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Shi A, Lin C, Wang J, Chen Y, Zhong J, Lyu J. EPRIM: An approach of identifying cancer immune-related epigenetic regulators. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102100. [PMID: 38222302 PMCID: PMC10784696 DOI: 10.1016/j.omtn.2023.102100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/08/2023] [Indexed: 01/16/2024]
Abstract
Epigenetic regulation contributes to the dysregulation of gene expression involved in cancer biology. Nevertheless, the roles of epigenetic regulators (ERs) in tumor immunity and immune response remain basically unclear. Here, we developed the epigenetic regulator in immunology (EPRIM) approach to identify immune-related ERs and comprehensively dissected the ER regulation in tumor immune response across 33 cancers. The identified immune-related ERs were related to immune infiltration and could stratify cancer patients into two risk groups in multiple independent datasets. These patient groups were characterized by distinct immune functions, immune infiltrates, driver gene mutations, and prognoses. Furthermore, we constructed an immune ER-based signature and highlighted its potential utility in predicting clinical benefit from immunotherapy and selecting therapeutic agents. Taken together, our identification and evaluation of immune-related ERs highlight the usefulness of EPRIM for the understanding of ERs in immune regulation and the clinical relevance in evaluation of cancer patient prognosis and response to immune checkpoint blockade therapy.
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Affiliation(s)
- Aiai Shi
- Joint Centre of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, People’s Republic of China
- Joint Centre of Translational Medicine, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, People’s Republic of China
- Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Chaohuan Lin
- Postgraduate Training Base Alliance of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, People’s Republic of China
| | - Jilu Wang
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Ying’ao Chen
- Postgraduate Training Base Alliance of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, People’s Republic of China
| | - Jinjin Zhong
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Jie Lyu
- Joint Centre of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, People’s Republic of China
- Joint Centre of Translational Medicine, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, People’s Republic of China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang 325001, People’s Republic of China
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2
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Wang J, Shi A, Lyu J. A comprehensive atlas of epigenetic regulators reveals tissue-specific epigenetic regulation patterns. Epigenetics 2023; 18:2139067. [PMID: 36305095 PMCID: PMC9980636 DOI: 10.1080/15592294.2022.2139067] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Epigenetic machinery contributes to gene regulation in eukaryotic species. However, the machinery including more than 600 epigenetic regulator (ER) genes responsible for reading, writing, and erasing histone modifications and DNA modifications remains largely uncharacterized across species. We compile a comprehensive list of ERs based on an evolutionary analysis across 23 species, which is the most comprehensive ER list in various species until recently. We further perform comparative transcriptomic analyses across different tissues in humans, mice, as well as other amniote species. We observe a consistent tissue-of-origin expression specificity pattern of duplicated ER genes across species and suggest links between expression specificity and ER gene evolution as well as ER function. Additional analyses further suggest that ER duplication can generate tissue-specific ER genes with the same epigenetic substrates, which may be closely related to their regulatory specificity in tissue development. Our work can serve as a foundation to better comprehend the tissue-specific expression patterns of ER genes from an evolutionary perspective and also the functional implications of ERs in tissue-specific epigenetic regulation.
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Affiliation(s)
- Jilu Wang
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, People's Republic of China
| | - Aiai Shi
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, People's Republic of China
| | - Jie Lyu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, People's Republic of China.,Joint Centre of Translational Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China.,Joint Centre of Translational Medicine, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, People's Republic of China.,Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, People's Republic of China
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3
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Martin BJE, Ablondi EF, Goglia C, Mimoso CA, Espinel-Cabrera PR, Adelman K. Global identification of SWI/SNF targets reveals compensation by EP400. Cell 2023; 186:5290-5307.e26. [PMID: 37922899 PMCID: PMC11307202 DOI: 10.1016/j.cell.2023.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 08/11/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023]
Abstract
Mammalian SWI/SNF chromatin remodeling complexes move and evict nucleosomes at gene promoters and enhancers to modulate DNA access. Although SWI/SNF subunits are commonly mutated in disease, therapeutic options are limited by our inability to predict SWI/SNF gene targets and conflicting studies on functional significance. Here, we leverage a fast-acting inhibitor of SWI/SNF remodeling to elucidate direct targets and effects of SWI/SNF. Blocking SWI/SNF activity causes a rapid and global loss of chromatin accessibility and transcription. Whereas repression persists at most enhancers, we uncover a compensatory role for the EP400/TIP60 remodeler, which reestablishes accessibility at most promoters during prolonged loss of SWI/SNF. Indeed, we observe synthetic lethality between EP400 and SWI/SNF in cancer cell lines and human cancer patient data. Our data define a set of molecular genomic features that accurately predict gene sensitivity to SWI/SNF inhibition in diverse cancer cell lines, thereby improving the therapeutic potential of SWI/SNF inhibitors.
