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Gautam P, Gupta S, Sachan M. Comprehensive DNA methylation profiling by MeDIP-NGS identifies potential genes and pathways for epithelial ovarian cancer. J Ovarian Res 2024; 17:83. [PMID: 38627856 PMCID: PMC11022481 DOI: 10.1186/s13048-024-01395-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/16/2024] [Indexed: 04/19/2024] Open
Abstract
Ovarian cancer, among all gynecologic malignancies, exhibits the highest incidence and mortality rate, primarily because it is often presents with non-specific or no symptoms during its early stages. For the advancement of Ovarian Cancer Diagnosis, it is crucial to identify the potential molecular signatures that could significantly differentiate between healthy and ovarian cancerous tissues and can be used further as a diagnostic biomarker for detecting ovarian cancer. In this study, we investigated the genome-wide methylation patterns in ovarian cancer patients using Methylated DNA Immunoprecipitation (MeDIP-Seq) followed by NGS. Identified differentially methylated regions (DMRs) were further validated by targeted bisulfite sequencing for CpG site-specific methylation profiles. Furthermore, expression validation of six genes by Quantitative Reverse Transcriptase-PCR was also performed. Out of total 120 differentially methylated genes (DMGs), 68 genes were hypermethylated, and 52 were hypomethylated in their promoter region. After analysis, we identified the top 6 hub genes, namely POLR3B, PLXND1, GIGYF2, STK4, BMP2 and CRKL. Interestingly we observed Non-CpG site methylation in the case of POLR3B and CRKL which was statistically significant in discriminating ovarian cancer samples from normal controls. The most significant pathways identified were focal adhesion, the MAPK signaling pathway, and the Ras signaling pathway. Expression analysis of hypermethylated genes was correlated with the downregulation of the genes. POLR3B and GIGYF2 turned out to be the novel genes associated with the carcinogenesis of EOC. Our study demonstrated that methylation profiling through MeDIP-sequencing has effectively identified six potential hub genes and pathways that might exacerbate our understanding of underlying molecular mechanisms of ovarian carcinogenesis.
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Affiliation(s)
- Priyanka Gautam
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Prayagraj, 211004, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Prayagraj, 211004, India.
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Dvorak O, Ndukwe M, Slavickova M, Laco J, Spacek J. DNA methylation of selected tumor suppressor genes in endometrial hyperplasia. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2024; 168:68-73. [PMID: 36628559 DOI: 10.5507/bp.2022.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 12/14/2022] [Indexed: 01/12/2023] Open
Abstract
AIMS To investigate DNA methylation of specific gene promoters in endometrial hyperplasia compared to normal endometrial tissue. MATERIALS AND METHODS To search for epigenetic events, methylation-specific multiplex ligation-dependent probe amplification was employed to compare the methylation status of 64 tissue samples with atypical endometrial hyperplasia, 60 tissue samples with endometrial hyperplasia without atypia, and 40 control tissue samples with normal endometrium. RESULTS Differences in DNA methylation among the groups were found in PTEN, CDH13, and MSH6 promoters (PTEN: atypical hyperplasia 32%, benign hyperplasia 6.8%, normal endometrium 10%; P=0.004; CDH13: atypical hyperplasia, 50%; benign hyperplasia, 43%; normal endometrium 8.1%; P=0.003; MSH6 atypical hyperplasia 84%, benign hyperplasia, 62%; normal endometrium, 52%; P=0.008.) Higher rates of CDH13 promoter methylation were identified in the groups with both forms of endometrial hyperplasia when compared to the control group (atypical hyperplasia, P=0.003, benign hyperplasia, P=0.0002). A higher rate of DNA methylation of the PTEN and MSH6 promoters was observed in samples with atypical endometrial hyperplasia than in samples with benign endometrial hyperplasia (PTEN: P=0.02; MSH6: P=0.01) and samples with normal endometrial tissue (PTEN, P=0.04; MSH6, P=0.006). CONCLUSION DNA methylation of CDH13, PTEN, and MSH6 appear to be involved in the development of endometrial hyperplasia.
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Affiliation(s)
- Ondrej Dvorak
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove and Faculty of Medicine, Charles University, Hradec Kralove, Czech Republic
| | - Munachiso Ndukwe
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove and Faculty of Medicine, Charles University, Hradec Kralove, Czech Republic
| | - Marcela Slavickova
- Department of Clinical Biochemistry and Diagnostics and Osteocenter, University Hospital Hradec Kralove and Faculty of Medicine, Charles University, Hradec Kralove, Czech Republic
| | - Jan Laco
- The Fingerland Department of Pathology, University Hospital Hradec Kralove and Faculty of Medicine, Charles University, Hradec Kralove, Czech Republic
| | - Jiri Spacek
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove and Faculty of Medicine, Charles University, Hradec Kralove, Czech Republic
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Wei Y, Zhao X, Tang H, Ma J, Wang Y, Li L. SIM2: Its Prognostic Significance and Oncogenic Role in Endometrial Carcinoma. Onco Targets Ther 2024; 17:45-61. [PMID: 38292061 PMCID: PMC10826595 DOI: 10.2147/ott.s440788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
Background Endometrial carcinoma ranks as the second most widespread malignancy affecting the reproductive system in females. Effective prognostic biomarkers are required to further improve survival rates for patients. Single-minded homolog 2 (SIM2) is known to participate in neurogenesis as a transcription factor. However, the potential role of SIM2 in endometrial carcinoma remains elusive. Methods Multiple public databases, including TIMER2.0, GEIPA2, UALCAN, LinkedOmics, BioGRID, DAVID and cBioPortal, were used to investigate SIM2 mRNA expression, SIM2-associated genes, PPI network, functional enrichment analysis, SIM2 gene alterations and methylation. The association between SIM2 expression and immune cell infiltrates was explored using GSVA. The effects of gene alterations and methylation on patient survival and CD8+T infiltration were examined using GSCA. Moreover, the prognostic potential of SIM2 was evaluated using COX regression, ROC curves and a nomogram model. Finally, the differential expression and function of SIM2 in UCEC were explored using qPCR, WB, CCK8 and Transwell assays. Results Our findings revealed the heightened expression of SIM2 in endometrial carcinoma, and that its DNA methylation and CNV alterations were correlated with immune infiltration and patients' prognosis. Additionally, functional enrichment revealed the involvement of SIM2 in transcription regulation and signal transduction. Moreover, we performed cell-based experiments to corroborate the oncogenic function of SIM2 in facilitating cell proliferation, migration and invasion. Conclusion Collectively, these results suggest that SIM2 holds promise as both a potential prognostic indicator and a viable treatment target for endometrial carcinoma.
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Affiliation(s)
- Yunfang Wei
- Department of Obstetrics & Gynecology, Shanghai Seventh People’s Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 200137, People’s Republic of China
| | - Xianlei Zhao
- Department of Obstetrics & Gynecology, Shanghai Seventh People’s Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 200137, People’s Republic of China
| | - Hong Tang
- Department of Obstetrics & Gynecology, Shanghai Seventh People’s Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 200137, People’s Republic of China
| | - Jin Ma
- Department of Obstetrics & Gynecology, Shanghai Seventh People’s Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 200137, People’s Republic of China
| | - Yongfeng Wang
- Department of Obstetrics & Gynecology, Shanghai Seventh People’s Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 200137, People’s Republic of China
| | - Linxia Li
- Department of Obstetrics & Gynecology, Shanghai Seventh People’s Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 200137, People’s Republic of China
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4
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Fukuda T, Suzuki E, Fukuda R. Bone morphogenetic protein signaling is a possible therapeutic target in gynecologic cancer. Cancer Sci 2023; 114:722-729. [PMID: 36468782 PMCID: PMC9986083 DOI: 10.1111/cas.15682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/17/2022] [Accepted: 11/26/2022] [Indexed: 12/12/2022] Open
Abstract
Bone morphogenetic proteins (BMPs) belong to the transforming growth factor β (TGFβ) superfamily. BMPs play crucial roles in embryogenesis and bone remodeling. Recently, BMP signaling has been found to have diverse effects on different types of tumors. In this review, we summarized the effects of BMP signaling on gynecologic cancer. BMP signaling has tumor-promoting effects on ovarian cancer (OC) and endometrial cancer (EC), whereas it has tumor-suppressing effects on uterine cervical cancer (UCC). Interestingly, EC has frequent gain-of-function mutations in ACVR1, encoding one of the type I BMP receptors, which are also observed in fibrodysplasia ossificans progressiva and diffuse intrinsic pontine glioma. Little is known about the relationship between BMP signaling and other gynecologic cancers. Tumor-promoting effects of BMP signaling in OC and EC are dependent on the promotion of cancer stemness and epithelial-mesenchymal transition (EMT). In accordance, BMP receptor kinase inhibitors suppress the cell growth and migration of OC and EC. Since both cancer stemness and EMT are associated with chemoresistance, BMP signaling activation might also be an important mechanism by which OC and EC patients acquire chemoresistance. Therefore, BMP inhibitors are promising for OC and EC patients even if they become resistant to standard chemotherapy. In contrast, BMP signaling inhibits UCC growth in vitro. However, the in vivo effects of BMP signaling have not been elucidated in UCC. In conclusion, BMP signaling has a variety of functions, depending on the types of gynecologic cancer. Therefore, targeting BMP signaling should improve the treatment of patients with gynecologic cancer.
