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Ji Y, Wang L, Chang G, Yan J, Dai L, Ji Z, Liu J, He M, Xu H, Zhang L. Mir-421 and mir-550a-1 are potential prognostic markers in esophageal adenocarcinoma. Biol Direct 2023; 18:5. [PMID: 36829221 PMCID: PMC9951500 DOI: 10.1186/s13062-022-00352-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/24/2022] [Indexed: 02/26/2023] Open
Abstract
OBJECTIVE To identify the prognostic indicators of esophageal adenocarcinoma (EAC) for future EAC diagnosis and treatment. METHODS The EAC dataset from The Cancer Genome Atlas was screened for differentially expressed microRNAs (miRNAs) and mRNAs associated with EAC. Weighted gene coexpression network analysis was performed to cluster miRNAs or mRNA with similar expression patterns to identify the miRNAs or mRNA that are highly associated with EAC. Prognostic miRNAs for overall survival (OS) were identified using Cox proportional-hazards regression analysis and least absolute shrinkage and selection operator based on survival duration and status. Two types of miRNAs were selected to develop a prognostic signature model for EAC using multiple Cox regression analysis. Furthermore, the signature was validated using internal validation sets 1 and 2. The receiver operating characteristic curve and concordance index were used to evaluate the accuracy of the signature and validation sets. The expression of miR-421, miR-550a-3p, and miR-550a-5p was assessed using quantitative polymerase chain reaction (qPCR). The proliferation, invasion, and migration of EAC cells were assessed using CCK8 and transwell assays. The OS of target mRNAs was assessed using Kaplan-Meier analysis. Functional enrichment analysis of the target mRNAs was performed using Metascape. RESULTS The prognostic signature and validation sets comprising mir-421 and mir-550a-1 had favorable predictive power in OS. Compared with the patients with EAC in the high-expression group, those assigned to the low-expression group displayed increased OS according to survival analysis. Differential and qPCR analysis showed that miR-421, miR-550a-3p, and miR-550a-5p were highly expressed in the EAC tissues and cell lines. Moreover, the downregulation of miR-421 and miR-550a-3p with inhibitor markedly suppressed the proliferation, invasion, and migration in OE33 cells compared with the negative control. A total of 20 target mRNAs of three miRNAs were predicted, among which seven target mRNAs-ASAP3, BCL2L2, LMF1, PPM1L, PTPN21, SLC18A2, and NR3C2-had prognostic value; PRKACB, PDCD4, RPS6KA5, and BCL2L2 were enriched in the miRNA cancer pathway. CONCLUSION Prognostic indicators of EAC may be useful in future EAC diagnosis and treatment.
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Affiliation(s)
- Yun Ji
- BGI College, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450007, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450052, China.,Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450000, China.,Center For Disease Control And Prevention, Health Bureau of Menglian Daizu Lahuzu Wazu Autonomous County, Pu'er Menglian, 665800, China
| | - Lulu Wang
- BGI College, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450007, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450052, China.,Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450000, China
| | - Guanglei Chang
- BGI College, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450007, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450052, China.,Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450000, China
| | - Juan Yan
- BGI College, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450007, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450052, China.,Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450000, China
| | - Liping Dai
- BGI College, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450007, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450052, China.,Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450000, China
| | - Zhenyu Ji
- BGI College, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450007, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450052, China.,Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450000, China
| | - Jingjing Liu
- BGI College, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450007, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450052, China.,Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450000, China
| | - Meixia He
- BGI College, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450007, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450052, China.,Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450000, China
| | - Hongliang Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, China
| | - Liguo Zhang
- BGI College, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450007, China. .,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, No. 40 Daxue Road, Zhengzhou, 450052, China. .,Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450000, China.
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2
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Sun X, Kato H, Sato H, Han X, Hirofuji Y, Kato TA, Sakai Y, Ohga S, Fukumoto S, Masuda K. Dopamine-related oxidative stress and mitochondrial dysfunction in dopaminergic neurons differentiated from deciduous teeth-derived stem cells of children with Down syndrome. FASEB Bioadv 2022; 4:454-467. [PMID: 35812076 PMCID: PMC9254221 DOI: 10.1096/fba.2021-00086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 02/17/2022] [Accepted: 03/14/2022] [Indexed: 12/24/2022] Open
Abstract
Down syndrome (DS) is one of the common genetic disorders caused by the trisomy of human chromosome 21 (HSA21). Mitochondrial dysfunction and redox imbalance play important roles in DS pathology, and altered dopaminergic regulation has been demonstrated in the brain of individuals with DS. However, the pathological association of these elements is not yet fully understood. In this study, we analyzed dopaminergic neurons (DNs) differentiated from deciduous teeth-derived stem cells of children with DS or healthy control children. As previously observed in the analysis of a single case of DS, compared to controls, patient-derived DNs (DS-DNs) displayed shorter neurite outgrowth and fewer branches, as well as downregulated vesicular monoamine transporter 2 and upregulated dopamine transporter 1, both of which are key regulators of dopamine homeostasis in DNs. In agreement with these expression profiles, DS-DNs accumulated dopamine intracellularly and had increased levels of cellular and mitochondrial reactive oxygen species (ROS). DS-DNs showed downregulation of non-canonical Notch ligand, delta-like 1, which may contribute to dopamine accumulation and increased ROS levels through DAT1 upregulation. Furthermore, DS-DNs showed mitochondrial dysfunction in consistent with lower expression of peroxisome proliferator-activated receptor-gamma coactivator 1 alpha (PGC-1α) and upregulation of a HSA21-encoded negative regulator of PGC-1α, nuclear receptor-interacting protein 1. These results suggest that dysregulated dopamine homeostasis may participate in oxidative stress and mitochondrial dysfunction of the dopaminergic system in DS.
