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Yu J, Liu QC, Lu SY, Wang S, Zhang H. Detecting plasma SHOX2, HOXA9, SEPTIN9, and RASSF1A methylation and circulating cancer cells for cholangiocarcinoma clinical diagnosis and monitoring. World J Gastrointest Oncol 2025; 17:104253. [PMID: 40235897 PMCID: PMC11995335 DOI: 10.4251/wjgo.v17.i4.104253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 01/17/2025] [Accepted: 02/25/2025] [Indexed: 03/25/2025] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA), also known as bile duct cancer, is a devastating malignancy primarily affecting the biliary tract. AIM To assess their performance in clinical diagnosis and monitoring of CCA, plasma methylation and circulating tumor cells were detected. METHODS Plasma samples were collected from Hubei Cancer Hospital (n = 156). Plasma DNA was tested to detect SHOX2, HOXA9, SEPTIN9, and RASSF1A methylation using TaqMan PCR. Circulating tumor cells (CTCs) were detected in the peripheral blood of patients using the United States Food and Drug Administration-approved cell search system before and after clinical therapy. The CCA diagnostic value was estimated using the area under the curve. The independent prognosis risk factors for patients with CCA were estimated using Cox and logistic regression analyses. RESULTS The sensitivity and specificity of the four DNA plasma methylations exhibited 64.74% sensitivity and 93.88% specificity for detecting CCA. The receiver operating characteristic curve of the combined value for CCA diagnosis in plasma was 0.828 ± 0.032. RASSF1A plasma methylation was related to the prognosis of patients with CCA. We determined the prognostic hazard ratio for CCA using CTC count, tumor stage, methylation, and carbohydrate antigen 19-9 levels as key factors. Our overall survival nomogram achieved a C-index of 0.705 (0.605-0.805). CONCLUSION SHOX2, HOXA9, SEPTIN9, and RASSF1A plasma methylation demonstrated increased sensitivity for diagnosing CCA. RASSF1A plasma methylation and CTCs were valuable predictors to assess CCA prognosis and recurrence.
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Affiliation(s)
- Jing Yu
- Department of Laboratory, Wuhan Hospital of Traditional Chinese and Western Medicine (Wuhan's TCWM Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
- Department of Laboratory, Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan 442008, Hubei Province, China
| | - Qiu-Chen Liu
- Department of Laboratory, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430079, Hubei Province, China
| | - Shuang-Yan Lu
- Department of Blood Transfusion, Wuhan Chinese and Western Medicine Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Shun Wang
- Department of Laboratory, Wuhan Chinese and Western Medicine Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Hua Zhang
- Department of Laboratory, Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan 442008, Hubei Province, China
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Guerra E, Di Pietro R, Stati G, Alberti S. A non-mutated TROP2 fingerprint in cancer genetics. Front Oncol 2023; 13:1151090. [PMID: 37456256 PMCID: PMC10338868 DOI: 10.3389/fonc.2023.1151090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
The advent of high throughput DNA sequencing is providing massive amounts of tumor-associated mutation data. Implicit in these analyses is the assumption that, by acquiring a series of hallmark changes, normal cells evolve along a neoplastic path. However, the lack of correlation between cancer risk and global exposure to mutagenic factors provides arguments against this model. This suggested that additional, non-mutagenic factors are at work in cancer development. A candidate determinant is TROP2, that stands out for its expression in the majority of solid tumors in human, for its impact on the prognosis of most solid cancers and for its role as driver of cancer growth and metastatic diffusion, through overexpression as a wild-type form. The Trop-2 signaling network encompasses CREB1, Jun, NF-κB, Rb, STAT1 and STAT3, through induction of cyclin D1 and MAPK/ERK. Notably, Trop-2-driven pathways vastly overlap with those activated by most functionally relevant/most frequently mutated RAS and TP53, and are co-expressed in a large fraction of individual tumor cases, suggesting functional overlap. Mutated Ras was shown to synergize with the TROP2-CYCLIND1 mRNA chimera in transforming primary cells into tumorigenic ones. Genomic loss of TROP2 was found to promote carcinogenesis in squamous cell carcinomas through modulation of Src and mutated Ras pathways. DNA methylation and TP53 status were shown to cause genome instability and TROP gene amplification, together with Trop-2 protein overexpression. These findings suggest that mutagenic and the TROP2 non-mutagenic pathways deeply intertwine in driving transformed cell growth and malignant progression of solid cancers.
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Affiliation(s)
- Emanuela Guerra
- Laboratory of Cancer Pathology, Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
- Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Roberta Di Pietro
- Department of Medicine and Aging Sciences, Section of Biomorphology, G. d’Annunzio University of Chieti-Pescara, Chieti, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, United States
| | - Gianmarco Stati
- Department of Medicine and Aging Sciences, Section of Biomorphology, G. d’Annunzio University of Chieti-Pescara, Chieti, Italy
| | - Saverio Alberti
- Unit of Medical Genetics, Department of Biomedical Sciences - Biomedical Sciences (BIOMORF), University of Messina, Messina, Italy
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Hermawan A, Putri H. Bioinformatics analysis reveals the potential target of rosiglitazone as an antiangiogenic agent for breast cancer therapy. BMC Genom Data 2022; 23:72. [PMID: 36114448 PMCID: PMC9482259 DOI: 10.1186/s12863-022-01086-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 09/06/2022] [Indexed: 11/19/2022] Open
Abstract
Background Several studies have demonstrated the antitumor activity of rosiglitazone (RGZ) in cancer cells, including breast cancer cells. However, the molecular targets of RGZ in the inhibition of angiogenesis in breast cancer cells remain unclear. This study aimed to explore the potential targets of RGZ in inhibiting breast cancer angiogenesis using bioinformatics-based analysis. Results Venn diagram analysis revealed 29 TR proteins. KEGG pathway enrichment analysis demonstrated that TR regulated the adipocytokine, AMPK, and PPAR signaling pathways. Oncoprint analysis showed genetic alterations in FABP4 (14%), ADIPOQ (2.9%), PPARG (2.8%), PPARGC1A (1.5%), CD36 (1.7%), and CREBBP (11%) in patients with breast cancer in a TCGA study. The mRNA levels of FABP4, ADIPOQ, PPARG, CD36, and PPARGC1A were significantly lower in patients with breast cancer than in those without breast cancer. Analysis of gene expression using bc-GenExMiner showed that the mRNA levels of FABP, ADIPOQ, PPARG, CD36, PPARGC1A, and CREBBP were significantly lower in basal-like and triple-negative breast cancer (TNBC) cells than in non-basal-like and non-TNBC cells. In general, the protein levels of these genes were low, except for that of CREBBP. Patients with breast cancer who had low mRNA levels of FABP4, ADIPOQ, PPARG, and PPARGC1A had lower overall survival rates than those with high mRNA levels, which was supported by the overall survival related to DNA methylation. Correlation analysis of immune cell infiltration with TR showed a correlation between TR and immune cell infiltration, highlighting the potential of RGZ for immunotherapy. Conclusion This study explored the potential targets of RGZ as antiangiogenic agents in breast cancer therapy and highlighted FABP4, ADIPOQ, PPARG, PPARGC1A, CD36, and CREBBP as potential targets of RGZ. These findings require further validation to explore the potential of RGZ as an antiangiogenic agent. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01086-2.
Recent studies have focused on the development of indirect angiogenesis inhibitors. Bioinformatics-based identification of potential rosiglitazone target genes to inhibit breast cancer angiogenesis. FABP4, ADIPOQ, PPARG, PPARGC1A, CD36, and CREBBP are potential targets of rosiglitazone.
