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Dai Z, Chen H, Feng K, Li T, Liu W, Zhou Y, Yang D, Xue B, Zhu J. Promoter hypermethylation of Y-chromosome gene PRKY as a potential biomarker for the early diagnosis of prostate cancer. Epigenomics 2024:1-16. [PMID: 38979582 DOI: 10.1080/17501911.2024.2365625] [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: 01/17/2022] [Accepted: 06/04/2024] [Indexed: 07/10/2024] Open
Abstract
Aim: To develop a methylation marker of Y-chromosome gene in the early diagnosis of prostate cancer (PCa). Materials & methods: We utilized bioinformatics analysis to identify the expression and promoter methylation of Y-chromosome gene PRKY in PCa and other common malignancies. Single-center experiments were conducted to validate the diagnostic value of PRKY promoter methylation in PCa. Results: PRKY expression was significantly down-regulated in PCa and its mechanism may be related to promoter methylation. PRKY promoter methylation is highly specific for the diagnosis of early PCa, which may be superior to prostate-specific antigen, mpMRI and other excellent molecular biomarkers. Conclusion: PRKY promoter methylation may be a potential marker for the early and accurate diagnosis of PCa.
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Affiliation(s)
- Zheng Dai
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
- Department of Urology, The Third Affiliated Hospital of Anhui Medical University, Hefei, 230061, China
| | - Hongbing Chen
- Department of Urology, The Third Affiliated Hospital of Anhui Medical University, Hefei, 230061, China
| | - Kaiwen Feng
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Tuoxin Li
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Weifeng Liu
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Yibin Zhou
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Dongrong Yang
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Boxin Xue
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Jin Zhu
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
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Wang Y, Liu W, Chen Z, Zang Y, Xu L, Dai Z, Zhou Y, Zhu J. A noninvasive method for predicting clinically significant prostate cancer using magnetic resonance imaging combined with PRKY promoter methylation level: a machine learning study. BMC Med Imaging 2024; 24:60. [PMID: 38468226 DOI: 10.1186/s12880-024-01236-1] [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: 12/18/2023] [Accepted: 02/29/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Traditional process for clinically significant prostate cancer (csPCA) diagnosis relies on invasive biopsy and may bring pain and complications. Radiomic features of magnetic resonance imaging MRI and methylation of the PRKY promoter were found to be associated with prostate cancer. METHODS Fifty-four Patients who underwent prostate biopsy or photoselective vaporization of the prostate (PVP) from 2022 to 2023 were selected for this study, and their clinical data, blood samples and MRI images were obtained before the operation. Methylation level of two PRKY promoter sites, cg05618150 and cg05163709, were tested through bisulfite sequencing PCR (BSP). The PI-RADS score of each patient was estimated and the region of interest (ROI) was delineated by 2 experienced radiologists. After being extracted by a plug-in of 3D-slicer, radiomic features were selected through LASSCO regression and t-test. Selected radiomic features, methylation levels and clinical data were used for model construction through the random forest (RF) algorithm, and the predictive efficiency was analyzed by the area under the receiver operation characteristic (ROC) curve (AUC). RESULTS Methylation level of the site, cg05618150, was observed to be associated with prostate cancer, for which the AUC was 0.74. The AUC of T2WI in csPCA prediction was 0.84, which was higher than that of the apparent diffusion coefficient ADC (AUC = 0.81). The model combined with T2WI and clinical data reached an AUC of 0.94. The AUC of the T2WI-clinic-methylation-combined model was 0.97, which was greater than that of the model combined with the PI-RADS score, clinical data and PRKY promoter methylation levels (AUC = 0.86). CONCLUSIONS The model combining with radiomic features, clinical data and PRKY promoter methylation levels based on machine learning had high predictive efficiency in csPCA diagnosis.
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Affiliation(s)
- Yufei Wang
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215000, China
| | - Weifeng Liu
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215000, China
| | - Zeyu Chen
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215000, China
| | - Yachen Zang
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215000, China
| | - Lijun Xu
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215000, China
| | - Zheng Dai
- Department of Urology, Hefei First People's Hopital, Hefei, Anhui Province, 230000, China.
| | - Yibin Zhou
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215000, China.
| | - Jin Zhu
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215000, China.