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Affiliation(s)
- Tomohiko Fukuda
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
| | - Eri Suzuki
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
| | - Risa Fukuda
- Division of Dermatology, National Center for Child Health and Development, Tokyo, Japan
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Ho CM, Yen TL, Chien TY, Huang SH. Distinct promotor methylation at tumor suppressive genes in ovarian cancer stromal progenitor cells and ovarian cancer and its clinical implication. Am J Cancer Res 2022; 12:5325-5341. [PMID: 36504889 PMCID: PMC9729910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/12/2022] [Indexed: 12/15/2022] Open
Abstract
Aberrant CpG-island methylation affects ovarian cancer progression. The promotor methylation changes at tumor suppressive genes in ovarian cancer stromal progenitor cells (OCSPCs) and epithelial ovarian cancer (EOC) tissues and their clinical implication remains unexplored. We systemically analyzed the promoter methylation status of 40 tumor suppressor genes (TSGs) associated with cancer in paired epithelial-like and mesenchymal-like OCSPCs and ovarian cancer cells by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). The effect of DNA methylation on gene expression was confirmed using qRT-PCR. The differential frequencies of TSGs' promoter methylation among matched epithelial-like or mesenchymal-like OCSPCs from tissues and ascites and ovarian cancer tissues were further validated in cancer tissues and correlated with clinicopathological features and survival outcomes of patients. According to the promoter methylation frequencies of the 40 TSGs, promoters of RASSF1A were the only significantly hypomethylated in epithelial-like OCSPCs from tissues than those from ascites and bulk tumor cells (0% vs 38% vs 45%, P=0.039 by Fisher's exact test). The most frequencies at promotor hypermethylation of TSGs in mesenchymal-like OCSPCs from ascites which processed aggressiveness were CDKN2B (73%) followed by CCND2 (45%) and RASSF1A (45%). Forty-three percent (47/110) of RASSF1A and 45% of CCND2 were validated as a frequently hypermethylated gene in an independent set of 110 EOC tissues in contrast to none (0/60) and 12% (10/60) of benign ovarian cysts (both P<0.001). Functional experiments revealed overexpression of CCND2 or CDKN2B in MSc-OCSPCs decreases EMT, invasion, and spheroid formation in EOC, and abolishes DNMT1 and COL6A3 expression. However, for the expected 5-year overall survival (OS) for patients with methylated RASSF1A, CCND2, and CDKN2B, only RASSF1A was significantly worse than those without methylated RASSF1A (56% vs 80%, p=0.022). Taken together, overexpression of CCND2 and CDKN2B decreased the aggressiveness of mesenchymal-like OCSPCs from ascites which may represent a potential therapeutic target for EOC. Promotor hypomethylation at RASSF1A in OCSPCs from EOC tissues and changes to hypermethylation of EOC and OCSPCs from ascites could predict poor survival outcomes for EOC patients compared to without those changes of CCND2 and CDKN2B.
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Affiliation(s)
- Chih-Ming Ho
- Gynecologic Cancer Center, Department of Obstetrics and Gynecology, Cathay General HospitalTaipei, Taiwan,School of Medicine, Fu Jen Catholic UniversityHsinchuang, New Taipei City, Taiwan,Department of Medical Research, Cathay General HospitalNew Taipei City, Taiwan
| | - Ting-Lin Yen
- Department of Medical Research, Cathay General HospitalNew Taipei City, Taiwan
| | - Tsai-Yen Chien
- Gynecologic Cancer Center, Department of Obstetrics and Gynecology, Cathay General HospitalTaipei, Taiwan
| | - Shih-Hung Huang
- Department of Pathology, Cathay General HospitalTaipei, Taiwan
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6
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Understanding the versatile roles and applications of EpCAM in cancers: from bench to bedside. Exp Hematol Oncol 2022; 11:97. [PMID: 36369033 PMCID: PMC9650829 DOI: 10.1186/s40164-022-00352-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022] Open
Abstract
Epithelial cell adhesion molecule (EpCAM) functions not only in physiological processes but also participates in the development and progression of cancer. In recent decades, extensive efforts have been made to decipher the role of EpCAM in cancers. Great advances have been achieved in elucidating its structure, molecular functions, pathophysiological mechanisms, and clinical applications. Beyond its well-recognized role as a biomarker of cancer stem cells (CSCs) or circulating tumor cells (CTCs), EpCAM exhibits novel and promising value in targeted therapy. At the same time, the roles of EpCAM in cancer progression are found to be highly context-dependent and even contradictory in some cases. The versatile functional modules of EpCAM and its communication with other signaling pathways complicate the study of this molecule. In this review, we start from the structure of EpCAM and focus on communication with other signaling pathways. The impacts on the biology of cancers and the up-to-date clinical applications of EpCAM are also introduced and summarized, aiming to shed light on the translational prospects of EpCAM.
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Wu E, Fan X, Tang T, Li J, Wang J, Liu X, Zungar Z, Ren J, Wu C, Shen B. Biomarkers discovery for endometrial cancer: A graph convolutional sample network method. Comput Biol Med 2022; 150:106200. [PMID: 37859290 DOI: 10.1016/j.compbiomed.2022.106200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/20/2022] [Accepted: 10/09/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Endometrial carcinoma is the sixth most common cancer in women worldwide. Importantly, endometrial cancer is among the few types of cancers with patient mortality that is still increasing, which indicates that the improvement in its diagnosis and treatment is still urgent. Moreover, biomarker discovery is essential for precise classification and prognostic prediction of endometrial cancer. METHODS A novel graph convolutional sample network method was used to identify and validate biomarkers for the classification of endometrial cancer. The sample networks were first constructed for each sample, and the gene pairs with high frequencies were identified to construct a subtype-specific network. Putative biomarkers were then screened using the highest degrees in the subtype-specific network. Finally, simplified sample networks are constructed using the biomarkers for the graph convolutional network (GCN) training and prediction. RESULTS Putative biomarkers (23) were identified using the novel bioinformatics model. These biomarkers were then rationalised with functional analyses and were found to be correlated to disease survival with network entropy characterisation. These biomarkers will be helpful in future investigations of the molecular mechanisms and therapeutic targets of endometrial cancers. CONCLUSIONS A novel bioinformatics model combining sample network construction with GCN modelling is proposed and validated for biomarker discovery in endometrial cancer. The model can be generalized and applied to biomarker discovery in other complex diseases.
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Affiliation(s)
- Erman Wu
- Institutes for Systems Genetics, Frontiers Science Centre for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xuemeng Fan
- Institutes for Systems Genetics, Frontiers Science Centre for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Tong Tang
- Institutes for Systems Genetics, Frontiers Science Centre for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Department of Computer Science and Information Technologies, Elviña Campus, University of A Coruña, A Coruña, Spain
| | - Jingjing Li
- Institutes for Systems Genetics, Frontiers Science Centre for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Jiao Wang
- Institutes for Systems Genetics, Frontiers Science Centre for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xingyun Liu
- Institutes for Systems Genetics, Frontiers Science Centre for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Zayatta Zungar
- School of Medicine, University of New England, Armidale, NSW, 2351, Australia
| | - Jiaojiao Ren
- School of Electronic Information and Electrical Engineering, Chengdu University, Chengdu, China
| | - Cong Wu
- Institutes for Systems Genetics, Frontiers Science Centre for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Centre for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
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Xu T, Ding H, Chen J, Lei J, Zhao M, Ji B, Chen Y, Qin S, Gao Q. Research Progress of DNA Methylation in Endometrial Cancer. Biomolecules 2022; 12:biom12070938. [PMID: 35883495 PMCID: PMC9312849 DOI: 10.3390/biom12070938] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Endometrial cancer (EC)) is one of the most common malignant tumors of the female genital system, with an increasing incidence and mortality, worldwide. Although the therapeutic strategy of EC is still complicated and challenging, further understanding of carcinogenesis from a gene perspective would allow an effort to improve therapeutic precision in this complex malignancy. DNA methylation is the most widely studied epigenetic alteration in human tumors. Aberrant DNA methylation events, resulting in altered gene expression, are features of many tumor types. In this review, we provide an update on evidence about the roles of aberrant DNA methylation within some classical tumor suppressor genes and oncogenes in endometrial carcinogenesis, and report on recent advances in the understanding of the contribution of aberrant DNA methylation to EC, as well as opportunities and challenges of DNA methylation in EC management and prevention.
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Affiliation(s)
- Ting Xu
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (T.X.); (J.L.); (M.Z.); (B.J.)
| | - Hongmei Ding
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (H.D.); (J.C.)
| | - Jie Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (H.D.); (J.C.)
| | - Jiahui Lei
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (T.X.); (J.L.); (M.Z.); (B.J.)
| | - Meng Zhao
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (T.X.); (J.L.); (M.Z.); (B.J.)
| | - Bingyu Ji
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (T.X.); (J.L.); (M.Z.); (B.J.)
| | - Youguo Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (H.D.); (J.C.)
- Correspondence: (Y.C.); (S.Q.); (Q.G.); Tel.: +86-512-67781951 (Y.C. & S.Q. & Q.G.); Fax: +86-0512-67780922 (Y.C. & S.Q. & Q.G.)
| | - Songbing Qin
- Department of Radiation Oncology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
- Correspondence: (Y.C.); (S.Q.); (Q.G.); Tel.: +86-512-67781951 (Y.C. & S.Q. & Q.G.); Fax: +86-0512-67780922 (Y.C. & S.Q. & Q.G.)
| | - Qinqin Gao
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (T.X.); (J.L.); (M.Z.); (B.J.)
- Correspondence: (Y.C.); (S.Q.); (Q.G.); Tel.: +86-512-67781951 (Y.C. & S.Q. & Q.G.); Fax: +86-0512-67780922 (Y.C. & S.Q. & Q.G.)
