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Huang Y, Yang Z, Tang Y, Chen H, Liu T, Peng G, Huang X, He X, Mei M, Du C. Identification of a signature of histone modifiers in kidney renal clear cell carcinoma. Aging (Albany NY) 2024; 16:10489-10511. [PMID: 38888515 PMCID: PMC11236308 DOI: 10.18632/aging.205944] [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: 11/24/2023] [Accepted: 04/22/2024] [Indexed: 06/20/2024]
Abstract
Kidney renal clear cell carcinoma (KIRC) is a cancer that is closely associated with epigenetic alterations, and histone modifiers (HMs) are closely related to epigenetic regulation. Therefore, this study aimed to comprehensively explore the function and prognostic value of HMs-based signature in KIRC. HMs were first obtained from top journal. Then, the mRNA expression profiles and clinical information in KIRC samples were downloaded from The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) datasets. Cox regression analysis and least absolute shrinkage and selection operator (Lasso) analysis were implemented to find prognosis-related HMs and construct a risk model related to the prognosis in KIRC. Kaplan-Meier analysis was used to determine prognostic differences between high- and low-risk groups. Immune infiltration and drug sensitivity analysis were also performed between high- and low-risk groups. Eventually, 8 HMs were successfully identified for the construction of a risk model in KIRC. The results of the correlation analysis between risk signature and the prognosis showed HMs-based signature has good prognostic value in KIRC. Results of immune analysis of risk models showed there were significant differences in the level of immune cell infiltration and expression of immune checkpoints between high- and low-risk groups. The results of the drug sensitivity analysis showed that the high-risk group was more sensitive to several chemotherapeutic agents such as Sunitinib, Tipifarnib, Nilotinib and Bosutinib than the low-risk group. In conclusion, we successfully constructed HMs-based prognostic signature that can predict the prognosis of KIRC.
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Affiliation(s)
- Yongming Huang
- Department of Urology, Ganzhou People's Hospital, Ganzhou, Jiangxi 341000, China
| | - Zhongsheng Yang
- Department of Urology, Ganzhou People's Hospital, Ganzhou, Jiangxi 341000, China
| | - Ying Tang
- Department of Day Ward, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Hua Chen
- Department of Urology, Ganzhou People's Hospital, Ganzhou, Jiangxi 341000, China
| | - Tairong Liu
- Department of Urology, Ganzhou People's Hospital, Ganzhou, Jiangxi 341000, China
| | - Guanghua Peng
- Department of Urology, Ganzhou People's Hospital, Ganzhou, Jiangxi 341000, China
| | - Xin Huang
- Department of Urology, Ganzhou People's Hospital, Ganzhou, Jiangxi 341000, China
| | - Xiaolong He
- Department of Urology, Ganzhou People's Hospital, Ganzhou, Jiangxi 341000, China
| | - Ming Mei
- Department of Day Ward, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Chuance Du
- Department of Urology, Ganzhou People's Hospital, Ganzhou, Jiangxi 341000, China
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Bingyu W, Xi Y, Jiangfang L, Jianqing Z. Key chromatin regulator-related genes associated with the risk of coronary artery disease regulate the expression of HCFC1, RNF8, TNP1 and SET. Heliyon 2024; 10:e28685. [PMID: 38596069 PMCID: PMC11002600 DOI: 10.1016/j.heliyon.2024.e28685] [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: 06/28/2023] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/11/2024] Open
Abstract
Chromatin regulators are indispensable upstream epigenetic regulators.The emergence and progression of atherosclerosis has been demonstrated to be influenced by smooth muscle-related chromatin regulators, such as ZEB2 and MAFF. However, specific chromatin regulators and their possible roles have not been clarified. Information was gathered from 51 patients diagnosed with coronary artery disease (CAD) and 50 individuals in good health from the GEO database. 440 genes were identified as having differential expression across the two datasets, and these genes were linked to cellular reactions. Enrichment of pathways related to histone modification and transcriptional regulatory factors was observed in GO and KEGG analyses. Four machine learning models (RF, SVM, GLM, and XGB) were developed using the expression profiles of 440 chromatin-associated genes in the CAD cohort to pinpoint genes with significant diagnostic potential. After evaluating residuals, root mean square errors, receiver operating characteristic curves, and immune-infiltration, four key genes (HCFC1, RNF8, TNP1, and SET) were identified. Gene expression in different blood vessel levels in atherosclerotic plaques in a mouse model of coronary artery disease showed significant variations. The gene expression levels in macrophages aligned with clinical data from the GEO database as expected. This discovery is crucial for future analysis and the prediction of drug and miRNA targets. In conclusion, we found that the four hub genes are important in the mechanism of CAD. These findings provide new ideas for the study of potential epigenetic predictive markers and therapeutic targets to be used in determining a treatment strategy for CAD.
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Affiliation(s)
- Wang Bingyu
- Department of Cardiovascular, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Yang Xi
- Department of Cardiovascular, Ningbo Medical Center Lihuili Hospital, Ningbo, China
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Ningbo, China
| | - Lian Jiangfang
- Department of Cardiovascular, Ningbo Medical Center Lihuili Hospital, Ningbo, China
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Ningbo, China
| | - Zhou Jianqing
- Department of Cardiovascular, Ningbo Medical Center Lihuili Hospital, Ningbo, China
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Ningbo, China
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Luo L, Zhao L, Cui L, Peng C, Ou S, Zeng Y, Liu B. The roles of chromatin regulatory factors in endometriosis. J Assist Reprod Genet 2024; 41:863-873. [PMID: 38270747 PMCID: PMC11052748 DOI: 10.1007/s10815-024-03026-8] [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: 08/07/2023] [Accepted: 01/07/2024] [Indexed: 01/26/2024] Open
Abstract
PURPOSE Endometriosis is an estrogen-dependent inflammatory disease and one of the most common gynecological diseases in women of reproductive age. The aim of the review was to explore the relationship between the chromatin regulatory factors and endometriosis. METHODS By searching for literature on chromatin regulators and endometriosis in PuMed. Finally, 98 documents were selected. RESULTS Chromatin regulators (CRs) are essential epigenetic regulatory factors that can regulate chromatin structure changes and are usually divided into three categories: DNA methylation compounds, histone modification compounds, and chromatin remodeling complexes. Noncoding RNAs are also chromatin regulators and can form heterochromatin by binding to protein complexes. Chromatin regulators cause abnormal gene expression by regulating chromatin structure, thereby affecting the occurrence and development of endometriosis. CONCLUSION This review summarizes the participation of chromatin regulators in the mechanisms of endometriosis, and these changes in related chromatin regulators provide a comprehensive reference for diagnosis and treatment of endometriosis.
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Affiliation(s)
- Liumei Luo
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ling Zhao
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Lanyu Cui
- Key Laboratory of Longevity and Aging-Related Diseases of Chinese Ministry of Education; Guangxi Colleges and Universities, Key Laboratory of Biological Molecular Medicine Research, School of Basic Medical Sciences,, Guangxi Medical University, Nanning, China
| | - Chuyu Peng
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shanshan Ou
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yan Zeng
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Bo Liu
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.
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Ma Y, Fang F, Liao K, Zhang J, Wei C, Liao Y, Zhao B, Fang Y, Chen Y, Zhang X, Tang D. Identification and validation of the clinical prediction model and biomarkers based on chromatin regulators in colon cancer by integrated analysis of bulk- and single-cell RNA sequencing data. Transl Cancer Res 2024; 13:1290-1313. [PMID: 38617504 PMCID: PMC11009811 DOI: 10.21037/tcr-23-1886] [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: 10/12/2023] [Accepted: 02/08/2024] [Indexed: 04/16/2024]
Abstract
Background Chromatin regulators (CRs) are implicated in the development of cancer, but a comprehensive investigation of their role in colon adenocarcinoma (COAD) is inadequate. The purpose of this study is to find CRs that can provide recommendations for clinical diagnosis and treatment, and to explore the reasons why they serve as critical CRs. Methods We obtained data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Weighted Gene Co-Expression Network Analysis (WGCNA) screened tumor-associated CRs. LASSO-Cox regression was used to construct the model and to screen key CRs together with support vector machine (SVM), the univariate Cox regression. We used single-cell data to explore the expression of CRs in cells and their communication. Immune infiltration, immune checkpoints, mutation, methylation, and drug sensitivity analyses were performed. Gene expression was verified by quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR). Pan-cancer analysis was used to explore the importance of hub CRs. Results We finally obtained 32 tumor-associated CRs. The prognostic model was constructed based on RCOR2, PPARGC1A, PKM, RAC3, PHF19, MYBBP1A, ORC1, and EYA2 by the LASSO-Cox regression. Single-cell data revealed that the model was immune-related. Combined with immune infiltration analysis, immune checkpoint analysis, and tumor immune dysfunction and exclusion (TIDE) analysis, the low-score risk group had more immune cell infiltration and better immune response. Mutation and methylation analysis showed that multiple CRs may be mutated and methylated in colon cancer. Drug sensitivity analysis revealed that the low-risk group may be more sensitive to several drugs and PKM was associated with multiple drugs. Combined with machine learning, PKM is perhaps the most critical gene in CRs. Pan-cancer analysis showed that PKM plays a role in the prognosis of cancers. Conclusions We developed a prognostic model for COAD based on CRs. Increased expression of the core gene PKM is linked with a poor prognosis in several malignancies.
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Affiliation(s)
- Yichao Ma
- Clinical Medical College, Yangzhou University, Yangzhou, China
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Fang Fang
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Kai Liao
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Jingqiu Zhang
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Chen Wei
- Clinical Medical College, Yangzhou University, Yangzhou, China
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Yiqun Liao
- Department of Clinical Medical college, Dalian Medical University, Dalian, China
| | - Bin Zhao
- Department of Clinical Medical college, Dalian Medical University, Dalian, China
| | - Yongkun Fang
- Department of Clinical Medical college, Dalian Medical University, Dalian, China
| | - Yuji Chen
- Clinical Medical College, Yangzhou University, Yangzhou, China
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Xinyue Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Dong Tang
- Clinical Medical College, Yangzhou University, Yangzhou, China
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
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Felipe I, Martínez-de-Villarreal J, Patel K, Martínez-Torrecuadrada J, Grossmann LD, Roncador G, Cubells M, Farrell A, Kendsersky N, Sabroso-Lasa S, Sancho-Temiño L, Torres K, Martinez D, Perez JM, García F, Pogoriler J, Moreno L, Maris JM, Real FX. BPTF cooperates with MYCN and MYC to link neuroblastoma cell cycle control to epigenetic cellular states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.11.579816. [PMID: 38405949 PMCID: PMC10888818 DOI: 10.1101/2024.02.11.579816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The nucleosome remodeling factor BPTF is required for the deployment of the MYC-driven transcriptional program. Deletion of one Bptf allele delays tumor progression in mouse models of pancreatic cancer and lymphoma. In neuroblastoma, MYCN cooperates with the transcriptional core regulatory circuitry (CRC). High BPTF levels are associated with high-risk features and decreased survival. BPTF depletion results in a dramatic decrease of cell proliferation. Bulk RNA-seq, single-cell sequencing, and tissue microarrays reveal a positive correlation of BPTF and CRC transcription factor expression. Immunoprecipitation/mass spectrometry shows that BPTF interacts with MYCN and the CRC proteins. Genome-wide distribution analysis of BPTF and CRC in neuroblastoma reveals a dual role for BPTF: 1) it co-localizes with MYCN/MYC at the promoter of genes involved in cell cycle and 2) it co-localizes with the CRC at super-enhancers to regulate cell identity. The critical role of BPTF across neuroblastoma subtypes supports its relevance as a therapeutic target.
