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Brockett JS, Manalo T, Zein-Sabatto H, Lee J, Fang J, Chu P, Feng H, Patil D, Davidson P, Ogan K, Master VA, Pattaras JG, Roberts DL, Bergquist SH, Reyna MA, Petros JA, Lerit DA, Arnold RS. A missense SNP in the tumor suppressor SETD2 reduces H3K36me3 and mitotic spindle integrity in Drosophila. Genetics 2024; 226:iyae015. [PMID: 38290049 PMCID: PMC10990431 DOI: 10.1093/genetics/iyae015] [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: 09/08/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 02/01/2024] Open
Abstract
Mutations in SETD2 are among the most prevalent drivers of renal cell carcinoma (RCC). We identified a novel single nucleotide polymorphism (SNP) in SETD2, E902Q, within a subset of RCC patients, which manifests as both an inherited or tumor-associated somatic mutation. To determine if the SNP is biologically functional, we used CRISPR-based genome editing to generate the orthologous mutation within the Drosophila melanogaster Set2 gene. In Drosophila, the homologous amino acid substitution, E741Q, reduces H3K36me3 levels comparable to Set2 knockdown, and this loss is rescued by reintroduction of a wild-type Set2 transgene. We similarly uncovered significant defects in spindle morphogenesis, consistent with the established role of SETD2 in methylating α-Tubulin during mitosis to regulate microtubule dynamics and maintain genome stability. These data indicate the Set2 E741Q SNP affects both histone methylation and spindle integrity. Moreover, this work further suggests the SETD2 E902Q SNP may hold clinical relevance.
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Affiliation(s)
- Jovan S Brockett
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Tad Manalo
- Department of Urology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hala Zein-Sabatto
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jina Lee
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Junnan Fang
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Philip Chu
- Department of Urology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Harry Feng
- Department of Urology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dattatraya Patil
- Department of Urology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Priscilla Davidson
- Department of Urology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kenneth Ogan
- Department of Urology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Viraj A Master
- Department of Urology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John G Pattaras
- Department of Urology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David L Roberts
- Emory University Department of Medicine, Division of General Internal Medicine, Atlanta, GA 30322, USA
| | - Sharon H Bergquist
- Emory University Department of Medicine, Division of General Internal Medicine, Atlanta, GA 30322, USA
| | - Matthew A Reyna
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John A Petros
- Department of Urology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Dorothy A Lerit
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Rebecca S Arnold
- Department of Urology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
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2
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Takeda K, Bastacky S, Dhir R, Mohebnasab M, Quiroga-Garza GM. Morphological characteristics of SETD2-mutated locally advanced clear cell renal cell carcinoma: Comparison with BAP1-mutated clear cell renal cell carcinoma. Ann Diagn Pathol 2024; 68:152223. [PMID: 37976977 DOI: 10.1016/j.anndiagpath.2023.152223] [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: 09/02/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
SET-domain containing 2 (SETD2) and BRCA1-associated protein 1 (BAP1), both chromatin remodeling genes, are frequently mutated in clear cell renal cell carcinoma (ccRCC) and involved in tumor progression and metastasis. Herein, we studied clinicopathologic features of 7 cases of locally advanced ccRCC with single SETD2 mutation, and compared to 7 cases of locally advanced ccRCC with single BAP1 mutation. SETD2-mutated ccRCC showed high-grade transformation, comprising of enlarged tumor cells with voluminous clear cytoplasm, enlarged irregular nuclei with prominent nucleoli, eosinophilic cytoplasmic granules, arranged in various architectural patterns such as large nested, tubular, tubulopapillary and solid. 71 % (5 of 7 cases) of SETD2-mutated ccRCC showed a rhabdoid morphology. SETD2-mutated ccRCC have striking propensity for invasive growth; all cases have vascular invasion and perirenal (extracapsular) adipose tissue invasion. After nephrectomy, distant metastasis was found in 67 % (4 of 7 cases) of patients with SETD2-mutated ccRCC. The most common metastatic site was the lung (3 cases), followed by precaval lymph nodes (1 case). BAP1-mutated ccRCC also showed a similar high-grade morphology, with rhabdoid and/or sarcomatoid features. Their high-grade features mostly overlapped with those of SETD2-mutated ccRCC, which makes difficult to predict the presence of BAP1 or SETD2 mutation solely from morphology. These findings justify the use of molecular testing to detect these mutations, especially when we encounter high-grade ccRCC. Detecting SETD2 and BAP1 mutation in ccRCC is useful for risk stratification and proper therapeutic strategy.
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Affiliation(s)
- Kotaro Takeda
- Department of Pathology, Genitourinary Pathology Center of Excellence, University of Pittsburgh Medical Center, Pittsburgh, USA.
| | - Sheldon Bastacky
- Department of Pathology, Genitourinary Pathology Center of Excellence, University of Pittsburgh Medical Center, Pittsburgh, USA
| | - Rajiv Dhir
- Department of Pathology, Genitourinary Pathology Center of Excellence, University of Pittsburgh Medical Center, Pittsburgh, USA
| | - Maedeh Mohebnasab
- Department of Pathology, Division of Molecular Genetics Pathology, University of Pittsburgh Medical Center, Pittsburgh, USA
| | - Gabriela M Quiroga-Garza
- Department of Pathology, Genitourinary Pathology Center of Excellence, University of Pittsburgh Medical Center, Pittsburgh, USA
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Zheng X, Luo Y, Xiong Y, Liu X, Zeng C, Lu X, Wang X, Cheng Y, Wang S, Lan H, Wang K, Weng Z, Bi W, Gan X, Jia X, Wang L, Wang Y. Tumor cell-intrinsic SETD2 inactivation sensitizes cancer cells to immune checkpoint blockade through the NR2F1-STAT1 pathway. J Immunother Cancer 2023; 11:e007678. [PMID: 38056895 PMCID: PMC10711831 DOI: 10.1136/jitc-2023-007678] [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] [Accepted: 11/16/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Cancer immunotherapies can induce durable tumor regression, but most patients do not respond. SETD2 mutation has been linked to the efficacy of immune checkpoint inhibitors (ICIs) immunotherapy. The functional importance of the SETD2 inactivation and how to modulate immunotherapy response remains unclear. METHODS To explore the function of SETD2 in immunotherapy, knockout and subsequent functional experiments were conducted. Bulk RNA-seq, ATAC-seq, Chip-seq and single-cell RNA-seq were performed to dissect the mechanism and explore the immune microenvironment of mouse tumor. Flow cytometry was used to assess cell surface antigen and intratumoral T cell levels. RESULTS We comprehensively determine the effect of SETD2 inactivation in ICIs therapy and elucidate the mechanistic impact on tumor immunity. Murine syngeneic tumors harboring Setd2 inactivation are sensitive to ICIs. By bulk and single-cell RNA-seq, we further reveal that SETD2 inactivation reprograms intratumoral immune cells and inflames the tumor microenvironment, which is characterized by high infiltration of T cells and enhanced antigen presentation to activate CD8+ T cell-mediated killing. Mechanistically, via an integrated multiomics analysis using ATAC-seq, ChIP-seq and RNA-seq, we demonstrate that SETD2 inactivation reduces NR2F1 transcription by impairing H3K36me3 deposition and chromatin accessibility, which activates the STAT1 signaling pathway to promote chemokines and programmed cell death protein-1 (PD-1) expression and enhance antigen presentation. All these regulatory mechanisms synergistically promote the effects of anti-programmed cell death ligand 1 immunotherapy in Setd2-knockout syngeneic mouse models. The SETD2-NR2F1-STAT1 regulatory axis is conserved in human and murine cancers. Finally, cancer patients harboring SETD2 mutations who received ICIs show increased durable clinical benefits and survival. CONCLUSIONS These findings provide novel insights into the biology of SETD2 inactivation regulation and reveal a new potential therapeutic biomarker for ICIs immunotherapy in various refractory cancers.
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Affiliation(s)
- Xufen Zheng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuxiang Luo
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yangjie Xiong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoxiao Liu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chunling Zeng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaojing Lu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaofang Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yumei Cheng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Simin Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Haoqi Lan
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kai Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhonghui Weng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenbo Bi
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinxin Gan
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xiaona Jia
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Linhui Wang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yuexiang Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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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.
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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.
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5
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Sturgill IR, Raab JR, Hoadley KA. Expanded detection of BAP1 alterations in cancer and tumor type-specific expression score comparison. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568094. [PMID: 38045292 PMCID: PMC10690206 DOI: 10.1101/2023.11.21.568094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
BAP1 is a tumor suppressor gene that was originally studied in uveal melanoma (UVM), kidney renal cell clear cell carcinoma (KIRC), and malignant mesothelioma (MESO). Early analyses focused on single-nucleotide variants, but other alteration types such as larger indels and gene-level copy number (CN) loss can also lead to loss of BAP1 expression. We performed integrated multi-omic analyses using data from The Cancer Genome Atlas (TCGA) for 33 cancer types and more than 10,000 individuals. We combined and manually reviewed existing variant calls and new calls derived from a de novo local realignment pipeline across multiple independent variant callers including indel callers, increasing detection of high-quality somatic variant calls by 30% from 91 to 130, including 7 indels ≥40bp. Including CN loss alterations, 1561 samples from 32 cancer types were BAP1-altered, with alterations being predominantly CN-driven. Differential expression and survival analyses revealed both shared and tissue-specific consequences associated with BAP1 alteration. Our findings broadly emphasize the improvements that are gained by using new computational approaches in large cancer-genome studies such as TCGA.
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Affiliation(s)
- Ian R Sturgill
- Bioinformatics and Computational Biology Curriculum, Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jesse R Raab
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Katherine A Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
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6
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Velez J, Kaniskan HÜ, Jin J. Recent advances in developing degraders & inhibitors of lysine methyltransferases. Curr Opin Chem Biol 2023; 76:102356. [PMID: 37379717 PMCID: PMC10527319 DOI: 10.1016/j.cbpa.2023.102356] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/29/2023] [Accepted: 06/01/2023] [Indexed: 06/30/2023]
Abstract
Over the last several decades, there has been continued interest in developing novel therapeutic approaches targeting protein lysine methyltransferases (PKMTs). Along with PKMT inhibitors, targeted protein degradation (TPD) has emerged as a promising strategy to attenuate aberrant PKMT activity. Particularly, proteolysis targeting chimeras (PROTACs) effectively eliminate PKMTs of interest, suppressing all enzymatic and non-enzymatic functions. PROTACs and other TPD approaches add new depth to PKMT research and novel therapeutics discovery. This review focuses on recent advances in PKMT degrader and inhibitor development over the last several years.