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Zhang Z, Zhou Q, Ang X, Hu C, Ouyang J, Zhang J. The research of the application of a new urinary biomarker PCA-M of prostate cancer (PSA from 4 to 20 ng/ml). ALL LIFE 2022. [DOI: 10.1080/26895293.2022.2038689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Zhiyu Zhang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Qi Zhou
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Xiaojie Ang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Can Hu
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Jun Ouyang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Jianglei Zhang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
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Heydari R, Jangravi Z, Maleknia S, Seresht-Ahmadi M, Bahari Z, Salekdeh GH, Meyfour A. Y chromosome is moving out of sex determination shadow. Cell Biosci 2022; 12:4. [PMID: 34983649 PMCID: PMC8724748 DOI: 10.1186/s13578-021-00741-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/21/2021] [Indexed: 01/05/2023] Open
Abstract
Although sex hormones play a key role in sex differences in susceptibility, severity, outcomes, and response to therapy of different diseases, sex chromosomes are also increasingly recognized as an important factor. Studies demonstrated that the Y chromosome is not a ‘genetic wasteland’ and can be a useful genetic marker for interpreting various male-specific physiological and pathophysiological characteristics. Y chromosome harbors male‑specific genes, which either solely or in cooperation with their X-counterpart, and independent or in conjunction with sex hormones have a considerable impact on basic physiology and disease mechanisms in most or all tissues development. Furthermore, loss of Y chromosome and/or aberrant expression of Y chromosome genes cause sex differences in disease mechanisms. With the launch of the human proteome project (HPP), the association of Y chromosome proteins with pathological conditions has been increasingly explored. In this review, the involvement of Y chromosome genes in male-specific diseases such as prostate cancer and the cases that are more prevalent in men, such as cardiovascular disease, neurological disease, and cancers, has been highlighted. Understanding the molecular mechanisms underlying Y chromosome-related diseases can have a significant impact on the prevention, diagnosis, and treatment of diseases.
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Affiliation(s)
- Raheleh Heydari
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zohreh Jangravi
- Department of Biochemistry, Faculty of Medicine, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Samaneh Maleknia
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehrshad Seresht-Ahmadi
- Department of Basic Science and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Zahra Bahari
- Department of Physiology and Medical Physics, Faculty of Medicine, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran. .,Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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Dicitore A, Bacalini MG, Saronni D, Gaudenzi G, Cantone MC, Gelmini G, Grassi ES, Gentilini D, Borghi MO, Di Blasio AM, Persani L, Garagnani P, Franceschi C, Vitale G. Role of Epigenetic Therapy in the Modulation of Tumor Growth and Migration in Human Castration-Resistant Prostate Cancer Cells with Neuroendocrine Differentiation. Neuroendocrinology 2022; 112:580-594. [PMID: 34348348 DOI: 10.1159/000518801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/29/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Neuroendocrine transdifferentiation (NED) of prostate cancer (PC) cells is associated with the development of resistance to antiandrogen therapy and poor prognosis in patients with castration-resistant PC (CRPC). Many of the molecular events, involved in NED, appear to be mediated by epigenetic mechanisms. In this study, we evaluated the antitumor activity and epigenetic modulation of 2 epigenetic drugs, such as the demethylating agent 5-aza-2'-deoxycytidine (AZA) and the methyl donor S-adenosylmethionine (SAM), in 2 human CRPC cell lines with NED (DU-145 and PC-3). METHODS The effects of AZA and SAM on cell viability, cell cycle, apoptosis, migration, and genome-wide DNA methylation profiling have been evaluated. RESULTS Both drugs showed a prominent antitumor activity in DU-145 and PC-3 cells, through perturbation of cell cycle progression, induction of apoptosis, and inhibition of cell migration. AZA and SAM reversed NED in DU-145 and PC-3, respectively. Moreover, AZA treatment modified DNA methylation pattern in DU-145 cells, sustaining a pervasive hypomethylation of the genome, with a relevant effect on several pathways involved in the regulation of cell proliferation, apoptosis, and cell migration, in particular Wnt/β-catenin. CONCLUSIONS A relevant antitumor activity of these epigenetic drugs on CRPC cell lines with NED opens a new scenario in the therapy of this lethal variant of PC.
