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Xiong J, Zhu L, Fu Y, Ye Z, Deng C, Wang X, Chen Y. Prognostic and therapeutic roles of SETD2 in cutaneous melanoma. Aging (Albany NY) 2024; 16:9692-9708. [PMID: 38843391 PMCID: PMC11210245 DOI: 10.18632/aging.205894] [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: 09/18/2023] [Accepted: 04/16/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Cutaneous melanoma (CM) is an aggressive form of skin cancer with limited treatment options for advanced stages. Prognostic markers that accurately predict patients' outcomes and guide therapeutic strategies are crucial for improving melanoma management. SETD2 (SET Domain-Containing Protein 2), a histone methyltransferase involved in chromatin remodeling and gene regulation, has recently emerged as a tumor suppressor. Its dysfunction is involved in oncogenesis in some cancers, but little is known about its functions in progression and therapeutic response of melanoma. METHODS RNA-seq and clinical data from public database were used to evaluate the survival analysis, gene set enrichment, IC50 of therapeutics and immunotherapy response. SETD2 knock-out A375 cell line (A375SETD2ko) was developed by Crispr/cas9 and CCK-8 analysis and nude mice used to evaluate the proliferation and invasion of melanoma cells in vitro and in vivo, while Western blotting tested the MMR-related protein. RESULTS SETD2 was commonly down-regulated in melanoma samples which demonstrated an unfavorable survival. Cells without SETD2 expression tend to have a more progressive and invasive behavior, with resistance to chemotherapy. However, they are more sensitive to tyrosine kinase inhibitors (TKIs). They also exhibit inflamed features with lower TIDE (Tumor Immune Dysfunction and Exclusion) score and higher tumor mutation burden (TMB), showing that these patients may benefit from immunotherapy. CONCLUSIONS This study revealed that SETD2 dysfunction in melanoma implied a poor prognosis and chemotherapy resistance, but highly sensitive to TKIs and immunotherapy, highlighting the prognostic and therapeutic value of SETD2 in cutaneous melanoma.
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Affiliation(s)
- Jiani Xiong
- Department of Medical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
- Cancer Bio-immunotherapy Center, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Liping Zhu
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Yunrong Fu
- Department of Medical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
- Cancer Bio-immunotherapy Center, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
- Department of Pharmacology, College of Pharmacy, Fujian Medical University, Fuzhou, Fujian, China
| | - Zhoujie Ye
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Cuimin Deng
- Department of Pharmacology, QuanZhou Women’s and Children’s Hospital, Quanzhou, Fujian, China
| | - Xinrui Wang
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Yu Chen
- Department of Medical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
- Cancer Bio-immunotherapy Center, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
- College of Chemistry, Fuzhou University, Fuzhou, China
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2
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Zhang C, Zeng J, Ye C, Tian K, Xian Z. Construction and validation of a chromatin regulator-related gene signature for prognostic and therapeutic significance of clear cell renal cell carcinoma. Transl Cancer Res 2024; 13:150-172. [PMID: 38410230 PMCID: PMC10894348 DOI: 10.21037/tcr-23-1383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/29/2023] [Indexed: 02/28/2024]
Abstract
Background Epigenetic alterations driven by chromatin regulators (CRs) are well-recognized cancer hallmarks. Growing evidence suggests that the imbalance of CRs may lead to the occurrence of various diseases including tumors. However, the role and prognostic value of CRs in clear cell renal cell carcinoma (ccRCC) remain undefined. Methods Consensus clustering analysis was used to identify different subtypes. Univariate and multivariate Cox regression analysis were performed to identify prognosis-related CRs and constructed a risk model. Transcriptome sequencing was used to verify gene expression levels. Kaplan-Meier survival analysis was used to compare overall survival (OS) between high- and low-risk groups. The area under the curve (AUC) value of the receiver operating characteristic (ROC) curve was used to evaluate the performance of the model. The ESTIMATE algorithm and single-sample gene set enrichment analysis (ssGSEA) were executed to evaluate the immune characteristics of samples. Correlation analysis was used to assess the relationship between risk score and immune checkpoint genes, the relationship between expression levels of CRs and immune cell infiltration and drug therapeutic response. Finally, we also compared differences in drug sensitivity between low- and high-risk groups. Results We identified three CRs-related subtypes with different characteristics. A prognostic model was built with four CRs and can precisely predict the OS of patients in different risk groups. The model has good stability and applicability and was further verified in the internal and external dataset. The transcriptomic levels of the four CRs were also validated, and the risk score was an independent prognostic factor for ccRCC. Obvious differences in the immune microenvironment and the expression levels of immune checkpoints were observed in low- and high-risk group. Higher immune activity and immune cell infiltration were found in the high-risk group. Besides, the expression levels of CRs were associated with drug therapeutic response. Patients with high-risk score may be more sensitive to gemcitabine, vinblastine, paclitaxel, axitinib, sunitinib, and temsirolimus. Conclusions CRs were strongly associated with the occurrence and development of ccRCC. Targeting CRs may become a new therapeutic strategy for ccRCC. Besides, CRs-related gene signature can predict the prognosis and therapeutic significance of ccRCC, which provides an important reference for clinical decision-making.
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Affiliation(s)
- Changzheng Zhang
- Department of Urology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Jiayi Zeng
- Department of Urology, Guangdong Provincial People’s Hospital’s Nanhai Hospital, Foshan, China
| | - Chujin Ye
- Department of Urology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Kaiwen Tian
- Department of Urology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Zhiyong Xian
- Department of Urology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Department of Urology, Guangdong Provincial People’s Hospital’s Nanhai Hospital, Foshan, China
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3
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Wang T, Wagner RT, Hlady RA, Pan X, Zhao X, Kim S, Wang L, Lee J, Luo H, Castle EP, Lake DF, Ho TH, Robertson KD. SETD2 loss in renal epithelial cells drives epithelial-to-mesenchymal transition in a TGF-β-independent manner. Mol Oncol 2024; 18:44-61. [PMID: 37418588 PMCID: PMC10766198 DOI: 10.1002/1878-0261.13487] [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: 04/21/2023] [Revised: 05/25/2023] [Accepted: 07/04/2023] [Indexed: 07/09/2023] Open
Abstract
Histone-lysine N-methyltransferase SETD2 (SETD2), the sole histone methyltransferase that catalyzes trimethylation of lysine 36 on histone H3 (H3K36me3), is often mutated in clear cell renal cell carcinoma (ccRCC). SETD2 mutation and/or loss of H3K36me3 is linked to metastasis and poor outcome in ccRCC patients. Epithelial-to-mesenchymal transition (EMT) is a major pathway that drives invasion and metastasis in various cancer types. Here, using novel kidney epithelial cell lines isogenic for SETD2, we discovered that SETD2 inactivation drives EMT and promotes migration, invasion, and stemness in a transforming growth factor-beta-independent manner. This newly identified EMT program is triggered in part through secreted factors, including cytokines and growth factors, and through transcriptional reprogramming. RNA-seq and assay for transposase-accessible chromatin sequencing uncovered key transcription factors upregulated upon SETD2 loss, including SOX2, POU2F2 (OCT2), and PRRX1, that could individually drive EMT and stemness phenotypes in SETD2 wild-type (WT) cells. Public expression data from SETD2 WT/mutant ccRCC support the EMT transcriptional signatures derived from cell line models. In summary, our studies reveal that SETD2 is a key regulator of EMT phenotypes through cell-intrinsic and cell-extrinsic mechanisms that help explain the association between SETD2 loss and ccRCC metastasis.
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Affiliation(s)
- Tianchu Wang
- Molecular Pharmacology and Experimental Therapeutics Graduate Program, Mayo Clinic Graduate School of Biomedical SciencesMayo ClinicRochesterMNUSA
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Ryan T. Wagner
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Ryan A. Hlady
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Xiaoyu Pan
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Xia Zhao
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Sungho Kim
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Department of Health Science ResearchMayo ClinicRochesterMNUSA
| | - Jeong‐Heon Lee
- Epigenomics Development LaboratoryMayo ClinicRochesterMNUSA
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Huijun Luo
- Division of Hematology and OncologyMayo Clinic ArizonaPhoenixAZUSA
| | | | | | - Thai H. Ho
- Division of Hematology and OncologyMayo Clinic ArizonaPhoenixAZUSA
| | - Keith D. Robertson
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
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Contreras Yametti GP, Robbins G, Chowdhury A, Narang S, Ostrow TH, Kilberg H, Greenberg J, Kramer L, Raetz E, Tsirigos A, Evensen NA, Carroll WL. SETD2 mutations do not contribute to clonal fitness in response to chemotherapy in childhood B cell acute lymphoblastic leukemia. Leuk Lymphoma 2024; 65:78-90. [PMID: 37874744 DOI: 10.1080/10428194.2023.2273752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/14/2023] [Indexed: 10/26/2023]
Abstract
Mutations in genes encoding epigenetic regulators are commonly observed at relapse in B cell acute lymphoblastic leukemia (B-ALL). Loss-of-function mutations in SETD2, an H3K36 methyltransferase, have been observed in B-ALL and other cancers. Previous studies on mutated SETD2 in solid tumors and acute myelogenous leukemia support a role in promoting resistance to DNA damaging agents. We did not observe chemoresistance, an impaired DNA damage response, nor increased mutation frequency in response to thiopurines using CRISPR-mediated knockout in wild-type B-ALL cell lines. Likewise, restoration of SETD2 in cell lines with hemizygous mutations did not increase sensitivity. SETD2 mutations affected the chromatin landscape and transcriptional output that was unique to each cell line. Collectively our data does not support a role for SETD2 mutations in driving clonal evolution and relapse in B-ALL, which is consistent with the lack of enrichment of SETD2 mutations at relapse in most studies.
