title: Needle core biopsies provide ample material for genomic and proteomic studies of kidney cancer: observations on DNA, RNA, protein extractions and VHL mutation detection.
abstract: The use of needle biopsies in basic research is increasing, and our study provides a comprehensive analysis of their adequacy in genomic and proteomic studies of kidney cancer. Frozen clear cell renal cell carcinoma (ccRCC) needle core biopsies and sections from core biopsies embedded in optimal cutting temperature (OCT) compound were used to extract DNA, RNA and protein. Their integrity was determined using genomic and proteomic analyses. VHL mutation testing was performed on ccRCC biopsies and corresponding tumors using bulk and laser capture microdissection (LCM) extractions for comparison. Adequate amounts of good quality DNA (5.8-13.3 μg/whole core, 0.6-2.7 μg/20 sections), RNA (2.9-11.9 μg/whole core, 0.5-1.3 μg/20 sections) and protein (137.4-444 μg/whole core, 39.9-74.1 μg/20 sections) were obtained from whole core and frozen sections of ccRCC needle biopsies, respectively. We observed VHL sequence mutations in 75% of ccRCC tumors and, in most cases, the same mutations were detected in both tumors and corresponding biopsies. Mutations observed by bulk extractions from tumors and biopsies were also detected by LCM without significant differences between both methodologies. ccRCC needle biopsies provide ample material for genomic and proteomic studies of kidney cancer. They are good representatives of their corresponding tumors for VHL mutation detection using both bulk and LCM extractions. LCM does not increase sensitivity of VHL mutation detection.
authors.affiliation: Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, University of Toronto, Toronto, Canada.
authors.forename: Ghada
authors.initials: G
authors.lastname: Kurban
authors.forename: Brenda L
authors.initials: BL
authors.lastname: Gallie
authors.forename: Michael
authors.initials: M
authors.lastname: Leveridge
authors.forename: Andrew
authors.initials: A
authors.lastname: Evans
authors.forename: Diane
authors.initials: D
authors.lastname: Rushlow
authors.forename: Donco
authors.initials: D
authors.lastname: Matevski
authors.forename: Rashi
authors.initials: R
authors.lastname: Gupta
authors.forename: Antonio
authors.initials: A
authors.lastname: Finelli
authors.forename: Michael A S
authors.initials: MA
authors.lastname: Jewett
mesh_terms: D001707:Biopsy, Needle; D002292:Carcinoma, Renal Cell / Q000235:genetics* / Q000378:metabolism / Q000601:surgery; D004247:DNA / Q000032:analysis* / Q000235:genetics / Q000302:isolation & purification; D020869:Gene Expression Profiling / Q000379:methods; D023281:Genomics / Q000379:methods; D006801:Humans; D007150:Immunohistochemistry; D007680:Kidney Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000601:surgery; D061346:Laser Capture Microdissection; D060885:Multiplex Polymerase Chain Reaction; D009154:Mutation; D011506:Proteins / Q000032:analysis / Q000235:genetics / Q000302:isolation & purification; D040901:Proteomics / Q000379:methods; D012313:RNA / Q000032:analysis* / Q000235:genetics / Q000302:isolation & purification; D020133:Reverse Transcriptase Polymerase Chain Reaction; D051794:Von Hippel-Lindau Tumor Suppressor Protein / Q000235:genetics*
chemical_list: D011506:Proteins; D012313:RNA; D004247:DNA; D051794:Von Hippel-Lindau Tumor Suppressor Protein; C497446:VHL protein, human