1
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Franzén B, Auer G, Lewensohn R. Minimally invasive biopsy-based diagnostics in support of precision cancer medicine. Mol Oncol 2024. [PMID: 38519839 DOI: 10.1002/1878-0261.13640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/31/2024] [Accepted: 03/14/2024] [Indexed: 03/25/2024] Open
Abstract
Precision cancer medicine (PCM) to support the treatment of solid tumors requires minimally invasive diagnostics. Here, we describe the development of fine-needle aspiration biopsy-based (FNA) molecular cytology which will be increasingly important in diagnostics and adaptive treatment. We provide support for FNA-based molecular cytology having a significant potential to replace core needle biopsy (CNB) as a patient-friendly potent technique for tumor sampling for various tumor types. This is not only because CNB is a more traumatic procedure and may be associated with more complications compared to FNA-based sampling, but also due to the recently developed molecular methods used with FNA. Recent studies show that image-guided FNA in combination with ultrasensitive molecular methods also offers opportunities for characterization of the tumor microenvironment which can aid therapeutic decisions. Here we provide arguments for an increased implementation of molecular FNA-based sampling as a patient-friendly diagnostic method, which may, due to its repeatability, facilitate regular sampling that is needed during different treatment lines, to provide tumor information, supporting treatment decisions, shortening lead times in healthcare, and benefit healthcare economics.
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Affiliation(s)
- Bo Franzén
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Cancer Centre Karolinska (CCK) Foundation, Karolinska University Hospital, Stockholm, Sweden
| | - Gert Auer
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Rolf Lewensohn
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Theme Cancer, Medical Unit Head and Neck, Lung, and Skin Tumors, Thoracic Oncology Center, Karolinska University Hospital, Stockholm, Sweden
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2
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Zhong Q, Sun R, Aref AT, Noor Z, Anees A, Zhu Y, Lucas N, Poulos RC, Lyu M, Zhu T, Chen GB, Wang Y, Ding X, Rutishauser D, Rupp NJ, Rueschoff JH, Poyet C, Hermanns T, Fankhauser C, Rodríguez Martínez M, Shao W, Buljan M, Neumann JF, Beyer A, Hains PG, Reddel RR, Robinson PJ, Aebersold R, Guo T, Wild PJ. Proteomic-based stratification of intermediate-risk prostate cancer patients. Life Sci Alliance 2024; 7:e202302146. [PMID: 38052461 PMCID: PMC10698198 DOI: 10.26508/lsa.202302146] [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: 05/09/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023] Open
Abstract
Gleason grading is an important prognostic indicator for prostate adenocarcinoma and is crucial for patient treatment decisions. However, intermediate-risk patients diagnosed in the Gleason grade group (GG) 2 and GG3 can harbour either aggressive or non-aggressive disease, resulting in under- or overtreatment of a significant number of patients. Here, we performed proteomic, differential expression, machine learning, and survival analyses for 1,348 matched tumour and benign sample runs from 278 patients. Three proteins (F5, TMEM126B, and EARS2) were identified as candidate biomarkers in patients with biochemical recurrence. Multivariate Cox regression yielded 18 proteins, from which a risk score was constructed to dichotomize prostate cancer patients into low- and high-risk groups. This 18-protein signature is prognostic for the risk of biochemical recurrence and completely independent of the intermediate GG. Our results suggest that markers generated by computational proteomic profiling have the potential for clinical applications including integration into prostate cancer management.
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Affiliation(s)
- Qing Zhong
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Rui Sun
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Adel T Aref
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Zainab Noor
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Asim Anees
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Yi Zhu
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Natasha Lucas
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Rebecca C Poulos
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Mengge Lyu
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Tiansheng Zhu
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Guo-Bo Chen
- Urology & Nephrology Center, Department of Urology, Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Yingrui Wang
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xuan Ding
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Dorothea Rutishauser
- Department of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Niels J Rupp
- Department of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Jan H Rueschoff
- Department of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Cédric Poyet
- Department of Urology, University Hospital Zürich, Zürich, Switzerland
| | - Thomas Hermanns
- Department of Urology, University Hospital Zürich, Zürich, Switzerland
| | - Christian Fankhauser
- Department of Urology, University Hospital Zürich, Zürich, Switzerland
- Department of Urology, Cantonal Hospital Lucerne, Lucerne, Switzerland
| | | | - Wenguang Shao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Marija Buljan
- Empa - Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | - Peter G Hains
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Roger R Reddel
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Phillip J Robinson
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
- Faculty of Science, University of Zürich, Zürich, Switzerland
| | - Tiannan Guo
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Peter J Wild
- Goethe University Frankfurt, Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
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3
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An Y, Lu W, Li S, Lu X, Zhang Y, Han D, Su D, Jia J, Yuan J, Zhao B, Tu M, Li X, Wang X, Fang N, Ji S. Systematic review and integrated analysis of prognostic gene signatures for prostate cancer patients. Discov Oncol 2023; 14:234. [PMID: 38112859 PMCID: PMC10730790 DOI: 10.1007/s12672-023-00847-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023] Open
Abstract
Prostate cancer (PC) is one of the most common cancers in men and becoming the second leading cause of cancer fatalities. At present, the lack of effective strategies for prognosis of PC patients is still a problem to be solved. Therefore, it is significant to identify potential gene signatures for PC patients' prognosis. Here, we summarized 71 different prognostic gene signatures for PC and concluded 3 strategies for signature construction after extensive investigation. In addition, 14 genes frequently appeared in 71 different gene signatures, which enriched in mitotic and cell cycle. This review provides extensive understanding and integrated analysis of current prognostic signatures of PC, which may help researchers to construct gene signatures of PC and guide future clinical treatment.
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Affiliation(s)
- Yang An
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China.
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China.
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China.
| | - Wenyuan Lu
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Shijia Li
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Xiaoyan Lu
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Yuanyuan Zhang
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Dongcheng Han
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Dingyuan Su
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Jiaxin Jia
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Jiaxin Yuan
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Binbin Zhao
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Mengjie Tu
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Xinyu Li
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Xiaoqing Wang
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Na Fang
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China.
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China.
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China.
| | - Shaoping Ji
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China.
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China.
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China.
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4
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Röbeck P, Franzén B, Cantera-Ahlman R, Dragomir A, Auer G, Jorulf H, Jacobsson SP, Viktorsson K, Lewensohn R, Häggman M, Ladjevardi S. Multiplex protein analysis and ensemble machine learning methods of fine needle aspirates from prostate cancer patients reveal potential diagnostic signatures associated with tumour grade. Cytopathology 2023; 34:286-294. [PMID: 36840380 DOI: 10.1111/cyt.13226] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/06/2023] [Accepted: 02/16/2023] [Indexed: 02/26/2023]
Abstract
BACKGROUND Improved molecular diagnosis is needed in prostate cancer (PC). Fine needle aspiration (FNA) is a minimally invasive biopsy technique, less traumatic compared to core needle biopsy, and could be useful for diagnosis of PC. Molecular biomarkers (BMs) in FNA-samples can be assessed for prediction, eg of immunotherapy efficacy before treatment as well as at treatment decision time points during disease progression. METHODS In the present pilot study, the expression levels of 151 BM proteins were analysed by proximity extension assay in FNA-samples from 16 patients, including benign prostate lesions (n = 3) and cancers (n = 13). An ensemble data analysis strategy was applied using several machine learning models. RESULTS Twelve potentially predictive BM proteins correlating with International Society of Urological Pathology grade groups were identified, among them vimentin, tissue factor pathway inhibitor 2, and integrin beta-5. The validity of the results was supported by network analysis that showed functional associations between most of the identified putative BMs. We also showed that multiple immune checkpoint targets can be assessed (eg PD-L1, CD137, and Galectin-9), which may support the selection of immunotherapy in advanced PC. Results are promising but need further validation in a larger cohort. CONCLUSIONS Our pilot study represents a "proof of concept" and shows that multiplex profiling of potential diagnostic and predictive BM proteins is feasible on tumour material obtained by FNA sampling of prostate cancer. Moreover, our results demonstrate that an ensemble data analysis strategy may facilitate the identification of BM signatures in pilot studies when the patient cohort is limited.
