrid-dependent manner, to promote histone deacetylation and chromatin condensation. This activity establishes a spatio-temporal boundary between open and closed chromatin, which is necessary for the correct termination of DNA end resection. The lack of the GATAD2B-NuRD complex leads to chromatin hyperrelaxation and extended DNA end resection, resulting in homologous recombination (HR) repair failure. Our results suggest that the GATAD2B-NuRD complex is a key coordinator of the dynamic interplay between transcription and the chromatin landscape, underscoring its biological significance in the RNA-dependent DNA damage response.
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Affiliation(s)
- Zhichao Liu
- Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, United Kingdom
| | - Kamal Ajit
- Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, United Kingdom
| | - Yupei Wu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, 518055, Shenzhen, China
| | - Wei-Guo Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, 518055, Shenzhen, China
| | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, United Kingdom.
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Priyanka P, Gopalakrishnan AP, Nisar M, Shivamurthy PB, George M, John L, Sanjeev D, Yandigeri T, Thomas SD, Rafi A, Dagamajalu S, Velikkakath AKG, Abhinand CS, Kanekar S, Prasad TSK, Balaya RDA, Raju R. A global phosphosite-correlated network map of Thousand And One Kinase 1 (TAOK1). Int J Biochem Cell Biol 2024; 170:106558. [PMID: 38479581 DOI: 10.1016/j.biocel.2024.106558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 02/19/2024] [Accepted: 03/09/2024] [Indexed: 03/25/2024]
Abstract
Thousand and one amino acid kinase 1 (TAOK1) is a sterile 20 family Serine/Threonine kinase linked to microtubule dynamics, checkpoint signaling, DNA damage response, and neurological functions. Molecular-level alterations of TAOK1 have been associated with neurodevelopment disorders and cancers. Despite their known involvement in physiological and pathophysiological processes, and as a core member of the hippo signaling pathway, the phosphoregulatory network of TAOK1 has not been visualized. Aimed to explore this network, we first analyzed the predominantly detected and differentially regulated TAOK1 phosphosites in global phosphoproteome datasets across diverse experimental conditions. Based on 709 qualitative and 210 quantitative differential cellular phosphoproteome datasets that were systematically assembled, we identified that phosphorylation at Ser421, Ser9, Ser965, and Ser445 predominantly represented TAOK1 in almost 75% of these datasets. Surprisingly, the functional role of all these phosphosites in TAOK1 remains unexplored. Hence, we employed a robust strategy to extract the phosphosites in proteins that significantly correlated in expression with predominant TAOK1 phosphosites. This led to the first categorization of the phosphosites including those in the currently known and predicted interactors, kinases, and substrates, that positively/negatively correlated with the expression status of each predominant TAOK1 phosphosites. Subsequently, we also analyzed the phosphosites in core proteins of the hippo signaling pathway. Based on the TAOK1 phosphoregulatory network analysis, we inferred the potential role of the predominant TAOK1 phosphosites. Especially, we propose pSer9 as an autophosphorylation and TAOK1 kinase activity-associated phosphosite and pS421, the most frequently detected phosphosite in TAOK1, as a significant regulatory phosphosite involved in the maintenance of genome integrity. Considering that the impact of all phosphosites that predominantly represent each kinase is essential for the efficient interpretation of global phosphoproteome datasets, we believe that the approach undertaken in this study is suitable to be extended to other kinases for accelerated research.
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Affiliation(s)
- Pahal Priyanka
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Athira Perunelly Gopalakrishnan
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Mahammad Nisar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | | | - Mejo George
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Levin John
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Diya Sanjeev
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Tanuja Yandigeri
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Sonet D Thomas
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Ahmad Rafi
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Anoop Kumar G Velikkakath
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Chandran S Abhinand
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Saptami Kanekar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | | | | | - Rajesh Raju
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
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Abad C, Robayo MC, Muñiz-Moreno MDM, Bernardi MT, Otero MG, Kosanovic C, Griswold AJ, Pierson TM, Walz K, Young JI. Gatad2b, associated with the neurodevelopmental syndrome GAND, plays a critical role in neurodevelopment and cortical patterning. Transl Psychiatry 2024; 14:33. [PMID: 38238293 PMCID: PMC10796954 DOI: 10.1038/s41398-023-02678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/06/2023] [Accepted: 11/23/2023] [Indexed: 01/22/2024] Open
Abstract
GATAD2B (GATA zinc finger domain containing 2B) variants are associated with the neurodevelopmental syndrome GAND, characterized by intellectual disability (ID), infantile hypotonia, apraxia of speech, epilepsy, macrocephaly and distinct facial features. GATAD2B encodes for a subunit of the Nucleosome Remodeling and Histone Deacetylase (NuRD) complex. NuRD controls transcriptional programs critical for proper neurodevelopment by coupling histone deacetylase with ATP-dependent chromatin remodeling activity. To study mechanisms of pathogenesis for GAND, we characterized a mouse model harboring an inactivating mutation in Gatad2b. Homozygous Gatad2b mutants die perinatally, while haploinsufficient Gatad2b mice exhibit behavioral abnormalities resembling the clinical features of GAND patients. We also observed abnormal cortical patterning, and cellular proportions and cell-specific alterations in the developmental transcriptome in these mice. scRNAseq of embryonic cortex indicated misexpression of genes key for corticogenesis and associated with neurodevelopmental syndromes such as Bcl11b, Nfia and H3f3b and Sox5. These data suggest a crucial role for Gatad2b in brain development.
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Affiliation(s)
- Clemer Abad
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Maria C Robayo
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Maria Del Mar Muñiz-Moreno
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Maria T Bernardi
- IQUIBICEN - CONICET, School of Exact and Natural Sciences - University of Buenos Aires, Buenos Aires, Argentina
| | - Maria G Otero
- The Board of Governors Regenerative Medicine Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Christina Kosanovic
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Tyler Mark Pierson
- The Board of Governors Regenerative Medicine Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
- Guerin Children's, Departments of Pediatrics, Cedars Sinai Medical Center, Los Angeles, CA, USA
- Department of Neurology, Cedars Sinai Medical Center, Los Angeles, CA, USA
- The Center for the Undiagnosed Patient, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Katherina Walz
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- IQUIBICEN - CONICET, School of Exact and Natural Sciences - University of Buenos Aires, Buenos Aires, Argentina
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Juan I Young
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA.
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA.
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6
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Sun Z, Cernilogar FM, Horvatic H, Yeroslaviz A, Abdullah Z, Schotta G, Hornung V. β1 integrin signaling governs necroptosis via the chromatin-remodeling factor CHD4. Cell Rep 2023; 42:113322. [PMID: 37883227 DOI: 10.1016/j.celrep.2023.113322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/29/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
Fibrosis, characterized by sustained activation of myofibroblasts and excessive extracellular matrix (ECM) deposition, is known to be associated with chronic inflammation. Receptor-interacting protein kinase 3 (RIPK3), the central kinase of necroptosis signaling, is upregulated in fibrosis and contributes to tumor necrosis factor (TNF)-mediated inflammation. In bile-duct-ligation-induced liver fibrosis, we found that myofibroblasts are the major cell type expressing RIPK3. Genetic ablation of β1 integrin, the major profibrotic ECM receptor in fibroblasts, not only abolished ECM fibrillogenesis but also blunted RIPK3 expression via a mechanism mediated by the chromatin-remodeling factor chromodomain helicase DNA-binding protein 4 (CHD4). While the function of CHD4 has been conventionally linked to the nucleosome-remodeling deacetylase (NuRD) and CHD4-ADNP-HP1(ChAHP) complexes, we found that CHD4 potently repressed a set of genes, including Ripk3, with high locus specificity but independent of either the NuRD or the ChAHP complex. Thus, our data uncover that β1 integrin intrinsically links fibrotic signaling to RIPK3-driven inflammation via a novel mode of action of CHD4.
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Affiliation(s)
- Zhiqi Sun
- Gene Center and Department of Biochemistry, Ludwig Maximilian University of Munich, Munich, Germany; Research Group Molecular Mechanisms of Inflammation, Max-Planck Institute of Biochemistry, Martinsried, Germany.
| | - Filippo M Cernilogar
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig Maximilian University of Munich, Munich, Germany
| | - Helena Horvatic
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Bonn, Germany
| | - Assa Yeroslaviz
- Computational Biology Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Zeinab Abdullah
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Bonn, Germany
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig Maximilian University of Munich, Munich, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig Maximilian University of Munich, Munich, Germany; Research Group Molecular Mechanisms of Inflammation, Max-Planck Institute of Biochemistry, Martinsried, Germany.
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Gederaas OA, Sharma A, Mbarak S, Sporsheim B, Høgset A, Bogoeva V, Slupphaug G, Hagen L. Proteomic analysis reveals mechanisms underlying increased efficacy of bleomycin by photochemical internalization in bladder cancer cells. Mol Omics 2023; 19:585-597. [PMID: 37345535 DOI: 10.1039/d2mo00337f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
Photochemical internalization (PCI) is a promising new technology for site-specific drug delivery, developed from photodynamic therapy (PDT). In PCI, light-induced activation of a photosensitizer trapped inside endosomes together with e.g. chemotherapeutics, nucleic acids or immunotoxins, allows cytosolic delivery and enhanced local therapeutic effect. Here we have evaluated the photosensitizer meso-tetraphenyl chlorine disulphonate (TPCS2a/fimaporfin) in a proteome analysis of AY-27 rat bladder cancer cells in combination with the chemotherapeutic drug bleomycin (BML). We find that BLMPCI attenuates oxidative stress responses induced by BLM alone, while concomitantly increasing transcriptional repression and DNA damage responses. BLMPCI also mediates downregulation of bleomycin hydrolase (Blmh), which is responsible for cellular degradation of BLM, as well as several factors known to be involved in fibrotic responses. PCI-mediated delivery might thus allow reduced dosage of BLM and alleviate unwanted side effects from treatment, including pulmonary fibrosis.