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Affiliation(s)
- Julia Velez
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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7
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Wu Y, Liu F, Wan R, Jiao B. A novel SETD2 variant causing global development delay without overgrowth in a Chinese 3-year-old boy. Front Genet 2023; 14:1153284. [PMID: 37025455 PMCID: PMC10072282 DOI: 10.3389/fgene.2023.1153284] [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: 01/29/2023] [Accepted: 03/07/2023] [Indexed: 04/08/2023] Open
Abstract
Background: Luscan-Lumish syndrome is characterized by macrocephaly, postnatal overgrowth, intellectual disability (ID), developmental delay (DD), which is caused by heterozygous SETD2 (SET domain containing 2) mutations. The incidence of Luscan-Lumish syndrome is unclear. The study was conducted to provide a novel pathogenic SETD2 variant causing atypical Luscan-Lumish syndrome and review all the published SETD2 mutations and corresponding symptoms, comprehensively understanding the phenotypes and genotypes of SETD2 mutations. Methods: Peripheral blood samples of the proband and his parents were collected for next-generation sequencing including whole-exome sequencing (WES), copy number variation (CNV) detection and mitochondrial DNA sequencing. Identified variant was verified by Sanger sequencing. Conservative analysis and structural analysis were performed to investigate the effect of mutation. Public databases such as PubMed, Clinvar and Human Gene Mutation Database (HGMD) were used to collect all cases with SETD2 mutations. Results: A novel pathogenic SETD2 variant (c.5835_c.5836insAGAA, p. A1946Rfs*2) was identified in a Chinese 3-year-old boy, who had speech and motor delay without overgrowth. Conservative analysis and structural analysis showed that the novel pathogenic variant would loss the conserved domains in the C-terminal region and result in loss of function of SETD2 protein. Frameshift mutations and non-sense mutations account for 68.5% of the total 51 SETD2 point mutations, suggesting that Luscan-Lumish syndrome is likely due to loss of function of SETD2. But we failed to find an association between genotype and phenotype of SETD2 mutations. Conclusion: Our findings expand the genotype-phenotype knowledge of SETD2-associated neurological disorder and provide new evidence for further genetic counselling.
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Affiliation(s)
- Yuanyuan Wu
- Department of Reproduction and Genetics, Bethune International Peace Hospital, Shijiazhuang, China
| | - Fang Liu
- Department of Pediatrics, Bethune International Peace Hospital, Shijiazhuang, China
| | - Ruihua Wan
- Department of Pediatrics, Bethune International Peace Hospital, Shijiazhuang, China
| | - Baoquan Jiao
- Department of Reproduction and Genetics, Bethune International Peace Hospital, Shijiazhuang, China
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8
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The role of histone methylation in renal cell cancer: an update. Mol Biol Rep 2023; 50:2735-2742. [PMID: 36575323 DOI: 10.1007/s11033-022-08124-3] [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: 08/10/2022] [Accepted: 11/15/2022] [Indexed: 12/29/2022]
Abstract
Renal cell carcinoma accounts for 2-3% of all cancers. It is difficult to diagnose early. Recently, genome-wide studies have identified that histone methylation was one of the functional classes that is most frequently dysregulated in renal cell cancer. Mutation or mis-regulation of histone methylation, methyltransferases, demethylases are associated with gene expression and tumor progression in renal cell cancer. Herein, we summarize histone methylations, demethylases and their alterations and mechanisms in renal cell cancer.
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9
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Yu M, Qian K, Wang G, Xiao Y, Zhu Y, Ju L. Histone methyltransferase SETD2: An epigenetic driver in clear cell renal cell carcinoma. Front Oncol 2023; 13:1114461. [PMID: 37025591 PMCID: PMC10070805 DOI: 10.3389/fonc.2023.1114461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/09/2023] [Indexed: 04/08/2023] Open
Abstract
SET domain-containing 2 (SETD2) is a lysine methyltransferase that catalyzes histone H3 lysine36 trimethylation (H3K36me3) and has been revealed to play important roles in the regulation of transcriptional elongation, RNA splicing, and DNA damage repair. SETD2 mutations have been documented in several cancers, including clear cell renal cell carcinoma (ccRCC). SETD2 deficiency is associated with cancer occurrence and progression by regulating autophagy flux, general metabolic activity, and replication fork speed. Therefore, SETD2 is considered a potential epigenetic therapeutic target and is the subject of ongoing research on cancer-related diagnosis and treatment. This review presents an overview of the molecular functions of SETD2 in H3K36me3 regulation and its relationship with ccRCC, providing a theoretical basis for subsequent antitumor therapy based on SETD2 or H3K36me3 targets.
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Affiliation(s)
- Mengxue Yu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Gang Wang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
| | - Yu Xiao
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Yuan Zhu
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- *Correspondence: Yuan Zhu, ; Lingao Ju,
| | - Lingao Ju
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Medical Research Institute, Wuhan University, Wuhan, China
- *Correspondence: Yuan Zhu, ; Lingao Ju,
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10
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Sharda A, Humphrey TC. The role of histone H3K36me3 writers, readers and erasers in maintaining genome stability. DNA Repair (Amst) 2022; 119:103407. [PMID: 36155242 DOI: 10.1016/j.dnarep.2022.103407] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/03/2022]
Abstract
Histone Post-Translational Modifications (PTMs) play fundamental roles in mediating DNA-related processes such as transcription, replication and repair. The histone mark H3K36me3 and its associated methyltransferase SETD2 (Set2 in yeast) are archetypical in this regard, performing critical roles in each of these DNA transactions. Here, we present an overview of H3K36me3 regulation and the roles of its writers, readers and erasers in maintaining genome stability through facilitating DNA double-strand break (DSB) repair, checkpoint signalling and replication stress responses. Further, we consider how loss of SETD2 and H3K36me3, frequently observed in a number of different cancer types, can be specifically targeted in the clinic through exploiting loss of particular genome stability functions.
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Affiliation(s)
- Asmita Sharda
- CRUK and MRC Oxford Institute for Radiation Oncology, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Timothy C Humphrey
- CRUK and MRC Oxford Institute for Radiation Oncology, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
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11
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Thakur C, Qiu Y, Zhang Q, Carruthers NJ, Yu M, Bi Z, Fu Y, Wadgaonkar P, Almutairy B, Seno A, Stemmer PM, Chen F. Deletion of mdig enhances H3K36me3 and metastatic potential of the triple negative breast cancer cells. iScience 2022; 25:105057. [PMID: 36124233 PMCID: PMC9482110 DOI: 10.1016/j.isci.2022.105057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/06/2022] [Accepted: 08/26/2022] [Indexed: 11/25/2022] Open
Abstract
In this report, we provide evidence showing diminished expression of the mineral dust-induced gene (mdig), a previously identified oncogenic gene, in human triple negative breast cancer (TNBC). Using a mouse model of orthotopic xenograft of the TNBC MDA-MB-231 cells, we demonstrate that mdig promotes the growth of primary tumors but inhibits metastasis of these cells in vivo. Knockout of mdig resulted in an enhancement of H3K36me3 in the genome and upregulation of some X chromosome-linked genes for cell motility, invasion, and metastasis. Silencing MAGED2, one of the most upregulated and H3K36me3-enriched genes resulted from mdig depletion, can partially reverse the invasive migration of the mdig knockout cells. The anti-metastatic and inhibitory role of mdig on H3K36me3 was cross-validated in another cell line, A549 lung cancer cells. Together, our data suggest that mdig is antagonist against H3K36me3 that enforces expression of genes, such as MAGED2, for cell invasion and metastasis. Loss of mdig expression in TNBC and metastatic breast cancer Knockout of mdig enforces metastasis of the TNBC cells Mdig antagonizes H3K36me3 that promotes expression of X-linked metastatic genes Silencing MAGED2 reduces invasive migration of the mdig knockout cells
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Affiliation(s)
- Chitra Thakur
- Stony Brook Cancer Center and Department of Pathology, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY 11794, USA
| | - Yiran Qiu
- Stony Brook Cancer Center and Department of Pathology, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY 11794, USA
| | - Qian Zhang
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Nicholas J Carruthers
- Institute of Environmental Health Sciences, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Miaomiao Yu
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA.,Cancer Hospital of China Medical University, 44 Xiaoheyan Road, Dadong District, Shenyang, 110042 Liaoning Province, China
| | - Zhuoyue Bi
- Stony Brook Cancer Center and Department of Pathology, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY 11794, USA
| | - Yao Fu
- Stony Brook Cancer Center and Department of Pathology, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY 11794, USA
| | - Priya Wadgaonkar
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Bandar Almutairy
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA.,College of Pharmacy, Al-Dawadmi Campus, Shaqra University, P.O. Box 11961, Riyadh, Saudi Arabia
| | - Akimasa Seno
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA.,Faculty of Engineering, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan
| | - Paul M Stemmer
- Institute of Environmental Health Sciences, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Fei Chen
- Stony Brook Cancer Center and Department of Pathology, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY 11794, USA.,Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
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12
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NSD2 as a Promising Target in Hematological Disorders. Int J Mol Sci 2022; 23:ijms231911075. [PMID: 36232375 PMCID: PMC9569587 DOI: 10.3390/ijms231911075] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/16/2022] Open
Abstract
Alterations of the epigenetic machinery are critically involved in cancer development and maintenance; therefore, the proteins in charge of the generation of epigenetic modifications are being actively studied as potential targets for anticancer therapies. A very important and widespread epigenetic mark is the dimethylation of Histone 3 in Lysine 36 (H3K36me2). Until recently, it was considered as merely an intermediate towards the generation of the trimethylated form, but recent data support a more specific role in many aspects of genome regulation. H3K36 dimethylation is mainly carried out by proteins of the Nuclear SET Domain (NSD) family, among which NSD2 is one of the most relevant members with a key role in normal hematopoietic development. Consequently, NSD2 is frequently altered in several types of tumors—especially in hematological malignancies. Herein, we discuss the role of NSD2 in these pathological processes, and we review the most recent findings in the development of new compounds aimed against the oncogenic forms of this novel anticancer candidate.
