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Mehra R, Nallandhighal S, Cotta B, Knuth Z, Su F, Kasputis A, Zhang Y, Wang R, Cao X, Udager AM, Dhanasekaran SM, Cieslik MP, Morgan TM, Salami SS. Discovery and Validation of a 15-Gene Prognostic Signature for Clear Cell Renal Cell Carcinoma. JCO Precis Oncol 2024; 8:e2300565. [PMID: 38810179 DOI: 10.1200/po.23.00565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/11/2024] [Accepted: 03/15/2024] [Indexed: 05/31/2024] Open
Abstract
PURPOSE Develop and validate gene expression-based biomarker associated with recurrent disease to facilitate risk stratification of clear cell renal cell carcinoma (ccRCC). MATERIALS AND METHODS We retrospectively identified 110 patients who underwent radical nephrectomy for ccRCC (discovery cohort). Patients who recurred were matched on the basis of grade/stage to patients without recurrence. Capture whole-transcriptome sequencing was performed on RNA isolated from archival tissue using the Illumina platform. We developed a gene-expression signature to predict recurrence-free survival/disease-free survival (DFS) using a 15-fold lasso and elastic-net regularized linear Cox model. We derived the 31-gene cell cycle progression (mxCCP) score using RNA-seq data for each patient. Kaplan-Meier (KM) curves and multivariable Cox proportional hazard testing were used to validate the independent prognostic impact of the gene-expression signature on DFS, disease-specific survival (DSS), and overall survival (OS) in two validation data sets (combined n = 761). RESULTS After quality control, the discovery cohort comprised 50 patients with recurrence and 41 patients without, with a median follow-up of 26 and 36 months, respectively. We developed a 15-gene (15G) signature, which was independently associated with worse DFS and DSS (DFS: hazard ratio [HR], 11.08 [95% CI, 4.9 to 25.1]; DSS: HR, 9.67 [95% CI, 3.4 to 27.7]) in a multivariable model adjusting for clinicopathologic parameters (including stage, size, grade, and necrosis [SSIGN] score and Memorial Sloan Kettering Cancer Center nomogram) and mxCCP score. The 15G signature was also independently associated with worse DFS and DSS in both validation data sets (Validation A [n = 382], DFS: HR, 2.6 [95% CI, 1.6 to 4.3]; DSS: HR, 3 [95% CI, 1.4 to 6.1] and Validation B (n = 379), DFS: HR, 2.1 [95% CI, 1.2 to 3.6]; OS: HR, 3 [95% CI, 1.6 to 5.7]) adjusting for clinicopathologic variables and mxCCP score. CONCLUSION We developed and validated a novel 15G prognostic signature to improve risk stratification of patients with ccRCC. Pending further validation, this signature has the potential to facilitate optimal treatment allocation.
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Affiliation(s)
- Rohit Mehra
- University of Michigan Rogel Cancer Center, Ann Arbor, MI
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
| | | | | | - Zayne Knuth
- Department of Urology, Michigan Medicine, Ann Arbor, MI
| | - Fengyun Su
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
| | - Amy Kasputis
- Department of Urology, Michigan Medicine, Ann Arbor, MI
| | - Yuping Zhang
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
| | - Rui Wang
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
| | - Xuhong Cao
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI
| | - Aaron M Udager
- University of Michigan Rogel Cancer Center, Ann Arbor, MI
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
| | - Saravana M Dhanasekaran
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
| | - Marcin P Cieslik
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
- Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Todd M Morgan
- University of Michigan Rogel Cancer Center, Ann Arbor, MI
- Department of Urology, Michigan Medicine, Ann Arbor, MI
| | - Simpa S Salami
- University of Michigan Rogel Cancer Center, Ann Arbor, MI
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Urology, Michigan Medicine, Ann Arbor, MI
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Shen T, Song Y, Wang X, Wang H. Characterizing the molecular heterogeneity of clear cell renal cell carcinoma subgroups classified by miRNA expression profile. Front Mol Biosci 2022; 9:967934. [PMID: 36090028 PMCID: PMC9459094 DOI: 10.3389/fmolb.2022.967934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a heterogeneous disease that is associated with poor prognosis. Recent works have revealed the significant roles of miRNA in ccRCC initiation and progression. Comprehensive characterization of ccRCC based on the prognostic miRNAs would contribute to clinicians’ early detection and targeted treatment. Here, we performed unsupervised clustering using TCGA-retrieved prognostic miRNAs expression profiles. Two ccRCC subtypes were identified after assessing principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and consensus heatmaps. We found that the two subtypes are associated with distinct clinical features, overall survivals, and molecular characteristics. C1 cluster enriched patients in relatively early stage and have better prognosis while patients in C2 cluster have poor prognosis with relatively advanced state. Mechanistically, we found the differentially expressed genes (DEGs) between the indicated subgroups dominantly enriched in biological processes related to transmembrane transport activity. In addition, we also revealed a miRNA-centered DEGs regulatory network, which severed as essential regulators in both transmembrane transport activity control and ccRCC progression. Together, our work described the molecular heterogeneity among ccRCC cancers, provided potential targets served as effective biomarkers for ccRCC diagnosis and prognosis, and paved avenues to better understand miRNA-directed regulatory network in ccRCC progression.
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Affiliation(s)
- Tao Shen
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Key Laboratory of Biomedicine in Gene Diseases, Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, China
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
- *Correspondence: Tao Shen, ; Yingdong Song,
| | - Yingdong Song
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China
- *Correspondence: Tao Shen, ; Yingdong Song,
| | - Xiangting Wang
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China
| | - Haiyang Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Key Laboratory of Biomedicine in Gene Diseases, Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, China
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Prognostic and Predictive Factors in Metastatic Renal Cell Carcinoma: Current Perspective and a Look Into the Future. ACTA ACUST UNITED AC 2020; 26:365-375. [PMID: 32947304 DOI: 10.1097/ppo.0000000000000468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Metastatic renal cell carcinoma (mRCC) comprises a highly heterogeneous group of diseases with varied clinical outcomes. As a result, models to estimate prognosis were developed in an attempt to aid patient counseling, treatment selection, and clinical trial design. Contemporary prognostic models have been mostly generated based on clinical factors because of their ease of use. Recent advances in molecular techniques have allowed unprecedented molecular profiling of RCC and the discovery of genomic and proteotranscriptomic factors that may contribute to disease trajectory. With the advent of multiple systemic therapies in mRCC in recent years, predictive biomarkers have become increasingly relevant in treatment selection. In this review, we discuss the existing staging systems and prognostic models in mRCC. We also highlight various promising molecular biomarkers according to the subtypes of RCC and explore their integration into the traditional prognostic models. In addition, we discuss emerging predictive biomarkers in the era of immuno-oncology. Lastly, we explore future directions with a focus on liquid biopsies and composite biomarkers.