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Fabrizio FP, Castellana S, Centra F, Sparaneo A, Mastroianno M, Mazza T, Coco M, Trombetta D, Cingolani N, Centonza A, Graziano P, Maiello E, Fazio VM, Muscarella LA. Design and experimental validation of OPERA_MET-A panel for deep methylation analysis by next generation sequencing. Front Oncol 2022; 12:968804. [PMID: 36033501 PMCID: PMC9404304 DOI: 10.3389/fonc.2022.968804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methylation is the most recognized epigenetic mark that leads to a massive distortion in cancer cells. It has been observed that a large number of DNA aberrant methylation events occur simultaneously in a group of genes, thus providing a growth advantage to the cell in promoting cell differentiation and neoplastic transformation. Due to this reason, methylation profiles have been suggested as promising cancer biomarkers. Here, we designed and performed a first step of validation of a novel targeted next generation sequencing (NGS) panel for methylation analysis, which can simultaneously evaluate the methylation levels at CpG sites of multiple cancer-related genes. The OPERA_MET-A methylation panel was designed using the Ion AmpliSeq™ technology to amplify 155 regions with 125-175 bp mean length and covers a total of 1107 CpGs of 18 cancer-related genes. The performance of the panel was assessed by running commercially available fully methylated and unmethylated control human genomic DNA (gDNA) samples and a variable mixture of them. The libraries were run on Ion Torrent platform and the sequencing output was analyzed using the “methylation_analysis” plugin. DNA methylation calls on both Watson (W) and Crick (C) strands and methylated:unmethylated ratio for each CpG site were obtained. Cell lines, fresh frozen and formalin-fixed paraffin-embedded (FFPE) lung cancer tissues were tested. The OPERA_MET-A panel allows to run a minimum of 6 samples/530 chip to reach an observed mean target depth ≥2,500X (W and C strands) and an average number of mapped reads >750,000/sample. The conversion efficiency, determined by spiking-in unmethylated Lambda DNA into each sample before the bisulfite conversion process, was >97% for all samples. The observed percentage of global methylation for all CpGs was >95% and <5% for fully methylated and unmethylated gDNA samples, respectively, and the observed results for the variable mixtures were in agreement with what was expected. Methylation-specific NGS analysis represents a feasible method for a fast and multiplexed screening of cancer patients by a high-throughput approach. Moreover, it offers the opportunity to construct a more robust algorithm for disease prediction in cancer patients having a low quantity of biological material available.
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Affiliation(s)
- Federico Pio Fabrizio
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- *Correspondence: Federico Pio Fabrizio, ; Lucia Anna Muscarella,
| | - Stefano Castellana
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Flavia Centra
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Angelo Sparaneo
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Mario Mastroianno
- Scientific Direction, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Michelina Coco
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Domenico Trombetta
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Nicola Cingolani
- Unit of Pathology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Antonella Centonza
- Unit of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paolo Graziano
- Unit of Pathology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Evaristo Maiello
- Unit of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Vito Michele Fazio
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Laboratory of Molecular Medicine and Biotechnology, University Campus Bio-Medico of Rome, Rome, Italy
- Institute of Translational Pharmacology, National Research Council of Italy (CNR), Rome, Italy
| | - Lucia Anna Muscarella
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- *Correspondence: Federico Pio Fabrizio, ; Lucia Anna Muscarella,
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LI J, QI L, ZHANG M, YAO C, FENG J, ZHENG Z, CHEN C, DUAN S, QI Y. PRKCDBP Methylation is a Potential and Promising Candidate Biomarker for Non-small Cell Lung Cancer. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2022; 25:78-85. [PMID: 35224960 PMCID: PMC8913286 DOI: 10.3779/j.issn.1009-3419.2022.102.03] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND The occurrence and development of lung cancer are closely linked to epigenetic modification. Abnormal DNA methylation in the CpG island region of genes has been found in many cancers. Protein kinase C delta binding protein (PRKCDBP) is a potential tumor suppressor and its epigenetic changes are found in many human malignancies. This study investigated the possibility of PRKCDBP methylation as a potential biomarker for non-small cell lung cancer (NSCLC). METHODS We measured the methylation levels of PRKCDBP in the three groups of NSCLC tissues. Promoter activity was measured by the dual luciferase assay, with 5'-aza-deoxycytidine to examine the effect of demethylation on the expression level of PRKCDBP. RESULTS The methylation levels of PRKCDBP in tumor tissues and 3 cm para-tumor were higher than those of distant (>10 cm) non-tumor tissues. Receiver operating characteristic (ROC) curve analysis between tumor tissues and distant non-tumor tissues showed that the area under the line (AUC) was 0.717. Dual luciferase experiment confirmed that the promoter region was able to promote gene expression. Meanwhile, in vitro methylation of the fragment (PRKCDBP_Me) could significantly reduce the promoter activity of the fragment. Demethylation of 5'-aza-deoxycytidine in lung cancer cell lines A549 and H1299 showed a significant up-regulation of PRKCDBP mRNA levels. CONCLUSIONS PRKCDBP methylation is a potential and promising candidate biomarker for non-small cell lung cancer.
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Affiliation(s)
- Jing LI
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Lin QI
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Mingfang ZHANG
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Caiyun YAO
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Jinan FENG
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Zhonghua ZHENG
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo 315211, China
| | - Chujia CHEN
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo 315211, China
| | - Shiwei DUAN
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo 315211, China
| | - Yuanlin QI
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China,Yuanlin QI, E-mail:
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Ghalkhani E, Akbari MT, Izadi P, Mahmoodzadeh H, Kamali F. Assessment of DAPK1 and CAVIN3 Gene Promoter Methylation in Breast Invasive Ductal Carcinoma and Metastasis. CELL JOURNAL 2021; 23:397-405. [PMID: 34455714 PMCID: PMC8405083 DOI: 10.22074/cellj.2021.7251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/26/2020] [Indexed: 12/15/2022]
Abstract
Objective Metastasis might be latent or occur several years after primary tumor removal. Currently used methods for detection of distant metastasis have still some limitations. Blood tests may improve sensitivity and specificity of currently used screening procedures. The present study was designed to investigate promoter methylation status of DAPK1 and CAVIN3 genes in plasma circulating free DNA (cfDNA) samples in Iranian invasive ductal carcinoma (IDC) patients. We also investigated association of two gene promoter methylations with breast cancer (BC) and metastatic BC was also assessed. Materials and Methods In this case-control study, MethySYBR assay was performed to determine DAPK1 and CAVIN3 promoter methylation status in breast IDC from 90 patients and 30 controls. Based on clinicopathological information, patient samples subdivided into stage I, II/III and IV groups (each group contained 30 individuals). Results According to the results an increased promoter methylation level of the DAPK1 gene in BC patients was observed. It was found that as disease progressed, the percentage of methylation was changed while it was not significant. Methylation changes in metastatic and non-metastatic BC revealed that methylation levels were significantly increased in metastatic than non-metastatic group. Analysis revealed that promoter methylation of CAVIN3 gene in BC patients was significantly increased. The observed methylation changes from less to more invasive stages were not significant in the CAVIN3 gene. Moreover, promoter methylation was changed in metastatic rather than non-metastatic condition, although it was not significant. Conclusion Promoter hypermethylation of c and CAVIN3 genes in plasma are associated with the risk of BC and they can be potential diagnostic biomarkers along with current methods. Additionally, association of aberrant DAPK1 promoter methylation with metastasis suggests its potential usage as a non-invasive strategy for metastatic BC diagnosis.
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Affiliation(s)
- Esmat Ghalkhani
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Taghi Akbari
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Pantea Izadi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Habibollah Mahmoodzadeh
- Department of Surgery, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Kamali
- Iran National Tumor Bank, Cancer Institute of Iran, Tehran, University of Medical Sciences, Tehran, Iran
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Kosvyra A, Ntzioni E, Chouvarda I. Network analysis with biological data of cancer patients: A scoping review. J Biomed Inform 2021; 120:103873. [PMID: 34298154 DOI: 10.1016/j.jbi.2021.103873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 06/30/2021] [Accepted: 07/18/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND & OBJECTIVE Network Analysis (NA) is a mathematical method that allows exploring relations between units and representing them as a graph. Although NA was initially related to social sciences, the past two decades was introduced in Bioinformatics. The recent growth of the networks' use in biological data analysis reveals the need to further investigate this area. In this work, we attempt to identify the use of NA with biological data, and specifically: (a) what types of data are used and whether they are integrated or not, (b) what is the purpose of this analysis, predictive or descriptive, and (c) the outcome of such analyses, specifically in cancer diseases. METHODS & MATERIALS The literature review was conducted on two databases, PubMed & IEEE, and was restricted to journal articles of the last decade (January 2010 - December 2019). At a first level, all articles were screened by title and abstract, and at a second level the screening was conducted by reading the full text article, following the predefined inclusion & exclusion criteria leading to 131 articles of interest. A table was created with the information of interest and was used for the classification of the articles. The articles were initially classified to analysis studies and studies that propose a new algorithm or methodology. Each one of these categories was further screened by the following clustering criteria: (a) data used, (b) study purpose, (c) study outcome. Specifically for the studies proposing a new algorithm, the novelty presented in each one was detected. RESULTS & Conclusions: In the past five years researchers are focusing on creating new algorithms and methodologies to enhance this field. The articles' classification revealed that only 25% of the analyses are integrating multi-omics data, although 50% of the new algorithms developed follow this integrative direction. Moreover, only 20% of the analyses and 10% of the newly developed methodologies have a predictive purpose. Regarding the result of the works reviewed, 75% of the studies focus on identifying, prognostic or not, gene signatures. Concluding, this review revealed the need for deploying predictive and multi-omics integrative algorithms and methodologies that can be used to enhance cancer diagnosis, prognosis and treatment.
