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Lucchini S, Constantinou M, Marino S. Unravelling the mosaic: Epigenetic diversity in glioblastoma. Mol Oncol 2024. [PMID: 39148319 DOI: 10.1002/1878-0261.13706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 06/21/2024] [Accepted: 07/23/2024] [Indexed: 08/17/2024] Open
Abstract
Glioblastoma is the most common primary malignant brain tumour. Despite decades of intensive research in the disease, its prognosis remains poor, with an average survival of only 14 months after diagnosis. The remarkable level of intra- and interpatient heterogeneity is certainly contributing to the lack of progress in tackling this tumour. Epigenetic dysregulation plays an important role in glioblastoma biology and significantly contributes to intratumour heterogeneity. However, it is becoming increasingly clear that it also contributes to intertumour heterogeneity, which historically had mainly been linked to diverse genetic events occurring in different patients. In this review, we explore how DNA methylation, chromatin remodelling, microRNA (miRNA) dysregulation, and long noncoding RNA (lncRNA) alterations contribute to intertumour heterogeneity in glioblastoma, including its implications for advanced tumour stratification, which is the essential first step for developing more effective patient-specific therapeutic approaches.
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Affiliation(s)
- Sara Lucchini
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
| | - Myrianni Constantinou
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
| | - Silvia Marino
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
- Barts Brain Tumour Centre, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
- Barts Health NHS Trust, London, UK
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2
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Cheng JC, Swarup N, Morselli M, Huang WL, Aziz M, Caggiano C, Kordi M, Patel A, Chia D, Kim Y, Li F, Wei F, Zaitlen N, Krysan K, Dubinett S, Pellegrini M, Wong DW. Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA. Nucleic Acids Res 2024; 52:e50. [PMID: 38797520 PMCID: PMC11194076 DOI: 10.1093/nar/gkae276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 05/29/2024] Open
Abstract
Whole-genome bisulfite sequencing (BS-Seq) measures cytosine methylation changes at single-base resolution and can be used to profile cell-free DNA (cfDNA). In plasma, ultrashort single-stranded cfDNA (uscfDNA, ∼50 nt) has been identified together with 167 bp double-stranded mononucleosomal cell-free DNA (mncfDNA). However, the methylation profile of uscfDNA has not been described. Conventional BS-Seq workflows may not be helpful because bisulfite conversion degrades larger DNA into smaller fragments, leading to erroneous categorization as uscfDNA. We describe the '5mCAdpBS-Seq' workflow in which pre-methylated 5mC (5-methylcytosine) single-stranded adapters are ligated to heat-denatured cfDNA before bisulfite conversion. This method retains only DNA fragments that are unaltered by bisulfite treatment, resulting in less biased uscfDNA methylation analysis. Using 5mCAdpBS-Seq, uscfDNA had lower levels of DNA methylation (∼15%) compared to mncfDNA and was enriched in promoters and CpG islands. Hypomethylated uscfDNA fragments were enriched in upstream transcription start sites (TSSs), and the intensity of enrichment was correlated with expressed genes of hemopoietic cells. Using tissue-of-origin deconvolution, we inferred that uscfDNA is derived primarily from eosinophils, neutrophils, and monocytes. As proof-of-principle, we show that characteristics of the methylation profile of uscfDNA can distinguish non-small cell lung carcinoma from non-cancer samples. The 5mCAdpBS-Seq workflow is recommended for any cfDNA methylation-based investigations.
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Affiliation(s)
- Jordan C Cheng
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Neeti Swarup
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marco Morselli
- Department of Molecular, Cell, and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Wei-Lun Huang
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan, Taiwan
| | - Mohammad Aziz
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christa Caggiano
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Misagh Kordi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - David Chia
- Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yong Kim
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Feng Li
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fang Wei
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Noah Zaitlen
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Kostyantyn Krysan
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Steve Dubinett
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David T W Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
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3
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Hu S, Tao J, Peng M, Ye Z, Chen Z, Chen H, Yu H, Wang B, Fan JB, Ni B. Accurate detection of early-stage lung cancer using a panel of circulating cell-free DNA methylation biomarkers. Biomark Res 2023; 11:45. [PMID: 37101220 PMCID: PMC10134678 DOI: 10.1186/s40364-023-00486-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/14/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Lung cancer remains the leading cause of cancer mortality worldwide. Early detection of lung cancer helps improve treatment and survival. Numerous aberrant DNA methylations have been reported in early-stage lung cancer. Here, we sought to identify novel DNA methylation biomarkers that could potentially be used for noninvasive early diagnosis of lung cancers. METHODS This prospective-specimen collection and retrospective-blinded-evaluation trial enrolled a total of 317 participants (198 tissues and 119 plasmas) comprising healthy controls, patients with lung cancer and benign disease between January 2020 and December 2021. Tissue and plasma samples were subjected to targeted bisulfite sequencing with a lung cancer specific panel targeting 9,307 differential methylation regions (DMRs). DMRs associated with lung cancer were identified by comparing the methylation profiles of tissue samples from patients with lung cancer and benign disease. Markers were selected with minimum redundancy and maximum relevance algorithm. A prediction model for lung cancer diagnosis was built through logistic regression algorithm and validated independently in tissue samples. Furthermore, the performance of this developed model was evaluated in a set of plasma cell-free DNA (cfDNA) samples. RESULTS We identified 7 DMRs corresponding to 7 differentially methylated genes (DMGs) including HOXB4, HOXA7, HOXD8, ITGA4, ZNF808, PTGER4, and B3GNTL1 that were highly associated with lung cancer by comparing the methylation profiles of lung cancer and benign nodule tissue. Based on the 7-DMR biomarker panel, we developed a new diagnostic model in tissue samples, termed "7-DMR model", to distinguish lung cancers from benign diseases, achieving AUCs of 0.97 (95%CI: 0.93-1.00)/0.96 (0.92-1.00), sensitivities of 0.89 (0.82-0.95)/0.92 (0.86-0.98), specificities of 0.94 (0.89-0.99)/1.00 (1.00-1.00), and accuracies of 0.90 (0.84-0.96)/0.94 (0.89-0.99) in the discovery cohort (n = 96) and the independent validation cohort (n = 81), respectively. Furthermore, the 7-DMR model was applied to noninvasive discrimination of lung cancers and non-lung cancers including benign lung diseases and healthy controls in an independent validation cohort of plasma samples (n = 106), yielding an AUC of 0.94 (0.86-1.00), sensitivity of 0.81 (0.73-0.88), specificity of 0.98 (0.95-1.00), and accuracy of 0.93 (0.89-0.98). CONCLUSION The 7 novel DMRs could be promising methylation biomarkers that merits further development as a noninvasive test for early detection of lung cancer.
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Affiliation(s)
- Shuo Hu
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | | | | | - Zhujia Ye
- Anchordx Medical Co., Ltd, Guangzhou, China
| | - Zhiwei Chen
- Anchordx Medical Co., Ltd, Guangzhou, China
- AnchorDx Inc, Fremont, CA, USA
| | | | - Haifeng Yu
- The Fifth People's Hospital of Wuxi, Wuxi, China
| | - Bo Wang
- Anchordx Medical Co., Ltd, Guangzhou, China.
| | - Jian-Bing Fan
- Anchordx Medical Co., Ltd, Guangzhou, China.
- Department of Pathology, Southern Medical University, Guangzhou, China.
| | - Bin Ni
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.
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4
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Sun J, Chen J. [Research Progress of DNA Methylation in Cisplatin Resistance in Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2023; 26:52-58. [PMID: 36792081 PMCID: PMC9987084 DOI: 10.3779/j.issn.1009-3419.2023.101.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
As one of the most common malignant tumors, lung cancer poses a serious threat to human life and health. The platinum-based drug cisplatin (DDP) is used as the first-line treatment for lung cancer. The poor prognosis of lung cancer is mostly due to developed resistance to cisplatin, which poses a serious treatment challenge. The mechanism of cisplatin resistance is complex and unclear. Numerous studies have shown that DNA methylation plays a crucial role in the emergence of lung cancer cisplatin resistance. DNA hypermethylation results in the deactivation of numerous drug resistance genes and tumor suppressor genes through a change in chromatin conformation. Finding new therapeutic targets and indicators to predict the therapeutic effect can be aided by elucidating the complex mechanism. In order to discover novel strategies to overcome cisplatin resistance in lung cancer, this paper discusses DNA methylation-mediated cisplatin resistance and offers an overview of current demethylation procedures.
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Affiliation(s)
- Jinzhe Sun
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian 116000, China
| | - Jun Chen
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian 116000, China
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5
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Jie C, Li R, Cheng Y, Wang Z, Wu Q, Xie C. Prospects and feasibility of synergistic therapy with radiotherapy, immunotherapy, and DNA methyltransferase inhibitors in non-small cell lung cancer. Front Immunol 2023; 14:1122352. [PMID: 36875059 PMCID: PMC9981667 DOI: 10.3389/fimmu.2023.1122352] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/09/2023] [Indexed: 02/19/2023] Open
Abstract
The morbidity and mortality of lung cancer are increasing, seriously threatening human health and life. Non-small cell lung cancer (NSCLC) has an insidious onset and is not easy to be diagnosed in its early stage. Distant metastasis often occurs and the prognosis is poor. Radiotherapy (RT) combined with immunotherapy, especially with immune checkpoint inhibitors (ICIs), has become the focus of research in NSCLC. The efficacy of immunoradiotherapy (iRT) is promising, but further optimization is necessary. DNA methylation has been involved in immune escape and radioresistance, and becomes a game changer in iRT. In this review, we focused on the regulation of DNA methylation on ICIs treatment resistance and radioresistance in NSCLC and elucidated the potential synergistic effects of DNA methyltransferases inhibitors (DNMTis) with iRT. Taken together, we outlined evidence suggesting that a combination of DNMTis, RT, and immunotherapy could be a promising treatment strategy to improve NSCLC outcomes.
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Affiliation(s)
- Chen Jie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Rumeng Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yajie Cheng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhihao Wang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiuji Wu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
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6
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Cox OT, O’Sullivan N, Tresse E, Ward S, Buckley N, O’Connor R. PDLIM2 is highly expressed in Breast Cancer tumour-associated macrophages and is required for M2 macrophage polarization. Front Oncol 2022; 12:1028959. [DOI: 10.3389/fonc.2022.1028959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/04/2022] [Indexed: 12/03/2022] Open
Abstract
The PDZ-LIM domain-containing protein 2 (PDLIM2) regulates cell polarity and the protein stability of key transcription factors in epithelial and hemopoietic cells. We previously reported that PDLIM2 is more highly expressed in Triple Negative Breast Cancer (TNBC) than in other breast cancer types or normal breast tissue. In the course of the TNBC study, it was noted that PDLIM2 was highly expressed in the stroma of PDLIM2-expressing tumours. Here, we investigated the phenotype of these stromal cells and whether any infiltrating immune population was linked to PDLIM2 expression. We found that high PDLIM2 expression in breast tumours was associated with higher levels of infiltrating M2 macrophages, but was not associated with infiltrating T cell sub-populations. We then tested whether PDLIM2 contributes to macrophage differentiation or function by using cultures of bone marrow-derived macrophages from wildtype and Pdlim2 knockout mice. This demonstrated that PDLIM2 is required for naïve macrophage migration and for the full adoption of IL-4-induced M2 polarization, including expression of M2 phenotypic markers, cell adhesion and cell migration. TLR4-, TLR3- or IFNγ-induced M1 macrophage activity was less dependent on PDLIM2. Finally, analysis of publicly available breast cancer datasets showed that high PDLIM2 expression is associated with increased M2 macrophage infiltration. We conclude that PDLIM2 expression influences the tumour associated stroma and, in particular, M2 macrophage infiltration that may contribute to the progression of TNBC or other subsets of breast cancer.
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7
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Lau SCM, Pan Y, Velcheti V, Wong KK. Squamous cell lung cancer: Current landscape and future therapeutic options. Cancer Cell 2022; 40:1279-1293. [PMID: 36270277 DOI: 10.1016/j.ccell.2022.09.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/19/2022] [Accepted: 09/27/2022] [Indexed: 01/09/2023]
Abstract
Squamous cell lung cancers (lung squamous cell carcinomas [LUSCs]) are associated with high mortality and a lack of therapies specific to this disease. Although recurrent molecular aberrations are present in LUSCs, efforts to develop targeted therapies against receptor tyrosine kinases, signaling transduction, and cell cycle checkpoints in LUSCs were met with significant challenges. The present therapeutic landscape focuses on epigenetic therapies to modulate the expression of lineage-dependent survival pathways and undruggable oncogenes. Another important therapeutic approach is to exploit metabolic vulnerabilities unique to LUSCs. These novel therapies may synergize with immune checkpoint inhibitors in the right therapeutic context. For example, the recognition that alterations in KEAP1-NFE2L2 in LUSCs affected antitumor immune responses created unique opportunities for targeted, metabolic, and immune combinations. This article provides a perspective on how lessons learned from the past influence the current therapeutic landscape and opportunities for future drug development for LUSCs.
