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Yates J, Boeva V. Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype: a pan-cancer analysis. Brief Bioinform 2022; 23:6520307. [PMID: 35134107 PMCID: PMC8921629 DOI: 10.1093/bib/bbab610] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/06/2021] [Accepted: 12/30/2021] [Indexed: 12/25/2022] Open
Abstract
Numerous cancer types have shown to present hypermethylation of CpG islands, also known as a CpG island methylator phenotype (CIMP), often associated with survival variation. Despite extensive research on CIMP, the etiology of this variability remains elusive, possibly due to lack of consistency in defining CIMP. In this work, we utilize a pan-cancer approach to further explore CIMP, focusing on 26 cancer types profiled in the Cancer Genome Atlas (TCGA). We defined CIMP systematically and agnostically, discarding any effects associated with age, gender or tumor purity. We then clustered samples based on their most variable DNA methylation values and analyzed resulting patient groups. Our results confirmed the existence of CIMP in 19 cancers, including gliomas and colorectal cancer. We further showed that CIMP was associated with survival differences in eight cancer types and, in five, represented a prognostic biomarker independent of clinical factors. By analyzing genetic and transcriptomic data, we further uncovered potential drivers of CIMP and classified them in four categories: mutations in genes directly involved in DNA demethylation; mutations in histone methyltransferases; mutations in genes not involved in methylation turnover, such as KRAS and BRAF; and microsatellite instability. Among the 19 CIMP-positive cancers, very few shared potential driver events, and those drivers were only IDH1 and SETD2 mutations. Finally, we found that CIMP was strongly correlated with tumor microenvironment characteristics, such as lymphocyte infiltration. Overall, our results indicate that CIMP does not exhibit a pan-cancer manifestation; rather, general dysregulation of CpG DNA methylation is caused by heterogeneous mechanisms.
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Affiliation(s)
- Josephine Yates
- Institute for Machine Learning, Department of Computer Science, ETH Zürich, Zurich 8092, Switzerland
| | - Valentina Boeva
- Institute for Machine Learning, Department of Computer Science, ETH Zürich, Zurich 8092, Switzerland.,Swiss Institute for Bioinformatics (SIB), Zürich, Switzerland.,Cochin Institute, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, Paris 75014, France
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2
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Paweł K, Maria Małgorzata S. CpG Island Methylator Phenotype-A Hope for the Future or a Road to Nowhere? Int J Mol Sci 2022; 23:ijms23020830. [PMID: 35055016 PMCID: PMC8777692 DOI: 10.3390/ijms23020830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023] Open
Abstract
The CpG island methylator phenotype (CIMP) can be regarded as the most notable emanation of epigenetic instability in cancer. Since its discovery in the late 1990s, CIMP has been extensively studied, mainly in colorectal cancers (CRC) and gliomas. Consequently, knowledge on molecular and pathological characteristics of CIMP in CRC and other tumour types has rapidly expanded. Concordant and widespread hypermethylation of multiple CpG islands observed in CIMP in multiple cancers raised hopes for future epigenetically based diagnostics and treatments of solid tumours. However, studies on CIMP in solid tumours were hampered by a lack of generalisability and reproducibility of epigenetic markers. Moreover, CIMP was not a satisfactory marker in predicting clinical outcomes. The idea of targeting epigenetic abnormalities such as CIMP for cancer therapy has not been implemented for solid tumours, either. Twenty-one years after its discovery, we aim to cover both the fundamental and new aspects of CIMP and its future application as a diagnostic marker and target in anticancer therapies.