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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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Wang B, Feng Y, Li Z, Zhou F, Luo J, Yang B, Long S, Li X, Liu Z, Li X, Chen J, Wang L, Wei W. Identification and validation of chromatin regulator-related signatures as a novel prognostic model for low-grade gliomas using translational bioinformatics. Life Sci 2024; 336:122312. [PMID: 38042284 DOI: 10.1016/j.lfs.2023.122312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/04/2023]
Abstract
AIMS The purpose of this study is to explore the potential biological role and prognostic significance of chromatin regulators (CRs) in low-grade gliomas (LGGs). MAIN METHODS CRs were obtained from the FACER database. Transcription profiles of LGG patients were collected from the TCGA and CGGA databases. Differentially expressed CRs (DECRs) between LGGs and normal controls were identified using DESeq2. The consensus clustering algorithm was employed to distinguish subtypes of LGGs based on prognosis-related DECRs. The differences in clinical and molecular characteristics between different subtypes were explored. R packages, GSVA, ssGSEA, and ESTIMATE were utilized to elucidate the tumor microenvironment and activated pathways in different subtypes. Subsequently, a CRs-related signature was developed using LASSO Cox regression. Its performance was evaluated by Kaplan-Meier curve and ROC curve analyses. In vitro experiments were performed to explore the function of JADE3 in LGGs, which predominantly expressed in glioma cells. KEY FINDINGS We identified 43 DECRs and two CRs-related subtypes of LGGs. The subtype characterized by shorter survival displayed significant enrichment for pathways associated with DNA damage response and repair, along with heightened immune cell infiltration. Furthermore, the CRs-based signature exhibited excellent prognostic performance in both the TCGA and CGGA databases. Knockdown of JADE3 significantly increased the invasion, migration, and proliferation abilities of Hs683. SIGNIFICANCE Our study reveals the aberrant expression and prognostic value of CRs in LGGs. It emphasizes the potential regulatory role of CRs in the microenvironment and DNA damage repair in LGGs. JADE3 could be a possible therapeutic target for LGGs.
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Affiliation(s)
- Bo Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yu Feng
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Zhengwei Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Fan Zhou
- Huanggang Central Hospital of Yangtze University, Hubei 438000, China
| | - Jie Luo
- Huanggang Central Hospital of Yangtze University, Hubei 438000, China
| | - Bin Yang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shengrong Long
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xinyi Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Zhenyuan Liu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jincao Chen
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Lei Wang
- Huanggang Central Hospital of Yangtze University, Hubei 438000, China.
| | - Wei Wei
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China.
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Ren S, Yu H. The prognostic and biological importance of chromatin regulation-related genes for lung cancer is examined using bioinformatics and experimentally confirmed. Pathol Res Pract 2023; 248:154638. [PMID: 37379709 DOI: 10.1016/j.prp.2023.154638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND The pathogenesis and clinical diagnosis of lung adenocarcinoma (LUAD), a malignant illness with substantial morbidity and mortality, are still being investigated. Genes involved in chromatin regulation are crucial in the biological function of LUAD. METHODS The prognostic prediction model for LUAD was developed using multivariables and least absolute shrinkage and selection operator (LASSO) regression. It consisted of 10 chromatin regulators. The LUAD has been divided into two groups, high- and low-risk, using a predictive model. The model was shown to be accurate in predicting survival by the nomogram, receiver operating characteristic (ROC) curves, and principal component analysis (PCA). An analysis of differences in immune-cell infiltration, immunologicalfunction, and clinical traits between low- and high-risk populations was conducted. Protein-protein interaction (PPI) networks and Gene Ontology (GO) pathways of differentially expressed genes (DEGs) in the high versus low risk group were also examined to investigate the association between genes and biological pathways. The biological roles of chromatin regulators (CRs) in LUAD were finally estimated using colony formation and cell movement. The important genes' mRNA expression has been measured using real-time polymerase chain reaction (RT-PCR). RESULTS AND CONCLUSION Risk score and stage based on the model could be seen as separate prognostic indicators for patients with LUAD. The main signaling pathway difference across various risk groups was in cell cycle. The immunoinfiltration profile of the tumor microenvironment (TME) and individuals with different risk levels were correlated, suggesting that the interaction of immune cells with the tumor led to the creation of a favorable immunosuppressive microenvironment. These discoveries aid in the creation of individualized therapies for LUAD patients.
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Affiliation(s)
- Shanshan Ren
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, Henan, China.
| | - Haiyang Yu
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, Henan, China
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Li Y, Xiong C, Wu LL, Zhang BY, Wu S, Chen YF, Xu QH, Liao HF. Tumor subtypes and signature model construction based on chromatin regulators for better prediction of prognosis in uveal melanoma. Pathol Oncol Res 2023; 29:1610980. [PMID: 37362244 PMCID: PMC10287976 DOI: 10.3389/pore.2023.1610980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
Background: Uveal Melanoma (UM) is the most prevalent primary intraocular malignancy in adults. This study assessed the importance of chromatin regulators (CRs) in UM and developed a model to predict UM prognosis. Methods: Gene expression data and clinical information for UM were obtained from public databases. Samples were typed according to the gene expression of CRs associated with UM prognosis. The prognostic key genes were further screened by the protein interaction network, and the risk model was to predict UM prognosis using the least absolute shrinkage and selection operator (LASSO) regression analysis and performed a test of the risk mode. In addition, we performed gene set variation analysis, tumor microenvironment, and tumor immune analysis between subtypes and risk groups to explore the mechanisms influencing the development of UM. Results: We constructed a signature model consisting of three CRs (RUVBL1, SIRT3, and SMARCD3), which was shown to be accurate, and valid for predicting prognostic outcomes in UM. Higher immune cell infiltration in poor prognostic subtypes and risk groups. The Tumor immune analysis and Tumor Immune Dysfunction and Exclusion (TIDE) score provided a basis for clinical immunotherapy in UM. Conclusion: The risk model has prognostic value for UM survival and provides new insights into the treatment of UM.
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Affiliation(s)
- Yue Li
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Chao Xiong
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Li Li Wu
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Bo Yuan Zhang
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Sha Wu
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Yu Fen Chen
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Qi Hua Xu
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Hong Fei Liao
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
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Yang B, Rong X, Jiang C, Long M, Liu A, Chen Q. Comprehensive analyses reveal the prognosis and biological function roles of chromatin regulators in lung adenocarcinoma. Aging (Albany NY) 2023; 15:3598-3620. [PMID: 37155150 PMCID: PMC10449281 DOI: 10.18632/aging.204693] [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: 02/17/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
The present study explored the prognosis and biological function roles of chromatin regulators (CRs) in patients with lung adenocarcinoma (LUAD). Using transcriptome profile and clinical follow-up data of LUAD dataset, we explored the molecular classification, developed, and validated a CR prognostic model, built an individual risk scoring system in LUAD, and compared the clinical and molecular characteristics between different subtypes and risk stratifications. We investigated the chemotherapy sensitivity and predicted potential immunotherapy response. Lastly, we collected the clinical samples and validated the prognosis and potential function role of NAPS2. Our study indicated that LUAD patients could be classified into two subtypes that had obviously different clinical background and molecular features. We constructed a prognostic model with eight CR genes, which was well validated in several other population cohort. We built high- and low-risk stratifications for LUAD patients. Patients from high-risk group were totally different from low-risk groups in clinical, biological function, gene mutation, microenvironment, and immune infiltration levels. We idented several potential molecular compounds for high-risk group treatment. We predicted that high-risk group may have poor immunotherapy response. We finally found that Neuronal PAS Domain Protein 2 (NPAS2) involved in the progression of LUAD via regulating cell adhesion. Our study indicated that CR involved in the progression of LUAD and affect their prognosis. Different therapeutic strategies should be developed for different molecular subtypes and risk stratifications. Our comprehensive analyses uncover specific determinants of CRs in LUAD and provides implications for investigating disease-associated CRs.
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Affiliation(s)
- Baishuang Yang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xueyao Rong
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Chen Jiang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Meihua Long
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Aibin Liu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Qiong Chen
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China
- Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
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11
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Kumar A, Maurya P, Hayes JJ. Post-Translation Modifications and Mutations of Human Linker Histone Subtypes: Their Manifestation in Disease. Int J Mol Sci 2023; 24:ijms24021463. [PMID: 36674981 PMCID: PMC9860689 DOI: 10.3390/ijms24021463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/14/2023] Open
Abstract
Linker histones (LH) are a critical component of chromatin in addition to the canonical histones (H2A, H2B, H3, and H4). In humans, 11 subtypes (7 somatic and 4 germinal) of linker histones have been identified, and their diverse cellular functions in chromatin structure, DNA replication, DNA repair, transcription, and apoptosis have been explored, especially for the somatic subtypes. Delineating the unique role of human linker histone (hLH) and their subtypes is highly tedious given their high homology and overlapping expression patterns. However, recent advancements in mass spectrometry combined with HPLC have helped in identifying the post-translational modifications (PTMs) found on the different LH subtypes. However, while a number of PTMs have been identified and their potential nuclear and non-nuclear functions explored in cellular processes, there are very few studies delineating the direct relevance of these PTMs in diseases. In addition, recent whole-genome sequencing of clinical samples from cancer patients and individuals afflicted with Rahman syndrome have identified high-frequency mutations and therefore broadened the perspective of the linker histone mutations in diseases. In this review, we compile the identified PTMs of hLH subtypes, current knowledge of the relevance of hLH PTMs in human diseases, and the correlation of PTMs coinciding with mutations mapped in diseases.
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Affiliation(s)
- Ashok Kumar
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA
- Correspondence:
| | - Preeti Maurya
- Aab Cardiovascular Research Institute, University of Rochester, Rochester, NY 14642, USA
| | - Jeffrey J. Hayes
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA
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12
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Zhang Y, Zhang Y, Song C, Zhao X, Ai B, Wang Y, Zhou L, Zhu J, Feng C, Xu L, Wang Q, Sun H, Fang Q, Xu X, Li E, Li C. CRdb: a comprehensive resource for deciphering chromatin regulators in human. Nucleic Acids Res 2023; 51:D88-D100. [PMID: 36318256 PMCID: PMC9825595 DOI: 10.1093/nar/gkac960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
Chromatin regulators (CRs) regulate epigenetic patterns on a partial or global scale, playing a critical role in affecting multi-target gene expression. As chromatin immunoprecipitation sequencing (ChIP-seq) data associated with CRs are rapidly accumulating, a comprehensive resource of CRs needs to be built urgently for collecting, integrating, and processing these data, which can provide abundant annotated information on CR upstream and downstream regulatory analyses as well as CR-related analysis functions. This study established an integrative CR resource, named CRdb (http://cr.liclab.net/crdb/), with the aim of curating a large number of available resources for CRs and providing extensive annotations and analyses of CRs to help biological researchers clarify the regulation mechanism and function of CRs. The CRdb database comprised a total of 647 CRs and 2,591 ChIP-seq samples from more than 300 human tissues and cell types. These samples have been manually curated from NCBI GEO/SRA and ENCODE. Importantly, CRdb provided the abundant and detailed genetic annotations in CR-binding regions based on ChIP-seq. Furthermore, CRdb supported various functional annotations and upstream regulatory information on CRs. In particular, it embedded four types of CR regulatory analyses: CR gene set enrichment, CR-binding genomic region annotation, CR-TF co-occupancy analysis, and CR regulatory axis analysis. CRdb is a useful and powerful resource that can help in exploring the potential functions of CRs and their regulatory mechanism in diseases and biological processes.
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Affiliation(s)
- Yimeng Zhang
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
| | | | | | - Xilong Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Yuezhu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Liwei Zhou
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Jiang Zhu
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Liyan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Cancer Research Center, Shantou University Medical College, Shantou 515041, China
| | - Qiuyu Wang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Hong Sun
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - Qiaoli Fang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
| | - Xiaozheng Xu
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Enmin Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - Chunquan Li
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South
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13
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Zhang X, Qin X, Yu T, Wang K, Chen Y, Xing Q. Chromatin regulators-related lncRNA signature predicting the prognosis of kidney renal clear cell carcinoma and its relationship with immune microenvironment: A study based on bioinformatics and experimental validation. Front Genet 2022; 13:974726. [PMID: 36338996 PMCID: PMC9630733 DOI: 10.3389/fgene.2022.974726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/05/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Kidney Renal Clear cell carcinoma (KIRC) is a major concern in the urinary system. A lot of researches were focused on Chromatin Regulators (CRs) in tumors. In this study, CRs-related lncRNAs (CRlncRNAs) were investigated for their potential impact on the prognosis of KIRC and the immune microenvironment. Methods: The TCGA database was used to obtain transcriptome and related clinical information. CRs were obtained from previous studies, whereas CRlncRNAs were obtained by differential and correlation analysis. We screened the lncRNAs for the signature construction using regression analysis and LASSO regression analysis. The effectiveness of the signature was evaluated using the Kaplan-Meier (K-M) curve and Receiver Operating Characteristic curve (ROC). Additionally, we examined the associations between the signature and Tumor Microenvironment (TME), and the efficacy of drug therapy. Finally, we further verified whether these lncRNAs could affect the biological function of KIRC cells by functional experiments such as CCK8 and transwell assay. Results: A signature consisting of 8 CRlncRNAs was constructed to predict the prognosis of KIRC. Quantitative Real-Time PCR verified the expression of 8 lncRNAs at the cell line and tissue level. The signature was found to be an independent prognostic indicator for KIRC in regression analysis. This signature was found to predict Overall Survival (OS) better for patients in the subgroups of age, gender, grade, stage, M, N0, and T. Furthermore, a significant correlation was found between riskScore and immune cell infiltration and immune checkpoint. Finally, we discovered several drugs with different IC50 values in different risk groups using drug sensitivity analysis. And functional experiments showed that Z97200.1 could affect the proliferation, migration and invasion of KIRC cells. Conclusion: Overall, the signature comprised of these 8 lncRNAs were reliable prognostic biomarkers for KIRC. Moreover, the signature had significant potential for assessing the immunological landscape of tumors and providing individualized treatment.