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Affiliation(s)
- Odrun A Gederaas
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, N-7489 Trondheim, Norway
- Department of Natural Sciences, UiA, University of Agder, N-4630, Kristiansand, Norway.
| | - Animesh Sharma
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, N-7489 Trondheim, Norway
- Proteomics and Modomics Experimental Core, PROMEC, at NTNU and the Central Norway Regional Health Authority, Trondheim, Norway
| | - Saide Mbarak
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, N-7489 Trondheim, Norway
| | - Bjørnar Sporsheim
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, N-7489 Trondheim, Norway
- CMIC Cellular & Molecular Imaging Core Facility, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Trondheim, Norway
| | - Anders Høgset
- PCI Biotech AS, Ullernchaussen 64, 0379 Oslo, Norway
| | - Vanya Bogoeva
- Department of Molecular Biology and Cell Cycle, Institute of Molecular Biology "Roumen Tsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, N-7489 Trondheim, Norway
- Proteomics and Modomics Experimental Core, PROMEC, at NTNU and the Central Norway Regional Health Authority, Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, N-7489 Trondheim, Norway
- Proteomics and Modomics Experimental Core, PROMEC, at NTNU and the Central Norway Regional Health Authority, Trondheim, Norway
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8
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Werren EA, Guxholli A, Jones N, Wagner M, Hannibal I, Granadillo JL, Tyndall AV, Moccia A, Kuehl R, Levandoski KM, Day-Salvatore DL, Wheeler M, Chong JX, Bamshad MJ, Innes AM, Pierson TM, Mackay JP, Bielas SL, Martin DM. De novo variants in GATAD2A in individuals with a neurodevelopmental disorder: GATAD2A-related neurodevelopmental disorder. HGG ADVANCES 2023; 4:100198. [PMID: 37181331 PMCID: PMC10172836 DOI: 10.1016/j.xhgg.2023.100198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/07/2023] [Indexed: 05/16/2023] Open
Abstract
GATA zinc finger domain containing 2A (GATAD2A) is a subunit of the nucleosome remodeling and deacetylase (NuRD) complex. NuRD is known to regulate gene expression during neural development and other processes. The NuRD complex modulates chromatin status through histone deacetylation and ATP-dependent chromatin remodeling activities. Several neurodevelopmental disorders (NDDs) have been previously linked to variants in other components of NuRD's chromatin remodeling subcomplex (NuRDopathies). We identified five individuals with features of an NDD that possessed de novo autosomal dominant variants in GATAD2A. Core features in affected individuals include global developmental delay, structural brain defects, and craniofacial dysmorphology. These GATAD2A variants are predicted to affect protein dosage and/or interactions with other NuRD chromatin remodeling subunits. We provide evidence that a GATAD2A missense variant disrupts interactions of GATAD2A with CHD3, CHD4, and CHD5. Our findings expand the list of NuRDopathies and provide evidence that GATAD2A variants are the genetic basis of a previously uncharacterized developmental disorder.
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Affiliation(s)
- Elizabeth A. Werren
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alba Guxholli
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Natasha Jones
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Matias Wagner
- Institute of Human Genetics, Technical University of Munich, 80333 Munich, Germany
| | - Iris Hannibal
- Institute of Human Genetics, Technical University of Munich, 80333 Munich, Germany
| | - Jorge L. Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amanda V. Tyndall
- Department of Medical Genetics, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Amanda Moccia
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ryan Kuehl
- Saint Peter’s University Hospital, New Brunswick, NJ 08901, USA
| | | | | | - Marsha Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - University of Washington Center for Mendelian Genomics
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
- Institute of Human Genetics, Technical University of Munich, 80333 Munich, Germany
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Medical Genetics, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Saint Peter’s University Hospital, New Brunswick, NJ 08901, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute, Seattle, WA 98195, USA
- Department of Pediatrics, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Division of Pediatric Neurology, Department of Pediatrics, Guerin Children’s, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Center for the Undiagnosed Patient, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jessica X. Chong
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute, Seattle, WA 98195, USA
| | - Michael J. Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute, Seattle, WA 98195, USA
| | - A. Micheil Innes
- Department of Medical Genetics, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Pediatrics, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Tyler Mark Pierson
- Division of Pediatric Neurology, Department of Pediatrics, Guerin Children’s, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Center for the Undiagnosed Patient, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Joel P. Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Stephanie L. Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Donna M. Martin
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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9
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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] [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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10
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Sachdev S, Dmello C, Sonabend AM. Radiosensitization of IDH-Mutated Gliomas through ZMYND8 - a Pathway to Improved Outcomes. Clin Cancer Res 2023; 29:1648-1650. [PMID: 36826993 PMCID: PMC10159893 DOI: 10.1158/1078-0432.ccr-23-0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023]
Abstract
Isocitrate dehydrogenase 1-mutant (IDH1m) gliomas are recalcitrant tumors for which radiotherapy remains a standard treatment. A recent study identified ZMYND8 as a key mediator of radioresistance for IDH1m gliomas, and pharmacologic targeting of this pathway may heighten radiotherapy-induced tumor response, providing a prospect of improved clinical outcomes. See related article by Carney et al., p. 1763.
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Affiliation(s)
- Sean Sachdev
- Department of Radiation Oncology, Northwestern Lou and Jean Malnati Brain Tumor Institute, Northwestern University Robert H. Lurie Comprehensive Cancer Center, 676 N. St Clair Street, Suite 1820, Chicago, IL, 60611, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL
| | - Crismita Dmello
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago IL
| | - Adam M. Sonabend
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago IL
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11
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Ma J, Zhou Y, Pan P, Yu H, Wang Z, Li LL, Wang B, Yan Y, Pan Y, Ye Q, Liu T, Feng X, Xu S, Wang K, Wang X, Jian Y, Ma B, Fan Y, Gao Y, Huang H, Li L. TRABID overexpression enables synthetic lethality to PARP inhibitor via prolonging 53BP1 retention at double-strand breaks. Nat Commun 2023; 14:1810. [PMID: 37002234 PMCID: PMC10066190 DOI: 10.1038/s41467-023-37499-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/17/2023] [Indexed: 04/03/2023] Open
Abstract
53BP1 promotes nonhomologous end joining (NHEJ) over homologous recombination (HR) repair by mediating inactivation of DNA end resection. Ubiquitination plays an important role in regulating dissociation of 53BP1 from DNA double-strand breaks (DSBs). However, how this process is regulated remains poorly understood. Here, we demonstrate that TRABID deubiquitinase binds to 53BP1 at endogenous level and regulates 53BP1 retention at DSB sites. TRABID deubiquitinates K29-linked polyubiquitination of 53BP1 mediated by E3 ubiquitin ligase SPOP and prevents 53BP1 dissociation from DSBs, consequently inducing HR defects and chromosomal instability. Prostate cancer cells with TRABID overexpression exhibit a high sensitivity to poly (ADP-ribose) polymerase (PARP) inhibitors. Our work shows that TRABID facilitates NHEJ repair over HR during DNA repair by inducing prolonged 53BP1 retention at DSB sites, suggesting that TRABID overexpression may predict HR deficiency and the potential therapeutic use of PARP inhibitors in prostate cancer.
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Affiliation(s)
- Jian Ma
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA
| | - Yingke Zhou
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Penglin Pan
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Haixin Yu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zixi Wang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Lei Lily Li
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Bing Wang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Yuqian Yan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA
| | - Yunqian Pan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA
| | - Qi Ye
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Tianjie Liu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Xiaoyu Feng
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Shan Xu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Ke Wang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Xinyang Wang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Yanlin Jian
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Bohan Ma
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Yizeng Fan
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Yang Gao
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA.
- Mayo Clinic Cancer Center, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA.
- Department of Urology, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA.
| | - Lei Li
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China.
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12
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Oberdoerffer P, Miller KM. Histone H2A variants: Diversifying chromatin to ensure genome integrity. Semin Cell Dev Biol 2023; 135:59-72. [PMID: 35331626 PMCID: PMC9489817 DOI: 10.1016/j.semcdb.2022.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/12/2022]
Abstract
Histone variants represent chromatin components that diversify the structure and function of the genome. The variants of H2A, primarily H2A.X, H2A.Z and macroH2A, are well-established participants in DNA damage response (DDR) pathways, which function to protect the integrity of the genome. Through their deposition, post-translational modifications and unique protein interaction networks, these variants guard DNA from endogenous threats including replication stress and genome fragility as well as from DNA lesions inflicted by exogenous sources. A growing body of work is now providing a clearer picture on the involvement and mechanistic basis of H2A variant contribution to genome integrity. Beyond their well-documented role in gene regulation, we review here how histone H2A variants promote genome stability and how alterations in these pathways contribute to human diseases including cancer.
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Affiliation(s)
- Philipp Oberdoerffer
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA.
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.
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13
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Reid XJ, Low JKK, Mackay JP. A NuRD for all seasons. Trends Biochem Sci 2023; 48:11-25. [PMID: 35798615 DOI: 10.1016/j.tibs.2022.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 12/27/2022]
Abstract
The nucleosome-remodeling and deacetylase (NuRD) complex is an essential transcriptional regulator in all complex animals. All seven core subunits of the complex exist as multiple paralogs, raising the question of whether the complex might utilize paralog switching to achieve cell type-specific functions. We examine the evidence for this idea, making use of published quantitative proteomic data to dissect NuRD composition in 20 different tissues, as well as a large-scale CRISPR knockout screen carried out in >1000 human cancer cell lines. These data, together with recent reports, provide strong support for the idea that distinct permutations of the NuRD complex with tailored functions might regulate tissue-specific gene expression programs.
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Affiliation(s)
- Xavier J Reid
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.
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14
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Zhou CD, Pettersson A, Plym A, Tyekucheva S, Penney KL, Sesso HD, Kantoff PW, Mucci LA, Stopsack KH. Differences in Prostate Cancer Transcriptomes by Age at Diagnosis: Are Primary Tumors from Older Men Inherently Different? Cancer Prev Res (Phila) 2022; 15:815-825. [PMID: 36125434 PMCID: PMC9722523 DOI: 10.1158/1940-6207.capr-22-0212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/03/2022] [Accepted: 09/01/2022] [Indexed: 01/31/2023]
Abstract
Older age at diagnosis is consistently associated with worse clinical outcomes in prostate cancer. We sought to characterize gene expression profiles of prostate tumor tissue by age at diagnosis. We conducted a discovery analysis in The Cancer Genome Atlas prostate cancer dataset (n = 320; 29% of men >65 years at diagnosis), using linear regressions of age at diagnosis and mRNA expression and adjusting for TMPRSS2:ERG fusion status and race. This analysis identified 13 age-related candidate genes at FDR < 0.1, six of which were also found in an analysis additionally adjusted for Gleason score. We then validated the 13 age-related genes in a transcriptome study nested in the Health Professionals Follow-up Study and Physicians' Health Study (n = 374; 53% of men >65 years). Gene expression differences by age in the 13 candidate genes were directionally consistent, and age at diagnosis was weakly associated with the 13-gene score. However, the age-related genes were not consistently associated with risk of metastases and prostate cancer-specific death. Collectively, these findings argue against tumor genomic differences as a main explanation for age-related differences in prostate cancer prognosis. PREVENTION RELEVANCE Older age at diagnosis is consistently associated with worse clinical outcomes in prostate cancer. This study with independent discovery and validation sets and long-term follow-up suggests that prevention of lethal prostate cancer should focus on implementing appropriate screening, staging, and treatment among older men without expecting fundamentally different tumor biology.