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Holdbrook DA, Singh M, Choudhury Y, Kalaw EM, Koh V, Tan HS, Kanesvaran R, Tan PH, Peng JYS, Tan MH, Lee HK. Automated Renal Cancer Grading Using Nuclear Pleomorphic Patterns. JCO Clin Cancer Inform 2019; 2:1-12. [PMID: 30652593 DOI: 10.1200/cci.17.00100] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
PURPOSE Nuclear pleomorphic patterns are essential for Fuhrman grading of clear cell renal cell carcinoma (ccRCC). Manual observation of renal histopathologic slides may lead to subjective and inconsistent assessment between pathologists. An automated, image-based system that classifies ccRCC slides by quantifying nuclear pleomorphic patterns in an objective and consistent interpretable fashion can aid pathologists in histopathologic assessment. METHODS In the current study, histopathologic tissue slides of 59 patients with ccRCC who underwent surgery at Singapore General Hospital were assembled retrospectively. An automated image classification pipeline detects and analyzes prominent nucleoli in ccRCC images to classify them as either low (Fuhrman grade 1 and 2) or high (Fuhrman grade 3 and 4). The pipeline uses machine learning and image pixel intensity-based feature extraction techniques for nuclear analysis. We trained classification systems that concurrently analyze different permutations of multiple prominent nucleoli image patches. RESULTS Given the parameters for feature combination and extraction, we present experimental results across various configurations for the classification of a given ccRCC histopathologic image. We also demonstrate that the image score used by the pipeline, termed fraction value, is correlated ( R = 0.59) with an existing multigene assay-based scoring system that has previously been demonstrated to be a strong indicator of prognosis in patients with ccRCC. CONCLUSION The current method provides an objective and fully automated way by which to process pathologic slides. The correlation study with a multigene assay-based scoring system also allows us to provide quantitative interpretation for already established nuclear pleomorphic patterns in ccRCC. This method can be extended to other cancers whose corresponding grading systems use nuclear pattern information.
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Affiliation(s)
- Daniel Aitor Holdbrook
- Daniel Aitor Holdbrook, Malay Singh, Emarene Mationg Kalaw, and Hwee Kuan Lee, Bioinformatics Institute; Malay Singh and Hwee Kuan Lee, National University of Singapore; Yukti Choudhury and Min-Han Tan, Lucence Diagnostics; Yukti Choudhury and Min-Han Tan, Institute of Bioengineering and Nanotechnology; Valerie Koh, Puay Hoon Tan, and John Yuen Shyi Peng, Singapore General Hospital; Hui Shan Tan, Ravindran Kanesvaran, and Min-Han Tan, National Cancer Center Singapore; and Hwee Kuan Lee, Institute for Infocomm Research, Singapore
| | - Malay Singh
- Daniel Aitor Holdbrook, Malay Singh, Emarene Mationg Kalaw, and Hwee Kuan Lee, Bioinformatics Institute; Malay Singh and Hwee Kuan Lee, National University of Singapore; Yukti Choudhury and Min-Han Tan, Lucence Diagnostics; Yukti Choudhury and Min-Han Tan, Institute of Bioengineering and Nanotechnology; Valerie Koh, Puay Hoon Tan, and John Yuen Shyi Peng, Singapore General Hospital; Hui Shan Tan, Ravindran Kanesvaran, and Min-Han Tan, National Cancer Center Singapore; and Hwee Kuan Lee, Institute for Infocomm Research, Singapore
| | - Yukti Choudhury
- Daniel Aitor Holdbrook, Malay Singh, Emarene Mationg Kalaw, and Hwee Kuan Lee, Bioinformatics Institute; Malay Singh and Hwee Kuan Lee, National University of Singapore; Yukti Choudhury and Min-Han Tan, Lucence Diagnostics; Yukti Choudhury and Min-Han Tan, Institute of Bioengineering and Nanotechnology; Valerie Koh, Puay Hoon Tan, and John Yuen Shyi Peng, Singapore General Hospital; Hui Shan Tan, Ravindran Kanesvaran, and Min-Han Tan, National Cancer Center Singapore; and Hwee Kuan Lee, Institute for Infocomm Research, Singapore
| | - Emarene Mationg Kalaw
- Daniel Aitor Holdbrook, Malay Singh, Emarene Mationg Kalaw, and Hwee Kuan Lee, Bioinformatics Institute; Malay Singh and Hwee Kuan Lee, National University of Singapore; Yukti Choudhury and Min-Han Tan, Lucence Diagnostics; Yukti Choudhury and Min-Han Tan, Institute of Bioengineering and Nanotechnology; Valerie Koh, Puay Hoon Tan, and John Yuen Shyi Peng, Singapore General Hospital; Hui Shan Tan, Ravindran Kanesvaran, and Min-Han Tan, National Cancer Center Singapore; and Hwee Kuan Lee, Institute for Infocomm Research, Singapore
| | - Valerie Koh
- Daniel Aitor Holdbrook, Malay Singh, Emarene Mationg Kalaw, and Hwee Kuan Lee, Bioinformatics Institute; Malay Singh and Hwee Kuan Lee, National University of Singapore; Yukti Choudhury and Min-Han Tan, Lucence Diagnostics; Yukti Choudhury and Min-Han Tan, Institute of Bioengineering and Nanotechnology; Valerie Koh, Puay Hoon Tan, and John Yuen Shyi Peng, Singapore General Hospital; Hui Shan Tan, Ravindran Kanesvaran, and Min-Han Tan, National Cancer Center Singapore; and Hwee Kuan Lee, Institute for Infocomm Research, Singapore
| | - Hui Shan Tan
- Daniel Aitor Holdbrook, Malay Singh, Emarene Mationg Kalaw, and Hwee Kuan Lee, Bioinformatics Institute; Malay Singh and Hwee Kuan Lee, National University of Singapore; Yukti Choudhury and Min-Han Tan, Lucence Diagnostics; Yukti Choudhury and Min-Han Tan, Institute of Bioengineering and Nanotechnology; Valerie Koh, Puay Hoon Tan, and John Yuen Shyi Peng, Singapore General Hospital; Hui Shan Tan, Ravindran Kanesvaran, and Min-Han Tan, National Cancer Center Singapore; and Hwee Kuan Lee, Institute for Infocomm Research, Singapore
| | - Ravindran Kanesvaran
- Daniel Aitor Holdbrook, Malay Singh, Emarene Mationg Kalaw, and Hwee Kuan Lee, Bioinformatics Institute; Malay Singh and Hwee Kuan Lee, National University of Singapore; Yukti Choudhury and Min-Han Tan, Lucence Diagnostics; Yukti Choudhury and Min-Han Tan, Institute of Bioengineering and Nanotechnology; Valerie Koh, Puay Hoon Tan, and John Yuen Shyi Peng, Singapore General Hospital; Hui Shan Tan, Ravindran Kanesvaran, and Min-Han Tan, National Cancer Center Singapore; and Hwee Kuan Lee, Institute for Infocomm Research, Singapore
| | - Puay Hoon Tan
- Daniel Aitor Holdbrook, Malay Singh, Emarene Mationg Kalaw, and Hwee Kuan Lee, Bioinformatics Institute; Malay Singh and Hwee Kuan Lee, National University of Singapore; Yukti Choudhury and Min-Han Tan, Lucence Diagnostics; Yukti Choudhury and Min-Han Tan, Institute of Bioengineering and Nanotechnology; Valerie Koh, Puay Hoon Tan, and John Yuen Shyi Peng, Singapore General Hospital; Hui Shan Tan, Ravindran Kanesvaran, and Min-Han Tan, National Cancer Center Singapore; and Hwee Kuan Lee, Institute for Infocomm Research, Singapore