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Affiliation(s)
- Xiao Sun
- Section of Oral Medicine for Children, Division of Oral Health, Growth and DevelopmentFaculty of Dental Science, Kyushu UniversityFukuokaJapan
| | - Hiroki Kato
- Department of Molecular Cell Biology and Oral AnatomyKyushu University Graduate School of Dental ScienceFukuokaJapan
| | - Hiroshi Sato
- Section of Oral Medicine for Children, Division of Oral Health, Growth and DevelopmentFaculty of Dental Science, Kyushu UniversityFukuokaJapan
| | - Xu Han
- Section of Oral Medicine for Children, Division of Oral Health, Growth and DevelopmentFaculty of Dental Science, Kyushu UniversityFukuokaJapan
| | - Yuta Hirofuji
- Section of Oral Medicine for Children, Division of Oral Health, Growth and DevelopmentFaculty of Dental Science, Kyushu UniversityFukuokaJapan
| | - Takahiro A. Kato
- Department of NeuropsychiatryGraduate School of Medical Sciences, Kyushu UniversityFukuokaJapan
| | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Shouichi Ohga
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Satoshi Fukumoto
- Section of Oral Medicine for Children, Division of Oral Health, Growth and DevelopmentFaculty of Dental Science, Kyushu UniversityFukuokaJapan
| | - Keiji Masuda
- Section of Oral Medicine for Children, Division of Oral Health, Growth and DevelopmentFaculty of Dental Science, Kyushu UniversityFukuokaJapan
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3
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Zhang L, Li Y, Wang X, Ping Y, Wang D, Cao Y, Dai Y, Liu W, Tao Z. Five-gene signature associating with Gleason score serve as novel biomarkers for identifying early recurring events and contributing to early diagnosis for Prostate Adenocarcinoma. J Cancer 2021; 12:3626-3647. [PMID: 33995639 PMCID: PMC8120165 DOI: 10.7150/jca.52170] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 04/12/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Compared to non-recurrent type, recurrent prostate adenocarcinoma (PCa) is highly fatal, and significantly shortens the survival time of affected patients. Early and accurate laboratory diagnosis is particularly important in identifying patients at high risk of recurrence, necessary for additional systemic intervention. We aimed to develop efficient and accurate diagnostic and prognostic biomarkers for new PCa following radical therapy. Methods: We identified differentially expressed genes (DEGs) and clinicopathological data of PCa patients from Gene Expression Omnibus (GEO) datasets and The Cancer Genome Atlas (TCGA) repositories. We then uncovered the most relevant clinical traits and genes modules associated with PCa prognosis using the Weighted gene correlation network analysis (WGCNA). Univariate Cox regression analysis and multivariate Cox proportional hazards (Cox-PH) models were performed to identify candidate gene signatures related to Disease-Free Interval (DFI). Data for internal and external cohorts were utilized to test and validate the accuracy and clinical utility of the prognostic models. Results: We constructed and validated an accurate and reliable model for predicting the prognosis of PCa using 5 Gleason score-associated gene signatures (ZNF695, CENPA, TROAP, BIRC5 and KIF20A). The ROC and Kaplan-Meier analysis revealed the model was highly accurate in diagnosing and predicting the recurrence and metastases of PCa. The accuracy of the model was validated using the calibration curves based on internal TCGA cohort and external GEO cohort. Using the model, patients could be prognostically stratified in to various groups including TNM classification and Gleason score. Multivariate analysis revealed the model could independently predict the prognosis of PCa patients and its utility was superior to that of clinicopathological characteristics. In addition, we fund the expression of the 5 gene signatures strongly and positively correlated with tumor purity but negatively correlated with infiltration CD8+ T cells to the tumor microenvironment. Conclusions: A 5 gene signatures can accurately be used in the diagnosis and prediction of PCa prognosis. Thus this can guide the treatment and management prostate adenocarcinoma.
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Affiliation(s)
- Lingyu Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Yu Li
- Department of Biochemistry and Molecular Biology, Bengbu Medical College, Anhui 233030, China
| | - Xuchu Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Ying Ping
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Danhua Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Ying Cao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Yibei Dai
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Weiwei Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Zhihua Tao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
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4
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Sopyllo K, Erickson AM, Mirtti T. Grading Evolution and Contemporary Prognostic Biomarkers of Clinically Significant Prostate Cancer. Cancers (Basel) 2021; 13:cancers13040628. [PMID: 33562508 PMCID: PMC7914622 DOI: 10.3390/cancers13040628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Prostate cancer treatment decisions are based on clinical stage and histological diagnosis, including Gleason grading assessed by a pathologist, in biopsies. Prior to staging and grading, serum or blood prostate-specific antigen (PSA) levels are measured and often trigger diagnostic examinations. However, PSA is best suited as a marker of cancer relapse after initial treatment. In this review, we first narratively describe the evolution of histological grading, the current status of Gleason pattern-based diagnostics and glance into future methodology of risk assessment by histological examination. In the second part, we systematically review the biomarkers that have been shown, independent from clinical characteristics, to correlate with clinically relevant end-points, i.e., occurrence of metastases, disease-specific mortality and overall survival after initial treatment of localized prostate cancer. Abstract Gleason grading remains the strongest prognostic parameter in localized prostate adenocarcinoma. We have here outlined the evolution and contemporary practices in pathological evaluation of prostate tissue samples for Gleason score and Grade group. The state of more observer-independent grading methods with the aid of artificial intelligence is also reviewed. Additionally, we conducted a systematic review of biomarkers that hold promise in adding independent prognostic or predictive value on top of clinical parameters, Grade group and PSA. We especially focused on hard end points during the follow-up, i.e., occurrence of metastasis, disease-specific mortality and overall mortality. In peripheral blood, biopsy-detected prostate cancer or in surgical specimens, we can conclude that there are more than sixty biomarkers that have been shown to have independent prognostic significance when adjusted to conventional risk assessment or grouping. Our search brought up some known putative markers and panels, as expected. Also, the synthesis in the systematic review indicated markers that ought to be further studied as part of prospective trials and in well characterized patient cohorts in order to increase the resolution of the current clinico-pathological prognostic factors.