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Affiliation(s)
- Gloria P Contreras Yametti
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Gabriel Robbins
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Ashfiyah Chowdhury
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Sonali Narang
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Talia H Ostrow
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Harrison Kilberg
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Joshua Greenberg
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Lindsay Kramer
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Elizabeth Raetz
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Aristotelis Tsirigos
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Nikki A Evensen
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - William L Carroll
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Langone Health, New York, NY, USA
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5
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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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Brocato ER, Wolstenholme JT. Adolescent binge ethanol impacts H3K36me3 regulation of synaptic genes. Front Mol Neurosci 2023; 16:1082104. [PMID: 36937047 PMCID: PMC10020663 DOI: 10.3389/fnmol.2023.1082104] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
Adolescence is marked in part by the ongoing development of the prefrontal cortex (PFC). Binge ethanol use during this critical stage in neurodevelopment induces significant structural changes to the PFC, as well as cognitive and behavioral deficits that can last into adulthood. Previous studies showed that adolescent binge ethanol causes lasting deficits in working memory, decreases in the expression of chromatin remodeling genes responsible for the methylation of histone 3 lysine 36 (H3K36), and global decreases in H3K36 in the PFC. H3K36me3 is present within the coding region of actively-transcribed genes, and safeguards against aberrant, cryptic transcription by RNA Polymerase II. We hypothesize that altered methylation of H3K36 could play a role in adolescent binge ethanol-induced memory deficits. To investigate this at the molecular level, ethanol (4 g/kg, i.g.) or water was administered intermittently to adolescent mice. RNA-and ChIP-sequencing were then performed within the same tissue to determine gene expression changes and identify genes and loci where H3K36me3 was disrupted by ethanol. We further assessed ethanol-induced changes at the transcription level with differential exon-use and cryptic transcription analysis - a hallmark of decreased H3K36me3. Here, we found ethanol-induced changes to the gene expression and H3K36me3-regulation of synaptic-related genes in all our analyses. Notably, H3K36me3 was differentially trimethylated between ethanol and control conditions at synaptic-related genes, and Snap25 and Cplx1 showed evidence of cryptic transcription in males and females treated with ethanol during adolescence. Our results provide preliminary evidence that ethanol-induced changes to H3K36me3 during adolescent neurodevelopment may be linked to synaptic dysregulation at the transcriptional level, which may explain the reported ethanol-induced changes to PFC synaptic function.
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Affiliation(s)
- Emily R. Brocato
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, United States
| | - Jennifer T. Wolstenholme
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, United States
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, United States
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7
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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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8
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Xie Y, Sahin M, Wakamatsu T, Inoue-Yamauchi A, Zhao W, Han S, Nargund AM, Yang S, Lyu Y, Hsieh JJ, Leslie CS, Cheng EH. SETD2 regulates chromatin accessibility and transcription to suppress lung tumorigenesis. JCI Insight 2023; 8:e154120. [PMID: 36810256 PMCID: PMC9977508 DOI: 10.1172/jci.insight.154120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/18/2023] [Indexed: 02/23/2023] Open
Abstract
SETD2, a H3K36 trimethyltransferase, is the most frequently mutated epigenetic modifier in lung adenocarcinoma, with a mutation frequency of approximately 9%. However, how SETD2 loss of function promotes tumorigenesis remains unclear. Using conditional Setd2-KO mice, we demonstrated that Setd2 deficiency accelerated the initiation of KrasG12D-driven lung tumorigenesis, increased tumor burden, and significantly reduced mouse survival. An integrated chromatin accessibility and transcriptome analysis revealed a potentially novel tumor suppressor model of SETD2 in which SETD2 loss activates intronic enhancers to drive oncogenic transcriptional output, including the KRAS transcriptional signature and PRC2-repressed targets, through regulation of chromatin accessibility and histone chaperone recruitment. Importantly, SETD2 loss sensitized KRAS-mutant lung cancer to inhibition of histone chaperones, the FACT complex, or transcriptional elongation both in vitro and in vivo. Overall, our studies not only provide insight into how SETD2 loss shapes the epigenetic and transcriptional landscape to promote tumorigenesis, but they also identify potential therapeutic strategies for SETD2 mutant cancers.
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Affiliation(s)
- Yuchen Xie
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York, USA
| | - Merve Sahin
- Computational and Systems Biology Program, MSKCC, New York, New York, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York, USA
| | - Toru Wakamatsu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Akane Inoue-Yamauchi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Wanming Zhao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Song Han
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Amrita M. Nargund
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Shaoyuan Yang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Yang Lyu
- Molecular Oncology, Department of Medicine, Washington University, St. Louis, Missouri, USA
| | - James J. Hsieh
- Molecular Oncology, Department of Medicine, Washington University, St. Louis, Missouri, USA
| | | | - Emily H. Cheng
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
- Department of Pathology and Laboratory Medicine, MSKCC, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
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9
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Alternative Splicing in the Regulatory Circuit of Plant Temperature Response. Int J Mol Sci 2023; 24:ijms24043878. [PMID: 36835290 PMCID: PMC9962249 DOI: 10.3390/ijms24043878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
As sessile organisms, plants have evolved complex mechanisms to rapidly respond to ever-changing ambient temperatures. Temperature response in plants is modulated by a multilayer regulatory network, including transcriptional and post-transcriptional regulations. Alternative splicing (AS) is an essential post-transcriptional regulatory mechanism. Extensive studies have confirmed its key role in plant temperature response, from adjustment to diurnal and seasonal temperature changes to response to extreme temperatures, which has been well documented by previous reviews. As a key node in the temperature response regulatory network, AS can be modulated by various upstream regulations, such as chromatin modification, transcription rate, RNA binding proteins, RNA structure and RNA modifications. Meanwhile, a number of downstream mechanisms are affected by AS, such as nonsense-mediated mRNA decay (NMD) pathway, translation efficiency and production of different protein variants. In this review, we focus on the links between splicing regulation and other mechanisms in plant temperature response. Recent advances regarding how AS is regulated and the following consequences in gene functional modulation in plant temperature response will be discussed. Substantial evidence suggests that a multilayer regulatory network integrating AS in plant temperature response has been unveiled.
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10
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Walton J, Lawson K, Prinos P, Finelli A, Arrowsmith C, Ailles L. PBRM1, SETD2 and BAP1 - the trinity of 3p in clear cell renal cell carcinoma. Nat Rev Urol 2023; 20:96-115. [PMID: 36253570 DOI: 10.1038/s41585-022-00659-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2022] [Indexed: 02/08/2023]
Abstract
Biallelic inactivation of the tumour suppressor gene Von Hippel-Lindau (VHL) occurs in the vast majority of clear cell renal cell carcinoma (ccRCC) instances, disrupting cellular oxygen-sensing mechanisms to yield a state of persistent pseudo-hypoxia, defined as a continued hypoxic response despite the presence of adequate oxygen levels. However, loss of VHL alone is often insufficient to drive oncogenesis. Results from genomic studies have shown that co-deletions of VHL with one (or more) of three genes encoding proteins involved in chromatin modification and remodelling, polybromo-1 gene (PBRM1), BRCA1-associated protein 1 (BAP1) and SET domain-containing 2 (SETD2), are common and important co-drivers of tumorigenesis. These genes are all located near VHL on chromosome 3p and are often altered following cytogenetic rearrangements that lead to 3p loss and precede the establishment of ccRCC. These three proteins have multiple roles in the regulation of crucial cancer-related pathways, including protection of genomic stability, antagonism of polycomb group (PcG) complexes to maintain a permissive transcriptional landscape in physiological conditions, and regulation of genes that mediate responses to immune checkpoint inhibitor therapy. An improved understanding of these mechanisms will bring new insights regarding cellular drivers of ccRCC growth and therapy response and, ultimately, will support the development of novel translational therapeutics.
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Affiliation(s)
- Joseph Walton
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Keith Lawson
- Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Panagiotis Prinos
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Antonio Finelli
- Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Cheryl Arrowsmith
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laurie Ailles
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
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11
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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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12
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Hadar S, Meller A, Saida N, Shalgi R. Stress-induced transcriptional readthrough into neighboring genes is linked to intron retention. iScience 2022; 25:105543. [PMID: 36505935 PMCID: PMC9732411 DOI: 10.1016/j.isci.2022.105543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/10/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Exposure to certain stresses leads to readthrough transcription. Using polyA-selected RNA-seq in mouse fibroblasts subjected to heat shock, oxidative, or osmotic stress, we found that readthrough transcription can proceed into proximal downstream genes, in a phenomenon previously termed "read-in." We found that read-in genes share distinctive genomic characteristics; they are GC-rich and extremely short , with genomic features conserved in human. Using ribosome profiling, we found that read-in genes show significantly reduced translation. Strikingly, read-in genes demonstrate marked intron retention, mostly in their first introns, which could not be explained solely by their short introns and GC-richness, features often associated with intron retention. Finally, we revealed H3K36me3 enrichment upstream to read-in genes. Moreover, demarcation of exon-intron junctions by H3K36me3 was absent in read-in first introns. Our data portray a relationship between read-in and intron retention, suggesting they may have co-evolved to facilitate reduced translation of read-in genes during stress.
