1
|
Ma S, Long G, Jiang Z, Zhang Y, Sun L, Pan Y, You Q, Guo X. Recent advances in targeting histone H3 lysine 36 methyltransferases for cancer therapy. Eur J Med Chem 2024; 274:116532. [PMID: 38805937 DOI: 10.1016/j.ejmech.2024.116532] [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: 04/09/2024] [Revised: 05/14/2024] [Accepted: 05/22/2024] [Indexed: 05/30/2024]
Abstract
Histone H3 lysine 36 (H3K36) methylation is a typical epigenetic histone modification that is involved in various biological processes such as DNA transcription, repair and recombination in vivo. Mutations, translocations, and aberrant gene expression associated with H3K36 methyltransferases have been implicated in different malignancies such as acute myeloid leukemia, lung cancer, multiple myeloma, and others. Herein, we provided a comprehensive overview of the latest advances in small molecule inhibitors targeting H3K36 methyltransferases. We analyzed the structures and biological functions of the H3K36 methyltransferases family members. Additionally, we discussed the potential directions for future development of inhibitors targeting H3K36 methyltransferases.
Collapse
Affiliation(s)
- Sai Ma
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Guanlu Long
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Zheng Jiang
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Yan Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Liangkui Sun
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Yun Pan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Xiaoke Guo
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| |
Collapse
|
2
|
Li TW, Park Y, Watters EG, Wang X, Zhou D, Fiches GN, Wu Z, Badley AD, Sacha JB, Ho WZ, Santoso NG, Qi J, Zhu J. KDM5A/B contribute to HIV-1 latent infection and survival of HIV-1 infected cells. Antiviral Res 2024; 228:105947. [PMID: 38925368 DOI: 10.1016/j.antiviral.2024.105947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 06/22/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
Combinational antiretroviral therapy (cART) suppresses human immunodeficiency virus type 1 (HIV-1) viral replication and pathogenesis in acquired immunodeficiency syndrome (AIDS) patients. However, HIV-1 remains in the latent stage of infection by suppressing viral transcription, which hinders an HIV-1 cure. One approach for an HIV-1 cure is the "shock and kill" strategy. The strategy focuses on reactivating latent HIV-1, inducing the viral cytopathic effect and facilitating the immune clearance for the elimination of latent HIV-1 reservoirs. Here, we reported that the H3K4 trimethylation (H3K4me3)-specific demethylase KDM5A/B play a role in suppressing HIV-1 Tat/LTR-mediated viral transcription in HIV-1 latent cells. Furthermore, we evaluated the potential of KDM5-specific inhibitor JQKD82 as an HIV-1 "shock and kill" agent. Our results showed that JQKD82 increases the H3K4me3 level at HIV-1 5' LTR promoter regions, HIV-1 reactivation, and the cytopathic effects in an HIV-1-latent T cell model. In addition, we identified that the combination of JQKD82 and AZD5582, a non-canonical NF-κB activator, generates a synergistic impact on inducing HIV-1 lytic reactivation and cell death in the T cell. The latency-reversing potency of the JQKD82 and AZD5582 pair was also confirmed in peripheral blood mononuclear cells (PBMCs) isolated from HIV-1 aviremic patients and in an HIV-1 latent monocyte. In latently infected microglia (HC69) of the brain, either deletion or inhibition of KDM5A/B results in a reversal of the HIV-1 latency. Overall, we concluded that KDM5A/B function as a host repressor of the HIV-1 lytic reactivation and thus promote the latency and the survival of HIV-1 infected reservoirs.
Collapse
Affiliation(s)
- Tai-Wei Li
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Youngmin Park
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Emily G Watters
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Xu Wang
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Dawei Zhou
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Guillaume N Fiches
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Zhenyu Wu
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Andrew D Badley
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN, 55902, USA
| | - Jonah B Sacha
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Wen-Zhe Ho
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Netty G Santoso
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Jun Qi
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Jian Zhu
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA; Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
3
|
Lysenkova Wiklander M, Arvidsson G, Bunikis I, Lundmark A, Raine A, Marincevic-Zuniga Y, Gezelius H, Bremer A, Feuk L, Ameur A, Nordlund J. A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing. Life Sci Alliance 2024; 7:e202302481. [PMID: 38777370 PMCID: PMC11111970 DOI: 10.26508/lsa.202302481] [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: 11/14/2023] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
The B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21) ETV6::RUNX1 translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-yr-old at relapse, the cell line offers a practical model for the study of pediatric B-ALL. In recent years, short- and long-read DNA and RNA sequencing have emerged as a complement to karyotyping techniques in the resolution of structural variants in an oncological context. Here, we explore the integration of long-read PacBio and Oxford Nanopore whole-genome sequencing, IsoSeq RNA sequencing, and short-read Illumina sequencing to create a detailed genomic and transcriptomic characterization of the REH cell line. Whole-genome sequencing clarified the molecular traits of disrupted ALL-associated genes including CDKN2A, PAX5, BTG1, VPREB1, and TBL1XR1, as well as the glucocorticoid receptor NR3C1 Meanwhile, transcriptome sequencing identified seven fusion genes within the genomic breakpoints. Together, our extensive whole-genome investigation makes high-quality open-source data available to the leukemia genomics community.
Collapse
Affiliation(s)
- Mariya Lysenkova Wiklander
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Gustav Arvidsson
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Anders Lundmark
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Yanara Marincevic-Zuniga
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Henrik Gezelius
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Anna Bremer
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/01apvbh93 Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Lars Feuk
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| |
Collapse
|
4
|
Zhang J, Huang H, Ding B, Liu Z, Chen D, Li S, Shen T, Zhu Q. Histone demethylase KDM4A mediating macrophage polarization: A potential mechanism of trichloroethylene induced liver injury. Cell Biol Int 2024; 48:1148-1159. [PMID: 38800986 DOI: 10.1002/cbin.12187] [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: 01/20/2024] [Revised: 03/26/2024] [Accepted: 05/02/2024] [Indexed: 05/29/2024]
Abstract
Trichloroethylene (TCE) is a commonly used organic solvent in industry. Our previous studies have found that TCE can cause liver injury accompanied by macrophage polarization, but the specific mechanism is unclear. The epigenetic regulation of macrophage polarization is mainly focused on histone modification. Histone lysine demethylase 4A (KDM4A) is involved in the activation of macrophages. In this study, we used a mouse model we investigated the role of KDM4A in the livers of TCE-drinking mice and found that the expression of KDM4A, M1-type polarization indicators, and related inflammatory factors in the livers of TCE-drinking mice. In the study, BALB/c mice were randomly divided into four groups: 2.5 mg/mL TCE dose group and 5.0 mg/mL TCE dose group, the vehicle control group, and the blank control group. We found that TCE triggered M1 polarization of mouse macrophages, characterized by the expression of CD11c and robust production of inflammatory cytokines. Notably, exposure to TCE resulted in markedly increased expression of KDM4A in macrophages. Functionally, the increased expression of KDM4A significantly impaired the expression of H3K9me3 and H3K9me2 and increased the expression of H3K9me1. In addition, KDM4A potentially represents a novel epigenetic modulator, with its upregulation connected to β-catenin activation, a signal critical for the pro-inflammatory activation of macrophages. Furthermore, KDM4A inhibitor JIB-04 treatment resulted in a decrease in β-catenin expression and prevented TCE-induced M1 polarization and the expression of the pro-inflammatory cytokines TNF-α and IL-1β. These results suggest that the association of KDM4A and Wnt/β-catenin cooperatively establishes the activation and polarization of macrophages and global changes in H3K9me3/me2/me1. Our findings identify KDM4A as an essential regulator of the polarization of macrophages and the expression of inflammatory cytokines, which might serve as a potential target for preventing and treating liver injury caused by TCE.
Collapse
Affiliation(s)
- Jiaxiang Zhang
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Key Laboratory of Dermatology, Ministry of Education, Hefei, Anhui, China
| | - Hua Huang
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department Of Infectious Disease Prevention and Control, Linan District Center for Disease Control and Prevention, Hangzhou City, Zhejiang Province, China
| | - Baiwang Ding
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department Of Infectious Disease Prevention and Control, Linan District Center for Disease Control and Prevention, Hangzhou City, Zhejiang Province, China
| | - Zhibing Liu
- Institute of Dermatology, Key Laboratory of Dermatology, Ministry of Education, Hefei, Anhui, China
- Department of Dermatology, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Daojun Chen
- Institute of Medical Technology, Anhui Medical College, Hefei, Anhui, China
| | - Shulong Li
- The Center for Scientific Research, Anhui Medical University, Hefei, Anhui, China
| | - Tong Shen
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Key Laboratory of Dermatology, Ministry of Education, Hefei, Anhui, China
| | - Qixing Zhu
- Institute of Dermatology, Key Laboratory of Dermatology, Ministry of Education, Hefei, Anhui, China
- Department of Dermatology, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| |
Collapse
|
5
|
Chen L, Liu J, Chen K, Su Y, Chen Y, Lei Y, Si J, Zhang J, Zhang Z, Zou W, Zhang X, Rondina MT, Wang QF, Li Y. SET domain containing 2 promotes megakaryocyte polyploidization and platelet generation through methylation of α-tubulin. J Thromb Haemost 2024; 22:1727-1741. [PMID: 38537781 DOI: 10.1016/j.jtha.2024.03.010] [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: 08/29/2023] [Revised: 02/23/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Megakaryocytes (MKs) are polyploid cells responsible for producing ∼1011 platelets daily in humans. Unraveling the mechanisms regulating megakaryopoiesis holds the promise for the production of clinical-grade platelets from stem cells, overcoming significant current limitations in platelet transfusion medicine. Previous work identified that loss of the epigenetic regulator SET domain containing 2 (SETD2) was associated with an increased platelet count in mice. However, the role of SETD2 in megakaryopoiesis remains unknown. OBJECTIVES Here, we examined how SETD2 regulated MK development and platelet production using complementary murine and human systems. METHODS We manipulated the expression of SETD2 in multiple in vitro and ex vivo models to assess the ploidy of MKs and the function of platelets. RESULTS The genetic ablation of Setd2 increased the number of high-ploidy bone marrow MKs. Peripheral platelet counts in Setd2 knockout mice were significantly increased ∼2-fold, and platelets exhibited normal size, morphology, and function. By knocking down and overexpressing SETD2 in ex vivo human cell systems, we demonstrated that SETD2 negatively regulated MK polyploidization by controlling methylation of α-tubulin, microtubule polymerization, and MK nuclear division. Small-molecule inactivation of SETD2 significantly increased the production of high-ploidy MKs and platelets from human-induced pluripotent stem cells and cord blood CD34+ cells. CONCLUSION These findings identify a previously unrecognized role for SETD2 in regulating megakaryopoiesis and highlight the potential of targeting SETD2 to increase platelet production from human cells for transfusion practices.
Collapse
Affiliation(s)
- Lei Chen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jingkun Liu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Kunying Chen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yanxun Su
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yihe Chen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ying Lei
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jia Si
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jie Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zhaojun Zhang
- University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center of Bioinformation, Beijing, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Weiguo Zou
- Shanghai Institute of Microsurgery on Extremities, and Department of Orthopedic Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China; State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiaohui Zhang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing, China; National Clinical Research Center for Hematologic Disease, Beijing, China; Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China; Collaborative Innovation Center of Hematology, Peking University, Beijing, China
| | - Matthew T Rondina
- Departments of Internal Medicine and Pathology, Molecular Medicine Program, University of Utah, Salt Lake City, Utah, USA; Department of Internal Medicine and the Geriatric Research, Education, and Clinical Center, George E. Wahlen Veterans Affairs Medical Center, Salt Lake City, Utah, USA.
| | - Qian-Fei Wang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Yueying Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
6
|
Chen S, Zhang Z, Peng H, Jiang S, Xu C, Ma X, Zhang L, Zhou H, Xing X, Chen L, Wang Q, Chen W, Li D. Histone H3K36me3 mediates the genomic instability of Benzo[a]pyrene in human bronchial epithelial cells. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123564. [PMID: 38367693 DOI: 10.1016/j.envpol.2024.123564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/13/2023] [Accepted: 02/11/2024] [Indexed: 02/19/2024]
Abstract
Histone modifications maintain genomic stability and orchestrate gene expression at the chromatin level. Benzo [a]pyrene (BaP) is the ubiquitous carcinogen widely spread in the environment, but the role and regulatory mechanism of histone modification in its toxic effects remain largely undefined. In this study, we found a dose-dependent reduction of histone H3 methylations at lysine4, lysine9, lysine27, lysine36 in HBE cells treated with BaP. We observed that inhibiting H3K27 and H3K36 methylation impaired cell proliferation, whereas the loss of H3K4, H3K9, H3K27, and H3K36 methylation led to increased genomic instability and delayed DNA repair. H3K36 mutation at both H3.1 and H3.3 exhibited the most significant impacts. In addition, we found that the expression of SET domain containing 2 (SETD2), the unique methyltransferase catalyzed H3K36me3, was downregulated by BaP dose-dependently in vitro and in vivo. Knockdown of SETD2 aggravated DNA damage of BaP exposure, which was consistent with the effects of H3K36 mutation. With the aid of chromatin immunoprecipitation (ChIP) -seq and RNA-seq, we found that H3K36me3 was responsible for transcriptional regulation of genes involved in pathways related to cell survival, lung cancer, metabolism and inflammation. The enhanced enrichment of H3K36me3 in genes (CYP1A1, ALDH1A3, ACOXL, WNT5A, WNT7A, RUNX2, IL1R2) was positively correlated with their expression levels, while the reduction of H3K36me3 distribution in genes (PPARGC1A, PDE4D, GAS1, RNF19A, KSR1) were in accordance with the downregulation of gene expression. Taken together, our findings emphasize the critical roles and mechanisms of histone lysine methylation in mediating cellular homeostasis during BaP exposure.