| | - John Yuen Shyi Peng
- Daniel Aitor Holdbrook, Malay Singh, Emarene Mationg Kalaw, and Hwee Kuan Lee, Bioinformatics Institute; Malay Singh and Hwee Kuan Lee, National University of Singapore; Yukti Choudhury and Min-Han Tan, Lucence Diagnostics; Yukti Choudhury and Min-Han Tan, Institute of Bioengineering and Nanotechnology; Valerie Koh, Puay Hoon Tan, and John Yuen Shyi Peng, Singapore General Hospital; Hui Shan Tan, Ravindran Kanesvaran, and Min-Han Tan, National Cancer Center Singapore; and Hwee Kuan Lee, Institute for Infocomm Research, Singapore
| | - Min-Han Tan
- Daniel Aitor Holdbrook, Malay Singh, Emarene Mationg Kalaw, and Hwee Kuan Lee, Bioinformatics Institute; Malay Singh and Hwee Kuan Lee, National University of Singapore; Yukti Choudhury and Min-Han Tan, Lucence Diagnostics; Yukti Choudhury and Min-Han Tan, Institute of Bioengineering and Nanotechnology; Valerie Koh, Puay Hoon Tan, and John Yuen Shyi Peng, Singapore General Hospital; Hui Shan Tan, Ravindran Kanesvaran, and Min-Han Tan, National Cancer Center Singapore; and Hwee Kuan Lee, Institute for Infocomm Research, Singapore
| | - Hwee Kuan Lee
- Daniel Aitor Holdbrook, Malay Singh, Emarene Mationg Kalaw, and Hwee Kuan Lee, Bioinformatics Institute; Malay Singh and Hwee Kuan Lee, National University of Singapore; Yukti Choudhury and Min-Han Tan, Lucence Diagnostics; Yukti Choudhury and Min-Han Tan, Institute of Bioengineering and Nanotechnology; Valerie Koh, Puay Hoon Tan, and John Yuen Shyi Peng, Singapore General Hospital; Hui Shan Tan, Ravindran Kanesvaran, and Min-Han Tan, National Cancer Center Singapore; and Hwee Kuan Lee, Institute for Infocomm Research, Singapore
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miR-9-5p in Nephrectomy Specimens is a Potential Predictor of Primary Resistance to First-Line Treatment with Tyrosine Kinase Inhibitors in Patients with Metastatic Renal Cell Carcinoma. Cancers (Basel) 2018; 10:cancers10090321. [PMID: 30201928 PMCID: PMC6162741 DOI: 10.3390/cancers10090321] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/22/2018] [Accepted: 08/29/2018] [Indexed: 12/21/2022] Open
Abstract
Approximately 20–30% of patients with metastatic renal cell carcinoma (mRCC) in first-line treatment with tyrosine kinase inhibitors (TKIs) do not respond due to primary resistance to this drug. At present, suitable robust biomarkers for prediction of a response are not available. Therefore, the aim of this study was to evaluate a panel of microRNAs (miRNAs) in nephrectomy specimens for use as predictive biomarkers for TKI resistance. Archived formalin-fixed, paraffin embedded nephrectomy samples from 60 mRCC patients treated with first-line TKIs (sunitinib, n = 51; pazopanib, n = 6; sorafenib, n = 3) were categorized into responders and non-responders. Using the standard Response Evaluation Criteria in Solid Tumors, patients with progressive disease within 3 months after the start of treatment with TKI were considered as non-responders and those patients with stable disease and complete or partial response under the TKI treatment for at least 6 months as responders. Based on a miRNA microarray expression profile in the two stratified groups of patients, seven differentially expressed miRNAs were validated using droplet digital reverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) assays in the two groups. Receiver operating characteristic curve analysis and binary logistic regression of response prediction were performed. MiR-9-5p and miR-489-3p were able to discriminate between the two groups. MiR-9-5p, as the most significant miRNA, improved the correct prediction of primary resistance against TKIs in comparison to that of conventional clinicopathological variables. The results of the decision curve analyses, Kaplan-Meier analyses and Cox regression analyses confirmed the potential of miR-9-5p in the prediction of response to TKIs and the prediction of progression-free survival after the initiation of TKI treatment.
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Salinas-Sánchez AS, Serrano-Oviedo L, Nam-Cha SY, Roche-Losada O, Sánchez-Prieto R, Giménez-Bachs JM. Prognostic Value of the VHL, HIF-1α, and VEGF Signaling Pathway and Associated MAPK (ERK1/2 and ERK5) Pathways in Clear-Cell Renal Cell Carcinoma. A Long-Term Study. Clin Genitourin Cancer 2017. [DOI: 10.1016/j.clgc.2017.05.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Verbiest A, Couchy G, Job S, Zucman-Rossi J, Caruana L, Lerut E, Oyen R, de Reyniès A, Laguerre B, Rioux-Leclercq N, Wozniak A, Joniau S, Van Poppel H, Van Den Eynde K, Beuselinck B. Molecular Subtypes of Clear Cell Renal Cell Carcinoma Are Associated With Outcome During Pazopanib Therapy in the Metastatic Setting. Clin Genitourin Cancer 2017; 16:e605-e612. [PMID: 29239846 DOI: 10.1016/j.clgc.2017.10.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/25/2017] [Accepted: 10/30/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND We previously described 4 molecular subtypes of metastatic clear cell renal cell carcinoma (mccRCC), named ccrcc1-4 (Beuselinck et al, 2015). These have both prognostic and predictive value for patients treated with first-line sunitinib, with distinctive objective response rate (ORR), progression-free survival (PFS), and overall survival (OS). The ccrcc2 and ccrcc3 tumors have the best outcomes, followed by ccrcc1 and then ccrcc4. We hypothesized that these molecular subtypes would show similar outcomes with first-line pazopanib treatment. PATIENTS AND METHODS We classified 28 mccRCC tumors treated with pazopanib as first-line therapy, as described previously. The primary endpoints were PFS and OS from the start of pazopanib. A secondary endpoint was ORR. Because there were only 2 ccrcc3 tumors, they were pooled with the ccrcc2 tumors for outcome analysis. RESULTS PFS was 9 months for the ccrcc2 and ccrcc3 tumors, 5 months for ccrcc1 tumors, and 3 months for the ccrcc4 tumors (P = .011). The corresponding OS duration was 69, 19, and 5 months (P = .003). The corresponding ORR was 50%, 33%, and 0%. The corresponding mean tumor size decreased by 34%, 6%, and 2% (P = .032). The ccrcc1-4 classification was a stronger predictor of outcome than the International Metastatic Renal Cell Carcinoma Database Consortium score on univariate analysis (P = .011 vs. P = .094 for PFS and P = .003 vs. .013 for OS). Both remained independent on bivariate analysis. CONCLUSION The molecular subtypes of mccRCC are associated with outcome on pazopanib as first-line therapy. The prognostic and predictive value of the ccrcc1-4 molecular classification requires validation in prospective trials.