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3
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Willscher E, Hopp L, Kreuz M, Schmidt M, Hakobyan S, Arakelyan A, Hentschel B, Jones DTW, Pfister SM, Loeffler M, Loeffler-Wirth H, Binder H. High-Resolution Cartography of the Transcriptome and Methylome Landscapes of Diffuse Gliomas. Cancers (Basel) 2021; 13:3198. [PMID: 34206856 PMCID: PMC8268631 DOI: 10.3390/cancers13133198] [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: 06/03/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 02/01/2023] Open
Abstract
Molecular mechanisms of lower-grade (II-III) diffuse gliomas (LGG) are still poorly understood, mainly because of their heterogeneity. They split into astrocytoma- (IDH-A) and oligodendroglioma-like (IDH-O) tumors both carrying mutations(s) at the isocitrate dehydrogenase (IDH) gene and into IDH wild type (IDH-wt) gliomas of glioblastoma resemblance. We generated detailed maps of the transcriptomes and DNA methylomes, revealing that cell functions divided into three major archetypic hallmarks: (i) increased proliferation in IDH-wt and, to a lesser degree, IDH-O; (ii) increased inflammation in IDH-A and IDH-wt; and (iii) the loss of synaptic transmission in all subtypes. Immunogenic properties of IDH-A are diverse, partly resembling signatures observed in grade IV mesenchymal glioblastomas or in grade I pilocytic astrocytomas. We analyzed details of coregulation between gene expression and DNA methylation and of the immunogenic micro-environment presumably driving tumor development and treatment resistance. Our transcriptome and methylome maps support personalized, case-by-case views to decipher the heterogeneity of glioma states in terms of data portraits. Thereby, molecular cartography provides a graphical coordinate system that links gene-level information with glioma subtypes, their phenotypes, and clinical context.
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Affiliation(s)
- Edith Willscher
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Lydia Hopp
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Markus Kreuz
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, Universität of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.K.); (B.H.); (M.L.)
| | - Maria Schmidt
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Siras Hakobyan
- Research Group of Bioinformatics, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
| | - Arsen Arakelyan
- Research Group of Bioinformatics, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
| | - Bettina Hentschel
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, Universität of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.K.); (B.H.); (M.L.)
| | - David T. W. Jones
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Stefan M. Pfister
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Markus Loeffler
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, Universität of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.K.); (B.H.); (M.L.)
| | - Henry Loeffler-Wirth
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Hans Binder
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
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4
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Padmanabhan N, Kyon HK, Boot A, Lim K, Srivastava S, Chen S, Wu Z, Lee HO, Mukundan VT, Chan C, Chan YK, Xuewen O, Pitt JJ, Isa ZFA, Xing M, Lee MH, Tan ALK, Ting SHW, Luftig MA, Kappei D, Kruger WD, Bian J, Ho YS, Teh M, Rozen SG, Tan P. Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation. Genome Biol 2021; 22:167. [PMID: 34074348 PMCID: PMC8170989 DOI: 10.1186/s13059-021-02375-2] [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: 01/28/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
Background CIMP (CpG island methylator phenotype) is an epigenetic molecular subtype, observed in multiple malignancies and associated with the epigenetic silencing of tumor suppressors. Currently, for most cancers including gastric cancer (GC), mechanisms underlying CIMP remain poorly understood. We sought to discover molecular contributors to CIMP in GC, by performing global DNA methylation, gene expression, and proteomics profiling across 14 gastric cell lines, followed by similar integrative analysis in 50 GC cell lines and 467 primary GCs. Results We identify the cystathionine beta-synthase enzyme (CBS) as a highly recurrent target of epigenetic silencing in CIMP GC. Likewise, we show that CBS epimutations are significantly associated with CIMP in various other cancers, occurring even in premalignant gastroesophageal conditions and longitudinally linked to clinical persistence. Of note, CRISPR deletion of CBS in normal gastric epithelial cells induces widespread DNA methylation changes that overlap with primary GC CIMP patterns. Reflecting its metabolic role as a gatekeeper interlinking the methionine and homocysteine cycles, CBS loss in vitro also causes reductions in the anti-inflammatory gasotransmitter hydrogen sulfide (H2S), with concomitant increase in NF-κB activity. In a murine genetic model of CBS deficiency, preliminary data indicate upregulated immune-mediated transcriptional signatures in the stomach. Conclusions Our results implicate CBS as a bi-faceted modifier of aberrant DNA methylation and inflammation in GC and highlights H2S donors as a potential new therapy for CBS-silenced lesions. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02375-2.