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Affiliation(s)
- Pontus Röbeck
- Department of Urology, Uppsala University, Uppsala, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Bo Franzén
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Rafaele Cantera-Ahlman
- Department of Urology, Uppsala University, Uppsala, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Anca Dragomir
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Gert Auer
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Håkan Jorulf
- Department of Urology, Uppsala University, Uppsala, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Sven P Jacobsson
- Department of Analytical Chemistry, Stockholm University, Stockholm, Sweden
| | - Kristina Viktorsson
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Rolf Lewensohn
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
- Theme Cancer, Medical Unit Head and Neck, Lung, and Skin Tumors, Thoracic Oncology Center, Karolinska University Hospital, Solna, Sweden
| | - Michael Häggman
- Department of Urology, Uppsala University, Uppsala, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Sam Ladjevardi
- Department of Urology, Uppsala University, Uppsala, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
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5
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Röbeck P, Xu L, Ahmed D, Dragomir A, Dahlman P, Häggman M, Ladjevardi S. P-score in preoperative biopsies accurately predicts P-score in final pathology at radical prostatectomy in patients with localized prostate cancer. Prostate 2023; 83:831-839. [PMID: 36938873 DOI: 10.1002/pros.24523] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/13/2023] [Accepted: 03/03/2023] [Indexed: 03/21/2023]
Abstract
BACKGROUND Prostate cancer (PCa) is a highly heterogeneous, multifocal disease, and identification of clinically significant lesions is challenging, which complicates the choice of adequate treatment. The Prostatype® score (P-score) is intended to guide treatment decisions for newly diagnosed PCa patients based on a three-gene signature (IGFBP3, F3, and VGLL3) and clinicopathological information obtained at diagnosis. This study evaluated association of the P-score measured in preoperative magnetic resonance imaging/transrectal ultrasound fusion-guided core needle biopsies (CNBs) and the P-score measured in radical prostatectomy (RP) specimens of PCa patients. We also evaluated the P-score association with the pathology of RP specimens. Furthermore, concordance of the P-score in paired CNB and RP specimens, as well as in index versus concomitant nonindex tumor foci from the same RP was investigated. METHODS The study included 100 patients with localized PCa. All patients were diagnosed by CNB and underwent RP between 2015 and 2018. Gene expression was assessed with the Prostatype® real-time quantitative polymerase chain reaction kit and the P-score was calculated. Patients were categorized into three P-score risk groups according to previously defined cutoffs. RESULTS For 71 patients, sufficient CNB tumor material was available for comparison with the RP specimens. The CNB-based P-score was associated with the pathological T-stage in RP specimens (p = 0.02). Moreover, the CNB-based P-score groups were in substantial agreement with the RP-based P-score groups (weighted κ score: 0.76 [95% confidence interval, 95% CI: 0.60-0.92]; Spearman's rank correlation coefficient r = 0.83 [95% CI: 0.74-0.89]; p < 0.0001). Similarly, the P-score groups based on paired index tumor and concomitant nonindex tumor foci (n = 64) were also in substantial agreement (weighted κ score: 0.74 [95% CI: 0.57-0.91]; r = 0.83 [95% CI: 0.73-0.89], p < 0.0001). CONCLUSIONS Our findings suggest that the P-score based on preoperative CNB accurately reflects the pathology of the whole tumor, highlighting its value as a decision support tool for newly diagnosed PCa patients.
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Affiliation(s)
- Pontus Röbeck
- Department of Urology, Uppsala University Hospital, Uppsala, Sweden
| | - Lidi Xu
- Prostatype Genomics AB, Stockholm, Sweden
| | | | - Anca Dragomir
- Department of Pathology, Uppsala University Hospital, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Pär Dahlman
- Department of Surgical Sciences, Radiology, Uppsala University Hospital, Uppsala, Sweden
| | - Michael Häggman
- Department of Urology, Uppsala University Hospital, Uppsala, Sweden
| | - Sam Ladjevardi
- Department of Urology, Uppsala University Hospital, Uppsala, Sweden
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6
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Lelong EIJ, Khelifi G, Adjibade P, Joncas FH, Grenier St-Sauveur V, Paquette V, Gris T, Zoubeidi A, Audet-Walsh E, Lambert JP, Toren P, Mazroui R, Hussein SMI. Prostate cancer resistance leads to a global deregulation of translation factors and unconventional translation. NAR Cancer 2022; 4:zcac034. [PMID: 36348939 PMCID: PMC9634437 DOI: 10.1093/narcan/zcac034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/29/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Emerging evidence associates translation factors and regulators to tumorigenesis. However, our understanding of translational changes in cancer resistance is still limited. Here, we generated an enzalutamide-resistant prostate cancer (PCa) model, which recapitulated key features of clinical enzalutamide-resistant PCa. Using this model and poly(ribo)some profiling, we investigated global translation changes that occur during acquisition of PCa resistance. We found that enzalutamide-resistant cells exhibit an overall decrease in mRNA translation with a specific deregulation in the abundance of proteins involved in mitochondrial processes and in translational regulation. However, several mRNAs escape this translational downregulation and are nonetheless bound to heavy polysomes in enzalutamide-resistant cells suggesting active translation. Moreover, expressing these corresponding genes in enzalutamide-sensitive cells promotes resistance to enzalutamide treatment. We also found increased association of long non-coding RNAs (lncRNAs) with heavy polysomes in enzalutamide-resistant cells, suggesting that some lncRNAs are actively translated during enzalutamide resistance. Consistent with these findings, expressing the predicted coding sequences of known lncRNAs JPX, CRNDE and LINC00467 in enzalutamide-sensitive cells drove resistance to enzalutamide. Taken together, this suggests that aberrant translation of specific mRNAs and lncRNAs is a strong indicator of PCa enzalutamide resistance, which points towards novel therapeutic avenues that may target enzalutamide-resistant PCa.
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Affiliation(s)
- Emeline I J Lelong
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - Gabriel Khelifi
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - Pauline Adjibade
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - France-Hélène Joncas
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - Valérie Grenier St-Sauveur
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - Virginie Paquette
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Endocrinology and Nephrology Division , Quebec City, Québec G1V 4G2, Canada
| | - Typhaine Gris
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, Faculty of Medicine, University of British Columbia , Vancouver, British Columbia V6H 3Z6, Canada
| | - Etienne Audet-Walsh
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Endocrinology and Nephrology Division , Quebec City, Québec G1V 4G2, Canada
| | - Jean-Philippe Lambert
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Endocrinology and Nephrology Division , Quebec City, Québec G1V 4G2, Canada
| | - Paul Toren
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - Rachid Mazroui
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - Samer M I Hussein
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
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7
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Xin S, Sun X, Jin L, Li W, Liu X, Zhou L, Ye L. The Prognostic Signature and Therapeutic Value of Phagocytic Regulatory Factors in Prostate Adenocarcinoma (PRAD). Front Genet 2022; 13:877278. [PMID: 35706452 PMCID: PMC9190300 DOI: 10.3389/fgene.2022.877278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/19/2022] [Indexed: 01/03/2023] Open
Abstract
There is growing evidence that phagocytosis regulatory factors (PRFs) play important roles in tumor progression, and therefore, identifying and characterizing these factors is crucial for understanding the mechanisms of cellular phagocytosis in tumorigenesis. Our research aimed to comprehensively characterize PRFs in prostate adenocarcinoma (PRAD) and to screen and determine important PRFs in PRAD which may help to inform tumor prognostic and therapeutic signatures based on these key PRFs. Here, we first systematically described the expression of PRFs in PRAD and evaluated their expression patterns and their prognostic value. We then analyzed prognostic phagocytic factors by Cox and Lasso analysis and constructed a phagocytic factor-mediated risk score. We then divided the samples into two groups with significant differences in overall survival (OS) based on the risk score. Then, we performed correlation analysis between the risk score and clinical features, immune infiltration levels, immune characteristics, immune checkpoint expression, IC50 of several classical sensitive drugs, and immunotherapy efficacy. Finally, the Human Protein Atlas (HPA) database was used to determine the protein expression of 18 PRF characteristic genes. The aforementioned results confirmed that multilayer alterations of PRFs were associated with the prognosis of patients with PRAD and the degree of macrophage infiltration. These findings may provide us with potential new therapies for PRAD.