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Affiliation(s)
- Annelies Verbiest
- Laboratory of Experimental Oncology, Department of Oncology, University of Leuven, Leuven, Belgium; Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Gabrielle Couchy
- Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, Institut Universitaire Hématologie, Paris, France
| | - Sylvie Job
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Jessica Zucman-Rossi
- Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, Institut Universitaire Hématologie, Paris, France
| | - Laure Caruana
- Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, Institut Universitaire Hématologie, Paris, France
| | - Evelyne Lerut
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Raymond Oyen
- Department of Radiology, University Hospitals Leuven, Leuven, Belgium
| | - Aurélien de Reyniès
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Brigitte Laguerre
- Department of Medical Oncology, Centre Eugène Marquis, Rennes, France
| | | | - Agnieszka Wozniak
- Laboratory of Experimental Oncology, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Steven Joniau
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | | | | | - Benoit Beuselinck
- Laboratory of Experimental Oncology, Department of Oncology, University of Leuven, Leuven, Belgium; Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium; Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, Institut Universitaire Hématologie, Paris, France.
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Tan MH, Choudhury Y, Tan PH, Ng QS, Toh CK, Kanesvaran R. The Issue of Tissue in Molecular Stratification. Oncologist 2017; 22:1560. [PMID: 28894016 PMCID: PMC5728023 DOI: 10.1634/theoncologist.2017-0165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Min-Han Tan
- Lucence Diagnostics Pte Ltd, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | | | - Puay Hoon Tan
- Division of Pathology, Singapore General Hospital, Singapore
| | - Quan Sing Ng
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Chee Keong Toh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
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Wei X, Choudhury Y, Lim WK, Anema J, Kahnoski RJ, Lane B, Ludlow J, Takahashi M, Kanayama HO, Belldegrun A, Kim HL, Rogers C, Nicol D, Teh BT, Tan MH. Recognizing the Continuous Nature of Expression Heterogeneity and Clinical Outcomes in Clear Cell Renal Cell Carcinoma. Sci Rep 2017; 7:7342. [PMID: 28779136 PMCID: PMC5544702 DOI: 10.1038/s41598-017-07191-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 06/23/2017] [Indexed: 01/06/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) has been previously classified into putative discrete prognostic subtypes by gene expression profiling. To investigate the robustness of these proposed subtype classifications, we evaluated 12 public datasets, together with a new dataset of 265 ccRCC gene expression profiles. Consensus clustering showed unstable subtype and principal component analysis (PCA) showed a continuous spectrum both within and between datasets. Considering the lack of discrete delineation and continuous spectrum observed, we developed a continuous quantitative prognosis score (Continuous Linear Enhanced Assessment of RCC, or CLEAR score). Prognostic performance was evaluated in independent cohorts from The Cancer Genome Atlas (TCGA) (n = 414) and EMBL-EBI (n = 53), CLEAR score demonstrated both superior prognostic estimates and inverse correlation with anti-angiogenic tyrosine-kinase inhibition in comparison to previously proposed discrete subtyping classifications. Inverse correlation with high-dose interleukin-2 outcomes was also observed for the CLEAR score. Multiple somatic mutations (VHL, PBRM1, SETD2, KDM5C, TP53, BAP1, PTEN, MTOR) were associated with the CLEAR score. Application of the CLEAR score to independent expression profiling of intratumoral ccRCC regions demonstrated that average intertumoral heterogeneity exceeded intratumoral expression heterogeneity. Wider investigation of cancer biology using continuous approaches may yield insights into tumor heterogeneity; single cell analysis may provide a key foundation for this approach.
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Affiliation(s)
- Xiaona Wei
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, 138669, Singapore, Republic of Singapore
- MRL IT, MSD International GmbH (Singapore Branch), 1 Fusionopolis Place, #06-10/07-18, Galaxis, Singapore, 138522, Republic of Singapore
| | - Yukti Choudhury
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, 138669, Singapore, Republic of Singapore
- Lucence Diagnostics Pte Ltd, Singapore, Republic of Singapore
| | - Weng Khong Lim
- Cancer Stem Cell Biology Program, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Republic of Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore, 117599, Republic of Singapore
| | - John Anema
- Urologic Consultants, 25 Michigan Street, Suite 3300, Grand Rapids, MI, 49503, USA
| | - Richard J Kahnoski
- Division of Urology, Spectrum Health Medical Group, 4069 Lake Drive SE, Suite 313, Grand Rapids, MI, 49546, USA
| | - Brian Lane
- Division of Urology, Spectrum Health Medical Group, 4069 Lake Drive SE, Suite 313, Grand Rapids, MI, 49546, USA
| | - John Ludlow
- Western Michigan Urological Associates, 577 Michigan Avenue, Suite 201, Holland, MI, 49423, USA
| | - Masayuki Takahashi
- Department of Urology, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15, Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Hiro-Omi Kanayama
- Department of Urology, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15, Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Arie Belldegrun
- FACS, Institute of Urologic Oncology, Department of Urology, David Geffen School of Medicine, University of California Los Angeles, 66-118 Center for Health Sciences Box 951738, Los Angeles, CA, 90095, USA
| | - Hyung L Kim
- Division of Urology, Cedars-Sinai Medical Center, 8635W. Third Street, Suite 1070, Los Angeles, CA, 90048, USA
| | - Craig Rogers
- Vattikuti Urology Institute, Henry Ford Hospital, 2799W. Grand Blvd, Detroit, MI, USA
| | - David Nicol
- Department of Urology, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, London, SW3 6JJ, UK
- The Institute of Cancer Research, 123 Old Brompton Road, London, SW7 3RP, UK
| | - Bin Tean Teh
- Cancer Stem Cell Biology Program, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Republic of Singapore.