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Affiliation(s)
- A Kosvyra
- Laboratory of Computing, Medical Informatics and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - E Ntzioni
- Laboratory of Computing, Medical Informatics and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - I Chouvarda
- Laboratory of Computing, Medical Informatics and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Ruscito I, Gasparri ML, De Marco MP, Costanzi F, Besharat AR, Papadia A, Kuehn T, Gentilini OD, Bellati F, Caserta D. The Clinical and Pathological Profile of BRCA1 Gene Methylated Breast Cancer Women: A Meta-Analysis. Cancers (Basel) 2021; 13:cancers13061391. [PMID: 33808555 PMCID: PMC8003261 DOI: 10.3390/cancers13061391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/09/2021] [Accepted: 03/16/2021] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND DNA aberrant hypermethylation is the major cause of transcriptional silencing of the breast cancer gene 1 (BRCA1) gene in sporadic breast cancer patients. The aim of the present meta-analysis was to analyze all available studies reporting clinical characteristics of BRCA1 gene hypermethylated breast cancer in women, and to pool the results to provide a unique clinical profile of this cancer population. METHODS On September 2020, a systematic literature search was performed. Data were retrieved from PubMed, MEDLINE, and Scopus by searching the terms: "BRCA*" AND "methyl*" AND "breast". All studies evaluating the association between BRCA1 methylation status and breast cancer patients' clinicopathological features were considered for inclusion. RESULTS 465 studies were retrieved. Thirty (6.4%) studies including 3985 patients met all selection criteria. The pooled analysis data revealed a significant correlation between BRCA1 gene hypermethylation and advanced breast cancer disease stage (OR = 0.75: 95% CI: 0.58-0.97; p = 0.03, fixed effects model), lymph nodes involvement (OR = 1.22: 95% CI: 1.01-1.48; p = 0.04, fixed effects model), and pre-menopausal status (OR = 1.34: 95% CI: 1.08-1.66; p = 0.008, fixed effects model). No association could be found between BRCA1 hypermethylation and tumor histology (OR = 0.78: 95% CI: 0.59-1.03; p = 0.08, fixed effects model), tumor grading (OR = 0.78: 95% CI :0.46-1.32; p = 0.36, fixed effects model), and breast cancer molecular classification (OR = 1.59: 95% CI: 0.68-3.72; p = 0.29, random effects model). CONCLUSIONS hypermethylation of the BRCA1 gene significantly correlates with advanced breast cancer disease, lymph nodes involvement, and pre-menopausal cancer onset.
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Affiliation(s)
- Ilary Ruscito
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
- Correspondence: ; Tel.: +39-06-3377-5696
| | - Maria Luisa Gasparri
- Department of Gynecology and Obstetrics, Ente Ospedaliere Cantonale (EOC), Via Tesserete 46, 6900 Lugano, Switzerland; (M.L.G.); (A.P.)
- University of the Italian Switzerland (USI), Via Giuseppe Buffi 13, 6900 Lugano, Switzerland
| | - Maria Paola De Marco
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Flavia Costanzi
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Aris Raad Besharat
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Andrea Papadia
- Department of Gynecology and Obstetrics, Ente Ospedaliere Cantonale (EOC), Via Tesserete 46, 6900 Lugano, Switzerland; (M.L.G.); (A.P.)
- University of the Italian Switzerland (USI), Via Giuseppe Buffi 13, 6900 Lugano, Switzerland
| | - Thorsten Kuehn
- Interdisciplinary Breast Center, Department of Gynecology and Obstetrics, Klinikum Esslingen, 73730 Neckar, Germany;
| | - Oreste Davide Gentilini
- Breast Surgery Unit, San Raffaele University Hospital, via Olgettina 60, 20132 Milan, Italy;
| | - Filippo Bellati
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Donatella Caserta
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
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Fu J, Zhou H, Chen J, Wang Y. Low expression of PRKCDBP promoted cisplatin resistance in lung adenocarcinoma by DNMT1 and TNF‑α. Oncol Rep 2020; 44:1616-1626. [PMID: 32945503 PMCID: PMC7448504 DOI: 10.3892/or.2020.7721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/09/2020] [Indexed: 12/15/2022] Open
Abstract
The aim of the present study was to explore the mechanism of protein kinase C delta binding protein (PRKCDBP) promoting cisplatin resistance in lung adenocarcinoma (LAD). The PRKCDBP expression level was herein detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). We overexpressed PRKCDBP and tumor necrosis factor-α (TNF-α) in A549/DDP cell line, DNMT1 in A549 cells and siRNA TNF-α in A549 cells with lentivirus-mediated technique, and then, analyzed their biological diversification. The results showed a significantly lower expression level of PRKCDBP was lowly expressed in the A549/DDP cell line and LAD tissues than that in A549 cells and adjacent cancer tissues (P<0.05 and P<0.01), while the DNMT1 mRNA level was remarkably increased (P=0.000) and the promoter of PRKCDBP was hypermethylated in the A549/DDP cell line. Additionally, DNMT1 mRNA level in cisplatin-insensitive group was markedly higher than that in cisplatin-sensitive group (t=7.233, P<0.0001), while PRKCDBP mRNA level in cisplatin insensitive group was notably lower than that in cisplatin-sensitive group (t=8.784, P<0.0001). The results showed that PRKCDBP mRNA level was significantly elevated following treatment with 5 µM decitabine for 24 h (P<0.0001), while the DNMT1 mRNA level was notably reduced (P=0.000). When PRKCDBP was overexpressed, the DNMT1 mRNA level was markedly decreased (P=0.007), the rate of proliferation (P<0.05 or P<0.01), IC50 of cisplatin (P<0.001), G2/M phase and S phase cells were obviously reduced (P<0.001), while G0/G1 phase cells, apoptosis (P<0.001) distinctly increased, but migration ability did not significantly change. TNF-α overexpression resulted in an increase of PRKCDBP mRNA level (P<0.001), while TNF-α siRNA led to PRKCDBP mRNA level distinctly reduced (P<0.001). Overexpression of DNMT1 improved IC50 in A549 cells. Thus, findings of the present study ascertained the promoter of PRKCDBP was hypermethylated in A549/DDP cells. In conclusion, low expression of PRKCDBP promoted cisplatin resistance in LAD by DNMT1 and TNF-α.
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Affiliation(s)
- Jiali Fu
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
| | - Huixin Zhou
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
| | - Jie Chen
- Department of Intensive Care Unit, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
| | - Yumin Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
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10
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Zhao T, Khadka VS, Deng Y. Identification of lncRNA biomarkers for lung cancer through integrative cross-platform data analyses. Aging (Albany NY) 2020; 12:14506-14527. [PMID: 32675385 PMCID: PMC7425463 DOI: 10.18632/aging.103496] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/01/2020] [Indexed: 02/07/2023]
Abstract
This study was designed to identify lncRNA biomarker candidates using lung cancer data from RNA-Seq and microarray platforms separately.Lung cancer datasets were obtained from the Gene Expression Omnibus (GEO, n = 287) and The Cancer Genome Atlas (TCGA, n = 216) repositories, only common lncRNAs were used. Differentially expressed (DE) lncRNAs in tumors with respect to normal were selected from the Affymetrix and TCGA datasets. A training model consisting of the top 20 DE Affymetrix lncRNAs was used for validation in the TCGA and Agilent datasets. A second similar training model was generated using the TCGA dataset.First, a model using the top 20 DE lncRNAs from Affymetrix for training and validated using TCGA and Agilent, achieved high prediction accuracy for both training (98.5% AUC for Affymetrix) and validation (99.2% AUC for TCGA and 92.8% AUC for Agilent). A similar model using the top 20 DE lncRNAs from TCGA for training and validated using Affymetrix and Agilent, also achieved high prediction accuracy for both training (97.7% AUC for TCGA) and validation (96.5% AUC for Affymetrix and 80.9% AUC for Agilent). Eight lncRNAs were found to be overlapped from these two lists.