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Affiliation(s)
- Sally C M Lau
- Department of Medical Oncology, Laura & Issac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, Smilow Building 10th Floor, Suite 1001, New York, NY 10016, USA
| | - Yuanwang Pan
- Department of Medical Oncology, Laura & Issac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, Smilow Building 10th Floor, Suite 1001, New York, NY 10016, USA
| | - Vamsidhar Velcheti
- Department of Medical Oncology, Laura & Issac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, Smilow Building 10th Floor, Suite 1001, New York, NY 10016, USA
| | - Kwok Kin Wong
- Department of Medical Oncology, Laura & Issac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, Smilow Building 10th Floor, Suite 1001, New York, NY 10016, USA.
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8
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Wu Q, Yan Y, Shi S, Qi Q, Han J. DNMT3b-mediated SPAG6 promoter hypermethylation affects lung squamous cell carcinoma development through the JAK/STAT pathway. Am J Transl Res 2022; 14:6964-6977. [PMID: 36398260 PMCID: PMC9641444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND DNA methylation controls the transcription of genes and is involved in the development of lung cancer. Our preliminary bioinformatics prediction revealed that sperm associated antigen 6 (SPAG6) was considerably hypermethylated in lung squamous cell carcinoma (LUSC). Thus, this study aimed to probe the mechanism underlying its hypermethylation. METHODS The effect of DNA methylation of SPAG6 on its expression in LUSC was analyzed. The contributors to SPAG6 DNA hypermethylation were sought. CCK-8, EdU, and Transwell assays were carried out to assess the malignant phenotype of LUSC cells. KEGG pathway enrichment analysis was used to screen for pathways affected by SPAG6, which were confirmed by dual-luciferase assays. Bioinformatics analysis was conducted to dissect the impact of SPAG6 on the immune response and cancer cell stemness in LUSC. RESULTS DNA methyltransferase 3b (DNMT3b)-mediated hypermethylation of the SPAG6 promoter in LUSC led to SPAG6 downregulation. SPAG6 reverted the malignant phenotype of LUSC cells. SPAG6 regulated the JAK/STAT pathway by inhibiting the transcription of STAT1 and STAT3. The expression of SPAG6 was positively related to immune infiltration in LUSC and inversely related to the expressions of the immunosuppressive genes CTLA4 and PDCD1. SPAG6 expression was negatively correlated with cancer cell stemness in LUSC, and its expression inhibited the expressions of Nanog, ALDH1, and Sox2, markers of cancer cell stemness. CONCLUSIONS DNMT3b-mediated SPAG6 promoter hypermethylation activates the JAK/STAT pathway to promote LUSC progression.
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Affiliation(s)
- Qianbiao Wu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical UniversityNo. 6, Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Yibo Yan
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical UniversityNo. 6, Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Shuo Shi
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical UniversityNo. 6, Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Quan Qi
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical UniversityNo. 6, Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Jiahui Han
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical UniversityNo. 6, Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, China
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Hoang PH, Landi MT. DNA Methylation in Lung Cancer: Mechanisms and Associations with Histological Subtypes, Molecular Alterations, and Major Epidemiological Factors. Cancers (Basel) 2022; 14:cancers14040961. [PMID: 35205708 PMCID: PMC8870477 DOI: 10.3390/cancers14040961] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/14/2021] [Accepted: 02/11/2022] [Indexed: 01/27/2023] Open
Abstract
Lung cancer is the major leading cause of cancer-related mortality worldwide. Multiple epigenetic factors-in particular, DNA methylation-have been associated with the development of lung cancer. In this review, we summarize the current knowledge on DNA methylation alterations in lung tumorigenesis, as well as their associations with different histological subtypes, common cancer driver gene mutations (e.g., KRAS, EGFR, and TP53), and major epidemiological risk factors (e.g., sex, smoking status, race/ethnicity). Understanding the mechanisms of DNA methylation regulation and their associations with various risk factors can provide further insights into carcinogenesis, and create future avenues for prevention and personalized treatments. In addition, we also highlight outstanding questions regarding DNA methylation in lung cancer to be elucidated in future studies.
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10
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Zhang J, Li Q, Sun Q, Wang B, Cui Y, Lou C, Yao Y, Zhang Y. Epigenetic modifications inhibit the expression of MARVELD1 and in turn tumorigenesis by regulating the Wnt/β-catenin pathway in pan-cancer. J Cancer 2022; 13:225-242. [PMID: 34976185 PMCID: PMC8692698 DOI: 10.7150/jca.63608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/21/2021] [Indexed: 12/15/2022] Open
Abstract
MARVEL domain-containing 1 (MARVELD1) is one of the MARVEL domain-containing proteins. Expression of MARVELD1 in tumor and non-tumor tissues, the relationship between its expression and cancer prognosis, and upstream regulation of MARVELD1 were examined using pan-cancer data from The Cancer Genome Atlas. MARVELD1 expression was significantly downregulated in tissues used for pan-cancer analysis compared to that in normal tissues. Low expression of MARVELD1 was associated with poor disease outcomes in pan-cancer. Colon cancer patients with low expression of MARVELD1 had worse progression free survival and overall survival than those with high expression levels in our cohort. Hypermethylation and histone modification in the MARVELD1 promoter locus synergistically affected its expression in pan-cancer. The function of MARVELD1 in colon cancer remains to be studied. Gene Ontology enrichment analysis revealed that MARVELD1 may modulate processes associated with inhibition of tumorigenesis in colon cancer. Both upstream transcription factors and downstream functional enrichment of MARVELD1 were related to the Wnt/β-catenin signaling pathway. Overexpression of MARVELD1 inhibited the expression of β-catenin and its entry into the nucleus. MARVELD1 also inhibited the proliferation, migration, and invasion of colon cancer cells. With Wnt/β-catenin activator LiCl treatment, rescue experiments demonstrated that the role of MARVELD1 in colon cancer progression was dependent on the Wnt/β-catenin pathway. These results indicate that MARVELD1 acts as a tumor suppressor and inhibits tumorigenesis via the Wnt/β-catenin pathway.
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Affiliation(s)
- Jingchun Zhang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang Province, China
| | - Qingwei Li
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang Province, China
| | - Qinliang Sun
- Department of Ultrasound, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Bojun Wang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang Province, China
| | - Ying Cui
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang Province, China
| | - Changjie Lou
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang Province, China
| | - Yuanfei Yao
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang Province, China
| | - Yanqiao Zhang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, China
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11
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Peralta-Arrieta I, Trejo-Villegas OA, Armas-López L, Ceja-Rangel HA, Ordóñez-Luna MDC, Pineda-Villegas P, González-López MA, Ortiz-Quintero B, Mendoza-Milla C, Zatarain-Barrón ZL, Arrieta O, Zúñiga J, Ávila-Moreno F. Failure to EGFR-TKI-based therapy and tumoural progression are promoted by MEOX2/GLI1-mediated epigenetic regulation of EGFR in the human lung cancer. Eur J Cancer 2021; 160:189-205. [PMID: 34844838 DOI: 10.1016/j.ejca.2021.10.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/26/2021] [Indexed: 01/22/2023]
Abstract
BACKGROUND Mesenchyme homeobox-2 (MEOX2)-mediated regulation of glioma-associated oncogene-1 (GLI1) has been associated with poor overall survival, conferring chemoresistance in lung cancer. However, the role of MEOX2/GLI1 in resistance to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs)-based therapy remains unexplored in human lung cancer. METHODS Functional assays using genetic silencing strategy by short hairpin RNAs, as well as cytotoxic (tetrazolium dye MTT) and clonogenic assays, were performed to evaluate MEOX2/GLI1-induced malignancy capacity in lung cancer cells. Further analysis performed includes western blot, qPCR and ChIP-qPCR assays to identify whether MEOX2/GLI1 promote EGFR/AKT/ERK activation, as well as EGFR overexpression through epigenetic mechanisms. Finally, preclinical tumour progression in vivo and progression-free disease interval analyses in patients treated with EGFR-TKI were included. RESULTS Overexpressed MEOX2/GLI1 in both EGFR wild-type and EGFR/KRAS-mutated lung cancer cells were detected and involved in the activation/expression of EGFR/AKT/ERK biomarkers. In addition, MEOX2/GLI1 was shown to be involved in the increased proliferation of tumour cells and resistance capacity to cisplatin, EGFR-TKIs (erlotinib and AZD9291 'osimertinib'), AZD8542-SMO, and AZD6244-MEKK1/2. In addition, we identified that MEOX2/GLI1 promote lung tumour cells progression in vivo and are clinically associated with poorer progression-free disease intervals. Finally, both MEOX2 and GLI1 were detected to be epigenetically involved in EGFR expression by reducing both repressive markers polycomb-EZH2 and histone H3K27me3, but, particularly, increasing an activated histone profile H3K27Ac/H3K4me3 at EGFR-gene enhancer-promoter sequences that probably representing a novel EGFR-TKI-based therapy resistance mechanism. CONCLUSION MEOX2/GLI1 promote resistance to cisplatin and EGFR-TKI-based therapy in lung cancer cells, modulating EGFR/AKT/ERK signalling pathway activation, as well as inducing an aberrant epigenetic modulation of the EGFR-gene expression in human lung cancer.
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Affiliation(s)
- Irlanda Peralta-Arrieta
- Universidad Nacional Autónoma de México (UNAM), Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores (FES) Iztacala, Tlalnepantla de Baz, 54090, Estado de México, Mexico.
| | - Octavio A Trejo-Villegas
- Universidad Nacional Autónoma de México (UNAM), Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores (FES) Iztacala, Tlalnepantla de Baz, 54090, Estado de México, Mexico.
| | - Leonel Armas-López
- Universidad Nacional Autónoma de México (UNAM), Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores (FES) Iztacala, Tlalnepantla de Baz, 54090, Estado de México, Mexico.
| | - Hugo A Ceja-Rangel
- Universidad Nacional Autónoma de México (UNAM), Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores (FES) Iztacala, Tlalnepantla de Baz, 54090, Estado de México, Mexico.
| | - María Del Carmen Ordóñez-Luna
- Universidad Nacional Autónoma de México (UNAM), Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores (FES) Iztacala, Tlalnepantla de Baz, 54090, Estado de México, Mexico.
| | - Priscila Pineda-Villegas
- Universidad Nacional Autónoma de México (UNAM), Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores (FES) Iztacala, Tlalnepantla de Baz, 54090, Estado de México, Mexico.
| | - Marco A González-López
- Unidad Funcional de Oncología Torácica, Instituto Nacional de Cancerología (INCan), Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, 14080, Ciudad de México, Mexico.
| | - Blanca Ortiz-Quintero
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calz de Tlalpan, 14080, Ciudad de México, Mexico.
| | - Criselda Mendoza-Milla
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calz de Tlalpan, 14080, Ciudad de México, Mexico.
| | - Zyanya L Zatarain-Barrón
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Campus Ciudad de México, Mexico.
| | - Oscar Arrieta
- Unidad Funcional de Oncología Torácica, Instituto Nacional de Cancerología (INCan), Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, 14080, Ciudad de México, Mexico.
| | - Joaquín Zúñiga
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calz de Tlalpan, 14080, Ciudad de México, Mexico; Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Campus Ciudad de México, Mexico.
| | - Federico Ávila-Moreno
- Universidad Nacional Autónoma de México (UNAM), Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores (FES) Iztacala, Tlalnepantla de Baz, 54090, Estado de México, Mexico; Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calz de Tlalpan, 14080, Ciudad de México, Mexico.
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Guo ZS, Qu Z. PDLIM2: Signaling pathways and functions in cancer suppression and host immunity. Biochim Biophys Acta Rev Cancer 2021; 1876:188630. [PMID: 34571051 DOI: 10.1016/j.bbcan.2021.188630] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/30/2021] [Accepted: 09/22/2021] [Indexed: 12/20/2022]
Abstract
PDZ and LIM domains-containing proteins play pivotal functions in cell cytoskeleton organization, cell polarization and differentiation. As a key member of the family, PDLIM2 regulates stability and activity of transcription factors such as NF-κB, STATs and β-catenin, and thus exert it functions in inflammation, immunity, and cancer. PDLIM2 functions as a tumor suppressor in multiple tissues and it is often genetically mutated or epigenetically silenced in human cancers derived from lung, breast, ovarian and other histologies. However, in certain types of cancers, PDLIM2 may promote cancer cell proliferation and metastases. Therefore, PDLIM2 is added to a long list of genes that can function as tumor suppressor or oncogenic protein. During tumorigenesis induced by oncogenic viruses, PDLIM2 is a key target. Through promotion of NF-κB/RelA and STAT3 degradation, PDLIM2 enhances expression of proteins involved in antigen presentation and promotes T-cell activation while repressing multidrug resistance genes, thereby rendering mutated cells susceptible to immune surveillance and cytotoxicity mediated by immune cells and chemotherapeutic drugs. Intriguingly, PDLIM2 in alveolar macrophages (AMs) plays key roles in monitoring lung tumorigenesis, as its selective genetic deletion leads to constitutive activation of STAT3, driving monocyte differentiation to AMs with pro-tumorigenic polarization and activation. PDLIM2 has also been explored as a therapeutic target for cancer therapy. At the end of this review, we provide perspectives on this important molecule and discuss the future directions of both basic and translational studies.