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Affiliation(s)
- Shani Hadar
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa 31096, Israel
| | - Anatoly Meller
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa 31096, Israel
| | - Naseeb Saida
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa 31096, Israel
| | - Reut Shalgi
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa 31096, Israel
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13
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Kerschbamer E, Arnoldi M, Tripathi T, Pellegrini M, Maturi S, Erdin S, Salviato E, Di Leva F, Sebestyén E, Dassi E, Zarantonello G, Benelli M, Campos E, Basson M, Gusella J, Gustincich S, Piazza S, Demichelis F, Talkowski M, Ferrari F, Biagioli M. CHD8 suppression impacts on histone H3 lysine 36 trimethylation and alters RNA alternative splicing. Nucleic Acids Res 2022; 50:12809-12828. [PMID: 36537238 PMCID: PMC9825192 DOI: 10.1093/nar/gkac1134] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022] Open
Abstract
Disruptive mutations in the chromodomain helicase DNA-binding protein 8 gene (CHD8) have been recurrently associated with autism spectrum disorders (ASDs). Here we investigated how chromatin reacts to CHD8 suppression by analyzing a panel of histone modifications in induced pluripotent stem cell-derived neural progenitors. CHD8 suppression led to significant reduction (47.82%) in histone H3K36me3 peaks at gene bodies, particularly impacting on transcriptional elongation chromatin states. H3K36me3 reduction specifically affects highly expressed, CHD8-bound genes and correlates with altered alternative splicing patterns of 462 genes implicated in 'regulation of RNA splicing' and 'mRNA catabolic process'. Mass spectrometry analysis uncovered a novel interaction between CHD8 and the splicing regulator heterogeneous nuclear ribonucleoprotein L (hnRNPL), providing the first mechanistic insights to explain the CHD8 suppression-derived splicing phenotype, partly implicating SETD2, a H3K36me3 methyltransferase. In summary, our results point toward broad molecular consequences of CHD8 suppression, entailing altered histone deposition/maintenance and RNA processing regulation as important regulatory processes in ASD.
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Affiliation(s)
- Emanuela Kerschbamer
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, (CIBIO) University of Trento, Trento, Italy
| | - Michele Arnoldi
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, (CIBIO) University of Trento, Trento, Italy
| | - Takshashila Tripathi
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, (CIBIO) University of Trento, Trento, Italy
| | - Miguel Pellegrini
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, (CIBIO) University of Trento, Trento, Italy
| | - Samuele Maturi
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, (CIBIO) University of Trento, Trento, Italy
| | - Serkan Erdin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Elisa Salviato
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Francesca Di Leva
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, (CIBIO) University of Trento, Trento, Italy
| | - Endre Sebestyén
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational and Integrative Biology, (CIBIO), University of Trento, Trento, Italy
| | - Giulia Zarantonello
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, (CIBIO) University of Trento, Trento, Italy
| | - Matteo Benelli
- Bioinformatics Unit, Hospital of Prato, Istituto Toscano Tumori, Prato, Italy
| | - Eric Campos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - M Albert Basson
- Centre for Craniofacial and Regenerative Biology and MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - James F Gusella
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Silvano Piazza
- Bioinformatic facility, Department of Cellular, Computational and Integrative Biology (CIBIO) University of Trento, Italy
| | - Francesca Demichelis
- Laboratory of Computational and Functional Oncology, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Francesco Ferrari
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- CNR Institute of Molecular Genetics ‘Luigi Luca Cavalli-Sforza’, Pavia, Italy
| | - Marta Biagioli
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, (CIBIO) University of Trento, Trento, Italy
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14
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Hapke R, Venton L, Rose KL, Sheng Q, Reddy A, Prather R, Jones A, Rathmell WK, Haake SM. SETD2 regulates the methylation of translation elongation factor eEF1A1 in clear cell renal cell carcinoma. KIDNEY CANCER JOURNAL : OFFICIAL JOURNAL OF THE KIDNEY CANCER ASSOCIATION 2022; 6:179-193. [PMID: 36684483 PMCID: PMC9851421 DOI: 10.3233/kca-220009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND SET domain-containing protein 2 (SETD2) is commonly mutated in renal cell carcinoma. SETD2 methylates histone H3 as well as a growing list of non-histone proteins. OBJECTIVE Initially, we sought to explore SETD2-dependent changes in lysine methylation of proteins in proximal renal tubule cells. Subsequently, we focused on changes in lysine methylation of the translation elongation factor eEF1A1. METHODS To accomplish these objectives, we initially performed a systems-wide analysis of protein lysine-methylation and expression in wild type (WT) and SETD2-knock out (KO) kidney cells and later focused our studies on eEF1A1 as well as the expression of lysine methyltransferases that regulate its lysine methylation. RESULTS We observed decreased lysine methylation of the translation elongation factor eEF1A1. EEF1AKMT2 and EEF1AKMT3 are known to methylate eEF1A1, and we show here that their expression is dependent on SET-domain function of SETD2. Globally, we observe differential expression of hundreds of proteins in WT versus SETD2-KO cells, including increased expression of many involved in protein translation. Finally, we observe decreased progression free survival and loss of EEF1AKMT2 gene expression in SETD2-mutated tumors predicted to have loss of function of the SET domain. CONCLUSION Overall, these data suggest that SETD2-mutated ccRCC, via loss of enzymatic function of the SET domain, displays dysregulation of protein translation as a potentially important component of the transformed phenotype.
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Affiliation(s)
- Robert Hapke
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lindsay Venton
- Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kristie Lindsay Rose
- Mass Spectrometry Research Center, Proteomics Core Laboratory, Vanderbilt University, Nashville, TN, USA
| | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Rebecca Prather
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Angela Jones
- Vanderbilt Technologies for Advanced Genomics (VANTAGE), Vanderbilt University Medical Center, Nashville, TN, USA
| | - W. Kimryn Rathmell
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott M. Haake
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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15
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Petrova V, Song R, Nordström KJV, Walter J, Wong JJL, Armstrong N, Rasko JEJ, Schmitz U. Increased chromatin accessibility facilitates intron retention in specific cell differentiation states. Nucleic Acids Res 2022; 50:11563-11579. [PMID: 36354002 PMCID: PMC9723627 DOI: 10.1093/nar/gkac994] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/05/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022] Open
Abstract
Dynamic intron retention (IR) in vertebrate cells is of widespread biological importance. Aberrant IR is associated with numerous human diseases including several cancers. Despite consistent reports demonstrating that intrinsic sequence features can help introns evade splicing, conflicting findings about cell type- or condition-specific IR regulation by trans-regulatory and epigenetic mechanisms demand an unbiased and systematic analysis of IR in a controlled experimental setting. We integrated matched mRNA sequencing (mRNA-Seq), whole-genome bisulfite sequencing (WGBS), nucleosome occupancy methylome sequencing (NOMe-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) data from primary human myeloid and lymphoid cells. Using these multi-omics data and machine learning, we trained two complementary models to determine the role of epigenetic factors in the regulation of IR in cells of the innate immune system. We show that increased chromatin accessibility, as revealed by nucleosome-free regions, contributes substantially to the retention of introns in a cell-specific manner. We also confirm that intrinsic characteristics of introns are key for them to evade splicing. This study suggests an important role for chromatin architecture in IR regulation. With an increasing appreciation that pathogenic alterations are linked to RNA processing, our findings may provide useful insights for the development of novel therapeutic approaches that target aberrant splicing.
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Affiliation(s)
- Veronika Petrova
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | | | - Karl J V Nordström
- Laboratory of EpiGenetics, Saarland University, Campus A2 4, D-66123 Saarbrücken, Germany
| | - Jörn Walter
- Laboratory of EpiGenetics, Saarland University, Campus A2 4, D-66123 Saarbrücken, Germany
| | - Justin J L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Nicola J Armstrong
- Mathematics and Statistics, Curtin University, Bentley, WA 6102, Australia
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16
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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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17
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Molenaar TM, Malik M, Silva J, Liu NQ, Haarhuis JHI, Ambrosi C, Kwesi-Maliepaard EM, van Welsem T, Baubec T, Faller WJ, van Leeuwen F. The histone methyltransferase SETD2 negatively regulates cell size. J Cell Sci 2022; 135:jcs259856. [PMID: 36052643 PMCID: PMC9659392 DOI: 10.1242/jcs.259856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 08/23/2022] [Indexed: 11/20/2022] Open
Abstract
Cell size varies between cell types but is tightly regulated by cell intrinsic and extrinsic mechanisms. Cell size control is important for cell function, and changes in cell size are frequently observed in cancer. Here, we uncover a role for SETD2 in regulating cell size. SETD2 is a lysine methyltransferase and a tumor suppressor protein involved in transcription, RNA processing and DNA repair. At the molecular level, SETD2 is best known for associating with RNA polymerase II through its Set2-Rbp1 interacting (SRI) domain and methylating histone H3 on lysine 36 (H3K36) during transcription. Using multiple independent perturbation strategies, we identify SETD2 as a negative regulator of global protein synthesis rates and cell size. We provide evidence that overexpression of the H3K36 demethylase KDM4A or the oncohistone H3.3K36M also increase cell size. In addition, ectopic overexpression of a decoy SRI domain increased cell size, suggesting that the relevant substrate is engaged by SETD2 via its SRI domain. These data add a central role of SETD2 in regulating cellular physiology and warrant further studies on separating the different functions of SETD2 in cancer development.
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Affiliation(s)
- Thom M. Molenaar
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Muddassir Malik
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Joana Silva
- Division of Oncogenomics, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Ning Qing Liu
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Judith H. I. Haarhuis
- Division of Cell Biology, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Christina Ambrosi
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
- Life Science Zurich Graduate School, University of Zurich and ETH Zurich, CH-8057 Zurich, Switzerland
| | | | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - William J. Faller
- Division of Oncogenomics, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
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18
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Wang X, Xia Z, Li Z, Zhang C. Development of a SETD2-related immune prognostic signature in clear cell renal cell carcinoma. Medicine (Baltimore) 2022; 101:e29561. [PMID: 35945780 PMCID: PMC9351884 DOI: 10.1097/md.0000000000029561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Renal cell carcinoma (RCC) is a malignant tumor of urinary system, and clear cell RCC (ccRCC) is the major pathological subtype. A high-frequency mutation in SETD2 gene is related to the occurrence, development, and poor prognosis of RCC. OBJECTIVE The research of immune-related genes (IRGs) is important to the success of immunotherapy in RCC. The aim of this study was to develop SETD2-related immune prognostic signature (IPS) potentially useful in the prognosis prediction of ccRCC. METHODS The expression profile, mutation profile, and clinical data related to ccRCC were obtained from the TCGA (Cancer Genome Atlas) and cBioPortal databases. The data of IRGs were downloaded from the ImmPort database. RESULTS An IPS with 5 genes (PDIA2, PAEP, AMELX, GREM2, and INHA) was constructed by analyzing the correlation between prognosis data and IRGs associated with ccRCC patients with wild type and mutant SETD2 genes. The clinical utility of the IPS and its relationship with immune microenvironment were also studied. CONCLUSIONS According to the results of this study, the IPS can be a promising biomarker of ccRCC to guide its prognosis and treatment.