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Affiliation(s)
- Nisha Padmanabhan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Huang Kie Kyon
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Arnoud Boot
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Kevin Lim
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Supriya Srivastava
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Zhiyuan Wu
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
| | - Hyung-Ok Lee
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Vineeth T Mukundan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Charlene Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Yarn Kit Chan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Ong Xuewen
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Zul Fazreen Adam Isa
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Manjie Xing
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Ming Hui Lee
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Angie Lay Keng Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Shamaine Ho Wei Ting
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke Centre for Virology, Duke University School of Medicine, Durham, NC, USA
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Warren D Kruger
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Jinsong Bian
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore.,National University of Singapore (Suzhou) Research Institute, Suzhou, 215123, China
| | - Ying Swan Ho
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Ming Teh
- Department of Pathology, National University of Singapore, Singapore, 119228, Singapore
| | - Steve George Rozen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Patrick Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore. .,Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Genome Institute of Singapore, Singapore, 138672, Singapore. .,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, 169856, Singapore. .,Singapore Gastric Cancer Consortium, Singapore, 119074, Singapore. .,Department of Physiology, National University of Singapore, Singapore, 117593, Singapore.
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5
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Li L, Li N, Liu N, Huo F, Zheng J. MBD2 Correlates with a Poor Prognosis and Tumor Progression in Renal Cell Carcinoma. Onco Targets Ther 2020; 13:10001-10012. [PMID: 33116585 PMCID: PMC7548338 DOI: 10.2147/ott.s256226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/27/2020] [Indexed: 01/21/2023] Open
Abstract
Purpose DNA methylation plays an important role in regulating gene expression. Methyl-CpG-binding domain (MBD) proteins recognize and bind to methylated DNA, which mediate gene silencing by the interaction with deacetylases and histone methyltransferases. MBD2 has been reported in various human cancers; however, its clinical implication and potential regulatory role in renal cell carcinoma (RCC) have not been elaborated. Materials and Methods In the study, we estimated the expression and prognostic value of MBD2 in RCC cell lines and tissues by Western blotting and immunohistochemistry. The associations of MBD2 expression and pathological characters and survival in RCC patients were performed using χ2 and Kaplan-Meier survival analysis, respectively. Univariate and multivariable Cox regression analyses suggested the independent predictors in RCC prognosis. The functional role of MBD2 in RCC progression was assessed by in vitro cell experiments. In addition, we identified the MBD2-mediated alterations of protein-related proliferation and EMT markers in RCC cells after MBD2 overexpression and knockdown. Results We found that the protein levels of MBD2 were upregulated in RCC cells and tissues. High MBD2 expression was related to TNM stage and predicted poorer survival in RCC. Enforced expression of MBD2 significantly promoted the proliferation, cycle progress, invasion and migration of RCC cells in vitro. However, downregulating MBD2 remarkably weakened the above cell functions. Mechanistically, the promotive effect of MBD2 overexpression may be regulated by its effects onp21, p53 and Cyclin D1 expression and EMT process. Conclusion These results indicated that MBD2confers an oncogenic function in the malignant progression of RCC. MBD2 could be served as a meaningful prognostic biomarker and a latent therapeutic target in RCC patients.
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Affiliation(s)
- Liantao Li
- Cancer Institute, Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou 221000, People's Republic of China
| | - Na Li
- Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| | - Nianli Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou 221000, People's Republic of China
| | - Fuchun Huo
- Department of Pathology, Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| | - Junnian Zheng
- Cancer Institute, Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China
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6
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Samad A, Haque F, Nain Z, Alam R, Al Noman MA, Rahman Molla MH, Hossen MS, Islam MR, Khan MI, Ahammad F. Computational assessment of MCM2 transcriptional expression and identification of the prognostic biomarker for human breast cancer. Heliyon 2020; 6:e05087. [PMID: 33024849 PMCID: PMC7530310 DOI: 10.1016/j.heliyon.2020.e05087] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/09/2020] [Accepted: 09/24/2020] [Indexed: 12/24/2022] Open
Abstract
Minichromosome maintenance protein 2 (MCM2) is a highly conserved protein from the MCM protein family that plays an important role in eukaryotic DNA replication as well as in cell cycle progression. In addition, it maintains the ploidy level consistency in eukaryotic cells, hence, mutations or alteration of this protein could result in the disintegration of the fine-tuned molecular machinery that can lead to uncontrolled cell proliferation. Moreover, MCM2 has been found to be an important marker for progression and prognosis in different cancers. Therefore, we aimed to analyze the MCM2 expression and the associated outcome in breast cancer (BC) patients based on the publicly available online databases. In this study, server-based gene expression analyses indicate the upregulation of MCM2 (p < 10-6; fold change>2.0) in various BC subtypes as compared to the respective normal tissues. Besides, the evaluation of histological sections from healthy and cancer tissues showed strong staining signals indicating higher expression of MCM2 protein. The overexpression of MCM2 was significantly correlated to promoter methylation and was related to patients' clinical features. Further, mutation analysis suggested missense as the predominant type of mutation (71.4%) with 18 copy-number alterations and 0.2% mutation frequency in the MCM2 gene. This study revealed a significant correlation (Cox p ≤ 0.05) between the higher MCM2 expression and lower patient survival. Finally, we identified the co-expressed genes with gene ontological features and signaling pathways associated in BC development. We believe that this study will provide a basis for MCM2 to be a significant biomarker for human BC prognosis.