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Affiliation(s)
- Benjamin J E Martin
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA
| | - Eileen F Ablondi
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Christine Goglia
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Claudia A Mimoso
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Piero R Espinel-Cabrera
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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4
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Cheng MW, Mitra M, Coller HA. Pan-cancer landscape of epigenetic factor expression predicts tumor outcome. Commun Biol 2023; 6:1138. [PMID: 37973839 PMCID: PMC10654613 DOI: 10.1038/s42003-023-05459-w] [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: 02/08/2023] [Accepted: 10/13/2023] [Indexed: 11/19/2023] Open
Abstract
Oncogenic pathways that drive cancer progression reflect both genetic changes and epigenetic regulation. Here we stratified primary tumors from each of 24 TCGA adult cancer types based on the gene expression patterns of epigenetic factors (epifactors). The tumors for five cancer types (ACC, KIRC, LGG, LIHC, and LUAD) separated into two robust clusters that were better than grade or epithelial-to-mesenchymal transition in predicting clinical outcomes. The majority of epifactors that drove the clustering were also individually prognostic. A pan-cancer machine learning model deploying epifactor expression data for these five cancer types successfully separated the patients into poor and better outcome groups. Single-cell analysis of adult and pediatric tumors revealed that expression patterns associated with poor or worse outcomes were present in individual cells within tumors. Our study provides an epigenetic map of cancer types and lays a foundation for discovering pan-cancer targetable epifactors.
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Affiliation(s)
- Michael W Cheng
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Mithun Mitra
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Hilary A Coller
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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5
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Uncovering Oncogenic Mechanisms of Tumor Suppressor Genes in Breast Cancer Multi-Omics Data. Int J Mol Sci 2022; 23:ijms23179624. [PMID: 36077026 PMCID: PMC9455665 DOI: 10.3390/ijms23179624] [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: 07/03/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
Tumor suppressor genes (TSGs) are essential genes in the development of cancer. While they have many roles in normal cells, mutation and dysregulation of the TSGs result in aberrant molecular processes in cancer cells. Therefore, understanding TSGs and their roles in the oncogenic process is crucial for prevention and treatment of cancer. In this research, multi-omics breast cancer data were used to identify molecular mechanisms of TSGs in breast cancer. Differentially expressed genes and differentially coexpressed genes were identified in four large-scale transcriptomics data from public repositories and multi-omics data analyses of copy number, methylation and gene expression were performed. The results of the analyses were integrated using enrichment analysis and meta-analysis of a p-value summation method. The integrative analysis revealed that TSGs have a significant relationship with genes of gene ontology terms that are related to cell cycle, genome stability, RNA processing and metastasis, indicating the regulatory mechanisms of TSGs on cancer cells. The analysis frame and research results will provide valuable information for the further identification of TSGs in different types of cancers.
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Yedier-Bayram O, Gokbayrak B, Kayabolen A, Aksu AC, Cavga AD, Cingöz A, Kala EY, Karabiyik G, Günsay R, Esin B, Morova T, Uyulur F, Syed H, Philpott M, Cribbs AP, Kung SHY, Lack NA, Onder TT, Bagci-Onder T. EPIKOL, a chromatin-focused CRISPR/Cas9-based screening platform, to identify cancer-specific epigenetic vulnerabilities. Cell Death Dis 2022; 13:710. [PMID: 35973998 PMCID: PMC9381743 DOI: 10.1038/s41419-022-05146-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/24/2022] [Accepted: 07/28/2022] [Indexed: 01/21/2023]
Abstract
Dysregulation of the epigenome due to alterations in chromatin modifier proteins commonly contribute to malignant transformation. To interrogate the roles of epigenetic modifiers in cancer cells, we generated an epigenome-wide CRISPR-Cas9 knockout library (EPIKOL) that targets a wide-range of epigenetic modifiers and their cofactors. We conducted eight screens in two different cancer types and showed that EPIKOL performs with high efficiency in terms of sgRNA distribution and depletion of essential genes. We discovered novel epigenetic modifiers that regulate triple-negative breast cancer (TNBC) and prostate cancer cell fitness. We confirmed the growth-regulatory functions of individual candidates, including SS18L2 and members of the NSL complex (KANSL2, KANSL3, KAT8) in TNBC cells. Overall, we show that EPIKOL, a focused sgRNA library targeting ~800 genes, can reveal epigenetic modifiers that are essential for cancer cell fitness under in vitro and in vivo conditions and enable the identification of novel anti-cancer targets. Due to its comprehensive epigenome-wide targets and relatively high number of sgRNAs per gene, EPIKOL will facilitate studies examining functional roles of epigenetic modifiers in a wide range of contexts, such as screens in primary cells, patient-derived xenografts as well as in vivo models.