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Affiliation(s)
- Xinyu Zhang
- Department of Urology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xinyue Qin
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu, China
| | - Tiannan Yu
- Department of Urology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Kexin Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Yinhao Chen
- Department of Urology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
- *Correspondence: Qianwei Xing, ; Yinhao Chen,
| | - Qianwei Xing
- Department of Urology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- *Correspondence: Qianwei Xing, ; Yinhao Chen,
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14
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Liu Z, Yang H, Chen Z, Jing C. A novel chromatin regulator-related immune checkpoint related gene prognostic signature and potential candidate drugs for endometrial cancer patients. Hereditas 2022; 159:40. [PMID: 36253800 PMCID: PMC9578220 DOI: 10.1186/s41065-022-00253-w] [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: 07/28/2022] [Accepted: 09/22/2022] [Indexed: 11/14/2022] Open
Abstract
Background Endometrial cancer (EC) is the most common gynecologic malignancy in developed countries and its prevalence is increasing. As an emerging therapy with a promising efficacy, immunotherapy has been extensively applied in the treatment of solid tumors. In addition, chromatin regulators (CRs), as essential upstream regulators of epigenetics, play a significant role in tumorigenesis and cancer development. Methods CRs and immune checkpoint-related genes (ICRGs) were obtained from the previous top research. The Genome Cancer Atlas (TCGA) was utilized to acquire the mRNA expression and clinical information of patients with EC. Correlation analysis was utilized for screen CRs-related ICRGs (CRRICRGs). By Cox regression and least absolute shrinkage and selection operator (LASSO) analysis, prognosis related CRRICRGs were screened out and risk model was constructed. The Kaplan–Meier curve was used to estimate the prognosis between high- and low-risk group. By comparing the IC50 value, the drugs sensitivity difference was explored. We obtained small molecule drugs for the treatment of UCEC patients based on CAMP dataset. Results We successfully constructed a 9 CRRICRs-based prognostic signature for patients with UCEC and found the riskscore was an independent prognostic factor. The results of functional analysis suggested that CRRICRGs may be involved in immune processes associated with cancer. Immune characteristics analysis provided further evidence that the CRRICRGs-based model was correlated with immune cells infiltration and immune checkpoint. Eight small molecule drugs that may be effective for the treatment of UCEC patients were screened. Effective drugs identified by drug sensitivity profiling in high- and low-risk groups. Conclusion In summary, our study provided novel insights into the function of CRRICRGs in UCEC. We also developed a reliable prognostic panel for the survival of patients with UCEC. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-022-00253-w.
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Affiliation(s)
- Zesi Liu
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China
| | - Hongxia Yang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China
| | - Ziyu Chen
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China
| | - Chunli Jing
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China.
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15
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Dai YW, Chen HB, Pan YT, Lv LX, Wang WM, Chen XH, Zhou X. Characterization of chromatin regulators identified prognosis and heterogeneity in hepatocellular carcinoma. Front Oncol 2022; 12:1002781. [PMID: 36158697 PMCID: PMC9505021 DOI: 10.3389/fonc.2022.1002781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Liver carcinogenesis is a multiprocess that involves complicated interactions between genetics, epigenetics, and transcriptomic alterations. Aberrant chromatin regulator (CR) expressions, which are vital regulatory epigenetics, have been found to be associated with multiple biological processes. Nevertheless, the impression of CRs on tumor microenvironment remodeling and hepatocellular carcinoma (HCC) prognosis remains obscure. Thus, this study aimed to systematically analyze CR-related patterns and their correlation with genomic features, metabolism, cuproptosis activity, and clinicopathological features of patients with HCC in The Cancer Genome Atlas, International Cancer Genome Consortium-LIRI-JP cohort, and GSE14520 that utilized unsupervised consensus clustering. Three CR-related patterns were recognized, and the CRs phenotype-related gene signature (CRsscore) was developed using the least absolute shrinkage and selection operator-Cox regression and multivariate Cox algorithms to represent the individual CR-related pattern. Additionally, the CRsscore was an independent prognostic index that served as a fine predictor for energy metabolism and cuproptosis activity in HCC. Accordingly, describing a wide landscape of CR characteristics may assist us to illustrate the sealed association between epigenetics, energy metabolism, and cuproptosis activity. This study may discern new tumor therapeutic targets and exploit personalized therapy for patients.
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Affiliation(s)
- Yin-wei Dai
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Han-bin Chen
- Department of Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ya-ting Pan
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lin-xi Lv
- Wenzhou Medical University, Wenzhou, China
| | - Wei-ming Wang
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiao-Hu Chen
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Xiao-Hu Chen, ; Xiang Zhou,
| | - Xiang Zhou
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Xiao-Hu Chen, ; Xiang Zhou,
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16
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Jia X, Zhang G. Characterization of chromatin regulators in hepatocellular carcinoma to guide clinical therapy. Front Genet 2022; 13:961018. [PMID: 36092923 PMCID: PMC9452841 DOI: 10.3389/fgene.2022.961018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is notorious for its high mortality and incidence. Accumulating evidence confirms that chromatin regulators (CRs) have a significant impact on cancer. Therefore, exploring the mode of action and prognostic value of CRs is imminent for the treatment of hepatocellular carcinoma. Method: Transcriptome and clinical data for this study have been downloaded from TCGA (https://portal.gdc.cancer.gov/) and ICGC (https://dcc.icgc.org/). Univariate analysis was used to screen CRs with prognostic value, and our prognostic risk score signature was developed using least absolute shrinkage along with selection operator (lasso) Cox regression analysis. The CRs-based prognostic model was constructed in the TCGA dataset, and low-risk HCC patients had a better prognosis, which was finally validated in the ICGC dataset. We used the receiver operating characteristic curve to identify the accuracy of the prediction model and establish a line chart to prove the clinical effectiveness of the model. We also discussed the differences in drug sensitivity via CellMiner database, tumor immune microenvironment via ssGSEA algorithm, and clinical characteristics among different risk groups. Results: A prognostic model consisting of seven CRs was constructed and verified in HCC patients. Furthermore, we found that this risk score prognostic signature could independently predict the prognosis of HCC patients. Functional enrichment analysis revealed that CRs are mainly associated with cancer-related signaling pathways and metabolic pathways. In addition, immune cell abundance correlates with risk score levels Conclusion: In brief, we systematically explored the mode of action of CRs in HCC patients and established a reliable prognostic prediction model.
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Affiliation(s)
- Xiangen Jia
- North China University of Science and Technology Affiliated Hospital, Tangshan, China
- North China University of Science and Technology, Tangshan, China
| | - Guozhi Zhang
- North China University of Science and Technology Affiliated Hospital, Tangshan, China
- North China University of Science and Technology, Tangshan, China
- *Correspondence: Guozhi Zhang,
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17
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Role of SWI/SNF chromatin remodeling genes in lung cancer development. Biochem Soc Trans 2022; 50:1143-1150. [PMID: 35587173 DOI: 10.1042/bst20211084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/26/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022]
Abstract
SWI/SNF family of chromatin remodeling complexes uses the energy of ATP to change the structure of DNA, playing key roles in DNA regulation and repair. It is estimated that up to 25% of all human cancers contain alterations in SWI/SNF, although the precise molecular mechanisms for their involvement in tumor progression are largely unknown. Despite the improvements achieved in the last decades on our knowledge of lung cancer molecular biology, it remains the major cause of cancer-related deaths worldwide and it is in urgent need for new therapeutic alternatives. We and others have described recurrent alterations in different SWI/SNF genes in nearly 20% of lung cancer patients, some of them with a significant association with worse prognosis, indicating an important role of SWI/SNF in this fatal disease. These alterations might be therapeutically exploited, as it has been shown in cellular and animal models with the use of EGFR inhibitors, DNA-damaging agents and several immunotherapy approaches. Therefore, a better knowledge of the molecular mechanisms regulated by SWI/SNF alterations in lung cancer might be translated into a therapeutic improvement of this frequently lethal disease. In this review, we summarize all the evidence of SWI/SNF alterations in lung cancer, the current knowledge about the potential mechanisms involved in their tumorigenic role, as well as the results that support a potential exploitation of these alterations to improve the treatment of lung cancer patients.
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18
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Weir WH, Mucha PJ, Kim WY. A bipartite graph-based expected networks approach identifies DDR genes not associated with TMB yet predictive of immune checkpoint blockade response. Cell Rep Med 2022; 3:100602. [PMID: 35584624 PMCID: PMC9133403 DOI: 10.1016/j.xcrm.2022.100602] [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: 07/14/2021] [Revised: 01/07/2022] [Accepted: 03/20/2022] [Indexed: 11/26/2022]
Abstract
Immune checkpoint blockade (ICB) has had remarkable success for treatment of solid tumors. However, as only a subset of patients exhibit responses, there is a continued need for biomarker development. Numerous reports have shown a link between tumor mutational burden (TMB) and ICB response, while others have identified a link between ICB response and mutation in DNA damage repair (DDR) genes. However, it remains unclear to what extent mutations in DDR genes hold predictive value above and beyond their association with TMB. Herein, we present a networks-based test and bipartite graph-based expected TMB score (BiG-BETS) with higher specificity for discriminating DDR genes and pathways that are associated with elevated TMB. Moreover, we find that mutations in certain DDR genes that are not associated with elevated TMB (low BiG-BETS) are nevertheless predictive of ICB benefit in high TMB patients, demonstrating that their inactivation contributes to ICB response in a TMB-independent manner.
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Affiliation(s)
- William H Weir
- Curriculum in Bioinformatics & Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Peter J Mucha
- Curriculum in Bioinformatics & Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Mathematics, Dartmouth College, Hanover, NH, USA.
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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19
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Deng S, Feng Y, Pauklin S. 3D chromatin architecture and transcription regulation in cancer. J Hematol Oncol 2022; 15:49. [PMID: 35509102 PMCID: PMC9069733 DOI: 10.1186/s13045-022-01271-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/21/2022] [Indexed: 12/18/2022] Open
Abstract
Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation. In turn, aberrant 3D structures play a vital role in developing abnormalities and diseases such as cancer. This review discusses key 3D chromatin structures (topologically associating domain, lamina-associated domain, and enhancer-promoter interactions) and corresponding structural protein elements mediating 3D chromatin interactions [CCCTC-binding factor, polycomb group protein, cohesin, and Brother of the Regulator of Imprinted Sites (BORIS) protein] with a highlight of their associations with cancer. We also summarise the recent development of technologies and bioinformatics approaches to study the 3D chromatin interactions in gene expression regulation, including crosslinking and proximity ligation methods in the bulk cell population (ChIA-PET and HiChIP) or single-molecule resolution (ChIA-drop), and methods other than proximity ligation, such as GAM, SPRITE, and super-resolution microscopy techniques.
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Affiliation(s)
- Siwei Deng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Siim Pauklin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK.
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20
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Stauffer KM, Elion DL, Cook RS, Stricker T. MLL3 is a de novo cause of endocrine therapy resistance. Cancer Med 2021; 10:7692-7711. [PMID: 34581028 PMCID: PMC8559462 DOI: 10.1002/cam4.4285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/12/2021] [Accepted: 08/21/2021] [Indexed: 12/14/2022] Open
Abstract
Background Cancer resequencing studies have revealed epigenetic enzymes as common targets for recurrent mutations. The monomethyltransferase MLL3 is among the most recurrently mutated enzymes in ER+ breast cancer. The H3K4me1 marks created by MLL3 can define enhancers. In ER+ breast cancer, ERα genome‐binding sites are primarily distal enhancers. Thus, we hypothesize that mutation of MLL3 will alter the genomic binding and transcriptional regulatory activity of ERα. Methods We investigated the genomic consequences of knocking down MLL3 in an MLL3/PIK3CA WT ER+ breast cancer cell line. Results Loss of MLL3 led to a large loss of H3K4me1 across the genome, and a shift in genomic location of ERα‐binding sites, which was accompanied by a re‐organization of the breast cancer transcriptome. Gene set enrichment analyses of ERα‐binding sites in MLL3 KD identified endocrine therapy resistance terms, and we showed that MLL3 KD cells are resistant to tamoxifen and fulvestrant. Many differentially expressed genes are controlled by the small collection of new locations of H3K4me1 deposition and ERα binding, suggesting that loss of functional MLL3 leads to new transcriptional regulation of essential genes. Motif analysis of RNA‐seq and ChIP‐seq data highlighted SP1 as a critical transcription factor in the MLL3 KD cells. Differentially expressed genes that display a loss of ERα binding upon MLL3 KD also harbor increased SP1 binding. Conclusions Our data show that a decrease in functional MLL3 leads to endocrine therapy resistance. This highlights the importance of genotyping patient tumor samples for MLL3 mutation upon initial resection, prior to deciding upon treatment plans.
