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Murali R, Gopalakrishnan AV. Molecular insight into renal cancer and latest therapeutic approaches to tackle it: an updated review. Med Oncol 2023; 40:355. [PMID: 37955787 DOI: 10.1007/s12032-023-02225-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023]
Abstract
Renal cell carcinoma (RCC) is one of the most lethal genitourinary cancers, with the highest mortality rate, and may remain undetected throughout its development. RCC can be sporadic or hereditary. Exploring the underlying genetic abnormalities in RCC will have important implications for understanding the origins of nonhereditary renal cancers. The treatment of RCC has evolved over centuries from the era of cytokines to targeted therapy to immunotherapy. A surgical cure is the primary treatment modality, especially for organ-confined diseases. Furthermore, the urologic oncology community focuses on nephron-sparing surgical approaches and ablative procedures when small renal masses are detected incidentally in conjunction with interventional radiologists. In addition to new combination therapies approved for RCC treatment, several trials have been conducted to investigate the potential benefits of certain drugs. This may lead to durable responses and more extended survival benefits for patients with metastatic RCC (mRCC). Several approved drugs have reduced the mortality rate of patients with RCC by targeting VEGF signaling and mTOR. This review better explains the signaling pathways involved in the RCC progression, oncometabolites, and essential biomarkers in RCC that can be used for its diagnosis. Further, it provides an overview of the characteristics of RCC carcinogenesis to assist in combating treatment resistance, as well as details about the current management and future therapeutic options. In the future, multimodal and integrated care will be available, with new treatment options emerging as we learn more about the disease.
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Affiliation(s)
- Reshma Murali
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology VIT, Vellore, Tamil Nadu, 632014, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology VIT, Vellore, Tamil Nadu, 632014, India.
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2
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Chang P, Bing Z, Tian J, Zhang J, Li X, Ge L, Ling J, Yang K, Li Y. Comprehensive assessment gene signatures for clear cell renal cell carcinoma prognosis. Medicine (Baltimore) 2018; 97:e12679. [PMID: 30383629 PMCID: PMC6221654 DOI: 10.1097/md.0000000000012679] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
There are many prognostic gene signature models in clear cell renal cell carcinoma (ccRCC). However, different results from various methods and samples are hard to contribute to clinical practice. It is necessary to develop a robust gene signature for improving clinical practice in ccRCC.A method was proposed to integrate least absolute shrinkage and selection operator and multiple Cox regression to obtain mRNA and microRNA signature from the cancer genomic atlas database for predicting prognosis of ccRCC. The gene signature model consisted by 5 mRNAs and 1 microRNA was identified. Prognosis index (PI) model was constructed from RNA expression and median value of PI is used to classified patients into high- and low-risk groups.The results showed that high-risk patients showed significantly decrease survival comparison with low-risk groups [hazard ratio (HR) =7.13, 95% confidence interval = 3.71-13.70, P < .001]. As the gene signature was mainly consisted by mRNA, the validation data can use transcriptomic data to verify. For comparison of the performance with previous works, other gene signature models and 4 datasets of ccRCC were retrieved from publications and public database. For estimating PI in each model, 3 indicators including HR, concordance index , and the area under the curve of receiver operating characteristic for 3 years were calculated across 4 independent datasets.The comparison results showed that the integrative model from our study was more robust than other models via comprehensive analysis. These findings provide some genes for further study their functions and mechanisms in ccRCC tumorigenesis and malignance, and may be useful for effective clinical decision making of ccRCC patients.