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Affiliation(s)
- Ozlem Yedier-Bayram
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Bengul Gokbayrak
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Alisan Kayabolen
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Ali Cenk Aksu
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Ayse Derya Cavga
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
- Biostatistics, Bioinformatics and Data Management Core, KUTTAM, Istanbul, Türkiye
| | - Ahmet Cingöz
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Ezgi Yagmur Kala
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Goktug Karabiyik
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Rauf Günsay
- Koç University School of Medicine, Istanbul, Türkiye
| | - Beril Esin
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Tunc Morova
- Koç University School of Medicine, Istanbul, Türkiye
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Fırat Uyulur
- Koç University Department of Computational Biology, Istanbul, Türkiye
| | - Hamzah Syed
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
- Biostatistics, Bioinformatics and Data Management Core, KUTTAM, Istanbul, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
| | - Martin Philpott
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Adam P Cribbs
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Sonia H Y Kung
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Nathan A Lack
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Tamer T Onder
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye.
- Koç University School of Medicine, Istanbul, Türkiye.
| | - Tugba Bagci-Onder
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye.
- Koç University School of Medicine, Istanbul, Türkiye.
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7
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Vicente ALSA, Novoloaca A, Cahais V, Awada Z, Cuenin C, Spitz N, Carvalho AL, Evangelista AF, Crovador CS, Reis RM, Herceg Z, de Lima Vazquez V, Ghantous A. Cutaneous and acral melanoma cross-OMICs reveals prognostic cancer drivers associated with pathobiology and ultraviolet exposure. Nat Commun 2022; 13:4115. [PMID: 35840550 PMCID: PMC9287446 DOI: 10.1038/s41467-022-31488-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 06/16/2022] [Indexed: 11/08/2022] Open
Abstract
Ultraviolet radiation (UV) is causally linked to cutaneous melanoma, yet the underlying epigenetic mechanisms, known as molecular sensors of exposure, have not been characterized in clinical biospecimens. Here, we integrate clinical, epigenome (DNA methylome), genome and transcriptome profiling of 112 cutaneous melanoma from two multi-ethnic cohorts. We identify UV-related alterations in regulatory regions and immunological pathways, with multi-OMICs cancer driver potential affecting patient survival. TAPBP, the top gene, is critically involved in immune function and encompasses several UV-altered methylation sites that were validated by targeted sequencing, providing cost-effective opportunities for clinical application. The DNA methylome also reveals non UV-related aberrations underlying pathological differences between the cutaneous and 17 acral melanomas. Unsupervised epigenomic mapping demonstrated that non UV-mutant cutaneous melanoma more closely resembles acral rather than UV-exposed cutaneous melanoma, with the latter showing better patient prognosis than the other two forms. These gene-environment interactions reveal translationally impactful mechanisms in melanomagenesis.
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Affiliation(s)
- Anna Luiza Silva Almeida Vicente
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France.
| | - Alexei Novoloaca
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Vincent Cahais
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Zainab Awada
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Natália Spitz
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - André Lopes Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
- Early Detection Prevention and Infections Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Camila Souza Crovador
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Vinicius de Lima Vazquez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
- Department of Surgery-Melanoma and Sarcoma, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France.
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8
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Thakur S, Cahais V, Turkova T, Zikmund T, Renard C, Stopka T, Korenjak M, Zavadil J. Chromatin Remodeler Smarca5 Is Required for Cancer-Related Processes of Primary Cell Fitness and Immortalization. Cells 2022; 11:808. [PMID: 35269430 PMCID: PMC8909548 DOI: 10.3390/cells11050808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 12/04/2022] Open
Abstract
Smarca5, an ATPase of the ISWI class of chromatin remodelers, is a key regulator of chromatin structure, cell cycle and DNA repair. Smarca5 is deregulated in leukemia and breast, lung and gastric cancers. However, its role in oncogenesis is not well understood. Chromatin remodelers often play dosage-dependent roles in cancer. We therefore investigated the epigenomic and phenotypic impact of controlled stepwise attenuation of Smarca5 function in the context of primary cell transformation, a process relevant to tumor formation. Upon conditional single- or double-allele Smarca5 deletion, the cells underwent both accelerated growth arrest and senescence entry and displayed gradually increased sensitivity to genotoxic insults. These phenotypic characteristics were explained by specific remodeling of the chromatin structure and the transcriptome in primary cells prior to the immortalization onset. These molecular programs implicated Smarca5 requirement in DNA damage repair, telomere maintenance, cell cycle progression and in restricting apoptosis and cellular senescence. Consistent with the molecular programs, we demonstrate for the first time that Smarca5-deficient primary cells exhibit dramatically decreased capacity to bypass senescence and immortalize, an indispensable step during cell transformation and cancer development. Thus, Smarca5 plays a crucial role in key homeostatic processes and sustains cancer-promoting molecular programs and cellular phenotypes.
