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Zhou R, Lu D, Mi J, Wang C, Lu W, Wang Z, Li X, Wei C, Zhang H, Ji J, Zhang Y, Zhang D, Wang F. Disulfidptosis-related genes serve as potential prognostic biomarkers and indicate tumor microenvironment characteristics and immunotherapy response in prostate cancer. Sci Rep 2024; 14:14107. [PMID: 38898043 PMCID: PMC11187134 DOI: 10.1038/s41598-024-61679-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/08/2024] [Indexed: 06/21/2024] Open
Abstract
Disulfidptosis, a newly identified programmed cell death pathway in prostate cancer (PCa), is closely associated with intracellular disulfide stress and glycolysis. This study aims to elucidate the roles of disulfidptosis-related genes (DRGs) in the pathogenesis and progression of PCa, with the goal of improving diagnostic and therapeutic approaches. We analyzed PCa datasets and normal tissue transcriptome data from TCGA, GEO, and MSKCC. Using consensus clustering analysis and LASSO regression, we developed a risk scoring model, which was validated in an independent cohort. The model's predictive accuracy was confirmed through Kaplan-Meier curves, receiver operating characteristic (ROC) curves, and nomograms. Additionally, we explored the relationship between the risk score and immune cell infiltration, and examined the tumor microenvironment and somatic mutations across different risk groups. We also investigated responses to immunotherapy and drug sensitivity. Our analysis identified two disulfidosis subtypes with significant differences in survival, immune environments, and treatment responses. According to our risk score, the high-risk group exhibited poorer progression-free survival (PFS) and higher tumor mutational burden (TMB), associated with increased immune suppression. Functional enrichment analysis linked high-risk features to key cancer pathways, including the IL-17 signaling pathway. Moreover, drug sensitivity analysis revealed varied responses to chemotherapy, suggesting the potential for disulfidosis-based personalized treatment strategies. Notably, we identified PROK1 as a crucial prognostic marker in PCa, with its reduced expression correlating with disease progression. In summary, our study comprehensively assessed the clinical implications of DRGs in PCa progression and prognosis, offering vital insights for tailored precision medicine approaches.
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Affiliation(s)
- Rongbin Zhou
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-Constructed By the Province and Ministry, Guangxi Medical University, No. 22, Shuangyong Road, Qingxiu District, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Dingjin Lu
- Department of Urology, People's Hospital of Beihai, Beihai, 536000, Guangxi, China
| | - Junhao Mi
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-Constructed By the Province and Ministry, Guangxi Medical University, No. 22, Shuangyong Road, Qingxiu District, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Chengbang Wang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Wenhao Lu
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-Constructed By the Province and Ministry, Guangxi Medical University, No. 22, Shuangyong Road, Qingxiu District, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zuheng Wang
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Xiao Li
- School of Life Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Chunmeng Wei
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Huiyong Zhang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jin Ji
- Department of Urology, Shanghai Changhai Hospital, Naval Medical University, Shanghai, 200433, China
- Department of Urology, Naval Medical Center, Naval Medical Univiersiy, 338 Huaihai West Road, Shanghai, 200433, China
| | - Yifeng Zhang
- Department of Urology, Naval Medical Center, Naval Medical Univiersiy, 338 Huaihai West Road, Shanghai, 200433, China.
| | - Duobing Zhang
- Department of Urology, Suzhou Hospital of Anhui Medical University, 616 The Third Bianyang Road, Yongqiao District, Suzhou, 234000, Anhui, China.
| | - Fubo Wang
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-Constructed By the Province and Ministry, Guangxi Medical University, No. 22, Shuangyong Road, Qingxiu District, Nanning, 530021, Guangxi Zhuang Autonomous Region, China.
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- School of Life Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Department of Urology, Affiliated Tumor Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China.