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Affiliation(s)
- Zong Sheng Guo
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Zhaoxia Qu
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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Abstract
The epigenetic landscape, which in part includes DNA methylation, chromatin organization, histone modifications, and noncoding RNA regulation, greatly contributes to the heterogeneity that makes developing effective therapies for lung cancer challenging. This review will provide an overview of the epigenetic alterations that have been implicated in all aspects of cancer pathogenesis and progression as well as summarize clinical applications for targeting epigenetics in the treatment of lung cancer.
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Affiliation(s)
- Yvonne L Chao
- Department of Medicine, Division of Hematology and Oncology, University of North Carolina, Chapel Hill, North Carolina 27514, USA
| | - Chad V Pecot
- Department of Medicine, Division of Hematology and Oncology, University of North Carolina, Chapel Hill, North Carolina 27514, USA
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Liu W, Jiang K, Wang J, Mei T, Zhao M, Huang D. Upregulation of GNPNAT1 Predicts Poor Prognosis and Correlates With Immune Infiltration in Lung Adenocarcinoma. Front Mol Biosci 2021; 8:605754. [PMID: 33842535 PMCID: PMC8027087 DOI: 10.3389/fmolb.2021.605754] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Glucosamine 6-phosphate N-acetyltransferase (GNPNAT1) is a key enzyme in the hexosamine biosynthetic pathway (HBP), which functions as promoting proliferation in some tumors, yet its potential biological function and mechanism in lung adenocarcinoma (LUAD) have not been explored. METHODS The mRNA differential expression of GNPNAT1 in LUAD and normal tissues was analyzed using the Cancer Genome Atlas (TCGA) database and validated by real-time PCR. The clinical value of GNPNAT1 in LUAD was investigated based on the data from the TCGA database. Then, immunohistochemistry (IHC) of GNPNAT1 was applied to verify the expression and clinical significance in LUAD from the protein level. The relationship between GNPNAT1 and epigenetics was explored using the cBioPortal database, and the miRNAs regulating GNPNAT1 were found using the miRNA database. The association between GNPNAT1 expression and tumor-infiltrating immune cells in LUAD was observed through the Tumor IMmune Estimation Resource (TIMER). Finally, Gene set enrichment analysis (GSEA) was used to explore the biological signaling pathways involved in GNPNAT1 in LUAD. RESULTS GNPNAT1 was upregulated in LUAD compared with normal tissues, which was verified through qRT-PCR in different cell lines (P < 0.05), and associated with patients' clinical stage, tumor size, and lymphatic metastasis status (all P < 0.01). Kaplan-Meier (KM) analysis suggested that patients with upregulated GNPNAT1 had a relatively poor prognosis (P < 0.0001). Furthermore, multivariate Cox regression analysis indicated that GNPNAT1 was an independent prognostic factor for LUAD (OS, TCGA dataset: HR = 1.028, 95% CI: 1.013-1.044, P < 0.001; OS, validation set: HR = 1.313, 95% CI: 1.130-1.526, P < 0.001). GNPNAT1 overexpression was correlated with DNA copy amplification (P < 0.0001), low DNA methylation (R = -0.52, P < 0.0001), and downregulation of hsa-miR-30d-3p (R = -0.17, P < 0.001). GNPNAT1 expression was linked to B cells (R = -0.304, P < 0.0001), CD4+T cells (R = -0.218, P < 0.0001), and dendritic cells (R = -0.137, P = 0.002). Eventually, GSEA showed that the signaling pathways of the cell cycle, ubiquitin-mediated proteolysis, mismatch repair and p53 were enriched in the GNPNAT1 overexpression group. CONCLUSION GNPNAT1 may be a potential prognostic biomarker and novel target for intervention in LUAD.
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Affiliation(s)
| | | | | | | | | | - Dingzhi Huang
- Department of Thoracic Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
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Huang G, Zhang J, Gong L, Liu D, Wang X, Chen Y, Guo S. Specific Lung Squamous Cell Carcinoma Prognosis-Subtype Distinctions Based on DNA Methylation Patterns. Med Sci Monit 2021; 27:e929524. [PMID: 33661858 PMCID: PMC7942209 DOI: 10.12659/msm.929524] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background Lung squamous cell carcinoma (LUSC) is one of the major types of non-small-cell lung cancer. Epigenetic alterations, such as DNA methylation, have been recognized to be closely associated with the tumorigenesis and progression. Material/Methods In this study, we investigated the prognosis subgroups and assessed their correlation with clinical characteristics in LUSC using a methylation array acquired from The Cancer Genome Atlas (TCGA) database. Results A total of 196 DNA methylation sites exhibited a significant association with patient prognosis, and patients were further stratified into 7 prognosis subgroups based upon the consensus clustering. The patients in every subgroup were different in terms of prognosis and TNM stage. In addition, we found these 196 significant methylation sites corresponded to 258 genes. The function enrichment analysis revealed that these 258 genes enriched in biological pathways were closely related to cancers, such as DNA methylation and demethylation, cell cycle DNA replication, regulation of signal transduction by p53 class mediator, and genetic imprinting. Subsequently, we determined the levels of methylation sites in 7 subgroups, and found 24 intra-subgroup-specific methylation sites. Meanwhile, we selected 3 subgroups-specific methylation sites to construct the prognosis model for LUSC patients using multivariate Cox proportional risk regression model analysis. This model can effectively predict the prognosis of LUSC patients. Conclusions Our study identified a new classification of LUSC into 7 prognosis subgroups on the basis of DNA methylation data in TCGA, which demonstrated that molecular subtypes are independent factor for prognosis in LUSC. This may provide a more detailed explanation for LUSC heterogeneity. Additionally, this classification will contribute to discovery of new biomarkers of LUSC and provide more accurate subdivision of LUSC. Furthermore, these specific DNA methylation sites and corresponding genes can serve as biomarkers for early diagnosis, accurate therapy, and prognosis prediction.
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Affiliation(s)
- Guichuan Huang
- Department of Pulmonary and Critical Care Medicine, The First People's hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China (mainland)
| | - Jing Zhang
- Department of Pulmonary and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China (mainland)
| | - Ling Gong
- Department of Pulmonary and Critical Care Medicine, The First People's hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China (mainland)
| | - Daishun Liu
- Department of Pulmonary and Critical Care Medicine, The First People's hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China (mainland)
| | - Xin Wang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China (mainland)
| | - Yi Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China (mainland)
| | - Shuliang Guo
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China (mainland)
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Hernandez Cordero AI, Yang CX, Obeidat M, Yang J, MacIsaac J, McEwen L, Lin D, Kobor M, Novak R, Hudson F, Klinker H, Dharan N, Man SP, Sin DD, Kunisaki K, Leung J. DNA methylation is associated with airflow obstruction in patients living with HIV. Thorax 2020; 76:448-455. [PMID: 33443234 PMCID: PMC8070606 DOI: 10.1136/thoraxjnl-2020-215866] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 11/30/2022]
Abstract
Introduction People living with HIV (PLWH) suffer from age-related comorbidities such as COPD. The processes responsible for reduced lung function in PLWH are largely unknown. We performed an epigenome-wide association study to investigate whether blood DNA methylation is associated with impaired lung function in PLWH. Methods Using blood DNA methylation profiles from 161 PLWH, we tested the effect of methylation on FEV1, FEV1/FVC ratio and FEV1 decline over a median of 5 years. We evaluated the global methylation of PLWH with airflow obstruction by testing the differential methylation of transposable elements Alu and LINE-1, a well-described marker of epigenetic ageing. Results Airflow obstruction as defined by a FEV1/FVC<0.70 was associated with 1393 differentially methylated positions (DMPs), while 4676 were associated with airflow obstruction based on the FEV1/FVC<lower limit of normal. These DMPs were enriched for biological pathways associated with chronic viral infections. The airflow obstruction group was globally hypomethylated compared with those without airflow obstruction. 103 and 7112 DMPs were associated with FEV1 and FEV1/FVC, respectively. No positions were associated with FEV1 decline. Conclusion A large number of DMPs were associated with airflow obstruction and lung function in a unique cohort of PLWH. Airflow obstruction in even relatively young PLWH is associated with global hypomethylation, suggesting advanced epigenetic ageing compared with those with normal lung function. The disturbance of the epigenetic regulation of key genes not previously identified in non-HIV COPD cohorts could explain the unique risk of COPD in PLWH.
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Affiliation(s)
- Ana I Hernandez Cordero
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Chen Xi Yang
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Maen Obeidat
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia Yang
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Julie MacIsaac
- Center for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lisa McEwen
- Center for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - David Lin
- Center for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael Kobor
- Center for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard Novak
- Section of Infectious Diseases, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Fleur Hudson
- MRC Clinical Trials Unit, University College London, London, UK
| | - Hartwig Klinker
- Medizinische Klinik und Poliklinik II, Universitatsklinikum Wurzburg, Wurzburg, Germany
| | - Nila Dharan
- The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Sf Paul Man
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Don D Sin
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Ken Kunisaki
- Minneapolis Veterans Affairs Health Care System, Section of Pulmonary, Critical Care and Sleep Medicine and the Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Janice Leung
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
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Yu H, Pan R, Gao T, Wu D, Ying J, Duan S. FANCF hypomethylation is associated with colorectal cancer in Han Chinese. TURKISH JOURNAL OF GASTROENTEROLOGY 2020; 31:558-565. [PMID: 32915143 DOI: 10.5152/tjg.2020.19394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND/AIMS Fanconi anemia complement group F (FANCF) is known to be involved in DNA repair, and the overexpression of FANCF protein leads to cell proliferation and ultimately to cancer. The purpose of this study was to assess whether FANCF methylation was associated with colorectal cancer (CRC). MATERIALS AND METHODS A case-control experiment was conducted to study the association between FANCF methylation and CRC. We used quantitative methylation-specific PCR to measure the FANCF promoter methylation, and the percentage of methylation reference (PMR) to quantify the FANCF promoter methylation level. To investigate the effect of the selected FANCF fragment on gene expression regulation, we also performed a dual-luciferase reporter gene assay. RESULTS The results indicated that FANCF methylation in CRC tumor tissues was significantly lower than that in the nontumor tissues (median PMR: 44.86% vs. 65.77%, p=0.00001). Analysis of receiver-operating characteristic curves showed that FANCF hypomethylation had a diagnostic value for CRC (area under curve [AUC]: 0.670, sensitivity: 55.8%, specificity: 71.7%, p=0.00001). The dual-luciferase reporter assay showed that the FANCF fragment upregulated gene expression (fold change: 1.93, p=0.002). CONCLUSION Research demonstrates for the first time that FANCF hypomethylation is significantly associated with CRC risk. FANCF hypomethylation may ultimately increase the risk of CRC by upregulating the expression of FANCF.
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Affiliation(s)
- Hang Yu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Ranran Pan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Tong Gao
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Dongping Wu
- Department of Medical Oncology, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, Zhejiang, China
| | - Jieer Ying
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
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Kezeminasab S, Emamalizadeh B, Khoubnasabjafari M, Jouyban A. Exhaled Breath Condensate: A Non-Invasive Source for Tracking of Genetic and Epigenetic Alterations in Lung Diseases. PHARMACEUTICAL SCIENCES 2020. [DOI: 10.34172/ps.2020.46] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Lung diseases have been recognized as an extensive cause of morbidity and mortality in the worldwide. The high degree of clinical heterogeneity and nonspecific initial symptoms of lung diseases contribute to a delayed diagnosis. So, the molecular and genomic profiling play a pivotal role in promoting the pulmonary diseases. Exhaled breath condensate (EBC) as a novel and potential method for sampling the respiratory epithelial lining fluid is to assess the inflammatory and oxidative stress biomarkers, drugs and genetic alterations in the pathophysiologic processes of lung diseases. The recent studies on the analysis of EBC from both a genetic and epigenetic point of view were searched from database and reviewed. This review provides an overview of the current findings in the tracking of genomic and epigenetic alterations which are potentially effective in better management of cancer detection. In addition, respiratory microbiota DNA using EBC samples in association with pulmonary disease especially lung cancer were investigated. Various studies have concluded that EBC has a great potential for analysis of nuclear and mitochondrial DNA alterations as well as epigenetic modifications and identification of respiratory microbiome. Next-generation sequencing (NGS) based genomic profiling of EBC samples is recommended as a promising approach to establish personalized based prevention, diagnosis, treatment and post-treatment follow-ups for patients with lung diseases especially lung cancer.