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Tumor Promoting Effect of BMP Signaling in Endometrial Cancer. Int J Mol Sci 2021; 22:ijms22157882. [PMID: 34360647 PMCID: PMC8346149 DOI: 10.3390/ijms22157882] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/10/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
The effects of bone morphogenetic proteins (BMPs), members of the transforming growth factor-β (TGF-β) family, in endometrial cancer (EC) have yet to be determined. In this study, we analyzed the TCGA and MSK-IMPACT datasets and investigated the effects of BMP2 and of TWSG1, a BMP antagonist, on Ishikawa EC cells. Frequent ACVR1 mutations and high mRNA expressions of BMP ligands and receptors were observed in EC patients of the TCGA and MSK-IMPACT datasets. Ishikawa cells secreted higher amounts of BMP2 compared with ovarian cancer cell lines. Exogenous BMP2 stimulation enhanced EC cell sphere formation via c-KIT induction. BMP2 also induced EMT of EC cells, and promoted migration by induction of SLUG. The BMP receptor kinase inhibitor LDN193189 augmented the growth inhibitory effects of carboplatin. Analyses of mRNAs of several BMP antagonists revealed that TWSG1 mRNA was abundantly expressed in Ishikawa cells. TWSG1 suppressed BMP7-induced, but not BMP2-induced, EC cell sphere formation and migration. Our results suggest that BMP signaling promotes EC tumorigenesis, and that TWSG1 antagonizes BMP7 in EC. BMP signaling inhibitors, in combination with chemotherapy, might be useful in the treatment of EC patients.
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Functional Implications of the Dynamic Regulation of EpCAM during Epithelial-to-Mesenchymal Transition. Biomolecules 2021; 11:biom11070956. [PMID: 34209658 PMCID: PMC8301972 DOI: 10.3390/biom11070956] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 12/12/2022] Open
Abstract
Epithelial cell adhesion molecule (EpCAM) is a transmembrane glycoprotein expressed in epithelial tissues. EpCAM forms intercellular, homophilic adhesions, modulates epithelial junctional protein complex formation, and promotes epithelial tissue homeostasis. EpCAM is a target of molecular therapies and plays a prominent role in tumor biology. In this review, we focus on the dynamic regulation of EpCAM expression during epithelial-to-mesenchymal transition (EMT) and the functional implications of EpCAM expression on the regulation of EMT. EpCAM is frequently and highly expressed in epithelial cancers, while silenced in mesenchymal cancers. During EMT, EpCAM expression is downregulated by extracellular signal-regulated kinases (ERK) and EMT transcription factors, as well as by regulated intramembrane proteolysis (RIP). The functional impact of EpCAM expression on tumor biology is frequently dependent on the cancer type and predominant oncogenic signaling pathways, suggesting that the role of EpCAM in tumor biology and EMT is multifunctional. Membrane EpCAM is cleaved in cancers and its intracellular domain (EpICD) is transported into the nucleus and binds β-catenin, FHL2, and LEF1. This stimulates gene transcription that promotes growth, cancer stem cell properties, and EMT. EpCAM is also regulated by epidermal growth factor receptor (EGFR) signaling and the EpCAM ectoderm (EpEX) is an EGFR ligand that affects EMT. EpCAM is expressed on circulating tumor and cancer stem cells undergoing EMT and modulates metastases and cancer treatment responses. Future research exploring EpCAM’s role in EMT may reveal additional therapeutic opportunities.
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A ten-gene methylation signature as a novel biomarker for improving prediction of prognosis and indicating gene targets in endometrial cancer. Genomics 2021; 113:2032-2044. [PMID: 33915245 DOI: 10.1016/j.ygeno.2021.04.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 03/10/2021] [Accepted: 04/23/2021] [Indexed: 12/17/2022]
Abstract
Endometrial cancer (EC) is a common female reproductive tumor worldwide. Nonetheless, the pathogenesis of EC still remains ambiguous and associated epigenetic mechanism still to be explored. The goal of this study is to investigate whether gene methylation signature is associated with overall survival (OS) for EC patients. In this study, a 10-gene methylation risk model was built and the OS in high- and low-risk groups was significant different. The area under the ROC curve (AUC) of this model was 0.856 at 5 years survival. The nomogram could accurately predict the OS in EC patients, with concordance index and AUC at 5 year survival reached 0.796 and 0.792, respectively. Furthermore, we verified the nomogram with 24 patients in our center and the Kaplan-Meier survival curve also proved to be significantly different (p < 0.01). WGCNA revealed a key gene group for the model and further bioinformatics analysis indicated 6 genes as the hub genes in the module. Knockdown of MMP12 inhibited the proliferation, invasion and metastasis of EC cells. After all, a methylation signature and a nomogram based on this signature were constructed, and they could both predict survival in patients with EC. Moreover, WGCNA model identified MMP12 as a potential target for the treatment of EC.
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12
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Fan Y, Li X, Tian L, Wang J. Identification of a Metabolism-Related Signature for the Prediction of Survival in Endometrial Cancer Patients. Front Oncol 2021; 11:630905. [PMID: 33763366 PMCID: PMC7982602 DOI: 10.3389/fonc.2021.630905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/27/2021] [Indexed: 12/13/2022] Open
Abstract
Objective Endometrial cancer (EC) is one of the most common gynecologic malignancies. The present study aims to identify a metabolism-related biosignature for EC and explore the molecular immune-related mechanisms underlying the tumorigenesis of EC. Methods Transcriptomics and clinical data of EC were retrieved from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Common differentially expressed metabolism-related genes were extracted and a risk signature was identified by using the least absolute shrinkage and selection operator (LASSO) regression analysis method. A nomogram integrating the prognostic model and the clinicopathological characteristics was established and validated by a cohort of clinical EC patients. Furthermore, the immune and stromal scores were observed and the infiltration of immune cells in EC cells was analyzed. Results Six genes, including CA3, HNMT, PHGDH, CD38, PSAT1, and GPI, were selected for the development of the risk prediction model. The Kaplan-Meier curve indicated that patients in the low-risk group had considerably better overall survival (OS) (P = 7.874e-05). Then a nomogram was constructed and could accurately predict the OS (AUC = 0.827, 0.821, 0.845 at 3-, 5-, and 7-year of OS). External validation with clinical patients showed that patients with low risk scores had a longer OS (p = 0.04). Immune/stromal scores and infiltrating density of six types of immune cells were lower in high-risk group. Conclusions In summary, our work provided six potential metabolism-related biomarkers as well as a nomogram for the prognosis of EC patients, and explored the underlying mechanism involved in the progression of EC.
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Affiliation(s)
- Yuan Fan
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Xingchen Li
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Li Tian
- Reproductive Medical Center, Peking University People's Hospital, Beijing, China
| | - Jianliu Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
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13
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Li X, Yin F, Fan Y, Cheng Y, Dong Y, Zhou J, Wang Z, Li X, Wang J. Establishment and validation of a prognostic nomogram based on a novel five-DNA methylation signature for survival in endometrial cancer patients. Cancer Med 2020; 10:693-708. [PMID: 33350104 PMCID: PMC7877372 DOI: 10.1002/cam4.3576] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/06/2020] [Accepted: 10/03/2020] [Indexed: 12/12/2022] Open
Abstract
Background This study aimed to explore the prognostic role of DNA methylation pattern in endometrial cancer (EC) patients. Methods Differentially methylated genes (DMGs) of EC patients with distinct survival from The Cancer Genome Atlas (TCGA) database were analyzed to identify methylated genes as biomarkers for EC prognosis. The Least Absolute Shrinkage and Selection Operator (LASSO) analysis was used to construct a risk score model. A nomogram was built based on analysis combining the risk score model with clinicopathological signatures together, and then verified in the validation cohort and patients in our own center. Results In total, 157 DMGs were identified between different prognostic groups. Based on the LASSO analysis, five genes (GBP4, OR8K3, GABRA2, RIPPLY2, and TRBV5‐7) were screened for the establishment of risk score model. The model outperformed in prognostic accuracy at varying follow‐up times (AUC for 3 years: 0.824, 5 years: 0.926, and 7 years: 0.853). Multivariate analysis identified four independent risk factors including menopausal status (HR = 3.006, 95%CI: 1.062–8.511, p = 0.038), recurrence (HR = 2.116, 95%CI: 1.061–4.379, p = 0.046), lymph node metastasis (LNM, HR = 3.465, 95%CI: 1.225–9.807, p = 0.019), and five‐DNA methylation risk model (HR = 3.654, 95%CI: 1.458–9.161, p = 0.006) in training cohort. The performance of the nomogram was good in the training (AUC = 0.828), validation (AUC = 0.866) and the whole cohorts (AUC = 0.843). Furthermore, we verified the nomogram with 24 patients in our center and the Kaplan–Meier survival curve also proved to be significantly different (p < 0.01). The subgroup analysis in different stratifications indicated that the accuracy was high in different subgroups for age, histological type, tumor grade, and clinical stage (all p < 0.01). Conclusions Briefly, our work established and verified a five‐DNA methylation risk model, and a nomogram merging the model with clinicopathological characteristics to facilitate individual prediction of EC patients for clinicians.
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Affiliation(s)
- Xingchen Li
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Fufen Yin
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Yuan Fan
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Yuan Cheng
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Yangyang Dong
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Jingyi Zhou
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China.,Beijing Key Laboratory of Female Pelvic Floor Disorders Diseases, Beijing, China
| | - Zhiqi Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Xiaoping Li
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Jianliu Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China.,Beijing Key Laboratory of Female Pelvic Floor Disorders Diseases, Beijing, China
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14
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Gires O, Pan M, Schinke H, Canis M, Baeuerle PA. Expression and function of epithelial cell adhesion molecule EpCAM: where are we after 40 years? Cancer Metastasis Rev 2020; 39:969-987. [PMID: 32507912 PMCID: PMC7497325 DOI: 10.1007/s10555-020-09898-3] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
EpCAM (epithelial cell adhesion molecule) was discovered four decades ago as a tumor antigen on colorectal carcinomas. Owing to its frequent and high expression on carcinomas and their metastases, EpCAM serves as a prognostic marker, a therapeutic target, and an anchor molecule on circulating and disseminated tumor cells (CTCs/DTCs), which are considered the major source for metastatic cancer cells. Today, EpCAM is reckoned as a multi-functional transmembrane protein involved in the regulation of cell adhesion, proliferation, migration, stemness, and epithelial-to-mesenchymal transition (EMT) of carcinoma cells. To fulfill these functions, EpCAM is instrumental in intra- and intercellular signaling as a full-length molecule and following regulated intramembrane proteolysis, generating functionally active extra- and intracellular fragments. Intact EpCAM and its proteolytic fragments interact with claudins, CD44, E-cadherin, epidermal growth factor receptor (EGFR), and intracellular signaling components of the WNT and Ras/Raf pathways, respectively. This plethora of functions contributes to shaping intratumor heterogeneity and partial EMT, which are major determinants of the clinical outcome of carcinoma patients. EpCAM represents a marker for the epithelial status of primary and systemic tumor cells and emerges as a measure for the metastatic capacity of CTCs. Consequentially, EpCAM has reclaimed potential as a prognostic marker and target on primary and systemic tumor cells.