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Affiliation(s)
- Alessandra Dicitore
- Istituto Auxologico Italiano, IRCCS, Laboratory of Geriatric and Oncologic Neuroendocrinology Research, Milan, Italy
| | | | - Davide Saronni
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Milan, Italy
| | - Germano Gaudenzi
- Istituto Auxologico Italiano, IRCCS, Laboratory of Geriatric and Oncologic Neuroendocrinology Research, Milan, Italy
| | - Maria Celeste Cantone
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Milan, Italy
| | - Giulia Gelmini
- Laboratory of Endocrine and Metabolic Research, Istituto Auxologico Italiano IRCCS, Milan, Italy
| | - Elisa Stellaria Grassi
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Milan, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Istituto Auxologico Italiano IRCCS, Bioinformatics and Statistical Genomics Unit, Milan, Italy
| | - Maria Orietta Borghi
- Istituto Auxologico Italiano, IRCCS, Experimental Laboratory of Immuno-rheumatology, Milan, Italy
- Department of Clinical Sciences and Community Health (DISCCO), University of Milan, Milan, Italy
| | | | - Luca Persani
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Milan, Italy
- Laboratory of Endocrine and Metabolic Research, Istituto Auxologico Italiano IRCCS, Milan, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- Department of Applied Mathematics, Institute of Information Technology, Mathematics and Mechanics, Lobachevsky State University of Nizhny Novgorod-National Research University, Nizhny Novgorod, Russian Federation
| | - Giovanni Vitale
- Istituto Auxologico Italiano, IRCCS, Laboratory of Geriatric and Oncologic Neuroendocrinology Research, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Milan, Italy
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Identification of prostate cancer specific methylation biomarkers from a multi-cancer analysis. BMC Bioinformatics 2021; 22:492. [PMID: 34641790 PMCID: PMC8507340 DOI: 10.1186/s12859-021-04416-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 09/29/2021] [Indexed: 01/14/2023] Open
Abstract
Background Detecting prostate cancer at a non-aggressive stage is the main goal of prostate cancer screening. DNA methylation has been widely used as biomarkers for cancer diagnosis and prognosis, however, with low clinical translation rate. By taking advantage of multi-cancer data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), we aimed to identify prostate cancer specific biomarkers which can separate between non-aggressive and aggressive prostate cancer based on DNA methylation patterns. Results We performed a comparison analysis of DNA methylation status between normal prostate tissues and prostate adenocarcinoma (PRAD) samples at different Gleason stages. The candidate biomarkers were selected by excluding the biomarkers existing in multiple cancers (pan-cancer) and requiring significant difference between PRAD and other urinary samples. By least absolute shrinkage and selection operator (LASSO) selection, 8 biomarkers (cg04633600, cg05219445, cg05796128, cg10834205, cg16736826, cg23523811, cg23881697, cg24755931) were identified and in-silico validated by model constructions. First, all 8 biomarkers could separate PRAD at different stages (Gleason 6 vs. Gleason 3 + 4: AUC = 0.63; Gleason 6 vs. Gleason 4 + 3 and 8–10: AUC = 0.87). Second, 5 biomarkers (cg04633600, cg05796128, cg23523811, cg23881697, cg24755931) effectively detected PRAD from normal prostate tissues (AUC ranged from 0.88 to 0.92). Last, 6 biomarkers (cg04633600, cg05219445, cg05796128, cg23523811, cg23881697, cg24755931) completely distinguished PRAD with other urinary samples (AUC = 1). Conclusions Our study identified and in-silico validated a panel of prostate cancer specific DNA methylation biomarkers with diagnosis value. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04416-w.