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Affiliation(s)
- Peng Chang
- School of Life Sciences, Lanzhou University
- Lanzhou University Second Hospital
- Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University
| | - Zhitong Bing
- Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province
| | - Jinhui Tian
- Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province
| | - Jingyun Zhang
- Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province
| | - Xiuxia Li
- Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Long Ge
- Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province
| | - Juan Ling
- Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province
| | - Kehu Yang
- School of Life Sciences, Lanzhou University
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province
| | - Yumin Li
- School of Life Sciences, Lanzhou University
- Lanzhou University Second Hospital
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3
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Poetz O, Dieze T, Hammer H, Weiß F, Sommersdorf C, Templin MF, Esdar C, Zimmermann A, Stevanovic S, Bedke J, Stenzl A, Joos TO. Peptide-Based Sandwich Immunoassay for the Quantification of the Membrane Transporter Multidrug Resistance Protein 1. Anal Chem 2018; 90:5788-5794. [DOI: 10.1021/acs.analchem.8b00152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Oliver Poetz
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
- SIGNATOPE GmbH Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Theresa Dieze
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Helen Hammer
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
- SIGNATOPE GmbH Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Frederik Weiß
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
- SIGNATOPE GmbH Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Cornelia Sommersdorf
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
- SIGNATOPE GmbH Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Markus F. Templin
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Christina Esdar
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | | | - Stefan Stevanovic
- Eberhard Karls University, Department of Immunology, 72076 Tübingen, Germany
| | - Jens Bedke
- Eberhard Karls University, Department of Urology, 72076 Tübingen, Germany
| | - Arnulf Stenzl
- Eberhard Karls University, Department of Urology, 72076 Tübingen, Germany
| | - Thomas O. Joos
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
- SIGNATOPE GmbH Markwiesenstrasse 55, 72770 Reutlingen, Germany
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4
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Xu Q, Junttila S, Scherer A, Giri KR, Kivelä O, Skovorodkin I, Röning J, Quaggin SE, Marti HP, Shan J, Samoylenko A, Vainio SJ. Renal carcinoma/kidney progenitor cell chimera organoid as a novel tumorigenesis gene discovery model. Dis Model Mech 2017; 10:1503-1515. [PMID: 29084770 PMCID: PMC5769601 DOI: 10.1242/dmm.028332] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/16/2017] [Indexed: 12/13/2022] Open
Abstract
Three-dimensional (3D) organoids provide a new way to model various diseases, including cancer. We made use of recently developed kidney-organ-primordia tissue-engineering technologies to create novel renal organoids for cancer gene discovery. We then tested whether our novel assays can be used to examine kidney cancer development. First, we identified the transcriptomic profiles of quiescent embryonic mouse metanephric mesenchyme (MM) and of MM in which the nephrogenesis program had been induced ex vivo. The transcriptome profiles were then compared to the profiles of tumor biopsies from renal cell carcinoma (RCC) patients, and control samples from the same kidneys. Certain signature genes were identified that correlated in the developmentally induced MM and RCC, including components of the caveolar-mediated endocytosis signaling pathway. An efficient siRNA-mediated knockdown (KD) of Bnip3, Gsn, Lgals3, Pax8, Cav1, Egfr or Itgb2 gene expression was achieved in mouse RCC (Renca) cells. The live-cell imaging analysis revealed inhibition of cell migration and cell viability in the gene-KD Renca cells in comparison to Renca controls. Upon siRNA treatment, the transwell invasion capacity of Renca cells was also inhibited. Finally, we mixed E11.5 MM with yellow fluorescent protein (YFP)-expressing Renca cells to establish chimera organoids. Strikingly, we found that the Bnip3-, Cav1- and Gsn-KD Renca-YFP+ cells as a chimera with the MM in 3D organoid rescued, in part, the RCC-mediated inhibition of the nephrogenesis program during epithelial tubules formation. Altogether, our research indicates that comparing renal ontogenesis control genes to the genes involved in kidney cancer may provide new growth-associated gene screens and that 3D RCC-MM chimera organoids can serve as a novel model with which to investigate the behavioral roles of cancer cells within the context of emergent complex tissue structures. Editor’s Choice: Chimeras between embryonic kidney cells and renal carcinoma cells serve as a novel model to assay the roles of co-regulated genes in kidney development and renal carcinogenesis.