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Affiliation(s)
- Xingyuan Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zhinan Xia
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zhiyuan Li
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Cheng Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- *Correspondence: Cheng Zhang, Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, China (e-mail: )
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19
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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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20
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Grillo G, Lupien M. Cancer-associated chromatin variants uncover the oncogenic role of transposable elements. Curr Opin Genet Dev 2022; 74:101911. [PMID: 35487182 DOI: 10.1016/j.gde.2022.101911] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/08/2022] [Accepted: 03/24/2022] [Indexed: 11/26/2022]
Abstract
The vast array of cell states found across human tissue arises from chromatin variants, which correspond to segments of the genome, known as DNA elements, adopting a different chromatin state over cell state transitions. Oncogenesis stems from alterations to the chromatin states over DNA elements that result in cancer-associated chromatin variants. Here, we review how cancer-associated chromatin variants call attention to repetitive DNA elements, and guide the functional characterization of transposable elements to decode their role in oncogenesis. We further discuss prevailing opportunities in the study of repetitive DNA elements to move towards the 'complete cancer genome' goal for precision medicine in oncology.
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Affiliation(s)
- Giacomo Grillo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
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21
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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] [MESH Headings] [Grants] [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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22
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González-Rodríguez P, Klionsky DJ, Joseph B. Autophagy regulation by RNA alternative splicing and implications in human diseases. Nat Commun 2022; 13:2735. [PMID: 35585060 PMCID: PMC9117662 DOI: 10.1038/s41467-022-30433-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/29/2022] [Indexed: 02/06/2023] Open
Abstract
Autophagy and RNA alternative splicing are two evolutionarily conserved processes involved in overlapping physiological and pathological processes. However, the extent of functional connection is not well defined. Here, we consider the role for alternative splicing and generation of autophagy-related gene isoforms in the regulation of autophagy in recent work. The impact of changes to the RNA alternative splicing machinery and production of alternative spliced isoforms on autophagy are reviewed with particular focus on disease relevance. The use of drugs targeting both alternative splicing and autophagy as well as the selective regulation of single autophagy-related protein isoforms, are considered as therapeutic strategies.
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Affiliation(s)
- Patricia González-Rodríguez
- Institute of Environmental Medicine, Toxicology Unit, Karolinska Institutet, Stockholm, Sweden
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Daniel J Klionsky
- Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Bertrand Joseph
- Institute of Environmental Medicine, Toxicology Unit, Karolinska Institutet, Stockholm, Sweden.
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23
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Abstract
Chromatin dysfunction has been implicated in a growing number of cancers especially in children and young adults. In addition to chromatin modifying and remodeling enzymes, mutations in histone genes are linked to human cancers. Since the first reports of hotspot missense mutations affecting key residues at histone H3 tail, studies have revealed how these so-called "oncohistones" dominantly (H3K27M and H3K36M) or locally (H3.3G34R/W) inhibit corresponding histone methyltransferases and misregulate epigenome and transcriptome to promote tumorigenesis. More recently, widespread mutations in all four core histones are identified in diverse cancer types. Furthermore, an "oncohistone-like" protein EZHIP has been implicated in driving childhood ependymomas through a mechanism highly reminiscent of H3K27M mutation. We will review recent progresses on understanding the biochemical, molecular and biological mechanisms underlying the canonical and novel histone mutations. Importantly, these mechanistic insights have identified therapeutic opportunities for oncohistone-driven tumors.
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Affiliation(s)
- Varun Sahu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Chao Lu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA,Corresponding author: Chao Lu:
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24
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SETD2 loss perturbs the kidney cancer epigenetic landscape to promote metastasis and engenders actionable dependencies on histone chaperone complexes. NATURE CANCER 2022; 3:188-202. [PMID: 35115713 PMCID: PMC8885846 DOI: 10.1038/s43018-021-00316-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 11/24/2021] [Indexed: 12/13/2022]
Abstract
SETD2 is a H3K36 trimethyltransferase that is mutated with high prevalence (13%) in clear cell renal cell carcinoma (ccRCC). Genomic profiling of primary ccRCC tumors reveals a positive correlation between SETD2 mutations and metastasis. However, whether and how SETD2 loss promotes metastasis remains unclear. In this study, we used SETD2-mutant metastatic ccRCC patient-derived cell line and xenograft models and showed that H3K36me3 restoration greatly reduced distant metastases of ccRCC in mice in an MMP1-dependent manner. An integrated multi-omics analysis using ATAC-seq, ChIP-seq, and RNA-seq established a tumor suppressor model in which loss of SETD2-mediated H3K36me3 activates enhancers to drive oncogenic transcriptional output through regulation of chromatin accessibility. Furthermore, we uncovered mechanism-based therapeutic strategies for SETD2-deficient cancer through the targeting of specific histone chaperone complexes including ASF1A/B and SPT16. Overall, SETD2 loss creates a permissive epigenetic landscape for cooperating oncogenic drivers to amplify transcriptional output, providing unique therapeutic opportunities.
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25
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Wong CH, Li CH, Man Tong JH, Zheng D, He Q, Luo Z, Lou UK, Wang J, To KF, Chen Y. The Establishment of CDK9/ RNA PolII/H3K4me3/DNA Methylation Feedback Promotes HOTAIR Expression by RNA Elongation Enhancement in Cancer. Mol Ther 2022; 30:1597-1609. [PMID: 35121112 PMCID: PMC9077372 DOI: 10.1016/j.ymthe.2022.01.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/07/2021] [Accepted: 01/28/2022] [Indexed: 11/28/2022] Open
Abstract
Long non-coding RNA HOX Transcript Antisense RNA (HOTAIR) is overexpressed in multiple cancers with diverse genetic profiles. Importantly, since HOTAIR heavily contributes to cancer progression by promoting tumor growth and metastasis, HOTAIR becomes a potential target for cancer therapy. However, the underlying mechanism leading to HOTAIR deregulation is largely unexplored. Here, we performed a pan-cancer analysis using more than 4,200 samples and found that intragenic exon CpG island (Ex-CGI) was hypermethylated and was positively correlated to HOTAIR expression. Also, we revealed that Ex-CGI methylation promotes HOTAIR expression through enhancing the transcription elongation process. Furthermore, we linked up the aberrant intragenic tri-methylation on H3 at lysine 4 (H3K4me3) and Ex-CGI DNA methylation in promoting transcription elongation of HOTAIR. Targeting the oncogenic CDK7-CDK9-H3K4me3 axis downregulated HOTAIR expression and inhibited cell growth in many cancers. To our knowledge, this is the first time that a positive feedback loop that involved CDK9-mediated phosphorylation of RNA Polymerase II Serine 2 (RNA PolII Ser2), H3K4me3, and intragenic DNA methylation, which induced robust transcriptional elongation and heavily contributed to the upregulation of oncogenic lncRNA in cancer has been demonstrated. Targeting the oncogenic CDK7-CDK9-H3K4me3 axis could be a novel therapy in many cancers through inhibiting the HOTAIR expression.
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Affiliation(s)
- Chi Hin Wong
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Chi Han Li
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Joanna Hung Man Tong
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Duo Zheng
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen University International Cancer Center, Department of Cell Biology and Genetics, School of Medicine, Shenzhen University, Shenzhen 518055, China
| | - Qifang He
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Zhiyuan Luo
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Ut Kei Lou
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Jiatong Wang
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yangchao Chen
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518087, China.
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26
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Abstract
BACKGROUND: Alternative splicing is a mechanism to produce different proteins with diverse functions from one gene. Many splicing factors play an important role in cancer progression. PRPF8 is a core protein component of the spliceosome complex, U4/U6-U5 tri-snRNP. OBJECTIVE: However, PRPF8 involved in mRNA alternative splicing are rarely included in the prognosis. METHODS: We found that PRPF8 was expressed in all examined cancer types. Further analyses found that PRPF8 expression was significantly different between the breast cancer and paracancerous tissues. RESULTS: Survival analyses showed that PRPF8-high patients had a poor prognosis, and the expression of PRPF8 is associated with distant metastasis-free survival (DMFS) and post progression survival (PPS). Gene Set Enrichment Analysis (GSEA) has revealed that PRPF8 expression is correlated with TGF-β, JAK-STAT, and cell cycle control pathways. Consistent with these results, upon PRPF8 silencing, the growth of MCF-7 cells was reduced, the ability of cell clone formation was weakened, and p21 expression was increased. CONCLUSIONS: These results have revealed that PRPF8 is a significant factor for splicing in breast cancer progression.