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Geng K, Merino LG, Veiga RG, Sommerauer C, Epperlein J, Brinkman EK, Kutter C. Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles. Life Sci Alliance 2024; 7:e202302128. [PMID: 37984988 PMCID: PMC10662290 DOI: 10.26508/lsa.202302128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
The CRISPR-Cas9 system is a powerful tool for studying gene functions and holds potential for disease treatment. However, precise genome editing requires thorough assessments to minimize unintended on- and off-target effects. Here, we report an unexpected 283-kb deletion on Chromosome 10 (10q23.31) in chronic myelogenous leukemia-derived HAP1 cells, which are frequently used in CRISPR screens. The deleted region encodes regulatory genes, including PAPSS2, ATAD1, KLLN, and PTEN We found that this deletion was not a direct consequence of CRISPR-Cas9 off-targeting but rather occurred frequently during the generation of CRISPR-Cas9-modified cells. The deletion was associated with global changes in histone acetylation and gene expression, affecting fundamental cellular processes such as cell cycle and DNA replication. We detected this deletion in cancer patient genomes. As in HAP1 cells, the deletion contributed to similar gene expression patterns among cancer patients despite interindividual differences. Our findings suggest that the unintended deletion of 10q23.31 can confound CRISPR-Cas9 studies and underscore the importance to assess unintended genomic changes in CRISPR-Cas9-modified cells, which could impact cancer research.
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Affiliation(s)
- Keyi Geng
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Lara G Merino
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Raül G Veiga
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Christian Sommerauer
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Janine Epperlein
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Eva K Brinkman
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Claudia Kutter
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
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3
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Luo Y, Chen R, Ning Z, Fu N, Xie M. Identification of a Four-Gene Signature for Determining the Prognosis of Papillary Thyroid Carcinoma by Integrated Bioinformatics Analysis. Int J Gen Med 2022; 15:1147-1160. [PMID: 35153506 PMCID: PMC8824688 DOI: 10.2147/ijgm.s346058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 01/21/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Although well-differentiated papillary thyroid carcinoma (PTC) has an indolent nature and usually an excellent prognosis, some patients experience disease recurrence or death. The aim of this study was to identify prognostic markers to stratify PTC patients. Patients and Methods Eight gene-expression profiles (GSE3467, GSE3678, GSE5364, GSE27155, GSE33630, GSE53157, GSE60542, and GSE104005) were obtained from the Gene Expression Omnibus and used to analyze differentially expressed genes (DEGs) between PTC tissues and non-tumor tissues. Univariable Cox regression survival analysis and Lasso-penalized Cox regression analysis were performed to identify prognostic genes and establish a risk-score model based on the integrated DEGs. Kaplan–Meier (KM) and receiver operating characteristic (ROC) curves were used to validate the prognostic performance of the risk score. A nomogram was constructed based on The Cancer Genome Atlas dataset and Multivariable Cox regression analysis. Results A total of 165 upregulated and 207 downregulated DEGs were screened. A four-gene signature including PAPSS2, PCOLCE2, PTX3, and TGFBR3 was identified. The risk-score model showed a strong diagnosis performance for identifying patients with a poor prognosis. KM analysis showed that patients with low risk scores had a significantly more favorable overall survival (OS) than those with high risk scores (p = 0.0002). ROC curves based on the four-gene signature showed better performances in predicting 1-, 3-, and 5-year survival than did the American Joint Committee on Cancer staging system (area under the curve: 0.86 vs 0.84, 0.80 vs 0.63, and 0.79 vs 0.73, respectively). Furthermore, when combined with age and tumor status from the nomogram, the four-gene signature achieved a good performance in guiding postoperative follow-up surveillance of patients with PTC. Conclusion The four-gene signature was found to be a novel and reliable biomarker with great potential for clinical application in risk stratification and OS prediction in patients with PTC.