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Affiliation(s)
- Somayeh Kezeminasab
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Babak Emamalizadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Khoubnasabjafari
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abolghasem Jouyban
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Kimia Idea Pardaz Azerbaijan (KIPA) Science-Based Company, Tabriz University of Medical Sciences, Tabriz, Iran
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Genome-Wide DNA Methylation Profiling in Early Stage I Lung Adenocarcinoma Reveals Predictive Aberrant Methylation in the Promoter Region of the Long Noncoding RNA PLUT: An Exploratory Study. J Thorac Oncol 2020; 15:1338-1350. [PMID: 32272161 DOI: 10.1016/j.jtho.2020.03.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 03/27/2020] [Accepted: 03/29/2020] [Indexed: 01/27/2023]
Abstract
INTRODUCTION Surgical procedure is the treatment of choice in early stage I lung adenocarcinoma. However, a considerable number of patients experience recurrence within the first 2 years after complete resection. Suitable prognostic biomarkers that identify patients at high risk of recurrence (who may probably benefit from adjuvant treatment) are still not available. This study aimed at identifying methylation markers for early recurrence that may become important tools for the development of new treatment modalities. METHODS Genome-wide DNA methylation profiling was performed on 30 stage I lung adenocarcinomas, comparing 14 patients with early metastatic recurrence with 16 patients with a long-term relapse-free survival period using methylated-CpG-immunoprecipitation followed by high-throughput next-generation sequencing. The differentially methylated regions between the two subgroups were validated for their prognostic value in two independent cohorts using the MassCLEAVE assay, a high-resolution quantitative methylation analysis. RESULTS Unsupervised clustering of patients in the discovery cohort on the basis of differentially methylated regions identified patients with shorter relapse-free survival (hazard ratio: 2.23; 95% confidence interval: 0.66-7.53; p = 0.03). In two validation cohorts, promoter hypermethylation of the long noncoding RNA PLUT was significantly associated with shorter relapse-free survival (hazard ratio: 0.54; 95% confidence interval: 0.31-0.93; p < 0.026) and could be reported as an independent prognostic factor in the multivariate Cox regression analysis. CONCLUSIONS Promoter hypermethylation of the long noncoding RNA PLUT is predictive in patients with early stage I adenocarcinoma at high risk for early recurrence. Further studies are needed to validate its role in carcinogenesis and its use as a biomarker to facilitate patient selection and risk stratification.
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Šutić M, Motzek A, Bubanović G, Linke M, Sabol I, Vugrek O, Ozretić P, Brčić L, Seiwerth S, Debeljak Ž, Jakovčević A, Janevski Z, Stančić-Rokotov D, Vukić-Dugac A, Jakopović M, Samaržija M, Zechner U, Knežević J. Promoter methylation status of ASC/TMS1/PYCARD is associated with decreased overall survival and TNM status in patients with early stage non-small cell lung cancer (NSCLC). Transl Lung Cancer Res 2019; 8:1000-1015. [PMID: 32010578 PMCID: PMC6976376 DOI: 10.21037/tlcr.2019.12.08] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related death worldwide, with 5-year overall survival less than 15%. Therefore, it is essential to find biomarkers for early detection and prognosis. Aberrant DNA methylation is a common feature of human cancers and its utility is already recognized in cancer management. The aim of this study was to explore the diagnostic and prognostic value of the promoter methylation status of the ASC/TMS1/PYCARD and MyD88 genes, key adaptor molecules in the activation of the innate immune response and apoptosis pathways. METHODS A total of 50 non-small cell lung cancer (NSCLC) patients were enrolled in the study. Methylation of bisulphite converted DNA was quantified by pyrosequencing in fresh frozen malignant tissues and adjacent non-malignant tissues. Associations between methylation and lung function, tumor grade and overall survival were evaluated using receiver-operating characteristics (ROC) analysis and statistical tests of hypothesis. RESULTS Methylation level of tested genes is generally low but significantly decreased in tumor tissues (ASC/TMS1/PYCARD, P<0.0001; MyD88, P<0.0002), which correlates with increased protein expression. Three CpG sites were identified as promising diagnostic marker candidates; CpG11 (-63 position) in ASC/TMS1/PYCARD and CpG1 (-253 position) and 2 (-265 position) in MyD88. The association study showed that the methylation status of the ASC/TMS1 CpG4 site (-34 position) in malignant and non-malignant tissues is associated with the overall survival (P=0.019) and the methylation status of CpG8 site (-92 position) is associated with TNM-stage (P=0.011). CONCLUSIONS The methylation status of the ASC/TMS1/PYCARD and MyD88 promoters are promising prognostic biomarker candidates. However, presented results should be considered as a preliminary and should be confirmed on the larger number of the samples.
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Affiliation(s)
- Maja Šutić
- Ruđer Bošković Institute, Division for Molecular Medicine, Zagreb, Croatia
| | - Antje Motzek
- Institute for Human Genetics, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Gordana Bubanović
- Department of Pathology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Matthias Linke
- Institute for Human Genetics, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Ivan Sabol
- Ruđer Bošković Institute, Division for Molecular Medicine, Zagreb, Croatia
| | - Oliver Vugrek
- Ruđer Bošković Institute, Division for Molecular Medicine, Zagreb, Croatia
| | - Petar Ozretić
- Ruđer Bošković Institute, Division for Molecular Medicine, Zagreb, Croatia
| | - Luka Brčić
- Department of Pathology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Sven Seiwerth
- Department of Pathology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Željko Debeljak
- Institute of Clinical Laboratory Diagnostics, University Hospital Osijek, Osijek, Croatia
- Faculty of Medicine, Department of Pharmacology, JJ Strossmayer University of Osijek, Osijek, Croatia
| | - Antonija Jakovčević
- Department of Pathology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Zoran Janevski
- Department of Thoracic Surgery Jordanovac, Clinical Hospital Centre Zagreb, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Dinko Stančić-Rokotov
- Department of Thoracic Surgery Jordanovac, Clinical Hospital Centre Zagreb, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Andrea Vukić-Dugac
- Department for Respiratory Diseases, Clinic for Respiratory Diseases Jordanovac, University Hospital Centre Zagreb, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Marko Jakopović
- Department for Respiratory Diseases, Clinic for Respiratory Diseases Jordanovac, University Hospital Centre Zagreb, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Miroslav Samaržija
- Department for Respiratory Diseases, Clinic for Respiratory Diseases Jordanovac, University Hospital Centre Zagreb, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Ulrich Zechner
- Institute for Human Genetics, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Jelena Knežević
- Ruđer Bošković Institute, Division for Molecular Medicine, Zagreb, Croatia
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21
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Epigenetic Regulation of Inflammatory Cytokine-Induced Epithelial-To-Mesenchymal Cell Transition and Cancer Stem Cell Generation. Cells 2019; 8:cells8101143. [PMID: 31557902 PMCID: PMC6829508 DOI: 10.3390/cells8101143] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/20/2019] [Accepted: 09/24/2019] [Indexed: 12/12/2022] Open
Abstract
The neoplastic transformation of normal to metastatic cancer cells is a complex multistep process involving the progressive accumulation of interacting genetic and epigenetic changes that alter gene function and affect cell physiology and homeostasis. Epigenetic changes including DNA methylation, histone modifications and changes in noncoding RNA expression, and deregulation of epigenetic processes can alter gene expression during the multistep process of carcinogenesis. Cancer progression and metastasis through an ‘invasion–metastasis cascade’ involving an epithelial-to-mesenchymal cell transition (EMT), the generation of cancer stem cells (CSCs), invasion of adjacent tissues, and dissemination are fueled by inflammation, which is considered a hallmark of cancer. Chronic inflammation is generated by inflammatory cytokines secreted by the tumor and the tumor-associated cells within the tumor microenvironment. Inflammatory cytokine signaling initiates signaling pathways leading to the activation of master transcription factors (TFs) such as Smads, STAT3, and NF-κB. Moreover, the same inflammatory responses also activate EMT-inducing TF (EMT-TF) families such as Snail, Twist, and Zeb, and epigenetic regulators including DNA and histone modifying enzymes and micoRNAs, through complex interconnected positive and negative feedback loops to regulate EMT and CSC generation. Here, we review the molecular regulatory feedback loops and networks involved in inflammatory cytokine-induced EMT and CSC generation.
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22
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Yan P, Yang X, Wang J, Wang S, Ren H. A novel CpG island methylation panel predicts survival in lung adenocarcinomas. Oncol Lett 2019; 18:1011-1022. [PMID: 31423161 PMCID: PMC6607393 DOI: 10.3892/ol.2019.10431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 02/27/2018] [Indexed: 12/23/2022] Open
Abstract
The lack of clinically useful biomarkers compromise the personalized management of lung adenocarcinomas (ADCs); epigenetic events and DNA methylation in particular have exhibited potential value as biomarkers. By comparing genome-wide DNA methylation data of paired lung ADCs and normal tissues from 6 public datasets, cancer-specific CpG island (CGI) methylation changes were identified with a pre-specified criterion. Correlations between DNA methylation and expression data for each gene were assessed by Pearson correlation analysis. A prognostically relevant CGI methylation signature was constructed by risk-score analysis, and was validated using a training-validation approach. Survival data were analyzed by log-rank test and Cox regression model. In total, 134 lung ADC-specific CGI CpGs were identified, among which, a panel of 9 CGI loci were selected as prognostic candidates, and were used to construct a risk-score signature. The novel CGI methylation signature was identified to classify distinct prognostic subgroups across different datasets, and was demonstrated to be a potent independent prognostic factor for overall survival time of patients with lung ADCs. In addition, it was identified that cancer-specific CGI hypomethylation of RPL39L, along with the corresponding gene expression, provided optimized prognostication of lung ADCs. In summary, cancer-specific CGI methylation aberrations are optimal candidates for novel biomarkers of lung ADCs; the 9-CpG methylation panel and hypomethylation of RPL39L exhibited particularly promising significance.
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Affiliation(s)
- Pingzhao Yan
- Department of General Surgery, People's Hospital of Tongchuan, Tongchuan, Shaanxi 727000, P.R. China
| | - Xiaohua Yang
- Department of Respiratory and Hematology Medicine, People's Hospital of Tongchuan, Tongchuan, Shaanxi 727000, P.R. China
| | - Jianhua Wang
- Department of General Surgery, People's Hospital of Tongchuan, Tongchuan, Shaanxi 727000, P.R. China
| | - Shichang Wang
- Department of General Surgery, People's Hospital of Tongchuan, Tongchuan, Shaanxi 727000, P.R. China
| | - Hong Ren
- Department of Oncology Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
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23
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Li B, Huang Q, Wei GH. The Role of HOX Transcription Factors in Cancer Predisposition and Progression. Cancers (Basel) 2019; 11:cancers11040528. [PMID: 31013831 PMCID: PMC6520925 DOI: 10.3390/cancers11040528] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/08/2019] [Accepted: 04/10/2019] [Indexed: 12/12/2022] Open
Abstract
Homeobox (HOX) transcription factors, encoded by a subset of homeodomain superfamily genes, play pivotal roles in many aspects of cellular physiology, embryonic development, and tissue homeostasis. Findings over the past decade have revealed that mutations in HOX genes can lead to increased cancer predisposition, and HOX genes might mediate the effect of many other cancer susceptibility factors by recognizing or executing altered genetic information. Remarkably, several lines of evidence highlight the interplays between HOX transcription factors and cancer risk loci discovered by genome-wide association studies, thereby gaining molecular and biological insight into cancer etiology. In addition, deregulated HOX gene expression impacts various aspects of cancer progression, including tumor angiogenesis, cell autophagy, proliferation, apoptosis, tumor cell migration, and metabolism. In this review, we will discuss the fundamental roles of HOX genes in cancer susceptibility and progression, highlighting multiple molecular mechanisms of HOX involved gene misregulation, as well as their potential implications in clinical practice.
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Affiliation(s)
- Bo Li
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China.
| | - Qilai Huang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China.
| | - Gong-Hong Wei
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, 90220 Oulu, Finland.