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Affiliation(s)
- Olivier Gires
- Department of Otorhinolaryngology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany.
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum, Neuherberg, Germany.
| | - Min Pan
- Department of Otorhinolaryngology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, China
| | - Henrik Schinke
- Department of Otorhinolaryngology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Martin Canis
- Department of Otorhinolaryngology, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Patrick A Baeuerle
- Institute for Immunology, LMU Munich, Grosshadernerstr. 9, 82152 Planegg, Martinsried, Germany
- MPM Capital, Cambridge MA, 450 Kendall Street, Cambridge, MA, 02142, USA
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15
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Eze IC, Jeong A, Schaffner E, Rezwan FI, Ghantous A, Foraster M, Vienneau D, Kronenberg F, Herceg Z, Vineis P, Brink M, Wunderli JM, Schindler C, Cajochen C, Röösli M, Holloway JW, Imboden M, Probst-Hensch N. Genome-Wide DNA Methylation in Peripheral Blood and Long-Term Exposure to Source-Specific Transportation Noise and Air Pollution: The SAPALDIA Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2020; 128:67003. [PMID: 32484729 PMCID: PMC7263738 DOI: 10.1289/ehp6174] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 04/27/2020] [Accepted: 04/30/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Few epigenome-wide association studies (EWAS) on air pollutants exist, and none have been done on transportation noise exposures, which also contribute to environmental burden of disease. OBJECTIVE We performed mutually independent EWAS on transportation noise and air pollution exposures. METHODS We used data from two time points of the Swiss Cohort Study on Air Pollution and Lung and Heart Diseases in Adults (SAPALDIA) from 1,389 participants contributing 2,542 observations. We applied multiexposure linear mixed-effects regressions with participant-level random intercept to identify significant Cytosine-phosphate-Guanine (CpG) sites and differentially methylated regions (DMRs) in relation to 1-y average aircraft, railway, and road traffic day-evening-night noise (Lden); nitrogen dioxide (NO 2 ); and particulate matter (PM) with aerodynamic diameter < 2.5 μ m (PM 2.5 ). We performed candidate (CpG-based; cross-systemic phenotypes, combined into "allostatic load") and agnostic (DMR-based) pathway enrichment tests, and replicated previously reported air pollution EWAS signals. RESULTS We found no statistically significant CpGs at false discovery rate < 0.05 . However, 14, 48, 183, 8, and 71 DMRs independently associated with aircraft, railway, and road traffic Lden; NO 2 ; and PM 2.5 , respectively, with minimally overlapping signals. Transportation Lden and air pollutants tendentially associated with decreased and increased methylation, respectively. We observed significant enrichment of candidate DNA methylation related to C-reactive protein and body mass index (aircraft, road traffic Lden, and PM 2.5 ), renal function and "allostatic load" (all exposures). Agnostic functional networks related to cellular immunity, gene expression, cell growth/proliferation, cardiovascular, auditory, embryonic, and neurological systems development were enriched. We replicated increased methylation in cg08500171 (NO 2 ) and decreased methylation in cg17629796 (PM 2.5 ). CONCLUSIONS Mutually independent DNA methylation was associated with source-specific transportation noise and air pollution exposures, with distinct and shared enrichments for pathways related to inflammation, cellular development, and immune responses. These findings contribute in clarifying the pathways linking these exposures and age-related diseases but need further confirmation in the context of mediation analyses. https://doi.org/10.1289/EHP6174.
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Affiliation(s)
- Ikenna C Eze
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Ayoung Jeong
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Emmanuel Schaffner
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- School of Water, Energy and Environment, Cranfield University, Cranfield, UK
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Maria Foraster
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- University Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiologia y Salud Publica, Madrid, Spain
- Blanquerna School of Health Science, Universitat Ramon Llull, Barcelona, Spain
| | - Danielle Vienneau
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, UK
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Mark Brink
- Federal Office for the Environment, Bern, Switzerland
| | - Jean-Marc Wunderli
- Empa Laboratory for Acoustics/Noise Control, Swiss Federal Laboratories for Material Science and Technology, Dübendorf, Switzerland
| | - Christian Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Christian Cajochen
- Center for Chronobiology, Psychiatric Hospital of the University of Basel, and Transfaculty Research Platform Molecular and Cognitive Neurosciences (MCN), Basel, Switzerland
| | - Martin Röösli
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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16
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Yahyazadeh Mashhadi SM, Kazemimanesh M, Arashkia A, Azadmanesh K, Meshkat Z, Golichenari B, Sahebkar A. Shedding light on the EpCAM: An overview. J Cell Physiol 2019; 234:12569-12580. [DOI: 10.1002/jcp.28132] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/30/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Seyed Muhammad Yahyazadeh Mashhadi
- Department of Virology Pasteur Institute of Iran Tehran Iran
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences Mashhad Iran
- Production Expert at Samandaroo 8 (Biotech Pharmaceutical) Co. Mashhad Iran
| | | | - Arash Arashkia
- Department of Virology Pasteur Institute of Iran Tehran Iran
| | | | - Zahra Meshkat
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences Mashhad Iran
| | - Behrouz Golichenari
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences Mashhad Iran
| | - Amirhosein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences Mashhad Iran
- Neurogenic inflammation Research Center, Mashhad University of Medical Sciences Mashhad Iran
- School of Pharmacy, Mashhad University of Medical Sciences Mashhad Iran
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17
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Mu W, Wang Z, Zöller M. Ping-Pong-Tumor and Host in Pancreatic Cancer Progression. Front Oncol 2019; 9:1359. [PMID: 31921628 PMCID: PMC6927459 DOI: 10.3389/fonc.2019.01359] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
Metastasis is the main cause of high pancreatic cancer (PaCa) mortality and trials dampening PaCa mortality rates are not satisfying. Tumor progression is driven by the crosstalk between tumor cells, predominantly cancer-initiating cells (CIC), and surrounding cells and tissues as well as distant organs, where tumor-derived extracellular vesicles (TEX) are of major importance. A strong stroma reaction, recruitment of immunosuppressive leukocytes, perineural invasion, and early spread toward the peritoneal cavity, liver, and lung are shared with several epithelial cell-derived cancer, but are most prominent in PaCa. Here, we report on the state of knowledge on the PaCIC markers Tspan8, alpha6beta4, CD44v6, CXCR4, LRP5/6, LRG5, claudin7, EpCAM, and CD133, which all, but at different steps, are engaged in the metastatic cascade, frequently via PaCIC-TEX. This includes the contribution of PaCIC markers to TEX biogenesis, targeting, and uptake. We then discuss PaCa-selective features, where feedback loops between stromal elements and tumor cells, including distorted transcription, signal transduction, and metabolic shifts, establish vicious circles. For the latter particularly pancreatic stellate cells (PSC) are responsible, furnishing PaCa to cope with poor angiogenesis-promoted hypoxia by metabolic shifts and direct nutrient transfer via vesicles. Furthermore, nerves including Schwann cells deliver a large range of tumor cell attracting factors and Schwann cells additionally support PaCa cell survival by signaling receptor binding. PSC, tumor-associated macrophages, and components of the dysplastic stroma contribute to perineural invasion with signaling pathway activation including the cholinergic system. Last, PaCa aggressiveness is strongly assisted by the immune system. Although rich in immune cells, only immunosuppressive cells and factors are recovered in proximity to tumor cells and hamper effector immune cells entering the tumor stroma. Besides a paucity of immunostimulatory factors and receptors, immunosuppressive cytokines, myeloid-derived suppressor cells, regulatory T-cells, and M2 macrophages as well as PSC actively inhibit effector cell activation. This accounts for NK cells of the non-adaptive and cytotoxic T-cells of the adaptive immune system. We anticipate further deciphering the molecular background of these recently unraveled intermingled phenomena may turn most lethal PaCa into a curatively treatable disease.
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Affiliation(s)
- Wei Mu
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Wei Mu
| | - Zhe Wang
- Department of Oncology, The First Affiliated Hospital of Guangdong, Pharmaceutical University, Guangzhou, China
| | - Margot Zöller
- Department of Oncology, The First Affiliated Hospital of Guangdong, Pharmaceutical University, Guangzhou, China
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18
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Zhang W, Chen JH, Shan T, Aguilera-Barrantes I, Wang LS, Huang THM, Rader JS, Sheng X, Huang YW. miR-137 is a tumor suppressor in endometrial cancer and is repressed by DNA hypermethylation. J Transl Med 2018; 98:1397-1407. [PMID: 29955087 PMCID: PMC6214735 DOI: 10.1038/s41374-018-0092-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 01/24/2023] Open
Abstract
Endometrial cancer is the most common gynecological cancer in the United States. We wanted to identify epigenetic aberrations involving microRNAs (miRNAs), whose genes become hypermethylated in endometrial primary tumors. By integrating known miRNA sequences from the miRNA database (miRBase) with DNA methylation data from methyl-CpG-capture sequencing, we identified 111 differentially methylated regions (DMRs) associated with CpG islands (CGIs) and miRNAs. Among them, 22 DMRs related to 29 miRNAs and within 8 kb of CGIs were hypermethylated in endometrial tumors but not in normal endometrium. miR-137 was further validated in additional endometrial primary tumors. Hypermethylation of miR-137 was found in both endometrioid and serous endometrial cancer (P < 0.01), and it led to the loss of miR-137 expression. Treating hypermethylated endometrial cancer cells with epigenetic inhibitors reactivated miR-137. Moreover, genetic overexpression of miR-137 suppressed cancer cell proliferation and colony formation in vitro. When transfected cancer cells were implanted into nude mice, the cells that overexpressed miR-137 grew more slowly and formed smaller tumors (P < 0.05) than vector transfectants. Histologically, xenograft tumors from cancer cells expressing miR-137 were less proliferative (P < 0.05), partly due to inhibition of EZH2 and LSD1 expression (P < 0.01) in both the transfected cancer cells and tumors. Reporter assays indicated that miR-137 targets EZH2 and LSD1. These results suggest that miR-137 is a tumor suppressor that is repressed in endometrial cancer because the promoter of its gene becomes hypermethylated.