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Affiliation(s)
- Difei Cao
- Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, Heilongjiang, China
| | - Jiaying Xue
- Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, Heilongjiang, China
| | - Guoqing Huang
- Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, Heilongjiang, China
| | - Jing An
- Institute of Cancer Prevention and Treatment, Heilongjiang Province Academy of Medical Sciences, Harbin, Heilongjiang, China
| | - Weiwei An
- Institute of Cancer Prevention and Treatment, Heilongjiang Province Academy of Medical Sciences, Harbin, Heilongjiang, China
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27
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Alternative Splicing, Epigenetic Modifications and Cancer: A Dangerous Triangle, or a Hopeful One? Cancers (Basel) 2022; 14:cancers14030560. [PMID: 35158828 PMCID: PMC8833605 DOI: 10.3390/cancers14030560] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Epigenetics studies the alteration of gene expression without changing DNA sequence and very often, epigenetic dysregulation causes cancer. Alternative splicing is a mechanism that results in the production of several mRNA isoforms from a single gene and aberrant splicing is also a frequent cause of cancer. The present review is built on the interrelations of epigenetics and alternative splicing. In an intuitive way, we say that epigenetic modifications and alternative splicing are at two vertices of a triangle, the third vertex being occupied by cancer. Interconnection between alternative splicing and epigenetic modifications occurs backward and forward and the mechanisms involved are widely reviewed. These connections also provide novel diagnostic or prognostic tools, which are listed. Finally, as epigenetic alterations are reversible and aberrant alternative splicing may be corrected, the therapeutic possibilities to break the triangle are discussed. Abstract The alteration of epigenetic modifications often causes cancer onset and development. In a similar way, aberrant alternative splicing may result in oncogenic products. These issues have often been individually reviewed, but there is a growing body of evidence for the interconnection of both causes of cancer. Actually, aberrant splicing may result from abnormal epigenetic signalization and epigenetic factors may be altered by alternative splicing. In this way, the interrelation between epigenetic marks and alternative splicing form the base of a triangle, while cancer may be placed at the vertex. The present review centers on the interconnections at the triangle base, i.e., between alternative splicing and epigenetic modifications, which may result in neoplastic transformations. The effects of different epigenetic factors, including DNA and histone modifications, the binding of non-coding RNAs and the alterations of chromatin organization on alternative splicing resulting in cancer are first considered. Other less-frequently considered questions, such as the epigenetic regulation of the splicing machinery, the aberrant splicing of epigenetic writers, readers and erasers, etc., are next reviewed in their connection with cancer. The knowledge of the above-mentioned relationships has allowed increasing the collection of biomarkers potentially useful as cancer diagnostic and/or prognostic tools. Finally, taking into account on one hand that epigenetic changes are reversible, and some epigenetic drugs already exist and, on the other hand, that drugs intended for reversing aberrations in alternative splicing, therapeutic possibilities for breaking the mentioned cancer-related triangle are discussed.
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28
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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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29
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Marcel SS, Quimby AL, Noel MP, Jaimes OC, Mehrab-Mohseni M, Ashur SA, Velasco B, Tsuruta JK, Kasoji SK, Santos CM, Dayton PA, Parker JS, Davis IJ, Pattenden SG. Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors. Genome Res 2021; 31:2327-2339. [PMID: 34815311 PMCID: PMC8647830 DOI: 10.1101/gr.275219.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 10/22/2021] [Indexed: 01/01/2023]
Abstract
Chromatin accessibility states that influence gene expression and other nuclear processes can be altered in disease. The constellation of transcription factors and chromatin regulatory complexes in cells results in characteristic patterns of chromatin accessibility. The study of these patterns in tissues has been limited because existing chromatin accessibility assays are ineffective for archival formalin-fixed, paraffin-embedded (FFPE) tissues. We have developed a method to efficiently extract intact chromatin from archival tissue via enhanced cavitation with a nanodroplet reagent consisting of a lipid shell with a liquid perfluorocarbon core. Inclusion of nanodroplets during the extraction of chromatin from FFPE tissues enhances the recovery of intact accessible and nucleosome-bound chromatin. We show that the addition of nanodroplets to the chromatin accessibility assay formaldehyde-assisted isolation of regulatory elements (FAIRE), does not affect the accessible chromatin signal. Applying the technique to FFPE human tumor xenografts, we identified tumor-relevant regions of accessible chromatin shared with those identified in primary tumors. Further, we deconvoluted non-tumor signal to identify cellular components of the tumor microenvironment. Incorporation of this method of enhanced cavitation into FAIRE offers the potential for extending chromatin accessibility to clinical diagnosis and personalized medicine, while also enabling the exploration of gene regulatory mechanisms in archival samples.
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Affiliation(s)
- Shelsa S Marcel
- Curriculum in Bioinformatics and Computational Biology, Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Austin L Quimby
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Melodie P Noel
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Oscar C Jaimes
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Marjan Mehrab-Mohseni
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Joint Department of Biomedical Engineering, The University of North Carolina and North Carolina State University, Chapel Hill, North Carolina 27599, USA
| | - Suud A Ashur
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Brian Velasco
- Joint Department of Biomedical Engineering, The University of North Carolina and North Carolina State University, Chapel Hill, North Carolina 27599, USA
| | - James K Tsuruta
- Joint Department of Biomedical Engineering, The University of North Carolina and North Carolina State University, Chapel Hill, North Carolina 27599, USA
| | - Sandeep K Kasoji
- Triangle Biotechnology, Incorporated, Chapel Hill, North Carolina 27517, USA
| | - Charlene M Santos
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Paul A Dayton
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Joint Department of Biomedical Engineering, The University of North Carolina and North Carolina State University, Chapel Hill, North Carolina 27599, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Samantha G Pattenden
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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30
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Koenning M, Wang X, Karki M, Jangid RK, Kearns S, Tripathi DN, Cianfrocco M, Verhey KJ, Jung SY, Coarfa C, Ward CS, Kalish BT, Grimm SL, Rathmell WK, Mostany R, Dere R, Rasband MN, Walker CL, Park IY. Neuronal SETD2 activity links microtubule methylation to an anxiety-like phenotype in mice. Brain 2021; 144:2527-2540. [PMID: 34014281 PMCID: PMC8418347 DOI: 10.1093/brain/awab200] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/22/2021] [Accepted: 05/02/2021] [Indexed: 02/07/2023] Open
Abstract
Gene discovery efforts in autism spectrum disorder have identified heterozygous defects in chromatin remodeller genes, the 'readers, writers and erasers' of methyl marks on chromatin, as major contributors to this disease. Despite this advance, a convergent aetiology between these defects and aberrant chromatin architecture or gene expression has remained elusive. Recently, data have begun to emerge that chromatin remodellers also function directly on the cytoskeleton. Strongly associated with autism spectrum disorder, the SETD2 histone methyltransferase for example, has now been shown to directly methylate microtubules of the mitotic spindle. However, whether microtubule methylation occurs in post-mitotic cells, for example on the neuronal cytoskeleton, is not known. We found the SETD2 α-tubulin lysine 40 trimethyl mark occurs on microtubules in the brain and in primary neurons in culture, and that the SETD2 C-terminal SRI domain is required for binding and methylation of α-tubulin. A CRISPR knock-in of a pathogenic SRI domain mutation (Setd2SRI) that disables microtubule methylation revealed at least one wild-type allele was required in mice for survival, and while viable, heterozygous Setd2SRI/wtmice exhibited an anxiety-like phenotype. Finally, whereas RNA-sequencing (RNA-seq) and chromatin immunoprecipitation-sequencing (ChIP-seq) showed no concomitant changes in chromatin methylation or gene expression in Setd2SRI/wtmice, primary neurons exhibited structural deficits in axon length and dendritic arborization. These data provide the first demonstration that microtubules of neurons are methylated, and reveals a heterozygous chromatin remodeller defect that specifically disables microtubule methylation is sufficient to drive an autism-associated phenotype.
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Affiliation(s)
- Matthias Koenning
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xianlong Wang
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Menuka Karki
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rahul Kumar Jangid
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Kearns
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Durga Nand Tripathi
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Scott Ward
- Molecular Physiology and Biophysics, Mouse Metabolic and Phenotyping Core, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Sandra L Grimm
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - W Kimryn Rathmell
- Vanderbilt-Ingram Cancer Center, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ricardo Mostany
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Ruhee Dere
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Cheryl Lyn Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - In Young Park
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
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31
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Zhang LQ, Liu JJ, Liu L, Fan GL, Li YN, Li QZ. The impact of gene-body H3K36me3 patterns on gene expression level changes in chronic myelogenous leukemia. Gene 2021; 802:145862. [PMID: 34352296 DOI: 10.1016/j.gene.2021.145862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 07/07/2021] [Accepted: 07/30/2021] [Indexed: 11/29/2022]
Abstract
Chronic myelogenous leukemia (CML) is a malignant clonal disease of hematopoietic stem cells. Researches have exhibited that the progression of CML is related to histone modifications. Here, we perform the systematic analyses of H3K36me3 patterns and gene expression level changes. We observe that the genes with higher gene-body H3K36me3 levels in normal cells show fewer expression changes during leukemogenesis, while the genes with lower gene-body H3K36me3 levels in normal cells yield obvious expression changes during leukemogenesis (ρ = -0.98, P = 9.30 × 10-8). These findings are conserved in human lung/breast cancers and mouse CML, regardless of gene expression levels and gene lengths. Regulatory element analysis and Random Forest regression display that Hoxd13, Rara, Scl, Smad3, Smad4 and Tgif1 induce the up-regulation of genes with lower H3K36me3 levels (ρ = 0.97, P = 2.35 × 10-56). Enrichment analysis shows that the differentially expressed genes with lower H3K36me3 levels are involved in leukemia-related pathways, such as leukocyte migration and regulation of leukocyte activation. Finally, six driver genes (Tp53, Wt1, Dnmt3a, Cacna1b, Phactr1 and Gbp4) with lower H3K36me3 levels are identified. Our analyses indicate that lower gene-body H3K36me3 levels may serve as a biomarker for the progression of CML.