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Novillo A, Fernández-Santander A, Gaibar M, Galán M, Romero-Lorca A, El Abdellaoui-Soussi F, Gómez-Del Arco P. Role of Chromodomain-Helicase-DNA-Binding Protein 4 (CHD4) in Breast Cancer. Front Oncol 2021; 11:633233. [PMID: 33981601 PMCID: PMC8107472 DOI: 10.3389/fonc.2021.633233] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/23/2021] [Indexed: 12/15/2022] Open
Abstract
Chromodomain-helicase-DNA-binding protein 4 (CHD4) is an epigenetic regulator identified as an oncogenic element that may provide a novel therapeutic target for the treatment of breast cancer (BC). CHD4—the core component of the nucleosome remodeling and deacetylase (NuRD) complex—may be mutated in patients with this disease. However, information on CHD4 mutants that might allow their use as biomarkers of therapeutic success and prognosis is lacking. The present work examines mutations in CHD4 reported in patients with breast cancer and included in public databases and attempts to identify their roles in its development. The databases revealed 81 point mutations across different types of breast cancer (19 of which also appeared in endometrial, intestinal, nervous system, kidney, and lymphoid organ cancers). 71.6% of the detected mutations were missense mutations, 13.6% were silent, and 6.2% nonsense. Over 50% affected conserved residues of the ATPase motor (ATPase and helicase domains), and domains of unknown function in the C-terminal region. Thirty one mutations were classified in the databases as either ‘deleterious’, ‘probably/possibly damaging’ or as ‘high/medium pathogenic’; another five nonsense and one splice-site variant were predicted to produce potentially harmful truncated proteins. Eight of the 81 mutations were categorized as putative driver mutations and have been found in other cancer types. Some mutations seem to influence ATPase and DNA translocation activities (R1162W), while others may alter protein stability (R877Q/H, R975H) or disrupt DNA binding and protein activity (R572*, X34_splice) suggesting CHD4 function may be affected. In vivo tumorigenecity studies in endometrial cancer have revealed R975H and R1162W as mutations that lead to CHD4 loss-of-function. Our study provides insight into the molecular mechanism whereby CHD4, and some of its mutants could play a role in breast cancer and suggest important implications for the biological comprehension and prognosis of breast cancer, identifying CHD4 as a novel therapeutic target for BC patients.
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Affiliation(s)
- Apolonia Novillo
- Department of Pre-clinical Dentistry, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Villaviciosa de Odón, Madrid, Spain
| | - Ana Fernández-Santander
- Department of Medicine, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Villaviciosa de Odón, Madrid, Spain
| | - Maria Gaibar
- Department of Health Sciences, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Villaviciosa de Odón, Madrid, Spain
| | - Miguel Galán
- Department of Health Sciences, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Villaviciosa de Odón, Madrid, Spain
| | - Alicia Romero-Lorca
- Department of Medicine, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Villaviciosa de Odón, Madrid, Spain
| | | | - Pablo Gómez-Del Arco
- Institute of Rare Diseases Research, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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Munakata W, Shirasugi Y, Tobinai K, Onizuka M, Makita S, Suzuki R, Maruyama D, Kawai H, Izutsu K, Nakanishi T, Shiba S, Hojo S, Ando K. Phase 1 study of tazemetostat in Japanese patients with relapsed or refractory B-cell lymphoma. Cancer Sci 2021; 112:1123-1131. [PMID: 33492746 PMCID: PMC7935786 DOI: 10.1111/cas.14822] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
Background Tazemetostat is a selective and orally available inhibitor of enhancer of zeste homolog 2 (EZH2), a histone methyltransferase and epigenetic regulator of cellular differentiation programs. We carried out a phase I study of tazemetostat in Japanese patients with relapsed or refractory B‐cell non‐Hodgkin‐type lymphoma (B‐NHL) to evaluate its tolerability, safety, pharmacokinetics, and preliminary antitumor activity. Methods Tazemetostat was given orally at a single dose of 800 mg on the first day and 800 mg twice daily (BID: total 1600 mg/d) on following days in a 28‐day/cycle manner. Tazemetostat dose‐limiting toxicity (DLT) was evaluated up to the end of the first treatment cycle. Archival tumor tissues were analyzed for hotspot EZH2 mutations. Results As of 15 January 2018, seven patients (four follicular lymphoma [FL] and three diffuse large B‐cell lymphoma [DLBCL]) were enrolled. The median age was 73 (range, 59‐85) years, and the median number of prior chemotherapy regimens was three (range, one to five). No DLT was observed (one patient was not evaluable due to early disease progression). The common treatment‐related adverse events (AEs) were thrombocytopenia and dysgeusia (three patients each; 42.9%). No treatment‐related serious AEs were observed. The objective response rate was 57% (4/7 patients), including responses in three of four patients with FL and one of three patients with DLBCL. An EZH2 mutation was detected in one patient with FL responding to treatment. Conclusions Tazemetostat at 800 mg BID showed an acceptable safety profile and promising antitumor activity in Japanese patients with relapsed or refractory B‐NHL.
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Affiliation(s)
- Wataru Munakata
- Department of Hematology, National Cancer Center Hospital, Tokyo, Japan
| | - Yukari Shirasugi
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Japan
| | - Kensei Tobinai
- Department of Hematology, National Cancer Center Hospital, Tokyo, Japan
| | - Makoto Onizuka
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Japan
| | - Shinichi Makita
- Department of Hematology, National Cancer Center Hospital, Tokyo, Japan
| | - Rikio Suzuki
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Japan
| | - Dai Maruyama
- Department of Hematology, National Cancer Center Hospital, Tokyo, Japan
| | - Hidetsugu Kawai
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Japan
| | - Koji Izutsu
- Department of Hematology, National Cancer Center Hospital, Tokyo, Japan
| | | | - Sari Shiba
- Clinical Pharmacology Science Department, Eisai Co., Ltd., Tokyo, Japan
| | - Seichiro Hojo
- Clinical Data Science Department, Eisai Co., Ltd., Tokyo, Japan
| | - Kiyoshi Ando
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Japan
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Farcas AM, Nagarajan S, Cosulich S, Carroll JS. Genome-Wide Estrogen Receptor Activity in Breast Cancer. Endocrinology 2021; 162:bqaa224. [PMID: 33284960 PMCID: PMC7787425 DOI: 10.1210/endocr/bqaa224] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Indexed: 12/13/2022]
Abstract
The largest subtype of breast cancer is characterized by the expression and activity of the estrogen receptor alpha (ERalpha/ER). Although several effective therapies have significantly improved survival, the adaptability of cancer cells means that patients frequently stop responding or develop resistance to endocrine treatment. ER does not function in isolation and multiple associating factors have been reported to play a role in regulating the estrogen-driven transcriptional program. This review focuses on the dynamic interplay between some of these factors which co-occupy ER-bound regulatory elements, their contribution to estrogen signaling, and their possible therapeutic applications. Furthermore, the review illustrates how some ER association partners can influence and reprogram the genomic distribution of the estrogen receptor. As this dynamic ER activity enables cancer cell adaptability and impacts the clinical outcome, defining how this plasticity is determined is fundamental to our understanding of the mechanisms of disease progression.
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Affiliation(s)
- Anca M Farcas
- Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Sankari Nagarajan
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | | | - Jason S Carroll
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
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Ohsawa S, Umemura T, Terada T, Muto Y. Network and Evolutionary Analysis of Human Epigenetic Regulators to Unravel Disease Associations. Genes (Basel) 2020; 11:genes11121457. [PMID: 33291839 PMCID: PMC7761991 DOI: 10.3390/genes11121457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 12/15/2022] Open
Abstract
We carried out a system-level analysis of epigenetic regulators (ERs) and detailed the protein–protein interaction (PPI) network characteristics of disease-associated ERs. We found that most diseases associated with ERs can be clustered into two large groups, cancer diseases and developmental diseases. ER genes formed a highly interconnected PPI subnetwork, indicating a high tendency to interact and agglomerate with one another. We used the disease module detection (DIAMOnD) algorithm to expand the PPI subnetworks into a comprehensive cancer disease ER network (CDEN) and developmental disease ER network (DDEN). Using the transcriptome from early mouse developmental stages, we identified the gene co-expression modules significantly enriched for the CDEN and DDEN gene sets, which indicated the stage-dependent roles of ER-related disease genes during early embryonic development. The evolutionary rate and phylogenetic age distribution analysis indicated that the evolution of CDEN and DDEN genes was mostly constrained, and these genes exhibited older evolutionary age. Our analysis of human polymorphism data revealed that genes belonging to DDEN and Seed-DDEN were more likely to show signs of recent positive selection in human history. This finding suggests a potential association between positive selection of ERs and risk of developmental diseases through the mechanism of antagonistic pleiotropy.
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Affiliation(s)
- Shinji Ohsawa
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1, Yanagido, Gifu 501-1193, Japan; (S.O.); (T.T.)
- Department of Nursing, Ogaki Women’s College, 1-109, Nishinokawa-cho, Ogaki 503-8554, Japan
| | - Toshiaki Umemura
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630, Sugitani, Toyama 930-0194, Japan;
| | - Tomoyoshi Terada
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1, Yanagido, Gifu 501-1193, Japan; (S.O.); (T.T.)
- Department of Functional Bioscience, Gifu University School of Medicine, 1-1, Yanagido, Gifu 501-1193, Japan
| | - Yoshinori Muto
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1, Yanagido, Gifu 501-1193, Japan; (S.O.); (T.T.)
- Department of Functional Bioscience, Gifu University School of Medicine, 1-1, Yanagido, Gifu 501-1193, Japan
- Correspondence: ; Tel.: +81-58-293-3241
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Halaburkova A, Cahais V, Novoloaca A, Araujo MGDS, Khoueiry R, Ghantous A, Herceg Z. Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes. Genome Res 2020; 30:1517-1532. [PMID: 32963031 PMCID: PMC7605261 DOI: 10.1101/gr.268292.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/26/2020] [Indexed: 12/24/2022]
Abstract
The recent identification of recurrently mutated epigenetic regulator genes (ERGs) supports their critical role in tumorigenesis. We conducted a pan-cancer analysis integrating (epi)genome, transcriptome, and DNA methylome alterations in a curated list of 426 ERGs across 33 cancer types, comprising 10,845 tumor and 730 normal tissues. We found that, in addition to mutations, copy number alterations in ERGs were more frequent than previously anticipated and tightly linked to expression aberrations. Novel bioinformatics approaches, integrating the strengths of various driver prediction and multi-omics algorithms, and an orthogonal in vitro screen (CRISPR-Cas9) targeting all ERGs revealed genes with driver roles within and across malignancies and shared driver mechanisms operating across multiple cancer types and hallmarks. This is the largest and most comprehensive analysis thus far; it is also the first experimental effort to specifically identify ERG drivers (epidrivers) and characterize their deregulation and functional impact in oncogenic processes.
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Affiliation(s)
- Andrea Halaburkova
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Alexei Novoloaca
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | | | - Rita Khoueiry
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
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26
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Darwiche N. Epigenetic mechanisms and the hallmarks of cancer: an intimate affair. Am J Cancer Res 2020; 10:1954-1978. [PMID: 32774995 PMCID: PMC7407342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023] Open
Abstract
Epigenetic mechanisms comprising DNA methylation, histone modifications, and noncoding RNAs affect chromatin structure and regulate gene expression. These mechanisms control normal embryonic development and adult life and their deregulation contributes to several diseases including cancer. The process of tumorigenesis is complex and results from the evolution of different "hallmarks of cancer". Hanahan and Weinberg presented in 2000 and 2011 seminal contributions in the cancer field, first the six hallmarks of cancer and a decade later two additional hallmarks and two enabling characteristics were added. Here, we surmise that epigenetic mechanisms regulate and contribute to every single hallmark in cancer, and thus represent the hallmark of hallmarks in tumorigenesis. Focusing on epigenetics as a major hallmark in cancer formation has profound preventive, therapeutic, and clinical implications.