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Affiliation(s)
- Charlie D. Zhou
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Andreas Pettersson
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Anna Plym
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden,Department of Urology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Svitlana Tyekucheva
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kathryn L. Penney
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Howard D. Sesso
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Division of Preventative Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Philip W. Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Convergent Therapeutics Inc., Cambridge, MA, USA
| | - Lorelei A. Mucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Konrad H. Stopsack
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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15
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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: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [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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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] [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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17
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De Novo ZMYND8 variants result in an autosomal dominant neurodevelopmental disorder with cardiac malformations. Genet Med 2022; 24:1952-1966. [PMID: 35916866 DOI: 10.1016/j.gim.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 12/25/2022] Open
Abstract
PURPOSE ZMYND8 encodes a multidomain protein that serves as a central interactive hub for coordinating critical roles in transcription regulation, chromatin remodeling, regulation of super-enhancers, DNA damage response and tumor suppression. We delineate a novel neurocognitive disorder caused by variants in the ZMYND8 gene. METHODS An international collaboration, exome sequencing, molecular modeling, yeast two-hybrid assays, analysis of available transcriptomic data and a knockdown Drosophila model were used to characterize the ZMYND8 variants. RESULTS ZMYND8 variants were identified in 11 unrelated individuals; 10 occurred de novo and one suspected de novo; 2 were truncating, 9 were missense, of which one was recurrent. The disorder is characterized by intellectual disability with variable cardiovascular, ophthalmologic and minor skeletal anomalies. Missense variants in the PWWP domain of ZMYND8 abolish the interaction with Drebrin and missense variants in the MYND domain disrupt the interaction with GATAD2A. ZMYND8 is broadly expressed across cell types in all brain regions and shows highest expression in the early stages of brain development. Neuronal knockdown of the DrosophilaZMYND8 ortholog results in decreased habituation learning, consistent with a role in cognitive function. CONCLUSION We present genomic and functional evidence for disruption of ZMYND8 as a novel etiology of syndromic intellectual disability.
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Price JD, Lindtner S, Ypsilanti A, Binyameen F, Johnson JR, Newton BW, Krogan NJ, Rubenstein JLR. DLX1 and the NuRD complex cooperate in enhancer decommissioning and transcriptional repression. Development 2022; 149:dev199508. [PMID: 35695185 PMCID: PMC9245191 DOI: 10.1242/dev.199508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 03/17/2022] [Indexed: 09/27/2023]
Abstract
In the developing subpallium, the fate decision between neurons and glia is driven by expression of Dlx1/2 or Olig1/2, respectively, two sets of transcription factors with a mutually repressive relationship. The mechanism by which Dlx1/2 repress progenitor and oligodendrocyte fate, while promoting transcription of genes needed for differentiation, is not fully understood. We identified a motif within DLX1 that binds RBBP4, a NuRD complex subunit. ChIP-seq studies of genomic occupancy of DLX1 and six different members of the NuRD complex show that DLX1 and NuRD colocalize to putative regulatory elements enriched near other transcription factor genes. Loss of Dlx1/2 leads to dysregulation of genome accessibility at putative regulatory elements near genes repressed by Dlx1/2, including Olig2. Consequently, heterozygosity of Dlx1/2 and Rbbp4 leads to an increase in the production of OLIG2+ cells. These findings highlight the importance of the interplay between transcription factors and chromatin remodelers in regulating cell-fate decisions.
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Affiliation(s)
- James D. Price
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - Susan Lindtner
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Athena Ypsilanti
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Fadya Binyameen
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey R. Johnson
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institute of Data Science and Biosciences, J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Billy W. Newton
- Gladstone Institute of Data Science and Biosciences, J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Nevan J. Krogan
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institute of Data Science and Biosciences, J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John L. R. Rubenstein
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
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19
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Vitkevičienė A, Skliutė G, Žučenka A, Borutinskaitė V, Navakauskienė R. Potential Prognostic Markers for Relapsed/Refractory vs. Responsive Acute Myeloid Leukemia. Cancers (Basel) 2022; 14:cancers14112752. [PMID: 35681732 PMCID: PMC9179343 DOI: 10.3390/cancers14112752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary Acute myeloid leukemia (AML) is the most common blood cancer in the elderly, which progresses rapidly and is often fatal. The prognosis for AML remains poor in most older patients: only about 15% of patients over 60 years of age can recover. Our aim is to determine new potential AML clinical treatment prognosis markers. We analyzed certain genes, proteins and the epigenome profile in therapy-resistant and responsive AML patients at diagnosis stage and after clinical treatment. We determined that MYC, WT1, IDH1, CDKN1A, HDAC2, TET1, KAT6A and GATAD2A gene expression changes might characterize refractory AML. Therefore, these genes could have an impact for AML prognosis. Abstract Acute myeloid leukemia (AML) is a heterogeneous disease. A significant proportion of AML patients is refractory to clinical treatment or relapses. Our aim is to determine new potential AML clinical treatment prognosis markers. We investigated various cell fate and epigenetic regulation important gene level differences between refractory and responsive AML patient groups at diagnosis stage and after clinical treatment using RT-qPCR. We demonstrated that oncogenic MYC and WT1 and metabolic IDH1 gene expression was significantly higher and cell cycle inhibitor CDKN1A (p21) gene expression was significantly lower in refractory patients’ bone marrow cells compared to treatment responsive patients both at diagnosis and after clinical treatment. Moreover, we determined that, compared to clinical treatment responsive patients, refractory patients possess a significantly higher gene expression of histone deacetylase 2 (HDAC2) and epigenetic DNA modulator TET1 and a significantly lower gene expression of lysine acetyltransferase 6A (KAT6A) and nucleosome remodeling and deacetylase (NuRD) complex component GATAD2A. We suggest that MYC, WT1, IDH1, CDKN1A, HDAC2, TET1, KAT6A and GATAD2A gene expression changes might characterize refractory AML. Thus, they might be useful for AML prognosis. Additionally, we suggest that epigenetic modulation might be beneficial in combination with standard treatment.
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Affiliation(s)
- Aida Vitkevičienė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-01257 Vilnius, Lithuania; (A.V.); (G.S.); (V.B.)
| | - Giedrė Skliutė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-01257 Vilnius, Lithuania; (A.V.); (G.S.); (V.B.)
| | - Andrius Žučenka
- Hematology, Oncology and Transfusion Medicine Centre, Vilnius University Hospital Santaros Klinikos, Santariskiu str. 2, LT-08661 Vilnius, Lithuania;
| | - Veronika Borutinskaitė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-01257 Vilnius, Lithuania; (A.V.); (G.S.); (V.B.)
| | - Rūta Navakauskienė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-01257 Vilnius, Lithuania; (A.V.); (G.S.); (V.B.)
- Correspondence: ; Tel.: +370-5-223-4409
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20
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Sanchez A, Buck-Koehntop BA, Miller KM. Joining the PARty: PARP Regulation of KDM5A during DNA Repair (and Transcription?). Bioessays 2022; 44:e2200015. [PMID: 35532219 DOI: 10.1002/bies.202200015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 11/05/2022]
Abstract
The lysine demethylase KDM5A collaborates with PARP1 and the histone variant macroH2A1.2 to modulate chromatin to promote DNA repair. Indeed, KDM5A engages poly(ADP-ribose) (PAR) chains at damage sites through a previously uncharacterized coiled-coil domain, a novel binding mode for PAR interactions. While KDM5A is a well-known transcriptional regulator, its function in DNA repair is only now emerging. Here we review the molecular mechanisms that regulate this PARP1-macroH2A1.2-KDM5A axis in DNA damage and consider the potential involvement of this pathway in transcription regulation and cancer. Using KDM5A as an example, we discuss how multifunctional chromatin proteins transition between several DNA-based processes, which must be coordinated to protect the integrity of the genome and epigenome. The dysregulation of chromatin and loss of genome integrity that is prevalent in human diseases including cancer may be related and could provide opportunities to target multitasking proteins with these pathways as therapeutic strategies.
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Affiliation(s)
- Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, The University of Texas at Austin, Austin, Texas, USA
| | | | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, The University of Texas at Austin, Austin, Texas, USA.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, Texas, USA
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21
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Oliviero G, Kovalchuk S, Rogowska-Wrzesinska A, Schwämmle V, Jensen ON. Distinct and diverse chromatin-proteomes of ageing mouse organs reveal protein signatures that correlate with physiological functions. eLife 2022; 11:73524. [PMID: 35259090 PMCID: PMC8933006 DOI: 10.7554/elife.73524] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Temporal molecular changes in ageing mammalian organs are of relevance to disease aetiology because many age-related diseases are linked to changes in the transcriptional and epigenetic machinery that regulate gene expression. We performed quantitative proteome analysis of chromatin-enriched protein extracts to investigate the dynamics of the chromatin proteomes of the mouse brain, heart, lung, kidney, liver, and spleen at 3, 5, 10, and 15 months of age. Each organ exhibited a distinct chromatin proteome and sets of unique proteins. The brain and spleen chromatin proteomes were the most extensive, diverse, and heterogenous among the six organs. The spleen chromatin proteome appeared static during the lifespan, presenting a young phenotype that reflects the permanent alertness state and important role of this organ in physiological defence and immunity. We identified a total of 5928 proteins, including 2472 nuclear or chromatin-associated proteins across the six mouse organs. Up to 3125 proteins were quantified in each organ, demonstrating distinct and organ-specific temporal protein expression timelines and regulation at the post-translational level. Bioinformatics meta-analysis of these chromatin proteomes revealed distinct physiological and ageing-related features for each organ. Our results demonstrate the efficiency of organelle-specific proteomics for in vivo studies of a model organism and consolidate the hypothesis that chromatin-associated proteins are involved in distinct and specific physiological functions in ageing organs.
