Development and confirmation of potential gene classifiers of human clear cell renal cell carcinoma using next-generation RNA sequencing

References

• Ljungberg B, Campbell SC, Choi HY, Jacqmin D, Lee JE, Weikert S, et al. The epidemiology of renal cell carcinoma. Eur Urol 2011;60:615–21.
   PubMed Web of Science ®Google Scholar
• Maher ER. Genomics and epigenomics of renal cell carcinoma. Semin Cancer Biol 2013;23:10–7.
   PubMed Web of Science ®Google Scholar
• Oosterwijk E. Carbonic anhydrase expression in kidney and renal cancer: implications for diagnosis and treatment. Subcell Biochem 2014;75:181–98.
   PubMedGoogle Scholar
• Rydzanicz M, Wrzesinski T, Bluyssen HA, Wesoly J. Genomics and epigenomics of clear cell renal cell carcinoma: recent developments and potential applications. Cancer Lett 2013;341:111–26.
   PubMed Web of Science ®Google Scholar
• Tun HW, Marlow LA, von Roemeling CA, Cooper SJ, Kreinest P, Wu K, et al. Pathway signature and cellular differentiation in clear cell renal cell carcinoma. PLoS One 2010;5:e10696.
   PubMed Web of Science ®Google Scholar
• Eisengart LJ, MacVicar GR, Yang XJ. Predictors of response to targeted therapy in renal cell carcinoma. Arch Pathol Lab Med 2012;136:490–5.
   PubMed Web of Science ®Google Scholar
• Cho DS, Kim SI, Choo SH, Jang SH, Ahn HS, Kim SJ. Prognostic significance of modified Glasgow prognostic score in patients with non-metastatic clear cell renal cell carcinoma. Scand J Urol 2016;50:186–91.
   PubMed Web of Science ®Google Scholar
• Thorstenson A, Bergman M, Scherman-Plogell AH, Hosseinnia S, Ljungberg B, Adolfsson J, et al. Tumour characteristics and surgical treatment of renal cell carcinoma in Sweden 2005-2010: a population-based study from the national Swedish kidney cancer register. Scand J Urol 2014;48:231–8.
   PubMed Web of Science ®Google Scholar
• Thorstenson A, Harmenberg U, Lindblad P, Holmstrom B, Lundstam S, Ljungberg B. Cancer characteristics and current treatments of patients with renal cell carcinoma in Sweden. Biomed Res Int 2015;2015:456040.
   PubMed Web of Science ®Google Scholar
• Guethmundsson E, Hellborg H, Lundstam S, Erikson S, Ljungberg B, Swedish Kidney Cancer Quality Register Group. Metastatic potential in renal cell carcinomas ≤7 cm: Swedish kidney cancer quality register data. Eur Urol 2011;60:975–82.
   PubMed Web of Science ®Google Scholar
• Schrodter S, Braun M, Syring I, Klumper N, Deng M, Schmidt D, et al. Identification of the dopamine transporter SLC6A3 as a biomarker for patients with renal cell carcinoma. Mol Cancer 2016;15:10.
   PubMed Web of Science ®Google Scholar
• Escudier B, Porta C, Schmidinger M, Algaba F, Patard JJ, Khoo V, et al. Renal cell carcinoma: ESMO clinical practice guidelines for diagnosis, treatment and follow-up. Ann Oncol 2014;25:iii49–56.
   PubMed Web of Science ®Google Scholar
• Eikrem O, Beisland C, Hjelle K, Flatberg A, Scherer A, Landolt L, et al. Transcriptome sequencing (RNAseq) enables utilization of formalin-fixed, paraffin-embedded biopsies with clear cell renal cell carcinoma for exploration of disease biology and biomarker development. PLoS One 2016;11:e0149743.
   PubMed Web of Science ®Google Scholar
• Ljungberg B, Bensalah K, Canfield S, Dabestani S, Hofmann F, Hora M, et al. EAU guidelines on renal cell carcinoma: 2014 update. Eur Urol 2015;67:913–24.
   PubMed Web of Science ®Google Scholar
• Huang W, Goldfischer M, Babyeva S, Mao Y, Volyanskyy K, Dimitrova N, et al. Identification of a novel PARP14-TFE3 gene fusion from 10-year-old FFPE tissue by RNA-seq. Genes Chromosomes Cancer 2015;54:500–505.