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Affiliation(s)
- Qi Xu
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland
| | - Sanna Junttila
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland
| | | | - Khem Raj Giri
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland
| | - Oona Kivelä
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland.,ValiFinn, FI-90220 Oulu, Finland
| | - Ilya Skovorodkin
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland
| | - Juha Röning
- Department of Computer Science and Engineering, University of Oulu, FI-90014 Oulu, Finland
| | - Susan E Quaggin
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland.,Feinberg Cardiovascular Research Institute, Division of Medicine-Nephrology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, N-5020 Bergen, Norway
| | - Jingdong Shan
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland
| | - Anatoly Samoylenko
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland
| | - Seppo J Vainio
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland
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5
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Dalgin GS, Holloway DT, Liou LS, Delisi C. Identification and Characterization of Renal Cell Carcinoma Gene Markers. Cancer Inform 2017. [DOI: 10.1177/117693510700300006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Microarray gene expression profiling has been used to distinguish histological subtypes of renal cell carcinoma (RCC), and consequently to identify specific tumor markers. The analytical procedures currently in use find sets of genes whose average differential expression across the two categories differ significantly. In general each of the markers thus identified does not distinguish tumor from normal with 100% accuracy, although the group as a whole might be able to do so. For the purpose of developing a widely used economically viable diagnostic signature, however, large groups of genes are not likely to be useful. Here we use two different methods, one a support vector machine variant, and the other an exhaustive search, to reanalyze data previously generated in our Lab (Lenburg et al. 2003). We identify 158 genes, each having an expression level that is higher (lower) in every tumor sample than in any normal sample, and each having a minimum differential expression across the two categories at a significance of 0.01. The set is highly enriched in cancer related genes (p = 1.6 × 10–12), containing 43 genes previously associated with either RCC or other types of cancer. Many of the biomarkers appear to be associated with the central alterations known to be required for cancer transformation. These include the oncogenes JAZF1, AXL, ABL2; tumor suppressors RASD1, PTPRO, TFAP2A, CDKN1C; and genes involved in proteolysis or cell-adhesion such as WASF2, and PAPPA.
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Affiliation(s)
- Gul S. Dalgin
- Molecular Biology, Cell Biology and Biochemistry Program, Boston University, 2 Cummington Street, Boston, MA 02215, U.S.A
| | - Dustin T. Holloway
- Molecular Biology, Cell Biology and Biochemistry Program, Boston University, 2 Cummington Street, Boston, MA 02215, U.S.A
| | - Louis S. Liou
- Department of Urology, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, U.S.A
| | - Charles Delisi
- Biomedical Engineering, Boston University, 24 Cummington Street, Boston, MA 02215, U.S.A
- Bioinformatics and Systems Biology, Boston University, 24 Cummington Street, Boston, MA 02215, U.S.A
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6
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Banerjee S, Tian T, Wei Z, Peck KN, Shih N, Chalian AA, O'Malley BW, Weinstein GS, Feldman MD, Alwine J, Robertson ES. Microbial Signatures Associated with Oropharyngeal and Oral Squamous Cell Carcinomas. Sci Rep 2017; 7:4036. [PMID: 28642609 PMCID: PMC5481414 DOI: 10.1038/s41598-017-03466-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 04/26/2017] [Indexed: 12/18/2022] Open
Abstract
The microbiome is fundamentally one of the most unique organs in the human body. Dysbiosis can result in critical inflammatory responses and result in pathogenesis contributing to neoplastic events. We used a pan-pathogen array technology (PathoChip) coupled with next-generation sequencing to establish microbial signatures unique to human oral and oropharyngeal squamous cell carcinomas (OCSCC/OPSCC). Signatures for DNA and RNA viruses including oncogenic viruses, gram positive and negative bacteria, fungi and parasites were detected. Cluster and topological analyses identified 2 distinct groups of microbial signatures related to OCSCCs/OPSCCs. Results were validated by probe capture next generation sequencing; the data from which also provided a comprehensive map of integration sites and chromosomal hotspots for micro-organism genomic insertions. Identification of these microbial signatures and their integration sites may provide biomarkers for OCSCC/OPSCC diagnosis and prognosis as well as novel avenues for study of their potential role in OCSCCs/OPSCCs.