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Affiliation(s)
- Yuting Luo
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People’s Republic of China
| | - Rong Chen
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People’s Republic of China
| | - Zhikun Ning
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People’s Republic of China
| | - Nantao Fu
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People’s Republic of China
| | - Minghao Xie
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People’s Republic of China
- Correspondence: Minghao Xie, Department of General Surgery, The First Affiliated Hospital of Nanchang University, 17 Yongwai Road, Nanchang, Jiangxi, 330006, People’s Republic of China, Tel +8613672207521, Email
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Simpson BS, Camacho N, Luxton HJ, Pye H, Finn R, Heavey S, Pitt J, Moore CM, Whitaker HC. Genetic alterations in the 3q26.31-32 locus confer an aggressive prostate cancer phenotype. Commun Biol 2020; 3:440. [PMID: 32796921 PMCID: PMC7429505 DOI: 10.1038/s42003-020-01175-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 07/10/2020] [Indexed: 12/13/2022] Open
Abstract
Large-scale genetic aberrations that underpin prostate cancer development and progression, such as copy-number alterations (CNAs), have been described but the consequences of specific changes in many identified loci is limited. Germline SNPs in the 3q26.31 locus are associated with aggressive prostate cancer, and is the location of NAALADL2, a gene overexpressed in aggressive disease. The closest gene to NAALADL2 is TBL1XR1, which is implicated in tumour development and progression. Using publicly-available cancer genomic data we report that NAALADL2 and TBL1XR1 gains/amplifications are more prevalent in aggressive sub-types of prostate cancer when compared to primary cohorts. In primary disease, gains/amplifications occurred in 15.99% (95% CI: 13.02–18.95) and 14.96% (95% CI: 12.08–17.84%) for NAALADL2 and TBL1XR1 respectively, increasing in frequency in higher Gleason grade and stage tumours. Gains/amplifications result in transcriptional changes and the development of a pro-proliferative and aggressive phenotype. These results support a pivotal role for copy-number gains in this genetic region. Benjamin Simpson et al. use publicly available cancer genomic data to investigate copy number changes at the 3q26.31–32 locus, which has been associated with aggressive prostate cancer based on single-nucleotide polymorphisms. They find that gains of NAALADL2 and TBL1XR1 in this locus are associated with more aggressive subtypes of prostate cancer and the transcription of pro-proliferative signalling processes.
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Affiliation(s)
- Benjamin S Simpson
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK
| | - Niedzica Camacho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hayley J Luxton
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK
| | - Hayley Pye
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK
| | - Ron Finn
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK
| | - Susan Heavey
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK
| | - Jason Pitt
- Cancer Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Hayley C Whitaker
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK.
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5
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Zhou J, Yang X, Song P, Wang H, Wang X. HOXC6 in the prognosis of prostate cancer. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:2715-2720. [PMID: 31271305 DOI: 10.1080/21691401.2019.1635136] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Aims: Our study aimed to investigate the expression and prognostic role of homeobox C6 (HOXC6) in prostate cancer (PCa). Methods: Relative expression of HOXC6 at mRNA and protein levels in tissues and cell lines of PCa were measured using quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot analysis, respectively. Association between HOXC6 expression and clinical factors was analyzed by Chi-square test. HOXC6 effects on the proliferation, invasion and metastasis of PCa cells were severally examined through CCK-8 and transwell assays. Results: Relative expressions of HOXC6 at mRNA and protein levels were obviously higher in both PCa tissues and cells than in adjacent non-cancerous tissues and normal human prostate epithelial cells (p < .05). Chi-square test demonstrated that high expression of HOXC6 was significantly associated with PSA concentration, Gleason score and TNM stage (p < .05). The down-regulation of HOCX6 remarkably inhibited the proliferation, migration and invasion of PCa cells. Kaplan-Meier analysis showed that patients with high HOXC6 expression had shorter overall survival than those with low HOXC6 expression (log rank test, p < .001). Conclusion: Up-regulated HOXC6, in PCa patients, could not only participate in the progression of PCa but also function as an independent prognostic marker for the cancer.
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Affiliation(s)
- Junyu Zhou
- a Lihuili Hospital , Ningbo , Zhejiang , China
| | - Xiaogang Yang
- b Precision Medicine Center, The First Hospital of Handan City , Handan , Hebei , China