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Affiliation(s)
- Lu-Qiang Zhang
- Laboratory of Theoretical Biophysics, School oef Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
| | - Jun-Jie Liu
- Laboratory of Theoretical Biophysics, School oef Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Li Liu
- Laboratory of Theoretical Biophysics, School oef Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Guo-Liang Fan
- Laboratory of Theoretical Biophysics, School oef Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Yan-Nan Li
- Laboratory of Theoretical Biophysics, School oef Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Qian-Zhong Li
- Laboratory of Theoretical Biophysics, School oef Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China; The Research Center for Laboratory Animal Science, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
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32
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Pan-cancer analysis of SETD2 mutation and its association with the efficacy of immunotherapy. NPJ Precis Oncol 2021; 5:51. [PMID: 34127768 PMCID: PMC8203790 DOI: 10.1038/s41698-021-00193-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/26/2021] [Indexed: 01/10/2023] Open
Abstract
Histone methyltransferase SETD2 plays a critical role in maintaining genomic integrity and stability. Here, we investigated the characteristics of SETD2 somatic mutation in the cancer genome atlas pan-cancer cohort. Our data revealed that, compared with SETD2 nonmutant patients, SETD2 mutant patients had higher tumor mutation burden and microsatellite instability. In addition, the transcriptions of most genes related to immune activities were upregulated in patients with SETD2 mutant tumors. Further examination of cancer patients treated with immune checkpoint inhibitors suggested SETD2 mutation was associated with favorable clinical outcomes. These results have implication for the personalization of cancer immunotherapy.
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33
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Willbanks A, Wood S, Cheng JX. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes (Basel) 2021; 12:genes12050627. [PMID: 33922187 PMCID: PMC8145807 DOI: 10.3390/genes12050627] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases.
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34
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Tsang JY, Lai ST, Ni YB, Shao Y, Poon IK, Kwan JS, Chow C, Shea KH, Tse GM. SETD2 alterations and histone H3K36 trimethylation in phyllodes tumor of breast. Breast Cancer Res Treat 2021; 187:339-347. [PMID: 33844099 DOI: 10.1007/s10549-021-06181-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/05/2021] [Indexed: 12/23/2022]
Abstract
PURPOSE SETD2 is one of the key epigenetic regulatory genes involved in histone modifications. Its alterations were potentially oncogenic and commonly found in cancers. Interestingly, SETD2 is one of the most frequent mutated genes found exclusively in phyllodes tumor of the breast (PT). However, little has been done to further characterize SETD2 alterations in PT. METHODS In this study, we examined the alterations of SETD2 gene and protein expression in a large cohort of PTs. Their correlations with SETD2 downstream target, H3K36me3 expression, and clinicopathologic features in PT were also assessed. RESULTS SETD2 mutation was found in 15.9% of our cases and was mostly predicted to be damaging mutations. Interestingly, SETD2 mutations were associated with lower H3K36me3 expression, particularly those with damaging mutations (p = .041). Neither SETD2 mutations nor H3K36me3 expression was associated with PT grading and other clinicopathological features. By contrast, the SETD2 protein expression cannot reflect its mutation status and showed a different trend of clinicopathological correlations from H3K36me3. CONCLUSIONS Our findings may suggest a potential involvement of epigenetic regulation via SETD2 alterations and downstream H3K36me3 on PT development. SETD2 mutations may occur early in the pathogenic process of PTs and its loss per se may not be sufficient for progression to malignancy. Exclusive alterations of SETD2 in PT can be used as markers for the diagnosis of fibroepithelial lesions. The association of H3K36me3 with SETD2 mutations may also indicate the value of evaluation of H3K36me3 expression in the diagnosis of fibroepithelial lesions.
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Affiliation(s)
- Julia Y Tsang
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Ngan Shing Street, Shatin, NT, Hong Kong SAR
| | - Sui-Ting Lai
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Ngan Shing Street, Shatin, NT, Hong Kong SAR
| | - Yun-Bi Ni
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Ngan Shing Street, Shatin, NT, Hong Kong SAR
| | - Yan Shao
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Ngan Shing Street, Shatin, NT, Hong Kong SAR
| | | | - Johnny S Kwan
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Ngan Shing Street, Shatin, NT, Hong Kong SAR
| | - Chit Chow
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Ngan Shing Street, Shatin, NT, Hong Kong SAR
| | - Ka-Ho Shea
- Department of Pathology, Tuen Mun Hospital, Tuen Mun, NT, Hong Kong SAR
| | - Gary M Tse
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Ngan Shing Street, Shatin, NT, Hong Kong SAR.
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35
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El Khoury LY, Fu S, Hlady RA, Wagner RT, Wang L, Eckel-Passow JE, Castle EP, Stanton ML, Thompson RH, Parker AS, Ho TH, Robertson KD. Identification of DNA methylation signatures associated with poor outcome in lower-risk Stage, Size, Grade and Necrosis (SSIGN) score clear cell renal cell cancer. Clin Epigenetics 2021; 13:12. [PMID: 33461589 PMCID: PMC7814746 DOI: 10.1186/s13148-020-00998-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/21/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Despite using prognostic algorithms and standard surveillance guidelines, 17% of patients initially diagnosed with low risk clear cell renal cell carcinoma (ccRCC) ultimately relapse and die of recurrent disease, indicating additional molecular parameters are needed for improved prognosis. RESULTS To address the gap in ccRCC prognostication in the lower risk population, we performed a genome-wide analysis for methylation signatures capable of distinguishing recurrent and non-recurrent ccRCCs within the subgroup classified as 'low risk' by the Mayo Clinic Stage, Size, Grade, and Necrosis score (SSIGN 0-3). This approach revealed that recurrent patients have globally hypermethylated tumors and differ in methylation significantly at 5929 CpGs. Differentially methylated CpGs (DMCpGs) were enriched in regulatory regions and genes modulating cell growth and invasion. A subset of DMCpGs stratified low SSIGN groups into high and low risk of recurrence in independent data sets, indicating that DNA methylation enhances the prognostic power of the SSIGN score. CONCLUSIONS This study reports a global DNA hypermethylation in tumors of recurrent ccRCC patients. Furthermore, DMCpGs were capable of discriminating between aggressive and less aggressive tumors, in addition to SSIGN score. Therefore, DNA methylation presents itself as a potentially strong biomarker to further improve prognostic power in patients with low risk SSIGN score (0-3).
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Affiliation(s)
- Louis Y El Khoury
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Epigenomics Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Shuang Fu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Epigenomics Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.,Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Epigenomics Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Ryan T Wagner
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Epigenomics Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Jeanette E Eckel-Passow
- Division of Biomedical Statistics and Informatics, Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Erik P Castle
- Department of Urology, Mayo Clinic, Phoenix, AZ, USA
| | - Melissa L Stanton
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, AZ, USA
| | | | - Alexander S Parker
- Office of Research Affairs, University of Florida, Jacksonville, FL, USA
| | - Thai H Ho
- Division of Hematology and Medical Oncology, Mayo Clinic, 13400 E. Shea Blvd, Scottsdale, AZ, 85259, USA.
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA. .,Center for Individualized Medicine, Epigenomics Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
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36
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Liu Y, Liu X, Lin C, Jia X, Zhu H, Song J, Zhang Y. Noncoding RNAs regulate alternative splicing in Cancer. J Exp Clin Cancer Res 2021; 40:11. [PMID: 33407694 PMCID: PMC7789004 DOI: 10.1186/s13046-020-01798-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/03/2020] [Indexed: 12/14/2022] Open
Abstract
AS (alternative splicing) is a fundamental process by which a gene can generate multiple distinct mRNA transcripts to increase protein diversity. Defects in AS influence the occurrence and development of many diseases, including cancers, and are frequently found to participate in various aspects of cancer biology, such as promoting invasion, metastasis, apoptosis resistance and drug resistance. NcRNAs (noncoding RNAs) are an abundant class of RNAs that do not encode proteins. NcRNAs include miRNAs (microRNAs), lncRNAs (long noncoding RNAs), circRNAs (circular RNAs) and snRNAs (small nuclear RNAs) and have been proven to act as regulatory molecules that mediate cancer processes through AS. NcRNAs can directly or indirectly influence a plethora of molecular targets to regulate cis-acting elements, trans-acting factors, or pre-mRNA transcription at multiple levels, affecting the AS process and generating alternatively spliced isoforms. Consequently, ncRNA-mediated AS outcomes affect multiple cellular signaling pathways that promote or suppress cancer progression. In this review, we summarize the current mechanisms by which ncRNAs regulate AS in cancers and discuss their potential clinical applications as biomarkers and therapeutic targets.
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Affiliation(s)
- Yunze Liu
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
- Department of Traditional Chinese Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Xin Liu
- Department of Endocrinology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Changwei Lin
- Department of Gastrointestinal Surgery, the Third XiangYa Hospital of Central South University, Changsha, 410013, China
| | - Xianhong Jia
- Department of Traditional Chinese Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Hongmei Zhu
- Department of Traditional Chinese Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Jun Song
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China.
| | - Yi Zhang
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China.
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37
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Zhou Y, Zheng X, Xu B, Deng H, Chen L, Jiang J. Histone methyltransferase SETD2 inhibits tumor growth via suppressing CXCL1-mediated activation of cell cycle in lung adenocarcinoma. Aging (Albany NY) 2020; 12:25189-25206. [PMID: 33223508 PMCID: PMC7803529 DOI: 10.18632/aging.104120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 08/27/2020] [Indexed: 12/14/2022]
Abstract
The histone H3 lysine 36 methyltransferase SET-domain-containing 2 (SETD2) has been reported to be frequently mutated or deleted in many types of human cancer. However, the role of SETD2 in lung adenocarcinoma (LUAD) has not been well documented. In the present study, we found that SETD2 was significantly down-regulated both in LUAD tissues and cell lines. Functionally, the increased expression of SETD2 significantly attenuated the proliferation of cancer cells by affecting the cell cycle, whereas SETD2 deficiency dramatically improved these proliferative abilities of cancer cells. Through conjoint analysis of RNA-seq and ChIP data, we identified a functional target gene of SETD2, CXCL1, and its expression was negatively correlated with that of SETD2. Moreover, SETD2 deletion stimulated cell cycle-related proteins to promote LUAD. Further mechanistic studies demonstrated that histone H3 lysine 36 trimethylation (H3K36me3) catalyzed by SETD2 interacted with the promoter of CXCL1 to regulate its transcription and downstream signaling pathways, contributing to tumorigenesis in vitro and in vivo. Our findings suggested that SETD2 inhibited tumor growth via suppressing CXCL1-mediated activation of cell cycle, indicating that the regulation of H3K36me3 level by targeting SETD2 and/or the administration of downstream CXCL1 might represent a potential therapeutic way for new treatment in LUAD.