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Republic of Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore, 117599, Republic of Singapore.
| | - Min-Han Tan
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, 138669, Singapore, Republic of Singapore.
- Lucence Diagnostics Pte Ltd, Singapore, Republic of Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore, 117599, Republic of Singapore.
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Republic of Singapore.
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10
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Secreted miR-210-3p as non-invasive biomarker in clear cell renal cell carcinoma. Oncotarget 2017; 8:69551-69558. [PMID: 29050224 PMCID: PMC5642499 DOI: 10.18632/oncotarget.18449] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/06/2017] [Indexed: 12/22/2022] Open
Abstract
The most common subtype of renal cell carcinoma (RCC) is clear cell RCC (ccRCC). It accounts for 70-80% of all renal malignancies representing the third most common urological cancer after prostate and bladder cancer. The identification of non-invasive biomarkers for the diagnosis and responsiveness to therapy of ccRCC may represent a relevant step-forward in ccRCC management. The aim of this study is to evaluate whether specific miRNAs deregulated in ccRCC tissues present altered levels also in urine specimens. To this end we first assessed that miR-21-5p, miR-210-3p and miR-221-3p resulted upregulated in ccRCC fresh frozen tissues compared to matched normal counterparts. Next, we evidenced that miR-210-3p resulted significantly up-regulated in 38 urine specimens collected from two independent cohorts of ccRCC patients at the time of surgery compared to healthy donors samples. Of note, miR-210-3p levels resulted significantly reduced in follow-up samples. These results point to miR-210-3p as a potential non-invasive biomarker useful not only for diagnosis but also for the assessment of complete resection or response to treatment in ccRCC management.
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11
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12
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de Velasco G, Culhane AC, Fay AP, Hakimi AA, Voss MH, Tannir NM, Tamboli P, Appleman LJ, Bellmunt J, Kimryn Rathmell W, Albiges L, Hsieh JJ, Heng DYC, Signoretti S, Choueiri TK. Molecular Subtypes Improve Prognostic Value of International Metastatic Renal Cell Carcinoma Database Consortium Prognostic Model. Oncologist 2017; 22:286-292. [PMID: 28220024 DOI: 10.1634/theoncologist.2016-0078] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 12/11/2016] [Indexed: 01/09/2023] Open
Abstract
INTRODUCTION Gene-expression signatures for prognosis have been reported in localized renal cell carcinoma (RCC). The aim of this study was to test the predictive power of two different signatures, ClearCode34, a 34-gene signature model [Eur Urol 2014;66:77-84], and an 8-gene signature model [Eur Urol 2015;67:17-20], in the setting of systemic therapy for metastatic disease. MATERIALS AND METHODS Metastatic RCC (mRCC) patients from five institutions who were part of TCGA were identified and clinical data were retrieved. We trained and implemented each gene model as described by the original study. The latter was demonstrated by faithful regeneration of a figure and results from the original study. mRCC patients were dichotomized to good or poor prognostic risk groups using each gene model. Cox proportional hazard regression and concordance index (C-Index) analysis were used to investigate an association between each prognostic risk model and overall survival (OS) from first-line therapy. RESULTS Overall, 54 patients were included in the final analysis. The primary endpoint was OS. Applying the ClearCode34 model, median survival for the low-risk-ccA (n = 17)-and the high-risk-ccB (n = 37)-subtypes were 27.6 and 22.3 months (hazard ratio (HR): 2.33; p = .039), respectively. ClearCode34 ccA/ccB and International Metastatic Renal Cell Carcinoma Database Consortium (IMDC) classifications appear to represent distinct risk criteria in mRCC, and we observed no significant overlap in classification (p > .05, chi-square test). On multivariable analyses and adjusting for IMDC groups, ccB remained independently associated with a worse OS (p = .044); the joint model of ccA/ccB and IMDC was significantly more accurate in predicting OS than a model with IMDC alone (p = .045, F-test). This was also observed in C-Index analysis; a model with both ccA and ccB subtypes had higher accuracy (C-Index 0.63, 95% confidence interval [CI] = 0.51-0.75) and 95% CIs of the C-Index that did not include the null value of 0.5 in contrast to a model with IMDC alone (0.60, CI = 0.47-0.72). The 8-gene signature molecular subtype model was a weak but insignificant predictor of survival in this cohort (p = .13). A model that included both the 8-gene signature and IMDC (C-Index 0.62, CI = 0.49-0.76) was more prognostic than IMDC alone but did not reach significance, as the 95% CI included the null value of 0.5. These two genomic signatures share no genes in common and are enriched in different biological pathways. The ClearCode34 included genes ARNT and EPAS1 (also known as HIF2a), which are involved in regulation of gene expression by hypoxia-inducible factor. CONCLUSION The ClearCode34 but not the 8-gene molecular model improved the prognostic predictive power of the IMDC model in this cohort of 54 patients with metastatic clear cell RCC. The Oncologist 2017;22:286-292 IMPLICATIONS FOR PRACTICE: The clinical and laboratory factors included in the International Metastatic Renal Cell Carcinoma Database Consortium model provide prognostic information in metastatic renal cell carcinoma (mRCC). The present study shows that genomic signatures, originally validated in localized RCC, may add further complementary prognostic information in the metastatic setting. This study may provide new insights into the molecular basis of certain mRCC subgroups. The integration of clinical and molecular data has the potential to redefine mRCC classification, enhance the understanding of mRCC biology, and potentially predict response to treatment in the future.