| | - Peng Song
- c Department of Oncology, The Second Medical Center, Chinese PLA General Hospital , Beijing , China
| | - Hongwei Wang
- d School of Safety Engineering, China University of Labor Relations , Beijing , China
| | - Xiumei Wang
- e Affiliated People's Hospital of Inner Mongolia Medical University , Hohhot , Inner Mongolia , China
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6
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Bednarz-Knoll N, Eltze E, Semjonow A, Brandt B. BRCAness in prostate cancer. Oncotarget 2019; 10:2421-2422. [PMID: 31069005 PMCID: PMC6497433 DOI: 10.18632/oncotarget.26818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 03/19/2019] [Indexed: 02/03/2023] Open
Affiliation(s)
- Natalia Bednarz-Knoll
- Natalia Bednarz-Knoll: Laboratory of Cell Biology, Department of Medical Biotechnology, Medical University of Gdańsk, Gdańsk, Poland
| | - Elke Eltze
- Natalia Bednarz-Knoll: Laboratory of Cell Biology, Department of Medical Biotechnology, Medical University of Gdańsk, Gdańsk, Poland
| | - Axel Semjonow
- Natalia Bednarz-Knoll: Laboratory of Cell Biology, Department of Medical Biotechnology, Medical University of Gdańsk, Gdańsk, Poland
| | - Burkhard Brandt
- Natalia Bednarz-Knoll: Laboratory of Cell Biology, Department of Medical Biotechnology, Medical University of Gdańsk, Gdańsk, Poland
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7
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Álvarez-Garcia V, Tawil Y, Wise HM, Leslie NR. Mechanisms of PTEN loss in cancer: It's all about diversity. Semin Cancer Biol 2019; 59:66-79. [PMID: 30738865 DOI: 10.1016/j.semcancer.2019.02.001] [Citation(s) in RCA: 201] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/22/2019] [Accepted: 02/05/2019] [Indexed: 01/04/2023]
Abstract
PTEN is a phosphatase which metabolises PIP3, the lipid product of PI 3-Kinase, directly opposing the activation of the oncogenic PI3K/AKT/mTOR signalling network. Accordingly, loss of function of the PTEN tumour suppressor is one of the most common events observed in many types of cancer. Although the mechanisms by which PTEN function is disrupted are diverse, the most frequently observed events are deletion of a single gene copy of PTEN and gene silencing, usually observed in tumours with little or no PTEN protein detectable by immunohistochemistry. Accordingly, with the exceptions of glioblastoma and endometrial cancer, mutations of the PTEN coding sequence are uncommon (<10%) in most types of cancer. Here we review the data relating to PTEN loss in seven common tumour types and discuss mechanisms of PTEN regulation, some of which appear to contribute to reduced PTEN protein levels in cancers.
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Affiliation(s)
- Virginia Álvarez-Garcia
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Yasmine Tawil
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Helen M Wise
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Nicholas R Leslie
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
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8
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Jamaspishvili T, Berman DM, Ross AE, Scher HI, De Marzo AM, Squire JA, Lotan TL. Clinical implications of PTEN loss in prostate cancer. Nat Rev Urol 2018; 15:222-234. [PMID: 29460925 DOI: 10.1038/nrurol.2018.9] [Citation(s) in RCA: 364] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genomic aberrations of the PTEN tumour suppressor gene are among the most common in prostate cancer. Inactivation of PTEN by deletion or mutation is identified in ∼20% of primary prostate tumour samples at radical prostatectomy and in as many as 50% of castration-resistant tumours. Loss of phosphatase and tensin homologue (PTEN) function leads to activation of the PI3K-AKT (phosphoinositide 3-kinase-RAC-alpha serine/threonine-protein kinase) pathway and is strongly associated with adverse oncological outcomes, making PTEN a potentially useful genomic marker to distinguish indolent from aggressive disease in patients with clinically localized tumours. At the other end of the disease spectrum, therapeutic compounds targeting nodes in the PI3K-AKT-mTOR (mechanistic target of rapamycin) signalling pathway are being tested in clinical trials for patients with metastatic castration-resistant prostate cancer. Knowledge of PTEN status might be helpful to identify patients who are more likely to benefit from these therapies. To enable the use of PTEN status as a prognostic and predictive biomarker, analytically validated assays have been developed for reliable and reproducible detection of PTEN loss in tumour tissue and in blood liquid biopsies. The use of clinical-grade assays in tumour tissue has shown a robust correlation between loss of PTEN and its protein as well as a strong association between PTEN loss and adverse pathological features and oncological outcomes. In advanced disease, assessing PTEN status in liquid biopsies shows promise in predicting response to targeted therapy. Finally, studies have shown that PTEN might have additional functions that are independent of the PI3K-AKT pathway, including those affecting tumour growth through modulation of the immune response and tumour microenvironment.