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Affiliation(s)
- Sagarika Banerjee
- Department of Otorhinolaryngology-Head and neck surgery, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Tian Tian
- Department of Computer Science, New Jersey Institute of Technology, New Jersey, 07102, United States of America
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, New Jersey, 07102, United States of America
| | - Kristen N Peck
- Department of Otorhinolaryngology-Head and neck surgery, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Natalie Shih
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, 19104, Philadelphia, Pennsylvania, United States of America
| | - Ara A Chalian
- Department of Otorhinolaryngology-Head and neck surgery, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Bert W O'Malley
- Department of Otorhinolaryngology-Head and neck surgery, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Gregory S Weinstein
- Department of Otorhinolaryngology-Head and neck surgery, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Michael D Feldman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, 19104, Philadelphia, Pennsylvania, United States of America
| | - James Alwine
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Erle S Robertson
- Department of Otorhinolaryngology-Head and neck surgery, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America.
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7
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Jiang D, Sun J. Group Tests for High-dimensional Failure Time Data with the Additive Hazards Models. Int J Biostat 2017; 13:/j/ijb.ahead-of-print/ijb-2016-0085/ijb-2016-0085.xml. [PMID: 28493818 DOI: 10.1515/ijb-2016-0085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Statistical analysis of high-dimensional data has been attracting more and more attention due to the abundance of such data in various fields such as genetic studies or genomics and the existence of many interesting topics. Among them, one is the identification of a gene or genes that have significant effects on the occurrence of or are significantly related to a certain disease. In this paper, we will discuss such a problem that can be formulated as a group test or testing a group of variables or coefficients when one faces right-censored failure time response variable. For the problem, we develop a corrected variance reduced partial profiling (CVRPP) linear regression model and a likelihood ratio test procedure when the failure time of interest follows the additive hazards model. The numerical study suggests that the proposed method works well in practical situations and gives better performance than the existing one. An illustrative example is provided.
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Ghatalia P, Yang ES, Lasseigne BN, Ramaker RC, Cooper SJ, Chen D, Sudarshan S, Wei S, Guru AS, Zhao A, Cooper T, Della Manna DL, Naik G, Myers RM, Sonpavde G. Kinase Gene Expression Profiling of Metastatic Clear Cell Renal Cell Carcinoma Tissue Identifies Potential New Therapeutic Targets. PLoS One 2016; 11:e0160924. [PMID: 27574806 PMCID: PMC5004806 DOI: 10.1371/journal.pone.0160924] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/27/2016] [Indexed: 01/05/2023] Open
Abstract
Kinases are therapeutically actionable targets. Kinase inhibitors targeting vascular endothelial growth factor receptors (VEGFR) and mammalian target of rapamycin (mTOR) improve outcomes in metastatic clear cell renal cell carcinoma (ccRCC), but are not curative. Metastatic tumor tissue has not been comprehensively studied for kinase gene expression. Paired intra-patient kinase gene expression analysis in primary tumor (T), matched normal kidney (N) and metastatic tumor tissue (M) may assist in identifying drivers of metastasis and prioritizing therapeutic targets. We compared the expression of 519 kinase genes using NanoString in T, N and M in 35 patients to discover genes over-expressed in M compared to T and N tissue. RNA-seq data derived from ccRCC tumors in The Cancer Genome Atlas (TCGA) were used to demonstrate differential expression of genes in primary tumor tissue from patients that had metastasis at baseline (n = 79) compared to those that did not develop metastasis for at least 2 years (n = 187). Functional analysis was conducted to identify key signaling pathways by using Ingenuity Pathway Analysis. Of 10 kinase genes overexpressed in metastases compared to primary tumor in the discovery cohort, 9 genes were also differentially expressed in TCGA primary tumors with metastasis at baseline compared to primary tumors without metastasis for at least 2 years: EPHB2, AURKA, GSG2, IKBKE, MELK, CSK, CHEK2, CDC7 and MAP3K8; p<0.001). The top pathways overexpressed in M tissue were pyridoxal 5'-phosphate salvage, salvage pathways of pyrimidine ribonucleotides, NF-kB signaling, NGF signaling and cell cycle control of chromosomal replication. The 9 kinase genes validated to be over-expressed in metastatic ccRCC may represent currently unrecognized but potentially actionable therapeutic targets that warrant functional validation.