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13
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Puzanov GA. Identification of key genes of the ccRCC subtype with poor prognosis. Sci Rep 2022; 12:14588. [PMID: 36028558 PMCID: PMC9418309 DOI: 10.1038/s41598-022-18620-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 08/16/2022] [Indexed: 11/09/2022] Open
Abstract
Clear cell renal carcinoma has been reported in many research studies as a rather heterogeneous disease. Identification of different subtypes and their molecular characteristics can help in choosing a more effective treatment and predicting a response to it. In this study, using multi-omics clustering of RNA-Seq data of patients with clear cell renal carcinoma from TCGA. Specific genes were identified for the most aggressive ccRCC subtype associated with metastasis and a subtype associated with a more favorable course of the disease. Among them were genes associated with blood clotting (FGA, FGG) and genes associated with changes in the immune characteristics of a tumor (ENAM, IGFBP1, IL6). In addition, an association of hub genes of poor survival ccRCC subtype with the levels of infiltration of endothelial cells, hematopoietic stem cells, T cells NK and mast cells was revealed. It was shown that MFI2, CP, FGA, and FGG expression can predict the response to sunitinib, while the APOB, ENAM, IGFBP1, and MFI2 expression predict the response to nivolumab. The results obtained provide insight into the genetic characteristics underlying the aggressive subtype of ccRCC and may help develop new approaches to the treatment of this disease.
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Affiliation(s)
- Grigory Andreevich Puzanov
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Moscow, Russia, 119991. .,Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia.
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14
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Bhattacharya S, Reddy D, Zhang N, Li H, Workman JL. Elevated levels of the methyltransferase SETD2 causes transcription and alternative splicing changes resulting in oncogenic phenotypes. Front Cell Dev Biol 2022; 10:945668. [PMID: 36035998 PMCID: PMC9399737 DOI: 10.3389/fcell.2022.945668] [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: 05/16/2022] [Accepted: 07/18/2022] [Indexed: 11/23/2022] Open
Abstract
The methyltransferase SETD2 regulates cryptic transcription, alternative splicing, and the DNA damage response. It is mutated in a variety of cancers and is believed to be a tumor suppressor. Counterintuitively, despite its important role, SETD2 is robustly degraded by the proteasome keeping its levels low. Here we show that SETD2 accumulation results in a non-canonical deposition of the functionally important H3K36me3 histone mark, which includes its reduced enrichment over gene bodies and exons. This perturbed epigenetic landscape is associated with widespread changes in transcription and alternative splicing. Strikingly, contrary to its role as a tumor suppressor, excessive SETD2 results in the upregulation of cell cycle-associated pathways. This is also reflected in phenotypes of increased cell proliferation and migration. Thus, the regulation of SETD2 levels through its proteolysis is important to maintain its appropriate function, which in turn regulates the fidelity of transcription and splicing-related processes.
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Affiliation(s)
| | | | | | | | - Jerry L. Workman
- Stowers Institute for Medical Research, Kansas City, MO, United States
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15
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Yuen K, Liu Y, Zhou Y, Wang Y, Zhou D, Fang J, Xu L. Mutational landscape and clinical outcome of pediatric acute myeloid leukemia with 11q23/KMT2A rearrangements. Cancer Med 2022; 12:1418-1430. [PMID: 35833755 PMCID: PMC9883550 DOI: 10.1002/cam4.5026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/25/2022] [Accepted: 06/27/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Alterations of 11q23/KMT2A are the most prevalent cytogenetic abnormalities in acute myeloid leukemia (AML) and the prognostic significance of 11q23/KMT2A-rearranged AML based on various translocation partners varies among different studies. However, few studies evaluated the molecular characteristics of 11q23/KMT2A-rearranged pediatric AML. We aim to analyze the mutational landscape of 11q23/KMT2A-rearranged AML and assess their prognostic value in outcomes. METHODS The mutational landscape and clinical prognosis of 105 children with 11q23/KMT2A-rearranged AML in comparison with 277 children with non-11q23/KMT2A-rearranged AML were analyzed using publicly accessible next-generation sequencing data from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) dataset. RESULTS Pediatric AML patients with 11q23/KMT2A-rearrangements harbored a low number of mutations (Median, 1 mutation/patient, range, 1-22), 58% of which involved in RAS pathway mutations (KRAS, NRAS, and PTPN11) and 10.5% of which comprised of SETD2 mutations. Compared with non-11q23/KMT2A-rearranged AML, the incidence of KRAS (32.4% vs. 10.1%, P〈0.001) and SETD2 (10.5% vs. 1.4%, P=0.001) gene mutations in 11q23/KMT2A-rearranged AML was significantly higher. Both KRAS and SETD2 mutations occurred more often in t(10;11)(p12;q23). KRAS mutations were correlated with worse 5-year event-free survival [EFS] (Plog-rank = 0.001) and 5-year overall survival [OS] (Plog-rank = 0.009) and the presence of SETD2 mutations increases the 5-year relapse rate (PGray = 0.004). Multivariate analyses confirmed KRAS mutations in 11q23/KMT2A-rearranged AML as an independent predictor for poor EFS (hazard ratio [HR] = 2.10, P=0.05) and OS (HR = 2.39, P=0.054). CONCLUSION Our findings show that pediatric patients with 11q23/KMT2A rearrangements have characteristic mutation patterns and varying clinical outcomes depending on different translocation partners, which could be utilized to develop more accurate risk stratification and tailored therapies.
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Affiliation(s)
- Ka‐Yuk Yuen
- Department of PediatricsSun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdong ProvinceChina,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationSun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdong ProvinceChina
| | - Yong Liu
- Department of PediatricsSun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdong ProvinceChina,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationSun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdong ProvinceChina
| | - Yong‐Zhuo Zhou
- Department of Clinical LaboratorySun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdong ProvinceChina
| | - Yin Wang
- Department of PediatricsSun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdong ProvinceChina,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationSun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdong ProvinceChina
| | - Dun‐Hua Zhou
- Department of PediatricsSun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdong ProvinceChina,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationSun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdong ProvinceChina
| | - Jian‐Pei Fang
- Department of PediatricsSun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdong ProvinceChina,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationSun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdong ProvinceChina
| | - Lu‐Hong Xu
- Department of PediatricsSun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdong ProvinceChina,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationSun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdong ProvinceChina
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16
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Molenaar TM, van Leeuwen F. SETD2: from chromatin modifier to multipronged regulator of the genome and beyond. Cell Mol Life Sci 2022; 79:346. [PMID: 35661267 PMCID: PMC9167812 DOI: 10.1007/s00018-022-04352-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/09/2022] [Accepted: 05/05/2022] [Indexed: 12/13/2022]
Abstract
Histone modifying enzymes play critical roles in many key cellular processes and are appealing proteins for targeting by small molecules in disease. However, while the functions of histone modifying enzymes are often linked to epigenetic regulation of the genome, an emerging theme is that these enzymes often also act by non-catalytic and/or non-epigenetic mechanisms. SETD2 (Set2 in yeast) is best known for associating with the transcription machinery and methylating histone H3 on lysine 36 (H3K36) during transcription. This well-characterized molecular function of SETD2 plays a role in fine-tuning transcription, maintaining chromatin integrity, and mRNA processing. Here we give an overview of the various molecular functions and mechanisms of regulation of H3K36 methylation by Set2/SETD2. These fundamental insights are important to understand SETD2’s role in disease, most notably in cancer in which SETD2 is frequently inactivated. SETD2 also methylates non-histone substrates such as α-tubulin which may promote genome stability and contribute to the tumor-suppressor function of SETD2. Thus, to understand its role in disease, it is important to understand and dissect the multiple roles of SETD2 within the cell. In this review we discuss how histone methylation by Set2/SETD2 has led the way in connecting histone modifications in active regions of the genome to chromatin functions and how SETD2 is leading the way to showing that we also have to look beyond histones to truly understand the physiological role of an ‘epigenetic’ writer enzyme in normal cells and in disease.
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17
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Morgan M, Shiekhattar R, Shilatifard A, Lauberth SM. It's a DoG-eat-DoG world-altered transcriptional mechanisms drive downstream-of-gene (DoG) transcript production. Mol Cell 2022; 82:1981-1991. [PMID: 35487209 PMCID: PMC9208299 DOI: 10.1016/j.molcel.2022.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/24/2022] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
Abstract
The past decade has revolutionized our understanding of regulatory noncoding RNAs (ncRNAs). Among the most recently identified ncRNAs are downstream-of-gene (DoG)-containing transcripts that are produced by widespread transcriptional readthrough. The discovery of DoGs has set the stage for future studies to address many unanswered questions regarding the mechanisms that promote readthrough transcription, RNA processing, and the cellular functions of the unique transcripts. In this review, we summarize current findings regarding the biogenesis, function, and mechanisms regulating this exciting new class of RNA molecules.