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Affiliation(s)
- Konrad Sopyllo
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
| | - Andrew M. Erickson
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK;
| | - Tuomas Mirtti
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Department of Pathology, HUS Diagnostic Centre, Helsinki University Hospital, 00029 Helsinki, Finland
- Correspondence:
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5
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Haldrup J, Strand SH, Cieza-Borrella C, Jakobsson ME, Riedel M, Norgaard M, Hedensted S, Dagnaes-Hansen F, Ulhoi BP, Eeles R, Borre M, Olsen JV, Thomsen M, Kote-Jarai Z, Sorensen KD. FRMD6 has tumor suppressor functions in prostate cancer. Oncogene 2020; 40:763-776. [PMID: 33249427 DOI: 10.1038/s41388-020-01548-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/07/2020] [Accepted: 10/28/2020] [Indexed: 12/14/2022]
Abstract
Available tools for prostate cancer (PC) prognosis are suboptimal but may be improved by better knowledge about genes driving tumor aggressiveness. Here, we identified FRMD6 (FERM domain-containing protein 6) as an aberrantly hypermethylated and significantly downregulated gene in PC. Low FRMD6 expression was associated with postoperative biochemical recurrence in two large PC patient cohorts. In overexpression and CRISPR/Cas9 knockout experiments in PC cell lines, FRMD6 inhibited viability, proliferation, cell cycle progression, colony formation, 3D spheroid growth, and tumor xenograft growth in mice. Transcriptomic, proteomic, and phospho-proteomic profiling revealed enrichment of Hippo/YAP and c-MYC signaling upon FRMD6 knockout. Connectivity Map analysis and drug repurposing experiments identified pyroxamide as a new potential therapy for FRMD6 deficient PC cells. Finally, we established orthotropic Frmd6 and Pten, or Pten only (control) knockout in the ROSA26 mouse prostate. After 12 weeks, Frmd6/Pten double knockouts presented high-grade prostatic intraepithelial neoplasia (HG-PIN) and hyperproliferation, while Pten single-knockouts developed only regular PIN lesions and displayed lower proliferation. In conclusion, FRMD6 was identified as a novel tumor suppressor gene and prognostic biomarker candidate in PC.
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Affiliation(s)
- Jakob Haldrup
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Siri H Strand
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Clara Cieza-Borrella
- Oncogenetics, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Magnus E Jakobsson
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.,Department of Immunotechnology, Lund University, Medicon Village, 22100, Lund, Sweden
| | - Maria Riedel
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Maibritt Norgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Stine Hedensted
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | | | - Rosalind Eeles
- Oncogenetics, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.,The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Michael Borre
- Dept. of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Martin Thomsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Zsofia Kote-Jarai
- Oncogenetics, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Karina D Sorensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark. .,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
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6
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Shahzad N, Munir T, Javed M, Tasneem F, Aslam B, Ali M, Mutahir Z, Akhtar Ali M, Umer M, Ahmad M, Farooq K, Hassan U, Mustafa T, Anjum RS, Shakoori AR. SHISA3, an antagonist of the Wnt/β-catenin signaling, is epigenetically silenced and its ectopic expression suppresses growth in breast cancer. PLoS One 2020; 15:e0236192. [PMID: 32692756 PMCID: PMC7373276 DOI: 10.1371/journal.pone.0236192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/30/2020] [Indexed: 12/31/2022] Open
Abstract
Breast cancer (BC) is the foremost cause of cancer related deaths in women globally. Currently there is a scarcity of reliable biomarkers for its early stage diagnosis and theranostics monitoring. Altered DNA methylation patterns leading to the silencing of tumor suppressor genes are considered as an important mechanism underlying tumor development and progression in various cancer types, including BC. Very recently, epigenetic silencing of SHISA3, an antagonist of β-catenin, has been reported in various types of tumor. However, the role of SHISA3 in BC has not been investigated yet. Therefore, we aimed at evaluating the contribution of SHISA3 in BC causation by analyzing its expression and methylation levels in BC cell lines (MDA-MB231, MCF-7 and BT-474) and in 103 paired BC tissue samples. The SHISA3 expression and methylation status was determined by qPCR and methylation specific PCR (MSP) respectively. The role of SHISA3 in BC tumorigenesis was evaluated by proliferation and migration assays after ectopic expression of SHISA3. The association between SHISA3 hypermethylation and clinicopathological parameters of BC patients was also studied. The downregulation of SHISA3 expression was found in three BC cell lines used and in all BC tissue samples. However, SHISA3 promoter region was hypermethylated in 61% (63/103) tumorous tissues in comparison to the 18% of their matched normal tissues. The 5-aza-2’-deoxycytidine treatment restored SHISA3 expression by reversing promoter hypermethylation in both MDA-MB231 and MCF-7 cells. Furthermore, ectopic expression of SHISA3 significantly reduced the proliferation and migration ability of these cells. Taken together, our findings for the first time reveal epigenetic silencing and tumor suppressing role of SHISA3 in BC. Henceforth, this study has identified SHISA3 as potentially powerful target for the development of new therapies against BC, as well as novel diagnostic and therapy response monitoring approaches.