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Affiliation(s)
- Pooja Ghatalia
- Department of Internal Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, United States of America
| | - Eddy S. Yang
- Department of Radiation Oncology, UAB, Birmingham, AL, United States of America
| | | | - Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, UAB, Birmingham, AL, United States of America
| | - Sara J. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Dongquan Chen
- UAB Department of Preventive Medicine, Birmingham, AL, United States of America
| | - Sunil Sudarshan
- UAB Department of Urology, Birmingham, AL, United States of America
| | - Shi Wei
- UAB Department of Urologic Pathology, Birmingham, AL, United States of America
| | - Arjun S. Guru
- Department of Radiation Oncology, UAB, Birmingham, AL, United States of America
| | - Amy Zhao
- Department of Radiation Oncology, UAB, Birmingham, AL, United States of America
| | - Tiffiny Cooper
- Department of Radiation Oncology, UAB, Birmingham, AL, United States of America
| | | | - Gurudatta Naik
- UAB Department of Medicine, Section of Hematology-Oncology and the UAB Comprehensive Cancer Center, Birmingham, AL, United States of America
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Guru Sonpavde
- UAB Department of Medicine, Section of Hematology-Oncology and the UAB Comprehensive Cancer Center, Birmingham, AL, United States of America
- * E-mail:
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9
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Arlt D, Huber W, Liebel U, Schmidt C, Majety M, Sauermann M, Rosenfelder H, Bechtel S, Mehrle A, Bannasch D, Schupp I, Seiler M, Simpson JC, Hahne F, Moosmayer P, Ruschhaupt M, Guilleaume B, Wellenreuther R, Pepperkok R, Sültmann H, Poustka A, Wiemann S. Functional profiling: from microarrays via cell-based assays to novel tumor relevant modulators of the cell cycle. Cancer Res 2005; 65:7733-42. [PMID: 16140941 DOI: 10.1158/0008-5472.can-05-0642] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cancer transcription microarray studies commonly deliver long lists of "candidate" genes that are putatively associated with the respective disease. For many of these genes, no functional information, even less their relevance in pathologic conditions, is established as they were identified in large-scale genomics approaches. Strategies and tools are thus needed to distinguish genes and proteins with mere tumor association from those causally related to cancer. Here, we describe a functional profiling approach, where we analyzed 103 previously uncharacterized genes in cancer relevant assays that probed their effects on DNA replication (cell proliferation). The genes had previously been identified as differentially expressed in genome-wide microarray studies of tumors. Using an automated high-throughput assay with single-cell resolution, we discovered seven activators and nine repressors of DNA replication. These were further characterized for effects on extracellular signal-regulated kinase 1/2 (ERK1/2) signaling (G1-S transition) and anchorage-independent growth (tumorigenicity). One activator and one inhibitor protein of ERK1/2 activation and three repressors of anchorage-independent growth were identified. Data from tumor and functional profiling make these proteins novel prime candidates for further in-depth study of their roles in cancer development and progression. We have established a novel functional profiling strategy that links genomics to cell biology and showed its potential for discerning cancer relevant modulators of the cell cycle in the candidate lists from microarray studies.
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Affiliation(s)
- Dorit Arlt
- Division of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany
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