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Affiliation(s)
- Nadine Darwiche
- Department of Biochemistry and Molecular Genetics, American University of Beirut Beirut, Lebanon
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27
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Saha G, Singh R, Mandal A, Das S, Chattopadhyay E, Panja P, Roy P, DeSarkar N, Gulati S, Ghatak S, Ghosh S, Banerjee S, Roy B, Ghosh S, Chaudhuri D, Arora N, Biswas NK, Sikdar N. A novel hotspot and rare somatic mutation p.A138V, at TP53 is associated with poor survival of pancreatic ductal and periampullary adenocarcinoma patients. Mol Med 2020; 26:59. [PMID: 32552660 PMCID: PMC7302128 DOI: 10.1186/s10020-020-00183-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 06/03/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Pancreatic Ductal Adenocarcinoma (PDAC) is a cancer of the exocrine pancreas and 5-year survival rates remain constant at 7%. Along with PDAC, Periampullary Adenocarcinoma (PAC) accounts for 0.5-2% of all gastrointestinal malignancies. Genomic observations were well concluded for PDAC and PACs in western countries but no reports are available from India till now. METHODS Targeted Next Generation Sequencing were performed in 8 (5 PDAC and 3 PAC) tumour normal pairs, using a panel of 412 cancer related genes. Primary findings were replicated in 85 tumour samples (31 PDAC and 54 PAC) using the Sanger sequencing. Mutations were also validated by ASPCR, RFLP, and Ion Torrent sequencing. IHC along with molecular dynamics and docking studies were performed for the p.A138V mutant of TP53. Key polymorphisms at TP53 and its associated genes were genotyped by PCR-RFLP method and association with somatic mutations were evaluated. All survival analysis was done using the Kaplan-Meier survival method which revealed that the survival rates varied significantly depending on the somatic mutations the patients harboured. RESULTS Among the total 114 detected somatic mutations, TP53 was the most frequently mutated (41%) gene, followed by KRAS, SMAD4, CTNNB1, and ERBB3. We identified a novel hotspot TP53 mutation (p.A138V, in 17% of all patients). Low frequency of KRAS mutation (33%) was detected in these samples compared to patients from Western counties. Molecular Dynamics (MD) simulation and DNA-protein docking analysis predicted p.A138V to have oncogenic characteristics. Patients with p.A138V mutation showed poorer overall survival (p = 0.01). So, our finding highlights elevated prevalence of the p53p.A138V somatic mutation in PDAC and pancreatobiliary PAC patients. CONCLUSION Detection of p.A138V somatic variant in TP53 might serve as a prognostic marker to classify patients. It might also have a role in determining treatment regimes. In addition, low frequency of KRAS hotspot mutation mostly in Indian PDAC patient cohort indicates presence of other early drivers in malignant transformation.
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Affiliation(s)
- Gourab Saha
- Human Genetics Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata, 700108, India
| | - Richa Singh
- Human Genetics Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata, 700108, India
| | - Argha Mandal
- Department of Biotechnology, Heritage Institute of Technology, Kolkata, India
| | - Subrata Das
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Esita Chattopadhyay
- Human Genetics Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata, 700108, India
| | - Prasun Panja
- Human Genetics Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata, 700108, India
| | - Paromita Roy
- Department of Pathology & Department of Gastrointestinal Surgery, Tata Medical Center, Rajarhat, Kolkata, India
| | - Navonil DeSarkar
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, USA
| | - Sumit Gulati
- Department of Surgical Gastroenterology, Calcutta Medical Research Institute, Kolkata, India
| | - Supriyo Ghatak
- Department of Surgical Gastroenterology, Calcutta Medical Research Institute, Kolkata, India
| | - Shibajyoti Ghosh
- Department of General Surgery, Medical College and Hospital, Kolkata, India
| | - Sudeep Banerjee
- Department of Pathology & Department of Gastrointestinal Surgery, Tata Medical Center, Rajarhat, Kolkata, India
| | - Bidyut Roy
- Human Genetics Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata, 700108, India
| | - Saurabh Ghosh
- Human Genetics Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata, 700108, India
| | - Dipankar Chaudhuri
- Department of Biotechnology, Heritage Institute of Technology, Kolkata, India
| | - Neeraj Arora
- Department of Pathology & Department of Gastrointestinal Surgery, Tata Medical Center, Rajarhat, Kolkata, India
| | - Nidhan K Biswas
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Nilabja Sikdar
- Human Genetics Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata, 700108, India.
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Richart L, Margueron R. Drugging histone methyltransferases in cancer. Curr Opin Chem Biol 2020; 56:51-62. [DOI: 10.1016/j.cbpa.2019.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023]
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Richart L, Felipe I, Delgado P, Andrés MPD, Prieto J, Pozo ND, García JF, Piris MA, Ramiro A, Real FX. Bptf determines oncogenic addiction in aggressive B-cell lymphomas. Oncogene 2020; 39:4884-4895. [PMID: 32451433 DOI: 10.1038/s41388-020-1331-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 12/15/2022]
Abstract
Chromatin remodeling factors contribute to establish aberrant gene expression programs in cancer cells and therefore represent valuable targets for therapeutic intervention. BPTF (Bromodomain PhD Transcription Factor), a core subunit of the nucleosome remodeling factor (NURF), modulates c-MYC oncogenic activity in pancreatic cancer. Here, we analyze the role of BPTF in c-MYC-driven B-cell lymphomagenesis using the Eμ-Myc transgenic mouse model of aggressive B-cell lymphoma. We find that BPTF is required for normal B-cell differentiation without evidence of haploinsufficiency. In contrast, deletion of one Bptf allele is sufficient to delay lymphomagenesis in Eμ-Myc mice. Tumors arising in a Bptf heterozygous background display decreased c-MYC levels and pathway activity, together with increased activation of the NF-κB pathway, a molecular signature characteristic of human diffuse large B-cell lymphoma (DLBCL). In human B-cell lymphoma samples, we find a strong correlation between BPTF and c-MYC mRNA and protein levels, together with an anti-correlation between BPTF and NF-κB pathway activity. Our results indicate that BPTF is a relevant therapeutic target in B-cell lymphomas and that, upon its inhibition, cells acquire distinct oncogenic dependencies.
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Affiliation(s)
- Laia Richart
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre-CNIO, 28029, Madrid, Spain
| | - Irene Felipe
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre-CNIO, 28029, Madrid, Spain
| | - Pilar Delgado
- B Lymphocyte Biology Lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029, Madrid, Spain
| | - Mónica P de Andrés
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre-CNIO, 28029, Madrid, Spain
| | - Jaime Prieto
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre-CNIO, 28029, Madrid, Spain
| | - Natalia Del Pozo
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre-CNIO, 28029, Madrid, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Juan F García
- Department of Pathology, MD Anderson Cancer Center, 28033, Madrid, Spain
| | - Miguel A Piris
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain.,Department of Pathology, Fundación Jiménez Díaz, 28040, Madrid, Spain.,Department of Pathology, Hospital Universitario Marqués de Valdecilla, 39008, Santander, Spain
| | - Almudena Ramiro
- B Lymphocyte Biology Lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029, Madrid, Spain
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre-CNIO, 28029, Madrid, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain. .,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003, Barcelona, Spain.
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30
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Systematic analysis of alterations in the ubiquitin proteolysis system reveals its contribution to driver mutations in cancer. ACTA ACUST UNITED AC 2019; 1:122-135. [DOI: 10.1038/s43018-019-0001-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/11/2019] [Indexed: 12/21/2022]
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31
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Viarisio D, Robitaille A, Müller-Decker K, Flechtenmacher C, Gissmann L, Tommasino M. Cancer susceptibility of beta HPV49 E6 and E7 transgenic mice to 4-nitroquinoline 1-oxide treatment correlates with mutational signatures of tobacco exposure. Virology 2019; 538:53-60. [PMID: 31569015 DOI: 10.1016/j.virol.2019.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 12/27/2022]
Abstract
We have previously showed that a transgenic (Tg) mouse model with cytokeratin 14 promoter (K14)-driven expression of E6 and E7 from beta-3 HPV49 in the basal layer of the epidermis and of the mucosal epithelia of the digestive tract (K14 HPV49 E6/E7 Tg mice) are highly susceptible to upper digestive tract carcinogenesis upon exposure to 4-nitroquinoline 1-oxide (4NQO). Using whole-exome sequencing, we show that in K14 HPV49 E6/E7 Tg mice, development of 4NQO-induced cancers tightly correlates with the accumulation of somatic mutations in cancer-related genes. The mutational signature in 4NQO-treated mice was similar to the signature observed in humans exposed to tobacco smoking and tobacco chewing. Similar results were obtained with K14 Tg animals expressing mucosal high-risk HPV16 E6 and E7 oncogenes. Thus, beta-3 HPV49 share some functional similarities with HPV16 in Tg animals.
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Affiliation(s)
- Daniele Viarisio
- Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Alexis Robitaille
- International Agency for Research on Cancer (IARC), World Health Organization, 150 Cours Albert Thomas, 69372, Lyon Cedex 08, France
| | - Karin Müller-Decker
- Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Christa Flechtenmacher
- Department of Pathology, University Hospital of Heidelberg, Im Neuenheimer Feld 220, 69120, Heidelberg, Germany
| | - Lutz Gissmann
- Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany; Department of Botany and Microbiology (honorary MMember), King Saud University, Riyadh, Saudi Arabia
| | - Massimo Tommasino
- International Agency for Research on Cancer (IARC), World Health Organization, 150 Cours Albert Thomas, 69372, Lyon Cedex 08, France.
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Li XC, Wang MY, Yang M, Dai HJ, Zhang BF, Wang W, Chu XL, Wang X, Zheng H, Niu RF, Zhang W, Chen KX. A mutational signature associated with alcohol consumption and prognostically significantly mutated driver genes in esophageal squamous cell carcinoma. Ann Oncol 2019; 29:938-944. [PMID: 29351612 DOI: 10.1093/annonc/mdy011] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is often diagnosed at an advanced and incurable stage. Information on driver genes and prognosticators in ESCC remains incomplete. The objective was to elucidate significantly mutated genes (SMGs), mutational signatures, and prognosticators in ESCC. Patients and methods Three MutSig algorithms (i.e. MutSigCV, MutSigCL and MutSigFN) and '20/20+' ratio-metric were employed to identify SMGs. Nonnegative matrix factorization was used to decipher mutational signatures. Kaplan-Meier survival analysis, multivariate Cox and logistic regression models were applied to analyze association between mutational features and clinical parameters. Results We identified 26 SMGs, including 8 novel (NAV3, TENM3, PTCH1, TGFBR2, RIPK4, PBRM1, USP8 and BAP1) and 18 that have been previously reported. Three mutational signatures were identified to be prevalent in ESCC including clocklike C>T at CpG, APOBEC overactive C>T at TpCp[A/T], and a signature featured by T>C substitution. The T>C mutational signature was significantly correlated with alcohol consumption (OR: 3.59; 95% CI: 2.30-5.67; P < 0.001). This alcohol consumption signature was also observed in liver cancer and head and neck squamous cell carcinoma, and its mutational activity was substantially higher in samples with mutations in TP53. Survival analysis revealed that TENM3 mutations (HR: 5.54; CI: 2.68-11.45; P < 0.001) and TP53 hotspot mutation p.R213* (HR: 3.37; CI: 1.73-8.06; P < 0.001) were significantly associated with shortened survival outcome. The association remained statistically significant after controlling for age, gender, TNM stage and tumor grade. Conclusions We have uncovered several new SMGs in ESCC and defined an alcohol consumption related mutational signature. TENM3 mutations and the TP53 hotspot mutation p.R213* are independent prognosticators for poor survival in ESCC.
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Affiliation(s)
- X C Li
- Public Laborato, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - M Y Wang
- Beijing Genomics Institute-Shenzhen, Shenzhen, Guangdong, China
| | - M Yang
- Department of Epidemiology and Biostatisti, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - H J Dai
- Department of Epidemiology and Biostatisti, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - B F Zhang
- Beijing Genomics Institute-Shenzhen, Shenzhen, Guangdong, China
| | - W Wang
- Department of Epidemiology and Biostatisti, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - X L Chu
- Department of Epidemiology and Biostatisti, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - X Wang
- Department of Epidemiology and Biostatisti, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - H Zheng
- Department of Epidemiology and Biostatisti, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - R F Niu
- Public Laborato, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - W Zhang
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA.
| | - K X Chen
- Department of Epidemiology and Biostatisti, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.