Collapse
Affiliation(s)
- Shen Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Zhengbao Zhang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Department of Toxicology, School of Public Health, Guilin Medical University, Guilin, 541199, Guangxi, China
| | - Honghao Peng
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Shuyun Jiang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Chi Xu
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xingyu Ma
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Liying Zhang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Hao Zhou
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xiumei Xing
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Liping Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Qing Wang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Wen Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Daochuan Li
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China.
| |
Collapse
|
7
|
Yang G, Li C, Tao F, Liu Y, Zhu M, Du Y, Fei C, She Q, Chen J. The emerging roles of lysine-specific demethylase 4A in cancer: Implications in tumorigenesis and therapeutic opportunities. Genes Dis 2024; 11:645-663. [PMID: 37692513 PMCID: PMC10491877 DOI: 10.1016/j.gendis.2022.12.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 12/28/2022] [Indexed: 09/12/2023] Open
Abstract
Lysine-specific demethylase 4 A (KDM4A, also named JMJD2A, KIA0677, or JHDM3A) is a demethylase that can remove methyl groups from histones H3K9me2/3, H3K36me2/3, and H1.4K26me2/me3. Accumulating evidence suggests that KDM4A is not only involved in body homeostasis (such as cell proliferation, migration and differentiation, and tissue development) but also associated with multiple human diseases, especially cancers. Recently, an increasing number of studies have shown that pharmacological inhibition of KDM4A significantly attenuates tumor progression in vitro and in vivo in a range of solid tumors and acute myeloid leukemia. Although there are several reviews on the roles of the KDM4 subfamily in cancer development and therapy, all of them only briefly introduce the roles of KDM4A in cancer without systematically summarizing the specific mechanisms of KDM4A in various physiological and pathological processes, especially in tumorigenesis, which greatly limits advances in the understanding of the roles of KDM4A in a variety of cancers, discovering targeted selective KDM4A inhibitors, and exploring the adaptive profiles of KDM4A antagonists. Herein, we present the structure and functions of KDM4A, simply outline the functions of KDM4A in homeostasis and non-cancer diseases, summarize the role of KDM4A and its distinct target genes in the development of a variety of cancers, systematically classify KDM4A inhibitors, summarize the difficulties encountered in the research of KDM4A and the discovery of related drugs, and provide the corresponding solutions, which would contribute to understanding the recent research trends on KDM4A and advancing the progression of KDM4A as a drug target in cancer therapy.
Collapse
Affiliation(s)
- Guanjun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Changyun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Fan Tao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yanjun Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Minghui Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yu Du
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Chenjie Fei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Qiusheng She
- School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, Henan 467044, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
| |
Collapse
|
8
|
Li XX, Xu JK, Su WJ, Wu HL, Zhao K, Zhang CM, Chen XK, Yang LX. The role of KDM4A-mediated histone methylation on temozolomide resistance in glioma cells through the HUWE1/ROCK2 axis. Kaohsiung J Med Sci 2024; 40:161-174. [PMID: 37873881 DOI: 10.1002/kjm2.12768] [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: 07/19/2023] [Revised: 09/05/2023] [Accepted: 09/20/2023] [Indexed: 10/25/2023] Open
Abstract
Temozolomide (TMZ) resistance presents a significant challenge in the treatment of gliomas. Although lysine demethylase 4A (KDM4A) has been implicated in various cancer-related processes, its role in TMZ resistance remains unclear. This study aims to elucidate the contribution of KDM4A to TMZ resistance in glioma cells and its potential implications for glioma prognosis. We assessed the expression of KDM4A in glioma cells (T98G and U251MG) using qRT-PCR and Western blot assays. To explore the role of KDM4A in TMZ resistance, we transfected siRNA targeting KDM4A into drug-resistant glioma cells. Cell viability was assessed using the CCK-8 assay and the TMZ IC50 value was determined. ChIP assays were conducted to investigate KDM4A, H3K9me3, and H3K36me3 enrichment on the promoters of ROCK2 and HUWE1. Co-immunoprecipitation confirmed the interaction between HUWE1 and ROCK2, and we examined the levels of ROCK2 ubiquitination following MG132 treatment. Notably, T98G cells exhibited greater resistance to TMZ than U251MG cells, and KDM4A displayed high expression in T98G cells. Inhibiting KDM4A resulted in decreased cell viability and a reduction in the TMZ IC50 value. Mechanistically, KDM4A promoted ROCK2 transcription by modulating H3K9me3 levels. Moreover, disruption of the interaction between HUWE1 and ROCK2 led to reduced ROCK2 ubiquitination. Inhibition of HUWE1 or overexpression of ROCK2 counteracted the sensitization effect of si-KDM4A on TMZ responsiveness in T98G cells. Our findings highlight KDM4A's role in enhancing TMZ resistance in glioma cells by modulating ROCK2 and HUWE1 transcription and expression through H3K9me3 and H3K36me3 removal.
Collapse
Affiliation(s)
- Xi-Xi Li
- Department of Neurosurgery, Sun Yat-sen University 1st Affiliated Hospital, Guangzhou, China
| | - Jia-Kun Xu
- Department of Neurosurgery, Sun Yat-sen University 1st Affiliated Hospital, Guangzhou, China
| | - Wei-Jie Su
- Department of Neurosurgery, Sun Yat-sen University 1st Affiliated Hospital, Guangzhou, China
| | - Hong-Lin Wu
- Department of Neurosurgery, Sun Yat-sen University 1st Affiliated Hospital, Guangzhou, China
| | - Kun Zhao
- Department of Neurosurgery, Sun Yat-sen University 1st Affiliated Hospital, Guangzhou, China
| | - Chang-Ming Zhang
- Department of Neurosurgery, Sun Yat-sen University 1st Affiliated Hospital, Guangzhou, China
| | - Xiang-Kun Chen
- Department of Emergency, The First People's Hospital of Suqian, Suqian, China
| | - Li-Xuan Yang
- Department of Neurosurgery, Sun Yat-sen University 1st Affiliated Hospital, Guangzhou, China
| |
Collapse
|
9
|
Contreras Yametti GP, Robbins G, Chowdhury A, Narang S, Ostrow TH, Kilberg H, Greenberg J, Kramer L, Raetz E, Tsirigos A, Evensen NA, Carroll WL. SETD2 mutations do not contribute to clonal fitness in response to chemotherapy in childhood B cell acute lymphoblastic leukemia. Leuk Lymphoma 2024; 65:78-90. [PMID: 37874744 DOI: 10.1080/10428194.2023.2273752] [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: 06/19/2023] [Accepted: 10/14/2023] [Indexed: 10/26/2023]
Abstract
Mutations in genes encoding epigenetic regulators are commonly observed at relapse in B cell acute lymphoblastic leukemia (B-ALL). Loss-of-function mutations in SETD2, an H3K36 methyltransferase, have been observed in B-ALL and other cancers. Previous studies on mutated SETD2 in solid tumors and acute myelogenous leukemia support a role in promoting resistance to DNA damaging agents. We did not observe chemoresistance, an impaired DNA damage response, nor increased mutation frequency in response to thiopurines using CRISPR-mediated knockout in wild-type B-ALL cell lines. Likewise, restoration of SETD2 in cell lines with hemizygous mutations did not increase sensitivity. SETD2 mutations affected the chromatin landscape and transcriptional output that was unique to each cell line. Collectively our data does not support a role for SETD2 mutations in driving clonal evolution and relapse in B-ALL, which is consistent with the lack of enrichment of SETD2 mutations at relapse in most studies.
Collapse
Affiliation(s)
- Gloria P Contreras Yametti
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Gabriel Robbins
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Ashfiyah Chowdhury
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Sonali Narang
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Talia H Ostrow
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Harrison Kilberg
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Joshua Greenberg
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Lindsay Kramer
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Elizabeth Raetz
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Aristotelis Tsirigos
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Nikki A Evensen
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - William L Carroll
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Langone Health, New York, NY, USA
| |
Collapse
|
10
|
Liu H. SETD2 detection may reveal response to induction therapy and survival profile in acute myeloid leukemia patients. HEMATOLOGY (AMSTERDAM, NETHERLANDS) 2023; 28:2161194. [PMID: 36607144 DOI: 10.1080/16078454.2022.2161194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVE SET domain containing protein 2 (SETD2) involves in the progression and development of chemotherapy resistance in acute myeloid leukemia (AML). Hence, this study aimed to investigate the relationship of SETD2 expression with disease risk, features, treatment response, and survival profile in AML. METHODS One-hundred and sixty primary AML patients were retrospectively analyzed. Their bone marrow (BM) samples before and after induction therapy were retrieved for SETD2 detection by RT-qPCR. Moreover, SETD2 expression in BM samples of 20 disease controls (DCs) were also determined. RESULTS SETD2 expression was downregulated in AML patients compared to DCs (P < 0.001). Higher SETD2 expression related to white blood cells ≤10 × 109/L despite not reaching statistical significance (P = 0.062). One-hundred and nineteen (74.4%) AML patients achieved complete response (CR), while the remaining 41 (25.6%) did not achieve that. Furthermore, increased SETD2 expression was associated with CR achievement (P = 0.015). Survival analyses displayed that SETD2 high (vs. low) was related to prolonged event-free survival (EFS) (P = 0.001) and overall survival (OS) (P = 0.021). Moreover, increased SETD2 quartile was correlated with favorable EFS (P = 0.004) and OS (P = 0.042). After adjustment using multivariate Cox's regression analysis, higher SETD2 quartile was independently related to prolonged EFS [hazard ratio (HR): 0.766, P = 0.013] and OS (HR: 0.669, P = 0.013). It was also noticed that SETD2 expression was elevated during the induction therapy (P < 0.001). CONCLUSION Detection of SETD2 may assist in estimating treatment response and survival profile in AML patients.
Collapse
Affiliation(s)
- Hui Liu
- Department of Hematology, 3201 Hospital of Xi'an Jiaotong University Health Science Center, Hanzhong, People's Republic of China
| |
Collapse
|
11
|
Aziz N, Hong YH, Kim HG, Kim JH, Cho JY. Tumor-suppressive functions of protein lysine methyltransferases. Exp Mol Med 2023; 55:2475-2497. [PMID: 38036730 PMCID: PMC10766653 DOI: 10.1038/s12276-023-01117-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 12/02/2023] Open
Abstract
Protein lysine methyltransferases (PKMTs) play crucial roles in histone and nonhistone modifications, and their dysregulation has been linked to the development and progression of cancer. While the majority of studies have focused on the oncogenic functions of PKMTs, extensive evidence has indicated that these enzymes also play roles in tumor suppression by regulating the stability of p53 and β-catenin, promoting α-tubulin-mediated genomic stability, and regulating the transcription of oncogenes and tumor suppressors. Despite their contradictory roles in tumorigenesis, many PKMTs have been identified as potential therapeutic targets for cancer treatment. However, PKMT inhibitors may have unintended negative effects depending on the specific cancer type and target enzyme. Therefore, this review aims to comprehensively summarize the tumor-suppressive effects of PKMTs and to provide new insights into the development of anticancer drugs targeting PKMTs.
Collapse
Affiliation(s)
- Nur Aziz
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yo Han Hong
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Han Gyung Kim
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Ji Hye Kim
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Jae Youl Cho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| |
Collapse
|
12
|
Mason FM, Kounlavong ES, Tebeje AT, Dahiya R, Guess T, Khan A, Vlach L, Norris SR, Lovejoy CA, Dere R, Strahl BD, Ohi R, Ly P, Walker CL, Rathmell WK. SETD2 safeguards the genome against isochromosome formation. Proc Natl Acad Sci U S A 2023; 120:e2303752120. [PMID: 37722039 PMCID: PMC10523680 DOI: 10.1073/pnas.2303752120] [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: 03/06/2023] [Accepted: 08/11/2023] [Indexed: 09/20/2023] Open
Abstract
Isochromosomes are mirror-imaged chromosomes with simultaneous duplication and deletion of genetic material which may contain two centromeres to create isodicentric chromosomes. Although isochromosomes commonly occur in cancer and developmental disorders and promote genome instability, mechanisms that prevent isochromosomes are not well understood. We show here that the tumor suppressor and methyltransferase SETD2 is essential to prevent these errors. Using cellular and cytogenetic approaches, we demonstrate that loss of SETD2 or its epigenetic mark, histone H3 lysine 36 trimethylation (H3K36me3), results in the formation of isochromosomes as well as isodicentric and acentric chromosomes. These defects arise during DNA replication and are likely due to faulty homologous recombination by RAD52. These data provide a mechanism for isochromosome generation and demonstrate that SETD2 and H3K36me3 are essential to prevent the formation of this common mutable chromatin structure known to initiate a cascade of genomic instability in cancer.
Collapse
Affiliation(s)
- Frank M. Mason
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232
| | - Emily S. Kounlavong
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232
| | - Anteneh T. Tebeje
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232
| | - Rashmi Dahiya
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Tiffany Guess
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN37232
| | - Abid Khan
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Logan Vlach
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232
| | - Stephen R. Norris
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232
| | | | - Ruhee Dere
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX77030
| | - Brian D. Strahl
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI48109
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Cheryl Lyn Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX77030
| | - W. Kimryn Rathmell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232
| |
Collapse
|
13
|
Song YQ, Yang GJ, Ma DL, Wang W, Leung CH. The role and prospect of lysine-specific demethylases in cancer chemoresistance. Med Res Rev 2023; 43:1438-1469. [PMID: 37012609 DOI: 10.1002/med.21955] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 02/08/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023]
Abstract
Histone methylation plays a key function in modulating gene expression, and preserving genome integrity and epigenetic inheritance. However, aberrations of histone methylation are commonly observed in human diseases, especially cancer. Lysine methylation mediated by histone methyltransferases can be reversed by lysine demethylases (KDMs), which remove methyl marks from histone lysine residues. Currently, drug resistance is a main impediment for cancer therapy. KDMs have been found to mediate drug tolerance of many cancers via altering the metabolic profile of cancer cells, upregulating the ratio of cancer stem cells and drug-tolerant genes, and promoting the epithelial-mesenchymal transition and metastatic ability. Moreover, different cancers show distinct oncogenic addictions for KDMs. The abnormal activation or overexpression of KDMs can alter gene expression signatures to enhance cell survival and drug resistance in cancer cells. In this review, we describe the structural features and functions of KDMs, the KDMs preferences of different cancers, and the mechanisms of drug resistance resulting from KDMs. We then survey KDM inhibitors that have been used for combating drug resistance in cancer, and discuss the opportunities and challenges of KDMs as therapeutic targets for cancer drug resistance.