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Affiliation(s)
- Giorgio Oliviero
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Sergey Kovalchuk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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22
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Karl LA, Peritore M, Galanti L, Pfander B. DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling. Front Genet 2022; 12:821543. [PMID: 35096025 PMCID: PMC8790285 DOI: 10.3389/fgene.2021.821543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
DNA double strand breaks (DSBs) are repaired in eukaryotes by one of several cellular mechanisms. The decision-making process controlling DSB repair takes place at the step of DNA end resection, the nucleolytic processing of DNA ends, which generates single-stranded DNA overhangs. Dependent on the length of the overhang, a corresponding DSB repair mechanism is engaged. Interestingly, nucleosomes-the fundamental unit of chromatin-influence the activity of resection nucleases and nucleosome remodelers have emerged as key regulators of DSB repair. Nucleosome remodelers share a common enzymatic mechanism, but for global genome organization specific remodelers have been shown to exert distinct activities. Specifically, different remodelers have been found to slide and evict, position or edit nucleosomes. It is an open question whether the same remodelers exert the same function also in the context of DSBs. Here, we will review recent advances in our understanding of nucleosome remodelers at DSBs: to what extent nucleosome sliding, eviction, positioning and editing can be observed at DSBs and how these activities affect the DSB repair decision.
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Affiliation(s)
- Leonhard Andreas Karl
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Martina Peritore
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorenzo Galanti
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Boris Pfander
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
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23
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Adhikari S, Guha D, Mohan C, Mukherjee S, Tyler JK, Das C. Reprogramming Carbohydrate Metabolism in Cancer and Its Role in Regulating the Tumor Microenvironment. Subcell Biochem 2022; 100:3-65. [PMID: 36301490 PMCID: PMC10760510 DOI: 10.1007/978-3-031-07634-3_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Altered metabolism has become an emerging feature of cancer cells impacting their proliferation and metastatic potential in myriad ways. Proliferating heterogeneous tumor cells are surrounded by other resident or infiltrating cells, along with extracellular matrix proteins, and other secretory factors constituting the tumor microenvironment. The diverse cell types of the tumor microenvironment exhibit different molecular signatures that are regulated at their genetic and epigenetic levels. The cancer cells elicit intricate crosstalks with these supporting cells, exchanging essential metabolites which support their anabolic processes and can promote their survival, proliferation, EMT, angiogenesis, metastasis and even therapeutic resistance. In this context, carbohydrate metabolism ensures constant energy supply being a central axis from which other metabolic and biosynthetic pathways including amino acid and lipid metabolism and pentose phosphate pathway are diverged. In contrast to normal cells, increased glycolytic flux is a distinguishing feature of the highly proliferative cancer cells, which supports them to adapt to a hypoxic environment and also protects them from oxidative stress. Such rewired metabolic properties are often a result of epigenetic alterations in the cancer cells, which are mediated by several factors including, DNA, histone and non-histone protein modifications and non-coding RNAs. Conversely, epigenetic landscapes of the cancer cells are also dictated by their diverse metabolomes. Altogether, this metabolic and epigenetic interplay has immense potential for the development of efficient anti-cancer therapeutic strategies. In this book chapter we emphasize upon the significance of reprogrammed carbohydrate metabolism in regulating the tumor microenvironment and cancer progression, with an aim to explore the different metabolic and epigenetic targets for better cancer treatment.
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Affiliation(s)
- Swagata Adhikari
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Deblina Guha
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Chitra Mohan
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shravanti Mukherjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.
- Homi Bhaba National Institute, Mumbai, India.
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24
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Zhang Q, Zhang Y, Zhang J, Zhang D, Li M, Yan H, Zhang H, Song L, Wang J, Hou Z, Yang Y, Zou X. p66α Suppresses Breast Cancer Cell Growth and Migration by Acting as Co-Activator of p53. Cells 2021; 10:3593. [PMID: 34944103 PMCID: PMC8700327 DOI: 10.3390/cells10123593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/03/2021] [Accepted: 12/16/2021] [Indexed: 01/31/2023] Open
Abstract
p66α is a GATA zinc finger domain-containing transcription factor that has been shown to be essential for gene silencing by participating in the NuRD complex. Several studies have suggested that p66α is a risk gene for a wide spectrum of diseases such as diabetes, schizophrenia, and breast cancer; however, its biological role has not been defined. Here, we report that p66α functions as a tumor suppressor to inhibit breast cancer cell growth and migration, evidenced by the fact that the depletion of p66α results in accelerated tumor growth and migration of breast cancer cells. Mechanistically, immunoprecipitation assays identify p66α as a p53-interacting protein that binds the DNA-binding domain of p53 molecule predominantly via its CR2 domain. Depletion of p66α in multiple breast cells results in decreased expression of p53 target genes, while over-expression of p66α results in increased expression of these target genes. Moreover, p66α promotes the transactivity of p53 by enhancing p53 binding at target promoters. Together, these findings demonstrate that p66α is a tumor suppressor by functioning as a co-activator of p53.
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Affiliation(s)
- Qun Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Yihong Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Jie Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Dan Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Mengying Li
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Han Yan
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Hui Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Liwei Song
- Shanghai Pulmonary Tumor Medical Center, Shanghai Chest Hospital, Shanghai 200025, China;
- Naruiboen Biomedical Technology Corporation Limited, Linyi 277700, China
| | - Jiamin Wang
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Zhaoyuan Hou
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Yunhai Yang
- Shanghai Pulmonary Tumor Medical Center, Shanghai Chest Hospital, Shanghai 200025, China;
| | - Xiuqun Zou
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
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Comprehensive Combined Proteomics and Genomics Analysis Identifies Prognostic Related Transcription Factors in Breast Cancer and Explores the Role of DMAP1 in Breast Cancer. J Pers Med 2021; 11:jpm11111068. [PMID: 34834420 PMCID: PMC8625386 DOI: 10.3390/jpm11111068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/17/2021] [Accepted: 10/20/2021] [Indexed: 11/17/2022] Open
Abstract
Transcription factors (TFs) are important for regulating gene transcription and are the hallmark of many cancers. The identification of breast cancer TFs will help in developing new diagnostic and individualized cancer treatment tools. In this study, we used quantitative proteomic analyses of nuclear proteins and massive transcriptome data to identify enriched potential TFs and explore the possible role of the transcription factor DMAP1 in breast cancer. We identified 13 prognostic-related TFs and constructed their regulated genes, alternative splicing (AS) events, and splicing factor (SF) regulation networks. DMAP1 was reported less in breast cancer. The expression of DMAP1 decreased in breast cancer tumors compared with normal tissues. The poor prognosis of patients with low DMAP1 expression may relate to the activated PI3K/Akt signaling pathway, as well as other cancer-relevant pathways. This may be due to the low methylation and high expression of these pathway genes and the fact that such patients show more sensitivity to some PI3K/Akt signaling pathway inhibitors. The high expression of DMAP1 was correlated with low immune cell infiltration, and the response to immune checkpoint inhibitor treatment in patients with high DMAP1 expression was low. Our study identifies some transcription factors that are significant for breast cancer progression, which can be used as potential personalized prognostic markers in the future.
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26
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Sanchez A, Lee D, Kim DI, Miller KM. Making Connections: Integrative Signaling Mechanisms Coordinate DNA Break Repair in Chromatin. Front Genet 2021; 12:747734. [PMID: 34659365 PMCID: PMC8514019 DOI: 10.3389/fgene.2021.747734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/31/2021] [Indexed: 01/25/2023] Open
Abstract
DNA double-strand breaks (DSBs) are hazardous to genome integrity and can promote mutations and disease if not handled correctly. Cells respond to these dangers by engaging DNA damage response (DDR) pathways that are able to identify DNA breaks within chromatin leading ultimately to their repair. The recognition and repair of DSBs by the DDR is largely dependent on the ability of DNA damage sensing factors to bind to and interact with nucleic acids, nucleosomes and their modified forms to target these activities to the break site. These contacts orientate and localize factors to lesions within chromatin, allowing signaling and faithful repair of the break to occur. Coordinating these events requires the integration of several signaling and binding events. Studies are revealing an enormously complex array of interactions that contribute to DNA lesion recognition and repair including binding events on DNA, as well as RNA, RNA:DNA hybrids, nucleosomes, histone and non-histone protein post-translational modifications and protein-protein interactions. Here we examine several DDR pathways that highlight and provide prime examples of these emerging concepts. A combination of approaches including genetic, cellular, and structural biology have begun to reveal new insights into the molecular interactions that govern the DDR within chromatin. While many questions remain, a clearer picture has started to emerge for how DNA-templated processes including transcription, replication and DSB repair are coordinated. Multivalent interactions with several biomolecules serve as key signals to recruit and orientate proteins at DNA lesions, which is essential to integrate signaling events and coordinate the DDR within the milieu of the nucleus where competing genome functions take place. Genome architecture, chromatin structure and phase separation have emerged as additional vital regulatory mechanisms that also influence genome integrity pathways including DSB repair. Collectively, recent advancements in the field have not only provided a deeper understanding of these fundamental processes that maintain genome integrity and cellular homeostasis but have also started to identify new strategies to target deficiencies in these pathways that are prevalent in human diseases including cancer.
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Affiliation(s)
- Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Doohyung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Dae In Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
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27
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Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development. Cancers (Basel) 2021; 13:cancers13153801. [PMID: 34359703 PMCID: PMC8345099 DOI: 10.3390/cancers13153801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary Most epithelial ovarian cancer (EOC) patients, although initially responsive to standard treatment with platinum-based chemotherapy, develop platinum resistance over the clinical course and succumb due to drug-resistant metastases. It has long been hypothesized that resistance to platinum develops as a result of epigenetic changes within tumor cells evolving over time. In this study, we investigated epigenomic changes in EOC patient samples, as well as in cell lines, and showed that profound changes at enhancers result in a platinum-resistant phenotype. Through correlation of the epigenomic alterations with changes in the transcriptome, we could identify potential novel prognostic biomarkers for early patient stratification. Furthermore, we applied a combinatorial RNAi screening approach to identify suitable targets that prevent the enhancer remodeling process. Our results advance the molecular understanding of epigenetic mechanisms in EOC and therapy resistance, which will be essential for the further exploration of epigenetic drug targets and combinatorial treatment regimes. Abstract Epithelial ovarian cancer (EOC) is the most lethal disease of the female reproductive tract, and although most patients respond to the initial treatment with platinum (cPt)-based compounds, relapse is very common. We investigated the role of epigenetic changes in cPt-sensitive and -resistant EOC cell lines and found distinct differences in their enhancer landscape. Clinical data revealed that two genes (JAK1 and FGF10), which gained large enhancer clusters in resistant EOC cell lines, could provide novel biomarkers for early patient stratification with statistical independence for JAK1. To modulate the enhancer remodeling process and prevent the acquisition of cPt resistance in EOC cells, we performed a chromatin-focused RNAi screen in the presence of cPt. We identified subunits of the Nucleosome Remodeling and Deacetylase (NuRD) complex as critical factors sensitizing the EOC cell line A2780 to platinum treatment. Suppression of the Methyl-CpG Binding Domain Protein 3 (MBD3) sensitized cells and prevented the establishment of resistance under prolonged cPt exposure through alterations of H3K27ac at enhancer regions, which are differentially regulated in cPt-resistant cells, leading to a less aggressive phenotype. Our work establishes JAK1 as an independent prognostic marker and the NuRD complex as a potential target for combinational therapy.