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24
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Sarne V, Braunmueller S, Rakob L, Seeboeck R. The Relevance of Gender in Tumor-Influencing Epigenetic Traits. EPIGENOMES 2019; 3:epigenomes3010006. [PMID: 34991275 PMCID: PMC8594720 DOI: 10.3390/epigenomes3010006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/20/2019] [Accepted: 01/24/2019] [Indexed: 12/22/2022] Open
Abstract
Tumorigenesis as well as the molecular orchestration of cancer progression are very complex mechanisms that comprise numerous elements of influence and regulation. Today, many of the major concepts are well described and a basic understanding of a tumor's fine-tuning is given. Throughout the last decade epigenetics has been featured in cancer research and it is now clear that the underlying mechanisms, especially DNA and histone modifications, are important regulators of carcinogenesis and tumor progression. Another key regulator, which is well known but has been neglected in scientific approaches as well as molecular diagnostics and, consequently, treatment conceptualization for a long time, is the subtle influence patient gender has on molecular processes. Naturally, this is greatly based on hormonal differences, but from an epigenetic point of view, the diverse susceptibility to stress and environmental influences is of prime interest. In this review we present the current view on which and how epigenetic modifications, emphasizing DNA methylation, regulate various tumor diseases. It is our aim to elucidate gender and epigenetics and their interconnectedness, which will contribute to understanding of the prospect molecular orchestration of cancer in individual tumors.
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25
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Sharma B, Kanwar SS. Phosphatidylserine: A cancer cell targeting biomarker. Semin Cancer Biol 2018; 52:17-25. [DOI: 10.1016/j.semcancer.2017.08.012] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/12/2017] [Accepted: 08/30/2017] [Indexed: 12/11/2022]
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26
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Cermakova K, Hodges HC. Next-Generation Drugs and Probes for Chromatin Biology: From Targeted Protein Degradation to Phase Separation. Molecules 2018; 23:molecules23081958. [PMID: 30082609 PMCID: PMC6102721 DOI: 10.3390/molecules23081958] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/01/2018] [Accepted: 08/01/2018] [Indexed: 12/31/2022] Open
Abstract
Chromatin regulation is a critical aspect of nuclear function. Recent advances have provided detailed information about dynamic three-dimensional organization of chromatin and its regulatory factors. Mechanisms crucial for normal nuclear function and epigenetic control include compartmentalization of biochemical reactions by liquid-phase separated condensates and signal-dependent regulation of protein stability. Synthetic control of these phenomena by small molecules provides deep insight into essential activities such as histone modification, BAF (SWI/SNF) and PBAF remodeling, Polycomb repression, enhancer looping by cohesin and CTCF, as well as many other processes that contribute to transcription. As a result, a complete understanding of the spatiotemporal mechanisms that underlie chromatin regulation increasingly requires the use of fast-acting drugs and chemical probes. Here, we provide a comprehensive review of next-generation chemical biology tools to interrogate the chromatin regulatory landscape, including selective PROTAC E3 ubiquitin ligase degraders, degrons, fluorescent ligands, dimerizers, inhibitors, and other drugs. These small molecules provide important insights into the mechanisms that govern gene regulation, DNA repair, development, and diseases like cancer.
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Affiliation(s)
- Katerina Cermakova
- Department of Molecular & Cellular Biology, Center for Precision Environmental Health, and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - H Courtney Hodges
- Department of Molecular & Cellular Biology, Center for Precision Environmental Health, and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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27
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Feng X, Wang J, Gu X, Zhang J, Li X, Tao Z, Chen J, Chen B. Association of DNMT3B -283T>C polymorphism with risk of lung and gastric cancer: a case-control study and a meta-analysis. Int J Biol Markers 2018; 33:195-200. [PMID: 29027179 DOI: 10.5301/ijbm.5000306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
PURPOSE To investigate the association of DNMT3B -283T>C polymorphism with the risk of lung or gastric cancer, which was followed by a meta-analysis. METHODS The genotyping of -283T>C was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and was confirmed by sequencing. RESULTS The results of this case-control study showed that -283T>C was not associated with the risk of lung or gastric cancer, and further stratified analysis according to age, gender, smoking status, and alcohol status confirmed the present finding. However, data from a meta-analysis in the Asian population revealed a significant association between -283T>C and lung cancer risk in the allelic model (C vs. T: odds ratio [OR] = 1.28, 95% confidence interval [CI], 1.06-1.55, p = 0.01) and two genetic models (CC vs. TC: OR = 1.29, 95% CI, 1.04-1.59, p = 0.02; CC vs. TC + TT: OR = 1.30, 95% CI, 1.06-1.60, p = 0.01). CONCLUSIONS These results provided evidence that the DNMT3B -283T>C polymorphism might significantly contribute to the lung cancer risk in the Asian population, but not the gastric cancer risk in the Chinese population.
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Affiliation(s)
- Xianhong Feng
- 1 Clinical Laboratory, Wuhan Xinzhou District People's Hospital, Wuhan - PR China
| | - Jingdong Wang
- 2 Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan - PR China
| | - Xiuli Gu
- 3 Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan - PR China
| | - Jingli Zhang
- 2 Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan - PR China
| | - Xiaolin Li
- 1 Clinical Laboratory, Wuhan Xinzhou District People's Hospital, Wuhan - PR China
| | - Zhi Tao
- 1 Clinical Laboratory, Wuhan Xinzhou District People's Hospital, Wuhan - PR China
| | - Jiebing Chen
- 1 Clinical Laboratory, Wuhan Xinzhou District People's Hospital, Wuhan - PR China
| | - Bifeng Chen
- 2 Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan - PR China
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28
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Miousse IR, Ewing LE, Kutanzi KR, Griffin RJ, Koturbash I. DNA Methylation in Radiation-Induced Carcinogenesis: Experimental Evidence and Clinical Perspectives. Crit Rev Oncog 2018; 23:1-11. [PMID: 29953365 PMCID: PMC6369919 DOI: 10.1615/critrevoncog.2018025687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ionizing radiation is a valuable tool in many spheres of human life. At the same time, it is a genotoxic agent with a well-established carcinogenic potential. Progress achieved in the last two decades has demonstrated convincingly that ionizing radiation can also target the cellular epigenome. Epigenetics is defined as heritable changes in the expression of genes that are not due to alterations of DNA sequence but consist of specific covalent modifications of chromatin components, such as methylation of DNA, histone modifications, and control performed by non-coding RNAs. Accumulating evidence suggests that DNA methylation, a key epigenetic mechanism involved in the control of expression of genetic information, may serve as one of the driving mechanisms of radiation-induced carcinogenesis. Here, we review the literature on the effects of ionizing radiation on DNA methylation in various biological systems, discuss the role of DNA methylation in radiation carcinogenesis, and provide our opinion on the potential utilization of this knowledge in radiation oncology.
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Affiliation(s)
- Isabelle R. Miousse
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Laura E. Ewing
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Kristy R. Kutanzi
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Robert J. Griffin
- Department of Radiation Oncology, Radiation Biology Division, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Igor Koturbash
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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29
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Armas-López L, Piña-Sánchez P, Arrieta O, de Alba EG, Ortiz-Quintero B, Santillán-Doherty P, Christiani DC, Zúñiga J, Ávila-Moreno F. Epigenomic study identifies a novel mesenchyme homeobox2-GLI1 transcription axis involved in cancer drug resistance, overall survival and therapy prognosis in lung cancer patients. Oncotarget 2017; 8:67056-67081. [PMID: 28978016 PMCID: PMC5620156 DOI: 10.18632/oncotarget.17715] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 04/11/2017] [Indexed: 01/10/2023] Open
Abstract
Several homeobox-related gene (HOX) transcription factors such as mesenchyme HOX-2 (MEOX2) have previously been associated with cancer drug resistance, malignant progression and/or clinical prognostic responses in lung cancer patients; however, the mechanisms involved in these responses have yet to be elucidated. Here, an epigenomic strategy was implemented to identify novel MEOX2 gene promoter transcription targets and propose a new molecular mechanism underlying lung cancer drug resistance and poor clinical prognosis. Chromatin immunoprecipitation (ChIP) assays derived from non-small cell lung carcinomas (NSCLC) hybridized on gene promoter tiling arrays and bioinformatics analyses were performed, and quantitative, functional and clinical validation were also carried out. We statistically identified a common profile consisting of 78 gene promoter targets, including Hedgehog-GLI1 gene promoter sequences (FDR≤0.1 and FDR≤0.2). The GLI-1 gene promoter region from -2,192 to -109 was occupied by MEOX2, accompanied by transcriptionally active RNA Pol II and was epigenetically linked to the active histones H3K27Ac and H3K4me3; these associations were quantitatively validated. Moreover, siRNA genetic silencing assays identified a MEOX2-GLI1 axis involved in cellular cytotoxic resistance to cisplatinum in a dose-dependent manner, as well as cellular migration and proliferation. Finally, Kaplan-Maier survival analyses identified significant MEOX2-dependent GLI-1 protein expression associated with clinical progression and poorer overall survival using an independent cohort of NSCLC patients undergoing platinum-based oncological therapy with both epidermal growth factor receptor (EGFR)-non-mutated and EGFR-mutated status. In conclusion, this is the first study to investigate epigenome-wide MEOX2-transcription factor occupation identifying a novel overexpressed MEOX2-GLI1 axis and its clinical association with platinum-based cancer drug resistance and EGFR-tyrosine kinase inhibitor (TKI)-based therapy responses in NSCLC patients.
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Affiliation(s)
- Leonel Armas-López
- National University Autonomous of México (UNAM), Facultad de Estudios Superiores (FES) Iztacala, Biomedicine Research Unit (UBIMED), Lung Diseases And Cancer Epigenomics Laboratory, Mexico State, Mexico
| | - Patricia Piña-Sánchez
- Instituto Mexicano del Seguro Social (IMSS), Centro Medico Nacional (CMN) Siglo XXI, Unidad de Investigación Médica en Enfermedades Oncológicas (UIMEO), Molecular Oncology Laboratory, Mexico City, Mexico
| | - Oscar Arrieta
- National Cancer Institute (INCAN), Thoracic Oncology Clinic, Mexico City, Mexico
| | - Enrique Guzman de Alba
- National Institute of Respiratory Diseases (INER) “Ismael Cosío Villegas”, Mexico City, Mexico
| | - Blanca Ortiz-Quintero
- National Institute of Respiratory Diseases (INER) “Ismael Cosío Villegas”, Mexico City, Mexico
| | | | - David C. Christiani
- Harvard Medical School, Harvard School of Public Health, Department of Environmental Health, Boston, Massachusetts, USA
| | - Joaquín Zúñiga
- National Institute of Respiratory Diseases (INER) “Ismael Cosío Villegas”, Mexico City, Mexico
| | - Federico Ávila-Moreno
- National University Autonomous of México (UNAM), Facultad de Estudios Superiores (FES) Iztacala, Biomedicine Research Unit (UBIMED), Lung Diseases And Cancer Epigenomics Laboratory, Mexico State, Mexico
- National Institute of Respiratory Diseases (INER) “Ismael Cosío Villegas”, Mexico City, Mexico
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30
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Miousse IR, Tobacyk J, Melnyk S, James SJ, Cheema AK, Boerma M, Hauer-Jensen M, Koturbash I. One-carbon metabolism and ionizing radiation: a multifaceted interaction. Biomol Concepts 2017; 8:83-92. [PMID: 28574375 PMCID: PMC6693336 DOI: 10.1515/bmc-2017-0003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/03/2017] [Indexed: 01/20/2023] Open
Abstract
Ionizing radiation (IR) is a ubiquitous component of our environment and an important tool in research and medical treatment. At the same time, IR is a potent genotoxic and epigenotoxic stressor, exposure to which may lead to negative health outcomes. While the genotoxocity is well described and characterized, the epigenetic effects of exposure to IR and their mechanisms remain under-investigated. In this conceptual review, we propose the IR-induced changes to one-carbon metabolism as prerequisites to alterations in the cellular epigenome. We also provide evidence from both experimental and clinical studies describing the interactions between IR and one-carbon metabolism. We further discuss the potential for the manipulation of the one-carbon metabolism in clinical applications for the purpose of normal tissue protection and for increasing the radiosensitivity of cancerous cells.
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Affiliation(s)
- Isabelle R. Miousse
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Julia Tobacyk
- Departments of Environmental and Occupational Health, and Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Stepan Melnyk
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - S. Jill James
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Amrita K. Cheema
- Departments of Oncology and Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington DC 20057, USA
| | - Marjan Boerma
- Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Martin Hauer-Jensen
- Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Igor Koturbash
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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31
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Lu Y, Li S, Zhu S, Gong Y, Shi J, Xu L. Methylated DNA/RNA in Body Fluids as Biomarkers for Lung Cancer. Biol Proced Online 2017; 19:2. [PMID: 28331435 PMCID: PMC5356409 DOI: 10.1186/s12575-017-0051-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 03/02/2017] [Indexed: 12/21/2022] Open
Abstract
DNA/RNA methylation plays an important role in lung cancer initiation and progression. Liquid biopsy makes use of cells, nucleotides and proteins released from tumor cells into body fluids to help with cancer diagnosis and prognosis. Methylation of circulating tumor DNA (ctDNA) has gained increasing attention as biomarkers for lung cancer. Here we briefly introduce the biological basis and detection method of ctDNA methylation, and review various applications of methylated DNA in body fluids in lung cancer screening, diagnosis, prognosis, monitoring and treatment prediction. We also discuss the emerging role of RNA methylation as biomarkers for cancer.