Collapse
Affiliation(s)
- Ying-Qi Song
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Guan-Jun Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Wanhe Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao, China
| |
Collapse
|
14
|
Wei S, Luo S, Zhang H, Li Y, Zhao J. Paternal high-fat diet altered SETD2 gene methylation in sperm of F0 and F1 mice. GENES & NUTRITION 2023; 18:12. [PMID: 37598138 PMCID: PMC10439541 DOI: 10.1186/s12263-023-00731-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/11/2023] [Indexed: 08/21/2023]
Abstract
Paternal high-fat diet (HFD) can alter the epigenetics of sperm DNA, resulting in the transmission of obesity-related traits to the offspring. Previous studies have mainly focused on the HFD-induced changes in DNA methylation of imprinted genes, overlooking the potential involvement of non-imprinted genes in this process. SETD2, an important epigenetically-regulated gene known for its response to environmental stress, remains poorly understood in the context of high-fat diet-induced epigenetic changes. Here we examined the effect of obesity from a HFD on paternal SETD2 expression and methylation in sperm, and embryos at the blastocyst stage and during subsequent development, to determine the alteration of SETD2 in paternal intergenerational and transgenerational inheritance. The result showed that mice fed with HFD for two months had significantly increased SETD2 expression in testis and sperm. The paternal HFD significantly altered the DNA methylation level with 20 of the 26 CpG sites being changed in sperm from F0 mice. Paternal high-fat diet increased apoptotic index and decreased total cell number of blastocysts, which were closely correlated with DNA methylation level of sperm. Out of the 26 CpG sites, we also found three CpG sites that were significantly changed in the sperm from F1 mice, which meant that the methylation changes at these three CpG sites were maintained.In conclusion, we found that paternal exposure to an HFD disrupted the methylation pattern of SETD2 in the sperm of F0 mice and resulted in perturbed SETD2 expression. Furthermore, the paternal high-fat diet influenced embryo apoptosis and development, possibly through the SETD2 pathway. The altered methylation of SETD2 in sperm induced by paternal HFD partially persisted in the sperm of the F1 generation, highlighting the role of SETD2 as an epigenetic carrier for paternal intergenerational and transgenerational inheritance.
Collapse
Affiliation(s)
- Suhua Wei
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shiwei Luo
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University, Guangzhou, China
| | - Haifeng Zhang
- Xi'an International Medical Center Hospital, Xi'an, Shaanxi, China
| | - Yandong Li
- Xi'an International Medical Center Hospital, Xi'an, Shaanxi, China.
| | - Juan Zhao
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| |
Collapse
|
15
|
Leandro-García LJ, Landa I. Mechanistic Insights of Thyroid Cancer Progression. Endocrinology 2023; 164:bqad118. [PMID: 37503738 PMCID: PMC10403681 DOI: 10.1210/endocr/bqad118] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023]
Abstract
Differentiated thyroid cancers (DTCs) are primarily initiated by mutations that activate the MAPK signaling cascade, typically at BRAF or RAS oncoproteins. DTCs can evolve to more aggressive forms, specifically, poorly differentiated (PDTC) and anaplastic thyroid cancers (ATC), by acquiring additional genetic alterations which deregulate key pathways. In this review, we focused on bona fide mutations involved in thyroid cancer progression for which consistent mechanistic data exist. Here we summarized the relevant literature, spanning approximately 2 decades, highlighting genetic alterations that are unquestionably enriched in PDTC/ATC. We describe the relevant functional data obtained in multiple in vitro and in vivo thyroid cancer models employed to study genetic alterations in the following genes and functional groups: TP53, effectors of the PI3K/AKT pathway, TERT promoter, members of the SWI/SNF chromatin remodeling complex, NF2, and EIF1AX. In addition, we briefly discuss other genetic alterations that are selected in aggressive thyroid tumors but for which mechanistic data is still either limited or nonexistent. Overall, we argue for the importance conveyed by preclinical studies for the clinical translation of genomic knowledge of thyroid cancers.
Collapse
Affiliation(s)
- Luis Javier Leandro-García
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Iñigo Landa
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
16
|
He J, Xu T, Zhao F, Guo J, Hu Q. SETD2-H3K36ME3: an important bridge between the environment and tumors. Front Genet 2023; 14:1204463. [PMID: 37359376 PMCID: PMC10288198 DOI: 10.3389/fgene.2023.1204463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
Epigenetic regulation plays an important role in the occurrence, development and treatment of tumors. The histone methyltransferase SET-domain-containing 2 (SETD2) plays a key role in mammalian epigenetic regulation by catalyzing histone methylation and interacting with RNA polymerase II to mediate transcription elongation and mismatch repair. As an important bridge between the environment and tumors, SETD2-H3K36me3 plays an important role in the occurrence and development of tumors. Many tumors, including renal cancer, gastric cancer, lung cancer, are closely related to SETD2 gene mutations. As a key component of common tumor suppressor mechanisms, SETD2-H3K36me3is an important target for clinical disease diagnosis and treatment. Here, we reviewed the structure and function of the SETD2 and how SETD2-H3K36me3 functions as a bridge between the environment and tumors to provide an in-depth understanding of its role in the occurrence and development of various tumors, which is of great significance for future disease diagnosis and treatment.
Collapse
Affiliation(s)
- Jiahui He
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Tangpeng Xu
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Fangrui Zhao
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jin Guo
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Qinyong Hu
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| |
Collapse
|
17
|
Ribeiro ML, Sánchez Vinces S, Mondragon L, Roué G. Epigenetic targets in B- and T-cell lymphomas: latest developments. Ther Adv Hematol 2023; 14:20406207231173485. [PMID: 37273421 PMCID: PMC10236259 DOI: 10.1177/20406207231173485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 04/17/2023] [Indexed: 06/06/2023] Open
Abstract
Non-Hodgkin's lymphomas (NHLs) comprise a diverse group of diseases, either of mature B-cell or of T-cell derivation, characterized by heterogeneous molecular features and clinical manifestations. While most of the patients are responsive to standard chemotherapy, immunotherapy, radiation and/or stem cell transplantation, relapsed and/or refractory cases still have a dismal outcome. Deep sequencing analysis have pointed out that epigenetic dysregulations, including mutations in epigenetic enzymes, such as chromatin modifiers and DNA methyltransferases (DNMTs), are prevalent in both B- cell and T-cell lymphomas. Accordingly, over the past decade, a large number of epigenetic-modifying agents have been developed and introduced into the clinical management of these entities, and a few specific inhibitors have already been approved for clinical use. Here we summarize the main epigenetic alterations described in B- and T-NHL, that further supported the clinical development of a selected set of epidrugs in determined diseases, including inhibitors of DNMTs, histone deacetylases (HDACs), and extra-terminal domain proteins (bromodomain and extra-terminal motif; BETs). Finally, we highlight the most promising future directions of research in this area, explaining how bioinformatics approaches can help to identify new epigenetic targets in B- and T-cell lymphoid neoplasms.
Collapse
Affiliation(s)
- Marcelo Lima Ribeiro
- Lymphoma Translational Group, Josep Carreras
Leukaemia Research Institute, Badalona, Spain
- Laboratory of Immunopharmacology and Molecular
Biology, Sao Francisco University Medical School, Braganca Paulista,
Brazil
| | - Salvador Sánchez Vinces
- Laboratory of Immunopharmacology and Molecular
Biology, Sao Francisco University Medical School, Braganca Paulista,
Brazil
| | - Laura Mondragon
- T Cell Lymphoma Group, Josep Carreras Leukaemia
Research Institute, IJC. Ctra de Can Ruti, Camí de les Escoles s/n, 08916
Badalona, Barcelona, Spain
| | - Gael Roué
- Lymphoma Translational Group, Josep Carreras
Leukaemia Research Institute, IJC. Ctra de Can Ruti, Camí de les Escoles
s/n, 08916 Badalona, Barcelona, Spain
| |
Collapse
|
18
|
Tian H, Wang Y, Yang Z, Chen P, Xu J, Tian Y, Fan T, Xiao C, Bai G, Li L, Zheng B, Li C, He J. Genetic trajectory and clonal evolution of multiple primary lung cancer with lymph node metastasis. Cancer Gene Ther 2023; 30:507-520. [PMID: 36653483 PMCID: PMC10014582 DOI: 10.1038/s41417-022-00572-0] [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: 06/20/2022] [Revised: 11/10/2022] [Accepted: 11/25/2022] [Indexed: 01/20/2023]
Abstract
Multiple primary lung cancer (MPLC) with lymph node metastasis (LNM) is a rare phenomenon of multifocal lung cancer. The genomic landscapes of MPLC and the clonal evolution pattern between primary lung lesions and lymph node metastasis haven't been fully illustrated. We performed whole-exome sequencing (WES) on 52 FFPE (Formalin-fixed Paraffin-Embedded) samples from 11 patients diagnosed with MPLC with LNM. Genomic profiling and phylogenetic analysis were conducted to infer the evolutional trajectory within each patient. The top 5 most frequently mutated genes in our study were TTN (76.74%), MUC16 (62.79%), MUC19 (55.81%), FRG1 (46.51%), and NBPF20 (46.51%). For most patients in our study, a substantial of genetic alterations were mutually exclusive among the multiple pulmonary tumors of the same patient, suggesting their heterogenous origins. Individually, the genetic profile of lymph node metastatic lesions overlapped with that of multiple lung cancers in different degrees but are more genetically related to specific pulmonary lesions. SETD2 was a potential metastasis biomarker of MPLC. The mean putative neo-antigen number of the primary tumor (646.5) is higher than that of lymph node metastases (300, p = 0.2416). Primary lung tumors and lymph node metastases are highly heterogenous in immune repertoires. Our findings portrayed the comprehensive genomic landscape of MPLC with LNM. We characterized the genomic heterogeneity among different tumors. We offered novel clues to the clonal evolution between MPLC and their lymphatic metastases, thus advancing the treatment strategies and preventions of MPLC with LNM.
Collapse
Affiliation(s)
- He Tian
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Yalong Wang
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Zhenlin Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Ping Chen
- Department of Medical Oncology, Yancheng No. 1 People's Hospital, Yancheng, Jiangsu, 224000, China
| | - Jiachen Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Guangdong Provincial People's Hospital/Guangdong Provincial Academy of Medical Sciences, Guangdong Provincial Key Lab of Translational Medicine in Lung Cancer, Guangzhou, China
| | - Yanhua Tian
- Department of Thoracic Surgery/Head & Neck Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Tao Fan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Chu Xiao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Guangyu Bai
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Lin Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Bo Zheng
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Chunxiang Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China.
| |
Collapse
|
19
|
Kim R, Bergugnat H, Larcher L, Duchmann M, Passet M, Gachet S, Cuccuini W, Lafage-Pochitaloff M, Pastoret C, Grardel N, Asnafi V, Schäfer BW, Delabesse E, Itzykson R, Adès L, Hicheri Y, Chalandon Y, Graux C, Chevallier P, Hunault M, Leguay T, Huguet F, Lhéritier V, Dombret H, Soulier J, Rousselot P, Boissel N, Clappier E. Adult Low-Hypodiploid Acute Lymphoblastic Leukemia Emerges from Preleukemic TP53-Mutant Clonal Hematopoiesis. Blood Cancer Discov 2023; 4:134-149. [PMID: 36630200 PMCID: PMC9975768 DOI: 10.1158/2643-3230.bcd-22-0154] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/29/2022] [Accepted: 01/10/2023] [Indexed: 01/12/2023] Open
Abstract
Low hypodiploidy defines a rare subtype of B-cell acute lymphoblastic leukemia (B-ALL) with a dismal outcome. To investigate the genomic basis of low-hypodiploid ALL (LH-ALL) in adults, we analyzed copy-number aberrations, loss of heterozygosity, mutations, and cytogenetics data in a prospective cohort of Philadelphia (Ph)-negative B-ALL patients (n = 591, ages 18-84 years), allowing us to identify 80 LH-ALL cases (14%). Genomic analysis was critical for evidencing low hypodiploidy in many cases missed by cytogenetics. The proportion of LH-ALL within Ph-negative B-ALL dramatically increased with age, from 3% in the youngest patients (under 40 years old) to 32% in the oldest (over 55 years old). Somatic TP53 biallelic inactivation was the hallmark of adult LH-ALL, present in virtually all cases (98%). Strikingly, we detected TP53 mutations in posttreatment remission samples in 34% of patients. Single-cell proteogenomics of diagnosis and remission bone marrow samples evidenced a preleukemic, multilineage, TP53-mutant clone, reminiscent of age-related clonal hematopoiesis. SIGNIFICANCE We show that low-hypodiploid ALL is a frequent entity within B-ALL in older adults, relying on somatic TP53 biallelic alteration. Our study unveils a link between aging and low-hypodiploid ALL, with TP53-mutant clonal hematopoiesis representing a preleukemic reservoir that can give rise to aneuploidy and B-ALL. See related commentary by Saiki and Ogawa, p. 102. This article is highlighted in the In This Issue feature, p. 101.