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Affiliation(s)
- Wei Zhang
- Department of Gynecology Oncology, Shandong Provincial Cancer Hospital, Jinan, Shandong, China,Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jo-Hsin Chen
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Tianjiao Shan
- Department of Gynecology Oncology, Shandong Provincial Cancer Hospital, Jinan, Shandong, China,Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Li-Shu Wang
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Tim Hui-Ming Huang
- Department of Molecular Medicine, and Cancer Therapy & Research Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Janet S. Rader
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Xiugui Sheng
- Department of Gynecology Oncology, Shandong Provincial Cancer Hospital, Jinan, Shandong, China. .,Cancer Hospital of Chinese Academy of Medical Sciences, Shenzhen Center, Chaoyang Qu, Beijing Shi, China.
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA.
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19
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Zhu X, Zhang Q, Ho ED, Yu KHO, Liu C, Huang TH, Cheng ASL, Kao B, Lo E, Yip KY. START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries. BMC Genomics 2017; 18:749. [PMID: 28938868 PMCID: PMC5610441 DOI: 10.1186/s12864-017-4071-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/16/2017] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND A genomic signal track is a set of genomic intervals associated with values of various types, such as measurements from high-throughput experiments. Analysis of signal tracks requires complex computational methods, which often make the analysts focus too much on the detailed computational steps rather than on their biological questions. RESULTS Here we propose Signal Track Query Language (STQL) for simple analysis of signal tracks. It is a Structured Query Language (SQL)-like declarative language, which means one only specifies what computations need to be done but not how these computations are to be carried out. STQL provides a rich set of constructs for manipulating genomic intervals and their values. To run STQL queries, we have developed the Signal Track Analytical Research Tool (START, http://yiplab.cse.cuhk.edu.hk/start/ ), a system that includes a Web-based user interface and a back-end execution system. The user interface helps users select data from our database of around 10,000 commonly-used public signal tracks, manage their own tracks, and construct, store and share STQL queries. The back-end system automatically translates STQL queries into optimized low-level programs and runs them on a computer cluster in parallel. We use STQL to perform 14 representative analytical tasks. By repeating these analyses using bedtools, Galaxy and custom Python scripts, we show that the STQL solution is usually the simplest, and the parallel execution achieves significant speed-up with large data files. Finally, we describe how a biologist with minimal formal training in computer programming self-learned STQL to analyze DNA methylation data we produced from 60 pairs of hepatocellular carcinoma (HCC) samples. CONCLUSIONS Overall, STQL and START provide a generic way for analyzing a large number of genomic signal tracks in parallel easily.
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Affiliation(s)
- Xinjie Zhu
- Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Qiang Zhang
- School of Computing, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Eric Dun Ho
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Ken Hung-On Yu
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.,Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Chris Liu
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Tim H Huang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Alfred Sze-Lok Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Ben Kao
- Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong.
| | - Eric Lo
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong. .,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong. .,CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong. .,Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
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20
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Bartosch C, Lopes JM, Jerónimo C. Epigenetics in endometrial carcinogenesis - part 1: DNA methylation. Epigenomics 2017; 9:737-755. [PMID: 28470096 DOI: 10.2217/epi-2016-0166] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Carcinogenesis is a multistep multifactorial process that involves the accumulation of genetic and epigenetic alterations. In the past two decades, there has been an exponential growth of knowledge establishing the importance of epigenetic changes in cancer. Our work focused on reviewing the main role of epigenetics in the pathogenesis of endometrial carcinoma, highlighting the reported results concerning each epigenetic mechanistic layer. The present review is the first part of this work, in which we examined the contribution of DNA methylation alterations for endometrial carcinogenesis.
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Affiliation(s)
- Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology & Oncology, Medical Faculty, University of Porto, Porto, Portugal.,Porto Comprehensive Cancer Center (P.ccc), Porto, Portugal
| | - José Manuel Lopes
- Department of Pathology & Oncology, Medical Faculty, University of Porto, Porto, Portugal.,Department of Pathology, Centro Hospitalar São João (CHSJ), Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology & Immunology, University of Porto, Porto, Portugal.,I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal.,Porto Comprehensive Cancer Center (P.ccc), Porto, Portugal.,Department of Pathology & Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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21
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Fish TJ, Benninghoff AD. DNA methylation in lung tissues of mouse offspring exposed in utero to polycyclic aromatic hydrocarbons. Food Chem Toxicol 2017; 109:703-713. [PMID: 28476633 DOI: 10.1016/j.fct.2017.04.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/29/2017] [Accepted: 04/29/2017] [Indexed: 12/19/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) comprise an important class of environmental pollutants that are known to cause lung cancer in animals and are suspected lung carcinogens in humans. Moreover, evidence from cell-based studies points to PAHs as modulators of the epigenome. The objective of this work was to assess patterns of genome-wide DNA methylation in lung tissues of adult offspring initiated in utero with the transplacental PAH carcinogens dibenzo [def,p]chrysene (DBC) or benzo [a]pyrene (BaP). Genome-wide methylation patterns for normal (not exposed), normal adjacent and lung tumor tissues obtained from adult offspring were determined using methylated DNA immunoprecipitation (MeDIP) with the NimbleGen mouse DNA methylation CpG island array. Lung tumor incidence in 45-week old mice initiated with BaP was 32%, much lower than that of the DBC-exposed offspring at 96%. Also, male offspring appeared more susceptible to BaP as compared to females. Distinct patterns of DNA methylation were associated with non-exposed, normal adjacent and adenocarcinoma lung tissues, as determined by principal components, hierarchical clustering and gene ontology analyses. From these methylation profiles, a set of genes of interest was identified that includes potential important targets for epigenetic modification during the process of lung tumorigenesis in animals exposed to environmental PAHs.
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Affiliation(s)
- Trevor J Fish
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322, USA
| | - Abby D Benninghoff
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322, USA; School of Veterinary Medicine, Utah State University, Logan, UT 84322, USA.
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22
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Trimarchi MP, Yan P, Groden J, Bundschuh R, Goodfellow PJ. Identification of endometrial cancer methylation features using combined methylation analysis methods. PLoS One 2017; 12:e0173242. [PMID: 28278225 PMCID: PMC5344376 DOI: 10.1371/journal.pone.0173242] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/18/2017] [Indexed: 01/13/2023] Open
Abstract
Background DNA methylation is a stable epigenetic mark that is frequently altered in tumors. DNA methylation features are attractive biomarkers for disease states given the stability of DNA methylation in living cells and in biologic specimens typically available for analysis. Widespread accumulation of methylation in regulatory elements in some cancers (specifically the CpG island methylator phenotype, CIMP) can play an important role in tumorigenesis. High resolution assessment of CIMP for the entire genome, however, remains cost prohibitive and requires quantities of DNA not available for many tissue samples of interest. Genome-wide scans of methylation have been undertaken for large numbers of tumors, and higher resolution analyses for a limited number of cancer specimens. Methods for analyzing such large datasets and integrating findings from different studies continue to evolve. An approach for comparison of findings from a genome-wide assessment of the methylated component of tumor DNA and more widely applied methylation scans was developed. Methods Methylomes for 76 primary endometrial cancer and 12 normal endometrial samples were generated using methylated fragment capture and second generation sequencing, MethylCap-seq. Publically available Infinium HumanMethylation 450 data from The Cancer Genome Atlas (TCGA) were compared to MethylCap-seq data. Results Analysis of methylation in promoter CpG islands (CGIs) identified a subset of tumors with a methylator phenotype. We used a two-stage approach to develop a 13-region methylation signature associated with a “hypermethylator state.” High level methylation for the 13-region methylation signatures was associated with mismatch repair deficiency, high mutation rate, and low somatic copy number alteration in the TCGA test set. In addition, the signature devised showed good agreement with previously described methylation clusters devised by TCGA. Conclusion We identified a methylation signature for a “hypermethylator phenotype” in endometrial cancer and developed methods that may prove useful for identifying extreme methylation phenotypes in other cancers.
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Affiliation(s)
- Michael P. Trimarchi
- Department of Cancer Biology & Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Pearlly Yan
- Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Joanna Groden
- Department of Cancer Biology & Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Ralf Bundschuh
- Center for RNA Biology, Department of Physics, Department of Chemistry & Biochemistry, and Department of Internal Medicine, and Center for RNA Biology, The Ohio State University, Columbus, OH, United States of America
| | - Paul J. Goodfellow
- Department of Obstetrics and Gynecology, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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Abstract
microRNAs (miRNAs) and DNA methylation are the 2 epigenetic modifications that have emerged in recent years as the most critical players in the regulation of gene expression. Compelling evidence has indicated the roles of miRNAs and DNA methylation in modulating cellular transformation and tumorigenesis. miRNAs act as negative regulators of gene expression and are involved in the regulation of both physiologic conditions and during diseases, such as cancer, inflammatory diseases, and psychiatric disorders, among others. Meanwhile, aberrant DNA methylation manifests in both global genome changes and in localized gene promoter changes, which influences the transcription of cancer genes. In this review, we described the mutual regulation of miRNAs and DNA methylation in human cancers. miRNAs regulate DNA methylation by targeting DNA methyltransferases or methylation-related proteins. On the other hand, both hyper- and hypo-methylation of miRNAs occur frequently in human cancers and represent a new level of complexity in gene regulation. Therefore, understanding the mechanisms underlying the mutual regulation of miRNAs and DNA methylation may provide helpful insights in the development of efficient therapeutic approaches.
