Kryvenko ON, Jorda M, Argani P, Epstein JI. Diagnostic approach to eosinophilic renal neoplasms. Arch Pathol Lab Med. 2014;138(11):1531–41. https://doi.org/10.5858/arpa.2013-0653-RA.
Article
PubMed
PubMed Central
Google Scholar
Wu A. Oncocytic renal neoplasms on resections and core biopsies: our approach to this challenging differential diagnosis. Arch Pathol Lab Med. 2017;141(10):1336–41. https://doi.org/10.5858/arpa.2017-0240-RA.
Article
CAS
PubMed
Google Scholar
Moch H, Cubilla AL, Humphrey PA, Reuter VE, Ulbright TM. The 2016 WHO classification of tumours of the urinary system and male genital organs—part A: renal, penile, and testicular tumours. Eur Urol. 2016;70(1):93–105. https://doi.org/10.1016/j.eururo.2016.02.029.
Article
PubMed
Google Scholar
Gilbertson JA, Theis JD, Vrana JA, Lachmann H, Wechalekar A, Whelan C, et al. A comparison of immunohistochemistry and mass spectrometry for determining the amyloid fibril protein from formalin-fixed biopsy tissue. J Clin Pathol. 2015;68(4):314–7. https://doi.org/10.1136/jclinpath-2014-202722.
Article
PubMed
Google Scholar
Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B. Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem. 2007;389(4):1017–31. https://doi.org/10.1007/s00216-007-1486-6.
Article
CAS
PubMed
Google Scholar
Wiśniewski JR, Hein MY, Cox J, Mann M. A “proteomic ruler” for protein copy number and concentration estimation without spike-in standards. Mol Cell Proteomics. 2014;13(12):3497–506. https://doi.org/10.1074/mcp.M113.037309.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wiśniewski JR, Duś-Szachniewicz K, Ostasiewicz P, Ziółkowski P, Rakus D, Mann M. Absolute proteome analysis of colorectal mucosa, adenoma, and cancer reveals drastic changes in fatty acid metabolism and plasma membrane transporters. J Proteome Res. 2015;14(9):4005–18. https://doi.org/10.1021/acs.jproteome.5b00523.
Article
CAS
PubMed
Google Scholar
Wiśniewski JR, Vildhede A, Norén A, Artursson P. In-depth quantitative analysis and comparison of the human hepatocyte and hepatoma cell line HepG2 proteomes. J Proteomics. 2016;136:234–47. https://doi.org/10.1016/j.jprot.2016.01.016.
Article
CAS
PubMed
Google Scholar
Wiśniewski JR, Friedrich A, Keller T, Mann M, Koepsell H. The impact of high-fat diet on metabolism and immune defense in small intestine mucosa. J Proteome Res. 2015;14(1):353–65. https://doi.org/10.1021/pr500833v.
Article
CAS
PubMed
Google Scholar
Chinello C, L’imperio V, Stella M, Smith AJ, Bovo G, Grasso A, et al. The proteomic landscape of renal tumors. Expert Rev Proteomics. 2016;13(12):1103–20. https://doi.org/10.1080/14789450.2016.1248415.
Article
CAS
PubMed
Google Scholar
Valera VA, Li-Ning-T E, Walter BA, Roberts DD, Linehan WM, Merino MJ. Protein expression profiling in the spectrum of renal cell carcinomas. J Cancer. 2010;1:184–96. https://doi.org/10.7150/jca.1.184.
Article
CAS
PubMed
PubMed Central
Google Scholar
Siu KWM, DeSouza LV, Scorilas A, Romaschin AD, Honey RJ, Stewart R, et al. Differential protein expressions in renal cell carcinoma: new biomarker discovery by mass spectrometry. J Proteome Res. 2009;8(8):3797–807. https://doi.org/10.1021/pr800389e.
Article
CAS
PubMed
Google Scholar
Masui O, White NMA, DeSouza LV, Krakovska O, Matta A, Metias S, et al. Quantitative proteomic analysis in metastatic renal cell carcinoma reveals a unique set of proteins with potential prognostic significance. Mol Cell Proteomics. 2013;12(1):132–44. https://doi.org/10.1074/mcp.M112.020701.
Article
CAS
PubMed
Google Scholar
White NMA, Masui O, DeSouza LV, Krakovska O, Metias S, Romaschin AD, et al. Quantitative proteomic analysis reveals potential diagnostic markers and pathways involved in pathogenesis of renal cell carcinoma. Oncotarget. 2014;5:506–18. https://doi.org/10.18632/oncotarget.1529.