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Takahashi Y, Iwamoto T, Suzuki Y, Kajiwara Y, Hatono M, Tsukioki T, Kawada K, Kochi M, Ikeda H, Shien T, Taira N, Matsuoka J, Doihara H, Toyooka S. Evaluation of Therapeutic Target Gene Expression Based on Residual Cancer Burden Classification After Neoadjuvant Chemotherapy for HER2-Negative Breast Cancer. Clin Breast Cancer 2019; 20:117-124.e4. [PMID: 31570267 DOI: 10.1016/j.clbc.2019.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 10/26/2022]
Abstract
INTRODUCTION Patients with residual disease usually have a poor prognosis after neoadjuvant chemotherapy for breast cancer. The aim of this study was to explore therapeutic targets and potential additional adjuvant treatments for patients with residual disease after standard neoadjuvant chemotherapy. PATIENTS AND METHODS We retrieved publicly available complementary DNA microarray data from 399 human epidermal growth factor receptor 2 (HER2)-negative primary breast cancer samples from patients who underwent standard neoadjuvant chemotherapy. We analyzed the messenger RNA (mRNA) expression levels of key breast cancer markers and therapeutic target genes according to residual cancer burden (RCB) classification: RCB-0/I, RCB-II, and RCB-III. RESULTS Among hormone receptor-positive samples, there were more luminal A tumors by PAM50 (Prediction Analysis of Microarray 50 [Prosigna], aka Prosigna Breast Cancer Prognostic Gene Signature Assay) in RCB-III than in RCB-0/I and RCB-II (P < .01). The mRNA expressions of ESR1 and PGR were significantly higher, and that of MKI67 was lower in RCB-II and RCB-III than in RCB-0/I. The mRNA expression of cyclin D1 was up-regulated in RCB-III and that of CDKN2A was down-regulated in RCB-III (P = .027 and < .01). Among triple-negative (TN) samples, RCB-III had higher clinical stage and more lymph node-positive samples than RCB-0/1 and RCB-II (P < .01). In both subtypes, VEGF-C expression was significantly higher in RCB-III than in RCB-0/I and RCB-II. CONCLUSION In hormone receptor-positive breast cancer, biological features such as luminal A were associated with RCB; this trend was not observed in TN breast cancer. Further, some targeted therapies should be tested as new strategies after standard neoadjuvant chemotherapy in future clinical trials.
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Affiliation(s)
- Yuko Takahashi
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Takayuki Iwamoto
- Departments of Breast and Endocrine Surgery, Okayama University Hospital, Okayama, Japan.
| | - Yoko Suzuki
- Departments of Breast and Endocrine Surgery, Okayama University Hospital, Okayama, Japan
| | - Yukiko Kajiwara
- Departments of Breast and Endocrine Surgery, Okayama University Hospital, Okayama, Japan
| | - Minami Hatono
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Takahiro Tsukioki
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Kengo Kawada
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Mariko Kochi
- Departments of Breast and Endocrine Surgery, Okayama University Hospital, Okayama, Japan
| | - Hirokuni Ikeda
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Tadahiko Shien
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Naruto Taira
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Junji Matsuoka
- Departments of Palliative and Supportive Medicine, Okayama University Hospital, Okayama, Japan
| | - Hiroyoshi Doihara
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Shinichi Toyooka
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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Ru B, Sun J, Tong Y, Wong CN, Chandra A, Tang ATS, Chow LKY, Wun WL, Levitskaya Z, Zhang J. CR2Cancer: a database for chromatin regulators in human cancer. Nucleic Acids Res 2019; 46:D918-D924. [PMID: 29036683 PMCID: PMC5753221 DOI: 10.1093/nar/gkx877] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/28/2017] [Indexed: 12/19/2022] Open
Abstract
Chromatin regulators (CRs) can dynamically modulate chromatin architecture to epigenetically regulate gene expression in response to intrinsic and extrinsic signalling cues. Somatic alterations or misexpression of CRs might reprogram the epigenomic landscape of chromatin, which in turn lead to a wide range of common diseases, notably cancer. Here, we present CR2Cancer, a comprehensive annotation and visualization database for CRs in human cancer constructed by high throughput data analysis and literature mining. We collected and integrated genomic, transcriptomic, proteomic, clinical and functional information for over 400 CRs across multiple cancer types. We also built diverse types of CR-associated relations, including cancer type dependent (CR-target and miRNA-CR) and independent (protein-protein interaction and drug-target) ones. Furthermore, we manually curated around 6000 items of aberrant molecular alterations and interactions of CRs in cancer development from 5007 publications. CR2Cancer provides a user-friendly web interface to conveniently browse, search and download data of interest. We believe that this database would become a valuable resource for cancer epigenetics investigation and potential clinical application. CR2Cancer is freely available at http://cis.hku.hk/CR2Cancer.
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Affiliation(s)
- Beibei Ru
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Jianlong Sun
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Yin Tong
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Ching Ngar Wong
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Aditi Chandra
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Acacia Tsz So Tang
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Larry Ka Yue Chow
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Wai Lam Wun
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Zarina Levitskaya
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Jiangwen Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
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Lu J, Xu J, Li J, Pan T, Bai J, Wang L, Jin X, Lin X, Zhang Y, Li Y, Sahni N, Li X. FACER: comprehensive molecular and functional characterization of epigenetic chromatin regulators. Nucleic Acids Res 2019; 46:10019-10033. [PMID: 30102398 PMCID: PMC6212842 DOI: 10.1093/nar/gky679] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 08/04/2018] [Indexed: 01/09/2023] Open
Abstract
Epigenetic alterations, a well-recognized cancer hallmark, are driven by chromatin regulators (CRs). However, little is known about the extent of CR deregulation in cancer, and less is known about their common and specialized roles across various cancers. Here, we performed genome-wide analyses and constructed molecular signatures and network profiles of functional CRs in over 10 000 tumors across 33 cancer types. By integration of DNA mutation, genome-wide methylation, transcriptional/post-transcriptional regulation, and protein interaction networks with clinical outcomes, we identified CRs associated with cancer subtypes and clinical prognosis as potential oncogenic drivers. Comparative network analysis revealed principles of CR regulatory specificity and functionality. In addition, we identified common and specific CRs by assessing their prevalence across cancer types. Common CRs tend to be histone modifiers and chromatin remodelers with fundamental roles, whereas specialized CRs are involved in context-dependent functions. Finally, we have made a user-friendly web interface-FACER (Functional Atlas of Chromatin Epigenetic Regulators) available for exploring clinically relevant CRs for the development of CR biomarkers and therapeutic targets. Our integrative analysis reveals specific determinants of CRs across cancer types and presents a resource for investigating disease-associated CRs.
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Affiliation(s)
- Jianping Lu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang 150086, China
| | - Junyi Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Tao Pan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jing Bai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Liqiang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xiyun Jin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xiaoyu Lin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yongsheng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang 150086, China.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nidhi Sahni
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Quantitative and Computational Biosciences (QCB), Baylor College of Medicine, Houston, TX 77030, USA.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang 150086, China
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Ru B, Sun J, Kang Q, Tong Y, Zhang J. A framework for identifying dysregulated chromatin regulators as master regulators in human cancer. Bioinformatics 2019; 35:1805-1812. [PMID: 30358822 DOI: 10.1093/bioinformatics/bty836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/22/2018] [Accepted: 10/24/2018] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Chromatin regulators (CRs) are frequently dysregulated to reprogram the epigenetic landscape of the cancer genome. However, the underpinnings of the dysregulation of CRs and their downstream effectors remain to be elucidated. RESULTS Here, we designed an integrated framework based on multi-omics data to identify candidate master regulatory CRs affected by genomic alterations across eight cancer types in The Cancer Genome Atlas. Most of them showed consistent activated or repressed (i.e. oncogenic or tumor-suppressive) roles in cancer initiation and progression. In order to further explore the insight mechanism of the dysregulated CRs, we developed an R package ModReg based on differential connectivity to identify CRs as modulators of transcription factors (TFs) involved in tumorigenesis. Our analysis revealed that the connectivity between TFs and their target genes (TGs) tended to be disrupted in the patients who had a high expression of oncogenic CRs or low-expression of tumor-suppressive CRs. As a proof-of-principle study, 14 (82.4%) of the top-ranked 17 driver CRs in liver cancer were able to be validated by literature mining or experiments including shRNA knockdown and dCas9-based epigenetic editing. Moreover, we confirmed that CR SIRT7 physically interacted with TF NFE2L2, and positively modulated the transcriptional program of NFE2L2 by affecting ∼64% of its TGs. AVAILABILITY AND IMPLEMENTATION ModReg is freely accessible at http://cis.hku.hk/software/ModReg.tar.gz. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Aranda S, Alcaine-Colet A, Blanco E, Borràs E, Caillot C, Sabidó E, Di Croce L. Chromatin capture links the metabolic enzyme AHCY to stem cell proliferation. SCIENCE ADVANCES 2019; 5:eaav2448. [PMID: 30854431 PMCID: PMC6402848 DOI: 10.1126/sciadv.aav2448] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/28/2019] [Indexed: 05/19/2023]
Abstract
Profiling the chromatin-bound proteome (chromatome) in a simple, direct, and reliable manner might be key to uncovering the role of yet uncharacterized chromatin factors in physiology and disease. Here, we have designed an experimental strategy to survey the chromatome of proliferating cells by using the DNA-mediated chromatin pull-down (Dm-ChP) technology. Our approach provides a global view of cellular chromatome under normal physiological conditions and enables the identification of chromatin-bound proteins de novo. Integrating Dm-ChP with genomic and functional data, we have discovered an unexpected chromatin function for adenosylhomocysteinase, a major one-carbon pathway metabolic enzyme, in gene activation. Our study reveals a new regulatory axis between the metabolic state of pluripotent cells, ribosomal protein production, and cell division during the early phase of embryo development, in which the metabolic flux of methylation reactions is favored in a local milieu.
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Affiliation(s)
- Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Anna Alcaine-Colet
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Claire Caillot
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, Barcelona 08010, Spain
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38
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Genomic characterization of genes encoding histone acetylation modulator proteins identifies therapeutic targets for cancer treatment. Nat Commun 2019; 10:733. [PMID: 30760718 PMCID: PMC6374416 DOI: 10.1038/s41467-019-08554-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/18/2019] [Indexed: 02/07/2023] Open
Abstract
A growing emphasis in anticancer drug discovery efforts has been on targeting histone acetylation modulators. Here we comprehensively analyze the genomic alterations of the genes encoding histone acetylation modulator proteins (HAMPs) in the Cancer Genome Atlas cohort and observe that HAMPs have a high frequency of focal copy number alterations and recurrent mutations, whereas transcript fusions of HAMPs are relatively rare genomic events in common adult cancers. Collectively, 86.3% (63/73) of HAMPs have recurrent alterations in at least 1 cancer type and 16 HAMPs, including 9 understudied HAMPs, are identified as putative therapeutic targets across multiple cancer types. For example, the recurrent focal amplification of BRD9 is observed in 9 cancer types and genetic depletion of BRD9 inhibits tumor growth. Our systematic genomic analysis of HAMPs across a large-scale cancer specimen cohort may facilitate the identification and prioritization of potential drug targets and selection of suitable patients for precision treatment. Targeting histone acetylation modulators (HAMPs) is a promising avenue of drug discovery in cancer research. Here, the authors integrate multi-dimensional genomic profiles to systematically investigate recurrent genomic alterations in HAMPs, identifying potential therapeutic targets for precision epigenetic treatment.