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Affiliation(s)
- Yan Lu
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
| | - Shulin/Sl Li
- MD Anderson Cancer Center, the university of Texas, 1840 Old Spanish Trail, Houston, TX USA
| | - Shiguo/Sg Zhu
- Department of Immunology and Pathogenic Biology, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, 1200 Cai Lun Rd, Shanghai, China
| | - Yabin/Yb Gong
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
| | - Jun/J Shi
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
| | - Ling/L Xu
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
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32
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Vymetalkova V, Vodicka P, Pardini B, Rosa F, Levy M, Schneiderova M, Liska V, Vodickova L, Nilsson TK, Farkas SA. Epigenome-wide analysis of DNA methylation reveals a rectal cancer-specific epigenomic signature. Epigenomics 2016; 8:1193-207. [DOI: 10.2217/epi-2016-0044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim: The aim of the present study is to address a genome-wide search for novel methylation biomarkers in the rectal cancer (RC), as only scarce information on methylation profile is available. Materials & methods: We analyzed methylation status in 25 pairs of RC and adjacent healthy mucosa using the Illumina Human Methylation 450 BeadChip. Results: We found significantly aberrant methylation in 33 genes. After validation of our results by pyrosequencing, we found a good agreement with our findings. The BPIL3 and HBBP1 genes resulted hypomethylated in RC, whereas TIFPI2, ADHFE1, FLI1 and TLX1 were hypermethylated. An external validation by TCGA datasets confirmed the results. Conclusion: Our study, with external validation, has demonstrated the feasibility of using specific methylated DNA signatures for developing biomarkers in RC.
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Affiliation(s)
- Veronika Vymetalkova
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Biology & Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic
| | - Pavel Vodicka
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Biology & Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Czech Republic
| | | | - Fabio Rosa
- Human Genetics Foundation, (HuGeF), Torino, Italy
| | - Miroslav Levy
- Department of Surgery, 1st Faculty of Medicine, Charles University & Thomayer Hospital, Prague, Czech Republic
| | | | - Vaclav Liska
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Czech Republic
- Department of Surgery, Teaching Hospital & Medical School in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Biology & Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Czech Republic
| | | | - Sanja A Farkas
- Department of Laboratory Medicine, Örebro University; Örebro, Sweden
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33
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Pineda AL, Ogoe HA, Balasubramanian JB, Rangel Escareño C, Visweswaran S, Herman JG, Gopalakrishnan V. On Predicting lung cancer subtypes using 'omic' data from tumor and tumor-adjacent histologically-normal tissue. BMC Cancer 2016; 16:184. [PMID: 26944944 PMCID: PMC4778315 DOI: 10.1186/s12885-016-2223-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 02/28/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Adenocarcinoma (ADC) and squamous cell carcinoma (SCC) are the most prevalent histological types among lung cancers. Distinguishing between these subtypes is critically important because they have different implications for prognosis and treatment. Normally, histopathological analyses are used to distinguish between the two, where the tissue samples are collected based on small endoscopic samples or needle aspirations. However, the lack of cell architecture in these small tissue samples hampers the process of distinguishing between the two subtypes. Molecular profiling can also be used to discriminate between the two lung cancer subtypes, on condition that the biopsy is composed of at least 50 % of tumor cells. However, for some cases, the tissue composition of a biopsy might be a mix of tumor and tumor-adjacent histologically normal tissue (TAHN). When this happens, a new biopsy is required, with associated cost, risks and discomfort to the patient. To avoid this problem, we hypothesize that a computational method can distinguish between lung cancer subtypes given tumor and TAHN tissue. METHODS Using publicly available datasets for gene expression and DNA methylation, we applied four classification tasks, depending on the possible combinations of tumor and TAHN tissue. First, we used a feature selector (ReliefF/Limma) to select relevant variables, which were then used to build a simple naïve Bayes classification model. Then, we evaluated the classification performance of our models by measuring the area under the receiver operating characteristic curve (AUC). Finally, we analyzed the relevance of the selected genes using hierarchical clustering and IPA® software for gene functional analysis. RESULTS All Bayesian models achieved high classification performance (AUC > 0.94), which were confirmed by hierarchical cluster analysis. From the genes selected, 25 (93 %) were found to be related to cancer (19 were associated with ADC or SCC), confirming the biological relevance of our method. CONCLUSIONS The results from this study confirm that computational methods using tumor and TAHN tissue can serve as a prognostic tool for lung cancer subtype classification. Our study complements results from other studies where TAHN tissue has been used as prognostic tool for prostate cancer. The clinical implications of this finding could greatly benefit lung cancer patients.
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Affiliation(s)
- Arturo López Pineda
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, 5607 Baum Boulevard, 15206, Pittsburgh, PA, USA.
| | - Henry Ato Ogoe
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, 5607 Baum Boulevard, 15206, Pittsburgh, PA, USA.
| | - Jeya Balaji Balasubramanian
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, 5607 Baum Boulevard, 15206, Pittsburgh, PA, USA.
| | - Claudia Rangel Escareño
- Department of Computational Genomics, National Institute of Genomic Medicine, Periferico Sur No. 4809, Col. Arenal Tepepan, Tlalpan, 14610, Mexico City, Mexico.
| | - Shyam Visweswaran
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, 5607 Baum Boulevard, 15206, Pittsburgh, PA, USA.
| | - James Gordon Herman
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh School of Medicine, UPMC Cancer Pavilion, 5150 Centre Avenue, 15232, Pittsburgh, PA, USA.
| | - Vanathi Gopalakrishnan
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, 5607 Baum Boulevard, 15206, Pittsburgh, PA, USA.
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Bjaanæs MM, Fleischer T, Halvorsen AR, Daunay A, Busato F, Solberg S, Jørgensen L, Kure E, Edvardsen H, Børresen-Dale AL, Brustugun OT, Tost J, Kristensen V, Helland Å. Genome-wide DNA methylation analyses in lung adenocarcinomas: Association with EGFR, KRAS and TP53 mutation status, gene expression and prognosis. Mol Oncol 2016; 10:330-43. [PMID: 26601720 PMCID: PMC5528958 DOI: 10.1016/j.molonc.2015.10.021] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/25/2015] [Accepted: 10/28/2015] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND DNA methylation alterations are early events in tumorigenesis and important in the regulation of gene expression in cancer cells. Lung cancer patients have in general a poor prognosis, and a deeper insight into the epigenetic landscape in lung adenocarcinoma tumors and its prognostic implications is needed. RESULTS We determined whole-genome DNA methylation profiles of 164 fresh frozen lung adenocarcinoma samples and 19 samples of matched normal lung tissue using the Illumina Infinium 450K array. A large number of differentially methylated CpGs in lung adenocarcinoma tissue were identified, and specific methylation profiles were observed in tumors with mutations in the EGFR-, KRAS- or TP53 genes and according to the patients' smoking status. The methylation levels were correlated with gene expression and both positive and negative correlations were seen. Methylation profiles of the tumor samples identified subtypes of tumors with distinct prognosis, including one subtype enriched for TP53 mutant tumors. A prognostic index based on the methylation levels of 33 CpGs was established, and was significantly associated with prognosis in the univariate analysis using an independent cohort of lung adenocarcinoma patients from The Cancer Genome Atlas project. CpGs in the HOX B and HOX C gene clusters were represented in the prognostic signature. CONCLUSIONS Methylation differences mirror biologically important features in the etiology of lung adenocarcinomas and influence prognosis.
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Affiliation(s)
- Maria Moksnes Bjaanæs
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway; Department of Oncology, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway.
| | - Thomas Fleischer
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway; The K.G. Jebsen Censtre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway.
| | - Ann Rita Halvorsen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway.
| | - Antoine Daunay
- Laboratory for Functional Genomics, Fondation Jean Dausset - CEPH, 75010 Paris, France.
| | - Florence Busato
- Laboratory for Epigenetics and Environment (LEE), Centre National de Génotypage, CEA - Institut de Génomique, 91000 Evry, France.
| | - Steinar Solberg
- Department of Cardiothoracic Surgery, Oslo University Hospital-Rikshospitalet, Oslo, Norway.
| | - Lars Jørgensen
- Department of Cardiothoracic Surgery, Oslo University Hospital-Rikshospitalet, Oslo, Norway.
| | - Elin Kure
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway.
| | - Hege Edvardsen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway.
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway.
| | - Odd Terje Brustugun
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway; Department of Oncology, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway.
| | - Jörg Tost
- Laboratory for Epigenetics and Environment (LEE), Centre National de Génotypage, CEA - Institut de Génomique, 91000 Evry, France.
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway; The K.G. Jebsen Censtre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway; Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, Norway.
| | - Åslaug Helland
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway; Department of Oncology, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway.
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EZH2 in Bladder Cancer, a Promising Therapeutic Target. Int J Mol Sci 2015; 16:27107-32. [PMID: 26580594 PMCID: PMC4661858 DOI: 10.3390/ijms161126000] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 01/17/2023] Open
Abstract
Bladder Cancer (BC) represents a current clinical and social challenge. The recent studies aimed to describe the genomic landscape of BC have underscored the relevance of epigenetic alterations in the pathogenesis of these tumors. Among the epigenetic alterations, histone modifications occupied a central role not only in cancer, but also in normal organism homeostasis and development. EZH2 (Enhancer of Zeste Homolog 2) belongs to the Polycomb repressive complex 2 as its catalytic subunit, which through the trimethylation of H3 (Histone 3) on K27 (Lysine 27), produces gene silencing. EZH2 is frequently overexpressed in multiple tumor types, including BC, and plays multiple roles besides the well-recognized histone mark generation. In this review, we summarize the present knowledge on the oncogenic roles of EZH2 and its potential use as a therapeutic target, with special emphasis on BC pathogenesis and management.
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Heubach J, Monsior J, Deenen R, Niegisch G, Szarvas T, Niedworok C, Schulz WA, Hoffmann MJ. The long noncoding RNA HOTAIR has tissue and cell type-dependent effects on HOX gene expression and phenotype of urothelial cancer cells. Mol Cancer 2015; 14:108. [PMID: 25994132 PMCID: PMC4455698 DOI: 10.1186/s12943-015-0371-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 04/22/2015] [Indexed: 11/30/2022] Open
Abstract
Background Urothelial carcinoma (UC) is the fifth most common cancer in the developed world. Delineation of differentiation subtypes in UC highlighted the importance of aberrant differentiation. Understanding underlying mechanisms may facilitate diagnosis and development of efficient therapy strategies. It is well accepted that epigenetic mechanisms are involved. Long noncoding RNAs (lncRNAs), a new class of epigenetic factors, are thought to mediate molecular differences between cell types to control cellular identity. The present study focuses on the lncRNA HOTAIR, originating from the HOXC locus. Its overexpression induces an aggressive phenotype in many cancers and aberrant expression of homeotic HOX transcription factors, especially HOXD10, that regulate differentiation and tissue homeostasis. The aim of the present study was to determine the functional role of HOTAIR in UC with regard to aggressive phenotype, regulation of aberrant differentiation and altered HOX gene expression. Methods We determined RNA expression levels of HOTAIR and HOX genes in UC tissues and cell lines. Knockdown of HOTAIR and ectopic overexpression was performed to determine the effect on reported target genes in UC. Cell lines were stably transfected with HOTAIR to investigate changes in phenotype and HOX gene expression. Results HOTAIR was overexpressed in approximately half of UC tissues and cell lines. Effects of HOTAIR overexpression differed between cell lines. Whereas VM-CUB1 cells acquired the expected phenotype with increased proliferation, clonogenicity, anchorage independent growth, migratory activity and epithelial-to-mesenchymal transition, 5637 cells grew more slowly displaying induction of senescence and related immune response genes. Other UC lines showed intermediate effects. Expression profiling revealed divergent effects on HOX genes, cell cycle regulators and differentiation according with the phenotypic differences between HOTAIR-overexpressing VM-CUB1 and 5637 cells. Conclusions Our data indicate that HOTAIR overexpression may affect differentiation state and aggressiveness of UC cells, but in a cell-type dependent manner. Our functional studies and the comparison of our expression data sets with those from other cancer cell types, which revealed minimal overlaps, indicate that effects of HOTAIR are strongly tissue-dependent and can even differ within one cancer type. Thus, HOTAIR functions and target genes cannot simply be transferred from one cancer type to the other. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0371-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Judith Heubach
- Department of Urology, Medical Faculty, Heinrich-Heine-University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany.
| | - Juliana Monsior
- Department of Urology, Medical Faculty, Heinrich-Heine-University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany.
| | - René Deenen
- Biomedical and Medical Research Center, Heinrich-Heine-University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany.
| | - Günter Niegisch
- Department of Urology, Medical Faculty, Heinrich-Heine-University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany.
| | - Tibor Szarvas
- Department of Urology, University of Duisburg- Essen, Hufelandstr. 55, 45147, Essen, Germany. .,Department of Urology, Semmelweis University, Ülloi ut 78/b, 1082, Budapest, Hungary.
| | - Christian Niedworok
- Department of Urology, University of Duisburg- Essen, Hufelandstr. 55, 45147, Essen, Germany.
| | - Wolfgang Arthur Schulz
- Department of Urology, Medical Faculty, Heinrich-Heine-University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany.
| | - Michèle Janine Hoffmann
- Department of Urology, Medical Faculty, Heinrich-Heine-University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany.