Article
PubMed
PubMed Central
Google Scholar
Atrih A, Mudaliar MAVV, Zakikhani P, Lamont DJ, Huang JT-J, Bray SE, et al. Quantitative proteomics in resected renal cancer tissue for biomarker discovery and profiling. Br J Cancer. 2014;110(6):1622–33. https://doi.org/10.1038/bjc.2014.24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao Z, Wu F, Ding S, Sun L, Liu Z, Ding K, et al. Label-free quantitative proteomic analysis reveals potential biomarkers and pathways in renal cell carcinoma. Tumor Biol. 2015;36(2):939–51. https://doi.org/10.1007/s13277-014-2694-2.
Article
CAS
Google Scholar
Neely BA, Wilkins CE, Marlow LA, Malyarenko D, Kim Y, Ignatchenko A, et al. Proteotranscriptomic analysis reveals stage specific changes in the molecular landscape of clear-cell renal cell carcinoma. PLoS One. 2016;11(4):e0154074. https://doi.org/10.1371/journal.pone.0154074.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jorge S, Capelo JL, LaFramboise W, Dhir R, Lodeiro C, Santos HM. Development of a robust ultrasonic-based sample treatment to unravel the proteome of OCT-embedded solid tumor biopsies. J Proteome Res. 2019;18(7):2979–86. https://doi.org/10.1021/acs.jproteome.9b00248.
Article
CAS
PubMed
Google Scholar
Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 2019;47(D1):D442–50. https://doi.org/10.1093/nar/gky1106.
Article
CAS
PubMed
Google Scholar
Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008;26(12):1367–72. https://doi.org/10.1038/nbt.1511.
Article
CAS
PubMed
Google Scholar
Tyanova S, Temu T, Cox J. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc. 2016;11(12):2301–19. https://doi.org/10.1038/nprot.2016.136.
Article
CAS
PubMed
Google Scholar
Tyanova S, Temu T, Sinitcyn P, Carlson A, Hein MY, Geiger T, et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods. 2016;13(9):731–40. https://doi.org/10.1038/nmeth.3901.
Article
CAS
PubMed
Google Scholar
Tyanova S, Cox J. Perseus: a bioinformatics platform for integrative analysis of proteomics data in cancer research. In: Methods in Molecular Biology; 2018. p. 133–48. https://doi.org/10.1007/978-1-4939-7493-1_7.
Chapter
Google Scholar
Wiśniewski JR. Label-Free and standard-free absolute quantitative proteomics using the “total protein” and “proteomic ruler” approaches. In: Methods in Enzymology: Academic Press Inc.; 2017. p. 49–60. https://doi.org/10.1016/bs.mie.2016.10.002.
Akhtar M, Al-Bozom IA, Al HT. Papillary renal cell carcinoma (PRCC): an update. Adv Anat Pathol. 2019;26(2):124–32. https://doi.org/10.1097/PAP.0000000000000220.
Article
PubMed
Google Scholar
Sun CY, Zang YC, San YX, Sun W, Zhang L. Proteomic analysis of clear cell renal cell carcinoma. Identification of potential tumor markers. Saudi Med J. 2010;31(5):525–32. http://www.matrixscience. .
PubMed
Google Scholar
Raimondo F, Corbetta S, Savoia A, Chinello C, Cazzaniga M, Rocco F, et al. Comparative membrane proteomics: a technical advancement in the search of renal cell carcinoma biomarkers. Mol Biosyst. 2015;11(6):1708–16. https://doi.org/10.1039/C5MB00020C.
Article
CAS
PubMed
Google Scholar
Weißer J, Lai ZW, Bronsert P, Kuehs M, Drendel V, Timme S, et al. Quantitative proteomic analysis of formalin–fixed, paraffin–embedded clear cell renal cell carcinoma tissue using stable isotopic dimethylation of primary amines. BMC Genomics. 2015;16(1):559. https://doi.org/10.1186/s12864-015-1768-x.
Article
CAS
PubMed
PubMed Central
Google Scholar
Raimondo F, Morosi L, Chinello C, Perego R, Bianchi C, Albo G, et al. Protein profiling of microdomains purified from renal cell carcinoma and normal kidney tissue samples. Mol BioSyst. 2012;8(4):1007–16. https://doi.org/10.1039/C2MB05372A.
Article
CAS
PubMed
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(18):3141–8. https://doi.org/10.1016/j.ejca.2010.07.020.
Article
CAS
PubMed
Google Scholar
Lichtenfels R, Dressler SP, Zobawa M, Recktenwald CV, Ackermann A, Atkins D, et al. Systematic comparative protein expression profiling of clear cell renal cell carcinoma. Mol Cell Proteomics. 2009;8(12):2827–42. https://doi.org/10.1074/mcp.M900168-MCP200.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim DS, Choi YP, Kang S, Gao MQ, Kim B, Park HR, et al. Panel of candidate biomarkers for renal cell carcinoma. J Proteome Res. 2010;9(7):3710–9. https://doi.org/10.1021/pr100236r.