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Affiliation(s)
- Naveed Shahzad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
- * E-mail: (NS); (MU)
| | - Tehreem Munir
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Mariam Javed
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Fareeda Tasneem
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Bilal Aslam
- Department of Microbiology, Government College University, Faisalabad, Pakistan
| | - Moazzam Ali
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Zeeshan Mutahir
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | | | - Muhammad Umer
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Australia
- * E-mail: (NS); (MU)
| | - Munir Ahmad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Kokab Farooq
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Umair Hassan
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Tanveer Mustafa
- Department of Histopathology, Fatima Jinnah Medical University, Lahore, Pakistan
| | - Rana Salman Anjum
- School of Life Sciences, Forman Christian College University, Lahore, Pakistan
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7
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Epigenetic Analysis of Circulating Tumor DNA in Localized and Metastatic Prostate Cancer: Evaluation of Clinical Biomarker Potential. Cells 2020; 9:cells9061362. [PMID: 32486483 PMCID: PMC7349912 DOI: 10.3390/cells9061362] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022] Open
Abstract
Novel and minimally-invasive prostate cancer (PCa)-specific biomarkers are needed to improve diagnosis and risk stratification. Here, we investigated the biomarker potential in localized and de novo metastatic PCa (mPCa) of methylated circulating tumor DNA (ctDNA) in plasma. Using the Marmal-aid database and in-house datasets, we identified three top candidates specifically hypermethylated in PCa tissue: DOCK2, HAPLN3, and FBXO30 (specificity/sensitivity: 80%-100%/75-94%). These candidates were further analyzed in plasma samples from 36 healthy controls, 61 benign prostatic hyperplasia (BPH), 102 localized PCa, and 65 de novo mPCa patients using methylation-specific droplet digital PCR. Methylated ctDNA for DOCK2/HAPLN3/FBXO30 was generally not detected in healthy controls, BPH patients, nor in patients with localized PCa despite a positive signal in 98%-100% of matched radical prostatectomy tissue samples. However, ctDNA methylation of DOCK2, HAPLN3, and/or FBXO30 was detected in 61.5% (40/65) of de novo mPCa patients and markedly increased in high- compared to low-volume mPCa (89.3% (25/28) vs. 32.1% (10/31), p < 0.001). Moreover, detection of methylated ctDNA was associated with significantly shorter time to progression to metastatic castration resistant PCa, independent of tumor-volume. These results indicate that methylated ctDNA (DOCK2/HAPLN3/FBXO30) may be potentially useful for identification of hormone-naïve mPCa patients who could benefit from intensified treatment.
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8
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Nørgaard M, Haldrup C, Bjerre MT, Høyer S, Ulhøi B, Borre M, Sørensen KD. Epigenetic silencing of MEIS2 in prostate cancer recurrence. Clin Epigenetics 2019; 11:147. [PMID: 31640805 PMCID: PMC6805635 DOI: 10.1186/s13148-019-0742-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 09/10/2019] [Indexed: 01/23/2023] Open
Abstract
Background Current diagnostic and prognostic tools for prostate cancer (PC) are suboptimal, resulting in overdiagnosis and overtreatment of clinically insignificant tumors. Thus, to improve the management of PC, novel biomarkers are urgently needed. Results In this study, we integrated genome-wide methylome (Illumina 450K DNA methylation array (450K)) and RNA sequencing (RNAseq) data performed in a discovery set of 27 PC and 15 adjacent normal (AN) prostate tissue samples to identify candidate driver genes involved in PC development and/or progression. We found significant enrichment for homeobox genes among the most aberrantly methylated and transcriptionally dysregulated genes in PC. Specifically, homeobox gene MEIS2 (Myeloid Ecotropic viral Insertion Site 2) was significantly hypermethylated (p < 0.0001, Mann-Whitney test) and transcriptionally downregulated (p < 0.0001, Mann-Whitney test) in PC compared to non-malignant prostate tissue in our discovery sample set, which was also confirmed in an independent validation set including > 500 PC and AN tissue samples in total (TCGA cohort analyzed by 450K and RNAseq). Furthermore, in three independent radical prostatectomy (RP) cohorts (n > 700 patients in total), low MEIS2 transcriptional expression was significantly associated with poor biochemical recurrence (BCR) free survival (p = 0.0084, 0.0001, and 0.0191, respectively; log-rank test). Next, we analyzed another RP cohort consisting of > 200 PC, AN, and benign prostatic hyperplasia (BPH) samples by quantitative methylation-specific PCR (qMSP) and found that MEIS2 was significantly hypermethylated (p < 0.0001, Mann-Whitney test) in PC compared to non-malignant prostate tissue samples (AN and BPH) with an AUC > 0.84. Moreover, in this cohort, aberrant MEIS2 hypermethylation was significantly associated with post-operative BCR (p = 0.0068, log-rank test), which was subsequently confirmed (p = 0.0067; log-rank test) in the independent TCGA validation cohort (497 RP patients; 450K data). Conclusions To the best of our knowledge, this is the first study to investigate, demonstrate, and independently validate a prognostic biomarker potential for MEIS2 at the transcriptional expression level and at the DNA methylation level in PC.