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7
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Larsen LK, Lind GE, Guldberg P, Dahl C. DNA-Methylation-Based Detection of Urological Cancer in Urine: Overview of Biomarkers and Considerations on Biomarker Design, Source of DNA, and Detection Technologies. Int J Mol Sci 2019; 20:ijms20112657. [PMID: 31151158 PMCID: PMC6600406 DOI: 10.3390/ijms20112657] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/11/2022] Open
Abstract
Changes in DNA methylation have been causally linked with cancer and provide promising biomarkers for detection in biological fluids such as blood, urine, and saliva. The field has been fueled by genome-wide characterization of DNA methylation across cancer types as well as new technologies for sensitive detection of aberrantly methylated DNA molecules. For urological cancers, urine is in many situations the preferred "liquid biopsy" source because it contains exfoliated tumor cells and cell-free tumor DNA and can be obtained easily, noninvasively, and repeatedly. Here, we review recent advances made in the development of DNA-methylation-based biomarkers for detection of bladder, prostate, renal, and upper urinary tract cancers, with an emphasis on the performance characteristics of biomarkers in urine. For most biomarkers evaluated in independent studies, there was great variability in sensitivity and specificity. We discuss issues that impact the outcome of DNA-methylation-based detection of urological cancer and account for the great variability in performance, including genomic location of biomarkers, source of DNA, and technical issues related to the detection of rare aberrantly methylated DNA molecules. Finally, we discuss issues that remain to be addressed to fully exploit the potential of DNA-methylation-based biomarkers in the clinic, including the need for prospective trials and careful selection of control groups.
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Affiliation(s)
| | - Guro Elisabeth Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, NO-0424 Oslo, Norway.
| | - Per Guldberg
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark.
| | - Christina Dahl
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark.
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Li Y, Gu J, Xu F, Zhu Q, Ge D, Lu C. Novel methylation-driven genes identified as prognostic indicators for lung squamous cell carcinoma. Am J Transl Res 2019; 11:1997-2012. [PMID: 31105813 PMCID: PMC6511754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Abstract
Lung cancer remains the leading cause of cancer death. DNA methylation plays an essential role in carcinogenesis through regulating gene expression and gene alternative splicing. However, the role of methylation in the tumorigenesis of lung squamous cell carcinoma (SCC) and its association with prognosis remains unclear. Here, we used an integrative approach to evaluate the prognostic value of epigenetic processes in lung SCC by examining the data provided by The Cancer Genome Atlas (TCGA). We found that the mean methylation level was significantly decreased in lung SCC. We also identified methylation-driven genes which were associated with cancer-related pathways. The multivariate Cox regression analysis showed four methylation-driven genes, GCSAM, GPR75, NHLRC1, and TRIM58, could be served as prognostic indicators for lung SCC. Validation on two external GEO datasets showed consistent methylation alterations of the four genes. These findings may have important implications in the understanding of the potential therapeutic method for lung SCC.
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Affiliation(s)
- Yin Li
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University Shanghai, P. R. China
| | - Jie Gu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University Shanghai, P. R. China
| | - Fengkai Xu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University Shanghai, P. R. China
| | - Qiaoliang Zhu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University Shanghai, P. R. China
| | - Di Ge
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University Shanghai, P. R. China
| | - Chunlai Lu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University Shanghai, P. R. China
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Song C, Chen H, Song C. Research status and progress of the RNA or protein biomarkers for prostate cancer. Onco Targets Ther 2019; 12:2123-2136. [PMID: 30962694 PMCID: PMC6434918 DOI: 10.2147/ott.s194138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer is a kind of male malignancy. Recently, a large number of studies have reported many potential biomarkers for the diagnosis and prognosis of prostate cancer. In this literature review, we have collected a number of potential biomarkers for prostate cancer reported in the last 5 years. Among them, some are undergoing Phase III clinical trials, and others have been approved by the US Food and Drug Administration. However, most are still in the period of basic research. The review will contribute to future research to find the biomarkers to guide clinicians to make personalized treatment decisions for each prostate cancer patient.