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28
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Perfecting DNA double-strand break repair on transcribed chromatin. Essays Biochem 2021; 64:705-719. [PMID: 32309851 DOI: 10.1042/ebc20190094] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023]
Abstract
Timely repair of DNA double-strand break (DSB) entails coordination with the local higher order chromatin structure and its transaction activities, including transcription. Recent studies are uncovering how DSBs trigger transient suppression of nearby transcription to permit faithful DNA repair, failing of which leads to elevated chromosomal aberrations and cell hypersensitivity to DNA damage. Here, we summarize the molecular bases for transcriptional control during DSB metabolism, and discuss how the exquisite coordination between the two DNA-templated processes may underlie maintenance of genome stability and cell homeostasis.
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29
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Kumbhar R, Sanchez A, Perren J, Gong F, Corujo D, Medina F, Devanathan SK, Xhemalce B, Matouschek A, Buschbeck M, Buck-Koehntop BA, Miller KM. Poly(ADP-ribose) binding and macroH2A mediate recruitment and functions of KDM5A at DNA lesions. J Cell Biol 2021; 220:212163. [PMID: 34003252 PMCID: PMC8135068 DOI: 10.1083/jcb.202006149] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/15/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
The histone demethylase KDM5A erases histone H3 lysine 4 methylation, which is involved in transcription and DNA damage responses (DDRs). While DDR functions of KDM5A have been identified, how KDM5A recognizes DNA lesion sites within chromatin is unknown. Here, we identify two factors that act upstream of KDM5A to promote its association with DNA damage sites. We have identified a noncanonical poly(ADP-ribose) (PAR)–binding region unique to KDM5A. Loss of the PAR-binding region or treatment with PAR polymerase (PARP) inhibitors (PARPi’s) blocks KDM5A–PAR interactions and DNA repair functions of KDM5A. The histone variant macroH2A1.2 is also specifically required for KDM5A recruitment and function at DNA damage sites, including homology-directed repair of DNA double-strand breaks and repression of transcription at DNA breaks. Overall, this work reveals the importance of PAR binding and macroH2A1.2 in KDM5A recognition of DNA lesion sites that drive transcriptional and repair activities at DNA breaks within chromatin that are essential for maintaining genome integrity.
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Affiliation(s)
- Ramhari Kumbhar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Jullian Perren
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Fade Gong
- Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX
| | - David Corujo
- Cancer and Leukemia Epigenetics and Biology Program, Josep Carreras Leukaemia Cancer Institute, Barcelona, Spain
| | - Frank Medina
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Sravan K Devanathan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Blerta Xhemalce
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Marcus Buschbeck
- Cancer and Leukemia Epigenetics and Biology Program, Josep Carreras Leukaemia Cancer Institute, Barcelona, Spain.,Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, Badalona, Spain
| | | | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX
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30
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DNA double-strand break repair: Putting zinc fingers on the sore spot. Semin Cell Dev Biol 2021; 113:65-74. [DOI: 10.1016/j.semcdb.2020.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/22/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022]
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31
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van den Heuvel D, Spruijt CG, González-Prieto R, Kragten A, Paulsen MT, Zhou D, Wu H, Apelt K, van der Weegen Y, Yang K, Dijk M, Daxinger L, Marteijn JA, Vertegaal ACO, Ljungman M, Vermeulen M, Luijsterburg MS. A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair. Nat Commun 2021; 12:1342. [PMID: 33637760 PMCID: PMC7910549 DOI: 10.1038/s41467-021-21520-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 01/28/2021] [Indexed: 02/06/2023] Open
Abstract
Bulky DNA lesions in transcribed strands block RNA polymerase II (RNAPII) elongation and induce a genome-wide transcriptional arrest. The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking DNA lesions, but how transcription is restored in the genome following DNA repair remains unresolved. Here, we find that the TCR-specific CSB protein loads the PAF1 complex (PAF1C) onto RNAPII in promoter-proximal regions in response to DNA damage. Although dispensable for TCR-mediated repair, PAF1C is essential for transcription recovery after UV irradiation. We find that PAF1C promotes RNAPII pause release in promoter-proximal regions and subsequently acts as a processivity factor that stimulates transcription elongation throughout genes. Our findings expose the molecular basis for a non-canonical PAF1C-dependent pathway that restores transcription throughout the human genome after genotoxic stress. The transcription-coupled repair pathway removes transcription-blocking DNA lesions, but how transcription is restored following DNA repair is not clear. Here the authors reveal that the PAF1 complex, while dispensable for the repair process, restores transcription after DNA damage.
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Affiliation(s)
- Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Cornelia G Spruijt
- Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands.,Prinses Maxima Center, Utrecht, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Angela Kragten
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Rotterdam, The Netherlands
| | - Haoyu Wu
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Yana van der Weegen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kevin Yang
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Madelon Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Rotterdam, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Michiel Vermeulen
- Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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32
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Regulation of ZMYND8 to Treat Cancer. Molecules 2021; 26:molecules26041083. [PMID: 33670804 PMCID: PMC7923094 DOI: 10.3390/molecules26041083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 12/31/2022] Open
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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33
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van Mierlo G, Vermeulen M. Chromatin Proteomics to Study Epigenetics - Challenges and Opportunities. Mol Cell Proteomics 2021; 20:100056. [PMID: 33556626 PMCID: PMC7973309 DOI: 10.1074/mcp.r120.002208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Regulation of gene expression is essential for the functioning of all eukaryotic organisms. Understanding gene expression regulation requires determining which proteins interact with regulatory elements in chromatin. MS-based analysis of chromatin has emerged as a powerful tool to identify proteins associated with gene regulation, as it allows studying protein function and protein complex formation in their in vivo chromatin-bound context. Total chromatin isolated from cells can be directly analyzed using MS or further fractionated into transcriptionally active and inactive chromatin prior to MS-based analysis. Newly formed chromatin that is assembled during DNA replication can also be specifically isolated and analyzed. Furthermore, capturing specific chromatin domains facilitates the identification of previously unknown transcription factors interacting with these domains. Finally, in recent years, advances have been made toward identifying proteins that interact with a single genomic locus of interest. In this review, we highlight the power of chromatin proteomics approaches and how these provide complementary alternatives compared with conventional affinity purification methods. Furthermore, we discuss the biochemical challenges that should be addressed to consolidate and expand the role of chromatin proteomics as a key technology in the context of gene expression regulation and epigenetics research in health and disease. An overview of proteomics methods to study chromatin and gene regulation. Strength and limitations of the different approaches are highlighted. An outlook on the outstanding challenges for chromatin proteomics. Future directions for chromatin proteomics are discussed.
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Affiliation(s)
- Guido van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands.
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands.
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34
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Supercharging BRD4 with NUT in carcinoma. Oncogene 2021; 40:1396-1408. [PMID: 33452461 PMCID: PMC7914217 DOI: 10.1038/s41388-020-01625-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023]
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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35
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Farcas AM, Nagarajan S, Cosulich S, Carroll JS. Genome-Wide Estrogen Receptor Activity in Breast Cancer. Endocrinology 2021; 162:bqaa224. [PMID: 33284960 PMCID: PMC7787425 DOI: 10.1210/endocr/bqaa224] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Indexed: 12/13/2022]
Abstract
The largest subtype of breast cancer is characterized by the expression and activity of the estrogen receptor alpha (ERalpha/ER). Although several effective therapies have significantly improved survival, the adaptability of cancer cells means that patients frequently stop responding or develop resistance to endocrine treatment. ER does not function in isolation and multiple associating factors have been reported to play a role in regulating the estrogen-driven transcriptional program. This review focuses on the dynamic interplay between some of these factors which co-occupy ER-bound regulatory elements, their contribution to estrogen signaling, and their possible therapeutic applications. Furthermore, the review illustrates how some ER association partners can influence and reprogram the genomic distribution of the estrogen receptor. As this dynamic ER activity enables cancer cell adaptability and impacts the clinical outcome, defining how this plasticity is determined is fundamental to our understanding of the mechanisms of disease progression.
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Affiliation(s)
- Anca M Farcas
- Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Sankari Nagarajan
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | | | - Jason S Carroll
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
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36
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Dou C, Mo H, Chen T, Liu J, Zeng Y, Li S, Guo C, Zhang C. ZMYND8 promotes the growth and metastasis of hepatocellular carcinoma by promoting HK2-mediated glycolysis. Pathol Res Pract 2021; 219:153345. [PMID: 33517164 DOI: 10.1016/j.prp.2021.153345] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
The bromodomain protein zinc finger MYND-type containing 8 (ZMYND8) plays a critical role in human breast cancer. However, the expression and biological function of ZMYND8 in hepatocellular carcinoma (HCC) are poorly understood. In this study, ZMYND8 expression was found to be elevated in HCC based on the cancer genome atlas (TCGA) and gene expression omnibus (GEO) databases. Next, we confirmed that ZMYND8 was frequently overexpressed in HCC tissues compared with adjacent non-tumor tissues. The up-regulated level of ZMYND8 was also observed in HCC cell lines. Elevated ZMYND8 expression was correlated with unfavorable clinicopathological features and poor prognosis of HCC patients. Functionally, ectopic expression of ZMYND8 potentiated the proliferation, migration, and invasion of Hep3B cells. Conversely, ZMYND8 knockdown led to the reduced proliferation and invasiveness of HCCLM3 cells. ZMYND8 silencing restrained the growth of HCCLM3 cells in vivo. Mechanistically, ZMYND8 enhanced glucose consumption, lactate production, and ATP level in HCC cells. Pharmacological inhibition of glycolysis using 2-DG blocked the promoting effects of ZMYND8 on HCC cell proliferation and mobility. Furthermore, hexokinase 2 (HK2), a key enzyme of glycolysis, was identified as the downstream target of ZMYND8 in HCC cells. ZMYND8 promoted HK2 transcription by recruiting bromodomain containing 4 (BRD4) to its promoter. Knockdown of HK2 abrogated the oncogenic functions of ZMYND8 in HCC. Altogether, these data indicated that ZMYND8 promoted the growth and metastasis of HCC by promoting HK2-mediated glycolysis and might serve as a promising biomarker and therapeutic target for HCC.