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Affiliation(s)
- Maibritt Nørgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Christa Haldrup
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Marianne Trier Bjerre
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Høyer
- Department of Histopathology, Aarhus University Hospital, Aarhus, Denmark
| | - Benedicte Ulhøi
- Department of Histopathology, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Borre
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Karina D Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark. .,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
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9
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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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10
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Schmidt L, Møller M, Haldrup C, Strand SH, Vang S, Hedegaard J, Høyer S, Borre M, Ørntoft T, Sørensen KD. Exploring the transcriptome of hormone-naive multifocal prostate cancer and matched lymph node metastases. Br J Cancer 2018; 119:1527-1537. [PMID: 30449885 PMCID: PMC6288156 DOI: 10.1038/s41416-018-0321-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/09/2018] [Accepted: 10/09/2018] [Indexed: 11/09/2022] Open
Abstract
Background The current inability to predict whether a primary prostate cancer (PC) will progress to metastatic disease leads to overtreatment of indolent PCs as well as undertreatment of aggressive PCs. Here, we explored the transcriptional changes associated with metastatic progression of multifocal hormone-naive PC. Methods Using total RNA-sequencing, we analysed laser micro-dissected primary PC foci (n = 23), adjacent normal prostate tissue samples (n = 23) and lymph node metastases (n = 9) from ten hormone-naive PC patients. Genes important for PC progression were identified using differential gene expression and clustering analysis. From these, two multi-gene-based expression signatures (models) were developed, and their prognostic potential was evaluated using Cox-regression and Kaplan–Meier analyses in three independent radical prostatectomy (RP) cohorts (>650 patients). Results We identified several novel PC-associated transcripts deregulated during PC progression, and these transcripts were used to develop two novel gene-expression-based prognostic models. The models showed independent prognostic potential in three RP cohorts (n = 405, n = 107 and n = 91), using biochemical recurrence after RP as the primary clinical endpoint. Conclusions We identified several transcripts deregulated during PC progression and developed two new prognostic models for PC risk stratification, each of which showed independent prognostic value beyond routine clinicopathological factors in three independent RP cohorts.
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Affiliation(s)
- Linnéa Schmidt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mia Møller
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Christa Haldrup
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Siri H Strand
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jakob Hedegaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Høyer
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Borre
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Torben Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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11
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Lim MCJ, Baird AM, Aird J, Greene J, Kapoor D, Gray SG, McDermott R, Finn SP. RNAs as Candidate Diagnostic and Prognostic Markers of Prostate Cancer-From Cell Line Models to Liquid Biopsies. Diagnostics (Basel) 2018; 8:E60. [PMID: 30200254 PMCID: PMC6163368 DOI: 10.3390/diagnostics8030060] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 12/19/2022] Open
Abstract
The treatment landscape of prostate cancer has evolved rapidly over the past five years. The explosion in treatment advances has been witnessed in parallel with significant progress in the field of molecular biomarkers. The advent of next-generation sequencing has enabled the molecular profiling of the genomic and transcriptomic architecture of prostate and other cancers. Coupled with this, is a renewed interest in the role of non-coding RNA (ncRNA) in prostate cancer biology. ncRNA consists of several different classes including small non-coding RNA (sncRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). These families are under active investigation, given their essential roles in cancer initiation, development and progression. This review focuses on the evidence for the role of RNAs in prostate cancer, and their use as diagnostic and prognostic markers, and targets for treatment in this disease.
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Affiliation(s)
- Marvin C J Lim
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
- Department of Medical Oncology, Tallaght University Hospital, Dublin D24 NR0A, Ireland.
| | - Anne-Marie Baird
- Cancer and Ageing Research Programme, Queensland University of Technology, Brisbane, QLD 4000, Australia.
- Department of Clinical Medicine, Trinity College Dublin, College Green, Dublin D02 PN40, Ireland.
- Thoracic Oncology Research Group, Labmed Directorate, St. James's Hospital, Dublin 08 W9RT, Ireland.
| | - John Aird
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
| | - John Greene
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
| | - Dhruv Kapoor
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
| | - Steven G Gray
- Department of Clinical Medicine, Trinity College Dublin, College Green, Dublin D02 PN40, Ireland.
- Thoracic Oncology Research Group, Labmed Directorate, St. James's Hospital, Dublin 08 W9RT, Ireland.
- School of Biological Sciences, Dublin Institute of Technology, Dublin D08 NF82, Ireland.
| | - Ray McDermott
- Department of Medical Oncology, Tallaght University Hospital, Dublin D24 NR0A, Ireland.
- Department of Medical Oncology, St. Vincent's University Hospital, Dublin D04 YN26, Ireland.
| | - Stephen P Finn
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
- Department of Histopathology, St. James's Hospital, P.O. Box 580, James's Street, Dublin D08 X4RX, Ireland.
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12
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Yang J, Tang H, Huang J, An H. Upregulation of CXCR7 Is Associated with Poor Prognosis of Prostate Cancer. Med Sci Monit 2018; 24:5185-5191. [PMID: 30047547 PMCID: PMC6074061 DOI: 10.12659/msm.906180] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Background Prostate cancer (PCa) is a prevalent cancer in males. CXCR7 exhibits oncogenic actions in various cancers. The aim of our study was to explore the clinical significance of CXCR7 in patients with PCa. Material/Methods QRT-PCR was used to detect the expression level of CXCR7 in PCa tissues. The relationship between CXCR7 expression and clinicopathologic parameters was evaluated by chi-square test. Kaplan-Meier survival curve was used for the survival analysis of patients. Cox regression analyses were performed to assess the potential of CXCR7 as a prognosis biomarker for PCa patients. We performed MTT and Transwell assays to determine the effect of CXCR7 on proliferative and migratory abilities of PCa cells, respectively. Results CXCR7 was upregulated in PCa tissues (P<0.05) and was correlated with PSA (P=0.023), differentiation (P=0.022), and lymph node metastasis (P=0.018). The results of MTT and Transwell assays demonstrated that inhibition of CXCR7 suppressed PCa cells growth and migration. Additionally, high CXCR7 level predicted poor overall survival (log rank test, P=0.019). CXCR7 was a valuable prognostic biomarker for PCa patients (HR=2.271, 95%CI=1.093–4.719, P=0.028). Conclusions CXCR7 is an oncogene in PCa that can promote aggressive progression of PCa through enhancing proliferation and migration of the tumor cells. CXCR7 is an independent biomarker for the prognosis of PCa.
