Needle core biopsies provide ample material for genomic and proteomic studies of kidney cancer: Observations on DNA, RNA, protein extractions and VHL mutation detection

Pathology Research and Practice

Volumn 208, Issue 1, 2012, Pages 22-31

  Kurban, Ghada ^a   Gallie, Brenda L ^a,b,c,d   Leveridge, Michael ^e   Evans, Andrew ^f   Rushlow, Diane ^b   Matevski, Donco ^b   Gupta, Rashi ^d   Finelli, Antonio ^a   Jewett, Michael A S ^a  

^a PRINCESS MARGARET HOSPITAL   (Canada)

^b TORONTO WESTERN HOSPITAL   (Canada)

^c HOSPITAL FOR SICK CHILDREN   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

^e QUEEN S UNIVERSITY   (Canada)

^f UNIVERSITY HEALTH NETWORK   (Canada)

Author keywords

Kidney cancer; Laser capture microdissection; Needle biopsy; VHL mutation analysis

Indexed keywords

DNA; PROTEIN; RNA; VON HIPPEL LINDAU PROTEIN;

ARTICLE; CONTROLLED STUDY; DNA EXTRACTION; FROZEN SECTION; FUNCTIONAL GENOMICS; FUNCTIONAL PROTEOMICS; GENE MUTATION; GENE SEQUENCE; GENETIC SCREENING; HUMAN; HUMAN TISSUE; KIDNEY BIOPSY; KIDNEY CARCINOMA; MICRODISSECTION; MUTATIONAL ANALYSIS; PROTEIN DETERMINATION; RNA EXTRACTION; SENSITIVITY AND SPECIFICITY; TUMOR SUPPRESSOR GENE; VON HIPPEL LINDAU GENE;

BIOPSY, NEEDLE; CARCINOMA, RENAL CELL; DNA; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; IMMUNOHISTOCHEMISTRY; KIDNEY NEOPLASMS; LASER CAPTURE MICRODISSECTION; MULTIPLEX POLYMERASE CHAIN REACTION; MUTATION; PROTEINS; PROTEOMICS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA; VON HIPPEL-LINDAU TUMOR SUPPRESSOR PROTEIN;

EID: 84855783148     PISSN: 03440338     EISSN: 16180631     Source Type: Journal    
DOI: 10.1016/j.prp.2011.11.001     Document Type: Article

References (32)