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Affiliation(s)
- Changwei Dou
- Department of Hepatopancreatobiliary Surgery & Minimally Invasive Surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China.
| | - Huanye Mo
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Tianxiang Chen
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Jie Liu
- Department of Hepatopancreatobiliary Surgery & Minimally Invasive Surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China.
| | - Yuqun Zeng
- Department of Nephrology, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang Province 310014, China.
| | - Shuangshuang Li
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China.
| | - Cheng Guo
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Chengwu Zhang
- Department of Hepatopancreatobiliary Surgery & Minimally Invasive Surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China.
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37
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Millard CJ, Fairall L, Ragan TJ, Savva CG, Schwabe JWR. The topology of chromatin-binding domains in the NuRD deacetylase complex. Nucleic Acids Res 2020; 48:12972-12982. [PMID: 33264408 PMCID: PMC7736783 DOI: 10.1093/nar/gkaa1121] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/22/2020] [Accepted: 11/03/2020] [Indexed: 01/22/2023] Open
Abstract
Class I histone deacetylase complexes play essential roles in many nuclear processes. Whilst they contain a common catalytic subunit, they have diverse modes of action determined by associated factors in the distinct complexes. The deacetylase module from the NuRD complex contains three protein domains that control the recruitment of chromatin to the deacetylase enzyme, HDAC1/2. Using biochemical approaches and cryo-electron microscopy, we have determined how three chromatin-binding domains (MTA1-BAH, MBD2/3 and RBBP4/7) are assembled in relation to the core complex so as to facilitate interaction of the complex with the genome. We observe a striking arrangement of the BAH domains suggesting a potential mechanism for binding to di-nucleosomes. We also find that the WD40 domains from RBBP4 are linked to the core with surprising flexibility that is likely important for chromatin engagement. A single MBD2 protein binds asymmetrically to the dimerisation interface of the complex. This symmetry mismatch explains the stoichiometry of the complex. Finally, our structures suggest how the holo-NuRD might assemble on a di-nucleosome substrate.
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Affiliation(s)
- Christopher J Millard
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Louise Fairall
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Timothy J Ragan
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Christos G Savva
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John W R Schwabe
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
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38
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Spruijt CG, Gräwe C, Kleinendorst SC, Baltissen MPA, Vermeulen M. Cross-linking mass spectrometry reveals the structural topology of peripheral NuRD subunits relative to the core complex. FEBS J 2020; 288:3231-3245. [PMID: 33283408 PMCID: PMC8246863 DOI: 10.1111/febs.15650] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 10/23/2020] [Accepted: 11/27/2020] [Indexed: 01/08/2023]
Abstract
The multi‐subunit nucleosome remodeling and deacetylase (NuRD) complex consists of seven subunits, each of which comprises two or three paralogs in vertebrates. These paralogs define mutually exclusive and functionally distinct complexes. In addition, several proteins in the complex are multimeric, which complicates structural studies. Attempts to purify sufficient amounts of endogenous complex or recombinantly reconstitute the complex for structural studies have proven quite challenging. Until now, only substructures of individual domains or proteins and low‐resolution densities of (partial) complexes have been reported. In this study, we comprehensively investigated the relative orientation of different subunits within the NuRD complex using multiple cross‐link IP mass spectrometry (xIP‐MS) experiments. Our results confirm that the core of the complex is formed by MTA, RBBP, and HDAC proteins. Assembly of a copy of MBD and GATAD2 onto this core enables binding of the peripheral CHD and CDK2AP proteins. Furthermore, our experiments reveal that not only CDK2AP1 but also CDK2AP2 interacts with the NuRD complex. This interaction requires the C terminus of CHD proteins. Our data provide a more detailed understanding of the topology of the peripheral NuRD subunits relative to the core complex. Database Proteomics data are available in the PRIDE database under the accession numbers PXD017244 and PXD017378.
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Affiliation(s)
- Cornelia G Spruijt
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Cathrin Gräwe
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Simone C Kleinendorst
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Marijke P A Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
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39
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Russo R, Russo V, Cecere F, Valletta M, Gentile MT, Colucci-D'Amato L, Angelini C, Riccio A, Pedone PV, Chambery A, Baglivo I. ZBTB2 protein is a new partner of the Nucleosome Remodeling and Deacetylase (NuRD) complex. Int J Biol Macromol 2020; 168:67-76. [PMID: 33301849 DOI: 10.1016/j.ijbiomac.2020.12.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/25/2020] [Accepted: 12/04/2020] [Indexed: 11/19/2022]
Abstract
ZBTB2 is a protein belonging to the BTB/POZ zinc-finger family whose members typically contain a BTB/POZ domain at the N-terminus and several zinc-finger domains at the C-terminus. Studies have been carried out to disclose the role of ZBTB2 in cell proliferation, in human cancers and in regulating DNA methylation. Moreover, ZBTB2 has been also described as an ARF, p53 and p21 gene repressor as well as an activator of genes modulating pluripotency. In this scenario, ZBTB2 seems to play many functions likely associated with other proteins. Here we report a picture of the ZBTB2 protein partners in U87MG cell line, identified by high-resolution mass spectrometry (MS) that highlights the interplay between ZBTB2 and chromatin remodeling multiprotein complexes. In particular, our analysis reveals the presence, as ZBTB2 candidate interactors, of SMARCA5 and BAZ1B components of the chromatin remodeling complex WICH and PBRM1, a subunit of the SWI/SNF complex. Intriguingly, we identified all the subunits of the NuRD complex among the ZBTB2 interactors. By co-immunoprecipitation experiments and ChIP-seq analysis we definitely identify ZBTB2 as a new partner of the NuRD complex.
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Affiliation(s)
- Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", via Vivaldi, 43, 81100 Caserta, Italy
| | - Veronica Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", via Vivaldi, 43, 81100 Caserta, Italy
| | - Francesco Cecere
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", via Vivaldi, 43, 81100 Caserta, Italy; Institute of Genetics and Biophysics "A. Buzzati-Traverso" - CNR, Via Pietro Castellino, 111, 80131 Naples, Italy
| | - Mariangela Valletta
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", via Vivaldi, 43, 81100 Caserta, Italy
| | - Maria Teresa Gentile
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", via Vivaldi, 43, 81100 Caserta, Italy
| | - Luca Colucci-D'Amato
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", via Vivaldi, 43, 81100 Caserta, Italy
| | - Claudia Angelini
- Institute for Applied Mathematics "Mauro Picone" (IAC), National Research Council, 80131 Naples, Italy
| | - Andrea Riccio
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", via Vivaldi, 43, 81100 Caserta, Italy; Institute of Genetics and Biophysics "A. Buzzati-Traverso" - CNR, Via Pietro Castellino, 111, 80131 Naples, Italy
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", via Vivaldi, 43, 81100 Caserta, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", via Vivaldi, 43, 81100 Caserta, Italy.
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", via Vivaldi, 43, 81100 Caserta, Italy.
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40
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A novel role of tumor suppressor ZMYND8 in inducing differentiation of breast cancer cells through its dual-histone binding function. J Biosci 2020. [DOI: 10.1007/s12038-019-9980-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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41
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Low JKK, Silva APG, Sharifi Tabar M, Torrado M, Webb SR, Parker BL, Sana M, Smits C, Schmidberger JW, Brillault L, Jackman MJ, Williams DC, Blobel GA, Hake SB, Shepherd NE, Landsberg MJ, Mackay JP. The Nucleosome Remodeling and Deacetylase Complex Has an Asymmetric, Dynamic, and Modular Architecture. Cell Rep 2020; 33:108450. [PMID: 33264611 PMCID: PMC8908386 DOI: 10.1016/j.celrep.2020.108450] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/23/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022] Open
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is essential for metazoan development but has been refractory to biochemical analysis. We present an integrated analysis of the native mammalian NuRD complex, combining quantitative mass spectrometry, cross-linking, protein biochemistry, and electron microscopy to define the architecture of the complex. NuRD is built from a 2:2:4 (MTA, HDAC, and RBBP) deacetylase module and a 1:1:1 (MBD, GATAD2, and Chromodomain-Helicase-DNA-binding [CHD]) remodeling module, and the complex displays considerable structural dynamics. The enigmatic GATAD2 controls the asymmetry of the complex and directly recruits the CHD remodeler. The MTA-MBD interaction acts as a point of functional switching, with the transcriptional regulator PWWP2A competing with MBD for binding to the MTA-HDAC-RBBP subcomplex. Overall, our data address the long-running controversy over NuRD stoichiometry, provide imaging of the mammalian NuRD complex, and establish the biochemical mechanism by which PWWP2A can regulate NuRD composition. Low et al. examine the architecture of the nucleosome remodeling and deacetylase complex. They define its stoichiometry, use cross-linking mass spectrometry to define subunit locations, and use electron microscopy to reveal large-scale dynamics. They also demonstrate that PWWP2A competes with MBD3 to sequester the HDAC-MTA-RBBP module from NuRD.
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Affiliation(s)
- Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia.
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Mehdi Sharifi Tabar
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Sarah R Webb
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Benjamin L Parker
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Maryam Sana
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | | | | | - Lou Brillault
- School of Chemistry and Molecular Biosciences, University of Queensland, QLD, Australia
| | - Matthew J Jackman
- School of Chemistry and Molecular Biosciences, University of Queensland, QLD, Australia
| | - David C Williams
- Dept of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, NC, USA
| | - Gerd A Blobel
- The Division of Hematology, Children's Hospital of Philadelphia, and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sandra B Hake
- Institute for Genetics, FB08 Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Nicholas E Shepherd
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, University of Queensland, QLD, Australia.
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia.