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Affiliation(s)
- Chunjiao Song
- Medical Research Center, Shaoxing People's Hospital/Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang Province, China,
| | - Huan Chen
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang, China
| | - Chunyu Song
- Department of Anesthesia, The Second Clinical Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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The Long Noncoding RNA TTTY15, Which Is Located on the Y Chromosome, Promotes Prostate Cancer Progression by Sponging let-7. Eur Urol 2018; 76:315-326. [PMID: 30527798 DOI: 10.1016/j.eururo.2018.11.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/06/2018] [Indexed: 01/04/2023]
Abstract
BACKGROUND The link between prostate cancer (PCa) development and aberrant expression of genes located on the Y chromosome remains unclear. OBJECTIVE To identify Y-chromosomal long noncoding RNAs (lncRNAs) with critical roles in PCa and to clarify the corresponding mechanisms. DESIGN, SETTING, AND PARTICIPANTS Aberrantly expressed lncRNAs on the Y chromosome were identified using transcriptome analysis of PCa clinical samples and cell lines. Biological functions and molecular mechanisms of the lncRNAs were revealed using in vitro and in vivo experimental methods. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Experiments and outcome measurements were performed in duplicate or triplicate. Wilcoxon signed-rank test was employed for comparison of RNA levels in clinical cohorts. Analysis of variance was employed for comparisons among multiple groups. RESULTS AND LIMITATIONS In most patients with PCa, TTTY15 was the most elevated lncRNA located on the Y chromosome. Knockout of this lncRNA by two different CRISPR-Cas9 strategies suppressed PCa cell growth both in vitro and in vivo. TTTY15 promoted PCa by sponging the microRNA let-7, consequently increasing CDK6 and FN1 expression. FOXA1 is an upstream regulatory factor of TTTY15 transcription. CONCLUSIONS The Y-chromosomal lncRNA TTTY15 was upregulated in most PCa tissues and could promote PCa progression by sponging let-7. PATIENT SUMMARY We found that TTTY15 levels were frequently elevated in prostate cancer (PCa) tissues compared with those in paracancerous normal tissues in a large group of PCa patients, and we observed a tumour suppressive effect after TTTY15 knockout using CRISPR/Cas9. These results may have therapeutic implications for PCa patients.
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RankProd Combined with Genetic Algorithm Optimized Artificial Neural Network Establishes a Diagnostic and Prognostic Prediction Model that Revealed C1QTNF3 as a Biomarker for Prostate Cancer. EBioMedicine 2018; 32:234-244. [PMID: 29861410 PMCID: PMC6021271 DOI: 10.1016/j.ebiom.2018.05.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/08/2018] [Accepted: 05/08/2018] [Indexed: 01/09/2023] Open
Abstract
Prostate cancer (PCa) is the most commonly diagnosed cancer in males in the Western world. Although prostate-specific antigen (PSA) has been widely used as a biomarker for PCa diagnosis, its results can be controversial. Therefore, new biomarkers are needed to enhance the clinical management of PCa. From publicly available microarray data, differentially expressed genes (DEGs) were identified by meta-analysis with RankProd. Genetic algorithm optimized artificial neural network (GA-ANN) was introduced to establish a diagnostic prediction model and to filter candidate genes. The diagnostic and prognostic capability of the prediction model and candidate genes were investigated in both GEO and TCGA datasets. Candidate genes were further validated by qPCR, Western Blot and Tissue microarray. By RankProd meta-analyses, 2306 significantly up- and 1311 down-regulated probes were found in 133 cases and 30 controls microarray data. The overall accuracy rate of the PCa diagnostic prediction model, consisting of a 15-gene signature, reached up to 100% in both the training and test dataset. The prediction model also showed good results for the diagnosis (AUC = 0.953) and prognosis (AUC of 5 years overall survival time = 0.808) of PCa in the TCGA database. The expression levels of three genes, FABP5, C1QTNF3 and LPHN3, were validated by qPCR. C1QTNF3 high expression was further validated in PCa tissue by Western Blot and Tissue microarray. In the GEO datasets, C1QTNF3 was a good predictor for the diagnosis of PCa (GSE6956: AUC = 0.791; GSE8218: AUC = 0.868; GSE26910: AUC = 0.972). In the TCGA database, C1QTNF3 was significantly associated with PCa patient recurrence free survival (P < .001, AUC = 0.57). In this study, we have developed a diagnostic and prognostic prediction model for PCa. C1QTNF3 was revealed as a promising biomarker for PCa. This approach can be applied to other high-throughput data from different platforms for the discovery of oncogenes or biomarkers in different kinds of diseases.