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Rampias T, Karagiannis D, Avgeris M, Polyzos A, Kokkalis A, Kanaki Z, Kousidou E, Tzetis M, Kanavakis E, Stravodimos K, Manola KN, Pantelias GE, Scorilas A, Klinakis A. The lysine-specific methyltransferase KMT2C/MLL3 regulates DNA repair components in cancer. EMBO Rep 2019; 20:embr.201846821. [PMID: 30665945 PMCID: PMC6399616 DOI: 10.15252/embr.201846821] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 12/11/2022] Open
Abstract
Genome‐wide studies in tumor cells have indicated that chromatin‐modifying proteins are commonly mutated in human cancers. The lysine‐specific methyltransferase 2C (KMT2C/MLL3) is a putative tumor suppressor in several epithelia and in myeloid cells. Here, we show that downregulation of KMT2C in bladder cancer cells leads to extensive changes in the epigenetic status and the expression of DNA damage response and DNA repair genes. More specifically, cells with low KMT2C activity are deficient in homologous recombination‐mediated double‐strand break DNA repair. Consequently, these cells suffer from substantially higher endogenous DNA damage and genomic instability. Finally, these cells seem to rely heavily on PARP1/2 for DNA repair, and treatment with the PARP1/2 inhibitor olaparib leads to synthetic lethality, suggesting that cancer cells with low KMT2C expression are attractive targets for therapies with PARP1/2 inhibitors.
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Affiliation(s)
| | | | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Antonis Kokkalis
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Zoi Kanaki
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Evgenia Kousidou
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Maria Tzetis
- Department of Medical Genetics, Medical School, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Emmanouil Kanavakis
- Department of Medical Genetics, Medical School, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece.,University Research Institute for the Study and Treatment of Childhood Genetic and Malignant Diseases, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Stravodimos
- First Department of Urology, "Laiko" General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Kalliopi N Manola
- Laboratory of Health Physics, Radiobiology & Cytogenetics, National Center for Scientific Research (NCSR) "Demokritos", Athens, Greece
| | - Gabriel E Pantelias
- Laboratory of Health Physics, Radiobiology & Cytogenetics, National Center for Scientific Research (NCSR) "Demokritos", Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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Youn A, Kim KI, Rabadan R, Tycko B, Shen Y, Wang S. A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes. BMC Med Genomics 2018; 11:98. [PMID: 30400878 PMCID: PMC6218985 DOI: 10.1186/s12920-018-0425-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 10/19/2018] [Indexed: 01/08/2023] Open
Abstract
Background Recent large-scale cancer sequencing studies have discovered many novel cancer driver genes (CDGs) in human cancers. Some studies also suggest that CDG mutations contribute to cancer-associated epigenomic and transcriptomic alterations across many cancer types. Here we aim to improve our understanding of the connections between CDG mutations and altered cancer cell epigenomes and transcriptomes on pan-cancer level and how these connections contribute to the known association between epigenome and transcriptome. Method Using multi-omics data including somatic mutation, DNA methylation, and gene expression data of 20 cancer types from The Cancer Genome Atlas (TCGA) project, we conducted a pan-cancer analysis to identify CDGs, when mutated, have strong associations with genome-wide methylation or expression changes across cancer types, which we refer as methylation driver genes (MDGs) or expression driver genes (EDGs), respectively. Results We identified 32 MDGs, among which, eight are known chromatin modification or remodeling genes. Many of the remaining 24 MDGs are connected to chromatin regulators through either regulating their transcription or physically interacting with them as potential co-factors. We identified 29 EDGs, 26 of which are also MDGs. Further investigation on target genes’ promoters methylation and expression alteration patterns of these 26 overlapping driver genes shows that hyper-methylation of target genes’ promoters are significantly associated with down-regulation of the same target genes and hypo-methylation of target genes’ promoters are significantly associated with up-regulation of the same target genes. Conclusion This finding suggests a pivotal role for genetically driven changes in chromatin remodeling in shaping DNA methylation and gene expression patterns during tumor development. Electronic supplementary material The online version of this article (10.1186/s12920-018-0425-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ahrim Youn
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York, USA.,The Jackson Laboratory For Genomic Medicine, Farmington, Connecticut, USA
| | - Kyung In Kim
- The Jackson Laboratory For Genomic Medicine, Farmington, Connecticut, USA
| | - Raul Rabadan
- Department of System Biology, Columbia University, New York, New York, USA.,Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | - Benjamin Tycko
- Division of Genetics & Epigenetics, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | - Yufeng Shen
- Department of System Biology, Columbia University, New York, New York, USA.,Department of Biomedical Informatics, Columbia University, New York, New York, USA.,Columbia Genome Center, Columbia University, New York, New York, USA
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York, USA.
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41
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Affiliation(s)
- Jung-Ae Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, South Korea
| | - Minjung Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
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Zaini MN, Patel SA, Syafruddin SE, Rodrigues P, Vanharanta S. Endogenous HIF2A reporter systems for high-throughput functional screening. Sci Rep 2018; 8:12063. [PMID: 30104738 PMCID: PMC6089976 DOI: 10.1038/s41598-018-30499-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/01/2018] [Indexed: 11/24/2022] Open
Abstract
Tissue-specific transcriptional programs control most biological phenotypes, including disease states such as cancer. However, the molecular details underlying transcriptional specificity is largely unknown, hindering the development of therapeutic approaches. Here, we describe novel experimental reporter systems that allow interrogation of the endogenous expression of HIF2A, a critical driver of renal oncogenesis. Using a focused CRISPR-Cas9 library targeting chromatin regulators, we provide evidence that these reporter systems are compatible with high-throughput screening. Our data also suggests redundancy in the control of cancer type-specific transcriptional traits. Reporter systems such as those described here could facilitate large-scale mechanistic dissection of transcriptional programmes underlying cancer phenotypes, thus paving the way for novel therapeutic approaches.
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Affiliation(s)
- M Nazhif Zaini
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge, CB2 0XZ, United Kingdom
| | - Saroor A Patel
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge, CB2 0XZ, United Kingdom
| | - Saiful E Syafruddin
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge, CB2 0XZ, United Kingdom.,UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Jalan Yaa'cob Latiff, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Paulo Rodrigues
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge, CB2 0XZ, United Kingdom
| | - Sakari Vanharanta
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge, CB2 0XZ, United Kingdom.
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43
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Herceg Z, Ghantous A, Wild CP, Sklias A, Casati L, Duthie SJ, Fry R, Issa JP, Kellermayer R, Koturbash I, Kondo Y, Lepeule J, Lima SC, Marsit CJ, Rakyan V, Saffery R, Taylor JA, Teschendorff AE, Ushijima T, Vineis P, Walker CL, Waterland RA, Wiemels J, Ambatipudi S, Esposti DD, Hernandez-Vargas H. Roadmap for investigating epigenome deregulation and environmental origins of cancer. Int J Cancer 2018; 142:874-882. [PMID: 28836271 PMCID: PMC6027626 DOI: 10.1002/ijc.31014] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/25/2017] [Accepted: 08/03/2017] [Indexed: 12/11/2022]
Abstract
The interaction between the (epi)genetic makeup of an individual and his/her environmental exposure record (exposome) is accepted as a determinant factor for a significant proportion of human malignancies. Recent evidence has highlighted the key role of epigenetic mechanisms in mediating gene-environment interactions and translating exposures into tumorigenesis. There is also growing evidence that epigenetic changes may be risk factor-specific ("fingerprints") that should prove instrumental in the discovery of new biomarkers in cancer. Here, we review the state of the science of epigenetics associated with environmental stimuli and cancer risk, highlighting key developments in the field. Critical knowledge gaps and research needs are discussed and advances in epigenomics that may help in understanding the functional relevance of epigenetic alterations. Key elements required for causality inferences linking epigenetic changes to exposure and cancer are discussed and how these alterations can be incorporated in carcinogen evaluation and in understanding mechanisms underlying epigenome deregulation by the environment.
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Affiliation(s)
- Zdenko Herceg
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, Lyon 69008, France
| | - Akram Ghantous
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, Lyon 69008, France
| | - Christopher P. Wild
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, Lyon 69008, France
| | - Athena Sklias
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, Lyon 69008, France
| | - Lavinia Casati
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Susan J. Duthie
- School of Pharmacy and Life Sciences, The Robert Gordon University, Aberdeen, United Kingdom
| | - Rebecca Fry
- Gillings School of Global Public Health, UNC, Chapel Hill, NC
| | - Jean-Pierre Issa
- Fels Institute for Cancer Research & Molecular Biology, Philadelphia, PA
| | | | | | - Yukata Kondo
- Aichi Cancer Center Research Institute, Nagoya, Japan
| | | | | | | | - Vardhman Rakyan
- Centre for Genomics and Child Health, Blizard Institute, London, United Kingdom
| | | | | | - Andrew E. Teschendorff
- Statistical Cancer Genomics, UCL Cancer Institute & Dept. of Woman’s Cancer, University College London, United Kingdom
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China
| | | | - Paolo Vineis
- MRC/PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Cheryl Lyn Walker
- Departments of Molecular & Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX
| | - Robert A. Waterland
- Baylor College of Medicine, USDA/ARS Children’s Nutrition Research Center, Houston, TX
| | - Joe Wiemels
- UCSF School of Medicine, Epidemiology & Biostatistics, San Francisco, CA
| | - Srikant Ambatipudi
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, Lyon 69008, France
| | - Davide Degli Esposti
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, Lyon 69008, France
| | - Hector Hernandez-Vargas
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, Lyon 69008, France
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44
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Wang X, Sheu JJC, Lai MT, Yin-Yi Chang C, Sheng X, Wei L, Gao Y, Wang X, Liu N, Xie W, Chen CM, Ding WY, Sun L. RSF-1 overexpression determines cancer progression and drug resistance in cervical cancer. Biomedicine (Taipei) 2018; 8:4. [PMID: 29480799 PMCID: PMC5825929 DOI: 10.1051/bmdcn/2018080104] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 11/16/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Remodeling spacing factor 1 (RSF-1/HBXAP) has been linked to a variety of cancer types, however, its roles and the therapeutic potential are not clear in cervical cancer. METHODS RSF-1 expression in cancer tissues was analyzed by immunohistochemical staining followed by statistical analysis with SPSS. Anti-RSF-1 studies were performed by treating cells with specific siRNA or a dominant mutant form (RSF-D4). RESULTS RSF-1 expression correlates with cancer progression that strongly-positive staining can be found in 67.7% carcinomas and 66.7% CIN lesions, but none in normal tissues. Such overexpression also associated with increased tumor size, poor differentiation, higher nodal metastasis and advanced clinical stages. Kaplan- Meier analysis confirmed that cancer patients with high RSF-1 levels exhibited a significantly shorter survival time than those with low RSF-1 levels. Downregulation of RSF-1 by siRNA silencing or RSF-D4 reduced cell growth and increased drug sensitivity toward paclitaxel treatment in HeLa cells. CONCLUSIONS RSF-1 participates in the tumor progression of cervical cancer and could be considered as an early prognostic marker for cancer development and clinical outcome. Therapies based on anti-RSF-1 activity may be beneficial for patients with RSF-1 overexpression in their tumors.