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42
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Rother MB, Pellegrino S, Smith R, Gatti M, Meisenberg C, Wiegant WW, Luijsterburg MS, Imhof R, Downs JA, Vertegaal ACO, Huet S, Altmeyer M, van Attikum H. CHD7 and 53BP1 regulate distinct pathways for the re-ligation of DNA double-strand breaks. Nat Commun 2020; 11:5775. [PMID: 33188175 PMCID: PMC7666215 DOI: 10.1038/s41467-020-19502-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 10/15/2020] [Indexed: 01/16/2023] Open
Abstract
Chromatin structure is dynamically reorganized at multiple levels in response to DNA double-strand breaks (DSBs). Yet, how the different steps of chromatin reorganization are coordinated in space and time to differentially regulate DNA repair pathways is insufficiently understood. Here, we identify the Chromodomain Helicase DNA Binding Protein 7 (CHD7), which is frequently mutated in CHARGE syndrome, as an integral component of the non-homologous end-joining (NHEJ) DSB repair pathway. Upon recruitment via PARP1-triggered chromatin remodeling, CHD7 stimulates further chromatin relaxation around DNA break sites and brings in HDAC1/2 for localized chromatin de-acetylation. This counteracts the CHD7-induced chromatin expansion, thereby ensuring temporally and spatially controlled 'chromatin breathing' upon DNA damage, which we demonstrate fosters efficient and accurate DSB repair by controlling Ku and LIG4/XRCC4 activities. Loss of CHD7-HDAC1/2-dependent cNHEJ reinforces 53BP1 assembly at the damaged chromatin and shifts DSB repair to mutagenic NHEJ, revealing a backup function of 53BP1 when cNHEJ fails.
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Grants
- 25715 Cancer Research UK
- 714326 European Research Council
- MR/N02155X/2 Medical Research Council
- MR/N02155X/1 Medical Research Council
- This research was financially supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERC-StG 714326 to M.A.; ERC-StG 310913 to A.C.O.V.; ERC-CoG 50364 to H.v.A), the Swiss National Science Foundation (grants 150690 and 179057 to M.A.), grants from the Danish Research Council (DFF 1333-00037B and 1331-00732B to M.A.), NWO-VENI (863.11.007) and NWO-VIDI (016.161.320) grants to M.S.L., People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/ 2007-2013) under REA grant agreement [(PCOFUND-GA-2013-609102), through the PRESTIGE program coordinated by Campus France (PRESTIGE-2017-2-0042), the Université Bretagne-Loire and the Fondation ARC pour la recherche sur le cancer (PDF20181208405) to R.S., the Ligue contre le Cancer du Grand-Ouest (committees 22 and 35), the Fondation ARC pour la recherche sur le cancer (20161204883), the Agence Nationale de la Recherche (PRC-2018 REPAIRCHROM) and the Institut Universitaire de France to S.H., and the Medical Research Council (MR/N02155X/1) to C.M. and J.A.D..
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Affiliation(s)
- Magdalena B Rother
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stefania Pellegrino
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)-UMR 6290, BIOSIT-UMS3480, F-35000, Rennes, France
| | - Marco Gatti
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | | | - Wouter W Wiegant
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Ralph Imhof
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Jessica A Downs
- The Institute of Cancer Research, Royal Cancer Hospital, London, UK
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)-UMR 6290, BIOSIT-UMS3480, F-35000, Rennes, France
- Institut Universitaire de France, Paris, France
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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43
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Wang Y, Luo M, Chen Y, Wang Y, Zhang B, Ren Z, Bao L, Wang Y, Wang JE, Fu YX, Luo W, Wang Y. ZMYND8 Expression in Breast Cancer Cells Blocks T-Lymphocyte Surveillance to Promote Tumor Growth. Cancer Res 2020; 81:174-186. [PMID: 33148660 DOI: 10.1158/0008-5472.can-20-1710] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 10/05/2020] [Accepted: 10/30/2020] [Indexed: 11/16/2022]
Abstract
Emerging studies indicate that DNA damage in cancer cells triggers antitumor immunity, but its intrinsic regulatory mechanism in breast cancer cells remains poorly understood. Here, we show that ZMYND8 is upregulated and inhibits micronucleus formation and DNA damage in breast cancer cells. Loss of ZMYND8 triggered activation of the DNA sensor cyclic guanosine monophosphate-adenosine monophosphate synthase in micronuclei, leading to further activation of the downstream signaling effectors stimulator of IFN genes and NF-κB, but not TANK-binding kinase 1 and IFN regulatory factor 3, thereby inducing the expression of IFNβ and IFN-stimulated genes (ISG) in breast cancer cells in vitro and tumors in vivo. ZMYND8 knockout (KO) in breast cancer cells promoted infiltration of CD4+ and CD8+ T cells, leading to tumor inhibition in syngeneic mouse models, which was significantly attenuated by treatment of anti-CD4/CD8-depleting antibodies or anti-IFNAR1 antibody and in immunodeficient Rag1 KO mice. In human breast tumors, ZMYND8 was negatively correlated with ISGs, CD4, CD8A, CD8B, and the tumor-lymphocyte infiltration phenotype. Collectively, these findings demonstrate that maintenance of genome stability by ZMYND8 causes breast cancer cells to evade cytotoxic T-lymphocyte surveillance, which leads to tumor growth. SIGNIFICANCE: These findings show that ZMYND8 is a new negative and intrinsic regulator of the innate immune response in breast tumor cells, and ZMYND8 may be a possible target for antitumor immunotherapy.
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Affiliation(s)
- Yong Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Maowu Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Yan Chen
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Yijie Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Bo Zhang
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Zhenhua Ren
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Lei Bao
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Yanan Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Jennifer E Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Yang-Xin Fu
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Weibo Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas. .,Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas
| | - Yingfei Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas. .,Department of Neurology, UT Southwestern Medical Center, Dallas, Texas
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44
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Scotto di Carlo F, Pazzaglia L, Mumm S, Benassi MS, De Chiara A, Franchi A, Parafioriti A, Righi A, Esposito T, Whyte MP, Gianfrancesco F. ZNF687 Mutations in an Extended Cohort of Neoplastic Transformations in Paget's Disease of Bone: Implications for Clinical Pathology. J Bone Miner Res 2020; 35:1974-1980. [PMID: 32106343 DOI: 10.1002/jbmr.3993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/17/2020] [Accepted: 01/27/2020] [Indexed: 01/06/2023]
Abstract
Neoplastic transformation is a rare but serious complication of Paget's disease of bone (PDB), occurring in fewer than 1% of individuals with polyostotic disease. Their prognosis is poor, with less than 50% surviving 5 years. In 2016, the genetic alteration of giant cell tumor (GCT) complicating PDB was identified as a founder germline mutation (P937R) in the ZNF687 gene. However, the study population was exclusively of Italian descent, and patients of different ethnic origins were not studied. To fill this gap, herein we performed mutation analysis of ZNF687 in a GCT in the pelvis of a 45-year-old black American woman with polyostotic PDB. The P937R mutation in ZNF687 was found in her tumor but, as expected, the ancestral haplotype that characterizes the Italian GCT/PDB patients was not found. Furthermore, we identified two additional Italian GCT/PDB patients with this ZNF687 mutation, now constituting a cohort of 18 GCT/PDB cases, all harboring the identical mutation. We also searched for ZNF687 mutations in a unique collection of tumor tissues derived from Italian PDB patients, including 28 osteosarcomas (OS/PDB), 8 undifferentiated sarcomas (SRC/PDB), 1 fibrosarcoma (FS/PDB), and 1 chondrosarcoma (CS/PDB). We identified the P937R mutation in one SRC/PDB and a different ZNF687 mutation (R331W) in 1 of 28 pagetic osteosarcomas. Thus, whereas GCT/PDB pathogenesis globally seems to involve the P937R mutation in ZNF687, other neoplasms associated with PDB seem to be less related to mutations in this gene. Finally, we identified the G34W mutation in the H3F3A gene in the maxillary tumor masses of two PDB patients, defining them as conventional GCT rather than GCT/PDB. Thus, combined molecular analysis of H3F3A and ZNF687 is essential to clarify the origin and diagnosis of tumors in PDB. © 2020 American Society for Bone and Mineral Research.
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Affiliation(s)
| | - Laura Pazzaglia
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Steven Mumm
- Division of Bone and Mineral Diseases, Department of Internal Medicine, Washington University School of Medicine at Barnes-Jewish Hospital, St. Louis, MO, USA.,Center for Metabolic Bone Disease and Molecular Research, Shriners Hospitals for Children-St. Louis, St. Louis, MO, USA
| | - Maria S Benassi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Annarosaria De Chiara
- Pathology Division, Istituto Nazionale Tumori IRCCS, Fondazione G. Pascale, Naples, Italy
| | - Alessandro Franchi
- Department of Translational Research and of New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Alberto Righi
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Teresa Esposito
- Institute of Genetics and Biophysics, National Research Council of Italy, Naples, Italy.,IRCCS INM Neuromed, Pozzilli, Italy
| | - Michael P Whyte
- Division of Bone and Mineral Diseases, Department of Internal Medicine, Washington University School of Medicine at Barnes-Jewish Hospital, St. Louis, MO, USA.,Center for Metabolic Bone Disease and Molecular Research, Shriners Hospitals for Children-St. Louis, St. Louis, MO, USA
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45
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Smits VAJ, Alonso-de Vega I, Warmerdam DO. Chromatin regulators and their impact on DNA repair and G2 checkpoint recovery. Cell Cycle 2020; 19:2083-2093. [PMID: 32730133 DOI: 10.1080/15384101.2020.1796037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Chromatin plays a pivotal role in regulating the DNA damage response and during DNA double-strand break repair. Upon the generation of DNA breaks, the chromatin structure is altered by post-translational modifications of histones and chromatin remodeling. How the chromatin structure, and the epigenetic information that it carries, is reestablished after the completion of DNA break repair remains unclear though. Also, how these processes influence recovery of the cell cycle remains poorly understood. We recently performed a reverse genetic screen for novel chromatin regulators that control checkpoint recovery after DNA damage. Here we discuss the implications of PHD finger protein 6 (PHF6) and additional candidates from the NuA4 ATPase-dependent chromatin-remodeling complex and the Cohesin complex, required for sister chromatid cohesion, in DNA repair and checkpoint recovery in more detail. In addition, the potential role of this novel function of PHF6 in cancer development and treatment is reviewed.