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Affiliation(s)
- Shiyong Xin
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xianchao Sun
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Liang Jin
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Weiyi Li
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiang Liu
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Liqing Zhou
- Department of Rheumatology and Immunology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Lin Ye
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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8
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Söderdahl F, Xu LD, Bring J, Häggman M. A Novel Risk Score (P-score) Based on a Three-Gene Signature, for Estimating the Risk of Prostate Cancer-Specific Mortality. Res Rep Urol 2022; 14:203-217. [PMID: 35586706 PMCID: PMC9109804 DOI: 10.2147/rru.s358169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/30/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose To develop and validate a risk score (P-score) algorithm which includes previously described three-gene signature and clinicopathological parameters to predict the risk of death from prostate cancer (PCa) in a retrospective cohort. Patients and Methods A total of 591 PCa patients diagnosed between 2003 and 2008 in Stockholm, Sweden, with a median clinical follow-up time of 7.6 years (1–11 years) were included in this study. Expression of a three-gene signature (IGFBP3, F3, VGLL3) was measured in formalin-fixed paraffin-embedded material from diagnostic core needle biopsies (CNB) of these patients. A point-based scoring system based on a Fine-Gray competing risk model was used to establish the P-score based on the three-gene signature combined with PSA value, Gleason score and tumor stage at diagnosis. The endpoint was PCa-specific mortality, while other causes of death were treated as a competing risk. Out of the 591 patients, 315 patients (estimation cohort) were selected to develop the P-score. The P-score was subsequently validated in an independent validation cohort of 276 patients. Results The P-score was established ranging from the integers 0 to 15. Each one-unit increase was associated with a hazard ratio of 1.39 (95% confidence interval: 1.27–1.51, p < 0.001). The P-score was validated and performed better in predicting PCa-specific mortality than both D’Amico (0.76 vs 0.70) and NCCN (0.76 vs 0.71) by using the concordance index for competing risk. Similar improvement patterns are shown by time-dependent area under the curve. As demonstrated by cumulative incidence function, both P-score and gene signature stratified PCa patients into significantly different risk groups. Conclusion We developed the P-score, a risk stratification system for newly diagnosed PCa patients by integrating a three-gene signature measured in CNB tissue. The P-score could provide valuable decision support to distinguish PCa patients with favorable and unfavorable outcomes and hence improve treatment decisions.
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Affiliation(s)
| | - Li-Di Xu
- Prostatype Genomics AB, Stockholm, Sweden
| | | | - Michael Häggman
- Department of Urology, Uppsala University Hospital, Uppsala, Sweden
- Correspondence: Michael Häggman, Department of Urology, Uppsala University Hospital, SE-751 85 Uppsala University Hospital, Uppsala, Sweden, Tel +46 70 520 42 87, Email
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Feng X, Zhang T, Chou J, Liu L, Miller LD, Sullivan CA, Browne JD. Comprehensive gene cluster analysis of head and neck squamous cell carcinoma TCGA RNA-seq data defines B cell immunity-related genes as a robust survival predictor. Head Neck 2022; 44:443-452. [PMID: 34841601 PMCID: PMC8766919 DOI: 10.1002/hed.26944] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/14/2021] [Accepted: 11/18/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The authors aimed to define novel gene expression signatures that are associated with patients' survival with head and neck squamous cell carcinoma (HNSCC). METHODS TCGA RNA-seq data were used for gene expression clusters extraction from 499 tumor samples by the "EPIG" method. Tumor samples were then partitioned into lower and higher than median level groups for survival relevant analysis by Kaplan-Meier estimator. RESULTS We found that two gene clusters (_1, _2) are favorably, while two (_3, _4) are unfavorably, associated with patients' survival with HNSCC. Notably, most genes on the top lists of cluster_2 are associated with B cells. A gene expression signature with combined genes from cluster_2 and _4 was further determined to be associated with HNSCC survival rate. CONCLUSION Our work strongly supported a favorable role of B cells in patients' survival with HNSCC and identified a novel coexpressed gene signature as prognostic biomarker for patients' survival with HNSCC estimation.
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Affiliation(s)
- Xin Feng
- Departments of Otolaryngology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Tan Zhang
- Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jeff Chou
- Center for Cancer Genomics and Precision Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Liang Liu
- Center for Cancer Genomics and Precision Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Lance D. Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Christopher A. Sullivan
- Departments of Otolaryngology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - James D. Browne
- Departments of Otolaryngology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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Buskin A, Singh P, Lorenz O, Robson C, Strand DW, Heer R. A Review of Prostate Organogenesis and a Role for iPSC-Derived Prostate Organoids to Study Prostate Development and Disease. Int J Mol Sci 2021; 22:ijms222313097. [PMID: 34884905 PMCID: PMC8658468 DOI: 10.3390/ijms222313097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/23/2021] [Accepted: 11/29/2021] [Indexed: 01/09/2023] Open
Abstract
The prostate is vulnerable to two major age-associated diseases, cancer and benign enlargement, which account for significant morbidity and mortality for men across the globe. Prostate cancer is the most common cancer reported in men, with over 1.2 million new cases diagnosed and 350,000 deaths recorded annually worldwide. Benign prostatic hyperplasia (BPH), characterised by the continuous enlargement of the adult prostate, symptomatically afflicts around 50% of men worldwide. A better understanding of the biological processes underpinning these diseases is needed to generate new treatment approaches. Developmental studies of the prostate have shed some light on the processes essential for prostate organogenesis, with many of these up- or downregulated genes expressions also observed in prostate cancer and/or BPH progression. These insights into human disease have been inferred through comparative biological studies relying primarily on rodent models. However, directly observing mechanisms of human prostate development has been more challenging due to limitations in accessing human foetal material. Induced pluripotent stem cells (iPSCs) could provide a suitable alternative as they can mimic embryonic cells, and iPSC-derived prostate organoids present a significant opportunity to study early human prostate developmental processes. In this review, we discuss the current understanding of prostate development and its relevance to prostate-associated diseases. Additionally, we detail the potential of iPSC-derived prostate organoids for studying human prostate development and disease.
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Affiliation(s)
- Adriana Buskin
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Paul O’Gorman Building, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (P.S.); (C.R.)
- Correspondence: (A.B.); (R.H.)
| | - Parmveer Singh
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Paul O’Gorman Building, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (P.S.); (C.R.)
| | - Oliver Lorenz
- Newcastle University School of Computing, Digital Institute, Urban Sciences Building, Newcastle University, Newcastle upon Tyne NE4 5TG, UK;
| | - Craig Robson
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Paul O’Gorman Building, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (P.S.); (C.R.)
| | - Douglas W. Strand
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Rakesh Heer
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Paul O’Gorman Building, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (P.S.); (C.R.)
- Department of Urology, Freeman Hospital, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
- Correspondence: (A.B.); (R.H.)
