title: Messenger RNA expression ratios among four genes predict subtypes of renal cell carcinoma and distinguish oncocytoma from carcinoma.
abstract: OBJECTIVE
  Morphologic distinction among clear cell, papillary, and chromophobe types of renal cell carcinoma (RCC) can be difficult, as is the differential diagnosis between oncocytoma and RCC. Whether these renal tumors can be distinguished by their mRNA expression profile of a few selected genes was examined.
  
  
  METHODS
  The expression of four genes in renal tumor was evaluated by quantitative reverse transcription-PCR: carbonic anhydrase IX (CA9), methylacyl-CoA racemase (AMACR), parvalbumin (PVALB), and chloride channel kb (CLCNKB). Thirty-one fresh-frozen and 63 formalin-fixed, paraffin-embedded tumor specimens were analyzed.
  
  
  RESULTS
  CA9 expression was highest in clear cell carcinoma and lowest in chromophobe RCC and in oncocytoma. AMACR expression was highest in papillary RCC, and CLCNKB was highest in chromophobe RCC/oncocytoma. PVALB was highest in chromophobe RCC, variable in oncocytoma, and low in clear cell and papillary types. Similar findings were observed in fresh-frozen and formalin-fixed specimens. The mRNA expression ratios among these genes (i.e., CA9/AMACR and AMACR/CLCNKB ratios) further accentuate the gene expression differences among these tumors, and a molecular diagnostic algorithm was established. This algorithm accurately classified the 31 fresh-frozen tumors into 14 clear cell, 5 papillary, 6 chromophobe, and 6 oncocytomas. In the formalin-fixed group, the molecular criteria accurately classified the cases into 15 clear cell, 16 papillary, and 32 in the chromophobe/oncocytoma group but could only separate some, but not all, oncocytomas from chromophobe RCC.
  
  
  CONCLUSIONS
  RNA expression ratios based on the four-gene panel can accurately classify subtypes of RCC as well as help distinguish some oncocytomas from chromophobe RCC.
authors.affiliation: Department of Pathology and Laboratory Medicine, Weill Medical College, Cornell University, New York, NY 10021, USA. ytchen@med.cornell.edu
authors.forename: Yao-Tseng
authors.initials: YT
authors.lastname: Chen
authors.forename: Jiangling J
authors.initials: JJ
authors.lastname: Tu
authors.forename: Jean
authors.initials: J
authors.lastname: Kao
authors.forename: Xi K
authors.initials: XK
authors.lastname: Zhou
authors.forename: Madhu
authors.initials: M
authors.lastname: Mazumdar
mesh_terms: D018262:Adenocarcinoma, Clear Cell / Q000235:genetics / Q000473:pathology; D018249:Adenoma, Oxyphilic / Q000235:genetics / Q000473:pathology; D000465:Algorithms; D027321:Anion Transport Proteins / Q000235:genetics; D000951:Antigens, Neoplasm / Q000235:genetics; D000071231:Carbonic Anhydrase IX; D002256:Carbonic Anhydrases / Q000235:genetics; D002292:Carcinoma, Renal Cell / Q000235:genetics / Q000473:pathology; D018118:Chloride Channels / Q000235:genetics; D003937:Diagnosis, Differential; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007680:Kidney Neoplasms / Q000235:genetics / Q000473:pathology*; D008565:Membrane Proteins / Q000235:genetics; D009363:Neoplasm Proteins / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D019998:Racemases and Epimerases / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D023083:beta-Defensins / Q000235:genetics
chemical_list: D027321:Anion Transport Proteins; D000951:Antigens, Neoplasm; C412733:CLCNKB protein, human; D018118:Chloride Channels; C406407:DEFB1 protein, human; D008565:Membrane Proteins; D009363:Neoplasm Proteins; D012333:RNA, Messenger; D023083:beta-Defensins; C089226:CA9 protein, human; D000071231:Carbonic Anhydrase IX; D002256:Carbonic Anhydrases; D019998:Racemases and Epimerases; C108352:alpha-methylacyl-CoA racemase