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Affiliation(s)
- Tamara Jamaspishvili
- Division of Cancer Biology and Genetics, Cancer Research Institute, Queen's University, Kingston, Ontario, Canada.,Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - David M Berman
- Division of Cancer Biology and Genetics, Cancer Research Institute, Queen's University, Kingston, Ontario, Canada.,Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Ashley E Ross
- Department of Urology, Johns Hopkins University, Baltimore, MD, USA
| | - Howard I Scher
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, USA
| | - Angelo M De Marzo
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University, Baltimore, MD, USA
| | - Jeremy A Squire
- Department of Pathology and Legal Medicine, University of Sao Paulo, Campus Universitario Monte Alegre, Ribeirão Preto, Brazil
| | - Tamara L Lotan
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University, Baltimore, MD, USA
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9
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Nowinski S, Santaolalla A, O'Leary B, Loda M, Mirchandani A, Emberton M, Van Hemelrijck M, Grigoriadis A. Systematic identification of functionally relevant risk alleles to stratify aggressive versus indolent prostate cancer. Oncotarget 2018; 9:12812-12824. [PMID: 29560112 PMCID: PMC5849176 DOI: 10.18632/oncotarget.24400] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/25/2018] [Indexed: 12/20/2022] Open
Abstract
Novel approaches for classification, including molecular features, are needed to direct therapy for men with low-grade prostate cancer (PCa), especially men on active surveillance. Risk alleles identified from genome-wide association studies (GWAS) could improve prognostication. Those risk alleles that coincided with genes and somatic copy number aberrations associated with progression of PCa were selected as the most relevant for prognostication. In a systematic literature review, a total of 698 studies were collated. Fifty-three unique SNPs residing in 29 genomic regions, including 8q24, 10q11 and 19q13, were associated with PCa progression. Functional studies implicated 21 of these single nucleotide polymorphisms (SNPs) as modulating the expression of genes in the androgen receptor pathway and several other oncogenes. In particular, 8q24, encompassing MYC, harbours a high density of SNPs conferring unfavourable pathological characteristics in low-grade PCa, while a copy number gain of MYC in low-grade PCa was associated with prostate-specific antigen recurrence after radical prostatectomy. By combining GWAS data with gene expression and structural rearrangements, risk alleles were identified that could provide a new basis for developing a prognostication tool to guide therapy for men with early prostate cancer.
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Affiliation(s)
- Salpie Nowinski
- Cancer Bioinformatics, Innovation Hub, Guy's Cancer Centre, King's College London, London, UK
| | - Aida Santaolalla
- Translational Oncology & Urology Research, King's College London, London, UK
| | - Ben O'Leary
- Breast Cancer NOW Centre, The Institute of Cancer Research, The Royal Marsden Hospital, London, UK
| | - Massimo Loda
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ayesha Mirchandani
- Cancer Bioinformatics, Innovation Hub, Guy's Cancer Centre, King's College London, London, UK
| | - Mark Emberton
- Division of Surgery and Interventional Science, University College London, London, UK
| | | | - Anita Grigoriadis
- Cancer Bioinformatics, Innovation Hub, Guy's Cancer Centre, King's College London, London, UK
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10
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Seim I, Jeffery PL, Thomas PB, Nelson CC, Chopin LK. Whole-Genome Sequence of the Metastatic PC3 and LNCaP Human Prostate Cancer Cell Lines. G3 (BETHESDA, MD.) 2017; 7:1731-1741. [PMID: 28413162 PMCID: PMC5473753 DOI: 10.1534/g3.117.039909] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/09/2017] [Indexed: 12/14/2022]
Abstract
The bone metastasis-derived PC3 and the lymph node metastasis-derived LNCaP prostate cancer cell lines are widely studied, having been described in thousands of publications over the last four decades. Here, we report short-read whole-genome sequencing (WGS) and de novo assembly of PC3 (ATCC CRL-1435) and LNCaP (clone FGC; ATCC CRL-1740) at ∼70 × coverage. A known homozygous mutation in TP53 and homozygous loss of PTEN were robustly identified in the PC3 cell line, whereas the LNCaP cell line exhibited a larger number of putative inactivating somatic point and indel mutations (and in particular a loss of stop codon events). This study also provides preliminary evidence that loss of one or both copies of the tumor suppressor Capicua (CIC) contributes to primary tumor relapse and metastatic progression, potentially offering a treatment target for castration-resistant prostate cancer (CRPC). Our work provides a resource for genetic, genomic, and biological studies employing two commonly-used prostate cancer cell lines.