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11
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Lutz CT, Livas L, Presnell SR, Sexton M, Wang P. Gender Differences in Urothelial Bladder Cancer: Effects of Natural Killer Lymphocyte Immunity. J Clin Med 2021; 10:jcm10215163. [PMID: 34768683 PMCID: PMC8584838 DOI: 10.3390/jcm10215163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/13/2021] [Accepted: 10/29/2021] [Indexed: 02/07/2023] Open
Abstract
Men are more likely to develop cancer than women. In fact, male predominance is one of the most consistent cancer epidemiology findings. Additionally, men have a poorer prognosis and an increased risk of secondary malignancies compared to women. These differences have been investigated in order to better understand cancer and to better treat both men and women. In this review, we discuss factors that may cause this gender difference, focusing on urothelial bladder cancer (UBC) pathogenesis. We consider physiological factors that may cause higher male cancer rates, including differences in X chromosome gene expression. We discuss how androgens may promote bladder cancer development directly by stimulating bladder urothelium and indirectly by suppressing immunity. We are particularly interested in the role of natural killer (NK) cells in anti-cancer immunity.
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Affiliation(s)
- Charles T. Lutz
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY 40536, USA; (L.L.); (S.R.P.); (M.S.)
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY 40536, USA
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA;
- Correspondence:
| | - Lydia Livas
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY 40536, USA; (L.L.); (S.R.P.); (M.S.)
| | - Steven R. Presnell
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY 40536, USA; (L.L.); (S.R.P.); (M.S.)
| | - Morgan Sexton
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY 40536, USA; (L.L.); (S.R.P.); (M.S.)
| | - Peng Wang
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA;
- Department of Internal Medicine, University of Kentucky, Lexington, KY 40536, USA
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12
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Ntala C, Salji M, Salmond J, Officer L, Teodosio AV, Blomme A, McGhee EJ, Powley I, Ahmad I, Kruithof-de Julio M, Thalmann G, Roberts E, Goodyear CS, Jamaspishvili T, Berman DM, Carlin LM, Le Quesne J, Leung HY. Analysis of Prostate Cancer Tumor Microenvironment Identifies Reduced Stromal CD4 Effector T-cell Infiltration in Tumors with Pelvic Nodal Metastasis. EUR UROL SUPPL 2021; 29:19-29. [PMID: 34337530 PMCID: PMC8317840 DOI: 10.1016/j.euros.2021.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Pelvic nodal metastasis in prostate cancer impacts patient outcome negatively. OBJECTIVE To explore tumor-infiltrating immune cells as a potential predictive tool for regional lymph node (LN) metastasis. DESIGN SETTING AND PARTICIPANTS We applied multiplex immunofluorescence and targeted transcriptomic analysis on 94 radical prostatectomy specimens in patients with (LN+) or without (LN-) pelvic nodal metastases. Both intraepithelial and stromal infiltrations of immune cells and differentially expressed genes (mRNA and protein levels) were correlated with the nodal status. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The identified CD4 effector cell signature of nodal metastasis was validated in a comparable independent patient cohort of 184 informative cases. Patient outcome analysis and decision curve analysis were performed with the CD4 effector cell density-based signature. RESULTS AND LIMITATIONS In the discovery cohort, both tumor epithelium and stroma from patients with nodal metastasis had significantly lower infiltration of multiple immune cell types, with stromal CD4 effector cells highlighted as the top candidate marker. Targeted gene expression analysis and confirmatory protein analysis revealed key alteration of extracellular matrix components in tumors with nodal metastasis. Of note, stromal CD4 immune cell density was a significant independent predictor of LN metastasis (odds ratio [OR] = 0.15, p = 0.004), and was further validated as a significant predictor of nodal metastasis in the validation cohort (OR = 0.26, p < 0.001). CONCLUSIONS Decreased T-cell infiltrates in the primary tumor (particularly CD4 effector cells) are associated with a higher risk of LN metastasis. Future evaluation of CD4-based assays on prostate cancer diagnostic biopsy materials may improve selection of at-risk patients for the treatment of LN metastasis. PATIENT SUMMARY In this report, we found that cancer showing evidence of cancer metastasis to the lymph nodes tends to have less immune cells present within the tumor. We conclude that the extent of immune cells present within a prostate tumor can help doctors determine the most appropriate treatment plan for individual patients.
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Affiliation(s)
- Chara Ntala
- CRUK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, UK
| | - Mark Salji
- CRUK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, UK
| | - Jonathan Salmond
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, UK
| | - Leah Officer
- CRUK Beatson Institute, Glasgow, UK
- Medical Research Council Toxicology Unit, University of Cambridge, Leicester, UK
| | - Ana Vieira Teodosio
- Medical Research Council Toxicology Unit, University of Cambridge, Leicester, UK
| | | | | | - Ian Powley
- CRUK Beatson Institute, Glasgow, UK
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Imran Ahmad
- CRUK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, UK
| | | | - George Thalmann
- Department of Urology, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Carl S. Goodyear
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Tamara Jamaspishvili
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
| | - David M. Berman
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
| | - Leo M. Carlin
- CRUK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, UK
| | - John Le Quesne
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, UK
- Medical Research Council Toxicology Unit, University of Cambridge, Leicester, UK
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Hing Y. Leung
- CRUK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, UK
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13
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Schäfer C, Ju Y, Tak Y, Vazquez C, Han SJ, Tan E, Shay JW, Holmqvist M, Danuser G, Schopperle WM, Bubley G. TRA-1-60-positive/CD45 low cells found in the peripheral blood of prostate cancer patients with metastatic disease - A proof-of-concept study. Heliyon 2020; 6:e03263. [PMID: 32021935 PMCID: PMC6994489 DOI: 10.1016/j.heliyon.2020.e03263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 02/04/2019] [Accepted: 01/15/2020] [Indexed: 11/18/2022] Open
Abstract
Purpose Over 90% of all cancer related deaths are due to metastasis. However, current diagnostic tools can't reliably discriminate between invasive and localized cancers. Patients and methods In this proof-of-concept study, we employed the embryonic stem cell marker TRA-1-60 (TRA+) to identify TRA + cells within the blood of prostate cancer patients and searched for TRA + cells in men with metastatic and localized cancers. We isolated whole peripheral blood mononuclear cells from 26 metastatic prostate cancer patients, from 13 patients with localized prostate cancer and from 17 healthy controls. Cells were stained for DAPI, CD45 and TRA + by immunofluorescence and imaged by epi-fluorescence microscopy. Imaged-based software was used both to identify TRA + cells, and to analyze CD45 levels in TRA+ and negative cells. Results We found high numbers of TRA + cells within the blood of metastatic cancer patients, whereas healthy individuals or men with localized prostate cancer showed none or very low numbers of TRA + cells. Further analysis of the CD45 levels of TRA + cells revealed a small population of TRA + cells with almost undetectable CD45 levels that were found frequently in metastatic prostate cancer patients. By excluding CD45 positive cells from the TRA + cell pool, we were able to refine the assay to be highly specific in identifying men with metastatic disease. In fact, the difference of CD45 levels between TRA+ and negative cells was a robust measure to distinguish between men with localized and metastatic prostate cancers in this small patient cohort. Conclusions The data suggest that metastatic prostate cancer patient have significant numbers of TRA+/CD45low cells which might represent a potential tool for diagnostic assessment in the future.