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Affiliation(s)
- Guillermo de Velasco
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medical Oncology, University Hospital 12 de Octubre, Madrid, Spain
| | - Aedín C Culhane
- Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - André P Fay
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Pontifical Catholic University of Rio Grande do Sul (PUCRS) School of Medicine, Porto Alegre, Brazil
| | - A Ari Hakimi
- Department of Surgery-Urology Service, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Martin H Voss
- Department of Medical Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nizar M Tannir
- Department of Medical Oncology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Pheroze Tamboli
- Department of Pathology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Leonard J Appleman
- Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Joaquim Bellmunt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - W Kimryn Rathmell
- Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Laurence Albiges
- Department of Medical Oncology, Institut Gustave Roussy, Villejuif, France
| | - James J Hsieh
- Department of Medical Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Daniel Y C Heng
- Department of Medical Oncology, Tom Baker Cancer Center and University of Calgary, Calgary, Canada
| | - Sabina Signoretti
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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13
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Gremel G, Djureinovic D, Niinivirta M, Laird A, Ljungqvist O, Johannesson H, Bergman J, Edqvist PH, Navani S, Khan N, Patil T, Sivertsson Å, Uhlén M, Harrison DJ, Ullenhag GJ, Stewart GD, Pontén F. A systematic search strategy identifies cubilin as independent prognostic marker for renal cell carcinoma. BMC Cancer 2017; 17:9. [PMID: 28052770 PMCID: PMC5215231 DOI: 10.1186/s12885-016-3030-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/23/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND There is an unmet clinical need for better prognostic and diagnostic tools for renal cell carcinoma (RCC). METHODS Human Protein Atlas data resources, including the transcriptomes and proteomes of normal and malignant human tissues, were searched for RCC-specific proteins and cubilin (CUBN) identified as a candidate. Patient tissue representing various cancer types was constructed into a tissue microarray (n = 940) and immunohistochemistry used to investigate the specificity of CUBN expression in RCC as compared to other cancers. Two independent RCC cohorts (n = 181; n = 114) were analyzed to further establish the sensitivity of CUBN as RCC-specific marker and to explore if the fraction of RCCs lacking CUBN expression could predict differences in patient survival. RESULTS CUBN was identified as highly RCC-specific protein with 58% of all primary RCCs staining positive for CUBN using immunohistochemistry. In venous tumor thrombi and metastatic lesions, the frequency of CUBN expression was increasingly lost. Clear cell RCC (ccRCC) patients with CUBN positive tumors had a significantly better prognosis compared to patients with CUBN negative tumors, independent of T-stage, Fuhrman grade and nodal status (HR 0.382, CI 0.203-0.719, P = 0.003). CONCLUSIONS CUBN expression is highly specific to RCC and loss of the protein is significantly and independently associated with poor prognosis. CUBN expression in ccRCC provides a promising positive prognostic indicator for patients with ccRCC. The high specificity of CUBN expression in RCC also suggests a role as a new diagnostic marker in clinical cancer differential diagnostics to confirm or rule out RCC.
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Affiliation(s)
- Gabriela Gremel
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dijana Djureinovic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marjut Niinivirta
- Department of Oncology, Radiology and Radiation Science, Uppsala University, Uppsala, Sweden
| | - Alexander Laird
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK.,Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | | | - Julia Bergman
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | | | - Åsa Sivertsson
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | | | - Gustav J Ullenhag
- Department of Oncology, Radiology and Radiation Science, Uppsala University, Uppsala, Sweden
| | - Grant D Stewart
- Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Academic Urology Group, University of Cambridge, Box 43, Addenbrooke's Hospital, Cambridge Biomedical Campus, Hill's Road, CB2 0QQ, Cambridge, UK
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Dag Hammarskjölds Väg 20, SE-751 85, Uppsala, Sweden.
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14
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Positive intratumoral chemokine (C-C motif) receptor 8 expression predicts high recurrence risk of post-operation clear-cell renal cell carcinoma patients. Oncotarget 2016; 7:8413-21. [PMID: 26716905 PMCID: PMC4885002 DOI: 10.18632/oncotarget.6761] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/07/2015] [Indexed: 11/25/2022] Open
Abstract
Chemokine (C-C motif) receptor 8 (CCR8) could drive cancer progress through recruiting certain immune cells. Recent evidences revealed the chemotaxis of CCR8+ human malignant tumor cells towards lymph node, and a significantly increased CCR8 expression in renal carcinomas patients. To assess the clinical association between CCR8 expression and the risk of post-surgery recurrence in patients with clear-cell renal cell carcinoma (ccRCC), we detected intratumoral CCR8 expression in 472 post-nephrectomy ccRCC patients retrospectively enrolled. Positive CCR8 staining tumor cell occurred in 26.1% (123 of 472) non-metastatic ccRCC cases, and the positive expression was associated with increased risks of recurrence (Log-Rank P < 0.001). In multivariate analyses, CCR8 expression was identified as an independent prognostic factor (P = 0.008) and entered into a newly-built nomogram together with T stage, Fuhrman grade, tumor size, necrosis and lymphovascular invasion. Calibration curves showed optimal agreement between predictions and observations, while its C-index was higher than that of Leibovich score for predicting recurrence-free survival (RFS) of localised RCC patients (0.854 vs 0.836, respectively; P = 0.044). The practical prognostic nomogram model may help clinicians in decision making and design of clinical studies.
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15
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Xia Y, Liu L, Bai Q, Wang J, Xi W, Qu Y, Xiong Y, Long Q, Xu J, Guo J. Dectin-1 predicts adverse postoperative prognosis of patients with clear cell renal cell carcinoma. Sci Rep 2016; 6:32657. [PMID: 27600310 PMCID: PMC5013447 DOI: 10.1038/srep32657] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/10/2016] [Indexed: 01/16/2023] Open
Abstract
Dectin-1, a classical pattern-recognition receptor, was now identified as an important regulator in immune homeostasis and cancer immunity through its extensive ligands binding functions and subsequent cytokines production. The aim of this study was to assess the clinical significance of dectin-1 expression in 290 patients with clear cell renal cell carcinoma (ccRCC) through immunohistochemistry on tissue microarrays. We found that dectin-1 was predominantly expressed on ccRCC cells, in accordance with several other online databases. Moreover, Kaplan-Meier method was conducted and high expression of tumoral dectin-1 was associated with shorter patient recurrence free survival (RFS) and overall survival (OS) (P < 0.001 for both). In multivariate analyses, tumoral dectin-1 expression was also confirmed as an independent prognostic factor for patients’ survival together with other clinical parameters (P < 0.001 for RFS and OS). After incorporating these characteristics including tumoral dectin-1 expression, two nomograms were constructed to predict ccRCC patients’ RFS and OS (c-index 0.796 and 0.812, respectively) and performed better than existed integrated models (P < 0.001 for all models comparisons). In conclusion, high tumoral dectin-1 expression was an independent predictor of adverse clinical outcome in ccRCC patients. This molecule and established nomograms might help clinicians in future decision making and therapeutic developments.
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Affiliation(s)
- Yu Xia
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Li Liu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qi Bai
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiajun Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Wei Xi
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yang Qu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ying Xiong
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qilai Long
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiejie Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jianming Guo
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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16
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Zimpfer A, Dammert F, Glass A, Zettl H, Kilic E, Maruschke M, Hakenberg OW, Erbersdobler A. Expression and clinicopathological correlations of retinoid acid receptor responder protein 1 in renal cell carcinomas. Biomark Med 2016; 10:721-32. [PMID: 27339486 DOI: 10.2217/bmm.16.12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To evaluate the expression and prognostic value of RARRES1 at protein level in renal cell carcinoma (RCC). MATERIALS & METHODS Expression profile of RARRES1 was analyzed in 903 documented RCC followed by clinicopathological correlations and survival analysis. RESULTS RARRES1 expression was seen in 72.5% of RCC. A stronger RARRES1 expression was seen in high grade compared with low grade RCC (p < 0.001). Logrank tests revealed shorter overall survival in RARRES1 positive RCC (p = 0.006) and in pT1/2 tumors with RARRES1 expression (p = 0.002). CONCLUSION The variable expression profile in low and high grade RCC may reflect and confirm the differences of previous gene expression analysis. There was a significant prognostic value of RARRES1 expression in patients with RCC, especially in pT1/2 tumors.