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Affiliation(s)
- Abdus Samad
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Farhana Haque
- Department of Biotechnology and Genetic Engineering, Khulna University, Khulna, 9208, Bangladesh
| | - Zulkar Nain
- Department of Genetic Engineering and Biotechnology, Faculty of Sciences and Engineering, East West University, Dhaka, 1212, Bangladesh.,Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003, Bangladesh
| | - Rahat Alam
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.,Molecular and Cellular Biology Laboratory, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Abdullah Al Noman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.,Molecular and Cellular Biology Laboratory, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Mohammad Habibur Rahman Molla
- Institute of Marine Sciences and Fisheries, University of Chittagong, Chittagong, 4331, Bangladesh.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Md Saddam Hossen
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Raquibul Islam
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Iqbal Khan
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.,Department of Biotechnology and Genetic Engineering, Khulna University, Khulna, 9208, Bangladesh
| | - Foysal Ahammad
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.,Molecular and Cellular Biology Laboratory, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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Scherer M, Nazarov PV, Toth R, Sahay S, Kaoma T, Maurer V, Vedeneev N, Plass C, Lengauer T, Walter J, Lutsik P. Reference-free deconvolution, visualization and interpretation of complex DNA methylation data using DecompPipeline, MeDeCom and FactorViz. Nat Protoc 2020; 15:3240-3263. [PMID: 32978601 DOI: 10.1038/s41596-020-0369-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
DNA methylation profiling offers unique insights into human development and diseases. Often the analysis of complex tissues and cell mixtures is the only feasible option to study methylation changes across large patient cohorts. Since DNA methylomes are highly cell type specific, deconvolution methods can be used to recover cell type-specific information in the form of latent methylation components (LMCs) from such 'bulk' samples. Reference-free deconvolution methods retrieve these components without the need for DNA methylation profiles of purified cell types. Currently no integrated and guided procedure is available for data preparation and subsequent interpretation of deconvolution results. Here, we describe a three-stage protocol for reference-free deconvolution of DNA methylation data comprising: (i) data preprocessing, confounder adjustment using independent component analysis (ICA) and feature selection using DecompPipeline, (ii) deconvolution with multiple parameters using MeDeCom, RefFreeCellMix or EDec and (iii) guided biological inference and validation of deconvolution results with the R/Shiny graphical user interface FactorViz. Our protocol simplifies the analysis and guides the initial interpretation of DNA methylation data derived from complex samples. The harmonized approach is particularly useful to dissect and evaluate cell heterogeneity in complex systems such as tumors. We apply the protocol to lung cancer methylomes from The Cancer Genome Atlas (TCGA) and show that our approach identifies the proportions of stromal cells and tumor-infiltrating immune cells, as well as associations of the detected components with clinical parameters. The protocol takes slightly >3 d to complete and requires basic R skills.