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Affiliation(s)
- Claudia Schäfer
- Department of Cell Biology, University of Texas, Southwestern Medical Center, Dallas, TX, USA
- Corresponding author.
| | | | | | - Cesar Vazquez
- Genitourinary Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Sangyoon J. Han
- Department of Cell Biology, University of Texas, Southwestern Medical Center, Dallas, TX, USA
- College of Engineering, Michigan Tech University, Houghton, MI, USA
| | | | - Jerry W. Shay
- Department of Cell Biology, University of Texas, Southwestern Medical Center, Dallas, TX, USA
| | | | - Gaudenz Danuser
- Department of Cell Biology, University of Texas, Southwestern Medical Center, Dallas, TX, USA
| | | | - Glenn Bubley
- Genitourinary Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
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A Novel Gene Signature-Based Model Predicts Biochemical Recurrence-Free Survival in Prostate Cancer Patients after Radical Prostatectomy. Cancers (Basel) 2019; 12:cancers12010001. [PMID: 31861273 PMCID: PMC7017310 DOI: 10.3390/cancers12010001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/11/2019] [Accepted: 12/14/2019] [Indexed: 12/24/2022] Open
Abstract
Abstract: Currently, decision-making regarding biochemical recurrence (BCR) following prostatectomy relies solely on clinical parameters. We therefore attempted to develop an integrated prediction model based on a molecular signature and clinicopathological features, in order to forecast the risk for BCR and guide clinical decision-making for postoperative therapy. Using high-throughput screening and least absolute shrinkage and selection operator (LASSO) in the training set, a novel gene signature for biochemical recurrence-free survival (BCRFS) was established. Validation of the prognostic value was performed in five other independent datasets, including our patient cohort. Multivariate Cox regression analysis was performed to evaluate the importance of risk for BCR. Time-dependent receiver operating characteristic (tROC) was used to evaluate the predictive power. In combination with relevant clinicopathological features, a decision tree was built to improve the risk stratification. The gene signature exhibited a strong capacity for identifying high-risk BCR patients, and multivariate Cox regression analysis demonstrated that the gene signature consistently acted as a risk factor for BCR. The decision tree was successfully able to identify the high-risk subgroup. Overall, the gene signature established in the present study is a powerful predictor and risk factor for BCR after radical prostatectomy.
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15
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Thiemeyer H, Taher L, Schille JT, Harder L, Hungerbuehler SO, Mischke R, Hewicker-Trautwein M, Kiełbowicz Z, Brenig B, Schütz E, Beck J, Murua Escobar H, Nolte I. Suitability of ultrasound-guided fine-needle aspiration biopsy for transcriptome sequencing of the canine prostate. Sci Rep 2019; 9:13216. [PMID: 31519932 PMCID: PMC6744464 DOI: 10.1038/s41598-019-49271-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 08/15/2019] [Indexed: 02/06/2023] Open
Abstract
Ultrasound-guided fine-needle aspiration (US-FNA) biopsy is a widely used minimally invasive sampling procedure for cytological diagnosis. This study investigates the feasibility of using US-FNA samples for both cytological diagnosis and whole transcriptome RNA-sequencing analysis (RNA-Seq), with the ultimate aim of improving canine prostate cancer management. The feasibility of the US-FNA procedure was evaluated intra vitam on 43 dogs. Additionally, aspirates from 31 euthanised dogs were collected for standardising the procedure. Each aspirate was separated into two subsamples: for cytology and RNA extraction. Additional prostate tissue samples served as control for RNA quantity and quality evaluation, and differential expression analysis. The US-FNA sampling procedure was feasible in 95% of dogs. RNA isolation of US-FNA samples was successfully performed using phenol-chloroform extraction. The extracted RNA of 56% of a subset of US-FNA samples met the quality requirements for RNA-Seq. Expression analysis revealed that only 153 genes were exclusively differentially expressed between non-malignant US-FNAs and tissues. Moreover, only 36 differentially expressed genes were associated with the US-FNA sampling technique and unrelated to the diagnosis. Furthermore, the gene expression profiles clearly distinguished between non-malignant and malignant samples. This proves US-FNA to be useful for molecular profiling.
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Affiliation(s)
- H Thiemeyer
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Department of Haematology/Oncology/Palliative Care, Rostock University Medical Centre, Rostock, Germany
| | - L Taher
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - J T Schille
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Department of Haematology/Oncology/Palliative Care, Rostock University Medical Centre, Rostock, Germany
| | - L Harder
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - S O Hungerbuehler
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - R Mischke
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - M Hewicker-Trautwein
- Institute of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Z Kiełbowicz
- Department and Clinic of Veterinary Surgery, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - B Brenig
- University of Göttingen, Institute of Veterinary Medicine, Göttingen, Germany
| | - E Schütz
- Chronix Biomedical, Göttingen, Germany
| | - J Beck
- Chronix Biomedical, Göttingen, Germany
| | - H Murua Escobar
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Department of Haematology/Oncology/Palliative Care, Rostock University Medical Centre, Rostock, Germany
| | - I Nolte
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany.
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Hernández G, Ramírez JL, Pedroza-Torres A, Herrera LA, Jiménez-Ríos MA. The Secret Life of Translation Initiation in Prostate Cancer. Front Genet 2019; 10:14. [PMID: 30761182 PMCID: PMC6363655 DOI: 10.3389/fgene.2019.00014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 01/11/2019] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer (PCa) is the second most prevalent cancer in men worldwide. Despite the advances understanding the molecular processes driving the onset and progression of this disease, as well as the continued implementation of screening programs, PCa still remains a significant cause of morbidity and mortality, in particular in low-income countries. It is only recently that defects of the translation process, i.e., the synthesis of proteins by the ribosome using a messenger (m)RNA as a template, have begun to gain attention as an important cause of cancer development in different human tissues, including prostate. In particular, the initiation step of translation has been established to play a key role in tumorigenesis. In this review, we discuss the state-of-the-art of three key aspects of protein synthesis in PCa, namely, misexpression of translation initiation factors, dysregulation of the major signaling cascades regulating translation, and the therapeutic strategies based on pharmacological compounds targeting translation as a novel alternative to those based on hormones controlling the androgen receptor pathway.
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Affiliation(s)
- Greco Hernández
- Translation and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer, Mexico City, Mexico
| | - Jorge L Ramírez
- Translation and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer, Mexico City, Mexico
| | - Abraham Pedroza-Torres
- Cátedra-CONACyT Program, Hereditary Cancer Clinic, National Institute of Cancer, Mexico City, Mexico
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, The National Autonomous University of Mexico, Mexico City, Mexico
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17
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Markers of clinical utility in the differential diagnosis and prognosis of prostate cancer. Mod Pathol 2018; 31:S143-155. [PMID: 29297492 DOI: 10.1038/modpathol.2017.168] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 12/13/2022]
Abstract
Molecular diagnostics is a rapidly evolving area of surgical pathology, that is gradually beginning to transform our diagnostical procedures for a variety of tumors. Next to molecular prognostication that has begun to complement our histological diagnosis in breast cancer, additional testing to detect targets and to predict therapy response has become common practice in breast and lung cancer. Prostate cancer is a bit slower in this respect, as it is still largely diagnosed and classified on morphological grounds. Our diagnostic immunohistochemical armamentarium of basal cell markers and positive markers of malignancy now allows to clarify the majority of lesions, if applied to the appropriate morphological context (and step sections). Prognostic immunohistochemistry remains a problematic and erratic yet tempting research field that provides information on tumor relevance of proteins, but little hard data to integrate into our diagnostic workflow. Main reasons are various issues of standardization that hamper the reproducibility of cut-off values to delineate risk categories. Molecular testing of DNA-methylation or transcript profiling may be much better standardized and this review discusses a couple of commercially available tests: The ConfirmDX test measures DNA-methylation to estimate the likelihood of cancer detection on a repeat biopsy and may help to reduce unnecessary biopsies. The tests Prolaris, OncotypeDX Prostate, and Decipher all are transcript tests that have shown to provide prognostic data independent of clinico-pathological parameters and that may aid in therapy planning. However, further validation and more comparative studies will be needed to clarify the many open questions concerning sampling bias and tumor heterogeneity.