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Affiliation(s)
- Annette Zimpfer
- Institute of Pathology, University Medicine Rostock, Strempelstr. 14, 18055 Rostock, Germany.,Institute of Pathology, University Hospital of Jena, Ziegelmühlenweg 1, 07743 Jena, Germany
| | - Friedericke Dammert
- Institute of Pathology, University Medicine Rostock, Strempelstr. 14, 18055 Rostock, Germany
| | - Aenne Glass
- Institute of Biostatistics, University of Rostock, Ernst-Heydemann-Str. 8, 18057 Rostock, Germany
| | - Heike Zettl
- Clinical Cancer Registry, University Medicine Rostock, Südring 75, 18059 Rostock, Germany
| | - Ergin Kilic
- Institute of Pathology, Charité University Medicine, Chariteplatz 1, 10177 Berlin Germany
| | - Matthias Maruschke
- Clinic of Urology, HELIOS Hanseklinikum Stralsund, Große Parower Straße 47-53, 18435 Stralsund, Germany.,Clinic of Urology, University Medicine Rostock, Ernst-Heydemann-Str. 8, 18057 Rostock, Germany
| | - Oliver W Hakenberg
- Clinic of Urology, University Medicine Rostock, Ernst-Heydemann-Str. 8, 18057 Rostock, Germany
| | - Andreas Erbersdobler
- Institute of Pathology, University Medicine Rostock, Strempelstr. 14, 18055 Rostock, Germany
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17
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Diekstra MHM, Swen JJ, Gelderblom H, Guchelaar HJ. A decade of pharmacogenomics research on tyrosine kinase inhibitors in metastatic renal cell cancer: a systematic review. Expert Rev Mol Diagn 2016; 16:605-18. [PMID: 26837796 DOI: 10.1586/14737159.2016.1148601] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The individual response to targeted tyrosine kinase inhibitors (TKIs) in the treatment of metastatic renal cell cancer (mRCC) is highly variable. Outlined in this article are findings on potential biomarkers for TKI treatment outcome in mRCC and an evaluation of the status of clinical implementation. METHODS Articles were selected by two independent reviewers using a systematic search in five medical databases on renal cell carcinoma, TKIs, and pharmacogenetics. RESULTS Many researchers have focused on predictive biomarkers for treatment outcome of targeted therapies in mRCC patients. Attempts to explain differences in efficacy and toxicity of TKIs by use of genetic variants in genes related to the pharmacokinetics and pharmacodynamics of the drug have been successful. CONCLUSION Most findings on potential biomarkers have not been validated and therefore biomarker testing to guide choice of therapy and dose in mRCC is not yet feasible.
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Affiliation(s)
- Meta H M Diekstra
- a Department of Clinical Pharmacy and Toxicology , Leiden University Medical Center , Leiden , Netherlands
| | - Jesse J Swen
- a Department of Clinical Pharmacy and Toxicology , Leiden University Medical Center , Leiden , Netherlands
| | - Hans Gelderblom
- b Department of Medical Oncology , Leiden University Medical Center , Leiden , Netherlands
| | - Henk-Jan Guchelaar
- a Department of Clinical Pharmacy and Toxicology , Leiden University Medical Center , Leiden , Netherlands
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18
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Higdon R, Earl RK, Stanberry L, Hudac CM, Montague E, Stewart E, Janko I, Choiniere J, Broomall W, Kolker N, Bernier RA, Kolker E. The promise of multi-omics and clinical data integration to identify and target personalized healthcare approaches in autism spectrum disorders. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:197-208. [PMID: 25831060 DOI: 10.1089/omi.2015.0020] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Complex diseases are caused by a combination of genetic and environmental factors, creating a difficult challenge for diagnosis and defining subtypes. This review article describes how distinct disease subtypes can be identified through integration and analysis of clinical and multi-omics data. A broad shift toward molecular subtyping of disease using genetic and omics data has yielded successful results in cancer and other complex diseases. To determine molecular subtypes, patients are first classified by applying clustering methods to different types of omics data, then these results are integrated with clinical data to characterize distinct disease subtypes. An example of this molecular-data-first approach is in research on Autism Spectrum Disorder (ASD), a spectrum of social communication disorders marked by tremendous etiological and phenotypic heterogeneity. In the case of ASD, omics data such as exome sequences and gene and protein expression data are combined with clinical data such as psychometric testing and imaging to enable subtype identification. Novel ASD subtypes have been proposed, such as CHD8, using this molecular subtyping approach. Broader use of molecular subtyping in complex disease research is impeded by data heterogeneity, diversity of standards, and ineffective analysis tools. The future of molecular subtyping for ASD and other complex diseases calls for an integrated resource to identify disease mechanisms, classify new patients, and inform effective treatment options. This in turn will empower and accelerate precision medicine and personalized healthcare.
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Affiliation(s)
- Roger Higdon
- 1 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington
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19
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Albiges L, Fay AP, McKay RR, Kaymakcalan MD, Choueiri TK. Diagnosis of Renal Cell Carcinoma: A Clinician's Perspective. Surg Pathol Clin 2015; 8:657-662. [PMID: 26612219 DOI: 10.1016/j.path.2015.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Renal cell carcinoma (RCC) is a heterogeneous disease. A rigorous diagnostic assessment by a pathologist with close communication with the clinician provides more accurate prognostication and informed treatment decisions. In the localized setting, an accurate prognostic assessment directs patients to potential adjuvant clinical trials. For patients with advanced disease, the pathologic assessment may have a direct impact on the systemic therapy algorithm. Additionally, it provides the basis for continuous efforts in biomarker development. In rare histologic subtypes, the interaction between clinicians and pathologists provides an opportunity to offer patients specific clinical trials. Molecular characterization platforms may identify targets for therapeutic intervention.