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Affiliation(s)
- Inge Seim
- Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia
- Australian Prostate Cancer Research Centre - Queensland, Princess Alexandra Hospital, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia
- Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Penny L Jeffery
- Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia
- Australian Prostate Cancer Research Centre - Queensland, Princess Alexandra Hospital, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia
- Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Patrick B Thomas
- Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia
- Australian Prostate Cancer Research Centre - Queensland, Princess Alexandra Hospital, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia
- Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Colleen C Nelson
- Australian Prostate Cancer Research Centre - Queensland, Princess Alexandra Hospital, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Lisa K Chopin
- Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia
- Australian Prostate Cancer Research Centre - Queensland, Princess Alexandra Hospital, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia
- Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia
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11
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Sekar V, Mehrotra DG, Majumder B. Molecular and Functional Diagnostic Tools in Precision Oncology for Urological Malignancies. Indian J Surg Oncol 2017; 8:24-32. [PMID: 28127179 PMCID: PMC5236026 DOI: 10.1007/s13193-016-0591-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 09/12/2016] [Indexed: 12/29/2022] Open
Abstract
Urological malignancies, represented mainly by prostate, bladder, and renal cancers, are some of the leading causes of cancer-related mortalities worldwide. Despite various efforts over decades to develop early detection tests and effective therapeutic paradigms, the response rate to the existing treatments remains low for both primary and late stage/recurrent phases of these cancers. The evolving landscape of molecular diagnostics, aiming to make the diagnosis and treatment more patient-driven, underpins precision oncology and particularly intends to rationally profile individual tumors and highlight the mechanistic insight and complexity of tumor microenvironment in order to develop biomarkers of toxicity risks and response prediction in a clinically oriented dynamical setting. The present review is an effort to capture some of the recent developments in the area of molecular diagnostics and functional testing platforms and their potential application in clinical decision making in the premises of precision oncology of urological malignancies.
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Affiliation(s)
- Vasanthakumar Sekar
- Department of Cancer Biology, Mitra Biotech, 202, Narayana Nethralaya, Health City, Hosur Main Road, Bangalore, 560099 India
| | - Debapriya Ghosh Mehrotra
- Department of Molecular Pathology, Mitra Biotech, 202, Narayana Nethralaya, Health City, Hosur Main Road, Bangalore, 560099 India
| | - Biswanath Majumder
- Department of Molecular Pathology, Mitra Biotech, 202, Narayana Nethralaya, Health City, Hosur Main Road, Bangalore, 560099 India
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12
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Brait M, Banerjee M, Maldonado L, Ooki A, Loyo M, Guida E, Izumchenko E, Mangold L, Humphreys E, Rosenbaum E, Partin A, Sidransky D, Hoque MO. Promoter methylation of MCAM, ERα and ERβ in serum of early stage prostate cancer patients. Oncotarget 2017; 8:15431-15440. [PMID: 28147335 PMCID: PMC5362497 DOI: 10.18632/oncotarget.14873] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 12/31/2016] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Prostate cancer (PC) is the second most common cancer among men worldwide. Currently, the most common non-invasive approach for screening and risk assessment of PC is measuring the level of serum prostate-specific antigen (PSA). However, the sensitivity of PSA is 42.8 % and specificity is 41.1%. As a result, the serum PSA test leads to numerous unneeded biopsies. Therefore, a rigorous search for biomarkers for early detection of PC is ongoing. In this study, we aim to assess a panel of epigenetic markers in an intend to develop an early detection test for PC. RESULTS The sensitivity and specificity of hypermethylation of MCAM was 66% and 73% respectively which is an improvement from the sensitivity and specificity of PSA. Considering a combination marker panel of MCAM, ERα and ERβ increased the sensitivity to 75% and the specificity became 70% for the minimally invasive early detection test of PC. MATERIALS AND METHODS Sixteen primary matched tumor and serum were analyzed by quantitative methylation specific PCR (QMSP) to determine analytical and clinical sensitivity of the genes tested (SSBP2, MCAM, ERα, ERβ, APC, CCND2, MGMT, GSTP1, p16 and RARβ2). Additionally, serum samples from eighty four cases of PC, thirty controls and seven cases diagnosed as high grade Prostatic Intraepithelial Neoplasia (HGPIN) were analyzed. CONCLUSIONS Promoter methylation of MCAM, ERα and ERβ have a potential to be utilized as biomarker for the early detection of prostate PC as their sensitivity and specificity seem to be better than serum PSA in our cohort of samples. After robust validation in a larger prospective cohort, our findings may reduce the numbers of unwarranted prostate biopsies.