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18
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Bowlt Blacklock KL, Ireland J, Stewart J, Murphy S, Blackwood L, Starkey M. A preliminary investigation of the effect of sample collection technique on the cell and RNA content of fine-needle aspirates of five canine tumours. J Small Anim Pract 2017; 59:211-221. [PMID: 29193082 DOI: 10.1111/jsap.12790] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 07/12/2017] [Accepted: 10/27/2017] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To evaluate the effect of syringe size, needle size, number of needle passes and operator experience on cell yield from tumour fine-needle aspirates, and the quantity and quality of extractable RNA. MATERIALS AND METHODS Fine-needle aspirates were collected from canine lymphoma, cutaneous mast cell tumour, anal gland adenocarcinoma, fibrosarcoma and oral malignant melanoma using nine different techniques. RESULTS There was a significant difference in cell yield between fine-needle aspirate techniques for melanoma, lymphoma and anal gland adenocarcinoma. The application of suction yielded the largest number of cells. Cell numbers in lymphoma and fibrosarcoma aspirates collected by different veterinary surgeons were not significantly different. Use of a smaller gauge needle and suction increased the quantity of RNA isolated from fibrosarcoma and anal gland adenocarcinoma aspirates, but did not influence RNA integrity. CLINICAL SIGNIFICANCE Suction during fine-needle aspiration increases cell numbers obtained from five common canine tumours. Suction increases the quantity of RNA isolated from anal gland adenocarcinoma and fibrosarcoma aspirates without affecting RNA quality. Junior veterinary surgeons gain comparable cell numbers to senior staff.
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Affiliation(s)
| | - J Ireland
- Department of Epidemiology, Animal Health Trust, Newmarket, Suffolk, CB7 5UU, UK
| | - J Stewart
- Department of Clinical Pathology, Animal Health Trust, Newmarket, Suffolk, CB7 5UU, UK
| | - S Murphy
- Department of Clinical Oncology, Animal Health Trust, Newmarket, Suffolk, CB7 5UU, UK
| | - L Blackwood
- School of Veterinary Science, University of Liverpool, Neston, Cheshire West and Chester, CH64 7TE, UK
| | - M Starkey
- Department of Molecular Oncology, Animal Health Trust, Newmarket, Suffolk, CB7 5UU, UK
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19
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Stefanovski D, Tang G, Wawrowsky K, Boston RC, Lambrecht N, Tajbakhsh J. Prostate cancer diagnosis using epigenetic biomarkers, 3D high-content imaging and probabilistic cell-by-cell classifiers. Oncotarget 2017; 8:57278-57301. [PMID: 28915670 PMCID: PMC5593641 DOI: 10.18632/oncotarget.18985] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 06/02/2017] [Indexed: 11/29/2022] Open
Abstract
Background Prostate cancer (PCa) management can benefit from novel concepts/biomarkers for reducing the current 20-30% chance of false-negative diagnosis with standard histopathology of biopsied tissue. Method We explored the potential of selected epigenetic markers in combination with validated histopathological markers, 3D high-content imaging, cell-by-cell analysis, and probabilistic classification in generating novel detailed maps of biomarker heterogeneity in patient tissues, and PCa diagnosis. We used consecutive biopsies/radical prostatectomies from five patients for building a database of ∼140,000 analyzed cells across all tissue compartments and for model development; and from five patients and the two well-characterized HPrEpiC primary and LNCaP cancer cell types for model validation. Results Principal component analysis presented highest covariability for the four biomarkers 4′,6-diamidino-2-phenylindole, 5-methylcytosine, 5-hydroxymethylcytosine, and alpha-methylacyl-CoA racemase in the epithelial tissue compartment. The panel also showed best performance in discriminating between normal and cancer-like cells in prostate tissues with a sensitivity and specificity of 85%, correctly classified 87% of HPrEpiC as healthy and 99% of LNCaP cells as cancer-like, identified a majority of aberrant cells within histopathologically benign tissues at baseline diagnosis of patients that were later diagnosed with adenocarcinoma. Using k-nearest neighbor classifier with cells from an initial patient biopsy, the biomarkers were able to predict cancer stage and grade of prostatic tissue that occurred at later prostatectomy with 79% accuracy. Conclusion Our approach showed favorable diagnostic values to identify the portion and pathological category of aberrant cells in a small subset of sampled tissue cells, correlating with the degree of malignancy beyond baseline.
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Affiliation(s)
- Darko Stefanovski
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - George Tang
- Translational Cytomics Group, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kolja Wawrowsky
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Raymond C Boston
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nils Lambrecht
- Pathology and Laboratory Medicine Service, Veterans Affairs Medical Center, Long Beach, CA, USA.,Department of Pathology and Laboratory Medicine, University of California Irvine, Orange, CA, USA
| | - Jian Tajbakhsh
- Translational Cytomics Group, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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20
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Chen Z, Gerke T, Bird V, Prosperi M. Trends in Gene Expression Profiling for Prostate Cancer Risk Assessment: A Systematic Review. Biomed Hub 2017; 2:1-15. [PMID: 31988908 PMCID: PMC6945900 DOI: 10.1159/000472146] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/07/2017] [Indexed: 12/12/2022] Open
Abstract
Objectives The aim of the study is to review biotechnology advances in gene expression profiling on prostate cancer (PCa), focusing on experimental platform development and gene discovery, in relation to different study designs and outcomes in order to understand how they can be exploited to improve PCa diagnosis and clinical management. Methods We conducted a systematic literature review on gene expression profiling studies through PubMed/MEDLINE and Web of Science between 2000 and 2016. Tissue biopsy and clinical gene profiling studies with different outcomes (e.g., recurrence, survival) were included. Results Over 3,000 papers were screened and 137 full-text articles were selected. In terms of technology used, microarray is still the most popular technique, increasing from 50 to 70% between 2010 and 2015, but there has been a rise in the number of studies using RNA sequencing (13% in 2015). Sample sizes have increased, as well as the number of genes that can be screened all at once, but we have also observed more focused targeting in more recent studies. Qualitative analysis on the specific genes found associated with PCa risk or clinical outcomes revealed a large variety of gene candidates, with a few consistent cross-studies. Conclusions The last 15 years of research in gene expression in PCa have brought a large volume of data and information that has been decoded only in part, but advancements in high-throughput sequencing technology are increasing the amount of data that can be generated. The variety of findings warrants the execution of both validation studies and meta-analyses. Genetic biomarkers have tremendous potential for early diagnosis of PCa and, if coupled with other diagnostics (e.g., imaging), can effectively be used to concretize less-invasive, personalized prediction of PCa risk and progression.
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Affiliation(s)
- Zhaoyi Chen
- Department of Epidemiology, College of Public Health and Health Professions, College of Medicine, University of Florida, Gainesville, FL, USA
| | | | - Victoria Bird
- Department of Urology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Mattia Prosperi
- Department of Epidemiology, College of Public Health and Health Professions, College of Medicine, University of Florida, Gainesville, FL, USA
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21
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Pimmett VL, Deng H, Haskins JA, Mercier RJ, LaPointe P, Simmonds AJ. The activity of the Drosophila Vestigial protein is modified by Scalloped-dependent phosphorylation. Dev Biol 2017; 425:58-69. [PMID: 28322734 DOI: 10.1016/j.ydbio.2017.03.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 02/01/2017] [Accepted: 03/14/2017] [Indexed: 12/18/2022]
Abstract
The Drosophila vestigial gene is required for proliferation and differentiation of the adult wing and for differentiation of larval and adult muscle identity. Vestigial is part of a multi-protein transcription factor complex, which includes Scalloped, a TEAD-class DNA binding protein. Binding Scalloped is necessary for translocation of Vestigial into the nucleus. We show that Vestigial is extensively post-translationally modified and at least one of these modifications is required for proper function during development. We have shown that there is p38-dependent phosphorylation of Serine 215 in the carboxyl-terminal region of Vestigial. Phosphorylation of Serine 215 occurs in the nucleus and requires the presence of Scalloped. Comparison of a phosphomimetic and non-phosphorylatable mutant forms of Vestigial shows differences in the ability to rescue the wing and muscle phenotypes associated with a null vestigial allele.