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Affiliation(s)
- Laurence Albiges
- Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue (DANA 1230), Boston, MA 02215, USA
| | - André P Fay
- Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue (DANA 1230), Boston, MA 02215, USA
| | - Rana R McKay
- Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue (DANA 1230), Boston, MA 02215, USA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marina D Kaymakcalan
- Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue (DANA 1230), Boston, MA 02215, USA
| | - Toni K Choueiri
- Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue (DANA 1230), Boston, MA 02215, USA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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20
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Postoperative surveillance imaging for patients undergoing nephrectomy for renal cell carcinoma. Urol Oncol 2015; 33:499-502. [PMID: 26411549 DOI: 10.1016/j.urolonc.2015.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/13/2015] [Accepted: 08/17/2015] [Indexed: 12/18/2022]
Abstract
The American Urological Association and the National Comprehensive Cancer Network guidelines regarding postoperative surveillance for renal cell carcinoma (RCC) have provided a standardized framework for imaging following nephrectomy. These stage-stratified recommendations are based on retrospective studies that identified the timeline and location of RCC recurrences. However, the simplified and generalizable protocols offered by the American Urological Association and the National Comprehensive Cancer Network are not without limitations. Studies have found that RCC recurrences continue to be missed even with perfect compliance to these protocols and that RCC recurrences occur not infrequently after the required surveillance window of 5 years. Furthermore, recent studies evaluating the use of adjuvant systemic therapy in patients who are at a high risk for RCC recurrence or metastasis after nephrectomy have yielded disappointing results. This calls into question what interventions we can offer patients to improve survival once RCC recurrences are detected during postoperative surveillance; an effective surveillance strategy requires effective treatment options. The future of personalized medicine with genetic profiling of patients with RCC may offer a potential solution by providing better risk stratification to determine the intensity of surveillance imaging as well as to determine which patients will actually derive survival benefit from intervention on recurrent disease.
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21
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Chan JY, Choudhury Y, Tan MH. Predictive molecular biomarkers to guide clinical decision making in kidney cancer: current progress and future challenges. Expert Rev Mol Diagn 2015; 15:631-46. [PMID: 25837857 DOI: 10.1586/14737159.2015.1032261] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Although the past decade has seen a surfeit of new targeted therapies for renal cell carcinoma (RCC), no predictive molecular biomarker is currently used in routine clinical practice to guide personalized therapy as a companion diagnostic. Many putative biomarkers have been suggested, but none have undergone rigorous validation. There have been considerable advances in the biological understanding of RCC in recent years, with the development of accompanying molecular diagnostics that with additional validation, may be helpful for routine clinical decision making. In this review, we summarize the current understanding of predictive biomarkers in RCC management and also highlight upcoming developments of interest in biomarker research for personalizing RCC diagnostics and therapeutics.
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Affiliation(s)
- Jason Yongsheng Chan
- Department of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore
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22
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Karamchandani JR, Gabril MY, Ibrahim R, Scorilas A, Filter E, Finelli A, Lee JY, Ordon M, Pasic M, Romaschin AD, Yousef GM. Profilin-1 expression is associated with high grade and stage and decreased disease-free survival in renal cell carcinoma. Hum Pathol 2014; 46:673-80. [PMID: 25704627 DOI: 10.1016/j.humpath.2014.11.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 11/13/2014] [Accepted: 11/14/2014] [Indexed: 12/18/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is associated with high mortality, although individual outcomes are highly variable. Identification of patients with increased risk of disease progression can guide customizing management plan according to disease severity. Profilin-1 (Pfn1) has been recently identified as overexpressed in metastatic ccRCC compared with primary tumors. We examined Pfn1 expression in a tissue microarray of 384 cases of histologically confirmed primary ccRCC with detailed clinical follow-up. Profilin-1 expression showed both cytoplasmic and nuclear staining patterns. The immunoexpression of Pfn1 was scored in a semiquantitative fashion. There was no significant difference in Pfn1 expression between normal kidney and kidney ccRCC. Our results show that strong cytoplasmic Pfn1 expression is associated with high-grade (P < .001) and high-stage (III-IV) (P = .018) disease. Univariate analysis of the data set showed that higher Pfn1 expression is associated with significantly shorter disease-free survival (hazard ratio 7.36, P = .047) and also lower overall survival. Kaplan-Meier analysis showed that high cytoplasmic expression of Pfn1 was also associated with a statistically significant lower disease-free survival (P = .018). It was also associated with lower overall survival, although this was not statistically significant. Profilin-1 lost its prognostic significance in the multivariate analysis when controlling for grade and stage. Profilin-1 expression was not associated with significant prognostic deference in the subgroup of patients with stage 1 disease. Our results suggest that the evaluation of Pfn1 by immunohistochemistry may help to identify patients with an increased risk of disease progression. We validated our results at the messenger RNA level on an independent patient cohort. Higher messenger RNA expression of Pfn1 is associated with significantly lower survival.
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Affiliation(s)
- Jason R Karamchandani
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8; Department of Laboratory Medicine and the Keenan Research Centre for Biomedical Science at the Li KaShing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada M5B 1T8
| | | | - Rania Ibrahim
- Department of Laboratory Medicine and the Keenan Research Centre for Biomedical Science at the Li KaShing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada M5B 1T8
| | | | - Emily Filter
- London Health Sciences, London, Ontario, Canada N6A 5A5
| | - Antonio Finelli
- Division of Urologic Oncology, Princess Margaret Hospital, University Health Network, Department of Surgery, University of Toronto, Toronto, Ontario, Canada M5G 2M9
| | - Jason Y Lee
- Division of Urology, St. Michael's Hospital, Toronto, Ontario, Canada M5B 1W8
| | - Michael Ordon
- Division of Urology, St. Michael's Hospital, Toronto, Ontario, Canada M5B 1W8
| | - Maria Pasic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8; Department of Laboratory Medicine, St. Joseph's Health Centre, Toronto, Ontario, Canada M6R 1B5
| | - Alexander D Romaschin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8; Department of Laboratory Medicine and the Keenan Research Centre for Biomedical Science at the Li KaShing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada M5B 1T8
| | - George M Yousef
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8; Department of Laboratory Medicine and the Keenan Research Centre for Biomedical Science at the Li KaShing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada M5B 1T8.
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23
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Laird A, Harrison DJ, Stewart GD. The development of prognostic and predictive biomarkers in renal cell cancer are not one and the same thing. Eur Urol 2014; 67:21-22. [PMID: 25123323 DOI: 10.1016/j.eururo.2014.07.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 07/28/2014] [Indexed: 10/24/2022]
Affiliation(s)
- Alexander Laird
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK; Edinburgh Urological Cancer Group, University of Edinburgh, Edinburgh, UK; Scottish Collaboration On Translational Research into Renal Cell Cancer, Scotland, UK.
| | - David J Harrison
- Scottish Collaboration On Translational Research into Renal Cell Cancer, Scotland, UK; School of Medicine, University of St. Andrews, St. Andrews, UK
| | - Grant D Stewart
- Edinburgh Urological Cancer Group, University of Edinburgh, Edinburgh, UK; Scottish Collaboration On Translational Research into Renal Cell Cancer, Scotland, UK
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