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Chen Y, Hong T, Wang S, Mo J, Tian T, Zhou X. Epigenetic modification of nucleic acids: from basic studies to medical applications. Chem Soc Rev 2018; 46:2844-2872. [PMID: 28352906 DOI: 10.1039/c6cs00599c] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The epigenetic modification of nucleic acids represents one of the most significant areas of study in the field of nucleic acids because it makes gene regulation more complex and heredity more complicated, thus indicating its profound impact on aspects of heredity, growth, and diseases. The recent characterization of epigenetic modifications of DNA and RNA using chemical labelling strategies has promoted the discovery of these modifications, and the newly developed single-base or single-cell resolution mapping strategies have enabled large-scale epigenetic studies in eukaryotes. Due to these technological breakthroughs, several new epigenetic marks have been discovered that have greatly extended the scope and impact of epigenetic modifications in nucleic acids over the past few years. Because epigenetics is reversible and susceptible to environmental factors, it could potentially be a promising direction for clinical medicine research. In this review, we have comprehensively discussed how these epigenetic marks are involved in disease, including the pathogenesis, prevention, diagnosis and treatment of disease. These findings have revealed that the epigenetic modification of nucleic acids has considerable significance in various areas from methodology to clinical medicine and even in biomedical applications.
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Affiliation(s)
- Yuqi Chen
- College of Chemistry and Molecular Sciences, Institute of Advanced Studies, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Hubei, Wuhan 430072, P. R. China.
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13
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Patel R, Khalifa AO, Isali I, Shukla S. Prostate cancer susceptibility and growth linked to Y chromosome genes. Front Biosci (Elite Ed) 2018; 10:423-436. [PMID: 29293466 PMCID: PMC6152832 DOI: 10.2741/e830] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The role of Y chromosome in prostate cancer progression and incidence is not well known. Among the 46 chromosomes, Y chromosome determines the male gender. The Y chromosome is smaller than the X chromosome and contains only 458 genes compared to over 2000 genes found in the X chromosome. The Y chromosome is prone to high mutation rates, created exclusively in sperm cells due to the highly oxidative environment of the testis. Y chromosome harbors epigenetic information, which affects the expression of genes associated with the incidence and progression of prostate cancer. In this review, we focus on Y chromosome related genetic abnormalities, likely to be involved in the development and progression of prostate cancer.
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Affiliation(s)
- Riddhi Patel
- Department of Urology, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH, USA
| | - Ahmad O Khalifa
- Urology Dept. Case Western Reserve University, Cleveland, Ohio and Menofia University, Shebin Al kom, Egpt
| | - Ilaha Isali
- Department of Urology, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH, USA
| | - Sanjeev Shukla
- Department of Urology, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH, USA,
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14
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Men C, Chai H, Song X, Li Y, Du H, Ren Q. Identification of DNA methylation associated gene signatures in endometrial cancer via integrated analysis of DNA methylation and gene expression systematically. J Gynecol Oncol 2018; 28:e83. [PMID: 29027401 PMCID: PMC5641533 DOI: 10.3802/jgo.2017.28.e83] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/02/2017] [Accepted: 08/10/2017] [Indexed: 12/22/2022] Open
Abstract
Objective Endometrial cancer (EC) is a common gynecologic cancer worldwide. However, the pathogenesis of EC has not been epigenetically elucidated. Here, this study aims to describe the DNA methylation profile and identify favorable gene signatures highly associated with aberrant DNA methylation changes in EC. Methods The data regarding DNA methylation and gene expression were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially methylated CpG sites (DMCs), differentially methylated regions (DMRs), and differentially expressed genes (DEGs) were identified, and the relationship between the 2 omics was further analyzed. In addition, weighted CpG site co-methylation network (WCCN) was constructed followed by an integrated analysis of DNA methylation and gene expression data. Results Four hundred thirty-one tumor tissues and 46 tissues adjacent tumor of EC patients were analyzed. One thousand one hundred thirty-five DMCs (merging to 10 DMRs), and 1,488 DEGs were obtained between tumor and normal groups, respectively. One hundred forty-eight DMCs-DEGs correlated pairs and 13 regional DMCs-DEGs pairs were obtained. Interestingly, we found that some hub genes in 2 modules among 8 modules of WCCN analysis were down-regulated in tumor samples. Furthermore, protocadherins (PCDHs) clusters, DDP6, TNXB, and ZNF154 were identified as novel deregulated genes with altered methylation in EC. Conclusion Based on the analysis of DNA methylation in a systematic view, the potential long-range epigenetic silencing (LRES) composed of PCDHs was reported in ECs for the first time. PCDHs clusters, DDP6, and TNXB were firstly found to be associated with tumorigenesis, and may be novel candidate biomarkers for EC.