Article
CAS
PubMed
Google Scholar
Morgan TM, Seeley EH, Fadare O, Caprioli RM, Clark PE. Imaging the clear cell renal cell carcinoma proteome. J Urol. 2013;189(3):1097–103. https://doi.org/10.1016/j.juro.2012.09.074.
Article
CAS
PubMed
Google Scholar
Raimondo F, Salemi C, Chinello C, Fumagalli D, Morosi L, Rocco F, et al. Proteomic analysis in clear cell renal cell carcinoma: identification of differentially expressed protein by 2-D DIGE. Mol Biosyst. 2012;8(4):1040–51. https://doi.org/10.1039/c2mb05390j.
Article
CAS
PubMed
Google Scholar
Jones EE, Powers TW, Neely BA, Cazares LH, Troyer DA, Parker AS, et al. MALDI imaging mass spectrometry profiling of proteins and lipids in clear cell renal cell carcinoma. Proteomics. 2014;14(7-8):924–35. https://doi.org/10.1002/pmic.201300434.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lebdai S, Verhoest G, Parikh H, Jacquet SF, Bensalah K, Chautard D, et al. Identification and validation of TGFBI as a promising prognosis marker of clear cell renal cell carcinoma. Urol Oncol Semin Orig Investig. 2015;33:69.e11–8. https://doi.org/10.1016/j.urolonc.2014.06.005.
Article
CAS
Google Scholar
Johann DJ, Wei B-R, Prieto DA, Chan KC, Ye X, Valera VA, et al. Combined blood/tissue analysis for cancer biomarker discovery: application to renal cell carcinoma. Anal Chem. 2010;82(5):1584–8. https://doi.org/10.1021/ac902204k.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yao Y, Lu Z, Song Q, Yang J, Zhao X, Yang P, et al. Metabolism-related enzyme alterations identified by proteomic analysis in human renal cell carcinoma. Onco Targets Ther. 2016;9:1327. https://doi.org/10.2147/OTT.S91953.
Article
PubMed
PubMed Central
Google Scholar
Song Y, Zhong L, Zhou J, Lu M, Xing T, Ma L, et al. Data-independent acquisition-based quantitative proteomic analysis reveals potential biomarkers of kidney cancer. PROTEOMICS - Clin Appl. 2017;11(11-12):1700066. https://doi.org/10.1002/prca.201700066.
Article
CAS
Google Scholar
Giribaldi G, Barbero G, Mandili G, Daniele L, Khadjavi A, Notarpietro A, et al. Proteomic identification of Reticulocalbin 1 as potential tumor marker in renal cell carcinoma. J Proteomics. 2013;91:385–92. https://doi.org/10.1016/j.jprot.2013.07.018.
Article
CAS
PubMed
Google Scholar
Oppenheimer SR, Mi D, Sanders ME, Caprioli RM. Molecular analysis of tumor margins by MALDI mass spectrometry in renal carcinoma. J Proteome Res. 2010;9(5):2182–90. https://doi.org/10.1021/pr900936z.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gabril M, Girgis H, Scorilas A, Rotondo F, Wala S, Bjarnason GA, et al. S100A11 is a potential prognostic marker for clear cell renal cell carcinoma. Clin Exp Metastasis. 2016;33(1):63–71. https://doi.org/10.1007/s10585-015-9758-6.
Article
CAS
PubMed
Google Scholar
Qi Y, Zhang Y, Peng Z, Wang L, Wang K, Feng D, et al. SERPINH1 overexpression in clear cell renal cell carcinoma: association with poor clinical outcome and its potential as a novel prognostic marker. J Cell Mol Med. 2018;22:1224–35. https://doi.org/10.1111/jcmm.13495.
Article
CAS
PubMed
Google Scholar
Guo T, Kouvonen P, Koh CC, Gillet LC, Wolski WE, Röst HL, et al. Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps. Nat Med. 2015;21(4):407–13. https://doi.org/10.1038/nm.3807.
Article
CAS
PubMed
PubMed Central
Google Scholar
Klatte T, Rossi SH, Stewart GD. Prognostic factors and prognostic models for renal cell carcinoma: a literature review. World J Urol. 2018;36(12):1943–52. https://doi.org/10.1007/s00345-018-2309-4.
Article
PubMed
Google Scholar
Inamura K. Renal Cell Tumors: Understanding their molecular pathological epidemiology and the 2016 WHO classification. Int J Mol Sci. 2017;18(10):2195. https://doi.org/10.3390/ijms18102195.
Article
CAS
PubMed Central
Google Scholar
Marsaud A, Dadone B, Ambrosetti D, Baudoin C, Chamorey E, Rouleau E, et al. Dismantling papillary renal cell carcinoma classification: the heterogeneity of genetic profiles suggests several independent diseases. Genes, Chromosom Cancer. 2015;54(6):369–82. https://doi.org/10.1002/gcc.22248.