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Affiliation(s)
- Tianying Zhao
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, The University of Hawaii at Manoa, Honolulu, HI 96813, USA
- Department of Molecular Biosciences and Bioengineering, The University of Hawaii at Manoa College of Tropical Agriculture and Human Resources, Agricultural Sciences 218, Honolulu, HI 96822, USA
| | - Vedbar Singh Khadka
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, The University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, The University of Hawaii at Manoa, Honolulu, HI 96813, USA
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11
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DNA methylation landscape of triple-negative ductal carcinoma in situ (DCIS) progressing to the invasive stage in canine breast cancer. Sci Rep 2020; 10:2415. [PMID: 32051475 PMCID: PMC7015930 DOI: 10.1038/s41598-020-59260-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/16/2020] [Indexed: 11/09/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a subtype of breast cancer unresponsive to traditional receptor-targeted treatments, leading to a disproportionate number of deaths. Invasive breast cancer is believed to evolve from non-invasive ductal carcinoma in situ (DCIS). Detection of triple-negative DCIS (TN-DCIS) is challenging, therefore strategies to study molecular events governing progression of pre-invasive TN-DCIS to invasive TNBC are needed. Here, we study a canine TN-DCIS progression and investigate the DNA methylation landscape of normal breast tissue, atypical ductal hyperplasia (ADH), DCIS and invasive breast cancer. We report hypo- and hypermethylation of genes within functional categories related to cancer such as transcriptional regulation, apoptosis, signal transduction, and cell migration. DNA methylation changes associated with cancer-related genes become more pronounced at invasive breast cancer stage. Importantly, we identify invasive-only and DCIS-specific DNA methylation alterations that could potentially determine which lesions progress to invasive cancer and which could remain as pre-invasive DCIS. Changes in DNA methylation during TN-DCIS progression in this canine model correspond with gene expression patterns in human breast tissues. This study provides evidence for utilizing methylation status of gene candidates to define late-stage (DCIS and invasive), invasive stage only or DCIS stage only of TN-DCIS progression.
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12
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Bomane A, Gonçalves A, Ballester PJ. Paclitaxel Response Can Be Predicted With Interpretable Multi-Variate Classifiers Exploiting DNA-Methylation and miRNA Data. Front Genet 2019; 10:1041. [PMID: 31708973 PMCID: PMC6823251 DOI: 10.3389/fgene.2019.01041] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/30/2019] [Indexed: 12/27/2022] Open
Abstract
To address the problem of resistance to paclitaxel treatment, we have investigated to which extent is possible to predict Breast Cancer (BC) patient response to this drug. We carried out a large-scale tumor-based prediction analysis using data from the US National Cancer Institute’s Genomic Data Commons. These data sets comprise the responses of BC patients to paclitaxel along with six molecular profiles of their tumors. We assessed 10 Machine Learning (ML) algorithms on each of these profiles and evaluated the resulting 60 classifiers on the same BC patients. DNA methylation and miRNA profiles were the most informative overall. In combination with these two profiles, ML algorithms selecting the smallest subset of molecular features generated the most predictive classifiers: a complexity-optimized XGBoost classifier based on CpG island methylation extracted a subset of molecular factors relevant to predict paclitaxel response (AUC = 0.74). A CpG site methylation-based Decision Tree (DT) combining only 2 of the 22,941 considered CpG sites (AUC = 0.89) and a miRNA expression-based DT employing just 4 of the 337 analyzed mature miRNAs (AUC = 0.72) reveal the molecular types associated to paclitaxel-sensitive and resistant BC tumors. A literature review shows that features selected by these three classifiers have been individually linked to the cytotoxic-drug sensitivities and prognosis of BC patients. Our work leads to several molecular signatures, unearthed from methylome and miRNome, able to anticipate to some extent which BC tumors respond or not to paclitaxel. These results may provide insights to optimize paclitaxel-therapies in clinical practice.
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Affiliation(s)
- Alexandra Bomane
- Cancer Research Center of Marseille, CRCM, INSERM, Institut Paoli-Calmettes, Aix-Marseille Univ, CNRS, Paris, France
| | - Anthony Gonçalves
- Cancer Research Center of Marseille, CRCM, INSERM, Institut Paoli-Calmettes, Aix-Marseille Univ, CNRS, Paris, France
| | - Pedro J Ballester
- Cancer Research Center of Marseille, CRCM, INSERM, Institut Paoli-Calmettes, Aix-Marseille Univ, CNRS, Paris, France
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13
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DNA Methylation Status in Cancer Disease: Modulations by Plant-Derived Natural Compounds and Dietary Interventions. Biomolecules 2019; 9:biom9070289. [PMID: 31323834 PMCID: PMC6680848 DOI: 10.3390/biom9070289] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/24/2022] Open
Abstract
The modulation of the activity of DNA methyltransferases (DNMTs) represents a crucial epigenetic mechanism affecting gene expressions or DNA repair mechanisms in the cells. Aberrant modifications in the function of DNMTs are a fundamental event and part of the pathogenesis of human cancer. Phytochemicals, which are biosynthesized in plants in the form of secondary metabolites, represent an important source of biomolecules with pleiotropic effects and thus provide a wide range of possible clinical applications. It is well documented that phytochemicals demonstrate significant anticancer properties, and in this regard, rapid development within preclinical research is encouraging. Phytochemicals affect several epigenetic molecular mechanisms, including DNA methylation patterns such as the hypermethylation of tumor-suppressor genes and the global hypomethylation of oncogenes, that are specific cellular signs of cancer development and progression. This review will focus on the latest achievements in using plant-derived compounds and plant-based diets targeting epigenetic regulators and modulators of gene transcription in preclinical and clinical research in order to generate novel anticancer drugs as sensitizers for conventional therapy or compounds suitable for the chemoprevention clinical setting in at-risk individuals. In conclusion, indisputable anticancer activities of dietary phytochemicals linked with proper regulation of DNA methylation status have been described. However, precisely designed and well-controlled clinical studies are needed to confirm their beneficial epigenetic effects after long-term consumption in humans.
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14
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Humphries B, Wang Z, Yang C. MicroRNA Regulation of Epigenetic Modifiers in Breast Cancer. Cancers (Basel) 2019; 11:E897. [PMID: 31252590 PMCID: PMC6678197 DOI: 10.3390/cancers11070897] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/16/2019] [Accepted: 06/24/2019] [Indexed: 12/20/2022] Open
Abstract
Epigenetics refers to the heritable changes in gene expression without a change in the DNA sequence itself. Two of these major changes include aberrant DNA methylation as well as changes to histone modification patterns. Alterations to the epigenome can drive expression of oncogenes and suppression of tumor suppressors, resulting in tumorigenesis and cancer progression. In addition to modifications of the epigenome, microRNA (miRNA) dysregulation is also a hallmark for cancer initiation and metastasis. Advances in our understanding of cancer biology demonstrate that alterations in the epigenome are not only a major cause of miRNA dysregulation in cancer, but that miRNAs themselves also indirectly drive these DNA and histone modifications. More explicitly, recent work has shown that miRNAs can regulate chromatin structure and gene expression by directly targeting key enzymes involved in these processes. This review aims to summarize these research findings specifically in the context of breast cancer. This review also discusses miRNAs as epigenetic biomarkers and as therapeutics, and presents a comprehensive summary of currently validated epigenetic targets in breast cancer.
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Affiliation(s)
- Brock Humphries
- Center for Molecular Imaging, Department of Radiology, University of Michigan, Ann Arbor, MI 48109; USA.
| | - Zhishan Wang
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Chengfeng Yang
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA.
- Center for Research on Environment Disease, College of Medicine, University of Kentucky, Lexington, KY 40536; USA.