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Affiliation(s)
- Marc Morgan
- Simpson Querrey Institute for Epigenetics and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ramin Shiekhattar
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shannon M Lauberth
- Simpson Querrey Institute for Epigenetics and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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18
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Lam UTF, Tan BKY, Poh JJX, Chen ES. Structural and functional specificity of H3K36 methylation. Epigenetics Chromatin 2022; 15:17. [PMID: 35581654 PMCID: PMC9116022 DOI: 10.1186/s13072-022-00446-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/04/2022] [Indexed: 12/20/2022] Open
Abstract
The methylation of histone H3 at lysine 36 (H3K36me) is essential for maintaining genomic stability. Indeed, this methylation mark is essential for proper transcription, recombination, and DNA damage response. Loss- and gain-of-function mutations in H3K36 methyltransferases are closely linked to human developmental disorders and various cancers. Structural analyses suggest that nucleosomal components such as the linker DNA and a hydrophobic patch constituted by histone H2A and H3 are likely determinants of H3K36 methylation in addition to the histone H3 tail, which encompasses H3K36 and the catalytic SET domain. Interaction of H3K36 methyltransferases with the nucleosome collaborates with regulation of their auto-inhibitory changes fine-tunes the precision of H3K36me in mediating dimethylation by NSD2 and NSD3 as well as trimethylation by Set2/SETD2. The identification of specific structural features and various cis-acting factors that bind to different forms of H3K36me, particularly the di-(H3K36me2) and tri-(H3K36me3) methylated forms of H3K36, have highlighted the intricacy of H3K36me functional significance. Here, we consolidate these findings and offer structural insight to the regulation of H3K36me2 to H3K36me3 conversion. We also discuss the mechanisms that underlie the cooperation between H3K36me and other chromatin modifications (in particular, H3K27me3, H3 acetylation, DNA methylation and N6-methyladenosine in RNAs) in the physiological regulation of the epigenomic functions of chromatin.
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Affiliation(s)
- Ulysses Tsz Fung Lam
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Bryan Kok Yan Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - John Jia Xin Poh
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,National University Health System (NUHS), Singapore, Singapore. .,NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Integrative Sciences & Engineering Programme, National University of Singapore, Singapore, Singapore.
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19
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Khaleel S, Katims A, Cumarasamy S, Rosenzweig S, Attalla K, Hakimi AA, Mehrazin R. Radiogenomics in Clear Cell Renal Cell Carcinoma: A Review of the Current Status and Future Directions. Cancers (Basel) 2022; 14:2085. [PMID: 35565216 PMCID: PMC9100795 DOI: 10.3390/cancers14092085] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/17/2021] [Accepted: 11/21/2021] [Indexed: 12/30/2022] Open
Abstract
Radiogenomics is a field of translational radiology that aims to associate a disease's radiologic phenotype with its underlying genotype, thus offering a novel class of non-invasive biomarkers with diagnostic, prognostic, and therapeutic potential. We herein review current radiogenomics literature in clear cell renal cell carcinoma (ccRCC), the most common renal malignancy. A literature review was performed by querying PubMed, Medline, Cochrane Library, Google Scholar, and Web of Science databases, identifying all relevant articles using the following search terms: "radiogenomics", "renal cell carcinoma", and "clear cell renal cell carcinoma". Articles included were limited to the English language and published between 2009-2021. Of 141 retrieved articles, 16 fit our inclusion criteria. Most studies used computed tomography (CT) images from open-source and institutional databases to extract radiomic features that were then modeled against common genomic mutations in ccRCC using a variety of machine learning algorithms. In more recent studies, we noted a shift towards the prediction of transcriptomic and/or epigenetic disease profiles, as well as downstream clinical outcomes. Radiogenomics offers a platform for the development of non-invasive biomarkers for ccRCC, with promising results in small-scale retrospective studies. However, more research is needed to identify and validate robust radiogenomic biomarkers before integration into clinical practice.
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Affiliation(s)
- Sari Khaleel
- Memorial Sloan Kettering Cancer Center, Department of Urology, New York, NY 10065, USA; (S.K.); (A.A.H.)
| | - Andrew Katims
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (A.K.); (S.C.); (S.R.); (K.A.)
| | - Shivaram Cumarasamy
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (A.K.); (S.C.); (S.R.); (K.A.)
| | - Shoshana Rosenzweig
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (A.K.); (S.C.); (S.R.); (K.A.)
| | - Kyrollis Attalla
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (A.K.); (S.C.); (S.R.); (K.A.)
| | - A Ari Hakimi
- Memorial Sloan Kettering Cancer Center, Department of Urology, New York, NY 10065, USA; (S.K.); (A.A.H.)
| | - Reza Mehrazin
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (A.K.); (S.C.); (S.R.); (K.A.)
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20
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Taylor-Papadimitriou J, Burchell JM. Histone Methylases and Demethylases Regulating Antagonistic Methyl Marks: Changes Occurring in Cancer. Cells 2022; 11:cells11071113. [PMID: 35406676 PMCID: PMC8997813 DOI: 10.3390/cells11071113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetic regulation of gene expression is crucial to the determination of cell fate in development and differentiation, and the Polycomb (PcG) and Trithorax (TrxG) groups of proteins, acting antagonistically as complexes, play a major role in this regulation. Although originally identified in Drosophila, these complexes are conserved in evolution and the components are well defined in mammals. Each complex contains a protein with methylase activity (KMT), which can add methyl groups to a specific lysine in histone tails, histone 3 lysine 27 (H3K27), by PcG complexes, and H3K4 and H3K36 by TrxG complexes, creating transcriptionally repressive or active marks, respectively. Histone demethylases (KDMs), identified later, added a new dimension to histone methylation, and mutations or changes in levels of expression are seen in both methylases and demethylases and in components of the PcG and TrX complexes across a range of cancers. In this review, we focus on both methylases and demethylases governing the methylation state of the suppressive and active marks and consider their action and interaction in normal tissues and in cancer. A picture is emerging which indicates that the changes which occur in cancer during methylation of histone lysines can lead to repression of genes, including tumour suppressor genes, or to the activation of oncogenes. Methylases or demethylases, which are themselves tumour suppressors, are highly mutated. Novel targets for cancer therapy have been identified and a methylase (KMT6A/EZH2), which produces the repressive H3K27me3 mark, and a demethylase (KDM1A/LSD1), which demethylates the active H3K4me2 mark, are now under clinical evaluation.
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21
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Rosa-Mercado NA, Steitz JA. Who let the DoGs out? - biogenesis of stress-induced readthrough transcripts. Trends Biochem Sci 2022; 47:206-217. [PMID: 34489151 PMCID: PMC8840951 DOI: 10.1016/j.tibs.2021.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/27/2021] [Accepted: 08/10/2021] [Indexed: 01/22/2023]
Abstract
Readthrough transcription caused by inefficient 3'-end cleavage of nascent mRNAs has emerged as a hallmark of the mammalian cellular stress response and results in the production of long noncoding RNAs known as downstream-of-gene (DoG)-containing transcripts. DoGs arise from around 10% of human protein-coding genes and are retained in the nucleus. They are produced minutes after cell exposure to stress and can be detected hours after stress removal. However, their biogenesis and the role(s) that DoGs or their production play in the cellular stress response are incompletely understood. We discuss findings that implicate host and viral proteins in the mechanisms underlying DoG production, as well as the transcriptional landscapes that accompany DoG induction under different stress conditions.
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Affiliation(s)
- Nicolle A Rosa-Mercado
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.
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22
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23
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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.
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24
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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.
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25
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Lampe JW, Alford JS, Boriak-Sjodin PA, Brach D, Cosmopoulos K, Duncan KW, Eckley ST, Foley MA, Harvey DM, Motwani V, Munchhof MJ, Raimondi A, Riera TV, Tang C, Thomenius MJ, Totman J, Farrow NA. Discovery of a First-in-Class Inhibitor of the Histone Methyltransferase SETD2 Suitable for Preclinical Studies. ACS Med Chem Lett 2021; 12:1539-1545. [PMID: 34671445 PMCID: PMC8521618 DOI: 10.1021/acsmedchemlett.1c00272] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/16/2021] [Indexed: 01/19/2023] Open
Abstract
![]()
SET domain-containing
protein 2 (SETD2), a histone methyltransferase,
has been identified as a target of interest in certain hematological
malignancies, including multiple myeloma. This account details the
discovery of EPZ-719, a novel and potent SETD2 inhibitor
with a high selectivity over other histone methyltransferases. A screening
campaign of the Epizyme proprietary histone methyltransferase-biased
library identified potential leads based on a 2-amidoindole core.
Structure-based drug design (SBDD) and drug metabolism/pharmacokinetics
(DMPK) optimization resulted in EPZ-719, an attractive
tool compound for the interrogation of SETD2 biology that enables in vivo target validation studies.
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Affiliation(s)
- John W. Lampe
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Joshua S. Alford
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - P. Ann Boriak-Sjodin
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Dorothy Brach
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Kat Cosmopoulos
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Kenneth W. Duncan
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Sean T. Eckley
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Megan A. Foley
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Darren M. Harvey
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Vinny Motwani
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Michael J. Munchhof
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Alejandra Raimondi
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Thomas V. Riera
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Cuyue Tang
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Michael J. Thomenius
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Jennifer Totman
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Neil A. Farrow
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
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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.
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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:
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The disordered regions of the methyltransferase SETD2 govern its function by regulating its proteolysis and phase separation. J Biol Chem 2021; 297:101075. [PMID: 34391778 PMCID: PMC8405934 DOI: 10.1016/j.jbc.2021.101075] [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: 06/14/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 12/14/2022] Open
Abstract
SETD2 is an important methyltransferase that methylates crucial substrates such as histone H3, tubulin, and STAT1 and also physically interacts with transcription and splicing regulators such as Pol II and various hnRNPs. Of note, SETD2 has a functionally uncharacterized extended N-terminal region, the removal of which leads to its stabilization. How this region regulates SETD2 half-life is unclear. Here we show that SETD2 consists of multiple long disordered regions across its length that cumulatively destabilize the protein by facilitating its proteasomal degradation. SETD2 disordered regions can reduce the half-life of the yeast homolog Set2 in mammalian cells as well as in yeast, demonstrating the importance of intrinsic structural features in regulating protein half-life. In addition to the shortened half-life, by performing fluorescence recovery after photobleaching assay we found that SETD2 forms liquid droplets in vivo, another property associated with proteins that contain disordered regions. The phase-separation behavior of SETD2 is exacerbated upon the removal of its N-terminal segment and results in activator-independent histone H3K36 methylation. Our findings reveal that disordered region-facilitated proteolysis is an important mechanism governing SETD2 function.