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Affiliation(s)
- Chuandi Men
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Graduate School, Bengbu Medical College, Bengbu, China
| | - Hongjuan Chai
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xumin Song
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue Li
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huawen Du
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qing Ren
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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15
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Han X, Zhao Z, Zhang M, Li G, Yang C, Du F, Wang J, Zhang Y, Wang Y, Jia Y, Li B, Sun Y. Maternal trans-general analysis of the human mitochondrial DNA pattern. Biochem Biophys Res Commun 2017; 493:643-649. [PMID: 28865962 DOI: 10.1016/j.bbrc.2017.08.138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 08/29/2017] [Indexed: 02/06/2023]
Abstract
There is an intimate connection between mitochondrial DNA (mtDNA) methylation and some diseases, such as cancer. MtDNA is almost strictly maternally inherited. However, whether the aberrant mtDNA methylation involved in breast cancer progression and whether mtDNA methylation can be transmitted through maternal line are poorly understood. Here we applied bisulfite sequencing to global mitochondrial DNA and whole genomic DNA methylation array from fifteen members of five three-female-generation families with one breast cancer patient in each family. We found that mtDNA methylation was maternally inherited in D-loop region and eight aberrant mtDNA methylation sites were correlated with breast cancer. Furthermore, conjoint analysis showed that mtDNA methylation sites could be potential biomarkers combined with nuclear DNA methylation sites for breast cancer risk prediction.
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Affiliation(s)
- Xiao Han
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zitong Zhao
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minjie Zhang
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guochao Li
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caiyun Yang
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fengxia Du
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Junyun Wang
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yuanyuan Wang
- Laboratory of Cancer Cell Biology, Key Laboratory of Breast Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Yongsheng Jia
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University, Tianjin 300060, China
| | - Binghui Li
- Laboratory of Cancer Cell Biology, Key Laboratory of Breast Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Yingli Sun
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
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16
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Zhang LJ, Chen B, Zhang JJ, Li J, Yang Q, Zhong QS, Zhan S, Liu H, Cai C. Serum polyunsaturated fatty acid metabolites as useful tool for screening potential biomarker of colorectal cancer. Prostaglandins Leukot Essent Fatty Acids 2017; 120:25-31. [PMID: 28515019 DOI: 10.1016/j.plefa.2017.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/14/2017] [Accepted: 04/04/2017] [Indexed: 02/08/2023]
Abstract
The biomarker identification of cancer is benefit for early detection and less invasion. Polyunsaturated fatty acid (PUFA) metabolite as inflammatory mediators can affect progression and treatment of cancer. In this work, the serum was collected from colorectal cancer patients and healthy volunteers, and then we tested the change of serum PUFA metabolites in both of them by ultra-high performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS). Of the 158 PUFA and their metabolites, we found that abnormal change of 2, 3-dinor-8-iso-PGF2α, 19-HETE and 12-keto-LTB4 from arachidonic acid were observed in colorectal cancer patients. Meanwhile, 9-HODE and 13-HODE from linoleic acid were significant lower in colorectal cancer patients. Our data suggested that some PUFA metabolites might be used as a potential biomarker of colorectal cancer, which might provide assistance in clinical diagnosis and treatment.
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Affiliation(s)
- Li-Jian Zhang
- Guangdong key laboratory for research and development of nature drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, China
| | - Bin Chen
- Guangdong key laboratory for research and development of nature drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, China
| | - Jun-Jie Zhang
- Guangdong key laboratory for research and development of nature drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, China
| | - Jian Li
- Guangdong key laboratory for research and development of nature drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, China
| | - Qingjing Yang
- Guangdong key laboratory for research and development of nature drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, China
| | - Qi-Sheng Zhong
- Shimadzu Global COE for Application& Technical Development, Guangzhou, Guangdong, 510010, China
| | - Song Zhan
- Shimadzu Global COE for Application& Technical Development, Guangzhou, Guangdong, 510010, China
| | - Huwei Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering Peking University Beijing, 100871, China.
| | - Chun Cai
- Guangdong key laboratory for research and development of nature drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, China.
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