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Affiliation(s)
- Xiangyu Wang
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences Jinan 250022 China
- Department of Gynecological Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences Jinan 250117 China
| | - Jim Jinn-Chyuan Sheu
- Institute of Biomedical Sciences, National Sun Yat-sen University Kaohsiung 804 Taiwan
- Human Genetic Center, China Medical University Hospital Taichung 404 Taiwan
- School of Chinese Medicine, China Medical University Taichung 404 Taiwan
| | - Ming-Tsung Lai
- Department of Pathology, Taichung Hospital, Ministry of Health and Welfare Taichung 403 Taiwan
| | | | - Xiugui Sheng
- Department of Gynecological Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences Jinan 250117 China
| | - Ling Wei
- Department of Gynecological Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences Jinan 250117 China
| | - Yongsheng Gao
- Department of Gynecological Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences Jinan 250117 China
| | - Xingwu Wang
- Department of Gynecological Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences Jinan 250117 China
| | - Naifu Liu
- Department of Gynecological Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences Jinan 250117 China
| | - Wenli Xie
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences Jinan 250022 China
| | - Chih-Mei Chen
- Human Genetic Center, China Medical University Hospital Taichung 404 Taiwan
| | - Wendy Y. Ding
- Human Genetic Center, China Medical University Hospital Taichung 404 Taiwan
| | - Li Sun
- Department of Gynecological Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences Jinan 250117 China
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45
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Viarisio D, Müller-Decker K, Accardi R, Robitaille A, Dürst M, Beer K, Jansen L, Flechtenmacher C, Bozza M, Harbottle R, Voegele C, Ardin M, Zavadil J, Caldeira S, Gissmann L, Tommasino M. Beta HPV38 oncoproteins act with a hit-and-run mechanism in ultraviolet radiation-induced skin carcinogenesis in mice. PLoS Pathog 2018; 14:e1006783. [PMID: 29324843 PMCID: PMC5764406 DOI: 10.1371/journal.ppat.1006783] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 11/30/2017] [Indexed: 11/19/2022] Open
Abstract
Cutaneous beta human papillomavirus (HPV) types are suspected to be involved, together with ultraviolet (UV) radiation, in the development of non-melanoma skin cancer (NMSC). Studies in in vitro and in vivo experimental models have highlighted the transforming properties of beta HPV E6 and E7 oncoproteins. However, epidemiological findings indicate that beta HPV types may be required only at an initial stage of carcinogenesis, and may become dispensable after full establishment of NMSC. Here, we further investigate the potential role of beta HPVs in NMSC using a Cre-loxP-based transgenic (Tg) mouse model that expresses beta HPV38 E6 and E7 oncogenes in the basal layer of the skin epidermis and is highly susceptible to UV-induced carcinogenesis. Using whole-exome sequencing, we show that, in contrast to WT animals, when exposed to chronic UV irradiation K14 HPV38 E6/E7 Tg mice accumulate a large number of UV-induced DNA mutations, which increase proportionally with the severity of the skin lesions. The mutation pattern detected in the Tg skin lesions closely resembles that detected in human NMSC, with the highest mutation rate in p53 and Notch genes. Using the Cre-lox recombination system, we observed that deletion of the viral oncogenes after development of UV-induced skin lesions did not affect the tumour growth. Together, these findings support the concept that beta HPV types act only at an initial stage of carcinogenesis, by potentiating the deleterious effects of UV radiation. Many epidemiological and biological findings support the hypothesis that beta HPV types cooperate with UV radiation in the induction of NMSC, the most common form of human cancer. We have previously shown that K14 HPV38 E6/E7 Tg mice, when exposed to long-term UV radiation, developed NMSC, whereas WT animals subjected to identical treatments did not develop any type of skin lesions. Here, we show that the high skin cancer susceptibility of these Tg animals tightly correlates with their tendency to accumulate UV-induced mutations in genes that are frequently mutated in human NMSC. Importantly, deletion of the HPV38 E6 and E7 genes in existing skin lesions did not affect the further growth of the cancer cells. Together, these findings support the model that beta HPV infection is a co-factor in skin carcinogenesis, facilitating the accumulation of the UV-induced DNA mutations.
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Affiliation(s)
| | | | - Rosita Accardi
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Alexis Robitaille
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Matthias Dürst
- Department of Gynecology, Jena University Hospital - Friedrich Schiller University, Jena, Germany
| | - Katrin Beer
- Department of Gynecology, Jena University Hospital - Friedrich Schiller University, Jena, Germany
| | - Lars Jansen
- Department of Gynecology, Jena University Hospital - Friedrich Schiller University, Jena, Germany
| | | | | | | | - Catherine Voegele
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Maude Ardin
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Jiri Zavadil
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | | | - Lutz Gissmann
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
- Department of Botany and Microbiology (honorary member), King Saud University, Riyadh, Saudi Arabia
| | - Massimo Tommasino
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- * E-mail:
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46
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Frigola J, Iturbide A, Lopez-Bigas N, Peiro S, Gonzalez-Perez A. Altered oncomodules underlie chromatin regulatory factors driver mutations. Oncotarget 2017; 7:30748-59. [PMID: 27095575 PMCID: PMC5058714 DOI: 10.18632/oncotarget.8752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 03/31/2016] [Indexed: 11/25/2022] Open
Abstract
Chromatin regulatory factors (CRFs), are known to be involved in tumorigenesis in several cancer types. Nevertheless, the molecular mechanisms through which driver alterations of CRFs cause tumorigenesis remain unknown. Here, we developed a CRFs Oncomodules Discovery approach, which mines several sources of cancer genomics and perturbaomics data. The approach prioritizes sets of genes significantly miss-regulated in primary tumors (oncomodules) bearing mutations of driver CRFs. We applied the approach to eleven TCGA tumor cohorts and uncovered oncomodules potentially associated to mutations of five driver CRFs in three cancer types. Our results revealed, for example, the potential involvement of the mTOR pathway in the development of tumors with loss-of-function mutations of MLL2 in head and neck squamous cell carcinomas. The experimental validation that MLL2 loss-of-function increases the sensitivity of cancer cell lines to mTOR inhibition lends further support to the validity of our approach. The potential oncogenic modules detected by our approach may guide experiments proposing ways to indirectly target driver mutations of CRFs.
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Affiliation(s)
- Joan Frigola
- Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Ane Iturbide
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - Nuria Lopez-Bigas
- Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Sandra Peiro
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - Abel Gonzalez-Perez
- Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
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47
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Neelamraju Y, Gonzalez-Perez A, Bhat-Nakshatri P, Nakshatri H, Janga SC. Mutational landscape of RNA-binding proteins in human cancers. RNA Biol 2017; 15:115-129. [PMID: 29023197 PMCID: PMC5786023 DOI: 10.1080/15476286.2017.1391436] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
RNA Binding Proteins (RBPs) are a class of post-transcriptional regulatory molecules which are increasingly documented to be dysfunctional in cancer genomes. However, our current understanding of these alterations is limited. Here, we delineate the mutational landscape of ∼1300 RBPs in ∼6000 cancer genomes. Our analysis revealed that RBPs have an average of ∼3 mutations per Mb across 26 cancer types. We identified 281 RBPs to be enriched for mutations (GEMs) in at least one cancer type. GEM RBPs were found to undergo frequent frameshift and inframe deletions as well as missense, nonsense and silent mutations when compared to those that are not enriched for mutations. Functional analysis of these RBPs revealed the enrichment of pathways associated with apoptosis, splicing and translation. Using the OncodriveFM framework, we also identified more than 200 candidate driver RBPs that were found to accumulate functionally impactful mutations in at least one cancer. Expression levels of 15% of these driver RBPs exhibited significant difference, when transcriptome groups with and without deleterious mutations were compared. Functional interaction network of the driver RBPs revealed the enrichment of spliceosomal machinery, suggesting a plausible mechanism for tumorogenesis while network analysis of the protein interactions between RBPs unambiguously revealed the higher degree, betweenness and closeness centrality for driver RBPs compared to non-drivers. Analysis to reveal cancer-specific Ribonucleoprotein (RNP) mutational hotspots showed extensive rewiring even among common drivers between cancer types. Knockdown experiments on pan-cancer drivers such as SF3B1 and PRPF8 in breast cancer cell lines, revealed cancer subtype specific functions like selective stem cell features, indicating a plausible means for RBPs to mediate cancer-specific phenotypes. Hence, this study would form a foundation to uncover the contribution of the mutational spectrum of RBPs in dysregulating the post-transcriptional regulatory networks in different cancer types.
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Affiliation(s)
- Yaseswini Neelamraju
- a Department of Bio Health Informatics, School of Informatics and Computing , Indiana University Purdue University , Indianapolis , Indiana , USA
| | - Abel Gonzalez-Perez
- b Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences , Universitat Pompeu Fabra , Barcelona , Spain
| | - Poornima Bhat-Nakshatri
- c Department of Surgery , Indiana University School of Medicine , Indianapolis , Indiana , USA
| | - Harikrishna Nakshatri
- c Department of Surgery , Indiana University School of Medicine , Indianapolis , Indiana , USA.,d Department of Biochemistry & Molecular Biology , Indiana University School of Medicine , Indianapolis , Indiana , USA.,e VA Roudebush Medical Center , Indianapolis , Indiana , USA
| | - Sarath Chandra Janga
- a Department of Bio Health Informatics, School of Informatics and Computing , Indiana University Purdue University , Indianapolis , Indiana , USA.,f Centre for Computational Biology and Bioinformatics , Indiana University School of Medicine , 5021 Health Information and Translational Sciences (HITS), Indianapolis , Indiana , USA.,g Department of Medical and Molecular Genetics , Indiana University School of Medicine , Medical Research and Library Building, Indianapolis , Indiana , USA
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48
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Huskova H, Ardin M, Weninger A, Vargova K, Barrin S, Villar S, Olivier M, Stopka T, Herceg Z, Hollstein M, Zavadil J, Korenjak M. Modeling cancer driver events in vitro using barrier bypass-clonal expansion assays and massively parallel sequencing. Oncogene 2017; 36:6041-6048. [PMID: 28692054 PMCID: PMC5666318 DOI: 10.1038/onc.2017.215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 03/30/2017] [Accepted: 05/12/2017] [Indexed: 12/14/2022]
Abstract
The information on candidate cancer driver alterations available from public databases is often descriptive and of limited mechanistic insight, which poses difficulties for reliable distinction between true driver and passenger events. To address this challenge, we performed in-depth analysis of whole-exome sequencing data from cell lines generated by a barrier bypass-clonal expansion (BBCE) protocol. The employed strategy is based on carcinogen-driven immortalization of primary mouse embryonic fibroblasts and recapitulates early steps of cell transformation. Among the mutated genes were almost 200 COSMIC Cancer Gene Census genes, many of which were recurrently affected in the set of 25 immortalized cell lines. The alterations affected pathways regulating DNA damage response and repair, transcription and chromatin structure, cell cycle and cell death, as well as developmental pathways. The functional impact of the mutations was strongly supported by the manifestation of several known cancer hotspot mutations among the identified alterations. We identified a new set of genes encoding subunits of the BAF chromatin remodeling complex that exhibited Ras-mediated dependence on PRC2 histone methyltransferase activity, a finding that is similar to what has been observed for other BAF subunits in cancer cells. Among the affected BAF complex subunits, we determined Smarcd2 and Smarcc1 as putative driver candidates not yet fully identified by large-scale cancer genome sequencing projects. In addition, Ep400 displayed characteristics of a driver gene in that it showed a mutually exclusive mutation pattern when compared with mutations in the Trrap subunit of the TIP60 complex, both in the cell line panel and in a human tumor data set. We propose that the information generated by deep sequencing of the BBCE cell lines coupled with phenotypic analysis of the mutant cells can yield mechanistic insights into driver events relevant to human cancer development.
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Affiliation(s)
- H Huskova
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - M Ardin
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
| | - A Weninger
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - K Vargova
- Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - S Barrin
- Dynamics of T cell Interactions Team, Institut Cochin, Inserm U1016, Paris, France
| | - S Villar
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
| | - M Olivier
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
| | - T Stopka
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Z Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - M Hollstein
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
- Faculty of Medicine and Health, University of Leeds, LIGHT Laboratories, Leeds, UK
| | - J Zavadil
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
| | - M Korenjak
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
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49
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Exome Sequencing Landscape Analysis in Ovarian Clear Cell Carcinoma Shed Light on Key Chromosomal Regions and Mutation Gene Networks. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:2246-2258. [PMID: 28888422 DOI: 10.1016/j.ajpath.2017.06.012] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 06/08/2017] [Indexed: 12/18/2022]
Abstract
Previous studies have reported genome-wide mutation profile analyses in ovarian clear cell carcinomas (OCCCs). This study aims to identify specific novel molecular alterations by combined analyses of somatic mutation and copy number variation. We performed whole exome sequencing of 39 OCCC samples with 16 matching blood tissue samples. Four hundred twenty-six genes had recurrent somatic mutations. Among the 39 samples, ARID1A (62%) and PIK3CA (51%) were frequently mutated, as were genes such as KRAS (10%), PPP2R1A (10%), and PTEN (5%), that have been reported in previous OCCC studies. We also detected mutations in MLL3 (15%), ARID1B (10%), and PIK3R1 (8%), which are associations not previously reported. Gene interaction analysis and functional assessment revealed that mutated genes were clustered into groups pertaining to chromatin remodeling, cell proliferation, DNA repair and cell cycle checkpointing, and cytoskeletal organization. Copy number variation analysis identified frequent amplification in chr8q (64%), chr20q (54%), and chr17q (46%) loci as well as deletion in chr19p (41%), chr13q (28%), chr9q (21%), and chr18q (21%) loci. Integration of the analyses uncovered that frequently mutated or amplified/deleted genes were involved in the KRAS/phosphatidylinositol 3-kinase (82%) and MYC/retinoblastoma (75%) pathways as well as the critical chromatin remodeling complex switch/sucrose nonfermentable (85%). The individual and integrated analyses contribute details about the OCCC genomic landscape, which could lead to enhanced diagnostics and therapeutic options.
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50
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EZH2 Inhibition by Tazemetostat Results in Altered Dependency on B-cell Activation Signaling in DLBCL. Mol Cancer Ther 2017; 16:2586-2597. [DOI: 10.1158/1535-7163.mct-16-0840] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 05/04/2017] [Accepted: 08/16/2017] [Indexed: 11/16/2022]
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