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Affiliation(s)
- Sumei Wang
- a Department of Oncology , Guangdong Provincial Hospital of Chinese Medicine , Guangzhou, Guangdong , P. R. China.,b Department of Systems Biology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Wanyin Wu
- a Department of Oncology , Guangdong Provincial Hospital of Chinese Medicine , Guangzhou, Guangdong , P. R. China
| | - Francois X Claret
- b Department of Systems Biology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA.,c Experimental Therapeutics Academic Program and Cancer Biology Program , The University of Texas Graduate School of Biomedical Sciences at Houston , Houston , TX , USA
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24
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Jadhav RR, Wang YV, Hsu YT, Liu J, Garcia D, Lai Z, Huang THM, Jin VX. Methyl-binding DNA capture Sequencing for Patient Tissues. J Vis Exp 2016. [PMID: 27842364 DOI: 10.3791/54131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Methylation is one of the essential epigenetic modifications to the DNA, which is responsible for the precise regulation of genes required for stable development and differentiation of different tissue types. Dysregulation of this process is often the hallmark of various diseases like cancer. Here, we outline one of the recent sequencing techniques, Methyl-Binding DNA Capture sequencing (MBDCap-seq), used to quantify methylation in various normal and disease tissues for large patient cohorts. We describe a detailed protocol of this affinity enrichment approach along with a bioinformatics pipeline to achieve optimal quantification. This technique has been used to sequence hundreds of patients across various cancer types as a part of the 1,000 methylome project (Cancer Methylome System).
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Affiliation(s)
- Rohit R Jadhav
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio
| | - Yao V Wang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio
| | - Ya-Ting Hsu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio
| | - Joseph Liu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio
| | - Dawn Garcia
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio
| | - Tim H M Huang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio;
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25
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Shen-Gunther J, Wang CM, Poage GM, Lin CL, Perez L, Banks NA, Huang THM. Molecular Pap smear: HPV genotype and DNA methylation of ADCY8, CDH8, and ZNF582 as an integrated biomarker for high-grade cervical cytology. Clin Epigenetics 2016; 8:96. [PMID: 27651839 PMCID: PMC5022163 DOI: 10.1186/s13148-016-0263-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/05/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The Pap smear has remained the foundation for cervical cancer screening for over 70 years. With advancements in molecular diagnostics, primary high-risk human papillomavirus (hrHPV) screening has recently become an accepted stand-alone or co-test with conventional cytology. However, both diagnostic tests have distinct limitations. The aim of this study was to determine the association between HPV genotypes and cellular epigenetic modifications in three grades of cervical cytology for screening biomarker discovery. METHODS This prospective, cross-sectional study used residual liquid-based cytology samples for HPV genotyping and epigenetic analysis. Extracted DNA was subjected to parallel polymerase chain reactions using three primer sets (MY09/11, FAP59/64, E6-E7 F/B) for HPV DNA amplification. HPV+ samples were genotyped by DNA sequencing. Promoter methylation of four candidate tumor suppressor genes (adenylate cyclase 8 (ADCY8), cadherin 8, type 2 (CDH8), MGMT, and zinc finger protein 582 (ZNF582)) out of 48 genes screened was quantified by bisulfite-pyrosequencing of genomic DNA. Independent validation of methylation profiles was performed by analyzing data from cervical cancer cell lines and clinical samples from The Cancer Genome Atlas (TCGA). RESULTS Two hundred seventy-seven quality cytology samples were analyzed. HPV was detected in 31/100 (31 %) negative for intraepithelial lesion or malignancy (NILM), 95/100 (95 %) low-grade squamous intraepithelial lesion (LSIL), and 71/77 (92 %) high-grade squamous intraepithelial lesion (HSIL) samples. The proportion of IARC-defined carcinogenic HPV types in sequenced samples correlated with worsening grade: NILM 7/29 (24 %), LSIL 53/92 (58 %), and HSIL 65/70 (93 %). Promoter methylation of ADCY8, CDH8, and ZNF582 was measured in 170 samples: NILM (N = 33), LSIL (N = 70), and HSIL (N = 67) also correlated with worsening grade. Similar hypermethylation patterns were found in cancer cell lines and TCGA samples. The combination of four biomarkers, i.e., HPV genotype and three-gene promoter methylation, predicted HSIL (AUC 0.89) better than HPV alone (AUC 0.74) by logistic regression and probabilistic modeling. CONCLUSIONS HPV genotype and DNA methylation of ADCY8, CDH8, and ZNF582 are correlated with cytological grade. Collectively, these biomarkers may serve as a molecular classifier of Pap smears.
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Affiliation(s)
- Jane Shen-Gunther
- Gynecologic Oncology & Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, 3698 Chambers Pass, Fort Sam Houston, TX 78234-6315 USA
| | - Chiou-Miin Wang
- Department of Molecular Medicine, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
| | - Graham M. Poage
- Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, TX 78234 USA
| | - Chun-Lin Lin
- Department of Molecular Medicine, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
| | - Luis Perez
- Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, TX 78234 USA
| | - Nancy A. Banks
- Department of Pathology and Area Laboratories, Brooke Army Medical Center, Fort Sam Houston, TX 78234 USA
| | - Tim Hui-Ming Huang
- Department of Molecular Medicine, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
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26
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Cheishvili D, Stefanska B, Yi C, Li CC, Yu P, Arakelian A, Tanvir I, Khan HA, Rabbani S, Szyf M. A common promoter hypomethylation signature in invasive breast, liver and prostate cancer cell lines reveals novel targets involved in cancer invasiveness. Oncotarget 2016; 6:33253-68. [PMID: 26427334 PMCID: PMC4741763 DOI: 10.18632/oncotarget.5291] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/10/2015] [Indexed: 01/08/2023] Open
Abstract
Cancer invasion and metastasis is the most morbid aspect of cancer and is governed by different cellular mechanisms than those driving the deregulated growth of tumors. We addressed here the question of whether a common DNA methylation signature of invasion exists in cancer cells from different origins that differentiates invasive from non-invasive cells. We identified a common DNA methylation signature consisting of hyper- and hypomethylation and determined the overlap of differences in DNA methylation with differences in mRNA expression using expression array analyses. A pathway analysis reveals that the hypomethylation signature includes some of the major pathways that were previously implicated in cancer migration and invasion such as TGF beta and ERBB2 triggered pathways. The relevance of these hypomethylation events in human tumors was validated by identification of the signature in several publicly available databases of human tumor transcriptomes. We shortlisted novel invasion promoting candidates and tested the role of four genes in cellular invasiveness from the list C11orf68, G0S2, SHISA2 and TMEM156 in invasiveness using siRNA depletion. Importantly these genes are upregulated in human cancer specimens as determined by immunostaining of human normal and cancer breast, liver and prostate tissue arrays. Since these genes are activated in cancer they constitute a group of targets for specific pharmacological inhibitors of cancer invasiveness.
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Affiliation(s)
- David Cheishvili
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Barbara Stefanska
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada.,Department of Nutrition Science, Purdue University, West Lafayette, Indiana, USA
| | - Cao Yi
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Chen Chen Li
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Patricia Yu
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Ani Arakelian
- Departments of Medicine, Oncology, and Pharmacology, McGill University, Montreal, Quebec, Canada
| | - Imrana Tanvir
- Department of Pathology, Fatima Memorial Hospital System, Lahore, Pakistan
| | - Haseeb Ahmed Khan
- Department of Pathology, Fatima Memorial Hospital System, Lahore, Pakistan
| | - Shafaat Rabbani
- Departments of Medicine, Oncology, and Pharmacology, McGill University, Montreal, Quebec, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada.,Department of Pharmacology and Therapeutics, Sackler Program for Epigenetics & Developmental Psychobiology, McGill University Medical School, Montreal, Quebec, Canada.,Department of Pharmacology and Therapeutics, Canadian Institute for Advanced Research, Montreal, Quebec, Canada
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27
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Hsu YT, Osmulski P, Wang Y, Huang YW, Liu L, Ruan J, Jin VX, Kirma NB, Gaczynska ME, Huang THM. EpCAM-Regulated Transcription Exerts Influences on Nanomechanical Properties of Endometrial Cancer Cells That Promote Epithelial-to-Mesenchymal Transition. Cancer Res 2016; 76:6171-6182. [PMID: 27569206 DOI: 10.1158/0008-5472.can-16-0752] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/15/2016] [Indexed: 12/24/2022]
Abstract
Overexpression of epithelial cell adhesion molecule (EpCAM) has been implicated in advanced endometrial cancer, but its roles in this progression remain to be elucidated. In addition to its structural role in modulating cell-surface adhesion, here we demonstrate that EpCAM is a regulatory molecule in which its internalization into the nucleus turns on a transcription program. Activation of EGF/EGFR signal transduction triggered cell-surface cleavage of EpCAM, leading to nuclear internalization of its cytoplasmic domain EpICD. ChIP-seq analysis identified target genes that are coregulated by EpICD and its transcription partner, LEF-1. Network enrichment analysis further uncovered a group of 105 genes encoding functions for tight junction, adherent, and cell migration. Furthermore, nanomechanical analysis by atomic force microscopy revealed increased softness and decreased adhesiveness of EGF-stimulated cancer cells, implicating acquisition of an epithelial-mesenchymal transition (EMT) phenotype. Thus, genome editing of EpCAM could be associated with altering these nanomechanical properties towards a less aggressive phenotype. Using this integrative genomic-biophysical approach, we demonstrate for the first time an intricate relationship between EpCAM-regulated transcription and altered biophysical properties of cells that promote EMT in advanced endometrial cancer. Cancer Res; 76(21); 6171-82. ©2016 AACR.