   Web of Science ®Google Scholar
• Walther C, Hofvander J, Nilsson J, Magnusson L, Domanski HA, Gisselsson D, et al. Gene fusion detection in formalin-fixed paraffin-embedded benign fibrous histiocytomas using fluorescence in situ hybridization and RNA sequencing. Lab Invest 2015;95:1071–6.
   PubMed Web of Science ®Google Scholar
• Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 2012;366:883–92.
   PubMed Web of Science ®Google Scholar
• Law CW, Chen Y, Shi W, Smyth GK. voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol 2014;15:R29.
   PubMed Web of Science ®Google Scholar
• von Roemeling CA, Radisky DC, Marlow LA, Cooper SJ, Grebe SK, Anastasiadis PZ, et al. Neuronal pentraxin 2 supports clear cell renal cell carcinoma by activating the AMPA-selective glutamate receptor-4. Cancer Res 2014;74:4796–810.
   PubMed Web of Science ®Google Scholar
• Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, et al. The Microarray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol 2010;28:827–38.
   PubMed Web of Science ®Google Scholar
• Li G, Feng G, Gentil-Perret A, Genin C, Tostain J. Serum carbonic anhydrase 9 level is associated with postoperative recurrence of conventional renal cell cancer. J Urol 2008;180:510–3. discussion 3-4.
   PubMed Web of Science ®Google Scholar
• Zhou GX, Ireland J, Rayman P, Finke J, Zhou M. Quantification of carbonic anhydrase IX expression in serum and tissue of renal cell carcinoma patients using enzyme-linked immunosorbent assay: prognostic and diagnostic potentials. Urology 2010;75:257–61.
   PubMed Web of Science ®Google Scholar
• Hulick P, Zimmer M, Margulis V, Skates S, Hamel M, Dahl DM, et al. Blood levels of carbonic anhydrase 9 correlate with clear cell renal cell carcinoma activity. Clin Proteom 2009;5:37–45.
   Google Scholar
• Tostain J, Li G, Gentil-Perret A, Gigante M. Carbonic anhydrase 9 in clear cell renal cell carcinoma: a marker for diagnosis, prognosis and treatment. Eur J Cancer 2010;46:3141–8.
   PubMed Web of Science ®Google Scholar
• Bommaya G, Meran S, Krupa A, Phillips AO, Steadman R. Tumour necrosis factor-stimulated gene (TSG)-6 controls epithelial-mesenchymal transition of proximal tubular epithelial cells. Int J Biochem Cell Biol 2011;43:1739–46.
   PubMed Web of Science ®Google Scholar
• Mikami S, Mizuno R, Kosaka T, Saya H, Oya M, Okada Y. Expression of TNF-α and CD44 is implicated in poor prognosis, cancer cell invasion, metastasis and resistance to the sunitinib treatment in clear cell renal cell carcinomas. Int J Cancer 2015;136:1504–14.
   PubMed Web of Science ®Google Scholar
• Chi JT, Wang Z, Nuyten DS, Rodriguez EH, Schaner ME, Salim A, et al. Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers. PLoS Med 2006;3:e47.
   PubMed Web of Science ®Google Scholar
• Zhou L, Chen J, Li Z, Li X, Hu X, Huang Y, et al. Integrated profiling of microRNAs and mRNAs: microRNAs located on Xq27.3 associate with clear cell renal cell carcinoma. PLoS One 2010;5:e15224.
   PubMed Web of Science ®Google Scholar
• Wu S, Lv Z, Wang Y, Sun L, Jiang Z, Xu C, et al. Increased expression of pregnancy up-regulated non-ubiquitous calmodulin kinase is associated with poor prognosis in clear cell renal cell carcinoma. PLoS One 2013;8:e59936.
   Google Scholar
• Deb TB, Zuo AH, Barndt RJ, Sengupta S, Jankovic R, Johnson MD. Pnck overexpression in HER-2 gene-amplified breast cancer causes Trastuzumab resistance through a paradoxical PTEN-mediated process. Breast Cancer Res Treat 2015;150:347–61.
   PubMed Web of Science ®Google Scholar