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Affiliation(s)
- Jihua Yang
- Department of Oncology, Naval General Hospital, Beijing, China (mainland)
| | - Hao Tang
- Department of Urology, Jinling Hospital, Nanjing, Jiangsu, China (mainland)
| | - Jingyu Huang
- Department of Thoracic and Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China (mainland)
| | - Huaijie An
- Central Laboratory, Naval General Hospital, Beijing, China (mainland)
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13
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FitzGerald LM, Jung CH, Wong EM, Joo JE, Gould JA, Vasic V, Bassett JK, O'Callaghan N, Nottle T, Pedersen J, Giles GG, Southey MC. Obtaining high quality transcriptome data from formalin-fixed, paraffin-embedded diagnostic prostate tumor specimens. J Transl Med 2018; 98:537-550. [PMID: 29339835 DOI: 10.1038/s41374-017-0001-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 01/27/2023] Open
Abstract
Prognostic genomic biomarkers that can be measured at diagnosis to aid choice of treatment options are unavailable for most common cancers. This is due in part to the poor quality and quantity of available diagnostic specimens for discovery research and to limitations in genomic technologies. Recent technical advances now enable high-density molecular analyses using suboptimal biological specimens. Here we describe the optimization of a transcriptome-specific protocol for use with formalin-fixed, paraffin-embedded (FFPE) diagnostic prostate cancer (PrCa) specimens. We applied the Ion AmpliSeq Transcriptome Human Gene Expression Kit (AmpliSeq Kit) to RNA samples extracted from 36 tumor-enriched and 16 adjacent normal tissues (ADJNT) from 37 FFPE PrCa specimens over a series of eight pilot studies, incorporating protocol modifications from Pilots 2 to 5. Data quality were measured by (1) the total number of mapped reads; (2) the percentage of reads that mapped to AmpliSeq target regions (OnTarget%); (3) the percentage of genes on the AmpliSeq panel with a read count ≥10 (TargetsDetected%); and (4) comparing the gene read-count distribution of the prostate tissue samples with the median gene read-count distribution of cell line-derived RNA samples. Modifications incorporated into Pilot study 5 provided gene expression data equivalent to cell line-derived RNA samples. These modifications included the use of freshly cut slides for macrodissection; increased tissue section thickness (8 µm); RNA extraction using the RecoverAll Total Nucleic Acid Isolation Kit for FFPE (ThermoFisher); 18 target amplification cycles; and processing six samples per Ion PI chip. This protocol will facilitate the discovery of prognostic biomarkers for cancer by allowing researchers to exploit previously underutilized diagnostic FFPE specimens.
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Affiliation(s)
- Liesel M FitzGerald
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia.,Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Chol-Hee Jung
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, Australia
| | - Ee Ming Wong
- Department of Pathology, The University of Melbourne, Parkville, VIC, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - JiHoon E Joo
- Department of Pathology, The University of Melbourne, Parkville, VIC, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Jodee A Gould
- Monash Health Translation Precinct, Medical Genomics Facility, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Vivien Vasic
- Monash Health Translation Precinct, Medical Genomics Facility, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Julie K Bassett
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Neil O'Callaghan
- Department of Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Tim Nottle
- TissuPath Specialist Pathology, Mount Waverley, VIC, Australia
| | - John Pedersen
- TissuPath Specialist Pathology, Mount Waverley, VIC, Australia
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia.,Centre for Epidemiology and Biostatistics, School of Global and Population Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Melissa C Southey
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia. .,Department of Pathology, The University of Melbourne, Parkville, VIC, Australia. .,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.
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14
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Haldrup C, Pedersen AL, Øgaard N, Strand SH, Høyer S, Borre M, Ørntoft TF, Sørensen KD. Biomarker potential of ST6GALNAC3 and ZNF660 promoter hypermethylation in prostate cancer tissue and liquid biopsies. Mol Oncol 2018; 12:545-560. [PMID: 29465788 PMCID: PMC5891052 DOI: 10.1002/1878-0261.12183] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 10/17/2017] [Accepted: 02/14/2018] [Indexed: 01/04/2023] Open
Abstract
Current diagnostic and prognostic tools for prostate cancer (PC) are suboptimal, leading to overdiagnosis and overtreatment. Aberrant promoter hypermethylation of specific genes has been suggested as novel candidate biomarkers for PC that may improve diagnosis and prognosis. We here analyzed ST6GALNAC3 and ZNF660 promoter methylation in prostate tissues, and ST6GALNAC3,ZNF660,CCDC181, and HAPLN3 promoter methylation in liquid biopsies. First, using four independent patient sample sets, including a total of 110 nonmalignant (NM) and 705 PC tissue samples, analyzed by methylation‐specific qPCR or methylation array, we found that hypermethylation of ST6GALNAC3 and ZNF660 was highly cancer‐specific with areas under the curve (AUC) of receiver operating characteristic (ROC) curve analysis of 0.917–0.995 and 0.846–0.903, respectively. Furthermore, ZNF660 hypermethylation was significantly associated with biochemical recurrence in two radical prostatectomy (RP) cohorts of 158 and 392 patients and remained significant also in the subsets of patients with Gleason score ≤7 (univariate Cox regression and log‐rank tests, P < 0.05), suggesting that ZNF660 methylation analysis can potentially help to stratify low‐/intermediate‐grade PCs into indolent vs. more aggressive subtypes. Notably, ZNF660 hypermethylation was also significantly associated with poor overall and PC‐specific survival in the RP cohort (n = 158) with long clinical follow‐up available. Moreover, as proof of principle, we successfully detected highly PC‐specific hypermethylated circulating tumor DNA (ctDNA) for ST6GALNAC3,ZNF660,HAPLN3, and CCDC181 in liquid biopsies (serum) from 27 patients with PC vs. 10 patients with BPH, using droplet digital methylation‐specific PCR analysis. Finally, we generated a three‐gene (ST6GALNAC3/CCDC181/HAPLN3) ctDNA hypermethylation model, which detected PC with 100% specificity and 67% sensitivity. In conclusion, we here for the first time demonstrate diagnostic biomarker potential of ST6GALNAC3 and ZNF660 methylation, as well as prognostic biomarker potential of ZNF660. Furthermore, we show that hypermethylation of four genes can be detected in ctDNA in liquid biopsies (serum) from patients with PC.