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Depletion of H3K36me2 recapitulates epigenomic and phenotypic changes induced by the H3.3K36M oncohistone mutation. Proc Natl Acad Sci U S A 2021; 118:2021795118. [PMID: 33619101 DOI: 10.1073/pnas.2021795118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hotspot histone H3 mutations have emerged as drivers of oncogenesis in cancers of multiple lineages. Specifically, H3 lysine 36 to methionine (H3K36M) mutations are recurrently identified in chondroblastomas, undifferentiated sarcomas, and head and neck cancers. While the mutation reduces global levels of both H3K36 dimethylation (H3K36me2) and trimethylation (H3K36me3) by dominantly inhibiting their respective specific methyltransferases, the relative contribution of these methylation states to the chromatin and phenotypic changes associated with H3K36M remains unclear. Here, we specifically deplete H3K36me2 or H3K36me3 in mesenchymal cells, using CRISPR-Cas9 to separately knock out the corresponding methyltransferases NSD1/2 or SETD2. By profiling and comparing the epigenomic and transcriptomic landscapes of these cells with cells expressing the H3.3K36M oncohistone, we find that the loss of H3K36me2 could largely recapitulate H3.3K36M's effect on redistribution of H3K27 trimethylation (H3K27me3) and gene expression. Consistently, knockout of Nsd1/2, but not Setd2, phenocopies the differentiation blockade and hypersensitivity to the DNA-hypomethylating agent induced by H3K36M. Together, our results support a functional divergence between H3K36me2 and H3K36me3 and their nonredundant roles in H3K36M-driven oncogenesis.
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SETD2-mediated H3K14 trimethylation promotes ATR activation and stalled replication fork restart in response to DNA replication stress. Proc Natl Acad Sci U S A 2021; 118:2011278118. [PMID: 34074749 PMCID: PMC8201831 DOI: 10.1073/pnas.2011278118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ataxia telangiectasia and Rad3 related (ATR) activation after replication stress involves a cascade of reactions, including replication protein A (RPA) complex loading onto single-stranded DNA and ATR activator loading onto chromatin. The contribution of histone modifications to ATR activation, however, is unclear. Here, we report that H3K14 trimethylation responds to replication stress by enhancing ATR activation. First, we confirmed that H3K14 monomethylation, dimethylation, and trimethylation all exist in mammalian cells, and that both SUV39H1 and SETD2 methyltransferases can catalyze H3K14 trimethylation in vivo and in vitro. Interestingly, SETD2-mediated H3K14 trimethylation markedly increases in response to replication stress induced with hydroxyurea, a replication stress inducer. Under these conditions, SETD2-mediated H3K14me3 recruited the RPA complex to chromatin via a direct interaction with RPA70. The increase in H3K14me3 levels was abolished, and RPA loading was attenuated when SETD2 was depleted or H3K14 was mutated. Rather, the cells were sensitive to replication stress such that the replication forks failed to restart, and cell-cycle progression was delayed. These findings help us understand how H3K14 trimethylation links replication stress with ATR activation.
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30
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Li X, Liu C, Zhu Y, Rao H, Liu M, Gui L, Feng W, Tang H, Xu J, Gao WQ, Li L. SETD2 epidermal deficiency promotes cutaneous wound healing via activation of AKT/mTOR Signalling. Cell Prolif 2021; 54:e13045. [PMID: 33949020 PMCID: PMC8168411 DOI: 10.1111/cpr.13045] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/26/2021] [Accepted: 04/06/2021] [Indexed: 12/13/2022] Open
Abstract
Objectives Cutaneous wound healing is one of the major medical problems worldwide. Epigenetic modifiers have been identified as important players in skin development, homeostasis and wound repair. SET domain–containing 2 (SETD2) is the only known histone H3K36 tri‐methylase; however, its role in skin wound healing remains unclear. Materials and Methods To elucidate the biological role of SETD2 in wound healing, conditional gene targeting was used to generate epidermis‐specific Setd2‐deficient mice. Wound‐healing experiments were performed on the backs of mice, and injured skin tissues were collected and analysed by haematoxylin and eosin (H&E) and immunohistochemical staining. In vitro, CCK8 and scratch wound‐healing assays were performed on Setd2‐knockdown and Setd2‐overexpression human immortalized keratinocyte cell line (HaCaT). In addition, RNA‐seq and H3K36me3 ChIP‐seq analyses were performed to identify the dysregulated genes modulated by SETD2. Finally, the results were validated in functional rescue experiments using AKT and mTOR inhibitors (MK2206 and rapamycin). Results Epidermis‐specific Setd2‐deficient mice were successfully established, and SETD2 deficiency resulted in accelerated re‐epithelialization during cutaneous wound healing by promoting keratinocyte proliferation and migration. Furthermore, the loss of SETD2 enhanced the scratch closure and proliferation of keratinocytes in vitro. Mechanistically, the deletion of Setd2 resulted in the activation of AKT/mTOR signalling pathway, while the pharmacological inhibition of AKT and mTOR with MK2206 and rapamycin, respectively, delayed wound closure. Conclusions Our results showed that SETD2 loss promoted cutaneous wound healing via the activation of AKT/mTOR signalling.
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Affiliation(s)
- Xiaoxue Li
- State Key Laboratory of Oncogenes and Related Genes, School of Medicine and School of Biomedical Engineering, Renji Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Changwei Liu
- State Key Laboratory of Oncogenes and Related Genes, School of Medicine and School of Biomedical Engineering, Renji Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Yiwen Zhu
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hanyu Rao
- State Key Laboratory of Oncogenes and Related Genes, School of Medicine and School of Biomedical Engineering, Renji Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Min Liu
- State Key Laboratory of Oncogenes and Related Genes, School of Medicine and School of Biomedical Engineering, Renji Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Liming Gui
- State Key Laboratory of Oncogenes and Related Genes, School of Medicine and School of Biomedical Engineering, Renji Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Wenxin Feng
- State Key Laboratory of Oncogenes and Related Genes, School of Medicine and School of Biomedical Engineering, Renji Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Huayuan Tang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Jin Xu
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Wei-Qiang Gao
- State Key Laboratory of Oncogenes and Related Genes, School of Medicine and School of Biomedical Engineering, Renji Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Li Li
- State Key Laboratory of Oncogenes and Related Genes, School of Medicine and School of Biomedical Engineering, Renji Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
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31
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Li XJ, Li QL, Ju LG, Zhao C, Zhao LS, Du JW, Wang Y, Zheng L, Song BL, Li LY, Li L, Wu M. Deficiency of Histone Methyltransferase SET Domain-Containing 2 in Liver Leads to Abnormal Lipid Metabolism and HCC. Hepatology 2021; 73:1797-1815. [PMID: 33058300 DOI: 10.1002/hep.31594] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 09/15/2020] [Accepted: 09/20/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND AND AIMS Trimethylation of Lys36 on histone 3 (H3K36me3) catalyzed by histone methyltransferase SET domain-containing 2 (SETD2) is one of the most conserved epigenetic marks from yeast to mammals. SETD2 is frequently mutated in multiple cancers and acts as a tumor suppressor. APPROACH AND RESULTS Here, using a liver-specific Setd2 depletion model, we found that Setd2 deficiency is sufficient to trigger spontaneous HCC. Meanwhile, Setd2 depletion significantly increased tumor and tumor size of a diethylnitrosamine-induced HCC model. The mechanistic study showed that Setd2 suppresses HCC not only through modulating DNA damage response, but also by regulating lipid metabolism in the liver. Setd2 deficiency down-regulated H3K36me3 enrichment and expression of cholesterol efflux genes and caused lipid accumulation. High-fat diet enhanced lipid accumulation and promoted the development of HCC in Setd2-deficient mice. Chromatin immunoprecipitation sequencing analysis further revealed that Setd2 depletion induced c-Jun/activator protein 1 (AP-1) activation in the liver, which was trigged by accumulated lipid. c-Jun acts as an oncogene in HCC and functions through inhibiting p53 in Setd2-deficient cells. CONCLUSIONS We revealed the roles of Setd2 in HCC and the underlying mechanisms in regulating cholesterol homeostasis and c-Jun/AP-1 signaling.
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Affiliation(s)
- Xue-Jing Li
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qing-Lan Li
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lin-Gao Ju
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chen Zhao
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lan-Shen Zhao
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jia-Wen Du
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yan Wang
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ling Zheng
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bao-Liang Song
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lian-Yun Li
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Wuhan University, Wuhan, China
| | - Li Li
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Min Wu
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Wuhan University, Wuhan, China
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Rao H, Li X, Liu M, Liu J, Feng W, Tang H, Xu J, Gao WQ, Li L. Multilevel Regulation of β-Catenin Activity by SETD2 Suppresses the Transition from Polycystic Kidney Disease to Clear Cell Renal Cell Carcinoma. Cancer Res 2021; 81:3554-3567. [PMID: 33910928 DOI: 10.1158/0008-5472.can-20-3960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/17/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022]
Abstract
Patients with polycystic kidney disease (PKD) are at a high risk of developing renal cell carcinoma (RCC). However, little is known about genetic alterations or changes in signaling pathways during the transition from PKD to RCC. SET domain-containing 2 (SETD2) is a histone methyltransferase, which catalyzes tri-methylation of H3K36 (H3K36me3) and has been identified as a tumor suppressor in clear cell renal cell carcinoma (ccRCC), but the underlying mechanism remains largely unexplored. Here we report that knockout of SETD2 in a c-MYC-driven PKD mouse model drove the transition to ccRCC. SETD2 inhibited β-catenin activity at transcriptional and posttranscriptional levels by competing with β-catenin for binding promoters of target genes and maintaining transcript levels of members of the β-catenin destruction complex. Thus, SETD2 deficiency enhanced the epithelial-to-mesenchymal transition and tumorigenesis through the hyperactivation of Wnt/β-catenin signaling. Our findings reveal previously unrecognized roles of SETD2-mediated competitive DNA binding and H3K36me3 modification in regulating Wnt/β-catenin signaling during the transition from PKD to ccRCC. The novel autochthonous mouse models of PKD and ccRCC will be useful for preclinical research into disease progression. SIGNIFICANCE: These findings characterize multiple mechanisms by which SETD2 inhibits β-catenin activity during the transition of polycystic kidney disease to renal cell carcinoma, providing a potential therapeutic strategy for high-risk patients. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/13/3554/F1.large.jpg.