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Affiliation(s)
- Ya-Ting Hsu
- Departments of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Pawel Osmulski
- Departments of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Yao Wang
- Departments of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Lu Liu
- Department of Computer Science, University of Texas at San Antonio, San Antonio, Texas
| | - Jianhua Ruan
- Department of Computer Science, University of Texas at San Antonio, San Antonio, Texas
| | - Victor X Jin
- Departments of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Nameer B Kirma
- Departments of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Maria E Gaczynska
- Departments of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas.
| | - Tim Hui-Ming Huang
- Departments of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas.
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28
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Huang RL, Su PH, Liao YP, Wu TI, Hsu YT, Lin WY, Wang HC, Weng YC, Ou YC, Huang THM, Lai HC. Integrated Epigenomics Analysis Reveals a DNA Methylation Panel for Endometrial Cancer Detection Using Cervical Scrapings. Clin Cancer Res 2016; 23:263-272. [DOI: 10.1158/1078-0432.ccr-16-0863] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/27/2016] [Accepted: 07/19/2016] [Indexed: 11/16/2022]
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29
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Ruan J, Jahid MJ, Gu F, Lei C, Huang YW, Hsu YT, Mutch DG, Chen CL, Kirma NB, Huang THM. A novel algorithm for network-based prediction of cancer recurrence. Genomics 2016; 111:17-23. [PMID: 27453286 PMCID: PMC5253120 DOI: 10.1016/j.ygeno.2016.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 07/08/2016] [Accepted: 07/18/2016] [Indexed: 10/21/2022]
Abstract
To develop accurate prognostic models is one of the biggest challenges in "omics"-based cancer research. Here, we propose a novel computational method for identifying dysregulated gene subnetworks as biomarkers to predict cancer recurrence. Applying our method to the DNA methylome of endometrial cancer patients, we identified a subnetwork consisting of differentially methylated (DM) genes, and non-differentially methylated genes, termed Epigenetic Connectors (EC), that are topologically important for connecting the DM genes in a protein-protein interaction network. The ECs are statistically significantly enriched in well-known tumorgenesis and metastasis pathways, and include known epigenetic regulators. Importantly, combining the DMs and ECs as features using a novel random walk procedure, we constructed a support vector machine classifier that significantly improved the prediction accuracy of cancer recurrence and outperformed several alternative methods, demonstrating the effectiveness of our network-based approach.
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Affiliation(s)
- Jianhua Ruan
- Department of Computer Science, University of Texas, San Antonio, TX, USA; Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA; Department of Electrical Engineering and Computer Science, McNeese State University, Lake Charles, LA, USA.
| | - Md Jamiul Jahid
- Department of Computer Science, University of Texas, San Antonio, TX, USA
| | - Fei Gu
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Chengwei Lei
- Department of Electrical Engineering and Computer Science, McNeese State University, Lake Charles, LA, USA
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ya-Ting Hsu
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - David G Mutch
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, USA
| | - Chun-Liang Chen
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Nameer B Kirma
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA; Cancer Therapy & Research Center, University of Texas Health Science Center, San Antonio, TX, USA.
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30
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Qiu X, Hu B, Huang Y, Deng Y, Wang X, Zheng F. Hypermethylation of ACP1, BMP4, and TSPYL5 in Hepatocellular Carcinoma and Their Potential Clinical Significance. Dig Dis Sci 2016; 61:149-57. [PMID: 26386860 DOI: 10.1007/s10620-015-3878-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/08/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIM Aberrant methylation of specific genes is frequent event in hepatocellular carcinoma (HCC). Our present study aims to explore the methylation levels of acid phosphatase locus 1 (ACP1), bone morphogenetic protein 4 (BMP4), and testis-specific protein, Y-encoded-like 5 (TSPYL5) and their potential clinical applications in HCC. METHODS The methylation levels of ACP1, BMP4 and TSPYL5 were analyzed in 188 HCC tissues, 163 matched adjacent non-tumor tissues, and 29 normal liver tissues using a method of methylation-sensitive restriction enzyme-based quantitative PCR, and their associations with clinicopathological features and prognosis were evaluated. RESULTS Compared with adjacent non-tumor tissues and normal liver tissues, the methylation levels of ACP1, BMP4, and TSPYL5 were significantly increased in HCC tissues (All p < 0.0001). The methylation of each individual gene could distinguish HCC tissues well from adjacent non-tumor tissues with the area under the receiver operating characteristic curves (AUC) of 0.753, 0.785 and 0.917, respectively. Furthermore, a higher methylation of BMP4 was statistically associated with worse disease-free survival (p = 0.006) and might be an independent unfavorable factor for disease-free survival by univariate and multivariate analysis (p = 0.011, HR 3.431, 95 % CI 1.333-8.833). CONCLUSIONS Our findings suggest that hypermethylation of ACP1, BMP4, and TSPYL5 are common events in HCC and could be used as potentially detectable biomarkers in HCC tissues. Moreover, BMP4 could be potentially served as a methylated biomarker to predict recurrence and metastasis after hepatectomy for HCC patients. However, their potential clinical application value need to be further clarified.
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Affiliation(s)
- Xueping Qiu
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Rd 169, Wuchang District, Wuhan, 430071, China.
| | - Bo Hu
- The Third Affiliated Hospital of Sun Yat-sen University, Guanzhou, Guandong, China.
| | - Yifang Huang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Rd 169, Wuchang District, Wuhan, 430071, China.
| | - Yunte Deng
- Department of Pathology, Hubei Cancer Hospital, Wuhan, Hubei, China.
| | - Xuebin Wang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Rd 169, Wuchang District, Wuhan, 430071, China.
| | - Fang Zheng
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Rd 169, Wuchang District, Wuhan, 430071, China.
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31
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Duan ZH, Wang HC, Zhao DM, Ji XX, Song M, Yang XJ, Cui W. Cooperatively transcriptional and epigenetic regulation of sonic hedgehog overexpression drives malignant potential of breast cancer. Cancer Sci 2015; 106:1084-91. [PMID: 25990213 PMCID: PMC4556399 DOI: 10.1111/cas.12697] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/12/2015] [Accepted: 05/14/2015] [Indexed: 01/24/2023] Open
Abstract
Sonic hedgehog (Shh), a ligand of Hedgehog signaling pathway, is considered an important oncogene and an exciting potential therapeutic target in several cancers. Comprehensive understanding of the regulation mechanism of Shh in cancer cells is necessary to find an effective approach to selectively block its tumorigenic function. We and others previously demonstrated that nuclear factor-kappa B (NF-κB) activation and promoter hypomethylation contributed to the overexpression of Shh. However, the relationship between transcriptional and epigenetic regulation of Shh, and their roles in the malignant phenotype of cancer cells are still not clearly elucidated. In the present study, our data showed that the level of Shh was higher in breast cancer tissues with positive NF-κB nuclear staining and promoter hypomethylation. In addition, survival analysis revealed that Shh overexpression, but not hypomethylation and NF-κB nuclear staining, was a poor prognosis indicator for breast cancers. Moreover, in vitro data demonstrated that both NF-κB activation and hypomethylation in promoter region were positively associated with the overexpression of Shh. Mechanistically, the hypomethylation in Shh promoter could facilitate NF-κB binding to its site, and subsequently cooperate to induce transcription of Shh. Furthermore, the biological function data indicated that overexpressed Shh enhanced the self-renewal capacity and migration ability of breast cancer cells, which could be augmented by promoter demethylation and NF-κB activation. Overall, our findings reveal multiple and cooperative mechanisms of Shh upregulation in cancer cells, and the roles of Shh in tumor malignant behavior, thus suggesting a new strategy for therapeutic interventions to reduce Shh in tumors and improve patients’ prognosis.