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Affiliation(s)
- Christa Haldrup
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
| | - Anne L Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
| | - Nadia Øgaard
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
| | - Siri H Strand
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
| | - Søren Høyer
- Department of Histopathology, Aarhus University Hospital, Denmark
| | - Michael Borre
- Department of Urology, Aarhus University Hospital, Denmark
| | - Torben F Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
| | - Karina D Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
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15
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Zhuang W, Zhang C, Hao F, Sun X. Baculoviral IAP Repeat Containing 6 (BIRC6) Is a Predictor of Prognosis in Prostate Cancer. Med Sci Monit 2018; 24:839-845. [PMID: 29429983 PMCID: PMC5816567 DOI: 10.12659/msm.904052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Wenzhen Zhuang
- Medical Record Management Section, Weifang People's Hospital, Weifang, Shandong, China (mainland)
| | - Cuixia Zhang
- Medical Record Management Section, Weifang People's Hospital, Weifang, Shandong, China (mainland)
| | - Furong Hao
- Department of Radiotherapy, Weifang People's Hospital, Weifang, Shandong, China (mainland)
| | - Xicai Sun
- Department of Health Management, Weifang People's Hospital, Weifang, Shandong, China (mainland)
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16
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Comprehensive Evaluation of TFF3 Promoter Hypomethylation and Molecular Biomarker Potential for Prostate Cancer Diagnosis and Prognosis. Int J Mol Sci 2017; 18:ijms18092017. [PMID: 28930171 PMCID: PMC5618665 DOI: 10.3390/ijms18092017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 09/08/2017] [Accepted: 09/13/2017] [Indexed: 01/03/2023] Open
Abstract
Overdiagnosis and overtreatment of clinically insignificant tumors remains a major problem in prostate cancer (PC) due to suboptimal diagnostic and prognostic tools. Thus, novel biomarkers are urgently needed. In this study, we investigated the biomarker potential of Trefoil factor 3 (TFF3) promoter methylation and RNA expression levels for PC. Initially, by quantitative methylation specific PCR (qMSP) analysis of a large radical prostatectomy (RP) cohort (n = 292), we found that the TFF3 promoter was significantly hypomethylated in PC compared to non-malignant (NM) prostate tissue samples (p < 0.001) with an AUC (area under the curve) of 0.908 by receiver operating characteristics (ROC) curve analysis. Moreover, significant TFF3 promoter hypomethylation (p ≤ 0.010) as well as overexpression (p < 0.001) was found in PC samples from another large independent patient sample set (498 PC vs. 67 NM) analyzed by Illumina 450K DNA methylation arrays and/or RNA sequencing. TFF3 promoter methylation and transcriptional expression levels were inversely correlated, suggesting that epigenetic mechanisms contribute to the regulation of gene activity. Furthermore, low TFF3 expression was significantly associated with high ERG, ETS transcription factor (ERG) expression (p < 0.001), as well as with high Gleason score (p < 0.001), advanced pathological T-stage (p < 0.001), and prostate-specific antigen (PSA) recurrence after RP (p = 0.013; univariate Cox regression analysis). There were no significant associations between TFF3 promoter methylation levels, ERG status, or PSA recurrence in these RP cohorts. In conclusion, our results demonstrated diagnostic biomarker potential of TFF3 promoter hypomethylation for PC as well as prognostic biomarker potential of TFF3 RNA expression. To the best of our knowledge, this is the most comprehensive study of TFF3 promoter methylation and transcriptional expression in PC to date.
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17
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SHISA3 Promoter Methylation Is a Potential Diagnostic and Prognostic Biomarker for Laryngeal Squamous Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9058749. [PMID: 28299336 PMCID: PMC5337399 DOI: 10.1155/2017/9058749] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 11/03/2016] [Accepted: 01/10/2017] [Indexed: 12/16/2022]
Abstract
The purpose of this study was to evaluate the contribution of SHISA3 promoter methylation to laryngeal squamous cell carcinoma (LSCC). SHISA3 promoter methylation status and expression were determined using methylation-specific polymerase chain reaction (MSP) and quantitative real-time PCR (qRT-PCR) in 93 paired LSCC and adjacent normal tissues, respectively. Furthermore, the regulatory function of the SHISA3 promoter fragment was analyzed using a luciferase reporter assay. The results reveal that there is a significant increase in SHISA3 methylation in LSCC tissues compared with corresponding nontumor tissues (P = 4.58E − 12). The qRT-PCR results show a significant association between SHISA3 methylation and expression in LSCC (P = 1.67E − 03). In addition, the area under the receiver operating characteristic curve was 0.91. Consequently, a log-rank test and multivariate Cox analysis suggest that SHISA3 promoter hypermethylation is a predictor of poor overall survival for LSCC (log-rank P = 0.024; HR = 2.71; 95% CI = 1.024–7.177; P = 0.047). The results indicate that SHISA3 promoter hypermethylation might increase the risk of LSCC through regulation of gene expression and is a potential diagnostic and prognostic biomarker for LSCC.