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15
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Crisafulli C, Romeo PD, Calabrò M, Epasto LM, Alberti S. Pharmacogenetic and pharmacogenomic discovery strategies. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2019; 2:225-241. [PMID: 35582724 PMCID: PMC8992635 DOI: 10.20517/cdr.2018.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 11/12/2022]
Abstract
Genetic/genomic profiling at a single-patient level is expected to provide critical information for determining inter-individual drug toxicity and potential efficacy in cancer therapy. A better definition of cancer subtypes at a molecular level, may correspondingly complement such pharmacogenetic and pharmacogenomic approaches, for more effective personalized treatments. Current pharmacogenetic/pharmacogenomic strategies are largely based on the identification of known polymorphisms, thus limiting the discovery of novel or rarer genetic variants. Recent improvements in cost and throughput of next generation sequencing (NGS) are now making whole-genome profiling a plausible alternative for clinical procedures. Beyond classical pharmacogenetic/pharmacogenomic traits for drug metabolism, NGS screening programs of cancer genomes may lead to the identification of novel cancer-driving mutations. These may not only constitute novel therapeutic targets, but also effector determinants for metabolic pathways linked to drug metabolism. An additional advantage is that cancer NGS profiling is now leading to discovering targetable mutations, e.g., in glioblastomas and pancreatic cancers, which were originally discovered in other tumor types, thus allowing for effective repurposing of active drugs already on the market.
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Affiliation(s)
- Concetta Crisafulli
- Department of Biomedical Sciences - BIOMORF, University of Messina, via Consolare Valeria, 98125 Messina, Italy
| | | | - Marco Calabrò
- Department of Biomedical Sciences - BIOMORF, University of Messina, via Consolare Valeria, 98125 Messina, Italy
| | - Ludovica Martina Epasto
- Unit of Medical Genetics, University of Messina, via Consolare Valeria, 98125 Messina, Italy
| | - Saverio Alberti
- Department of Biomedical Sciences - BIOMORF, University of Messina, via Consolare Valeria, 98125 Messina, Italy.,Unit of Medical Genetics, University of Messina, via Consolare Valeria, 98125 Messina, Italy.,Correspondence Address: Prof. Saverio Alberti, Unit of Medical Genetics, BIOMORF Department of Biomedical Sciences, University of Messina, via Consolare Valeria, 98125 Messina, Italy. E-mail:
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16
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Köhler CU, Bonberg N, Ahrens M, Behrens T, Hovanec J, Eisenacher M, Noldus J, Deix T, Braun K, Gohlke H, Walter M, Tannapfel A, Tam Y, Sommerer F, Marcus K, Jöckel KH, Erbel R, Cantor CR, Käfferlein HU, Brüning T. Noninvasive diagnosis of urothelial cancer in urine using DNA hypermethylation signatures-Gender matters. Int J Cancer 2019; 145:2861-2872. [PMID: 31008534 DOI: 10.1002/ijc.32356] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/01/2019] [Indexed: 01/28/2023]
Abstract
Urothelial cancer (UCa) is the most predominant cancer of the urinary tract and noninvasive diagnosis using hypermethylation signatures in urinary cells is promising. Here, we assess gender differences in a newly identified set of methylation biomarkers. UCa-associated hypermethylated sites were identified in urine of a male screening cohort (n = 24) applying Infinium-450K-methylation arrays and verified in two separate mixed-gender study groups (n = 617 in total) using mass spectrometry as an independent technique. Additionally, tissue samples (n = 56) of mixed-gender UCa and urological controls (UCt) were analyzed. The hypermethylation signature of UCa in urine was specific and sensitive across all stages and grades of UCa and independent on hematuria. Individual CpG sensitivities reached up to 81.3% at 95% specificity. Albeit similar methylation differences in tissue of both genders, differences were less pronounced in urine from women, most likely due to the frequent presence of squamous epithelial cells and leukocytes. Increased repression of methylation levels was observed at leukocyte counts ≥500/μl urine which was apparent in 30% of female and 7% of male UCa cases, further confirming the significance of the relative amounts of cancerous and noncancerous cells in urine. Our study shows that gender difference is a most relevant issue when evaluating the performance of urinary biomarkers in cancer diagnostics. In case of UCa, the clinical benefits of methylation signatures to male patients may outweigh those in females due to the general composition of women's urine. Accordingly, these markers offer a diagnostic option specifically in males to decrease the number of invasive cystoscopies.
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Affiliation(s)
- Christina U Köhler
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Nadine Bonberg
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Maike Ahrens
- Medical Proteome Center, Ruhr University Bochum, Bochum, Germany
| | - Thomas Behrens
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Jan Hovanec
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | | | - Joachim Noldus
- Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Thomas Deix
- Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Katharina Braun
- Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | | | - Michael Walter
- c.ATG Core Facility for NGS and Microarrays, University of Tübingen, Tübingen, Germany
| | - Andrea Tannapfel
- Institute of Pathology, Georgius Agricola Foundation, Ruhr-University Bochum, Bochum, Germany
| | - Yu Tam
- Institute of Pathology, Georgius Agricola Foundation, Ruhr-University Bochum, Bochum, Germany
| | - Florian Sommerer
- Institute of Pathology, Georgius Agricola Foundation, Ruhr-University Bochum, Bochum, Germany
| | - Katrin Marcus
- Medical Proteome Center, Ruhr University Bochum, Bochum, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Raimund Erbel
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Charles R Cantor
- Department of Biomedical Engineering, School of Medicine, Boston University, Boston, MA
| | - Heiko U Käfferlein
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
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17
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Liu S, Yin P, Kujawa SA, Coon JS, Okeigwe I, Bulun SE. Progesterone receptor integrates the effects of mutated MED12 and altered DNA methylation to stimulate RANKL expression and stem cell proliferation in uterine leiomyoma. Oncogene 2019; 38:2722-2735. [PMID: 30538295 PMCID: PMC6461478 DOI: 10.1038/s41388-018-0612-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/31/2018] [Accepted: 11/17/2018] [Indexed: 01/22/2023]
Abstract
Progesterone and its receptor, PR, are essential for uterine leiomyoma (LM, a.k.a., fibroid) tumorigenesis, but the underlying cellular and molecular mechanisms remain unclear. The receptor activator of NF-κB (RANKL) was recently identified as a novel progesterone/PR-responsive gene that plays an important role in promoting LM growth. Here, we used RANKL as a representative gene to investigate how steroid hormone, genetic, and epigenetic signals are integrated to regulate LM stem cell (LSC) function. We demonstrated that RANKL specifically upregulates LSC proliferation through activation of Cyclin D1. RANKL gene transcription was robustly induced by the progesterone agonist R5020, leading to a dramatically higher RANKL expression in LM compared to adjacent myometrial (MM) tissue. MethylCap-Seq revealed a differentially methylated region (DMR) adjacent to the distal PR-binding site (PRBS) 87 kb upstream of the RANKL transcription start site. Hypermethylation of the DMR inhibited recruitment of PR to the adjacent PRBS. Luciferase assays indicated that the DMR and distal PRBS constitute a novel RANKL distal regulatory element that actively regulates RANKL expression. Furthermore, MED12 physically interacts with PR in LM tissue. The interaction between MED12 and PR, binding of PR and MED12 to PRBS, and RANKL gene expression are significantly higher in LM containing a distinct MED12 mutation (G44D) than in LM with wild-type MED12. In summary, our findings suggest that DNA methylation and MED12 mutation together constitute a complex regulatory network that affects progesterone/PR-mediated RANKL gene expression, with an important role in activating stem cell proliferation and fibroid tumor development.