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Affiliation(s)
- Virginia L Pimmett
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7
| | - Hua Deng
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7; Howard Hughes Medical Institute, Dept. of Physiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Julie A Haskins
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7
| | - Rebecca J Mercier
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7
| | - Paul LaPointe
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G2H7
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22
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Liu Y. The context of prostate cancer genomics in personalized medicine. Oncol Lett 2017; 13:3347-3353. [PMID: 28521441 DOI: 10.3892/ol.2017.5911] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/26/2017] [Indexed: 12/31/2022] Open
Abstract
Prostate cancer is one of the most common types of cancer in males. Heterogeneous genomic aberrations may lead to prostate cancer onset, progression and metastasis. This heterogeneity also contributes to the variety in cancer risk and outcomes, different drug responses and progression, observed between individual patients. Classical prognostic factors, including prostate-specific antigen, Gleason Score and clinical tumor staging, are not sufficient to portray the complexity of a clinically relevant cancer diagnosis, risk prognosis, treatment choice and therapy monitoring. There is a requirement for novel genetic biomarkers in order to understand the oncogenic heterogeneity in a patient-personalized clinical setting and to improve the efficacy of risk prognosis and treatment choice. A number of biomarkers and gene panels have been established from patient sample cohort studies. These previous studies have provided distinct information to the investigation of heterogeneous malignancy in prostate cancer, which aids in clinical decision-making. Biomarker-guided therapies may facilitate the effective selection of drugs during early treatment; therefore, are beneficial to the individual patient. A non-invasive approach allows for convenient and repeated sampling to screen for cancer and monitor treatment response without the requirement for invasive tissue biopsies. With the current availability of numerous advanced technologies, reliable detection of the minimal tumor residues present following treatment may become clinical practice and, therefore, inform further in the field of personalized medicine.
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Affiliation(s)
- Yanling Liu
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm SE-171 76, Sweden
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23
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Hu BR, Fairey AS, Madhav A, Yang D, Li M, Groshen S, Stephens C, Kim PH, Virk N, Wang L, Martin SE, Erho N, Davicioni E, Jenkins RB, Den RB, Xu T, Xu Y, Gill IS, Quinn DI, Goldkorn A. AXIN2 expression predicts prostate cancer recurrence and regulates invasion and tumor growth. Prostate 2016; 76:597-608. [PMID: 26771938 PMCID: PMC7455032 DOI: 10.1002/pros.23151] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 12/31/2015] [Indexed: 01/16/2023]
Abstract
BACKGROUND Treatment of prostate cancer (PCa) may be improved by identifying biological mechanisms of tumor growth that directly impact clinical disease progression. We investigated whether genes associated with a highly tumorigenic, drug resistant, progenitor phenotype impact PCa biology and recurrence. METHODS Radical prostatectomy (RP) specimens (±disease recurrence, N = 276) were analyzed by qRT-PCR to quantify expression of genes associated with self-renewal, drug resistance, and tumorigenicity in prior studies. Associations between gene expression and PCa recurrence were confirmed by bootstrap internal validation and by external validation in independent cohorts (total N = 675) and in silico. siRNA knockdown and lentiviral overexpression were used to determine the effect of gene expression on PCa invasion, proliferation, and tumor growth. RESULTS Four candidate genes were differentially expressed in PCa recurrence. Of these, low AXIN2 expression was internally validated in the discovery cohort. Validation in external cohorts and in silico demonstrated that low AXIN2 was independently associated with more aggressive PCa, biochemical recurrence, and metastasis-free survival after RP. Functionally, siRNA-mediated depletion of AXIN2 significantly increased invasiveness, proliferation, and tumor growth. Conversely, ectopic overexpression of AXIN2 significantly reduced invasiveness, proliferation, and tumor growth. CONCLUSIONS Low AXIN2 expression was associated with PCa recurrence after RP in our test population as well as in external validation cohorts, and its expression levels in PCa cells significantly impacted invasiveness, proliferation, and tumor growth. Given these novel roles, further study of AXIN2 in PCa may yield promising new predictive and therapeutic strategies.
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Affiliation(s)
- Brian R. Hu
- USC Institute of Urology, Keck Medical Center of USC and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Adrian S. Fairey
- USC Institute of Urology, Keck Medical Center of USC and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Anisha Madhav
- Division of Medical Oncology, Department of Medicine, University of Southern California Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, Los Angeles, California
| | - Dongyun Yang
- Department of Preventive Medicine, Keck Medical Center of USC, University of Southern California, Los Angeles, California
| | - Meng Li
- Health Sciences Bioinformatics Core, USC Keck School of Medicine, Los Angeles, California
| | - Susan Groshen
- Department of Preventive Medicine, Keck Medical Center of USC, University of Southern California, Los Angeles, California
| | | | - Philip H. Kim
- USC Institute of Urology, Keck Medical Center of USC and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Navneet Virk
- Division of Medical Oncology, Department of Medicine, University of Southern California Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, Los Angeles, California
| | - Lina Wang
- Department of Pathology, Keck Medical Center of USC, University of Southern California, Los Angeles, California
| | - Sue Ellen Martin
- Department of Pathology, Keck Medical Center of USC, University of Southern California, Los Angeles, California
| | | | | | - Robert B. Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Robert B. Den
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Tong Xu
- Division of Medical Oncology, Department of Medicine, University of Southern California Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, Los Angeles, California
| | - Yucheng Xu
- Division of Medical Oncology, Department of Medicine, University of Southern California Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, Los Angeles, California
| | - Inderbir S. Gill
- USC Institute of Urology, Keck Medical Center of USC and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - David I. Quinn
- Division of Medical Oncology, Department of Medicine, University of Southern California Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, Los Angeles, California
| | - Amir Goldkorn
- Division of Medical Oncology, Department of Medicine, University of Southern California Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, Los Angeles, California
- Correspondence to: Amir Goldkorn, MD, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, 1441 Eastlake Avenue, Suite 3440, Los Angeles, CA 90033.
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24
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From vestigial to vestigial-like: the Drosophila gene that has taken wing. Dev Genes Evol 2016; 226:297-315. [DOI: 10.1007/s00427-016-0546-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/10/2016] [Indexed: 12/16/2022]
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25
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Peng Z, Andersson K, Lindholm J, Dethlefsen O, Pramana S, Pawitan Y, Nistér M, Nilsson S, Li C. Improving the Prediction of Prostate Cancer Overall Survival by Supplementing Readily Available Clinical Data with Gene Expression Levels of IGFBP3 and F3 in Formalin-Fixed Paraffin Embedded Core Needle Biopsy Material. PLoS One 2016; 11:e0145545. [PMID: 26731648 PMCID: PMC4701463 DOI: 10.1371/journal.pone.0145545] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 12/04/2015] [Indexed: 11/28/2022] Open
Abstract
Background A previously reported expression signature of three genes (IGFBP3, F3 and VGLL3) was shown to have potential prognostic value in estimating overall and cancer-specific survivals at diagnosis of prostate cancer in a pilot cohort study using freshly frozen Fine Needle Aspiration (FNA) samples. Methods We carried out a new cohort study with 241 prostate cancer patients diagnosed from 2004–2007 with a follow-up exceeding 6 years in order to verify the prognostic value of gene expression signature in formalin fixed paraffin embedded (FFPE) prostate core needle biopsy tissue samples. The cohort consisted of four patient groups with different survival times and death causes. A four multiplex one-step RT-qPCR test kit, designed and optimized for measuring the expression signature in FFPE core needle biopsy samples, was used. In archive FFPE biopsy samples the expression differences of two genes (IGFBP3 and F3) were measured. The survival time predictions using the current clinical parameters only, such as age at diagnosis, Gleason score, PSA value and tumor stage, and clinical parameters supplemented with the expression levels of IGFBP3 and F3, were compared. Results When combined with currently used clinical parameters, the gene expression levels of IGFBP3 and F3 are improving the prediction of survival time as compared to using clinical parameters alone. Conclusion The assessment of IGFBP3 and F3 gene expression levels in FFPE prostate cancer tissue would provide an improved survival prediction for prostate cancer patients at the time of diagnosis.