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Affiliation(s)
- You Zhou
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| | - Xiao Zheng
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| | - Bin Xu
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| | - Haifeng Deng
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| | - Lujun Chen
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| | - Jingting Jiang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
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38
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Phillips RE, Soshnev AA, Allis CD. Epigenomic Reprogramming as a Driver of Malignant Glioma. Cancer Cell 2020; 38:647-660. [PMID: 32916125 PMCID: PMC8248764 DOI: 10.1016/j.ccell.2020.08.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/21/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022]
Abstract
Malignant gliomas are central nervous system tumors and remain among the most treatment-resistant cancers. Exome sequencing has revealed significant heterogeneity and important insights into the molecular pathogenesis of gliomas. Mutations in chromatin modifiers-proteins that shape the epigenomic landscape through remodeling and regulation of post-translational modifications on chromatin-are very frequent and often define specific glioma subtypes. This suggests that epigenomic reprogramming may be a fundamental driver of glioma. Here, we describe the key chromatin regulatory pathways disrupted in gliomas, delineating their physiological function and our current understanding of how their dysregulation may contribute to gliomagenesis.
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Affiliation(s)
- Richard E Phillips
- Department of Neurology and Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA.
| | - Alexey A Soshnev
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA.
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39
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Reim NI, Chuang J, Jain D, Alver BH, Park PJ, Winston F. The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae. Nucleic Acids Res 2020; 48:10241-10258. [PMID: 32941642 PMCID: PMC7544207 DOI: 10.1093/nar/gkaa745] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/20/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022] Open
Abstract
Spn1/Iws1 is a conserved protein involved in transcription and chromatin dynamics, yet its general in vivo requirement for these functions is unknown. Using a Spn1 depletion system in Saccharomyces cerevisiae, we demonstrate that Spn1 broadly influences several aspects of gene expression on a genome-wide scale. We show that Spn1 is globally required for normal mRNA levels and for normal splicing of ribosomal protein transcripts. Furthermore, Spn1 maintains the localization of H3K36 and H3K4 methylation across the genome and is required for normal histone levels at highly expressed genes. Finally, we show that the association of Spn1 with the transcription machinery is strongly dependent on its binding partner, Spt6, while the association of Spt6 and Set2 with transcribed regions is partially dependent on Spn1. Taken together, our results show that Spn1 affects multiple aspects of gene expression and provide additional evidence that it functions as a histone chaperone in vivo.
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Affiliation(s)
- Natalia I Reim
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James Chuang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Dhawal Jain
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Burak H Alver
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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40
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Monteuuis G, Schmitz U, Petrova V, Kearney PS, Rasko JEJ. Holding on to Junk Bonds: Intron Retention in Cancer and Therapy. Cancer Res 2020; 81:779-789. [PMID: 33046441 DOI: 10.1158/0008-5472.can-20-1943] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/16/2020] [Accepted: 10/06/2020] [Indexed: 11/16/2022]
Abstract
Intron retention (IR) in cancer was for a long time overlooked by the scientific community, as it was previously considered to be an artifact of a dysfunctional spliceosome. Technological advancements made in the last decade offer unique opportunities to explore the role of IR as a widespread phenomenon that contributes to the transcriptional diversity of many cancers. Numerous studies in cancer have shed light on dysregulation of cellular mechanisms that lead to aberrant and pathologic IR. IR is not merely a mechanism of gene regulation, but rather it can mediate cancer pathogenesis and therapeutic resistance in various human diseases. The burden of IR in cancer is governed by perturbations to mechanisms known to regulate this phenomenon and include epigenetic variation, mutations within the gene body, and splicing factor dysregulation. This review summarizes possible causes for aberrant IR and discusses the role of IR in therapy or as a consequence of disease treatment. As neoepitopes originating from retained introns can be presented on the cancer cell surface, the development of personalized cancer vaccines based on IR-derived neoepitopes should be considered. Ultimately, a deeper comprehension about the origins and consequences of aberrant IR may aid in the development of such personalized cancer vaccines.
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Affiliation(s)
- Geoffray Monteuuis
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia
| | - Ulf Schmitz
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Sydney, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Veronika Petrova
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Sydney, Australia
| | - Padraic S Kearney
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia. .,Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
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41
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Amante SM, Montibus B, Cowley M, Barkas N, Setiadi J, Saadeh H, Giemza J, Contreras-Castillo S, Fleischanderl K, Schulz R, Oakey RJ. Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing. Nucleic Acids Res 2020; 48:8349-8359. [PMID: 32621610 PMCID: PMC7470969 DOI: 10.1093/nar/gkaa556] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/16/2020] [Accepted: 07/01/2020] [Indexed: 01/23/2023] Open
Abstract
Alternative splicing (AS) and alternative polyadenylation (APA) generate diverse transcripts in mammalian genomes during development and differentiation. Epigenetic marks such as trimethylation of histone H3 lysine 36 (H3K36me3) and DNA methylation play a role in generating transcriptome diversity. Intragenic CpG islands (iCGIs) and their corresponding host genes exhibit dynamic epigenetic and gene expression patterns during development and between different tissues. We hypothesise that iCGI-associated H3K36me3, DNA methylation and transcription can influence host gene AS and/or APA. We investigate H3K36me3 and find that this histone mark is not a major regulator of AS or APA in our model system. Genomewide, we identify over 4000 host genes that harbour an iCGI in the mammalian genome, including both previously annotated and novel iCGI/host gene pairs. The transcriptional activity of these iCGIs is tissue- and developmental stage-specific and, for the first time, we demonstrate that the premature termination of host gene transcripts upstream of iCGIs is closely correlated with the level of iCGI transcription in a DNA-methylation independent manner. These studies suggest that iCGI transcription, rather than H3K36me3 or DNA methylation, interfere with host gene transcription and pre-mRNA processing genomewide and contributes to the spatiotemporal diversification of both the transcriptome and proteome.
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Affiliation(s)
- Samuele M Amante
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Bertille Montibus
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Michael Cowley
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Nikolaos Barkas
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Jessica Setiadi
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Heba Saadeh
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Joanna Giemza
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK
| | | | - Karin Fleischanderl
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Reiner Schulz
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Rebecca J Oakey
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK
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42
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Leung CS, Douglass SM, Morselli M, Obusan MB, Pavlyukov MS, Pellegrini M, Johnson TL. H3K36 Methylation and the Chromodomain Protein Eaf3 Are Required for Proper Cotranscriptional Spliceosome Assembly. Cell Rep 2020; 27:3760-3769.e4. [PMID: 31242410 PMCID: PMC6904931 DOI: 10.1016/j.celrep.2019.05.100] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/08/2019] [Accepted: 05/27/2019] [Indexed: 12/14/2022] Open
Abstract
In the eukaryotic cell, spliceosomes assemble onto pre-mRNA cotranscriptionally. Spliceosome assembly takes place in the context of the chromatin environment, suggesting that the state of the chromatin may affect splicing. The molecular details and mechanisms through which chromatin affects splicing, however, are still unclear. Here, we show a role for the histone methyltransferase Set2 and its histone modification, H3K36 methylation, in pre-mRNA splicing through high-throughput sequencing. Moreover, the effect of H3K36 methylation on pre-mRNA splicing is mediated through the chromodomain protein Eaf3. We find that Eaf3 is recruited to intron-containing genes and that Eaf3 interacts with the splicing factor Prp45. Eaf3 acts with Prp45 and Prp19 after formation of the precatalytic B complex around the time of splicing activation, thus revealing the step in splicing that is regulated by H3K36 methylation. These studies support a model whereby H3K36 facilitates recruitment of an "adapter protein" to support efficient, constitutive splicing.
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Affiliation(s)
- Calvin S Leung
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stephen M Douglass
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marco Morselli
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matthew B Obusan
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marat S Pavlyukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russian Federation
| | - Matteo Pellegrini
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tracy L Johnson
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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43
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Abstract
The treatment landscape of metastatic renal cell carcinoma (RCC) has been revolutionized over the past two decades, bringing forth an era in which more than a dozen therapeutic agents are now available to treat patients. As a consequence, personalized care has become a critical part of developing effective treatment guidelines and improving patient outcomes. One of the most important emerging aspects of precision medicine in cancer is matching patients and treatments based on the genomic characteristics of an individual and their tumour. Despite the lack of a single genomic predictor of treatment response or prognostication feature in RCC, emerging research suggests that the identification of such markers remains promising. Mutations in VHL and alterations in its downstream pathways are the mainstay of RCC development and progression. However, the predictive value of VHL mutations has been questioned. Further research has examined mutations in genes involved in chromosome remodelling (for example, PBRM1, BAP1 and SETD2), DNA methylation and DNA damage repair, all of which have been associated with clinical outcomes. Here, we provide a comprehensive overview of genomic evidence in the context of RCC and its potential predictive and prognostic value.