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18
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Heterogeneous patterns of DNA methylation-based field effects in histologically normal prostate tissue from cancer patients. Sci Rep 2017; 7:40636. [PMID: 28084441 PMCID: PMC5233981 DOI: 10.1038/srep40636] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 12/09/2016] [Indexed: 12/26/2022] Open
Abstract
Prostate cancer (PC) diagnosis is based on histological evaluation of prostate needle biopsies, which have high false negative rates. Here, we investigated if cancer-associated epigenetic field effects in histologically normal prostate tissue may be used to increase sensitivity for PC. We focused on nine genes (AOX1, CCDC181 (C1orf114), GABRE, GAS6, HAPLN3, KLF8, MOB3B, SLC18A2, and GSTP1) known to be hypermethylated in PC. Using quantitative methylation-specific PCR, we analysed 66 malignant and 134 non-malignant tissue samples from 107 patients, who underwent ultrasound-guided prostate biopsy (67 patients had at least one cancer-positive biopsy, 40 had exclusively cancer-negative biopsies). Hypermethylation was detectable for all genes in malignant needle biopsy samples (AUC: 0.80 to 0.98), confirming previous findings in prostatectomy specimens. Furthermore, we identified a four-gene methylation signature (AOX1xGSTP1xHAPLN3xSLC18A2) that distinguished histologically non-malignant biopsies from patients with vs. without PC in other biopsies (AUC = 0.65; sensitivity = 30.8%; specificity = 100%). This signature was validated in an independent patient set (59 PC, 36 adjacent non-malignant, and 9 normal prostate tissue samples) analysed on Illumina 450 K methylation arrays (AUC = 0.70; sensitivity = 40.6%; specificity = 100%). Our results suggest that a novel four-gene signature may be used to increase sensitivity for PC diagnosis through detection of epigenetic field effects in histologically non-malignant prostate tissue samples.
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19
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New Progress of Epigenetic Biomarkers in Urological Cancer. DISEASE MARKERS 2016; 2016:9864047. [PMID: 27594736 PMCID: PMC4993951 DOI: 10.1155/2016/9864047] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 06/30/2016] [Indexed: 11/17/2022]
Abstract
Urological cancers consist of bladder, kidney, prostate, and testis cancers and they are generally silenced at their early stage, which leads to the loss of the best opportunity for early diagnosis and treatment. Desired biomarkers are scarce for urological cancers and current biomarkers are lack of specificity and sensitivity. Epigenetic alterations are characteristic of nearly all kinds of human malignances including DNA methylation, histone modification, and miRNA regulation. Besides, the detection of these epigenetic conditions is easily accessible especially for urine, best target for monitoring the diseases of urinary system. Here, we summarize some new progress about epigenetic biomarkers in urological cancers, hoping to provide new thoughts for the diagnosis, treatment, and prognosis of urological cancers.
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20
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Haldrup C, Lynnerup AS, Storebjerg TM, Vang S, Wild P, Visakorpi T, Arsov C, Schulz WA, Lindberg J, Grönberg H, Egevad L, Borre M, Ørntoft TF, Høyer S, Sørensen KD. Large-scale evaluation of SLC18A2 in prostate cancer reveals diagnostic and prognostic biomarker potential at three molecular levels. Mol Oncol 2016; 10:825-37. [PMID: 26905753 DOI: 10.1016/j.molonc.2016.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/23/2015] [Accepted: 02/01/2016] [Indexed: 12/18/2022] Open
Abstract
Limitations of current diagnostic and prognostic tools for prostate cancer (PC) have led to over-diagnosis and over-treatment. Here, we investigate the biomarker potential of the SLC18A2 (VMAT2) gene for PC at three molecular levels. Thus, SLC18A2 promoter methylation was analyzed in 767 malignant and 78 benign radical prostatectomy (RP) samples using methylation-specific qPCR and Illumina 450K methylation microarray data. SLC18A2 transcript levels were assessed in 412 malignant and 45 benign RP samples using RNAseq data. SLC18A2 protein was evaluated by immunohistochemistry in 502 malignant and 305 benign RP samples. Cancer-specificity of molecular changes was tested using Mann-Whitney U tests and/or receiver operating characteristic (ROC) analyses. Log rank, uni- and multivariate Cox regression tests were used for survival analyses. We found that SLC18A2 promoter hypermethylation was highly cancer-specific (area under the curve (AUC): 0.923-0.976) and associated with biochemical recurrence (BCR) after RP in univariate analyses. SLC18A2 transcript levels were reduced in PC and had independent prognostic value for BCR after RP (multivariate HR 0.13, P < 0.05). Likewise, SLC18A2 protein was down-regulated in PC (AUC 0.898) and had independent prognostic value for BCR (multivariate HR 0.51, P < 0.05). Reduced SLC18A2 protein expression was also associated with poor overall survival in univariate analysis (HR 0.29, P < 0.05). Our results highlight SLC18A2 as a new promising methylation marker candidate for PC diagnosis. Furthermore, SLC18A2 expression (RNA and protein) showed promising prognostic potential beyond routine clinicopathological variables. Thus, novel SLC18A2-based molecular tests could have useful future applications for PC detection and identification of high-risk patients.
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Affiliation(s)
- Christa Haldrup
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Anne-Sofie Lynnerup
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Tine Maj Storebjerg
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Peter Wild
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere, and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Christian Arsov
- Department of Urology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Lars Egevad
- Department of Oncolocy and Pathology, Karolinska Institute, Stockholm, Sweden
| | - Michael Borre
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Søren Høyer
- Institute of Pathology, Aarhus University Hospital, Aarhus, Denmark
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