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Affiliation(s)
- Shimeng Liu
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Ping Yin
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Stacy A Kujawa
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - John S Coon
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Ijeoma Okeigwe
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Serdar E Bulun
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
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18
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Circulating cell-free DNA in breast cancer: size profiling, levels, and methylation patterns lead to prognostic and predictive classifiers. Oncogene 2019; 38:3387-3401. [PMID: 30643192 DOI: 10.1038/s41388-018-0660-y] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/11/2018] [Accepted: 12/07/2018] [Indexed: 12/24/2022]
Abstract
Blood circulating cell-free DNA (ccfDNA) is a suggested biosource of valuable clinical information for cancer, meeting the need for a minimally-invasive advancement in the route of precision medicine. In this paper, we evaluated the prognostic and predictive potential of ccfDNA parameters in early and advanced breast cancer. Groups consisted of 150 and 16 breast cancer patients under adjuvant and neoadjuvant therapy respectively, 34 patients with metastatic disease and 35 healthy volunteers. Direct quantification of ccfDNA in plasma revealed elevated concentrations correlated to the incidence of death, shorter PFS, and non-response to pharmacotherapy in the metastatic but not in the other groups. The methylation status of a panel of cancer-related genes chosen based on previous expression and epigenetic data (KLK10, SOX17, WNT5A, MSH2, GATA3) was assessed by quantitative methylation-specific PCR. All but the GATA3 gene was more frequently methylated in all the patient groups than in healthy individuals (all p < 0.05). The methylation of WNT5A was statistically significantly correlated to greater tumor size and poor prognosis characteristics and in advanced stage disease with shorter OS. In the metastatic group, also SOX17 methylation was significantly correlated to the incidence of death, shorter PFS, and OS. KLK10 methylation was significantly correlated to unfavorable clinicopathological characteristics and relapse, whereas in the adjuvant group to shorter DFI. Methylation of at least 3 or 4 genes was significantly correlated to shorter OS and no pharmacotherapy response, respectively. Classification analysis by a fully automated, machine learning software produced a single-parametric linear model using ccfDNA plasma concentration values, with great discriminating power to predict response to chemotherapy (AUC 0.803, 95% CI [0.606, 1.000]) in the metastatic group. Two more multi-parametric signatures were produced for the metastatic group, predicting survival and disease outcome. Finally, a multiple logistic regression model was constructed, discriminating between patient groups and healthy individuals. Overall, ccfDNA emerged as a highly potent predictive classifier in metastatic breast cancer. Upon prospective clinical evaluation, all the signatures produced could aid accurate prognosis.
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19
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Mio C, Gerratana L, Bolis M, Caponnetto F, Zanello A, Barbina M, Di Loreto C, Garattini E, Damante G, Puglisi F. BET proteins regulate homologous recombination-mediated DNA repair: BRCAness and implications for cancer therapy. Int J Cancer 2018; 144:755-766. [PMID: 30259975 DOI: 10.1002/ijc.31898] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/28/2018] [Accepted: 09/20/2018] [Indexed: 12/29/2022]
Abstract
Bromodomain and Extra-Terminal (BET) proteins are historically involved in regulating gene expression and BRD4 was recently found to be involved in DNA damage regulation. Aims of our study were to assess BRD4 regulation in homologous recombination-mediated DNA repair and to explore novel clinical strategies through the combinations of the pharmacological induction of epigenetic BRCAness in BRCA1 wild-type triple negative breast cancer (TNBC) cells by means of BET inhibitors and compounds already available in clinic. Performing a dual approach (chromatin immunoprecipitation and RNA interference), the direct relationship between BRD4 and BRCA1/RAD51 expression was confirmed in TNBC cells. Moreover, BRD4 pharmacological inhibition using two BET inhibitors (JQ1 and GSK525762A) induced a dose-dependent reduction in BRCA1 and RAD51 levels and is able to hinder homologous recombination-mediated DNA damage repair, generating a BRCAness phenotype in TNBC cells. Furthermore, BET inhibition impaired the ability of TNBC cells to overcome the increase in DNA damage after platinum salts (i.e., CDDP) exposure, leading to massive cell death, and triggered synthetic lethality when combined with PARP inhibitors (i.e., AZD2281). Altogether, the present study confirms that BET proteins directly regulate the homologous recombination pathway and their inhibition induced a BRCAness phenotype in BRCA1 wild-type TNBC cells. Noteworthy, being this strategy based on drugs already available for human use, it is rapidly transferable and could potentially enable clinicians to exploit platinum salts and PARP inhibitors-based treatments in a wider population of TNBC patients and not just in a specific subgroup, after validating clinical trials.
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Affiliation(s)
- Catia Mio
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | | | - Marco Bolis
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | | | - Andrea Zanello
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Mattia Barbina
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Carla Di Loreto
- Department of Medicine (DAME), University of Udine, Udine, Italy.,Institute of Pathology, ASUIUD University Hospital of Udine, Udine, Italy
| | - Enrico Garattini
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giuseppe Damante
- Department of Medicine (DAME), University of Udine, Udine, Italy.,Institute of Medical Genetics, ASUIUD University Hospital of Udine, Udine, Italy
| | - Fabio Puglisi
- Department of Medicine (DAME), University of Udine, Udine, Italy.,Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
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Vu TL, Nguyen TT, Doan VTH, Vo LTT. Methylation Profiles of BRCA1, RASSF1A and GSTP1 in Vietnamese Women with Breast Cancer. Asian Pac J Cancer Prev 2018; 19:1887-1893. [PMID: 30049201 PMCID: PMC6165660 DOI: 10.22034/apjcp.2018.19.7.1887] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 05/03/2018] [Indexed: 12/13/2022] Open
Abstract
Objective: This study investigated the DNA promoter methylation profiles of BRCA1, RASSF1A and GSTP1 genes, both individually and in an integrative manner in order to clarify their correlation with clinicopathological parameters of breast cancer from Vietnamese patients, and establish new potential integrative methylation biomarkers for breast cancer detection. Material and methods: The methylation frequencies of BRCA1, RASSF1A and GSTP1 were analyzed by methylation specific polymerase chain reaction (MSP) in 70 specimens of breast carcinomas and 79 pairs of tumor and matched adjacent normal tissues from breast cancer patients. Results: All the three analyzed genes showed a concordance concerning their promoter methylation in tumor and adjacent normal tissue. The methylation of BRCA1, RASSF1A and GSTP1 was found in 58.23 %, 74.68 % and 59.49 % of tumor tissues and 51.90 %, 63.29 % and 35.44 % of corresponding adjacent tissues, respectively. When each gene was assessed individually, only the methylation of GSTP1 was significantly associated with tumor tissues (p=0.003). However, the methylation frequency of at least one of the three genes and the methylation frequency of all the three genes both showed significant association with tumor (p=0.008 and p=0.04, respectively). The methylation of BRCA1 was found to be significantly associated with tumor grade (p=0.01). Conclusion: This study emphasized that the panel of the three genes BRCA1, RASSF1A and GSTP1 can be further developed as potential biomarkers in diagnosis and classification of breast cancer in Vietnamese women.
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Affiliation(s)
- Trang Lan Vu
- Sorbonne University, UPMC Univ. Paris 06, École Normale Supérieure, PSL Research University, CNRS, INSERM, APHP, Laboratoire des Biomolécules (LBM), Paris, France.
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21
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Targeting the Epigenome as a Novel Therapeutic Approach for Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1026:287-313. [DOI: 10.1007/978-981-10-6020-5_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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22
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Crujeiras AB, Diaz-Lagares A, Stefansson OA, Macias-Gonzalez M, Sandoval J, Cueva J, Lopez-Lopez R, Moran S, Jonasson JG, Tryggvadottir L, Olafsdottir E, Tinahones FJ, Carreira MC, Casanueva FF, Esteller M. Obesity and menopause modify the epigenomic profile of breast cancer. Endocr Relat Cancer 2017; 24:351-363. [PMID: 28442560 DOI: 10.1530/erc-16-0565] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 04/25/2017] [Indexed: 12/20/2022]
Abstract
Obesity is a high risk factor for breast cancer. This relationship could be marked by a specific methylome. The current work was aimed to explore the impact of obesity and menopausal status on variation in breast cancer methylomes. Data from Infinium 450K array-based methylomes of 64 breast tumors were coupled with information on BMI and menopausal status. Additionally, DNA methylation results were validated in 18 non-tumor and 81 tumor breast samples. Breast tumors arising in either pre- or postmenopausal women stratified by BMI or menopausal status alone were not associated with a specific DNA methylation pattern. Intriguingly, the DNA methylation pattern identified in association with the high-risk group (postmenopausal women with high BMI (>25) and premenopausal women with normal or low BMI < 25) exclusively characterized by hypermethylation of 1287 CpG sites as compared with the low-risk group. These CpG sites included the promoter region of fourteen protein-coding genes of which CpG methylation over the ZNF577 promoter region represents the top scoring associated event. In an independent cohort, the ZNF577 promoter methylation remained statistically significant in association with the high-risk group. Additionally, the impact of ZNF577 promoter methylation on mRNA expression levels was demonstrated in breast cancer cell lines after treatment with a demethylating agent (5-azacytidine). In conclusion, the epigenome of breast tumors is affected by a complex interaction between BMI and menopausal status. The ZNF577 methylation quantification is clearly relevant for the development of novel biomarkers of precision therapy in breast cancer.