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Affiliation(s)
- Shefali Thakur
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France; (S.T.); (V.C.); (C.R.)
- Faculty of Science, Charles University, 128 43 Prague, Czech Republic; (S.T.)
- Biocev, First Faculty of Medicine, Charles University, 252 50 Vestec, Czech Republic; (T.T.); (T.Z.); (T.S.)
| | - Vincent Cahais
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France; (S.T.); (V.C.); (C.R.)
| | - Tereza Turkova
- Biocev, First Faculty of Medicine, Charles University, 252 50 Vestec, Czech Republic; (T.T.); (T.Z.); (T.S.)
| | - Tomas Zikmund
- Biocev, First Faculty of Medicine, Charles University, 252 50 Vestec, Czech Republic; (T.T.); (T.Z.); (T.S.)
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum, D-81377 München, Germany; (T.Z.)
| | - Claire Renard
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France; (S.T.); (V.C.); (C.R.)
| | - Tomáš Stopka
- Biocev, First Faculty of Medicine, Charles University, 252 50 Vestec, Czech Republic; (T.T.); (T.Z.); (T.S.)
| | - Michael Korenjak
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France; (S.T.); (V.C.); (C.R.)
| | - Jiri Zavadil
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France; (S.T.); (V.C.); (C.R.)
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9
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Bošković M, Roje B, Chung FFL, Gelemanović A, Cahais V, Cuenin C, Khoueiry R, Vilović K, Herceg Z, Terzić J. DNA Methylome Changes of Muscle- and Neuronal-Related Processes Precede Bladder Cancer Invasiveness. Cancers (Basel) 2022; 14:487. [PMID: 35158756 PMCID: PMC8833512 DOI: 10.3390/cancers14030487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/24/2022] Open
Abstract
Bladder cancer (BC) is the ninth leading cause of cancer death with one of the highest recurrence rates among all cancers. One of the main risks for BC development is exposure to nitrosamines present in tobacco smoke or in other products. Aberrant epigenetic (DNA methylation) changes accompanied by deregulated gene expression are an important element of cancer pathogenesis. Therefore, we aimed to determine DNA methylation signatures and their impacts on gene expression in mice treated with N-butyl-N-(4-hydroxybutyl) nitrosamine (BBN), a carcinogen similar to compounds found in tobacco smoke. Following BBN administration mice developed non-invasive or invasive bladder cancers. Surprisingly, muscle- and neuronal-related pathways emerged as the most affected in those tumors. Hypo- and hypermethylation changes were present within non-invasive BC, across CpGs mapping to the genes involved in muscle- and neuronal-related pathways, however, methylation differences were not sufficient to affect the expression of the majority of associated genes. Conversely, invasive tumors displayed hypermethylation changes that were linked with alterations in gene expression profiles. Together, these findings indicate that bladder cancer progression could be revealed through methylation profiling at the pre-invasive cancer stage that could assist monitoring of cancer patients and guide novel therapeutic approaches.
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Affiliation(s)
- Maria Bošković
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000 Split, Croatia; (M.B.); (B.R.); (K.V.)
| | - Blanka Roje
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000 Split, Croatia; (M.B.); (B.R.); (K.V.)
| | - Felicia Fei-Lei Chung
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; (F.F.-L.C.); (V.C.); (C.C.); (R.K.)
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Jalan Universiti, Bandar Sunway, Petaling Jaya 47500, Selangor, Malaysia
| | - Andrea Gelemanović
- Biology of Robustness Group, Mediterranean Institute for Life Sciences (MedILS), Šetalište Ivana Meštrovića 45, 21000 Split, Croatia;
| | - Vincent Cahais
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; (F.F.-L.C.); (V.C.); (C.C.); (R.K.)