1. Lipworth L., Tarone R.E., McLaughlin J.K. The epidemiology of renal cell carcinoma. J. Urol. 2006, 176:2353-2358.
2. Latif F., Tory K., Gnarra J., Yao M., Duh F.M., Orcutt M.L., et al. Identification of the von Hippel-Lindau disease tumor suppressor gene. Science 1993, 260:1317-1320.
3. Kaelin W.G. The von Hippel-Lindau tumor suppressor protein and clear cell renal carcinoma. Clin. Cancer Res. 2007, 13:680s-684s.
4. Volpe A., Panzarella T., Rendon R.A., Haider M.A., Kondylis F.I., Jewett M.A. The natural history of incidentally detected small renal masses. Cancer 2004, 100:738-745.
5. Volpe A., Jewett M.A. The role of surveillance for small renal masses. Nat. Clin. Pract. Urol. 2007, 4:2-3.
6. Volpe A., Kachura J.R., Geddie W.R., Evans A.J., Gharajeh A., Saravanan A., et al. Techniques, safety and accuracy of sampling of renal tumors by fine needle aspiration and core biopsy. J. Urol. 2007, 178:379-386.
7. Volpe A., Mattar K., Finelli A., Kachura J.R., Evans A.J., Geddie W.R., et al. Contemporary results of percutaneous biopsy of 100 small renal masses: a single center experience. J. Urol. 2008, 180:2333-2337.
8. Liu A. Laser capture microdissection in the tissue biorepository. J. Biomol. Tech. 2010, 21:120-125.
9. Yang S., Nan Y., Tian Y., Zhang W., Zhou B., Bu L., et al. Study of distinct protein profiles for early diagnosis of NSCLC using LCM and SELDI-TOF-MS. Med. Oncol. 2008, 25:380-386.
10. Gregg J.L., Brown K.E., Mintz E.M., Piontkivska H., Fraizer G.C. Analysis of gene expression in prostate cancer epithelial and interstitial stromal cells using laser capture microdissection. BMC Cancer 2010, 10:165.
11. Craven R.A., Totty N., Harnden P., Selby P.J., Banks R.E. Laser capture microdissection and two-dimensional polyacrylamide gel electrophoresis: evaluation of tissue preparation and sample limitations. Am. J. Pathol. 2002, 160:815-822.
12. Djalilvand A., Pal R., Goldman H., Antonioli D., Kocher O. Evaluation of p53 mutations in premalignant esophageal lesions and esophageal adenocarcinoma using laser capture microdissection. Mod. Pathol. 2004, 17:1323-1327.
13. Li T., Sotgia F., Vuolo M.A., Li M., Yang W.C., Pestell R.G., et al. Caveolin-1 mutations in human breast cancer: functional association with estrogen receptor alpha-positive status. Am. J. Pathol. 2006, 168:1998-2013.
14. Yang F., Foekens J.A., Yu J., Sieuwerts A.M., Timmermans M., Klijn J.G., et al. Laser microdissection and microarray analysis of breast tumors reveal ER-alpha related genes and pathways. Oncogene 2006, 25:1413-1419.
15. Harrell J.C., Dye W.W., Harvell D.M., Sartorius C.A., Horwitz K.B. Contaminating cells alter gene signatures in whole organ versus laser capture microdissected tumors: a comparison of experimental breast cancers and their lymph node metastases. Clin. Exp. Metastasis 2008, 25:81-88.
16. Banks R.E., Tirukonda P., Taylor C., Hornigold N., Astuti D., Cohen D., et al. Genetic and epigenetic analysis of von Hippel-Lindau (VHL) gene alterations and relationship with clinical variables in sporadic renal cancer. Cancer Res. 2006, 66:2000-2011.
17. Gnarra J.R., Tory K., Weng Y., Schmidt L., Wei M.H., Li H., et al. Mutations of the VHL tumour suppressor gene in renal carcinoma. Nat. Genet. 1994, 7:85-90.
18. Brauch H., Weirich G., Brieger J., Glavac D., Rodl H., Eichinger M., et al. VHL alterations in human clear cell renal cell carcinoma: association with advanced tumor stage and a novel hot spot mutation. Cancer Res. 2000, 60:1942-1948.
19. Nickerson M.L., Jaeger E., Shi Y., Durocher J.A., Mahurkar S., Zaridze D., et al. Improved identification of von Hippel-Lindau gene alterations in clear cell renal tumors. Clin. Cancer Res. 2008, 14:4726-4734.
20. Young A.C., Craven R.A., Cohen D., Taylor C., Booth C., Harnden P., et al. Analysis of VHL gene alterations and their relationship to clinical parameters in sporadic conventional renal cell carcinoma. Clin. Cancer Res. 2009, 15:7582-7592.
21. Li Y.L., Ye F., Hu Y., Lu W.G., Xie X. Identification of suitable reference genes for gene expression studies of human serous ovarian cancer by real-time polymerase chain reaction. Anal. Biochem. 2009, 394:110-116.
22. Yager T.D., Baron L., Batra R., Bouevitch A., Chan D., Chan K., et al. High performance DNA sequencing, and the detection of mutations and polymorphisms, on the Clipper sequencer. Electrophoresis 1999, 20:1280-1300.
23. Zeschnigk M., Lohmann D., Horsthemke B. A PCR test for the detection of hypermethylated alleles at the retinoblastoma locus. J. Med. Genet. 1999, 36:793-794.
24. Ishkanian A.S., Mallof C.A., Ho J., Meng A., Albert M., Syed A., et al. Bristow, High-resolution array CGH identifies novel regions of genomic alteration in intermediate-risk prostate cancer. Prostate 2009, 69:1091-1100.
25. Otto E.A., Hurd T.W., Airik R., Chaki M., Zhou W., Stoetzel C., et al. Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy. Nat. Genet. 2010, 42:840-850.
26. Wheeler D.A., Srinivasan M., Egholm M., Shen Y., Chen L., McGuire A., et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452:872-876.
27. Ozsolak F., Goren A., Gymrek M., Guttman M., Regev A., Bernstein B.E., et al. Digital transcriptome profiling from attomole-level RNA samples. Genome Res. 2010, 20:519-525.
28. Tauber S., Jais A., Jeitler M., Haider S., Husa J., Lindroos J. Transcriptome analysis of human cancer reveals a functional role of Heme Oxygenase-1 in tumor cell adhesion. Mol. Cancer 2010, 9:200.
29. Croner R.S., Lausen B., Schellerer V., Zeittraeger I., Wein A., Schildberg C., et al. Comparability of microarray data between amplified and non amplified RNA in colorectal carcinoma. J. Biomed. Biotechnol. 2009, 2009:837170.
30. Frohlich T., Arnold G.J., Fritsch R., Mayr T., Laforsch C. LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia. BMC Genomics 2009, 10:171.
31. Jorissen R.N., Gibbs P., Christie M., Prakash S., Lipton L., Desai J., et al. Metastasis-associated gene expression changes predict poor outcomes in patients with Dukes stage B and C colorectal cancer. Clin. Cancer Res. 2009, 15:7642-7651.
32. Beekman J.M., Reischl J., Henderson D., Bauer D., Ternes R., Pena C., et al. Recovery of microarray-quality RNA from frozen EDTA blood samples. J. Pharmacol. Toxicol. Methods 2009, 59:44-49.