Collapse
Affiliation(s)
- Rathana Kim
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), Institut National de la Santé et de la Recherche Médicale (INSERM) U944, Centre National de la Recherche Scientifique (CNRS) UMR 7212 GenCellDis, Paris, France
- Laboratoire d'Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Hugo Bergugnat
- Laboratoire d'Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Lise Larcher
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), Institut National de la Santé et de la Recherche Médicale (INSERM) U944, Centre National de la Recherche Scientifique (CNRS) UMR 7212 GenCellDis, Paris, France
- Laboratoire d'Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Matthieu Duchmann
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), Institut National de la Santé et de la Recherche Médicale (INSERM) U944, Centre National de la Recherche Scientifique (CNRS) UMR 7212 GenCellDis, Paris, France
| | - Marie Passet
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), Institut National de la Santé et de la Recherche Médicale (INSERM) U944, Centre National de la Recherche Scientifique (CNRS) UMR 7212 GenCellDis, Paris, France
- Laboratoire d'Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Stéphanie Gachet
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), Institut National de la Santé et de la Recherche Médicale (INSERM) U944, Centre National de la Recherche Scientifique (CNRS) UMR 7212 GenCellDis, Paris, France
| | - Wendy Cuccuini
- Laboratoire d'Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France
| | - Marina Lafage-Pochitaloff
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France
- Laboratoire de Cytogénétique Hématologique, Hôpital Timone Enfant, AP-HM, Aix-Marseille Université, Marseille, France
| | - Cédric Pastoret
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Nathalie Grardel
- Laboratoire d'Hématologie, Centre Hospitalier Régional Universitaire de Lille, Lille, France
| | - Vahid Asnafi
- Laboratoire d'Onco-hématologie, Hôpital Necker Enfants-Malades, AP-HP, Paris, France
| | - Beat W. Schäfer
- Department of Hematology, University Hospital, Zürich, Switzerland
| | - Eric Delabesse
- Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Raphaël Itzykson
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), Institut National de la Santé et de la Recherche Médicale (INSERM) U944, Centre National de la Recherche Scientifique (CNRS) UMR 7212 GenCellDis, Paris, France
- Département d'Hématologie Clinique, Hôpital Saint-Louis, AP-HP, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
| | - Lionel Adès
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), Institut National de la Santé et de la Recherche Médicale (INSERM) U944, Centre National de la Recherche Scientifique (CNRS) UMR 7212 GenCellDis, Paris, France
- Département d'Hématologie Clinique, Hôpital Saint-Louis, AP-HP, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
| | - Yosr Hicheri
- Hematology Department, Institut Paoli-Calmettes, Aix Marseille Univ, CNRS, INSERM, CRCM, Marseille, France
| | - Yves Chalandon
- Hématologie, Hôpitaux Universitaires de Genève, Genève, Switzerland
| | - Carlos Graux
- Université Catholique de Louvain, Centre Hospitalier Universitaire UCLouvaine Namur-Godinne, Service d'Hématologie, Yvoir, Belgium
| | - Patrice Chevallier
- Department of Hematology, CHU Nantes, INSERM UMR1232 and CNRS ERL6001 CRCINA IRS-UN, Nantes, France
| | - Mathilde Hunault
- Département des Maladies du sang, CHU Angers, FHU GOAL, Université d'Angers, Université de Nantes, INSERM, CNRS, CRCI2NA, SFR ICAT, Angers, France
| | - Thibaut Leguay
- Department of Hematology, CHU de Bordeaux, Hôpital du Haut-Levêque, Pessac, France
| | - Françoise Huguet
- Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | | | - Hervé Dombret
- Département d'Hématologie Clinique, Hôpital Saint-Louis, AP-HP, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
| | - Jean Soulier
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), Institut National de la Santé et de la Recherche Médicale (INSERM) U944, Centre National de la Recherche Scientifique (CNRS) UMR 7212 GenCellDis, Paris, France
- Laboratoire d'Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Philippe Rousselot
- Hematology Department, Centre Hospitalier de Versailles, UMR 1184 CEA, University Paris-Saclay, Le Chesnay, France
| | - Nicolas Boissel
- Département d'Hématologie Clinique, Hôpital Saint-Louis, AP-HP, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
| | - Emmanuelle Clappier
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), Institut National de la Santé et de la Recherche Médicale (INSERM) U944, Centre National de la Recherche Scientifique (CNRS) UMR 7212 GenCellDis, Paris, France
- Laboratoire d'Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| |
Collapse
|
20
|
Wang N, Ma T, Yu B. Targeting epigenetic regulators to overcome drug resistance in cancers. Signal Transduct Target Ther 2023; 8:69. [PMID: 36797239 PMCID: PMC9935618 DOI: 10.1038/s41392-023-01341-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 01/15/2023] [Accepted: 01/28/2023] [Indexed: 02/18/2023] Open
Abstract
Drug resistance is mainly responsible for cancer recurrence and poor prognosis. Epigenetic regulation is a heritable change in gene expressions independent of nucleotide sequence changes. As the common epigenetic regulation mechanisms, DNA methylation, histone modification, and non-coding RNA regulation have been well studied. Increasing evidence has shown that aberrant epigenetic regulations contribute to tumor resistance. Therefore, targeting epigenetic regulators represents an effective strategy to reverse drug resistance. In this review, we mainly summarize the roles of epigenetic regulation in tumor resistance. In addition, as the essential factors for epigenetic modifications, histone demethylases mediate the histone or genomic DNA modifications. Herein, we comprehensively describe the functions of the histone demethylase family including the lysine-specific demethylase family, the Jumonji C-domain-containing demethylase family, and the histone arginine demethylase family, and fully discuss their regulatory mechanisms related to cancer drug resistance. In addition, therapeutic strategies, including small-molecule inhibitors and small interfering RNA targeting histone demethylases to overcome drug resistance, are also described.
Collapse
Affiliation(s)
- Nan Wang
- Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Ting Ma
- Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Bin Yu
- Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| |
Collapse
|
21
|
Li P, Wang Y, Sun Y, Jiang S, Li J. N 6-methyladenosine RNA methylation: From regulatory mechanisms to potential clinical applications. Front Cell Dev Biol 2022; 10:1055808. [PMID: 36407103 PMCID: PMC9669580 DOI: 10.3389/fcell.2022.1055808] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/24/2022] [Indexed: 10/20/2023] Open
Abstract
Epitranscriptomics has emerged as another level of epigenetic regulation similar to DNA and histone modifications. N 6-methyladenosine (m6A) is one of the most prevalent and abundant posttranscriptional modifications, widely distributed in many biological species. The level of N 6-methyladenosine RNA methylation is dynamically and reversibly regulated by distinct effectors including methyltransferases, demethylases, histone modification and metabolites. In addition, N 6-methyladenosine RNA methylation is involved in multiple RNA metabolism pathways, such as splicing, localization, translation efficiency, stability and degradation, ultimately affecting various pathological processes, especially the oncogenic and tumor-suppressing activities. Recent studies also reveal that N 6-methyladenosine modification exerts the function in immune cells and tumor immunity. In this review, we mainly focus on the regulatory mechanisms of N 6-methyladenosine RNA methylation, the techniques for detecting N 6-methyladenosine methylation, the role of N 6-methyladenosine modification in cancer and other diseases, and the potential clinical applications.
Collapse
Affiliation(s)
- Peipei Li
- Department of Oncology, Weifang Medical University, Weifang, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yuntao Wang
- Department of Oncology, Weifang Medical University, Weifang, China
| | - Yiwen Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Jingjing Li
- Department of Oncology, Weifang Medical University, Weifang, China
| |
Collapse
|
22
|
Zeng Z, Zhang J, Li J, Li Y, Huang Z, Han L, Xie C, Gong Y. SETD2 regulates gene transcription patterns and is associated with radiosensitivity in lung adenocarcinoma. Front Genet 2022; 13:935601. [PMID: 36035179 PMCID: PMC9399372 DOI: 10.3389/fgene.2022.935601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) has high morbidity and mortality worldwide, and its prognosis remains unsatisfactory. Identification of epigenetic biomarkers associated with radiosensitivity is beneficial for precision medicine in LUAD patients. SETD2 is important in repairing DNA double-strand breaks and maintaining chromatin integrity. Our studies established a comprehensive analysis pipeline, which identified SETD2 as a radiosensitivity signature. Multi-omics analysis revealed enhanced chromatin accessibility and gene transcription by SETD2. In both LUAD bulk RNA sequencing (RNA-seq) and single-cell RNA sequencing (scRNA-seq), we found that SETD2-associated positive transcription patterns were associated with DNA damage responses. SETD2 knockdown significantly upregulated tumor cell apoptosis, attenuated proliferation and migration of LUAD tumor cells, and enhanced radiosensitivity in vitro. Moreover, SETD2 was a favorably prognostic factor whose effects were antagonized by the m6A-related genes RBM15 and YTHDF3 in LUAD. In brief, SETD2 was a promising epigenetic biomarker in LUAD patients.
Collapse
Affiliation(s)
- Zihang Zeng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jianguo Zhang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiali Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yangyi Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhengrong Huang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Linzhi Han
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- *Correspondence: Conghua Xie, ; Yan Gong,
| | - Yan Gong
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- *Correspondence: Conghua Xie, ; Yan Gong,
| |
Collapse
|
23
|
Wu Q, Young B, Wang Y, Davidoff AM, Rankovic Z, Yang J. Recent Advances with KDM4 Inhibitors and Potential Applications. J Med Chem 2022; 65:9564-9579. [PMID: 35838529 PMCID: PMC9531573 DOI: 10.1021/acs.jmedchem.2c00680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The histone lysine demethylase 4 (KDM4) family plays an important role in regulating gene transcription, DNA repair, and metabolism. The dysregulation of KDM4 functions is associated with many human disorders, including cancer, obesity, and cardiovascular diseases. Selective and potent KDM4 inhibitors may help not only to understand the role of KDM4 in these disorders but also to provide potential therapeutic opportunities. Here, we provide an overview of the field and discuss current status, challenges, and opportunities lying ahead in the development of KDM4-based anticancer therapeutics.
Collapse
Affiliation(s)
- Qiong Wu
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Brandon Young
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yan Wang
- Department of Geriatrics and Occupational Disease, Qingdao Central Hospital, Qingdao 266044, China
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jun Yang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Avenue, Suite 500, Memphis, Tennessee 38163, United States
| |
Collapse
|
24
|
Wei C, Deng X, Gao S, Wan X, Chen J. Cantharidin Inhibits Proliferation of Liver Cancer by Inducing DNA Damage via KDM4A-Dependent Histone H3K36 Demethylation. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:2197071. [PMID: 35860003 PMCID: PMC9293552 DOI: 10.1155/2022/2197071] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/19/2022] [Accepted: 05/27/2022] [Indexed: 12/18/2022]
Abstract
Objective To investigate the effect of cantharidin on DNA damage in hepatocellular carcinoma cells and its possible mechanism. Methods Cell proliferation assay and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) assay were used to analyze the effects of cantharidin on cell proliferation and apoptosis of hepatocellular carcinoma cells. The expression levels of DNA damage markers H2AX and P21 were analyzed by qRT-PCR. The expression of KDM4A and H3K36me3 was observed by western blot. The expression of KDM4A was regulated by siRNA or plasmid transfection. The effect of KDM4A on DNA damage induced by cantharidin in liver cancer was observed after overexpression and addiction of KDM4A. Results Cantharidin can significantly inhibit the growth of hepatocellular carcinoma cells and induce apoptosis of hepatocellular carcinoma cells. Cantharidin enhances the chemotherapy sensitivity of liver cancer by targeting the upregulation of KDM4A and the regulation of DNA damage induced by H3K36me3. Overexpression of KDM4A enhances DNA damage induced by cantharidin in HCC. KDM4A silencing attenuated the damage of cantharidin to the DNA of HCC cells. Conclusion Cantharidin can inhibit the growth and promote apoptosis of hepatocellular carcinoma cells. Meanwhile, cantharidin can induce DNA damage in HCC cells. Mechanism studies have shown that cantharidin induces DNA damage through the demethylation of KDM4A-dependent histone H3K36.
Collapse
Affiliation(s)
- Chao Wei
- Infectious Disease Department, Qijiang Hospital of the First Affiliated Hospital of Chongqing Medical University, Chongqing 401420, China
| | - Xiangui Deng
- Infectious Disease Department, Wenlong Hospital of Qijiang, Chongqing 401420, China
| | - Shudi Gao
- Infectious Disease Department, Taiyuan Hospital of Traditional Chinese Medicine, Taiyuan 030009, Shanxi Province, China
| | - Xuemei Wan
- Infectious Disease Department, Affiliated Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610032, Sichuan Province, China
| | - Jing Chen
- Infectious Disease Department, Affiliated Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610032, Sichuan Province, China
| |
Collapse
|
25
|
Leung W, Teater M, Durmaz C, Meydan C, Chivu AG, Chadburn A, Rice EJ, Muley A, Camarillo JM, Arivalagan J, Li Z, Flowers CR, Kelleher NL, Danko CG, Imielinski M, Dave SS, Armstrong SA, Mason CE, Melnick AM. SETD2 Haploinsufficiency Enhances Germinal Center-Associated AICDA Somatic Hypermutation to Drive B-cell Lymphomagenesis. Cancer Discov 2022; 12:1782-1803. [PMID: 35443279 PMCID: PMC9262862 DOI: 10.1158/2159-8290.cd-21-1514] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/08/2022] [Accepted: 04/18/2022] [Indexed: 01/26/2023]
Abstract
SETD2 is the sole histone methyltransferase responsible for H3K36me3, with roles in splicing, transcription initiation, and DNA damage response. Homozygous disruption of SETD2 yields a tumor suppressor effect in various cancers. However, SETD2 mutation is typically heterozygous in diffuse large B-cell lymphomas. Here we show that heterozygous Setd2 deficiency results in germinal center (GC) hyperplasia and increased competitive fitness, with reduced DNA damage checkpoint activity and apoptosis, resulting in accelerated lymphomagenesis. Impaired DNA damage sensing in Setd2-haploinsufficient germinal center B (GCB) and lymphoma cells associated with increased AICDA-induced somatic hypermutation, complex structural variants, and increased translocations including those activating MYC. DNA damage was selectively increased on the nontemplate strand, and H3K36me3 loss was associated with greater RNAPII processivity and mutational burden, suggesting that SETD2-mediated H3K36me3 is required for proper sensing of cytosine deamination. Hence, Setd2 haploinsufficiency delineates a novel GCB context-specific oncogenic pathway involving defective epigenetic surveillance of AICDA-mediated effects on transcribed genes. SIGNIFICANCE Our findings define a B cell-specific oncogenic effect of SETD2 heterozygous mutation, which unleashes AICDA mutagenesis of nontemplate strand DNA in the GC reaction, resulting in lymphomas with heavy mutational burden. GC-derived lymphomas did not tolerate SETD2 homozygous deletion, pointing to a novel context-specific therapeutic vulnerability. This article is highlighted in the In This Issue feature, p. 1599.