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44
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Monteuuis G, Wong JJL, Bailey CG, Schmitz U, Rasko JEJ. The changing paradigm of intron retention: regulation, ramifications and recipes. Nucleic Acids Res 2020; 47:11497-11513. [PMID: 31724706 PMCID: PMC7145568 DOI: 10.1093/nar/gkz1068] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/04/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022] Open
Abstract
Intron retention (IR) is a form of alternative splicing that has long been neglected in mammalian systems although it has been studied for decades in non-mammalian species such as plants, fungi, insects and viruses. It was generally assumed that mis-splicing, leading to the retention of introns, would have no physiological consequence other than reducing gene expression by nonsense-mediated decay. Relatively recent landmark discoveries have highlighted the pivotal role that IR serves in normal and disease-related human biology. Significant technical hurdles have been overcome, thereby enabling the robust detection and quantification of IR. Still, relatively little is known about the cis- and trans-acting modulators controlling this phenomenon. The fate of an intron to be, or not to be, retained in the mature transcript is the direct result of the influence exerted by numerous intrinsic and extrinsic factors at multiple levels of regulation. These factors have altered current biological paradigms and provided unexpected insights into the transcriptional landscape. In this review, we discuss the regulators of IR and methods to identify them. Our focus is primarily on mammals, however, we broaden the scope to non-mammalian organisms in which IR has been shown to be biologically relevant.
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Affiliation(s)
- Geoffray Monteuuis
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Justin J L Wong
- Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia
| | - Ulf Schmitz
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Computational Biomedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
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45
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Abstract
Multiple studies have confirmed that speckle-type pox virus and zinc finger (POZ) protein (SPOP) functions as a substrate adaptor of cullin 3-based E3 ligase and has a crucial role in various cellular processes via specific targeting of proteins for ubiquitination and subsequent proteasomal degradation. Dysregulation of SPOP-mediated proteolysis might be involved in the development and progression of human prostate and kidney cancers. In prostate cancer, SPOP seems to function as a tumour suppressor by targeting several proteins, including androgen receptor (AR), steroid receptor coactivator 3 (SRC3) and BRD4, for degradation, whereas it might function as an oncoprotein in kidney cancer, for example, by targeting phosphatase and tensin homologue (PTEN) for proteasomal degradation. In addition, nuclear SPOP targets AR for degradation and has a role as a tumour suppressor in prostate cancer; however, in kidney cancer, SPOP largely accumulates in the cytoplasm and fails to promote degradation of AR located in the nucleus, resulting in activation of AR-driven pathways and cancer progression. Owing to the context-dependent function of SPOP in human malignancies, further assessment of the molecular mechanisms involving SPOP in prostate and kidney cancers is needed to improve our understanding of its role in the development of these cancer types. Treatments that target SPOP might become therapeutic strategies in these malignancies in the future.
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SETD2 mutation in renal clear cell carcinoma suppress autophagy via regulation of ATG12. Cell Death Dis 2020; 11:69. [PMID: 31988284 PMCID: PMC6985262 DOI: 10.1038/s41419-020-2266-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 12/26/2022]
Abstract
Inactivating mutations in the SETD2 gene, encoding for a nonredundant histone H3 methyltransferase and regulator of transcription, is a frequent molecular feature in clear cell renal cell carcinomas (ccRCC). SETD2 deficiency is associated with recurrence of ccRCC and bears low prognostic values. Targeting autophagy, a conserved catabolic process with critical functions in maintenance of cellular homeostasis and cell conservation under stress condition, is emerging as a potential therapeutic strategy to combat ccRCC. Epigenetics-based pathways are now appreciated as key components in the regulation of autophagy. However, whether loss of function in the SETD2 histone modifying enzyme occurring in ccRCC cells may impact on their ability to undergo autophagy remained to be explored. Here, we report that SETD2 deficiency in RCC cells is associated with the aberrant accumulation of both free ATG12 and of an additional ATG12-containing complex, distinct from the ATG5–ATG12 complex. Rescue of SETD2 functions in the SETD2 deficiency in RCC cells, or reduction of SETD2 expression level in RCC cells wild type for this enzyme, demonstrates that SETD2 deficiency in RCC is directly involved in the acquisition of these alterations in the autophagic process. Furthermore, we revealed that deficiency in SETD2, known regulator of alternative splicing, is associated with increased expression of a short ATG12 spliced isoform at the depend of the canonical long ATG12 isoform in RCC cells. The defect in the ATG12-dependent conjugation system was found to be associated with a decrease autophagic flux, in accord with the role for this ubiquitin-like protein conjugation system in autophagosome formation and expansion. Finally, we report that SETD2 and ATG12 gene expression levels are associated with favorable respective unfavorable prognosis in ccRCC patients. Collectively, our findings bring further argument for considering the SETD2 gene status of ccRCC tumors, when therapeutic interventions, such as targeting the autophagic process, are considered to combat these kidney cancers.
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Li Y, Brooks M, Yeoh-Wang J, McCoy RM, Rock TM, Pasquino A, Moon CI, Patrick RM, Tanurdzic M, Ruffel S, Widhalm JR, McCombie WR, Coruzzi GM. SDG8-Mediated Histone Methylation and RNA Processing Function in the Response to Nitrate Signaling. PLANT PHYSIOLOGY 2020; 182:215-227. [PMID: 31641075 PMCID: PMC6945839 DOI: 10.1104/pp.19.00682] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/09/2019] [Indexed: 05/04/2023]
Abstract
Chromatin modification has gained increased attention for its role in the regulation of plant responses to environmental changes, but the specific mechanisms and molecular players remain elusive. Here, we show that the Arabidopsis (Arabidopsis thaliana) histone methyltransferase SET DOMAIN GROUP8 (SDG8) mediates genome-wide changes in H3K36 methylation at specific genomic loci functionally relevant to nitrate treatments. Moreover, we show that the specific H3K36 methyltransferase encoded by SDG8 is required for canonical RNA processing, and that RNA isoform switching is more prominent in the sdg8-5 deletion mutant than in the wild type. To demonstrate that SDG8-mediated regulation of RNA isoform expression is functionally relevant, we examined a putative regulatory gene, CONSTANS, CO-like, and TOC1 101 (CCT101), whose nitrogen-responsive isoform-specific RNA expression is mediated by SDG8. We show by functional expression in shoot cells that the different RNA isoforms of CCT101 encode distinct regulatory proteins with different effects on genome-wide transcription. We conclude that SDG8 is involved in plant responses to environmental nitrogen supply, affecting multiple gene regulatory processes including genome-wide histone modification, transcriptional regulation, and RNA processing, and thereby mediating developmental and metabolic processes related to nitrogen use.
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Affiliation(s)
- Ying Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Matthew Brooks
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Jenny Yeoh-Wang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Rachel M McCoy
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Tara M Rock
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Angelo Pasquino
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Chang In Moon
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Ryan M Patrick
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Milos Tanurdzic
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Sandrine Ruffel
- Biochimie et Physiologie Moléculaire des Plantes, French National Institute for Agricultural Research, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier SupAgro, 34090 Montpellier, France
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | | | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
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Kinyamu HK, Bennett BD, Bushel PR, Archer TK. Proteasome inhibition creates a chromatin landscape favorable to RNA Pol II processivity. J Biol Chem 2019; 295:1271-1287. [PMID: 31806706 DOI: 10.1074/jbc.ra119.011174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/02/2019] [Indexed: 11/06/2022] Open
Abstract
Proteasome activity is required for diverse cellular processes, including transcriptional and epigenetic regulation. However, inhibiting proteasome activity can lead to an increase in transcriptional output that is correlated with enriched levels of trimethyl H3K4 and phosphorylated forms of RNA polymerase (Pol) II at the promoter and gene body. Here, we perform gene expression analysis and ChIP followed by sequencing (ChIP-seq) in MCF-7 breast cancer cells treated with the proteasome inhibitor MG132, and we further explore genome-wide effects of proteasome inhibition on the chromatin state and RNA Pol II transcription. Analysis of gene expression programs and chromatin architecture reveals that chemically inhibiting proteasome activity creates a distinct chromatin state, defined by spreading of the H3K4me3 mark into the gene bodies of differentially-expressed genes. The distinct H3K4me3 chromatin profile and hyperacetylated nucleosomes at transcription start sites establish a chromatin landscape that facilitates recruitment of Ser-5- and Ser-2-phosphorylated RNA Pol II. Subsequent transcriptional events result in diverse gene expression changes. Alterations of H3K36me3 levels in the gene body reflect productive RNA Pol II elongation of transcripts of genes that are induced, underscoring the requirement for proteasome activity at multiple phases of the transcriptional cycle. Finally, by integrating genomics data and pathway analysis, we find that the differential effects of proteasome inhibition on the chromatin state modulate genes that are fundamental for cancer cell survival. Together, our results uncover underappreciated downstream effects of proteasome inhibitors that may underlie targeting of distinct chromatin states and key steps of RNA Pol II-mediated transcription in cancer cells.
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Affiliation(s)
- H Karimi Kinyamu
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| | - Brian D Bennett
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709.,Integrative Bioinformatics Support Group, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| | - Pierre R Bushel
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| | - Trevor K Archer
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
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Abstract
Renal cell carcinomas (RCCs) are a diverse set of malignancies that have recently been shown to harbour mutations in a number of chromatin modifier genes - including PBRM1, SETD2, BAP1, KDM5C, KDM6A, and MLL2 - through high-throughput sequencing efforts. Current research focuses on understanding the biological activities that chromatin modifiers employ to suppress tumorigenesis and on developing clinical approaches that take advantage of this knowledge. Unsurprisingly, several common themes unify the functions of these epigenetic modifiers, particularly regulation of histone post-translational modifications and nucleosome organization. Furthermore, chromatin modifiers also govern processes crucial for DNA repair and maintenance of genomic integrity as well as the regulation of splicing and other key processes. Many chromatin modifiers have additional non-canonical roles in cytoskeletal regulation, which further contribute to genomic stability, expanding the repertoire of functions that might be essential in tumorigenesis. Our understanding of how mutations in chromatin modifiers contribute to tumorigenesis in RCC is improving but remains an area of intense investigation. Importantly, elucidating the activities of chromatin modifiers offers intriguing opportunities for the development of new therapeutic interventions in RCC.
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Affiliation(s)
- Aguirre A de Cubas
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - W Kimryn Rathmell
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN, USA.
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