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Affiliation(s)
- Michael Scherer
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany.,Computational Biology, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Petr V Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Reka Toth
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Thoracic Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Shashwat Sahay
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany.,Center for Digital Health, Berlin Institute of Health and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Tony Kaoma
- Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Valentin Maurer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Lengauer
- Computational Biology, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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8
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He H, Chen D, Cui S, Wu G, Piao H, Wang X, Ye P, Jin S. HDNA methylation data-based molecular subtype classification related to the prognosis of patients with hepatocellular carcinoma. BMC Med Genomics 2020; 13:118. [PMID: 32831081 PMCID: PMC7447581 DOI: 10.1186/s12920-020-00770-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 08/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background DNA methylation is a common chemical modification of DNA in the carcinogenesis of hepatocellular carcinoma (HCC). Methods In this bioinformatics analysis, 348 liver cancer samples were collected from the Cancer Genome Atlas (TCGA) database to analyse specific DNA methylation sites that affect the prognosis of HCC patients. Results 10,699 CpG sites (CpGs) that were significantly related to the prognosis of patients were clustered into 7 subgroups, and the samples of each subgroup were significantly different in various clinical pathological data. In addition, by calculating the level of methylation sites in each subgroup, 119 methylation sites (corresponding to 105 genes) were selected as specific methylation sites within the subgroups. Moreover, genes in the corresponding promoter regions in which the above specific methylation sites were located were subjected to signalling pathway enrichment analysis, and it was discovered that these genes were enriched in the biological pathways that were reported to be closely correlated with HCC. Additionally, the transcription factor enrichment analysis revealed that these genes were mainly enriched in the transcription factor KROX. A naive Bayesian classification model was used to construct a prognostic model for HCC, and the training and test data sets were used for independent verification and testing. Conclusion This classification method can well reflect the heterogeneity of HCC samples and help to develop personalized treatment and accurately predict the prognosis of patients.
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Affiliation(s)
- Hui He
- Department of Laparoscopic Surgery, the First Affiliated Hospital of Dalian Medical University, Lianhe Road 193#, Shahekou District, Dalian, 116000, Liaoning Province, China
| | - Di Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd, Dalian, 116023, China
| | - Shimeng Cui
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China
| | - Gang Wu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of China Medical University, Shenyang, 110042, Liaoning Province, China
| | - Hailong Piao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd, Dalian, 116023, China
| | - Xun Wang
- Department of Laparoscopic Surgery, the First Affiliated Hospital of Dalian Medical University, Lianhe Road 193#, Shahekou District, Dalian, 116000, Liaoning Province, China
| | - Peng Ye
- Department of Urological Surgery, Liaoning Cancer Hospital & Institute, Shenyang, 110042, Liaoning Province, China
| | - Shi Jin
- Department of Laparoscopic Surgery, the First Affiliated Hospital of Dalian Medical University, Lianhe Road 193#, Shahekou District, Dalian, 116000, Liaoning Province, China.
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9
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Pan-cancer analysis of clinical relevance of alternative splicing events in 31 human cancers. Oncogene 2019; 38:6678-6695. [PMID: 31391553 DOI: 10.1038/s41388-019-0910-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 06/21/2019] [Accepted: 07/10/2019] [Indexed: 01/16/2023]
Abstract
Alternative splicing represents a critical posttranscriptional regulation of gene expression, which contributes to the protein complexity and mRNA processing. Defects of alternative splicing including genetic alteration and/or altered expression of both pre-mRNA and trans-acting factors give rise to many cancers. By integrally analyzing clinical data and splicing data from TCGA and SpliceSeq databases, a number of splicing events were found clinically relevant in tumor samples. Alternative splicing of KLK2 (KLK2_51239) was found as a potential inducement of nonsense-mediated mRNA decay and associated with poor survival in prostate cancer. Consensus K-means clustering analysis indicated that alternative splicing events could be potentially used for molecular subtype classification of cancers. By random forest survival algorithm, prognostic prediction signatures with well performances were constructed for 31 cancers by using survival-associated alternative splicing events. Furthermore, an online tool for visualization of Kaplan-Meier plots of splicing events in 31 cancers was explored. Briefly, alternative splicing was found of significant clinical relevance with cancers.