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Abstract
The lung develops from a very simple outpouching of the foregut into a highly complex, finely structured organ with multiple specialized cell types that are required for its normal physiological function. During both the development of the lung and its remodeling in the context of disease or response to injury, gene expression must be activated and silenced in a coordinated manner to achieve the tremendous phenotypic heterogeneity of cell types required for homeostasis and pathogenesis. Epigenetic mechanisms, consisting of DNA base modifications such as methylation, alteration of histones resulting in chromatin modification, and the action of noncoding RNA, control the regulation of information "beyond the genome" required for both lung modeling and remodeling. Epigenetic regulation is subject to modification by environmental stimuli, such as oxidative stress, infection, and aging, and is thus critically important in chronic remodeling disorders such as idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD), bronchopulmonary dysplasia (BPD), and pulmonary hypertension (PH). Technological advances have made it possible to evaluate genome-wide epigenetic changes (epigenomics) in diseases of lung remodeling, clarifying existing pathophysiological paradigms and uncovering novel mechanisms of disease. Many of these represent new therapeutic targets. Advances in epigenomic technology will accelerate our understanding of lung development and remodeling, and lead to novel treatments for chronic lung diseases.
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Affiliation(s)
- James S Hagood
- Department of Pediatrics, Division of Respiratory Medicine, University of California-San Diego and Rady Children's Hospital of San Diego, San Diego, California
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Liu K, Huang W, Gao W, He W. Effect of combined 5-aza-2'deoxycytidine and cisplatin treatment on the P15 lung adenocarcinoma cell line. Oncol Lett 2015; 9:2007-2012. [PMID: 26137003 DOI: 10.3892/ol.2015.2986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 02/10/2015] [Indexed: 11/06/2022] Open
Abstract
Aberrant promoter hypermethylation resulting in the epigenetic silencing of apoptosis-associated genes is a key process in the chemotherapeutic treatment of cancer. The nucleoside analog, 5-aza-2'deoxycytidine (DAC), inhibits the activity of DNA methyltransferase enzymes and is able to restore the expression levels of genes that have been silenced by aberrant DNA methylation. The aim of the present study was to investigate the effect of combined treatment with DAC and cisplatin (CDDP) on the lung adenocarcinoma cell line, P15. Growth inhibition was examined using a clone formation assay and growth inhibitory activities by cell counting during treatment with DAC alone, CDDP alone or DAC followed by CDDP. In addition, changes in the mRNA expression levels of various apoptosis-associated genes following treatment with increasing concentrations of DAC were determined using reverse transcription-polymerase chain reaction. Furthermore, terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) analysis was used to detect the number of apoptotic P15 tumor cells following treatment with DAC and/or CDDP. The results indicated that DAC treatment alone restored the mRNA expression levels of p73, p16INK4a , B-cell lymphoma (Bcl)-2-associated agonist of cell death and Bcl-2-associated X protein. In addition, combined therapy with DAC and CDDP was found to significantly suppress the growth of P15 tumor cells compared with DAC or CDDP treatment alone. In conclusion, DAC may enhance the chemosensitivity of the P15 cell line to treatment with CDDP.
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Affiliation(s)
- Kaishan Liu
- Department of Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Wenyan Huang
- Department of Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Weisong Gao
- Department of Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Wenfang He
- Department of Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
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Shi M, Wang S, Yao Y, Li Y, Zhang H, Han F, Nie H, Su J, Wang Z, Yue L, Cao J, Li Y. Biological and clinical significance of epigenetic silencing of MARVELD1 gene in lung cancer. Sci Rep 2014; 4:7545. [PMID: 25520033 PMCID: PMC4269892 DOI: 10.1038/srep07545] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 12/01/2014] [Indexed: 01/20/2023] Open
Abstract
Epigenetic silence in cancer frequently altered signal-transduction pathways during the early stages of tumor development. Recent progress in the field of cancer epigenetics has led to new opportunities for diagnosis and treatment of cancer. We previously demonstrated that novel identified nuclear factor MARVELD1 was widely expressed in human tissues, but down-regulated by promoter methylation in multiple cancers. This study was carried out to determine the biological and clinical significance of MARVELD1 gene silencing in lung cancer. Here, we found the reduced MARVELD1 expression significantly correlated with diagnostic histopathology and malignant degree of lung cancers. DNA hypermethylation and histone deacetylation synergistically inactivated MARVELD1 gene in lung cancer cells. Moreover, MARVELD1 modulated the efficiency of nonsense-mediated mRNA decay (NMD) through interaction with NMD core factor SMG1. The decreased MARVELD1 level in lung cancer reduces NMD efficiency through diminishing the association between NMD complex component UPF1/SMG1 and premature termination codons containing mRNA (PTC-mRNA). The results suggested that MARVELD1 silencing is an appealing diagnostic biomarker for lung cancer and epigenetic silencing of MARVELD1 gene links with the regulatory mechanism of NMD pathway in lung cancer, which may be required for tumorigenesis.
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Affiliation(s)
- Ming Shi
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Shan Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yuanfei Yao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yiqun Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Hao Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Fang Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Huan Nie
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jie Su
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Zeyu Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Lei Yue
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jingyan Cao
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yu Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
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Stott-Miller M, Zhao S, Wright JL, Kolb S, Bibikova M, Klotzle B, Ostrander EA, Fan JB, Feng Z, Stanford JL. Validation study of genes with hypermethylated promoter regions associated with prostate cancer recurrence. Cancer Epidemiol Biomarkers Prev 2014; 23:1331-9. [PMID: 24718283 PMCID: PMC4082437 DOI: 10.1158/1055-9965.epi-13-1000] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND One challenge in prostate cancer is distinguishing indolent from aggressive disease at diagnosis. DNA promoter hypermethylation is a frequent epigenetic event in prostate cancer, but few studies of DNA methylation in relation to features of more aggressive tumors or prostate cancer recurrence have been completed. METHODS We used the Infinium HumanMethylation450 BeadChip to assess DNA methylation in tumor tissue from 407 patients with clinically localized prostate cancer who underwent radical prostatectomy. Recurrence status was determined by follow-up patient surveys, medical record review, and linkage with the Surveillance, Epidemiology, and End Results (SEER) registry. The methylation status of 14 genes for which promoter hypermethylation was previously correlated with advanced disease or biochemical recurrence was evaluated. Average methylation level for promoter region CpGs in patients who recurred compared with those with no evidence of recurrence was analyzed. For two genes with differential methylation, time to recurrence was examined. RESULTS During an average follow-up of 11.7 years, 104 (26%) patients recurred. Significant promoter hypermethylation in at least 50% of CpG sites in two genes, ABHD9 and HOXD3, was found in tumors from patients who recurred compared with those without recurrence. Evidence was strongest for HOXD3 (lowest P = 9.46 × 10(-6)), with higher average methylation across promoter region CpGs associated with reduced recurrence-free survival (P = 2 × 10(-4)). DNA methylation profiles did not differ by recurrence status for the other genes. CONCLUSIONS These results validate the association between promoter hypermethylation of ADHB9 and HOXD3 and prostate cancer recurrence. IMPACT Tumor DNA methylation profiling may help to distinguish patients with prostate cancer at higher risk for disease recurrence.
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Affiliation(s)
- Marni Stott-Miller
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center
| | - Shanshan Zhao
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center
| | - Jonathan L Wright
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center; Department of Urology, University of Washington School of Medicine; Departments of
| | - Suzanne Kolb
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center
| | | | | | - Elaine A Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | | | - Ziding Feng
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center; Biostatistics and
| | - Janet L Stanford
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center; Epidemiology, University of Washington, Seattle, Washington;
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Chen LN, Rubin RS, Othepa E, Cer C, Yun E, Agarwal RP, Collins BT, McGeagh K, Pahira J, Bandi G, Kowalczyk K, Kumar D, Dritschilo A, Collins SP, Bostwick DG, Lynch JH, Suy S. Correlation of HOXD3 promoter hypermethylation with clinical and pathologic features in screening prostate biopsies. Prostate 2014; 74:714-21. [PMID: 24847526 PMCID: PMC4285328 DOI: 10.1002/pros.22790] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Molecular markers that can discriminate indolent cancers from aggressive ones may improve the management of prostate cancer and minimize unnecessary treatment.Aberrant DNA methylation is a common epigenetic event in cancers and HOXD3 promoter hypermethylation (H3PH) has been found in prostate cancer. Our objective was to evaluate the relationship between H3PH and clinicopathologic features in screening prostate biopsies. METHODS Ninety-two patients who underwent a prostate biopsy at our institution between October 2011 and May 2012 were included in this study. The core with the greatest percentage of the highest grade disease was analyzed for H3PH by methylation-specific PCR. Correlational analysis was used to analyze the relationship between H3PH and various clinical parameters. Chi-square analysis was used to compare H3PH status between benign and malignant disease. RESULTS Of the 80 biopsies with HOXD3 methylation status assessable, 66 sets were confirmed to have cancer. In the 14 biopsies with benign disease there was minimal H3PH with the mean percentage of methylation reference (PMR) of 0.7%. In contrast, the HOXD3 promoter was hypermethylated in 16.7% of all cancers and in 50% of high risk tumors with an average PMR of 4.3% (P=0.008). H3PH was significantly correlated with age (P=0.013), Gleason score (P=0.031) and the maximum involvement of the biopsy core (P=0.035). CONCLUSIONS H3PH is associated with clinicopathologic features. The data indicate that H3PH is more common in older higher risk patients. More research is needed to determine the role of this marker in optimizing management strategies in men with newly diagnosed prostate cancer.
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Affiliation(s)
- Leonard N Chen
- Department of Radiation Medicine, Georgetown University HospitalWashington, District of Columbia
| | - Rachel S Rubin
- Department of Urology, Georgetown University HospitalWashington, District of Columbia
| | - Eugide Othepa
- Department of Radiation Medicine, Georgetown University HospitalWashington, District of Columbia
| | - Caroline Cer
- Department of Radiation Medicine, Georgetown University HospitalWashington, District of Columbia
| | - Elizabeth Yun
- Department of Radiation Medicine, Georgetown University HospitalWashington, District of Columbia
| | - Raghunath P Agarwal
- Department of Radiation Medicine, Georgetown University HospitalWashington, District of Columbia
| | - Brian T Collins
- Department of Radiation Medicine, Georgetown University HospitalWashington, District of Columbia
| | - Kevin McGeagh
- Department of Urology, Georgetown University HospitalWashington, District of Columbia
| | - John Pahira
- Department of Urology, Georgetown University HospitalWashington, District of Columbia
| | - Guarav Bandi
- Department of Urology, Georgetown University HospitalWashington, District of Columbia
| | - Keith Kowalczyk
- Department of Urology, Georgetown University HospitalWashington, District of Columbia
| | - Deepak Kumar
- Deptartment of Biological & Environmental Sciences, University of the District of ColumbiaWashington, District of Columbia
| | - Anatoly Dritschilo
- Department of Radiation Medicine, Georgetown University HospitalWashington, District of Columbia
| | - Sean P Collins
- Department of Radiation Medicine, Georgetown University HospitalWashington, District of Columbia
| | | | - John H Lynch
- Department of Urology, Georgetown University HospitalWashington, District of Columbia
| | - Simeng Suy
- Department of Radiation Medicine, Georgetown University HospitalWashington, District of Columbia
- * Simeng Suy, PhD, 3800 Reservoir Rd. NW LL Bles, Washington, DC 20007. E-mail:
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Wrangle J, Machida EO, Danilova L, Hulbert A, Franco N, Zhang W, Glöckner SC, Tessema M, Van Neste L, Easwaran H, Schuebel KE, Licchesi J, Hooker CM, Ahuja N, Amano J, Belinsky SA, Baylin SB, Herman JG, Brock MV. Functional identification of cancer-specific methylation of CDO1, HOXA9, and TAC1 for the diagnosis of lung cancer. Clin Cancer Res 2014; 20:1856-64. [PMID: 24486589 DOI: 10.1158/1078-0432.ccr-13-2109] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PURPOSE Non-small cell lung cancer (NSCLC) is the leading cause of cancer mortality in the world. Novel diagnostic biomarkers may augment both existing NSCLC screening methods as well as molecular diagnostic tests of surgical specimens to more accurately stratify and stage candidates for adjuvant chemotherapy. Hypermethylation of CpG islands is a common and important alteration in the transition from normal tissue to cancer. EXPERIMENTAL DESIGN Following previously validated methods for the discovery of cancer-specific hypermethylation changes, we treated eight NSCLC cell lines with the hypomethylating agent deoxyazacitidine or trichostatin A. We validated the findings using a large publicly available database and two independent cohorts of primary samples. RESULTS We identified >300 candidate genes. Using The Cancer Genome Atlas (TCGA) and extensive filtering to refine our candidate genes for the greatest ability to distinguish tumor from normal, we define a three-gene panel, CDO1, HOXA9, and TAC1, which we subsequently validate in two independent cohorts of primary NSCLC samples. This three-gene panel is 100% specific, showing no methylation in 75 TCGA normal and seven primary normal samples and is 83% to 99% sensitive for NSCLC depending on the cohort. CONCLUSION This degree of sensitivity and specificity may be of high value to diagnose the earliest stages of NSCLC. Addition of this three-gene panel to other previously validated methylation biomarkers holds great promise in both early diagnosis and molecular staging of NSCLC.