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Affiliation(s)
- Zhao-Heng Duan
- Department of Pharmacology, College of Life Science and Biopharmaceutical of Shenyang Pharmaceutical University, Shenyang, China
| | - Hao-Chuan Wang
- Department of Pharmacology, College of Life Science and Biopharmaceutical of Shenyang Pharmaceutical University, Shenyang, China
| | - Dong-Mei Zhao
- Department of Pharmacology, College of Life Science and Biopharmaceutical of Shenyang Pharmaceutical University, Shenyang, China
| | - Xiao-Xin Ji
- Department of Pharmacology, College of Life Science and Biopharmaceutical of Shenyang Pharmaceutical University, Shenyang, China
| | - Min Song
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences of China Medical University, Shenyang, China
| | - Xiao-Jun Yang
- Center for Neuroscience, Medical College of Shantou University, Shantou, China
| | - Wei Cui
- Department of Pharmacology, College of Life Science and Biopharmaceutical of Shenyang Pharmaceutical University, Shenyang, China
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32
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Jadhav RR, Ye Z, Huang RL, Liu J, Hsu PY, Huang YW, Rangel LB, Lai HC, Roa JC, Kirma NB, Huang THM, Jin VX. Genome-wide DNA methylation analysis reveals estrogen-mediated epigenetic repression of metallothionein-1 gene cluster in breast cancer. Clin Epigenetics 2015; 7:13. [PMID: 25763113 PMCID: PMC4355986 DOI: 10.1186/s13148-015-0045-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 01/13/2015] [Indexed: 12/23/2022] Open
Abstract
Background Recent genome-wide analysis has shown that DNA methylation spans long stretches of chromosome regions consisting of clusters of contiguous CpG islands or gene families. Hypermethylation of various gene clusters has been reported in many types of cancer. In this study, we conducted methyl-binding domain capture (MBDCap) sequencing (MBD-seq) analysis on a breast cancer cohort consisting of 77 patients and 10 normal controls, as well as a panel of 38 breast cancer cell lines. Results Bioinformatics analysis determined seven gene clusters with a significant difference in overall survival (OS) and further revealed a distinct feature that the conservation of a large gene cluster (approximately 70 kb) metallothionein-1 (MT1) among 45 species is much lower than the average of all RefSeq genes. Furthermore, we found that DNA methylation is an important epigenetic regulator contributing to gene repression of MT1 gene cluster in both ERα positive (ERα+) and ERα negative (ERα−) breast tumors. In silico analysis revealed much lower gene expression of this cluster in The Cancer Genome Atlas (TCGA) cohort for ERα + tumors. To further investigate the role of estrogen, we conducted 17β-estradiol (E2) and demethylating agent 5-aza-2′-deoxycytidine (DAC) treatment in various breast cancer cell types. Cell proliferation and invasion assays suggested MT1F and MT1M may play an anti-oncogenic role in breast cancer. Conclusions Our data suggests that DNA methylation in large contiguous gene clusters can be potential prognostic markers of breast cancer. Further investigation of these clusters revealed that estrogen mediates epigenetic repression of MT1 cluster in ERα + breast cancer cell lines. In all, our studies identify thousands of breast tumor hypermethylated regions for the first time, in particular, discovering seven large contiguous hypermethylated gene clusters. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0045-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rohit R Jadhav
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Zhenqing Ye
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Rui-Lan Huang
- Department of Obstetrics and Gynecology, Taipei Medical University Shuang Ho Hospital, New Taipei City, 23561 Taiwan
| | - Joseph Liu
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Pei-Yin Hsu
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, 9200 West Wisconsin Avenue, Froedtert Medical College Lab Building (FMCLB) 258, Milwaukee, 53226 WI USA
| | - Leticia B Rangel
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Pharmaceutical Sciences, Biotechnology Program/RENORBIO, Health Sciences Center, Universidade Federal do Espirito Santo, Av. Marechal Campos, 1468, Maruipe, 29040-090 Vitoria ES Brazil ; Programa Ciencias Sem Fronteiras, CNPq, Brasilia, Brazil
| | - Hung-Cheng Lai
- Department of Obstetrics and Gynecology, Taipei Medical University Shuang Ho Hospital, New Taipei City, 23561 Taiwan ; School of Medicine, Taipei Medical University, No. 250, Wu-Hsing Street, Taipei, 110 Taiwan ; Graduate Institute of Life Sciences, Department and Graduate Institute of Biochemistry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Juan Carlos Roa
- Departamento de Pathologı'a, Universidad de la Frontera, Claro Solar 115, Temuco, Chile
| | - Nameer B Kirma
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Cancer Therapy and Research Center, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Epidemiology and Biostatistics, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Tim Hui-Ming Huang
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Cancer Therapy and Research Center, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Epidemiology and Biostatistics, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Victor X Jin
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Cancer Therapy and Research Center, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Epidemiology and Biostatistics, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
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Wang D, Cui W, Wu X, Qu Y, Wang N, Shi B, Hou P. RUNX3 site-specific hypermethylation predicts papillary thyroid cancer recurrence. Am J Cancer Res 2014; 4:725-737. [PMID: 25520863 PMCID: PMC4266707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 10/20/2014] [Indexed: 06/04/2023] Open
Abstract
Papillary thyroid cancer (PTC) is the most common epithelial thyroid tumor, accounting for more than 80% of all thyroid cancers. Although PTC shows an indolent character and excellent prognosis, patients with aggressive characteristics are more likely to have a disease recurrence and die in the end. The aim of this study was to analyze BRAF(V600E) mutation and methylation levels of CpG sites in the promoters of CDH1, DAPK, RARβ and RUNX3 genes in a cohort of PTCs, and investigate their association with tumor recurrence. In this study, we used pyrosequencing method to individually quantified methylation levels at multiple CpG sites within each gene promoter, and detect BRAF(V600E) mutation in 120 PTCs and 23 goiter tissues as normal control. Moreover, appropriate cut-off values for each CpG site were set up to predict disease recurrence. Our data showed that overall average methylation levels of CDH1 and RUNX3 genes were significantly higher in PTCs than that in control subjects. Conversely, overall average methylation levels of DAPK promoter were significantly lower in PTCs than that in control subjects. Moreover, BRAF(V600E) mutation and overall average methylation levels of all these genes were not significant difference between recurrent and non-recurrent cases. However, we found that hypermethylation of RUNX3 at CpG sites -1397, -1406, -1415 and -1417 significantly increased the risk of of disease recurrence by using appropriate site-specific cut-off values. Collectively, our findings suggest RUNX3 site-specific hypermethylation may offer value in predicting or monitoring postoperative recurrence of PTC patients.
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Affiliation(s)
- Dan Wang
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine Xi'an 710061, The People's Republic of China
| | - Wei Cui
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine Xi'an 710061, The People's Republic of China
| | - Xiaoyan Wu
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine Xi'an 710061, The People's Republic of China
| | - Yiping Qu
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine Xi'an 710061, The People's Republic of China
| | - Na Wang
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine Xi'an 710061, The People's Republic of China
| | - Bingyin Shi
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine Xi'an 710061, The People's Republic of China
| | - Peng Hou
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine Xi'an 710061, The People's Republic of China
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DNA methylation as a biomarker for the detection of hidden carcinoma in endometrial atypical hyperplasia. Gynecol Oncol 2014; 135:552-9. [PMID: 25449566 DOI: 10.1016/j.ygyno.2014.10.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/15/2014] [Accepted: 10/19/2014] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Women with atypical hyperplasia (AH) are often found to have endometrial carcinoma (EC) at hysterectomy. The purpose of this study was to evaluate whether the hypermethylation of specific genes found by methylomic approaches to the study of gynecologic cancers is a biomarker for EC in women with AH. METHODS We evaluated the methylation of AJAP1, HS3ST2, SOX1, and PTGDR from 61 AH patients undergoing hysterectomy. Endometrial biopsy samples were analyzed by bisulfite conversion and quantitative methylation-specific polymerase chain reaction. A methylation index was used to predict the presence of cancer. To confirm the silencing effects of DNA methylation, immunohistochemical analysis of AJAP1, HS3ST2, and SOX1 was performed using tissue microarray. RESULTS Fourteen (23%) patients had EC at hysterectomy. AJAP1, HS3ST2, and SOX1 were highly methylated in the EC patients' biopsy samples (p≤0.023). AJAP1, HS3ST2, and SOX1 protein expression was significantly higher in patients with AH only (p≤0.038). The predictive value of AJAP1, HS3ST2, and SOX1 methylation for EC was 0.81, 0.72, and 0.70, respectively. Combined testing of both AJAP1 and HS3ST2 methylation had a positive predictive value of 56%, methylation of any one of AJAP1, SOX1, or HS3ST2 had a 100% negative predictive value. CONCLUSIONS Hypermethylation of AJAP1, HS3ST2, and SOX1 is predictive of EC in AH patients. Testing for methylation of these genes in endometrial biopsy samples may be a hysterectomy-sparing diagnostic tool. Validation of these new genes as biomarkers for AH screening in a larger population-based study is warranted.
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Jeong HM, Kwon MJ, Shin YK. Overexpression of Cancer-Associated Genes via Epigenetic Derepression Mechanisms in Gynecologic Cancer. Front Oncol 2014; 4:12. [PMID: 24551595 PMCID: PMC3912470 DOI: 10.3389/fonc.2014.00012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Accepted: 01/20/2014] [Indexed: 12/15/2022] Open
Abstract
Like other cancers, most gynecologic cancers are caused by aberrant expression of cancer-related genes. Epigenetics is one of the most important gene expression mechanisms, which contribute to cancer development and progression by regulating cancer-related genes. Since the discovery of differential gene expression patterns in cancer cells when compared with normal cells, extensive efforts have been made to explore the origins of abnormal gene expression in cancer. Epigenetics, the study of inheritable changes in gene expression that do not alter DNA sequence is a key area of this research. DNA methylation and histone modification are well-known epigenetic mechanisms, while microRNAs and alternative splicing have recently been identified as important regulators of epigenetic mechanisms. These mechanisms not only affect specific target gene expression but also regulate the functioning of other epigenetic mechanisms. Moreover, these diverse epigenetic regulations occur simultaneously. Epigenetic regulation of gene expression is extraordinarily complicated and all epigenetic mechanisms to be studied at once to determine the exact gene regulation mechanisms. Traditionally, the contribution of epigenetics to cancer is thought to be mediated through the inactivation of tumor suppressor genes expression. But recently, it is arising that some oncogenes or cancer-promoting genes (CPGs) are overexpressed in diverse type of cancers through epigenetic derepression mechanism, such as DNA and histone demethylation. Epigenetic derepression arises from diverse epigenetic changes, and all of these mechanisms actively interact with each other to increase oncogenes or CPGs expression in cancer cell. Oncogenes or CPGs overexpressed through epigenetic derepression can initiate cancer development, and accumulation of these abnormal epigenetic changes makes cancer more aggressive and treatment resistance. This review discusses epigenetic mechanisms involved in the overexpression of oncogenes or CPGs via epigenetic derepression in gynecologic cancers. Therefore, improved understanding of these epigenetic mechanisms will provide new targets for gynecologic cancer treatment.
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Affiliation(s)
- Hae Min Jeong
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University , Seoul , South Korea
| | - Mi Jeong Kwon
- College of Pharmacy, Kyungpook National University , Daegu , South Korea ; Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University , Daegu , South Korea
| | - Young Kee Shin
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University , Seoul , South Korea ; Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul , South Korea ; Advanced Institutes of Convergence Technology , Suwon , South Korea ; Bio-MAX Institute, Seoul National University , Seoul , South Korea
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