Collapse
Affiliation(s)
- Wilfred Leung
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
- Department of Biomedical Sciences, Cornell University, Ithaca, New York
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
| | - Ceyda Durmaz
- Graduate Program of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, New York
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, New York
| | - Alexandra G Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Ashlesha Muley
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois
| | - Jaison Arivalagan
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher R Flowers
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Marcin Imielinski
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
- New York Genome Center, New York, New York
- Caryl and Israel Englander Institute for Precision Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Sandeep S Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, North Carolina
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, New York
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
| |
Collapse
|
26
|
Alford JS, Lampe JW, Brach D, Chesworth R, Cosmopoulos K, Duncan KW, Eckley ST, Kutok JL, Raimondi A, Riera TV, Shook B, Tang C, Totman J, Farrow NA. Conformational-Design-Driven Discovery of EZM0414: A Selective, Potent SETD2 Inhibitor for Clinical Studies. ACS Med Chem Lett 2022; 13:1137-1143. [PMID: 35859865 PMCID: PMC9290024 DOI: 10.1021/acsmedchemlett.2c00167] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
![]()
SETD2, a lysine N-methyltransferase, is a histone
methyltransferase that plays an important role in various cellular
processes and was identified as a target of interest in multiple myeloma
that features a t(4,14) translocation. We recently reported the discovery
of a novel small-molecule SETD2 inhibitor tool compound that is suitable
for preclinical studies. Herein we describe the conformational-design-driven
evolution of the advanced chemistry lead, which resulted in compounds
appropriate for clinical evaluation. Further optimization of this
chemical series led to the discovery of EZM0414, which is a potent,
selective, and orally bioavailable inhibitor of SETD2 with good pharmacokinetic
properties and robust pharmacodynamic activity in a mouse xenograft
model.
Collapse
Affiliation(s)
- Joshua S. Alford
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - John W. Lampe
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Dorothy Brach
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Richard Chesworth
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Kat Cosmopoulos
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Kenneth W. Duncan
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Sean T. Eckley
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Jeffrey L. Kutok
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Alejandra Raimondi
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Thomas V. Riera
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Brian Shook
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Cuyue Tang
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Jennifer Totman
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Neil A. Farrow
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
27
|
Selvam K, Plummer DA, Mao P, Wyrick JJ. Set2 histone methyltransferase regulates transcription coupled-nucleotide excision repair in yeast. PLoS Genet 2022; 18:e1010085. [PMID: 35263330 PMCID: PMC8936446 DOI: 10.1371/journal.pgen.1010085] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 03/21/2022] [Accepted: 02/08/2022] [Indexed: 12/17/2022] Open
Abstract
Helix-distorting DNA lesions, including ultraviolet (UV) light-induced damage, are repaired by the global genomic-nucleotide excision repair (GG-NER) and transcription coupled-nucleotide excision repair (TC-NER) pathways. Previous studies have shown that histone post-translational modifications (PTMs) such as histone acetylation and methylation can promote GG-NER in chromatin. Whether histone PTMs also regulate the repair of DNA lesions by the TC-NER pathway in transcribed DNA is unknown. Here, we report that histone H3 K36 methylation (H3K36me) by the Set2 histone methyltransferase in yeast regulates TC-NER. Mutations in Set2 or H3K36 result in UV sensitivity that is epistatic with Rad26, the primary TC-NER factor in yeast, and cause a defect in the repair of UV damage across the yeast genome. We further show that mutations in Set2 or H3K36 in a GG-NER deficient strain (i.e., rad16Δ) partially rescue its UV sensitivity. Our data indicate that deletion of SET2 rescues UV sensitivity in a GG-NER deficient strain by activating cryptic antisense transcription, so that the non-transcribed strand (NTS) of yeast genes is repaired by TC-NER. These findings indicate that Set2 methylation of H3K36 establishes transcriptional asymmetry in repair by promoting canonical TC-NER of the transcribed strand (TS) and suppressing cryptic TC-NER of the NTS.
Collapse
Affiliation(s)
- Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
| | - Dalton A. Plummer
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
| | - Peng Mao
- Department of Internal Medicine, Program in Cellular and Molecular Oncology, University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico, United States of America
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
- Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- * E-mail:
| |
Collapse
|
28
|
SETD2 loss perturbs the kidney cancer epigenetic landscape to promote metastasis and engenders actionable dependencies on histone chaperone complexes. NATURE CANCER 2022; 3:188-202. [PMID: 35115713 PMCID: PMC8885846 DOI: 10.1038/s43018-021-00316-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 11/24/2021] [Indexed: 12/13/2022]
Abstract
SETD2 is a H3K36 trimethyltransferase that is mutated with high prevalence (13%) in clear cell renal cell carcinoma (ccRCC). Genomic profiling of primary ccRCC tumors reveals a positive correlation between SETD2 mutations and metastasis. However, whether and how SETD2 loss promotes metastasis remains unclear. In this study, we used SETD2-mutant metastatic ccRCC patient-derived cell line and xenograft models and showed that H3K36me3 restoration greatly reduced distant metastases of ccRCC in mice in an MMP1-dependent manner. An integrated multi-omics analysis using ATAC-seq, ChIP-seq, and RNA-seq established a tumor suppressor model in which loss of SETD2-mediated H3K36me3 activates enhancers to drive oncogenic transcriptional output through regulation of chromatin accessibility. Furthermore, we uncovered mechanism-based therapeutic strategies for SETD2-deficient cancer through the targeting of specific histone chaperone complexes including ASF1A/B and SPT16. Overall, SETD2 loss creates a permissive epigenetic landscape for cooperating oncogenic drivers to amplify transcriptional output, providing unique therapeutic opportunities.
Collapse
|
29
|
|
30
|
Pan D, Richter J. Where We Stand With Precision Therapeutics in Myeloma: Prosperity, Promises, and Pipedreams. Front Oncol 2022; 11:819127. [PMID: 35127532 PMCID: PMC8811139 DOI: 10.3389/fonc.2021.819127] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Abstract
Multiple myeloma remains an incurable disease despite numerous novel agents being approved in the last decade. Furthermore, disease behavior and susceptibility to current treatments often vary drastically from patient to patient. To date there are no approved therapies in myeloma that are targeted to specific patient populations based on genomic or immunologic findings. Precision medicine, using biomarkers descriptive of a specific tumor’s biology and predictive of response to appropriate agents, may continue to push the field forward by expanding our treatment arsenal while refining our ability to expose patients to only those treatments likely to be efficacious. Extensive research efforts have been carried out in this endeavor including the use of agents targeting Bcl2 and the RAS/MAPK and PI3K/AKT/mTOR pathways. Thus far, clinical trials have yielded occasional successes intermixed with disappointments, reflecting significant hurdles which still remain including the complex crosstalk between oncogenic pathways and the nonlinear genetic development of myeloma, prone to cultivating sub-clones with distinctive mutations. In this review, we explore the landscape of precision therapeutics in multiple myeloma and underscore the degree to which research efforts have produced tangible clinical results.
Collapse
|
31
|
Molecular mechanisms in governing genomic stability and tumor suppression by the SETD2 H3K36 methyltransferase. Int J Biochem Cell Biol 2022; 144:106155. [PMID: 34990836 DOI: 10.1016/j.biocel.2021.106155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 01/15/2023]
Abstract
Epigenetic dysregulation is an important contributor to carcinogenesis. This is not surprising, as chromatin-genomic DNA organized around structural histone scaffolding-serves as the template on which occurs essential nuclear processes, such as transcription, DNA replication and DNA repair. Histone H3 lysine 36 (H3K36) methyltransferases, such as the SET-domain 2 protein (SETD2), have emerged as critical tumor suppressors. Previous work on mammalian SETD2 and its counterpart in model organisms, Set2, has highlighted the role of this protein in governing genomic stability through transcriptional elongation and splicing, as well as in DNA damage response processes and cell cycle progression. A compendium of SETD2 mutations have been documented, garnered from sequenced cancer patient genome data, and these findings underscore the cancer-driving properties of SETD2 loss-of-function. In this review, we consolidate the molecular mechanisms regulated by SETD2/Set2 and discuss evidence of its dysregulation in tumorigenesis. Insight into the genetic interactions that exist between SETD2 and various canonical intracellular signaling pathways has not only empowered pharmacological intervention by taking advantage of synthetic lethality but underscores SETD2 as a druggable target for precision cancer therapy.
Collapse
|
32
|
Bajusz D, Bognár Z, Ebner J, Grebien F, Keserű GM. Discovery of a Non-Nucleoside SETD2 Methyltransferase Inhibitor against Acute Myeloid Leukemia. Int J Mol Sci 2021; 22:ijms221810055. [PMID: 34576219 PMCID: PMC8471172 DOI: 10.3390/ijms221810055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/06/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022] Open
Abstract
Histone methyltransferases (HMTs) have attracted considerable attention as potential targets for pharmaceutical intervention in various malignant diseases. These enzymes are known for introducing methyl marks at specific locations of histone proteins, creating a complex system that regulates epigenetic control of gene expression and cell differentiation. Here, we describe the identification of first-generation cell-permeable non-nucleoside type inhibitors of SETD2, the only mammalian HMT that is able to tri-methylate the K36 residue of histone H3. By generating the epigenetic mark H3K36me3, SETD2 is involved in the progression of acute myeloid leukemia. We developed a structure-based virtual screening protocol that was first validated in retrospective studies. Next, prospective screening was performed on a large library of commercially available compounds. Experimental validation of 22 virtual hits led to the discovery of three compounds that showed dose-dependent inhibition of the enzymatic activity of SETD2. Compound C13 effectively blocked the proliferation of two acute myeloid leukemia (AML) cell lines with MLL rearrangements and led to decreased H3K36me3 levels, prioritizing this chemotype as a viable chemical starting point for drug discovery projects.
Collapse
Affiliation(s)
- Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (D.B.); (Z.B.)
| | - Zsolt Bognár
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (D.B.); (Z.B.)
| | - Jessica Ebner
- Institute for Medical Biochemistry, University of Veterinary Medicine, 1220 Vienna, Austria; (J.E.); (F.G.)
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, 1220 Vienna, Austria; (J.E.); (F.G.)
| | - György M. Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (D.B.); (Z.B.)
- Correspondence:
| |
Collapse
|
33
|
Pacella G, Capell BC. Epigenetic and metabolic interplay in cutaneous squamous cell carcinoma. Exp Dermatol 2021; 30:1115-1125. [PMID: 33844325 PMCID: PMC8324523 DOI: 10.1111/exd.14354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/16/2021] [Accepted: 04/06/2021] [Indexed: 12/14/2022]
Abstract
With the ageing of the population and increased levels of recreational sun exposure and immunosuppression, cutaneous squamous cell carcinoma (cSCC), is both an enormous and expanding clinical and economic issue. Despite advances in therapy, up to 5000-8000 people are estimated to die every year from cSCC in the U.S., highlighting the need for both better prevention and treatments. Two emerging areas of scientific discovery that may offer new therapeutic approaches for cSCC are epigenetics and metabolism. Importantly, these disciplines display extensive crosstalk, with metabolic inputs contributing to the chromatin landscape, while the dynamic epigenome shapes transcriptional and cellular responses that feedback into cellular metabolism. Recent evidence suggests that indeed, epigenetic and metabolic dysregulation may be critical contributors to cSCC pathogenesis. Here, we synthesize the latest findings from these fast-moving fields, including how they may drive cSCC, yet also be harnessed for therapy.
Collapse
Affiliation(s)
- Gina Pacella
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Brian C. Capell
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| |
Collapse
|
34
|
Zhao J, Li B, Ren Y, Liang T, Wang J, Zhai S, Zhang X, Zhou P, Zhang X, Pan Y, Gao F, Zhang S, Li L, Yang Y, Deng X, Li X, Chen L, Yang D, Zheng Y. Histone demethylase KDM4A plays an oncogenic role in nasopharyngeal carcinoma by promoting cell migration and invasion. Exp Mol Med 2021; 53:1207-1217. [PMID: 34385569 PMCID: PMC8417295 DOI: 10.1038/s12276-021-00657-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 02/07/2023] Open
Abstract
Compelling evidence has indicated the vital role of lysine-specific demethylase 4 A (KDM4A), hypoxia-inducible factor-1α (HIF1α) and the mechanistic target of rapamycin (mTOR) signaling pathway in nasopharyngeal carcinoma (NPC). Therefore, we aimed to investigate whether KDM4A affects NPC progression by regulating the HIF1α/DDIT4/mTOR signaling pathway. First, NPC and adjacent tissue samples were collected, and KDM4A protein expression was examined by immunohistochemistry. Then, the interactions among KDM4A, HIF1α and DDIT4 were assessed. Gain- and loss-of-function approaches were used to alter KDM4A, HIF1α and DDIT4 expression in NPC cells. The mechanism of KDM4A in NPC was evaluated both in vivo and in vitro via RT-qPCR, Western blot analysis, MTT assay, Transwell assay, flow cytometry and tumor formation experiments. KDM4A, HIF1α, and DDIT4 were highly expressed in NPC tissues and cells. Mechanistically, KDM4A inhibited the enrichment of histone H3 lysine 9 trimethylation (H3K9me3) in the HIF1α promoter region and thus inhibited the methylation of HIF1α to promote HIF1α expression, thus upregulating DDIT4 and activating the mTOR signaling pathway. Overexpression of KDM4A, HIF1α, or DDIT4 or activation of the mTOR signaling pathway promoted SUNE1 cell proliferation, migration, and invasion but inhibited apoptosis. KDM4A silencing blocked the mTOR signaling pathway by inhibiting the HIF1α/DDIT4 axis to inhibit the growth of SUNE1 cells in vivo. Collectively, KDM4A silencing could inhibit NPC progression by blocking the activation of the HIF1α/DDIT4/mTOR signaling pathway by increasing H3K9me3, highlighting a promising therapeutic target for NPC.