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Affiliation(s)
- John Wrangle
- Authors' Affiliations: The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland; Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; MDxHealth Inc, Irvine, California; Shinshu University School of Medicine, Asahi, Matsumoto, Nagano, Japan; and Lovelace Respiratory Research Institute, Albuquerque, New Mexico
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Lung cancer. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Surana R, Sikka S, Cai W, Shin EM, Warrier SR, Tan HJG, Arfuso F, Fox SA, Dharmarajan AM, Kumar AP. Secreted frizzled related proteins: Implications in cancers. Biochim Biophys Acta Rev Cancer 2013; 1845:53-65. [PMID: 24316024 DOI: 10.1016/j.bbcan.2013.11.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 11/26/2013] [Accepted: 11/30/2013] [Indexed: 12/31/2022]
Abstract
The Wnt (wingless-type) signaling pathway plays an important role in embryonic development, tissue homeostasis, and tumor progression becaluse of its effect on cell proliferation, migration, and differentiation. Secreted frizzled-related proteins (SFRPs) are extracellular inhibitors of Wnt signaling that act by binding directly to Wnt ligands or to Frizzled receptors. In recent years, aberrant expression of SFRPs has been reported to be associated with numerous cancers. As gene expression of SFRP members is often lost through promoter hypermethylation, inhibition of methylation through the use of epigenetic modifying agents could renew the expression of SFRP members and further antagonize deleterious Wnt signaling. Several reports have described epigenetic silencing of these Wnt signaling antagonists in various human cancers, suggesting their possible role as tumor suppressors. SFRP family members thus come across as potential tools in combating Wnt-driven tumorigenesis. However, little is known about SFRP family members and their role in different cancers. This review comprehensively covers all the available information on the role of SFRP molecules in various human cancers.
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Affiliation(s)
- Rohit Surana
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Sakshi Sikka
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Wanpei Cai
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Eun Myoung Shin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Sudha R Warrier
- Manipal Institute of Regenerative Medicine, Manipal University, Bangalore, India
| | - Hong Jie Gabriel Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Frank Arfuso
- School of Anatomy, Physiology and Human Biology, The University of Western Australia, Crawley, Western Australia, Australia; School of Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, 6845 Western Australia, Australia
| | - Simon A Fox
- Molecular Pharmacology Laboratory, School of Pharmacy, Western Australian Biomedical Research Institute & Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia
| | - Arun M Dharmarajan
- School of Anatomy, Physiology and Human Biology, The University of Western Australia, Crawley, Western Australia, Australia; School of Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, 6845 Western Australia, Australia.
| | - Alan Prem Kumar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; School of Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, 6845 Western Australia, Australia; Department of Biological Sciences, University of North Texas, Denton, TX 76203-5017, USA.
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Bowe RA, Cox OT, Ayllón V, Tresse E, Healy NC, Edmunds SJ, Huigsloot M, O'Connor R. PDLIM2 regulates transcription factor activity in epithelial-to-mesenchymal transition via the COP9 signalosome. Mol Biol Cell 2013; 25:184-95. [PMID: 24196835 PMCID: PMC3873889 DOI: 10.1091/mbc.e13-06-0306] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
PDLIM2 integrates cytoskeletal signaling with gene expression to enable reversible differentiation of epithelial cancer cells. PDLIM2 associates with the COP9 signalosome and controls its nuclear translocation and the stability of key transcription factors necessary for either a mesenchymal or an epithelial phenotype. Epithelial cell differentiation and polarized migration associated with epithelial-to-mesenchymal transition (EMT) in cancer requires integration of gene expression with cytoskeletal dynamics. Here we show that the PDZ-LIM domain protein PDLIM2 (Mystique/SLIM), a known cytoskeletal protein and promoter of nuclear nuclear factor κB (NFκB) and signal transducer and activator of transcription (STAT) degradation, regulates transcription factor activity and gene expression through the COP9 signalosome (CSN). Although repressed in certain cancers, PDLIM2 is highly expressed in invasive cancer cells. Here we show that PDLIM2 suppression causes loss of directional migration, inability to polarize the cytoskeleton, and reversal of the EMT phenotype. This is accompanied by altered activity of several transcription factor families, including β-catenin, Ap-1, NFκB, interferon regulatory factors, STATs, JUN, and p53. We also show that PDLIM2 associates with CSN5, and cells with suppressed PDLIM2 exhibit reduced nuclear accumulation and deneddylation activity of the CSN toward the cullin 1 and cullin 3 subunits of cullin-RING ubiquitin ligases. Thus PDLIM2 integrates cytoskeleton signaling with gene expression in epithelial differentiation by controlling the stability of key transcription factors and CSN activity.
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Affiliation(s)
- Rachael A Bowe
- Cell Biology Laboratory, Department of Biochemistry, BioSciences Institute, University College Cork, Cork, Ireland Pfizer-Universidad de Granada-Junta de Andalucía Centre for Genomics and Oncological Research (GENYO), Granada 18016, Spain
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Naumov VA, Generozov EV, Zaharjevskaya NB, Matushkina DS, Larin AK, Chernyshov SV, Alekseev MV, Shelygin YA, Govorun VM. Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips. Epigenetics 2013; 8:921-34. [PMID: 23867710 DOI: 10.4161/epi.25577] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Illumina's Infinium HumanMethylation450 BeadChip arrays were used to examine genome-wide DNA methylation profiles in 22 sample pairs from colorectal cancer (CRC) and adjacent tissues and 19 colon tissue samples from cancer-free donors. We show that the methylation profiles of tumors and healthy tissue samples can be clearly distinguished from one another and that the main source of methylation variability is associated with disease status. We used different statistical approaches to evaluate the methylation data. In general, at the CpG-site level, we found that common CRC-specific methylation patterns consist of at least 15,667 CpG sites that were significantly different from either adjacent healthy tissue or tissue from cancer-free subjects. Of these sites, 10,342 were hypermethylated in CRC, and 5,325 were hypomethylated. Hypermethylated sites were common in the maximum number of sample pairs and were mostly located in CpG islands, where they were significantly enriched for differentially methylated regions known to be cancer-specific. In contrast, hypomethylated sites were mostly located in CpG shores and were generally sample-specific. Despite the considerable variability in methylation data, we selected a panel of 14 highly robust candidates showing methylation marks in genes SND1, ADHFE1, OPLAH, TLX2, C1orf70, ZFP64, NR5A2, and COL4A. This set was successfully cross-validated using methylation data from 209 CRC samples and 38 healthy tissue samples from The Cancer Genome Atlas consortium (AUC = 0.981 [95% CI: 0.9677-0.9939], sensitivity = 100% and specificity = 82%). In summary, this study reports a large number of loci with novel differential methylation statuses, some of which may serve as candidate markers for diagnostic purposes.
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Affiliation(s)
- Vladimir A Naumov
- Research Institute of Physical Chemical Medicine of Federal Medical Biology Agency of Russian Federation; Moscow, Russia
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Kapetanaki MG, Mora AL, Rojas M. Influence of age on wound healing and fibrosis. J Pathol 2013; 229:310-22. [PMID: 23124998 DOI: 10.1002/path.4122] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 09/30/2012] [Accepted: 10/02/2012] [Indexed: 12/18/2022]
Abstract
The incidence and severity of fibrotic lung diseases increase with age, but very little is known about how age-related changes affect the mechanisms that underlie disease emergence and progression. Normal ageing includes accumulation of DNA mutations, oxidative and cell stresses, mitochondria dysfunction, increased susceptibility to apoptosis, telomere length dysfunction and differential gene expression as a consequence of epigenetic changes and miR regulation. These inevitable ageing-related phenomena may cause dysfunction and impaired repair capacity of lung epithelial cells, fibroblasts and MSCs. As a consequence, the composition of the extracellular matrix changes and the dynamic interaction between cells and their environment is damaged, resulting ultimately in predisposition for several diseases. This review summarizes what is known about age-related molecular changes that are implicated in the pathobiology of lung fibrosis in lung tissue.
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Affiliation(s)
- Maria G Kapetanaki
- Dorothy P and Richard P Simmons Center for Interstitial Lung Disease, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Blancafort P, Jin J, Frye S. Writing and rewriting the epigenetic code of cancer cells: from engineered proteins to small molecules. Mol Pharmacol 2012; 83:563-76. [PMID: 23150486 DOI: 10.1124/mol.112.080697] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The epigenomic era has revealed a well-connected network of molecular processes that shape the chromatin landscape. These processes comprise abnormal methylomes, transcriptosomes, genome-wide histone post-transcriptional modifications patterns, histone variants, and noncoding RNAs. The mapping of these processes in large scale by chromatin immunoprecipitation sequencing and other methodologies in both cancer and normal cells reveals novel therapeutic opportunities for anticancer intervention. The goal of this minireview is to summarize pharmacological strategies to modify the epigenetic landscape of cancer cells. These approaches include the use of novel small molecule inhibitors of epigenetic processes specifically deregulated in cancer cells and the design of engineered proteins able to stably reprogram the epigenetic code in cancer cells in a way that is similar to normal cells.
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Affiliation(s)
- Pilar Blancafort
- School of Anatomy, Physiology, and Human Biology, M309, the University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia.
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DNA Hypomethylation and Hemimethylation in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 754:31-56. [DOI: 10.1007/978-1-4419-9967-2_2] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Carvalho RH, Haberle V, Hou J, van Gent T, Thongjuea S, van Ijcken W, Kockx C, Brouwer R, Rijkers E, Sieuwerts A, Foekens J, van Vroonhoven M, Aerts J, Grosveld F, Lenhard B, Philipsen S. Genome-wide DNA methylation profiling of non-small cell lung carcinomas. Epigenetics Chromatin 2012; 5:9. [PMID: 22726460 PMCID: PMC3407794 DOI: 10.1186/1756-8935-5-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 06/22/2012] [Indexed: 12/15/2022] Open
Abstract
Background Non-small cell lung carcinoma (NSCLC) is a complex malignancy that owing to its heterogeneity and poor prognosis poses many challenges to diagnosis, prognosis and patient treatment. DNA methylation is an important mechanism of epigenetic regulation involved in normal development and cancer. It is a very stable and specific modification and therefore in principle a very suitable marker for epigenetic phenotyping of tumors. Here we present a genome-wide DNA methylation analysis of NSCLC samples and paired lung tissues, where we combine MethylCap and next generation sequencing (MethylCap-seq) to provide comprehensive DNA methylation maps of the tumor and paired lung samples. The MethylCap-seq data were validated by bisulfite sequencing and methyl-specific polymerase chain reaction of selected regions. Results Analysis of the MethylCap-seq data revealed a strong positive correlation between replicate experiments and between paired tumor/lung samples. We identified 57 differentially methylated regions (DMRs) present in all NSCLC tumors analyzed by MethylCap-seq. While hypomethylated DMRs did not correlate to any particular functional category of genes, the hypermethylated DMRs were strongly associated with genes encoding transcriptional regulators. Furthermore, subtelomeric regions and satellite repeats were hypomethylated in the NSCLC samples. We also identified DMRs that were specific to two of the major subtypes of NSCLC, adenocarcinomas and squamous cell carcinomas. Conclusions Collectively, we provide a resource containing genome-wide DNA methylation maps of NSCLC and their paired lung tissues, and comprehensive lists of known and novel DMRs and associated genes in NSCLC.
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Affiliation(s)
- Rejane Hughes Carvalho
- Department of Cell Biology, ErasmusMC, PO Box 2040, Rotterdam, CA, 3000, The Netherlands.
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