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Affiliation(s)
- Hanyu Rao
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoxue Li
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Min Liu
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Liu
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Wenxin Feng
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Huayuan Tang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Jin Xu
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Wei-Qiang Gao
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China. ; .,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Li Li
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China. ; .,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
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Sandström J, Balian A, Lockowandt R, Fornander T, Nordenskjöld B, Lindström L, Pérez-Tenorio G, Stål O. IP6K2 predicts favorable clinical outcome of primary breast cancer. Mol Clin Oncol 2021; 14:94. [PMID: 33767863 PMCID: PMC7976380 DOI: 10.3892/mco.2021.2256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/09/2021] [Indexed: 01/15/2023] Open
Abstract
The inositol hexakisphosphate kinase (IP6K) 1 and 2 genes are localized at 3p21.31, a highly altered gene-dense chromosomal region in cancer. The IP6Ks convert IP6 to IP7, which inhibits activation of the tumor-promoting PI3K/Akt/mTOR signaling pathway. IP6K2 has been suggested to be involved in p53-induced apoptosis, while IP6K1 may stimulate tumor growth and migration. The present study aimed to elucidate the role of the two IP6Ks in predicting outcome in patients with breast cancer. To the best of our knowledge, the role of IP6K was analyzed for the first time in tumors from three cohorts of patients with breast cancer; one Swedish low-risk cohort, one Dutch cohort and the TCGA dataset. Analyses of gene -and protein expression and subcellular localization were included. IP6K2 gene expression was associated with ER positivity and nuclear p-Akt. Improved prognosis was detected with high IP6K2 gene expression compared with low IP6K2 gene expression in systemically untreated patients in the Swedish low-risk and Dutch cohorts. In the TCGA dataset, IP6K2 prognostic value was significant when selecting for tumors with wild-type TP53. A multivariable analysis testing IP6K2 against other cancer-related genes at 3p.21.31, including IP6K1 and clinical biomarkers, revealed that IP6K2 was associated with decreased risk of distant recurrence. IP6K1 was associated with increased risk of distant recurrence in the multivariable test and protein analysis revealed trends of worse prognosis with high IP6K1 in the cytoplasm. The expression levels of IP6K1 and IP6K2 were associated to a high extent; however, a diverging prognostic value of the two genes was observed in breast cancer. The present data suggest that IP6K2 can be a favorable prognostic factor, while IP6K1 may not be.
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Affiliation(s)
- Josefine Sandström
- Department of Biomedical and Clinical Sciences and Department of Oncology, Linköping University, 581 83 Linköping, Sweden
| | - Alien Balian
- Department of Biomedical and Clinical Sciences and Department of Oncology, Linköping University, 581 83 Linköping, Sweden
| | - Rebecca Lockowandt
- Department of Biomedical and Clinical Sciences and Department of Oncology, Linköping University, 581 83 Linköping, Sweden
| | - Tommy Fornander
- Department of Oncology-Pathology, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Bo Nordenskjöld
- Department of Biomedical and Clinical Sciences and Department of Oncology, Linköping University, 581 83 Linköping, Sweden
| | - Linda Lindström
- Department of Biosciences and Nutrition, Karolinska Institute, 141 83 Stockholm, Sweden
| | - Gizeh Pérez-Tenorio
- Department of Biomedical and Clinical Sciences and Department of Oncology, Linköping University, 581 83 Linköping, Sweden
| | - Olle Stål
- Department of Biomedical and Clinical Sciences and Department of Oncology, Linköping University, 581 83 Linköping, Sweden
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34
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Udayaraja GK, Arnold Emerson I. Network-based gene deletion analysis identifies candidate genes and molecular mechanism involved in clear cell renal cell carcinoma. J Genet 2021. [DOI: 10.1007/s12041-021-01260-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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35
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Taylor EL, Westendorf JJ. Histone Mutations and Bone Cancers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1283:53-62. [PMID: 33155137 DOI: 10.1007/978-981-15-8104-5_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Primary bone tumors are rare cancers that cause significant morbidity and mortality. The recent identification of recurrent mutations in histone genes H3F3A and H3F3B within specific bone cancers, namely, chondroblastomas and giant cell tumors of bone (GCTB), has provided insights into the cellular and molecular origins of these neoplasms and enhanced understanding of how histone variants control chromatin function. Somatic mutations in H3F3A and H3F3B produce oncohistones, H3.3G34W and H3.3K36M, in more than nine of ten GCTB and chondroblastomas, respectively. Incorporation of the mutant histones into nucleosomes inhibits histone methyltransferases NSD2 and SETD2 to alter the chromatin landscape and change gene expression patterns that control cell proliferation, survival, and differentiation, as well as DNA repair and chromosome stability. The discovery of these histone mutations has facilitated more accurate diagnoses of these diseases and stratification of malignant tumors from benign tumors so that appropriate care can be delivered. The broad-scale epigenomic and transcriptomic changes that arise from incorporation of mutant histones into chromatin provide opportunities to develop new and disease-specific therapies. In this chapter, we review how mutant histones inhibit SETD2 and NSD2 function in bone tumors and discuss how this information could lead to better treatments for these cancers.
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Affiliation(s)
- Earnest L Taylor
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
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36
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Schuhmacher MK, Beldar S, Khella MS, Bröhm A, Ludwig J, Tempel W, Weirich S, Min J, Jeltsch A. Sequence specificity analysis of the SETD2 protein lysine methyltransferase and discovery of a SETD2 super-substrate. Commun Biol 2020; 3:511. [PMID: 32939018 PMCID: PMC7495481 DOI: 10.1038/s42003-020-01223-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 08/10/2020] [Indexed: 12/18/2022] Open
Abstract
SETD2 catalyzes methylation at lysine 36 of histone H3 and it has many disease connections. We investigated the substrate sequence specificity of SETD2 and identified nine additional peptide and one protein (FBN1) substrates. Our data showed that SETD2 strongly prefers amino acids different from those in the H3K36 sequence at several positions of its specificity profile. Based on this, we designed an optimized super-substrate containing four amino acid exchanges and show by quantitative methylation assays with SETD2 that the super-substrate peptide is methylated about 290-fold more efficiently than the H3K36 peptide. Protein methylation studies confirmed very strong SETD2 methylation of the super-substrate in vitro and in cells. We solved the structure of SETD2 with bound super-substrate peptide containing a target lysine to methionine mutation, which revealed better interactions involving three of the substituted residues. Our data illustrate that substrate sequence design can strongly increase the activity of protein lysine methyltransferases. Schuhmacher, Beldar et al. design a super-substrate peptide based on the substrate sequence specificity of the SETD2 protein lysine methyltransferase. SETD2 methylates this super-substrate 290-fold more efficiently than the original H3K36 peptide. This study illustrates that substrate sequence design can improve the activity of protein lysine methyltransferases.
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Affiliation(s)
- Maren Kirstin Schuhmacher
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Serap Beldar
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Mina S Khella
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.,Biochemistry Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Abbassia, Cairo, 11566, Egypt
| | - Alexander Bröhm
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Jan Ludwig
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Sara Weirich
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada.
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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Abstract
Radiomics allows for high throughput extraction of quantitative data from images. This is an area of active research as groups try to capture and quantify imaging parameters and convert these into descriptive phenotypes of organs or tumors. Texture analysis is one radiomics tool that extracts information about heterogeneity within a given region of interest. This is used with or without associated machine learning classifiers or a deep learning approach is applied to similar types of data. These tools have shown utility in characterizing renal masses, renal cell carcinoma, and assessing response to targeted therapeutic agents in metastatic renal cell carcinoma.
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Affiliation(s)
- Meghan G Lubner
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Avenue, Madison, WI 53792, USA.
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38
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Chen R, Zhao WQ, Fang C, Yang X, Ji M. Histone methyltransferase SETD2: a potential tumor suppressor in solid cancers. J Cancer 2020; 11:3349-3356. [PMID: 32231741 PMCID: PMC7097956 DOI: 10.7150/jca.38391] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 02/09/2020] [Indexed: 12/24/2022] Open
Abstract
Epigenetic regulation plays an important role in the occurrence, development and treatment of malignant tumors; and a great deal of attention has been paid to the histone methylation level in recent years. As a 230-kD epigenetic regulator, the histone H3 lysine 36 histone (H3K36) methyltransferase SETD2 is a key enzyme of the nuclear receptor SET domain-containing (NSD) family, which is associated with a specific hyperphosphorylated domain, a large subunit of RNA polymerase II (RNAPII), named RNAPII subunit B1 (RPB1), and SETD2 which methylates the ly-36 position of dimethylated histone H3 (H3K36me2) to generate trimethylated H3K36 (H3K36me3). SETD2 is involved in various cellular processes, including transcriptional regulation, DNA damage repair, non-histone protein-related functions and some other processes. Great efforts of high-throughput sequencing have revealed that SETD2 is mutated or its function is lost in a range of solid cancers, including renal cancer, gastrointestinal cancer, lung cancer, pancreatic cancer, osteosarcoma, and so on. Mutation, or functional loss, of the SETD2 gene produces dysfunction in corresponding tumor tissue proteins, leading to tumorigenesis, progression, chemotherapy resistance, and unfavorable prognosis, suggesting that SETD2 possibly acts as a tumor suppressor. However, its underlying mechanism remains largely unexplored. In the present study, we summarized the latest advances of effects of SETD2 expression at the mRNA and protein levels in solid cancers, and its potential molecular and cellular functions as well as clinical applications were also reviewed.