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Affiliation(s)
- Ana B Crujeiras
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Laboratory of Molecular and Cellular EndocrinologyInstituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela University (USC), Santiago de Compostela, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Translational Medical Oncology Group (Oncomet)Instituto de Investigación Sanitaria (IDIS); Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and CIBER de Cancer (CIBERONC), Santiago de Compostela, Spain
| | - Olafur A Stefansson
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Cancer Research LaboratoryFaculty of Medicine, University of Iceland, Reykjavic, Iceland
| | - Manuel Macias-Gonzalez
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
- Unidad de Gestión Clínica de Endocrinología y NutriciónInstituto de Investigación Biomédica de Málaga (IBIMA), Complejo Hospitalario de Málaga (Virgen de la Victoria), Universidad de Málaga, Málaga, Spain
| | - Juan Sandoval
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Juan Cueva
- Translational Medical Oncology Group (Oncomet)Instituto de Investigación Sanitaria (IDIS); Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and CIBER de Cancer (CIBERONC), Santiago de Compostela, Spain
| | - Rafael Lopez-Lopez
- Translational Medical Oncology Group (Oncomet)Instituto de Investigación Sanitaria (IDIS); Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and CIBER de Cancer (CIBERONC), Santiago de Compostela, Spain
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Jon G Jonasson
- Department of Pathology and the Icelandic Cancer RegistryIcelandic Cancer society and Landspitali University Hospital, Reykjavik, Iceland
| | - Laufey Tryggvadottir
- Department of Pathology and the Icelandic Cancer RegistryIcelandic Cancer society and Landspitali University Hospital, Reykjavik, Iceland
| | - Elinborg Olafsdottir
- Department of Pathology and the Icelandic Cancer RegistryIcelandic Cancer society and Landspitali University Hospital, Reykjavik, Iceland
| | - Francisco J Tinahones
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
- Unidad de Gestión Clínica de Endocrinología y NutriciónInstituto de Investigación Biomédica de Málaga (IBIMA), Complejo Hospitalario de Málaga (Virgen de la Victoria), Universidad de Málaga, Málaga, Spain
| | - Marcos C Carreira
- Laboratory of Molecular and Cellular EndocrinologyInstituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela University (USC), Santiago de Compostela, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
| | - Felipe F Casanueva
- Laboratory of Molecular and Cellular EndocrinologyInstituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela University (USC), Santiago de Compostela, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Department of Physiological Sciences IISchool of Medicine, University of Barcelona and Instituto Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
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Spitzwieser M, Entfellner E, Werner B, Pulverer W, Pfeiler G, Hacker S, Cichna-Markl M. Hypermethylation of CDKN2A exon 2 in tumor, tumor-adjacent and tumor-distant tissues from breast cancer patients. BMC Cancer 2017; 17:260. [PMID: 28403857 PMCID: PMC5389179 DOI: 10.1186/s12885-017-3244-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/29/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Breast carcinogenesis is a multistep process involving genetic and epigenetic changes. Tumor tissues are frequently characterized by gene-specific hypermethylation and global DNA hypomethylation. Aberrant DNA methylation levels have, however, not only been found in tumors, but also in tumor-surrounding tissue appearing histologically normal. This phenomenon is called field cancerization. Knowledge of the existence of a cancer field and its spread are of clinical relevance. If the tissue showing pre-neoplastic lesions is not removed by surgery, it may develop into invasive carcinoma. METHODS We investigated the prevalence of gene-specific and global DNA methylation changes in tumor-adjacent and tumor-distant tissues in comparison to tumor tissues from the same breast cancer patients (n = 18) and normal breast tissues from healthy women (n = 4). Methylation-sensitive high resolution melting (MS-HRM) analysis was applied to determine methylation levels in the promoters of APC, BRCA1, CDKN2A (p16), ESR1, HER2/neu and PTEN, in CDKN2A exon 2 and in LINE-1, as indicator for the global DNA methylation extent. The methylation status of the ESR2 promoter was determined by pyrosequencing. RESULTS Tumor-adjacent and tumor-distant tissues frequently showed pre-neoplastic gene-specific and global DNA methylation changes. The APC promoter (p = 0.003) and exon 2 of CDKN2A (p < 0.001) were significantly higher methylated in tumors than in normal breast tissues from healthy women. For both regions, significant differences were also found between tumor and tumor-adjacent tissues (p = 0.001 and p < 0.001, respectively) and tumor and tumor-distant tissues (p = 0.001 and p < 0.001, respectively) from breast cancer patients. In addition, tumor-adjacent (p = 0.002) and tumor-distant tissues (p = 0.005) showed significantly higher methylation levels of CDKN2A exon 2 than normal breast tissues serving as control. Significant correlations were found between the proliferative activity and the methylation status of CDKN2A exon 2 in tumor (r = -0.485, p = 0.041) and tumor-distant tissues (r = -0.498, p = 0.036). CONCLUSIONS From our results we can conclude that methylation changes in CDKN2A exon 2 are associated with breast carcinogenesis. Further investigations are, however, necessary to confirm that hypermethylation of CDKN2A exon 2 is associated with tumor proliferative activity.
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Affiliation(s)
- Melanie Spitzwieser
- Department of Analytical Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Elisabeth Entfellner
- Department of Analytical Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Bettina Werner
- Department of Analytical Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Walter Pulverer
- Molecular Diagnostics, Austrian Institute of Technology, Muthgasse 11, 1190, Vienna, Austria
| | - Georg Pfeiler
- Department of Obstetrics and Gynecology, Division of Gynecology and Gynecological Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Stefan Hacker
- Department of Plastic and Reconstructive Surgery, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria.
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Guerra E, Cimadamore A, Simeone P, Vacca G, Lattanzio R, Botti G, Gatta V, D'Aurora M, Simionati B, Piantelli M, Alberti S. p53, cathepsin D, Bcl-2 are joint prognostic indicators of breast cancer metastatic spreading. BMC Cancer 2016; 16:649. [PMID: 27538498 PMCID: PMC4991058 DOI: 10.1186/s12885-016-2713-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 08/11/2016] [Indexed: 02/04/2023] Open
Abstract
Background Traditional prognostic indicators of breast cancer, i.e. lymph node diffusion, tumor size, grading and estrogen receptor expression, are inadequate predictors of metastatic relapse. Thus, additional prognostic parameters appear urgently needed. Individual oncogenic determinants have largely failed in this endeavour. Only a few individual tumor growth drivers, e.g. mutated p53, Her-2, E-cadherin, Trops, did reach some prognostic/predictive power in clinical settings. As multiple factors are required to drive solid tumor progression, clusters of such determinants were expected to become stronger indicators of tumor aggressiveness and malignant progression than individual parameters. To identify such prognostic clusters, we went on to coordinately analyse molecular and histopathological determinants of tumor progression of post-menopausal breast cancers in the framework of a multi-institutional case series/case-control study. Methods A multi-institutional series of 217 breast cancer cases was analyzed. Twenty six cases (12 %) showed disease relapse during follow-up. Relapsed cases were matched with a set of control patients by tumor diameter, pathological stage, tumor histotype, age, hormone receptors and grading. Histopathological and molecular determinants of tumor development and aggressiveness were then analyzed in relapsed versus non-relapsed cases. Stepwise analyses and model structure fitness assessments were carried out to identify clusters of molecular alterations with differential impact on metastatic relapse. Results p53, Bcl-2 and cathepsin D were shown to be coordinately associated with unique levels of relative risk for disease relapse. As many Ras downstream targets, among them matrix metalloproteases, are synergistically upregulated by mutated p53, whole-exon sequence analyses were performed for TP53, Ki-RAS and Ha-RAS, and findings were correlated with clinical phenotypes. Notably, TP53 insertion/deletion mutations were only detected in relapsed cases. Correspondingly, Ha-RAS missense oncogenic mutations were only found in a subgroup of relapsing tumors. Conclusions We have identified clusters of specific molecular alterations that greatly improve prognostic assessment with respect to singularly-analysed indicators. The combined analysis of these multiple tumor-relapse risk factors promises to become a powerful approach to identify patients subgroups with unfavourable disease outcome. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2713-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emanuela Guerra
- Unit of Cancer Pathology, CeSI-MeT, University of Chieti, Chieti, Italy
| | | | - Pasquale Simeone
- Unit of Cancer Pathology, CeSI-MeT, University of Chieti, Chieti, Italy
| | - Giovanna Vacca
- Unit of Cancer Pathology, CeSI-MeT, University of Chieti, Chieti, Italy
| | - Rossano Lattanzio
- Unit of Cancer Pathology, CeSI-MeT, University of Chieti, Chieti, Italy.,Department of Medical, Oral and Biotechnological Sciences, University 'G. D'Annunzio', Chieti, Italy
| | - Gerardo Botti
- Department of Pathology "Foundation G.Pascale", National Cancer Institute, Naples, Italy
| | - Valentina Gatta
- Department of Psychological, Health ad Territorial Sciences, School of Medicine and Life Sciences, University 'G. D'Annunzio', Chieti, Italy
| | - Marco D'Aurora
- Department of Psychological, Health ad Territorial Sciences, School of Medicine and Life Sciences, University 'G. D'Annunzio', Chieti, Italy
| | | | - Mauro Piantelli
- Unit of Cancer Pathology, CeSI-MeT, University of Chieti, Chieti, Italy.,Department of Medical, Oral and Biotechnological Sciences, University 'G. D'Annunzio', Chieti, Italy
| | - Saverio Alberti
- Unit of Cancer Pathology, CeSI-MeT, University of Chieti, Chieti, Italy. .,Department of Neurosciences, Imaging and Clinical Sciences, University 'G. D'Annunzio', Chieti, Italy.