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Affiliation(s)
- Mariana Brait
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mithu Banerjee
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Leonel Maldonado
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pathology, University of South Alabama Medical Center, Mobile, Alabama, USA
| | - Akira Ooki
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Myriam Loyo
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elisa Guida
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Evgeny Izumchenko
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Leslie Mangold
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth Humphreys
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eli Rosenbaum
- Department of Urological Oncology, Davidoff Center, Beilinson Hospital, Eliahu Hakim, Ramat Aviv, Israel
| | - Alan Partin
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David Sidransky
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mohammad Obaidul Hoque
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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13
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Mlcochova H, Machackova T, Rabien A, Radova L, Fabian P, Iliev R, Slaba K, Poprach A, Kilic E, Stanik M, Redova-Lojova M, Svoboda M, Dolezel J, Vyzula R, Jung K, Slaby O. Epithelial-mesenchymal transition-associated microRNA/mRNA signature is linked to metastasis and prognosis in clear-cell renal cell carcinoma. Sci Rep 2016; 6:31852. [PMID: 27549611 PMCID: PMC4994011 DOI: 10.1038/srep31852] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/28/2016] [Indexed: 02/06/2023] Open
Abstract
Clear-cell renal cell carcinomas (ccRCCs) are genetically heterogeneous tumors presenting diverse clinical courses. Epithelial-mesenchymal transition (EMT) is a crucial process involved in initiation of metastatic cascade. The aim of our study was to identify an integrated miRNA/mRNA signature associated with metastasis and prognosis in ccRCC through targeted approach based on analysis of miRNAs/mRNAs associated with EMT. A cohort of 230 ccRCC was included in our study and further divided into discovery, training and validation cohorts. EMT markers were evaluated in ccRCC tumor samples, which were grouped accordingly to EMT status. By use of large-scale miRNA/mRNA expression profiling, we identified miRNA/mRNA with significantly different expression in EMT-positive tumors and selected 41 miRNAs/mRNAs for training phase of the study to evaluate their diagnostic and prognostic potential. Fifteen miRNAs/mRNAs were analyzed in the validation phase, where all evaluated miRNA/mRNA candidates were confirmed to be significantly deregulated in tumor tissue. Some of them significantly differed in metastatic tumors, correlated with clinical stage, with Fuhrman grade and with overall survival. Further, we established an EMT-based stage-independent prognostic scoring system enabling identification of ccRCC patients at high-risk of cancer-related death. Finally, we confirmed involvement of miR-429 in EMT regulation in RCC cells in vitro.
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Affiliation(s)
- Hana Mlcochova
- Masaryk University, Central European Institute of Technology (CEITEC), Kamenice 5, 625 00, Brno, Czech Republic.,Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Tana Machackova
- Masaryk University, Central European Institute of Technology (CEITEC), Kamenice 5, 625 00, Brno, Czech Republic
| | - Anja Rabien
- University Hospital Charite, Humboldt University, Department of Urology, Schumannstrasse 20/21, D-10117 Berlin, Germany.,Berlin Institute for Urologic Research, Robert-Koch Platz 7, 10115 Berlin, Germany
| | - Lenka Radova
- Masaryk University, Central European Institute of Technology (CEITEC), Kamenice 5, 625 00, Brno, Czech Republic
| | - Pavel Fabian
- Masaryk Memorial Cancer Institute, Department of Diagnostic and Experimental Pathology, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Robert Iliev
- Masaryk University, Central European Institute of Technology (CEITEC), Kamenice 5, 625 00, Brno, Czech Republic
| | - Katerina Slaba
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Alexandr Poprach
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Ergin Kilic
- University Hospital Charite, Humboldt University, Institute of Pathology, Schumannstrasse 20/21, D-10117 Berlin, Germany
| | - Michal Stanik
- Masaryk Memorial Cancer Institute, Department of Urologic Oncology, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Martina Redova-Lojova
- Masaryk University, Central European Institute of Technology (CEITEC), Kamenice 5, 625 00, Brno, Czech Republic
| | - Marek Svoboda
- Masaryk University, Central European Institute of Technology (CEITEC), Kamenice 5, 625 00, Brno, Czech Republic.,Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Jan Dolezel
- Masaryk Memorial Cancer Institute, Department of Urologic Oncology, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Rostislav Vyzula
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Klaus Jung
- University Hospital Charite, Humboldt University, Department of Urology, Schumannstrasse 20/21, D-10117 Berlin, Germany.,Berlin Institute for Urologic Research, Robert-Koch Platz 7, 10115 Berlin, Germany
| | - Ondrej Slaby
- Masaryk University, Central European Institute of Technology (CEITEC), Kamenice 5, 625 00, Brno, Czech Republic.,Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53, Brno, Czech Republic
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