Collapse
Affiliation(s)
- Jingyi Zhao
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Bingyan Li
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Yongxia Ren
- Radiotherapy Department, Huaihe Hospital of Henan University, Kaifeng, PR China
| | - Tiansong Liang
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Juan Wang
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Suna Zhai
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Xiqian Zhang
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Pengcheng Zhou
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Xiangxian Zhang
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Yuanyuan Pan
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Fangfang Gao
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Sulan Zhang
- Institute of Radiation Therapy and Tumor Critical Care of Zhengzhou University, Zhengzhou, PR China
| | - Liming Li
- Henan Key Laboratory of Molecular Radiotherapy, Zhengzhou, PR China
| | - Yongqiang Yang
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Xiaoyu Deng
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Xiaole Li
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Linhui Chen
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Daoke Yang
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China.
| | - Yingjuan Zheng
- Radiotherapy Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China.
| |
Collapse
|
35
|
Berthelet J, Michail C, Bui LC, Le Coadou L, Sirri V, Wang L, Dulphy N, Dupret JM, Chomienne C, Guidez F, Rodrigues-Lima F. The benzene hematotoxic and reactive metabolite 1,4-benzoquinone impairs the activity of the histone methyltransferase SETD2 and causes aberrant H3K36 trimethylation (H3K36me3). Mol Pharmacol 2021; 100:283-294. [PMID: 34266924 DOI: 10.1124/molpharm.121.000303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/28/2021] [Indexed: 11/22/2022] Open
Abstract
Human SETD2 is the unique histone methyltransferase that generates H3K36me3, an epigenetic mark that plays a key role in normal hematopoiesis. Interestingly, recurrent-inactivating mutations of SETD2 and aberrant H3K36 trimethylation (H3K36me3) are increasingly reported to be involved in hematopoietic malignancies. Benzene (BZ) is an ubiquitous environmental pollutant and carcinogen that causes leukemia. The leukemogenic properties of BZ depend on its biotransformation in the bone marrow into oxidative metabolites in particular 1,4-benzoquinone (BQ). This hematotoxic metabolite can form DNA and protein adducts that result in the damage and the alteration of cellular processes. Recent studies suggest that BZ-depend leukemogenesis could depend on epigenetic perturbations notably aberrant histone methylation. We investigated whether H3K36 trimethylation by SETD2 could be impacted by BZ and its hematotoxic metabolites. Herein, we show that BQ, the major leukemogenic metabolite of BZ, inhibits irreversibly the human histone methyltransferase SETD2 resulting in decreased H3K36 trimethylation (H3K36me3). Our mechanistic studies further indicate that the BQ-dependent inactivation of SETD2 is due to covalent binding of BQ to reactive Zn-finger cysteines within the catalytic domain of the enzyme. The formation of these quinoprotein adducts results in loss of enzyme activity and protein cross-links/oligomers. Experiments conducted in hematopoietic cells confirm that exposure to BQ results in the formation of SETD2 cross-links/oligomers and concomitant loss of H3K36me3 in cells. Taken together, our data indicate that BQ, a major hematotoxic metabolite of BZ could contribute to BZ-dependent leukemogenesis by perturbing the functions of SETD2, an histone lysine methyltransferase of hematopoietic relevance. Significance Statement Benzoquinone is a major leukemogenic metabolite of benzene. Dysregulation of histone methyltransferase is involved in hematopoietic malignancies. We found that benzoquinone irreversibly impairs SETD2, a histone H3K36 methyltransferase that plays a key role in hematopoiesis. Benzoquinone forms covalent adducts on Zn-finger cysteines within the catalytic site leading to loss of activity, protein cross-links/oligomers and concomitant decrease of H3K36me3 histone mark. Our data provide evidence that a leukemogenic metabolite of benzene can impair a key epigenetic enzyme.
Collapse
Affiliation(s)
| | | | | | | | | | - Li Wang
- The First Affiliated Hospital of Chongqing Medical University, China
| | | | | | | | | | | |
Collapse
|
36
|
Ko EK, Capell BC. Methyltransferases in the Pathogenesis of Keratinocyte Cancers. Cancers (Basel) 2021; 13:cancers13143402. [PMID: 34298617 PMCID: PMC8304454 DOI: 10.3390/cancers13143402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 12/13/2022] Open
Abstract
Recent evidence suggests that the disruption of gene expression by alterations in DNA, RNA, and histone methylation may be critical contributors to the pathogenesis of keratinocyte cancers (KCs), made up of basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC), which collectively outnumber all other human cancers combined. While it is clear that methylation modifiers are frequently dysregulated in KCs, the underlying molecular and mechanistic changes are only beginning to be understood. Intriguingly, it has recently emerged that there is extensive cross-talk amongst these distinct methylation processes. Here, we summarize and synthesize the latest findings in this space and highlight how these discoveries may uncover novel therapeutic approaches for these ubiquitous cancers.
Collapse
Affiliation(s)
- Eun Kyung Ko
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Brian C. Capell
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA;
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence:
| |
Collapse
|
37
|
Song J, Du L, Liu P, Wang F, Zhang B, Xie Y, Lu J, Jin Y, Zhou Y, Lv G, Zhang J, Chen S, Chen Z, Sun X, Zhang Y, Huang Q. Intra-heterogeneity in transcription and chemoresistant property of leukemia-initiating cells in murine Setd2 -/- acute myeloid leukemia. Cancer Commun (Lond) 2021; 41:867-888. [PMID: 34196511 PMCID: PMC8441059 DOI: 10.1002/cac2.12189] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/09/2021] [Accepted: 06/19/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Heterogeneity of leukemia-initiating cells (LICs) is a major obstacle in acute myeloid leukemia (AML) therapy. Accumulated evidence indicates that the coexistence of multiple types of LICs with different pathogenicity in the same individual is a common feature in AML. However, the functional heterogeneity including the drug response of coexistent LICs remains unclear. Therefore, this study aimed to clarify the intra-heterogeneity in LICs that can help predict leukemia behavior and develop more effective treatments. METHODS Spleen cells from the primary Setd2-/- -AML mouse were transplanted into C57BL/6 recipient mice to generate a transplantable model. Flow cytometry was used to analyze the immunophenotype of the leukemic mice. Whole-genome sequencing was conducted to detect secondary hits responsible for leukemia transformation. A serial transplantation assay was used to determine the self-renewal potential of Setd2-/- -AML cells. A limiting-dilution assay was performed to identify the LIC frequency in different subsets of leukemia cells. Bulk and single-cell RNA sequencing were performed to analyze the transcriptional heterogeneity of LICs. Small molecular inhibitor screening and in vivo drug treatment were employed to clarify the difference in drug response between the different subsets of LICs. RESULTS In this study, we observed an aged Setd2-/- mouse developing AML with co-mutation of NrasG12S and BrafK520E . Further investigation identified two types of LICs residing in the c-Kit+ B220+ Mac-1- and c-Kit+ B220+ Mac-1+ subsets, respectively. In vivo transplantation assay disclosed the heterogeneity in differentiation between the coexistent LICs. Besides, an intrinsic doxorubicin-resistant transcriptional signature was uncovered in c-Kit+ B220+ Mac-1+ cells. Indeed, doxorubicin plus cytarabine (DA), the standard chemotherapeutic regimen used in AML treatment, could specifically kill c-Kit+ B220+ Mac-1- cells, but it hardly affected c-Kit+ B220+ Mac-1+ cells. Transcriptome analysis unveiled a higher activation of RAS downstream signaling pathways in c-Kit+ B220+ Mac-1+ cells than in c-Kit+ B220+ Mac-1- cells. Combined treatment with DA and RAS pathway inhibitors killed both c-Kit+ B220+ Mac-1- and c-Kit+ B220+ Mac-1+ cells and attenuated disease progression. CONCLUSIONS This study identified two cell subsets enriched for LICs in murine Setd2-/- -AML and disclosed the transcriptional and functional heterogeneity of LICs, revealing that the coexistence of different types of LICs in this model brings about diverse drug response.
Collapse
Affiliation(s)
- Jiachun Song
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Longting Du
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Ping Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Fuhui Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Bo Zhang
- Novel Bioinformatics Co., Ltd, Shanghai, 201114, P. R. China
| | - Yinyin Xie
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Jing Lu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Yi Jin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Yan Zhou
- Central Laboratory, Renji Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, P. R. China
| | - Gang Lv
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Jianmin Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Xiaojian Sun
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Yuanliang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Qiuhua Huang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| |
Collapse
|
38
|
Kearns S, Mason FM, Rathmell WK, Park IY, Walker C, Verhey KJ, Cianfrocco MA. Molecular determinants for α-tubulin methylation by SETD2. J Biol Chem 2021; 297:100898. [PMID: 34157286 PMCID: PMC8294582 DOI: 10.1016/j.jbc.2021.100898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 05/28/2021] [Accepted: 06/18/2021] [Indexed: 12/16/2022] Open
Abstract
Post-translational modifications to tubulin are important for many microtubule-based functions inside cells. It was recently shown that methylation of tubulin by the histone methyltransferase SETD2 occurs on mitotic spindle microtubules during cell division, with its absence resulting in mitotic defects. However, the catalytic mechanism of methyl addition to tubulin is unclear. We used a truncated version of human wild type SETD2 (tSETD2) containing the catalytic SET and C-terminal Set2-Rpb1-interacting (SRI) domains to investigate the biochemical mechanism of tubulin methylation. We found that recombinant tSETD2 had a higher activity toward tubulin dimers than polymerized microtubules. Using recombinant single-isotype tubulin, we demonstrated that methylation was restricted to lysine 40 of α-tubulin. We then introduced pathogenic mutations into tSETD2 to probe the recognition of histone and tubulin substrates. A mutation in the catalytic domain (R1625C) allowed tSETD2 to bind to tubulin but not methylate it, whereas a mutation in the SRI domain (R2510H) caused loss of both tubulin binding and methylation. Further investigation of the role of the SRI domain in substrate binding found that mutations within this region had differential effects on the ability of tSETD2 to bind to tubulin versus the binding partner RNA polymerase II for methylating histones in vivo, suggesting distinct mechanisms for tubulin and histone methylation by SETD2. Finally, we found that substrate recognition also requires the negatively charged C-terminal tail of α-tubulin. Together, this study provides a framework for understanding how SETD2 serves as a dual methyltransferase for both histone and tubulin methylation.
Collapse
Affiliation(s)
- Sarah Kearns
- Program of Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Frank M Mason
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Genetics, Vanderbilt University, Nashville, Tennessee, USA
| | - W Kimryn Rathmell
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Genetics, Vanderbilt University, Nashville, Tennessee, USA
| | - In Young Park
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA
| | - Cheryl Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| |
Collapse
|
39
|
Klintman J, Appleby N, Stamatopoulos B, Ridout K, Eyre TA, Robbe P, Pascua LL, Knight SJL, Dreau H, Cabes M, Popitsch N, Ehinger M, Martín-Subero JI, Campo E, Månsson R, Rossi D, Taylor JC, Vavoulis DV, Schuh A. Genomic and transcriptomic correlates of Richter transformation in chronic lymphocytic leukemia. Blood 2021; 137:2800-2816. [PMID: 33206936 PMCID: PMC8163497 DOI: 10.1182/blood.2020005650] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
The transformation of chronic lymphocytic leukemia (CLL) to high-grade B-cell lymphoma is known as Richter syndrome (RS), a rare event with dismal prognosis. In this study, we conducted whole-genome sequencing (WGS) of paired circulating CLL (PB-CLL) and RS biopsies (tissue-RS) from 17 patients recruited into a clinical trial (CHOP-O). We found that tissue-RS was enriched for mutations in poor-risk CLL drivers and genes in the DNA damage response (DDR) pathway. In addition, we identified genomic aberrations not previously implicated in RS, including the protein tyrosine phosphatase receptor (PTPRD) and tumor necrosis factor receptor-associated factor 3 (TRAF3). In the noncoding genome, we discovered activation-induced cytidine deaminase-related and unrelated kataegis in tissue-RS affecting regulatory regions of key immune-regulatory genes. These include BTG2, CXCR4, NFATC1, PAX5, NOTCH-1, SLC44A5, FCRL3, SELL, TNIP2, and TRIM13. Furthermore, differences between the global mutation signatures of pairs of PB-CLL and tissue-RS samples implicate DDR as the dominant mechanism driving transformation. Pathway-based clonal deconvolution analysis showed that genes in the MAPK and DDR pathways demonstrate high clonal-expansion probability. Direct comparison of nodal-CLL and tissue-RS pairs from an independent cohort confirmed differential expression of the same pathways by RNA expression profiling. Our integrated analysis of WGS and RNA expression data significantly extends previous targeted approaches, which were limited by the lack of germline samples, and it facilitates the identification of novel genomic correlates implicated in RS transformation, which could be targeted therapeutically. Our results inform the future selection of investigative agents for a UK clinical platform study. This trial was registered at www.clinicaltrials.gov as #NCT03899337.