Article
CAS
Google Scholar
Valladares Ayerbes M, Aparicio Gallego G, Díaz Prado S, Jiménez Fonseca P, García Campelo R, Antón Aparicio LM. Origin of renal cell carcinomas. Clin Transl Oncol. 2008;10(11):697–712. https://doi.org/10.1007/s12094-008-0276-8.
Article
CAS
PubMed
Google Scholar
Mori S, Takao S, Ikeda R, Noma H, Mataki Y, Wang X, et al. Thymidine phosphorylase suppresses Fas-induced apoptotic signal transduction independent of its enzymatic activity. Biochem Biophys Res Commun. 2002;295(2):300–5. https://doi.org/10.1016/S0006-291X(02)00662-9.
Article
CAS
PubMed
Google Scholar
Bijnsdorp IV, Capriotti F, Kruyt FAE, Losekoot N, Fukushima M, Griffioen AW, et al. Thymidine phosphorylase in cancer cells stimulates human endothelial cell migration and invasion by the secretion of angiogenic factors. Br J Cancer. 2011;104(7):1185–92. https://doi.org/10.1038/bjc.2011.74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Takayama T, Mugiya S, Sugiyama T, Aoki T, Furuse H, Liu H, et al. High levels of thymidine phosphorylase as an independent prognostic factor in renal cell carcinoma. Jpn J Clin Oncol. 2006;36(9):564–9. https://doi.org/10.1093/jjco/hyl063.
Article
PubMed
Google Scholar
Qiu B, Ackerman D, Sanchez DJ, Li B, Ochocki JD, Grazioli A, et al. HIF2α-dependent lipid storage promotes endoplasmic reticulum homeostasis in clear-cell renal cell carcinoma. Cancer Discov. 2015;5(6):652–67. https://doi.org/10.1158/2159-8290.CD-14-1507.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mylonis I, Simos G, Paraskeva E. Hypoxia-inducible factors and the regulation of lipid metabolism. Cells. 2019;8(3):214. https://doi.org/10.3390/cells8030214.
Article
CAS
PubMed Central
Google Scholar
Rybakin V, Clemen CS. Coronin proteins as multifunctional regulators of the cytoskeleton and membrane trafficking. BioEssays. 2005;27(6):625–32. https://doi.org/10.1002/bies.20235.
Article
CAS
PubMed
Google Scholar
Shen SS, Truong LD, Scarpelli M, Lopez-Beltran A. Role of immunohistochemistry in diagnosing renal neoplasms: when is it really useful? Arch Pathol Lab Med. 2012;136(4):410–7. https://doi.org/10.5858/arpa.2011-0472-RA.
Article
PubMed
Google Scholar
Alshenawy HA. Immunohistochemical panel for differentiating renal cell carcinoma with clear and papillary features. Pathol Oncol Res. 2015;21(4):893–9. https://doi.org/10.1007/s12253-015-9898-7.
Article
CAS
PubMed
Google Scholar
Ng KL, Morais C, Bernard A, Saunders N, Samaratunga H, Gobe G, et al. A systematic review and meta-analysis of immunohistochemical biomarkers that differentiate chromophobe renal cell carcinoma from renal oncocytoma. J Clin Pathol. 2016;69(8):661–71. https://doi.org/10.1136/jclinpath-2015-203585.
Article
CAS
PubMed
Google Scholar
Mariani M, Karki R, Spennato M, Pandya D, He S, Andreoli M, et al. Class III β-tubulin in normal and cancer tissues. Gene. 2015;563(2):109–14. https://doi.org/10.1016/j.gene.2015.03.061.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tsourlakis MC, Weigand P, Grupp K, Kluth M, Steurer S, Schlomm T, et al. βIII-tubulin overexpression is an independent predictor of prostate cancer progression tightly linked to ERG fusion status and PTEN deletion. Am J Pathol. 2014;184(3):609–17. https://doi.org/10.1016/j.ajpath.2013.11.007.
Article
CAS
PubMed
Google Scholar
Drendel V, Heckelmann B, Schell C, Kook L, Biniossek ML, Werner M, et al. Proteomic distinction of renal oncocytomas and chromophobe renal cell carcinomas. Clin Proteomics. 2018;15:25. https://doi.org/10.1186/s12014-018-9200-6.
Schindler A, Foley E. Hexokinase 1 blocks apoptotic signals at the mitochondria. Cell Signal. 2013;25(12):2685–92. https://doi.org/10.1016/j.cellsig.2013.08.035.
Article
CAS
PubMed
Google Scholar
He X, Lin X, Cai M, Zheng X, Lian L, Fan D, et al. Overexpression of Hexokinase 1 as a poor prognosticator in human colorectal cancer. Tumor Biol. 2016;37(3):3887–95. https://doi.org/10.1007/s13277-015-4255-8.
Article
CAS
Google Scholar