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Girotra S, Yeghiazaryan K, Golubnitschaja O. Potential biomarker panels in overall breast cancer management: advancements by multilevel diagnostics. Per Med 2016; 13:469-484. [PMID: 29767597 DOI: 10.2217/pme-2016-0020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Breast cancer (BC) prevalence has reached an epidemic scale with half a million deaths annually. Current deficits in BC management include predictive and preventive approaches, optimized screening programs, individualized patient profiling, highly sensitive detection technologies for more precise diagnostics and therapy monitoring, individualized prediction and effective treatment of BC metastatic disease. To advance BC management, paradigm shift from delayed to predictive, preventive and personalized medical services is essential. Corresponding step forwards requires innovative multilevel diagnostics procuring specific panels of validated biomarkers. Here, we discuss current instrumental advancements including genomics, proteomics, epigenetics, miRNA, metabolomics, circulating tumor cells and cancer stem cells with a focus on biomarker discovery and multilevel diagnostic panels. A list of the recommended biomarker candidates is provided.
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Sinnott JA, Cai T. Inference for survival prediction under the regularized Cox model. Biostatistics 2016; 17:692-707. [PMID: 27107008 DOI: 10.1093/biostatistics/kxw016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 03/23/2016] [Indexed: 12/31/2022] Open
Abstract
When a moderate number of potential predictors are available and a survival model is fit with regularization to achieve variable selection, providing accurate inference on the predicted survival can be challenging. We investigate inference on the predicted survival estimated after fitting a Cox model under regularization guaranteeing the oracle property. We demonstrate that existing asymptotic formulas for the standard errors of the coefficients tend to underestimate the variability for some coefficients, while typical resampling such as the bootstrap tends to overestimate it; these approaches can both lead to inaccurate variance estimation for predicted survival functions. We propose a two-stage adaptation of a resampling approach that brings the estimated error in line with the truth. In stage 1, we estimate the coefficients in the observed data set and in [Formula: see text] resampled data sets, and allow the resampled coefficient estimates to vote on whether each coefficient should be 0. For those coefficients voted as zero, we set both the point and interval estimates to [Formula: see text] In stage 2, to make inference about coefficients not voted as zero in stage 1, we refit the penalized model in the observed data and in the [Formula: see text] resampled data sets with only variables corresponding to those coefficients. We demonstrate that ensemble voting-based point and interval estimators of the coefficients perform well in finite samples, and prove that the point estimator maintains the oracle property. We extend this approach to derive inference procedures for survival functions and demonstrate that our proposed interval estimation procedures substantially outperform estimators based on asymptotic inference or standard bootstrap. We further illustrate our proposed procedures to predict breast cancer survival in a gene expression study.
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Affiliation(s)
- Jennifer A Sinnott
- Department of Statistics, The Ohio State University, Columbus, OH 43210, USA
| | - Tianxi Cai
- Department of Biostatistics, Harvard University, Boston, MA 02115, USA
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27
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Guerra E, Trerotola M, Tripaldi R, Aloisi AL, Simeone P, Sacchetti A, Relli V, D'Amore A, La Sorda R, Lattanzio R, Piantelli M, Alberti S. Trop-2 Induces Tumor Growth Through AKT and Determines Sensitivity to AKT Inhibitors. Clin Cancer Res 2016; 22:4197-205. [PMID: 27022065 DOI: 10.1158/1078-0432.ccr-15-1701] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 02/29/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE Inhibition of AKT is a key target area for personalized cancer medicine. However, predictive markers of response to AKT inhibitors are lacking. Correspondingly, the AKT-dependent chain of command for tumor growth, which will mediate AKT-dependent therapeutic responses, remains unclear. EXPERIMENTAL DESIGN Proteomic profiling was utilized to identify nodal hubs of the Trop-2 cancer growth-driving network. Kinase-specific inhibitors were used to dissect Trop-2-dependent from Trop-2-independent pathways. In vitro assays, in vivo preclinical models, and case series of primary human breast cancers were utilized to define the mechanisms of Trop-2-driven growth and the mode of action of Trop-2-predicted AKT inhibitors. RESULTS Trop-2 and AKT expression was shown to be tightly coordinated in human breast cancers, with virtual overlap with AKT activation profiles at T308 and S473, consistent with functional interaction in vivo AKT allosteric inhibitors were shown to only block the growth of Trop-2-expressing tumor cells, both in vitro and in preclinical models, being ineffective on Trop-2-null cells. Consistently, AKT-targeted siRNA only impacted on Trop-2-expressing cells. Lentiviral downregulation of endogenous Trop-2 abolished tumor response to AKT blockade, indicating Trop-2 as a mandatory activator of AKT. CONCLUSIONS Our findings indicate that the expression of Trop-2 is a stringent predictor of tumor response to AKT inhibitors. They also support the identification of target-activatory pathways, as efficient predictors of response in precision cancer therapy. Clin Cancer Res; 22(16); 4197-205. ©2016 AACR.
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Affiliation(s)
- Emanuela Guerra
- Unit of Cancer Pathology, CeSI-MeT, University 'G. d'Annunzio,' Chieti, Italy
| | - Marco Trerotola
- Unit of Cancer Pathology, CeSI-MeT, University 'G. d'Annunzio,' Chieti, Italy
| | - Romina Tripaldi
- Unit of Cancer Pathology, CeSI-MeT, University 'G. d'Annunzio,' Chieti, Italy
| | - Anna Laura Aloisi
- Unit of Cancer Pathology, CeSI-MeT, University 'G. d'Annunzio,' Chieti, Italy
| | - Pasquale Simeone
- Unit of Cancer Pathology, CeSI-MeT, University 'G. d'Annunzio,' Chieti, Italy
| | - Andrea Sacchetti
- Unit of Cancer Pathology, CeSI-MeT, University 'G. d'Annunzio,' Chieti, Italy
| | - Valeria Relli
- Unit of Cancer Pathology, CeSI-MeT, University 'G. d'Annunzio,' Chieti, Italy
| | - Antonella D'Amore
- Unit of Cancer Pathology, CeSI-MeT, University 'G. d'Annunzio,' Chieti, Italy
| | - Rossana La Sorda
- Unit of Cancer Pathology, CeSI-MeT, University 'G. d'Annunzio,' Chieti, Italy
| | - Rossano Lattanzio
- Unit of Cancer Pathology, CeSI-MeT, University 'G. d'Annunzio,' Chieti, Italy. Department of Medical, Oral and Biotechnological Sciences, University 'G. d'Annunzio,' Chieti, Italy
| | - Mauro Piantelli
- Unit of Cancer Pathology, CeSI-MeT, University 'G. d'Annunzio,' Chieti, Italy. Department of Medical, Oral and Biotechnological Sciences, University 'G. d'Annunzio,' Chieti, Italy
| | - Saverio Alberti
- Unit of Cancer Pathology, CeSI-MeT, University 'G. d'Annunzio,' Chieti, Italy. Department of Neuroscience, Imaging and Clinical Sciences, Unit of Physiology and Physiopathology, University 'G. d'Annunzio,' Chieti, Italy.
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