Collapse
MESH Headings
- Aged
- Aged, 80 and over
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/administration & dosage
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Base Sequence
- Clonal Evolution/genetics
- Clone Cells/pathology
- Combined Modality Therapy
- Cyclophosphamide/administration & dosage
- DNA Repair
- Disease Progression
- Doxorubicin/administration & dosage
- Female
- Gene Expression Regulation, Neoplastic/genetics
- Gene Regulatory Networks
- Genes, Neoplasm
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Male
- Middle Aged
- Mutation
- Neoplasm Proteins/genetics
- Prednisone/administration & dosage
- Prospective Studies
- RNA, Neoplasm/biosynthesis
- RNA, Neoplasm/genetics
- Syndrome
- Transcriptome
- Vincristine/administration & dosage
- Whole Genome Sequencing
Collapse
Affiliation(s)
- Jenny Klintman
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Translational Medicine, Skåne University Hospital, Lund University, Lund, Sweden
| | - Niamh Appleby
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Hematology, Oxford University Hospitals National Health Service (NHS) Trust, Oxford, United Kingdom
| | - Basile Stamatopoulos
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Laboratory of Clinical Cell Therapy, Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Katie Ridout
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Toby A Eyre
- Department of Hematology, Oxford University Hospitals National Health Service (NHS) Trust, Oxford, United Kingdom
| | - Pauline Robbe
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Laura Lopez Pascua
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Samantha J L Knight
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Helene Dreau
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Maite Cabes
- Department of Hematology, Oxford University Hospitals National Health Service (NHS) Trust, Oxford, United Kingdom
| | - Niko Popitsch
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- The Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Mats Ehinger
- Pathology, Department of Clinical Sciences, Skåne University Hospital, Lund University, Lund, Sweden
| | - Jose I Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Elías Campo
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
| | - Robert Månsson
- Center for Hematology and Regenerative Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Hematology Center, Karolinska University Hospital, Stockholm, Sweden; and
| | - Davide Rossi
- Institute of Oncology Research (IOR), Bellinzona, Switzerland
| | - Jenny C Taylor
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Dimitrios V Vavoulis
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Anna Schuh
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Hematology, Oxford University Hospitals National Health Service (NHS) Trust, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
40
|
The hematopoietic stem cell marker VNN2 is associated with chemoresistance in pediatric B-cell precursor ALL. Blood Adv 2021; 4:4052-4064. [PMID: 32853382 DOI: 10.1182/bloodadvances.2019000938] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 05/29/2020] [Indexed: 12/13/2022] Open
Abstract
Most relapses of acute lymphoblastic leukemia (ALL) occur in patients with a medium risk (MR) for relapse on the Associazione Italiana di Ematologia e Oncologia Pediatrica and Berlin-Frankfurt-Münster (AIEOP-BFM) ALL protocol, based on persistence of minimal residual disease (MRD). New insights into biological features that are associated with MRD are needed. Here, we identify the glycosylphosphatidylinositol-anchored cell surface protein vanin-2 (VNN2; GPI-80) by charting the cell surface proteome of MRD very high-risk (HR) B-cell precursor (BCP) ALL using a chemoproteomics strategy. The correlation between VNN2 transcript and surface protein expression enabled a retrospective analysis (ALL-BFM 2000; N = 770 cases) using quantitative polymerase chain reaction to confirm the association of VNN2 with MRD and independent prediction of worse outcome. Using flow cytometry, we detected VNN2 expression in 2 waves, in human adult bone marrow stem and progenitor cells and in the mature myeloid compartment, in line with proposed roles for fetal hematopoietic stem cells and inflammation. Prospective validation by flow cytometry in the ongoing clinical trial (AIEOP-BFM 2009) identified 10% (103/1069) of VNN2+ BCP ALL patients at first diagnosis, primarily in the MRD MR (48/103, 47%) and HR (37/103, 36%) groups, across various cytogenetic subtypes. We also detected frequent mutations in epigenetic regulators in VNN2+ ALLs, including histone H3 methyltransferases MLL2, SETD2, and EZH2 and demethylase KDM6A. Inactivation of the VNN2 gene did not impair leukemia repopulation capacity in xenografts. Taken together, VNN2 marks a cellular state of increased resistance to chemotherapy that warrants further investigations. Therefore, this marker should be included in diagnostic flow cytometry panels.
Collapse
|
41
|
van Gils N, Denkers F, Smit L. Escape From Treatment; the Different Faces of Leukemic Stem Cells and Therapy Resistance in Acute Myeloid Leukemia. Front Oncol 2021; 11:659253. [PMID: 34012921 PMCID: PMC8126717 DOI: 10.3389/fonc.2021.659253] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/08/2021] [Indexed: 12/26/2022] Open
Abstract
Standard induction chemotherapy, consisting of an anthracycline and cytarabine, has been the first-line therapy for many years to treat acute myeloid leukemia (AML). Although this treatment induces complete remissions in the majority of patients, many face a relapse (adaptive resistance) or have refractory disease (primary resistance). Moreover, older patients are often unfit for cytotoxic-based treatment. AML relapse is due to the survival of therapy-resistant leukemia cells (minimal residual disease, MRD). Leukemia cells with stem cell features, named leukemic stem cells (LSCs), residing within MRD are thought to be at the origin of relapse initiation. It is increasingly recognized that leukemia "persisters" are caused by intra-leukemic heterogeneity and non-genetic factors leading to plasticity in therapy response. The BCL2 inhibitor venetoclax, combined with hypomethylating agents or low dose cytarabine, represents an important new therapy especially for older AML patients. However, often there is also a small population of AML cells refractory to venetoclax treatment. As AML MRD reflects the sum of therapy resistance mechanisms, the different faces of treatment "persisters" and LSCs might be exploited to reach an optimal therapy response and prevent the initiation of relapse. Here, we describe the different epigenetic, transcriptional, and metabolic states of therapy sensitive and resistant AML (stem) cell populations and LSCs, how these cell states are influenced by the microenvironment and affect treatment outcome of AML. Moreover, we discuss potential strategies to target dynamic treatment resistance and LSCs.
Collapse
Affiliation(s)
- Noortje van Gils
- Department of Hematology, Amsterdam UMC, location VUmc, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Fedor Denkers
- Department of Hematology, Amsterdam UMC, location VUmc, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Linda Smit
- Department of Hematology, Amsterdam UMC, location VUmc, Cancer Center Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
42
|
Chen J, Feng J, Fang Z, Ye J, Chen Q, Chen Q, Chen K, Xiong X, Li G, Song H, Xu B. Anlotinib suppresses MLL-rearranged acute myeloid leukemia cell growth by inhibiting SETD1A/AKT-mediated DNA damage response. Am J Transl Res 2021; 13:1494-1504. [PMID: 33841673 PMCID: PMC8014360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
Leukemias driven by chromosomal translocation of the mixed-lineage leukemia (MLL) gene are highly prevalent in hematological malignancy. The poor survival rate and lack of effective targeted therapy for patients with MLL-rearranged (MLL-r) leukemias emphasize an urgent need for improved knowledge and novel therapeutic approaches for these malignancies. The present study aimed to investigate the potential effectiveness and mechanism of Anlotinib, a novel receptor tyrosine kinase inhibitor, in MLL-r acute myeloid leukemia (AML). The findings revealed that Anlotinib significantly inhibited the growth of MLL-r AML cells in both in vivo and a murine xenograft model. RNA sequencing identified that multiple genes involved in DNA damage response were responsible for Anlotinib activity. To further elucidate the correlation between the DNA damage response induced by Anlotinib and MLL fusion, Gene Expression Profiling Interactive Analysis (GEPIA) was conducted. It revealed that Anlotinib impaired DNA damage response via inhibiting SETD1A and AKT. In conclusion, Anlotinib exerts anti-leukemia function by inhibiting SETD1A/AKT-mediated DNA damage response and highlights a novel mechanism underlying Anlotinib in the treatment of MLL-r AML.
Collapse
Affiliation(s)
- Jinzhu Chen
- Department of Hematology, The First Hospital of Longhai 363199Fujian, P. R. China
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen UniversityXiamen 361003, P. R. China
- Key laboratory of Xiamen for Diagnosis and Treatment of Hematological MalignancyXiamen 361003, P. R. China
| | - Juan Feng
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen UniversityXiamen 361003, P. R. China
- Key laboratory of Xiamen for Diagnosis and Treatment of Hematological MalignancyXiamen 361003, P. R. China
| | - Zhihong Fang
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen UniversityXiamen 361003, P. R. China
- Key laboratory of Xiamen for Diagnosis and Treatment of Hematological MalignancyXiamen 361003, P. R. China
| | - Jing Ye
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen UniversityXiamen 361003, P. R. China
- Key laboratory of Xiamen for Diagnosis and Treatment of Hematological MalignancyXiamen 361003, P. R. China
| | - Qinwei Chen
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen UniversityXiamen 361003, P. R. China
- Key laboratory of Xiamen for Diagnosis and Treatment of Hematological MalignancyXiamen 361003, P. R. China
| | - Qiuling Chen
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen UniversityXiamen 361003, P. R. China
- Key laboratory of Xiamen for Diagnosis and Treatment of Hematological MalignancyXiamen 361003, P. R. China
| | - Kai Chen
- The First People’s Hospital of Foshan (The Affiliated Foshan Hospital of Sun Yat-sen University)Foshan 528000, Guangdong, P. R. China
| | - Xiaoming Xiong
- Department of Hematology, The First Hospital of Longhai 363199Fujian, P. R. China
| | - Guowei Li
- Department of Hematology, Huizhou Municipal Central HospitalHuizhou 516001, P. R. China
| | - Haihan Song
- Department of Immunology, DICAT Biomedical Computation CentreVancouver, BC, Canada
| | - Bing Xu
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen UniversityXiamen 361003, P. R. China
- Key laboratory of Xiamen for Diagnosis and Treatment of Hematological MalignancyXiamen 361003, P. R. China
| |
Collapse
|
43
|
T-lymphoblastic leukemia/lymphoma with interfollicular growth pattern and Castleman-like morphologic features. J Hematop 2021. [DOI: 10.1007/s12308-021-00446-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
|
44
|
Oner E, Kotmakci M, Baird AM, Gray SG, Debelec Butuner B, Bozkurt E, Kantarci AG, Finn SP. Development of EphA2 siRNA-loaded lipid nanoparticles and combination with a small-molecule histone demethylase inhibitor in prostate cancer cells and tumor spheroids. J Nanobiotechnology 2021; 19:71. [PMID: 33685469 PMCID: PMC7938557 DOI: 10.1186/s12951-021-00781-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/22/2021] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND siRNAs hold a great potential for cancer therapy, however, poor stability in body fluids and low cellular uptake limit their use in the clinic. To enhance the bioavailability of siRNAs in tumors, novel, safe, and effective carriers are needed. RESULTS Here, we developed cationic solid lipid nanoparticles (cSLNs) to carry siRNAs targeting EphA2 receptor tyrosine kinase (siEphA2), which is overexpressed in many solid tumors including prostate cancer. Using DDAB cationic lipid instead of DOTMA reduced nanoparticle size and enhanced both cellular uptake and gene silencing in prostate cancer cells. DDAB-cSLN showed better cellular uptake efficiency with similar silencing compared to commercial transfection reagent (Dharmafect 2). After verifying the efficacy of siEphA2-loaded nanoparticles, we further evaluated a potential combination with a histone lysine demethylase inhibitor, JIB-04. Silencing EphA2 by siEphA2-loaded DDAB-cSLN did not affect the viability (2D or 3D culture), migration, nor clonogenicity of PC-3 cells alone. However, upon co-administration with JIB-04, there was a decrease in cellular responses. Furthermore, JIB-04 decreased EphA2 expression, and thus, silencing by siEphA2-loaded nanoparticles was further increased with co-treatment. CONCLUSIONS We have successfully developed a novel siRNA-loaded lipid nanoparticle for targeting EphA2. Moreover, preliminary results of the effects of JIB-04, alone and in combination with siEphA2, on prostate cancer cells and prostate cancer tumor spheroids were presented for the first time. Our delivery system provides high transfection efficiency and shows great promise for targeting other genes and cancer types in further in vitro and in vivo studies.
Collapse
Affiliation(s)
- Ezgi Oner
- Department of Histopathology and Morbid Anatomy, Sir Patrick Dun Translational Research Lab, St. James's Hospital, Dublin, Ireland.,Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey.,Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Izmir Katip Celebi University, Balatcik, Izmir, Turkey
| | - Mustafa Kotmakci
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey
| | - Anne-Marie Baird
- Department of Histopathology and Morbid Anatomy, Sir Patrick Dun Translational Research Lab, St. James's Hospital, Dublin, Ireland.,Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland.,Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
| | - Steven G Gray
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland.,Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
| | - Bilge Debelec Butuner
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey
| | - Emir Bozkurt
- Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Balcova, Izmir, Turkey
| | - Ayse Gulten Kantarci
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey
| | - Stephen P Finn
- Department of Histopathology and Morbid Anatomy, Sir Patrick Dun Translational Research Lab, St. James's Hospital, Dublin, Ireland. .,Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland. .,Department of Histopathology, Labmed Directorate, St. James's Hospital, Dublin, Ireland. .,Cancer Molecular Diagnostics, Labmed Directorate, St. James's Hospital, Dublin, Ireland.
| |
Collapse
|
45
|
SETD2 deficiency accelerates MDS-associated leukemogenesis via S100a9 in NHD13 mice and predicts poor prognosis in MDS. Blood 2021; 135:2271-2285. [PMID: 32202636 DOI: 10.1182/blood.2019001963] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/08/2020] [Indexed: 02/06/2023] Open
Abstract
SETD2, the histone H3 lysine 36 methyltransferase, previously identified by us, plays an important role in the pathogenesis of hematologic malignancies, but its role in myelodysplastic syndromes (MDSs) has been unclear. In this study, low expression of SETD2 correlated with shortened survival in patients with MDS, and the SETD2 levels in CD34+ bone marrow cells of those patients were increased by decitabine. We knocked out Setd2 in NUP98-HOXD13 (NHD13) transgenic mice, which phenocopies human MDS, and found that loss of Setd2 accelerated the transformation of MDS into acute myeloid leukemia (AML). Loss of Setd2 enhanced the ability of NHD13+ hematopoietic stem and progenitor cells (HSPCs) to self-renew, with increased symmetric self-renewal division and decreased differentiation and cell death. The growth of MDS-associated leukemia cells was inhibited though increasing the H3K36me3 level by using epigenetic modifying drugs. Furthermore, Setd2 deficiency upregulated hematopoietic stem cell signaling and downregulated myeloid differentiation pathways in the NHD13+ HSPCs. Our RNA-seq and chromatin immunoprecipitation-seq analysis indicated that S100a9, the S100 calcium-binding protein, is a target gene of Setd2 and that the addition of recombinant S100a9 weakens the effect of Setd2 deficiency in the NHD13+ HSPCs. In contrast, downregulation of S100a9 leads to decreases of its downstream targets, including Ikba and Jnk, which influence the self-renewal and differentiation of HSPCs. Therefore, our results demonstrated that SETD2 deficiency predicts poor prognosis in MDS and promotes the transformation of MDS into AML, which provides a potential therapeutic target for MDS-associated acute leukemia.