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Affiliation(s)
- Rui Chen
- Department of Oncology, the Third Affiliated Hospital of Soochow University, The First People's Hospital of Changzhou, No. 185 Juqian Road, Tianning District, Changzhou 213003, China
| | - Wei-Qing Zhao
- Department of Oncology, the Third Affiliated Hospital of Soochow University, The First People's Hospital of Changzhou, No. 185 Juqian Road, Tianning District, Changzhou 213003, China
| | - Cheng Fang
- Department of Oncology, the Third Affiliated Hospital of Soochow University, The First People's Hospital of Changzhou, No. 185 Juqian Road, Tianning District, Changzhou 213003, China
| | - Xin Yang
- Department of Oncology, the Third Affiliated Hospital of Soochow University, The First People's Hospital of Changzhou, No. 185 Juqian Road, Tianning District, Changzhou 213003, China
| | - Mei Ji
- Department of Oncology, the Third Affiliated Hospital of Soochow University, The First People's Hospital of Changzhou, No. 185 Juqian Road, Tianning District, Changzhou 213003, China
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39
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Huang Y, Li GM. DNA mismatch repair in the context of chromatin. Cell Biosci 2020; 10:10. [PMID: 32025281 PMCID: PMC6996186 DOI: 10.1186/s13578-020-0379-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/24/2020] [Indexed: 12/11/2022] Open
Abstract
DNA mismatch repair (MMR) maintains replication fidelity by correcting mispaired nucleotides incorporated by DNA polymerases. Defects in MMR lead to cancers characterized by microsatellite instability. Recently, chromatin mechanisms that regulate MMR have been discovered, which sheds new light on MMR deficiency and its role in tumorigenesis. This review summarizes these chromatin-level mechanisms that regulate MMR and their implications for tumor development.
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Affiliation(s)
- Yaping Huang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
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40
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Sun Z, Zhang Y, Jia J, Fang Y, Tang Y, Wu H, Fang D. H3K36me3, message from chromatin to DNA damage repair. Cell Biosci 2020; 10:9. [PMID: 32021684 PMCID: PMC6995143 DOI: 10.1186/s13578-020-0374-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/09/2020] [Indexed: 12/17/2022] Open
Abstract
Histone marks control many cellular processes including DNA damage repair. This review will focus primarily on the active histone mark H3K36me3 in the regulation of DNA damage repair and the maintenance of genomic stability after DNA damage. There are diverse clues showing H3K36me3 participates in DNA damage response by directly recruiting DNA repair machinery to set the chromatin at a “ready” status, leading to a quick response upon damage. Reduced H3K36me3 is associated with low DNA repair efficiency. This review will also place a main emphasis on the H3K36me3-mediated DNA damage repair in the tumorigenesis of the newly found oncohistone mutant tumors. Gaining an understanding of different aspects of H3K36me3 in DNA damage repair, especially in cancers, would share the knowledge of chromatin and DNA repair to serve to the drug discovery and patient care.
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Affiliation(s)
- Zhongxing Sun
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Yanjun Zhang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Junqi Jia
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Yuan Fang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Yin Tang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Hongfei Wu
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Dong Fang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
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41
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Putative promoters within gene bodies control exon expression via TET1‐mediated H3K36 methylation. J Cell Physiol 2020; 235:6711-6724. [DOI: 10.1002/jcp.29566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 01/13/2020] [Indexed: 12/31/2022]
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42
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Lo Gullo R, Daimiel I, Morris EA, Pinker K. Combining molecular and imaging metrics in cancer: radiogenomics. Insights Imaging 2020; 11:1. [PMID: 31901171 PMCID: PMC6942081 DOI: 10.1186/s13244-019-0795-6] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/25/2019] [Indexed: 02/07/2023] Open
Abstract
Background Radiogenomics is the extension of radiomics through the combination of genetic and radiomic data. Because genetic testing remains expensive, invasive, and time-consuming, and thus unavailable for all patients, radiogenomics may play an important role in providing accurate imaging surrogates which are correlated with genetic expression, thereby serving as a substitute for genetic testing. Main body In this article, we define the meaning of radiogenomics and the difference between radiomics and radiogenomics. We provide an up-to-date review of the radiomics and radiogenomics literature in oncology, focusing on breast, brain, gynecological, liver, kidney, prostate and lung malignancies. We also discuss the current challenges to radiogenomics analysis. Conclusion Radiomics and radiogenomics are promising to increase precision in diagnosis, assessment of prognosis, and prediction of treatment response, providing valuable information for patient care throughout the course of the disease, given that this information is easily obtainable with imaging. Larger prospective studies and standardization will be needed to define relevant imaging biomarkers before they can be implemented into the clinical workflow.
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Affiliation(s)
- Roberto Lo Gullo
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, New York, NY, 10065, USA.
| | - Isaac Daimiel
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, New York, NY, 10065, USA
| | - Elizabeth A Morris
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, New York, NY, 10065, USA
| | - Katja Pinker
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, New York, NY, 10065, USA.,Department of Biomedical Imaging and Image-guided Therapy, Molecular and Gender Imaging Service, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Wien, Austria
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43
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Chen Z, Sun T, Yang Z, Zheng Y, Yu R, Wu X, Yan J, Shao YW, Shao X, Cao W, Wang X. Monitoring treatment efficacy and resistance in breast cancer patients via circulating tumor DNA genomic profiling. Mol Genet Genomic Med 2019; 8:e1079. [PMID: 31867841 PMCID: PMC7005625 DOI: 10.1002/mgg3.1079] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 09/16/2019] [Accepted: 10/23/2019] [Indexed: 01/03/2023] Open
Abstract
Background One of the major challenges in managing invasive breast cancer (BC) is the lack of reliable biomarkers to track response. Circulating tumor DNA (ctDNA) from liquid biopsy, as a candidate biomarker, provides a valuable assessment of BC patients. In this retrospective study, we evaluated the utility of ctDNA to reflect the efficacy of treatment and to monitor resistance mechanisms. Methods Targeted next‐generation sequencing (NGS) of 416 cancer‐relevant genes was performed on 41 plasma biopsy samples of 19 HER2+ and 12 HER2‐ BC patients. Longitudinal ctDNA samples were analyzed in three BC patients over the treatment course for detecting acquired mutations. Results In HER2+ BC patients, ERBB2 somatic copy numbers in ctDNA samples were significantly higher in patients progressed on HER2‐targeted therapy than those who were still responding to the treatment. Recurrent acquired mutations were detected in genes including ERBB2, TP53, EGFR, NF1, and SETD2, which may contribute to trastuzumab resistance. In longitudinal analyses, the observed mutation allele frequencies were tracked closely in concordance with treatment responses. A novel ERBB2 p.(Leu869Arg) mutation was acquired in one patient upon resistant to trastuzumab therapy, which was further validated as an oncogenic mutation in vitro and contributed to resistance. In HER2‐ BC patients with chemotherapy resistance, genetic alterations on TP53, PIK3CA, and DNA damage repair genes were frequently observed. Conclusions In summary, ctDNA monitoring, particularly longitudinal analyses, provides valuable insights into the assessment of targeted therapy efficacy and gene alterations underlying trastuzumab resistance and chemotherapy resistance in HER2+ and HER2‐ BC patients, respectively.
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Affiliation(s)
- Zhanhong Chen
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Tian Sun
- Translational Medicine Research Institute, Geneseeq Technology Inc, Toronto, Ontario, Canada
| | - Ziyan Yang
- The Second Clinical Medical College of Zhejiang, Chinese Medical University, Hangzhou, China
| | - Yabing Zheng
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Ruoying Yu
- Translational Medicine Research Institute, Geneseeq Technology Inc, Toronto, Ontario, Canada
| | - Xue Wu
- Translational Medicine Research Institute, Geneseeq Technology Inc, Toronto, Ontario, Canada
| | - Junrong Yan
- Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Yang W Shao
- Nanjing Geneseeq Technology Inc., Nanjing, China.,School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiying Shao
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Wenming Cao
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Xiaojia Wang
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
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44
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Wang Y, Wei H, Song L, Xu L, Bao J, Liu J. Gene Expression Microarray Data Meta-Analysis Identifies Candidate Genes and Molecular Mechanism Associated with Clear Cell Renal Cell Carcinoma. CELL JOURNAL 2019; 22:386-393. [PMID: 31863665 PMCID: PMC6947001 DOI: 10.22074/cellj.2020.6561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 06/10/2019] [Indexed: 12/21/2022]
Abstract
Objective We aimed to explore potential molecular mechanisms of clear cell renal cell carcinoma (ccRCC) and provide
candidate target genes for ccRCC gene therapy. Materials and Methods This is a bioinformatics-based study. Microarray datasets of GSE6344, GSE781 and GSE53000
were downloaded from Gene Expression Omnibus database. Using meta-analysis, differentially expressed genes
(DEGs) were identified between ccRCC and normal samples, followed by Kyoto Encyclopedia of Genes and Genomes
(KEGG) pathway and Gene Ontology (GO) function analyses. Then, protein-protein interaction (PPI) networks and
modules were investigated. Furthermore, miRNAs-target gene regulatory network was constructed.
Results Total of 511 up-regulated and 444 down-regulated DEGs were determined in the present gene expression
microarray data meta-analysis. These DEGs were enriched in functions like immune system process and pathways like
Toll-like receptor signaling pathway. PPI network and eight modules were further constructed. A total of 10 outstanding
DEGs including TYRO protein tyrosine kinase binding protein (TYROBP), interferon regulatory factor 7 (IRF7) and
PPARG co-activator 1 alpha (PPARGC1A) were detected in PPI network. Furthermore, the miRNAs-target gene
regulation analyses showed that miR-412 and miR-199b respectively targeted IRF7 and PPARGC1A to regulate the
immune response in ccRCC.
Conclusion TYROBP, IRF7 and PPARGC1A might play important roles in ccRCC via taking part in the immune
system process.
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Affiliation(s)
- Ying Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China. Electronic Address:
| | - Haibin Wei
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Lizhi Song
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Lu Xu
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jingyao Bao
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jiang Liu
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China. Electronic Address:
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45
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Histone lysine methyltransferases in biology and disease. Nat Struct Mol Biol 2019; 26:880-889. [PMID: 31582846 DOI: 10.1038/s41594-019-0298-7] [Citation(s) in RCA: 241] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 12/24/2022]
Abstract
The precise temporal and spatial coordination of histone lysine methylation dynamics across the epigenome regulates virtually all DNA-templated processes. A large number of histone lysine methyltransferase (KMT) enzymes catalyze the various lysine methylation events decorating the core histone proteins. Mutations, genetic translocations and altered gene expression involving these KMTs are frequently observed in cancer, developmental disorders and other pathologies. Therapeutic compounds targeting specific KMTs are currently being tested in the clinic, although overall drug discovery in the field is relatively underdeveloped. Here we review the biochemical and biological activities of histone KMTs and their connections to human diseases, focusing on cancer. We also discuss the scientific and clinical challenges and opportunities in studying KMTs.