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Su KY, Li MC, Lee NW, Ho BC, Cheng CL, Chuang YC, Yu SL, Guo YL. Perinatal polychlorinated biphenyls and polychlorinated dibenzofurans exposure are associated with DNA methylation changes lasting to early adulthood: Findings from Yucheng second generation. ENVIRONMENTAL RESEARCH 2019; 170:481-486. [PMID: 30640082 DOI: 10.1016/j.envres.2019.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/29/2018] [Accepted: 01/02/2019] [Indexed: 05/17/2023]
Abstract
Epigenome-wide DNA methylation has not been studied in men perinatally exposed to PCBs and dioxins. Therefore, we examined whether perinatal exposure to polychlorinated biphenyls (PCBs) and polychlorinated dibenzofurans (PCDFs) induces sustained methylation changes lasting to early adulthood. We used the Illumina HumanMethylation450 BeadChip to assess DNA methylation in whole blood among Yucheng second generation (people perinatal exposed to high PCBs and PCDFs) compared with referents. Thirty male offspring from the Yucheng cohort were randomly selected and matched with 30 male offspring from the Yucheng' neighborhood referents with similar backgrounds. Methylation differences between the Yucheng second generation and non-exposed referents were identified using a P value < 1.06 × 10-7. Differential DNA methylation with epigenome-wide statistical significance was observed for 20 CpGs mapped to 11 genes, and 19 CpGs were correlated with gestational levels of PCBs or PCDF toxic equivalency (PCDF-TEQ) with the same direction of effect. Among the 11 genes, AHRR and CYP1A1 are involved in the aryl hydrocarbon receptor signaling pathway known to mediate dioxin toxicity. MYO1G, FRMD4A, ARL4C, OLFM1, and WWC3 were previously reported to be related to carcinogenesis. This is the first study examining genome-wide DNA methylation among people perinatally exposed to high concentrations of PCBs and PCDFs. We observed novel differential methylation of several genes, indicating that modifications of DNA methylation associated with perinatal PCB and PCDF exposure may persist in exposed offspring for more than 20 years. Furthermore, involvement of several carcinogesis-related genes suggested a potential in utero epigenetic mechanisms.
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Affiliation(s)
- Kang-Yi Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 100, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 100, Taiwan; NTU Center for Genomic Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan
| | - Ming-Chieh Li
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli, 350, Taiwan; Department of Public Health, China Medical University College of Public Health, Taichung 404, Taiwan
| | - Nian-Wei Lee
- Institute of Occupational Medicine and Industrial Hygiene, National Taiwan University College of Public Health, Taipei, 100, Taiwan; Department of Environmental and Occupational Medicine, National Taiwan University Hospital, Yun-Lin Branch, Yunlin, 640, Taiwan
| | - Bing-Ching Ho
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 100, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 100, Taiwan; NTU Center for Genomic Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan
| | - Chiou-Ling Cheng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 100, Taiwan; NTU Center for Genomic Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan
| | - Yu-Chen Chuang
- Department of Environmental and Occupational Medicine, National Taiwan University and National Taiwan University Hospital, Taipei, 100, Taiwan
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 100, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 100, Taiwan; NTU Center for Genomic Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan; Department of Pathology and Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan; Institute of Medical Device and Imaging, College of Medicine, National Taiwan University, Taipei, 100, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, 100, Taiwan.
| | - Yue Leon Guo
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli, 350, Taiwan; Institute of Occupational Medicine and Industrial Hygiene, National Taiwan University College of Public Health, Taipei, 100, Taiwan; Department of Environmental and Occupational Medicine, National Taiwan University and National Taiwan University Hospital, Taipei, 100, Taiwan.
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Karpinski P, Patai AV, Hap W, Kielan W, Laczmanska I, Sasiadek MM. Multilevel omic data clustering reveals variable contribution of methylator phenotype to integrative cancer subtypes. Epigenomics 2018; 10:1289-1299. [PMID: 29896967 DOI: 10.2217/epi-2018-0057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AIM We aimed to assess to what extent CpG island methylator phenotype (CIMP) contributes to cancer subtypes obtained by multilevel omic data analysis. MATERIALS & METHODS 16 The Cancer Genome Atlas datasets encompassing three data layers in 4688 tumor samples were analyzed. We identified cancer integrative subtypes (ISs) by the use of similarity network fusion and consensus clustering. CIMP high (CIMP-H) associated ISs were profiled by gene sets and transcriptional regulators enrichment analysis. RESULTS & CONCLUSION In nine out of 16 cancer datasets CIMP-H clusters significantly overlaped with unique ISs. The contribution of CIMP-H on integrative molecular profiling is variable; therefore, only in a subset of cancer types does CIMP-H contribute to homogenous integrative subtype. CIMP-H associated ISs are heterogenous groups with regard to deregulated pathways and transcriptional regulators.
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Affiliation(s)
- Pawel Karpinski
- Department of Genetics; Wroclaw Medical University, Wroclaw, Poland
| | - Arpad V Patai
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Wojciech Hap
- 2nd Department of General & Oncological Surgery, Wroclaw Medical University, Wroclaw, Poland
| | - Wojciech Kielan
- 2nd Department of General & Oncological Surgery, Wroclaw Medical University, Wroclaw, Poland
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