Collapse
|
46
|
Leeksma AC, Baliakas P, Moysiadis T, Puiggros A, Plevova K, Van der Kevie-Kersemaekers AM, Posthuma H, Rodriguez-Vicente AE, Tran AN, Barbany G, Mansouri L, Gunnarsson R, Parker H, Van den Berg E, Bellido M, Davis Z, Wall M, Scarpelli I, Österborg A, Hansson L, Jarosova M, Ghia P, Poddighe P, Espinet B, Pospisilova S, Tam C, Ysebaert L, Nguyen-Khac F, Oscier D, Haferlach C, Schoumans J, Stevens-Kroef M, Eldering E, Stamatopoulos K, Rosenquist R, Strefford JC, Mellink C, Kater AP. Genomic arrays identify high-risk chronic lymphocytic leukemia with genomic complexity: a multi-center study. Haematologica 2021; 106:87-97. [PMID: 31974198 PMCID: PMC7776256 DOI: 10.3324/haematol.2019.239947] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/22/2020] [Indexed: 01/15/2023] Open
Abstract
Complex karyotype (CK) identified by chromosome-banding analysis (CBA) has shown prognostic value in chronic lymphocytic leukemia (CLL). Genomic arrays offer high-resolution genome-wide detection of copy-number alterations (CNAs) and could therefore be well equipped to detect the presence of a CK. Current knowledge on genomic arrays in CLL is based on outcomes of single center studies, in which different cutoffs for CNA calling were used. To further determine the clinical utility of genomic arrays for CNA assessment in CLL diagnostics, we retrospectively analyzed 2293 arrays from 13 diagnostic laboratories according to established standards. CNAs were found outside regions captured by CLL FISH probes in 34% of patients, and several of them including gains of 8q, deletions of 9p and 18p (p<0.01) were linked to poor outcome after correction for multiple testing. Patients (n=972) could be divided in three distinct prognostic subgroups based on the number of CNAs. Only high genomic complexity (high-GC), defined as ≥5 CNAs emerged as an independent adverse prognosticator on multivariable analysis for time to first treatment (Hazard ratio: 2.15, 95% CI: 1.36-3.41; p=0.001) and overall survival (Hazard ratio: 2.54, 95% CI: 1.54-4.17; p<0.001; n=528). Lowering the size cutoff to 1 Mb in 647 patients did not significantly improve risk assessment. Genomic arrays detected more chromosomal abnormalities and performed at least as well in terms of risk stratification compared to simultaneous chromosome banding analysis as determined in 122 patients. Our findings highlight genomic array as an accurate tool for CLL risk stratification.
Collapse
Affiliation(s)
| | - Panagiotis Baliakas
- Dept of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Theodoros Moysiadis
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | | | - Karla Plevova
- University Hospital Brno, Masaryk University, Brno, Czech Republic
| | | | - Hidde Posthuma
- Dept of Clinical Genetics, Amsterdam University Medical Centers, Univ of Amsterdam, The Netherlands
| | | | - Anh Nhi Tran
- Dept of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Gisela Barbany
- Dept of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Larry Mansouri
- Dept of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Rebeqa Gunnarsson
- Division of Clinical Genetics, Dept of Laboratory Medicine, Lund University, Lund, Sweden
| | - Helen Parker
- Cancer Genomics, Academic Unit of Cancer Sciences, University of Southampton, Southampton, UK
| | - Eva Van den Berg
- Dept of Genetics, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Mar Bellido
- Dept of Genetics, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Zadie Davis
- Dept of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Meaghan Wall
- Cytogenetics department, St Vincent Hospital Melbourne, Victoria, Australia
| | - Ilaria Scarpelli
- Oncogenomic laboratory, Dept of Hematology, Lausanne University Hospital (CHUV), Switzerland
| | - Anders Österborg
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Lotta Hansson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm
| | - Marie Jarosova
- University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Paolo Ghia
- Dept. of Experimental Oncology, IRCCS Ospedale San Raffaele, Università Vita-Salute, Milan
| | - Pino Poddighe
- Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, The Netherlands
| | - Blanca Espinet
- Laboratori de Citogenetica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | - Sarka Pospisilova
- CEITEC, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Constantine Tam
- St Vincent Hospital Melbourne, Peter MacCallum Cancer Center, University of Melbourne, Australia
| | - Loïc Ysebaert
- Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Florence Nguyen-Khac
- Service d'Hematologie Biologique, Hopital Pitié-Salpetriere, APHP, Paris, France
| | - David Oscier
- Dept of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | | | - Jacqueline Schoumans
- Oncogenomic laboratory, Dept of Hematology, Lausanne University Hospital (CHUV), Switzerland
| | - Marian Stevens-Kroef
- Radboud University Medical Center, Dept of Human Genetics, Nijmegen, The Netherlands
| | - Eric Eldering
- Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Richard Rosenquist
- Dept of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Clemens Mellink
- Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
| | - Arnon P Kater
- Hematology, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
| |
Collapse
|
47
|
Haase S, Nuñez FM, Gauss JC, Thompson S, Brumley E, Lowenstein P, Castro MG. Hemispherical Pediatric High-Grade Glioma: Molecular Basis and Therapeutic Opportunities. Int J Mol Sci 2020; 21:ijms21249654. [PMID: 33348922 PMCID: PMC7766684 DOI: 10.3390/ijms21249654] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
In this review, we discuss the molecular characteristics, development, evolution, and therapeutic perspectives for pediatric high-grade glioma (pHGG) arising in cerebral hemispheres. Recently, the understanding of biology of pHGG experienced a revolution with discoveries arising from genomic and epigenomic high-throughput profiling techniques. These findings led to identification of prevalent molecular alterations in pHGG and revealed a strong connection between epigenetic dysregulation and pHGG development. Although we are only beginning to unravel the molecular biology underlying pHGG, there is a desperate need to develop therapies that would improve the outcome of pHGG patients, as current therapies do not elicit significant improvement in median survival for this patient population. We explore the molecular and cell biology and clinical state-of-the-art of pediatric high-grade gliomas (pHGGs) arising in cerebral hemispheres. We discuss the role of driving mutations, with a special consideration of the role of epigenetic-disrupting mutations. We will also discuss the possibilities of targeting unique molecular vulnerabilities of hemispherical pHGG to design innovative tailored therapies.
Collapse
Affiliation(s)
- Santiago Haase
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Fernando M. Nuñez
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jessica C. Gauss
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Sarah Thompson
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Emily Brumley
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Pedro Lowenstein
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria G. Castro
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Correspondence:
| |
Collapse
|
48
|
Wang Y, Ma J, Martinez ED, Liang D, Xie H. A UHPLC-MS/MS method for the quantification of JIB-04 in rat plasma: Development, validation and application to pharmacokinetics study. J Pharm Biomed Anal 2020; 191:113587. [PMID: 32892084 PMCID: PMC7581536 DOI: 10.1016/j.jpba.2020.113587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022]
Abstract
Methylation of lysine by histone methyltransferases can be reversed by lysine demethylases (KDMs). Different KDMs have distinct oncogenic functions based on their cellular localization, stimulating cancer cell proliferation, reducing the expression of tumor suppressors, and/or promoting the development of drug resistance. JIB-04 is a small molecule that pan-selectively inhibits KDMs, showing maximal inhibitory activity against KDM5A, and as secondary targets, KDM4D/4B/4A/6B/4C. Recently, it was found that JIB-04 also potently and selectively blocks HIV-1 Tat expression, transactivation, and virus replication in T cell lines via the inhibition of a new target, serine hydroxymethyltransferase 2. Pharmacokinetic characterization and an analytical method for the quantification of JIB-04 are necessary for the further development of this small molecule. Herein, a sensitive, specific, fast and reliable UHPLC-MS/MS method for the quantification of JIB-04 in rat plasma samples was developed and fully validated using a SCIEX 6500+ triple QUAD LC-MS system equipped with an ExionLC UHPLC unit. The chromatographic separation was achieved on a reverse phase ACE Excel 2 Super C18 column with a flow rate of 0.5 mL/min under gradient elution. The calibration curves were linear (r2 > 0.999) over concentrations from 0.5 to 1000 ng/mL. The accuracy (RE%) was between -7.4% and 3.7%, and the precision (CV%) was 10.2% or less. The stability data showed that no significant degradation occurred under the experimental conditions. This method was successfully applied to the pharmacokinetic study of JIB-04 in rat plasma after intravenous and oral administration and the oral bioavailability of JIB-04 was found to be 44.4%.
Collapse
Affiliation(s)
- Yang Wang
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA
| | - Jing Ma
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA
| | - Elisabeth D Martinez
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dong Liang
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA
| | - Huan Xie
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA.
| |
Collapse
|
49
|
Oshima K, Zhao J, Pérez-Durán P, Brown JA, Patiño-Galindo JA, Chu T, Quinn A, Gunning T, Belver L, Ambesi-Impiombato A, Tosello V, Wang Z, Sulis ML, Kato M, Koh K, Paganin M, Basso G, Balbin M, Nicolas C, Gastier-Foster JM, Devidas M, Loh ML, Paietta E, Tallman MS, Rowe JM, Litzow M, Minden MD, Meijerink J, Rabadan R, Ferrando A. Mutational and functional genetics mapping of chemotherapy resistance mechanisms in relapsed acute lymphoblastic leukemia. ACTA ACUST UNITED AC 2020; 1:1113-1127. [PMID: 33796864 DOI: 10.1038/s43018-020-00124-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multi-agent combination chemotherapy can be curative in acute lymphoblastic leukemia (ALL). Still, patients with primary refractory disease or with relapsed leukemia have a very poor prognosis. Here we integrate an in-depth dissection of the mutational landscape across diagnostic and relapsed pediatric and adult ALL samples with genome-wide CRISPR screen analysis of gene-drug interactions across seven ALL chemotherapy drugs. By combining these analyses, we uncover diagnostic and relapse-specific mutational mechanisms as well as genetic drivers of chemoresistance. Functionally, our data identifies common and drug-specific pathways modulating chemotherapy response and underscores the effect of drug combinations in restricting the selection of resistance-driving genetic lesions. In addition, by identifying actionable targets for the reversal of chemotherapy resistance, these analyses open novel therapeutic opportunities for the treatment of relapse and refractory disease.
Collapse
Affiliation(s)
- Koichi Oshima
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,These authors contributed equally: Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie A. Brown
| | - Junfei Zhao
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA.,These authors contributed equally: Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie A. Brown
| | - Pablo Pérez-Durán
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,These authors contributed equally: Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie A. Brown
| | - Jessie A Brown
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,These authors contributed equally: Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie A. Brown
| | - Juan Angel Patiño-Galindo
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Timothy Chu
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Aidan Quinn
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Thomas Gunning
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Laura Belver
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Alberto Ambesi-Impiombato
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,Present address: PsychoGenics, Paramus, NJ, USA
| | | | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - Maria Luisa Sulis
- Department of Pediatric Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Motohiro Kato
- Department of Hematology-Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Katsuyoshi Koh
- Department of Hematology-Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Maddalena Paganin
- Fondazione Città della Speranza, Istituto di Ricerca Pediatrica, Padova, Italy.,Haematology-Oncology Division, Department of Woman's and Child's Health, University Hospital of Padua, Padua, Italy
| | - Giuseppe Basso
- Haematology-Oncology Division, Department of Woman's and Child's Health, University Hospital of Padua, Padua, Italy.,Present address: IIGM Italian Institute of Genomic Medicine, Turin, Italy
| | - Milagros Balbin
- Molecular Oncology Laboratory, Instituto Universitario de Oncologia del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Concepcion Nicolas
- Hematology Service, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Julie M Gastier-Foster
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Departments of Pathology and Pediatrics, Ohio State University School of Medicine, Columbus, OH, USA.,Children's Oncology Group, Arcadia, CA, USA
| | - Meenakshi Devidas
- Department of Biostatistics, University of Florida, Gainesville, FL, USA.,Present address: Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | | | - Martin S Tallman
- Department of Hematologic Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Mark D Minden
- Department of Oncology/Hematology, Princess Margaret Cancer Center, Toronto, ON, Canada
| | - Jules Meijerink
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Raul Rabadan
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.,Department of Pediatrics, Columbia University, New York, NY, USA
| |
Collapse
|
50
|
Yang Z, Jiang H. A chromatin perspective on metabolic and genotoxic impacts on hematopoietic stem and progenitor cells. Cell Mol Life Sci 2020; 77:4031-4047. [PMID: 32318759 PMCID: PMC7541408 DOI: 10.1007/s00018-020-03522-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/17/2020] [Accepted: 04/06/2020] [Indexed: 02/07/2023]
Abstract
Fate determination in self-renewal and differentiation of hematopoietic stem and progenitor cells (HSCs and HPCs) is ultimately controlled by gene expression, which is profoundly influenced by the global and local chromatin state. Cellular metabolism directly influences the chromatin state through the dynamic regulation of the enzymatic activities that modify DNA and histones, but also generates genotoxic metabolites that can damage DNA and thus pose threat to the genome integrity. On the other hand, mechanisms modulating the chromatin state impact metabolism by regulating the expression and activities of key metabolic enzymes. Moreover, through regulating either DNA damage response directly or expression of genes involved in this process, chromatin modulators play active and crucial roles in guarding the genome integrity, breaching of which results in defective HSPC function. Therefore, HSPC function is regulated by the dynamic and two-way interactions between metabolism and chromatin. Here, we review recent advances that provide a chromatin perspective on the major impacts the metabolic and genotoxic factors can have on HSPC function and fate determination.
Collapse
Affiliation(s)
- Zhenhua Yang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
| |
Collapse
|