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Affiliation(s)
- Veronique A J Smits
- Unidad de Investigación, Hospital Universitario de Canarias , La Laguna, Spain.,Instituto de Tecnologías Biomédicas, Universidad de La Laguna , Tenerife, Spain.,Universidad Fernando Pessoa Canarias , Las Palmas de Gran Canaria, Spain
| | - Ignacio Alonso-de Vega
- Unidad de Investigación, Hospital Universitario de Canarias , La Laguna, Spain.,Instituto de Tecnologías Biomédicas, Universidad de La Laguna , Tenerife, Spain
| | - Daniël O Warmerdam
- CRISPR Platform, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam , Amsterdam, The Netherlands
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46
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The two faces of giant cell tumor of bone. Cancer Lett 2020; 489:1-8. [PMID: 32502498 DOI: 10.1016/j.canlet.2020.05.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 12/31/2022]
Abstract
Giant cell tumor (GCT) is a bone-destructive benign neoplasm characterized by distinctive multinucleated osteoclast-like giant cells with osteolytic properties distributed among neoplastic stromal cells. GCT is locally aggressive with progressive invasion of adjacent tissues and occasionally displays malignant characteristics including lung metastasis. GCT is characterized genetically by highly recurrent somatic mutations at the G34 position of the H3F3A gene, encoding the histone variant H3.3, in stromal cells. This leads to deregulated gene expression and increased proliferation of mutation-bearing cells. However, when GCT complicates Paget disease of bone (GCT/PDB) it behaves differently, showing a more malignant phenotype with 5-year survival less than 50%. GCT/PDB is caused by a germline mutation in the ZNF687 gene, which encodes a transcription factor involved in the repression of genes surrounding DNA double-strand breaks to promote repair by homologous recombination. Identification of these driver mutations led to novel diagnostic tools for distinguishing between these two tumors and other osteoclast-rich neoplasms. Herein, we review the clinical, histological, and molecular features of GCT in different contexts focusing also on pharmacological treatments.
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Hou T, Cao Z, Zhang J, Tang M, Tian Y, Li Y, Lu X, Chen Y, Wang H, Wei FZ, Wang L, Yang Y, Zhao Y, Wang Z, Wang H, Zhu WG. SIRT6 coordinates with CHD4 to promote chromatin relaxation and DNA repair. Nucleic Acids Res 2020; 48:2982-3000. [PMID: 31970415 PMCID: PMC7102973 DOI: 10.1093/nar/gkaa006] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/02/2019] [Accepted: 01/03/2020] [Indexed: 01/08/2023] Open
Abstract
Genomic instability is an underlying hallmark of cancer and is closely associated with defects in DNA damage repair (DDR). Chromatin relaxation is a prerequisite for DDR, but how chromatin accessibility is regulated remains elusive. Here we report that the histone deacetylase SIRT6 coordinates with the chromatin remodeler CHD4 to promote chromatin relaxation in response to DNA damage. Upon DNA damage, SIRT6 rapidly translocates to DNA damage sites, where it interacts with and recruits CHD4. Once at the damage sites, CHD4 displaces heterochromatin protein 1 (HP1) from histone H3 lysine 9 trimethylation (H3K9me3). Notably, loss of SIRT6 or CHD4 leads to impaired chromatin relaxation and disrupted DNA repair protein recruitment. These molecular changes, in-turn, lead to defective homologous recombination (HR) and cancer cell hypersensitivity to DNA damaging agents. Furthermore, we show that SIRT6-mediated CHD4 recruitment has a specific role in DDR within compacted chromatin by HR in G2 phase, which is an ataxia telangiectasia mutated (ATM)-dependent process. Taken together, our results identify a novel function for SIRT6 in recruiting CHD4 onto DNA double-strand breaks. This newly identified novel molecular mechanism involves CHD4-dependent chromatin relaxation and competitive release of HP1 from H3K9me3 within the damaged chromatin, which are both essential for accurate HR.
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Affiliation(s)
- Tianyun Hou
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ziyang Cao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jun Zhang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Ming Tang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Yuan Tian
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Yinglu Li
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Xiaopeng Lu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Yongcan Chen
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Hui Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Fu-Zheng Wei
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lina Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yang Yang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ying Zhao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zimei Wang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Haiying Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Wei-Guo Zhu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
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48
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Páhi ZG, Borsos BN, Pantazi V, Ujfaludi Z, Pankotai T. PARylation During Transcription: Insights into the Fine-Tuning Mechanism and Regulation. Cancers (Basel) 2020; 12:cancers12010183. [PMID: 31940791 PMCID: PMC7017041 DOI: 10.3390/cancers12010183] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/19/2019] [Accepted: 01/09/2020] [Indexed: 01/31/2023] Open
Abstract
Transcription is a multistep, tightly regulated process. During transcription initiation, promoter recognition and pre-initiation complex (PIC) formation take place, in which dynamic recruitment or exchange of transcription activators occur. The precise coordination of the recruitment and removal of transcription factors, as well as chromatin structural changes, are mediated by post-translational modifications (PTMs). Poly(ADP-ribose) polymerases (PARPs) are key players in this process, since they can modulate DNA-binding activities of specific transcription factors through poly-ADP-ribosylation (PARylation). PARylation can regulate the transcription at three different levels: (1) by directly affecting the recruitment of specific transcription factors, (2) by triggering chromatin structural changes during initiation and as a response to cellular stresses, or (3) by post-transcriptionally modulating the stability and degradation of specific mRNAs. In this review, we principally focus on these steps and summarise the recent findings, demonstrating the mechanisms through which PARylation plays a potential regulatory role during transcription and DNA repair.
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Warmerdam DO, Alonso‐de Vega I, Wiegant WW, van den Broek B, Rother MB, Wolthuis RMF, Freire R, van Attikum H, Medema RH, Smits VAJ. PHF6 promotes non-homologous end joining and G2 checkpoint recovery. EMBO Rep 2020; 21:e48460. [PMID: 31782600 PMCID: PMC6944915 DOI: 10.15252/embr.201948460] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 12/12/2022] Open
Abstract
The cellular response to DNA breaks is influenced by chromatin compaction. To identify chromatin regulators involved in the DNA damage response, we screened for genes that affect recovery following DNA damage using an RNAi library of chromatin regulators. We identified genes involved in chromatin remodeling, sister chromatid cohesion, and histone acetylation not previously associated with checkpoint recovery. Among these is the PHD finger protein 6 (PHF6), a gene mutated in Börjeson-Forssman-Lehmann syndrome and leukemic cancers. We find that loss of PHF6 dramatically compromises checkpoint recovery in G2 phase cells. Moreover, PHF6 is rapidly recruited to sites of DNA lesions in a PARP-dependent manner and required for efficient DNA repair through classical non-homologous end joining. These results indicate that PHF6 is a novel DNA damage response regulator that promotes end joining-mediated repair, thereby stimulating timely recovery from the G2 checkpoint.
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Affiliation(s)
- Daniël O Warmerdam
- CRISPR PlatformCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Division of Cell BiologyOncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Ignacio Alonso‐de Vega
- Unidad de InvestigaciónHospital Universitario de CanariasLa LagunaTenerifeSpain
- Instituto de Tecnologías BiomédicasUniversidad de La LagunaTenerifeSpain
| | - Wouter W Wiegant
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Bram van den Broek
- Division of Cell BiologyOncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- BioImaging FacilityThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Magdalena B Rother
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Rob MF Wolthuis
- Section of OncogeneticsDepartment of Clinical GeneticsVrije Universiteit Amsterdam, Cancer Center AmsterdamAmsterdam UMCAmsterdamThe Netherlands
| | - Raimundo Freire
- Unidad de InvestigaciónHospital Universitario de CanariasLa LagunaTenerifeSpain
- Instituto de Tecnologías BiomédicasUniversidad de La LagunaTenerifeSpain
- Universidad Fernando Pessoa CanariasLas Palmas de Gran CanariaSpain
| | - Haico van Attikum
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - René H Medema
- Division of Cell BiologyOncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Veronique AJ Smits
- Unidad de InvestigaciónHospital Universitario de CanariasLa LagunaTenerifeSpain
- Instituto de Tecnologías BiomédicasUniversidad de La LagunaTenerifeSpain
- Universidad Fernando Pessoa CanariasLas Palmas de Gran CanariaSpain
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50
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Chen J, He Q, Wu P, Fu J, Xiao Y, Chen K, Xie D, Zhang X. ZMYND8 expression combined with pN and pM classification as a novel prognostic prediction model for colorectal cancer: Based on TCGA and GEO database analysis. Cancer Biomark 2020; 28:201-211. [PMID: 32224527 DOI: 10.3233/cbm-191261] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Zinc finger MYND (Myeloid, Nervy and DEAF-1)-type containing 8 (ZMYND8) is closely correlated with tumor proliferation and invasiveness. However, its prognostic value has not been estimated in colorectal cancer (CRC). OBJECTIVE We aimed to elucidate the prognostic significance of ZMYND8 expression and the pN and pM classification supplemented by its expression in CRCs. METHODS The candidate gene ZMYND8 is identified by TCGA database and GEO database, and then we retrospectively evaluated the status and prognostic significance of ZMYND8 expression of 174 patients with CRC. RESULTS Online data showed high expression of ZMYND8 is closely correlated with worse overall survival. Our study revealed high expression of ZMYND8 in CRC patients was significantly associated with worse overall and disease-free survival (P< 0.05), and was an independently adverse prognostic factor for overall survival (P< 0.001) and disease-free survival (P= 0.001) by univariate and multivariate analysis. C-index to combined prognostic model containing the pN, pM classification supplemented by the status of ZMYND8 expression showed improved predictive ability comparing with the pN and pM classification model (C-index of 0.597 vs. 0.545, respectively). CONCLUSION The combined prognostic model could improve the ability to determine the clinical outcome of patients with CRC.
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Affiliation(s)
- Jiewei Chen
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Guangdong Esophageal Cancer Institute, Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Qingmei He
- Guangdong Esophageal Cancer Institute, Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Peishan Wu
- Department of Pathology, The Second Affiliated Hospital of Shantou University Medical College, Guangdong, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Jianchang Fu
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Guangdong Esophageal Cancer Institute, Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yongbo Xiao
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Guangdong Esophageal Cancer Institute, Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Keming Chen
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Guangdong Esophageal Cancer Institute, Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Dan Xie
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Guangdong Esophageal Cancer Institute, Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Xinke Zhang
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Guangdong Esophageal Cancer Institute, Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
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