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; (F.F.-L.C.); (V.C.); (C.C.); (R.K.)
| | - Rita Khoueiry
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; (F.F.-L.C.); (V.C.); (C.C.); (R.K.)
| | - Katarina Vilović
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000 Split, Croatia; (M.B.); (B.R.); (K.V.)
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; (F.F.-L.C.); (V.C.); (C.C.); (R.K.)
| | - Janoš Terzić
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000 Split, Croatia; (M.B.); (B.R.); (K.V.)
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10
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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Sklias A, Halaburkova A, Vanzan L, Jimenez NF, Cuenin C, Bouaoun L, Cahais V, Ythier V, Sallé A, Renard C, Durand G, Le Calvez-Kelm F, Khoueiry R, Murr R, Herceg Z. Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation. Nucleic Acids Res 2021; 49:9738-9754. [PMID: 34403459 PMCID: PMC8464064 DOI: 10.1093/nar/gkab697] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/14/2021] [Indexed: 12/24/2022] Open
Abstract
Estrogen hormones are implicated in a majority of breast cancers and estrogen receptor alpha (ER), the main nuclear factor mediating estrogen signaling, orchestrates a complex molecular circuitry that is not yet fully elucidated. Here, we investigated genome-wide DNA methylation, histone acetylation and transcription after estradiol (E2) deprivation and re-stimulation to better characterize the ability of ER to coordinate gene regulation. We found that E2 deprivation mostly resulted in DNA hypermethylation and histone deacetylation in enhancers. Transcriptome analysis revealed that E2 deprivation leads to a global down-regulation in gene expression, and more specifically of TET2 demethylase that may be involved in the DNA hypermethylation following short-term E2 deprivation. Further enrichment analysis of transcription factor (TF) binding and motif occurrence highlights the importance of ER connection mainly with two partner TF families, AP-1 and FOX. These interactions take place in the proximity of E2 deprivation-mediated differentially methylated and histone acetylated enhancers. Finally, while most deprivation-dependent epigenetic changes were reversed following E2 re-stimulation, DNA hypermethylation and H3K27 deacetylation at certain enhancers were partially retained. Overall, these results show that inactivation of ER mediates rapid and mostly reversible epigenetic changes at enhancers, and bring new insight into early events, which may ultimately lead to endocrine resistance.
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Affiliation(s)
- Athena Sklias
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Andrea Halaburkova
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Ludovica Vanzan
- Department of Genetic Medicine and Development (GEDEV), University of Geneva, Geneva, Switzerland
| | - Nora Fernandez Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country 48940, Spain
| | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Liacine Bouaoun
- Section of Environment and Radiation, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Victor Ythier
- Department of Genetic Medicine and Development (GEDEV), University of Geneva, Geneva, Switzerland
| | - Aurélie Sallé
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Claire Renard
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Geoffroy Durand
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Florence Le Calvez-Kelm
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Rita Khoueiry
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Rabih Murr
- Department of Genetic Medicine and Development (GEDEV), University of Geneva, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
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Karkossa I, Raps S, von Bergen M, Schubert K. Systematic Review of Multi-Omics Approaches to Investigate Toxicological Effects in Macrophages. Int J Mol Sci 2020; 21:E9371. [PMID: 33317022 PMCID: PMC7764599 DOI: 10.3390/ijms21249371] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 12/19/2022] Open
Abstract
Insights into the modes of action (MoAs) of xenobiotics are of utmost importance for the definition of adverse outcome pathways (AOPs), which are essential for a mechanism-based risk assessment. A well-established strategy to reveal MoAs of xenobiotics is the use of omics. However, often an even more comprehensive approach is needed, which can be achieved using multi-omics. Since the immune system plays a central role in the defense against foreign substances and pathogens, with the innate immune system building a first barrier, we systematically reviewed multi-omics studies investigating the effects of xenobiotics on macrophages. Surprisingly, only nine publications were identified, combining proteomics with transcriptomics or metabolomics. We summarized pathways and single proteins, transcripts, or metabolites, which were described to be affected upon treatment with xenobiotics in the reviewed studies, thus revealing a broad range of effects. In summary, we show that macrophages are a relevant model system to investigate the toxicological effects induced by xenobiotics. Furthermore, the multi-omics approaches led to a more comprehensive overview compared to only one omics layer with slight advantages for combinations that complement each other directly, e.g., proteome and metabolome.
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Affiliation(s)
- Isabel Karkossa
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (I.K.); (S.R.); (M.v.B.)
| | - Stefanie Raps
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (I.K.); (S.R.); (M.v.B.)
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (I.K.); (S.R.); (M.v.B.)
- Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (I.K.); (S.R.); (M.v.B.)
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