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46
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Gao H, Li Y, Lin T, Cheng Y, Ma Y. Downregulation of CIP2A inhibits cancer cell proliferation and vascularization in renal clear cell carcinoma. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2019; 164:196-202. [PMID: 31431792 DOI: 10.5507/bp.2019.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 06/26/2019] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND CIP2A has been proved to play a role as an oncogene in various types of malignancies while its functionality in renal clear cell carcinoma has not been investigated. Our study aimed to investigate the role of CIP2A in renal clear cell carcinoma and to explore the possible mechanisms. METHODS A total of 80 patients with renal clear cell carcinoma and 32 healthy people were included in the study. Expression of CIP2A was detected by qRT-PCR. CIP2A silencing renal clear cell carcinoma cell line was established. Its effects on cell proliferation and migration were verified by CCK-8 assay and Transwell cell assay, respectively. The effects of CIP2A overexpression on AKT and VEGF were investigated. RESULTS CIP2A expression level was increased in tumor tissues compared to adjacent healthy tissues. Serum levels of CIP2A protein were higher in cancer patients than in healthy controls, and serum levels of CIP2A protein were increased with increased stage of primary tumor. Serum CIP2A protein can be used to accurately predict renal clear cell carcinoma and its prognosis. CIP2A siRNA silencing inhibited tumor cell proliferation, and treatment with Akt activator reduced this inhibitory effect. CIP2A siRNA silencing decreased the expression level of VEGF and phosphorylation levels of AKT in renal clear cell carcinoma cells, while AKT activator treatment showed no significant effects on CIP2A expression. CONCLUSION Downregulation of CIP2A can inhibit cancer cell proliferation and vascularization in renal clear cell carcinoma through inactivation of the Akt pathway and its downstream VEGF.
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Affiliation(s)
- Hui Gao
- Department of Urology, Liaocheng People's Hospital, Liaocheng City, Shandong Province, P. R. China, 252000
| | - Yuqiao Li
- Department of Urology, Liaocheng People's Hospital, Liaocheng City, Shandong Province, P. R. China, 252000
| | - Tao Lin
- Department of Urology, Liaocheng People's Hospital, Liaocheng City, Shandong Province, P. R. China, 252000
| | - Yan Cheng
- Department of Urology, Liaocheng People's Hospital, Liaocheng City, Shandong Province, P. R. China, 252000
| | - Yunbo Ma
- Department of Urology, Liaocheng People's Hospital, Liaocheng City, Shandong Province, P. R. China, 252000
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47
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Li J, Ahn JH, Wang GG. Understanding histone H3 lysine 36 methylation and its deregulation in disease. Cell Mol Life Sci 2019; 76:2899-2916. [PMID: 31147750 PMCID: PMC11105573 DOI: 10.1007/s00018-019-03144-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/13/2022]
Abstract
Methylation of histone H3 lysine 36 (H3K36) plays crucial roles in the partitioning of chromatin to distinctive domains and the regulation of a wide range of biological processes. Trimethylation of H3K36 (H3K36me3) demarcates body regions of the actively transcribed genes, providing signals for modulating transcription fidelity, mRNA splicing and DNA damage repair; and di-methylation of H3K36 (H3K36me2) spreads out within large intragenic regions, regulating distribution of histone H3 lysine 27 trimethylation (H3K27me3) and possibly DNA methylation. These H3K36 methylation-mediated events are biologically crucial and controlled by different classes of proteins responsible for either 'writing', 'reading' or 'erasing' of H3K36 methylation marks. Deregulation of H3K36 methylation and related regulatory factors leads to pathogenesis of disease such as developmental syndrome and cancer. Additionally, recurrent mutations of H3K36 and surrounding histone residues are detected in human tumors, further highlighting the importance of H3K36 in biology and medicine. This review will elaborate on current advances in understanding H3K36 methylation and related molecular players during various chromatin-templated cellular processes, their crosstalks with other chromatin factors, as well as their deregulations in the diseased contexts.
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Affiliation(s)
- Jie Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeong Hyun Ahn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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Gardner HL, Sivaprakasam K, Briones N, Zismann V, Perdigones N, Drenner K, Facista S, Richholt R, Liang W, Aldrich J, Trent JM, Shields PG, Robinson N, Johnson J, Lana S, Houghton P, Fenger J, Lorch G, Janeway KA, London CA, Hendricks WPD. Canine osteosarcoma genome sequencing identifies recurrent mutations in DMD and the histone methyltransferase gene SETD2. Commun Biol 2019; 2:266. [PMID: 31341965 PMCID: PMC6642146 DOI: 10.1038/s42003-019-0487-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/29/2019] [Indexed: 02/08/2023] Open
Abstract
Osteosarcoma (OS) is a rare, metastatic, human adolescent cancer that also occurs in pet dogs. To define the genomic underpinnings of canine OS, we performed multi-platform analysis of OS tumors from 59 dogs, including whole genome sequencing (n = 24) and whole exome sequencing (WES; n = 13) of primary tumors and matched normal tissue, WES (n = 10) of matched primary/metastatic/normal samples and RNA sequencing (n = 54) of primary tumors. We found that canine OS recapitulates features of human OS including low point mutation burden (median 1.98 per Mb) with a trend towards higher burden in metastases, high structural complexity, frequent TP53 (71%), PI3K pathway (37%), and MAPK pathway mutations (17%), and low expression of immune-associated genes. We also identified novel features of canine OS including putatively inactivating somatic SETD2 (42%) and DMD (50%) aberrations. These findings set the stage for understanding OS development in dogs and humans, and establish genomic contexts for future comparative analyses.
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Affiliation(s)
- Heather L. Gardner
- Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111 USA
| | | | - Natalia Briones
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Victoria Zismann
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | | | - Kevin Drenner
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | | | - Ryan Richholt
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Winnie Liang
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Jessica Aldrich
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Jeffrey M. Trent
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Peter G. Shields
- College of Medicine, The Ohio State University, Columbus, OH 43210 USA
| | - Nicholas Robinson
- Cummings School of Veterinary Medicine, Tufts University, Grafton, MA 01536 USA
| | | | - Susan Lana
- Colorado State University, Fort Collins, CO 80525 USA
| | - Peter Houghton
- University of Texas Health Science Center, San Antonio, TX 78229 USA
| | - Joelle Fenger
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, OH 43210 USA
| | - Gwendolen Lorch
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, OH 43210 USA
| | | | - Cheryl A. London
- Cummings School of Veterinary Medicine, Tufts University, Grafton, MA 01536 USA
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Li Y, Li Z, Zhu WG. Molecular Mechanisms of Epigenetic Regulators as Activatable Targets in Cancer Theranostics. Curr Med Chem 2019; 26:1328-1350. [PMID: 28933282 DOI: 10.2174/0929867324666170921101947] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 05/24/2017] [Accepted: 06/09/2017] [Indexed: 12/11/2022]
Abstract
Epigenetics is defined as somatically inheritable changes that are not accompanied by alterations in DNA sequence. Epigenetics encompasses DNA methylation, covalent histone modifications, non-coding RNA as well as nucleosome remodeling. Notably, abnormal epigenetic changes play a critical role in cancer development including malignant transformation, metastasis, prognosis, drug resistance and tumor recurrence, which can provide effective targets for cancer prognosis, diagnosis and therapy. Understanding these changes provide effective means for cancer diagnosis and druggable targets for better clinical applications. Histone modifications and related enzymes have been found to correlate well with cancer incidence and prognosis in recent years. Dysregulated expression or mutation of histone modification enzymes and histone modification status abnormalities have been considered to play essential roles in tumorigenesis and clinical outcomes of cancer treatment. Some of the histone modification inhibitors have been extensively employed in clinical practice and many others are still under laboratory research or pre-clinical assessment. Here we summarize the important roles of epigenetics, especially histone modifications in cancer diagnostics and therapeutics, and also discuss the developmental implications of activatable epigenetic targets in cancer theranostics.
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Affiliation(s)
- Yinglu Li
- Shenzhen University School of Medicine, Shenzhen 518060, China.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Zhiming Li
- Shenzhen University School of Medicine, Shenzhen 518060, China.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Wei-Guo Zhu
- Shenzhen University School of Medicine, Shenzhen 518060, China.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
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50
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Alessandrino F, Shinagare AB, Bossé D, Choueiri TK, Krajewski KM. Radiogenomics in renal cell carcinoma. Abdom Radiol (NY) 2019; 44:1990-1998. [PMID: 29713740 DOI: 10.1007/s00261-018-1624-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Radiogenomics, a field of radiology investigating the association between the imaging features of a disease and its gene expression pattern, has expanded considerably in the last few years. Recent advances in whole-genome sequencing of clear cell renal cell carcinoma (ccRCC) and the identification of mutations with prognostic significance have led to increased interest in the relationship between imaging and genomic data. ccRCC is particularly suitable for radiogenomic analysis as the relative paucity of mutated genes allows for more straightforward genomic-imaging associations. The ultimate aim of radiogenomics of ccRCC is to retrieve additional data for accurate diagnosis, prognostic stratification, and optimization of therapy. In this review article, we will present the state-of-the-art of radiogenomics of ccRCC, and after briefly reviewing updates in genomics, we will discuss imaging-genomic associations for diagnosis and staging, prognosis, and for assessment of optimal therapy in ccRCC.
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Affiliation(s)
- Francesco Alessandrino
- Department of Imaging, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02215, USA.
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
| | - Atul B Shinagare
- Department of Imaging, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02215, USA
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Dominick Bossé
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana 1230, Boston, MA, 02215, USA
| | - Toni K Choueiri
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana 1230, Boston, MA, 02215, USA
| | - Katherine M Krajewski
- Department of Imaging, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02215, USA
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
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