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Affiliation(s)
- Zhuochun Peng
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Chundsell Medicals AB, Stockholm, Sweden
| | - Karl Andersson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Ridgeview Instruments AB, Uppsala, Sweden
| | - Johan Lindholm
- Clinical Pathology/Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Olga Dethlefsen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Setia Pramana
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology/Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Sten Nilsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Chunde Li
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Oncology, Karolinska University Hospital, Stockholm, Sweden
- Chundsell Medicals AB, Stockholm, Sweden
- * E-mail:
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26
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Abstract
The cancer stem cell model in solid tumors has evolved significantly from the early paradigm shifting work highlighting parallels between the stem cell hierarchy in hematologic malignancies and solid tumors. Putative stem cells can dedifferentiated, be induced by context, and be the result of accumulated genetic mutations. The simple hypothesis that stem cell therapies will overcome the minority of cells that lead to recurrence has evolved with it. Nevertheless, the body of evidence that this field is clinically relevant in patients and patient care has grown with the complexity of the hypotheses, and numerous clinical strategies to target these cells have been identified. Herein we review this progress and highlight the work still outstanding.
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Affiliation(s)
- Wendy A Woodward
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Richard P Hill
- Princess Margaret Cancer Centre, Ontario Cancer Insitute, Toronto, ON, M5G 2M9, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
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27
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Pellegrini KL, Sanda MG, Moreno CS. RNA biomarkers to facilitate the identification of aggressive prostate cancer. Mol Aspects Med 2015; 45:37-46. [PMID: 26022941 PMCID: PMC4637232 DOI: 10.1016/j.mam.2015.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/20/2015] [Indexed: 02/07/2023]
Abstract
A large number of men are diagnosed with prostate cancer each year, but many will not experience morbidity or mortality as a result of their cancers. Therefore, biomarkers for prostate cancer are necessary to carefully select patients for initial diagnostic biopsy or to facilitate care decisions for men who have already been diagnosed with prostate cancer. RNA-based approaches to biomarker discovery allow the investigation of non-coding RNAs, gene fusion transcripts, splice variants, and multi-gene expression panels in tissue, urine, or blood as opportunities to improve care decisions. This review focuses on RNA biomarkers that are available as commercial assays, and therefore already available for potential clinical use, as well as providing an overview of newer RNA biomarkers that are in earlier stages of clinical development.
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Affiliation(s)
- Kathryn L Pellegrini
- Department of Urology, Emory University School of Medicine, Winship Cancer Institute at Emory University, Atlanta, GA 30322, USA
| | - Martin G Sanda
- Department of Urology, Emory University School of Medicine, Winship Cancer Institute at Emory University, Atlanta, GA 30322, USA
| | - Carlos S Moreno
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Winship Cancer Institute at Emory University, Atlanta, GA 30322, USA.
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28
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Martinez-Ledesma E, Verhaak RGW, Treviño V. Identification of a multi-cancer gene expression biomarker for cancer clinical outcomes using a network-based algorithm. Sci Rep 2015. [PMID: 26202601 PMCID: PMC5378879 DOI: 10.1038/srep11966] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cancer types are commonly classified by histopathology and more recently through molecular characteristics such as gene expression, mutations, copy number variations, and epigenetic alterations. These molecular characterizations have led to the proposal of prognostic biomarkers for many cancer types. Nevertheless, most of these biomarkers have been proposed for a specific cancer type or even specific subtypes. Although more challenging, it is useful to identify biomarkers that can be applied for multiple types of cancer. Here, we have used a network-based exploration approach to identify a multi-cancer gene expression biomarker highly connected by ESR1, PRKACA, LRP1, JUN and SMAD2 that can be predictive of clinical outcome in 12 types of cancer from The Cancer Genome Atlas (TCGA) repository. The gene signature of this biomarker is highly supported by cancer literature, biological terms, and prognostic power in other cancer types. Additionally, the signature does not seem to be highly associated with specific mutations or copy number alterations. Comparisons with cancer-type specific and other multi-cancer biomarkers in TCGA and other datasets showed that the performance of the proposed multi-cancer biomarker is superior, making the proposed approach and multi-cancer biomarker potentially useful in research and clinical settings.
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Affiliation(s)
- Emmanuel Martinez-Ledesma
- 1] Grupo de Enfoque e Investigación en Bioinformática, Departamento de Investigación e Innovación, Escuela Nacional de Medicina, Tecnológico de Monterrey, Monterrey, Nuevo León 64849, México [2] Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Roeland G W Verhaak
- 1] Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA [2] Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Victor Treviño
- Grupo de Enfoque e Investigación en Bioinformática, Departamento de Investigación e Innovación, Escuela Nacional de Medicina, Tecnológico de Monterrey, Monterrey, Nuevo León 64849, México
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29
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Peng Z, Andersson K, Lindholm J, Bodin I, Pramana S, Pawitan Y, Nistér M, Nilsson S, Li C. Operator dependent choice of prostate cancer biopsy has limited impact on a gene signature analysis for the highly expressed genes IGFBP3 and F3 in prostate cancer epithelial cells. PLoS One 2014; 9:e109610. [PMID: 25296164 PMCID: PMC4190108 DOI: 10.1371/journal.pone.0109610] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/01/2014] [Indexed: 11/20/2022] Open
Abstract
Background Predicting the prognosis of prostate cancer disease through gene expression analysis is receiving increasing interest. In many cases, such analyses are based on formalin-fixed, paraffin embedded (FFPE) core needle biopsy material on which Gleason grading for diagnosis has been conducted. Since each patient typically has multiple biopsy samples, and since Gleason grading is an operator dependent procedure known to be difficult, the impact of the operator's choice of biopsy was evaluated. Methods Multiple biopsy samples from 43 patients were evaluated using a previously reported gene signature of IGFBP3, F3 and VGLL3 with potential prognostic value in estimating overall survival at diagnosis of prostate cancer. A four multiplex one-step qRT-PCR test kit, designed and optimized for measuring the signature in FFPE core needle biopsy samples was used. Concordance of gene expression levels between primary and secondary Gleason tumor patterns, as well as benign tissue specimens, was analyzed. Results The gene expression levels of IGFBP3 and F3 in prostate cancer epithelial cell-containing tissue representing the primary and secondary Gleason patterns were high and consistent, while the low expressed VGLL3 showed more variation in its expression levels. Conclusion The assessment of IGFBP3 and F3 gene expression levels in prostate cancer tissue is independent of Gleason patterns, meaning that the impact of operator's choice of biopsy is low.
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Affiliation(s)
- Zhuochun Peng
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Chundsell Medicals AB, Stockholm, Sweden
| | - Karl Andersson
- Department of Oncology, Radiology and Radiation Sciences, Uppsala University, Uppsala, Sweden
- Ridgeview Instruments AB, Uppsala, Sweden
| | - Johan Lindholm
- Clinical Pathology/Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Inger Bodin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Setia Pramana
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Sekolah Tinggi Ilmu Statistik/Institute of Statistics, Jakarta, Indonesia
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology/Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Sten Nilsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Chunde Li
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Oncology, Karolinska University Hospital, Stockholm, Sweden
- Chundsell Medicals AB, Stockholm, Sweden
- * E-mail:
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