Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)

Nucleic Acids Research

Volumn 35, Issue 15, 2007, Pages

  Loudig, Olivier ^a   Milova, Ekaterina ^a   Brandwein Gensler, Margaret ^a   Massimi, Aldo ^a   Belbin, Thomas J ^a   Childs, Geoffrey ^a   Singer, Robert H ^a   Rohan, Thomas ^a   Prystowsky, Michael B ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; PARAFFIN; RNA; SINGLE STRANDED DNA; COMPLEMENTARY RNA; FIXATIVE; FORMALDEHYDE; PRIMER DNA;

ARTICLE; BREAST CANCER; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA SEQUENCE; DNA TEMPLATE; FEMALE; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE LIBRARY; HUMAN; HUMAN TISSUE; IN VITRO STUDY; MICROARRAY ANALYSIS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; RELIABILITY; REVERSE TRANSCRIPTION; RNA DEGRADATION; TISSUE SPECIFICITY; UTERINE CERVIX CANCER; VALIDATION PROCESS; BIOSYNTHESIS; BREAST TUMOR; CHEMISTRY; DNA MICROARRAY; GENETICS; HEALTH CARE FACILITY; METABOLISM; METHODOLOGY; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TUMOR GENE; VALIDATION STUDY;

BIOLOGICAL SPECIMEN BANKS; BREAST NEOPLASMS; DNA PRIMERS; DNA, COMPLEMENTARY; FEMALE; FIXATIVES; FORMALDEHYDE; GENE EXPRESSION PROFILING; GENES, NEOPLASM; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PARAFFIN EMBEDDING; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION; RNA, COMPLEMENTARY; TEMPLATES, GENETIC;

EID: 34548580290     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm510     Document Type: Article

References (47)

1. Mohr,S., Leikauf,G.D., Keith,G. and Rihn,B.H. (2002) Microarrays as cancer keys: An array of possibilities. J. Clin. Oncol., 20, 3165-3175.
2. Perou,C.M., Sorlie,T., Eisen,M.B., van de Rijn,M., Jeffrey,S.S., Rees,C.A., Pollack,J.R., Ross,D.T., Johnsen,H. et al. (2000) Molecular portraits of human breast tumours. Nature, 406, 747-752.
3. Sorlie,T., Perou,C.M., Tibshirani,R., Aas,T., Geisler,S., Johnsen,H., Hastie,T., Eisen,M.B., van de Rijn,M. et al. (2001) Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl Acad. Sci. USA, 98, 10869-10874.
4. Sorlie,T., Tibshirani,R., Parker,J., Hastie,T., Marron,J.S., Nobel,A., Deng,S., Johnsen,H., Pesich,R. et al. (2003) Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc. Natl Acad. Sci. USA, 100, 8418-8423.
5. Golub,T.R. (2001) Genome-wide views of cancer. N. Engl. J. Med., 344, 601-602.
6. Abramovitz,M. and Leyland-Jones,B.R. (2006) A systems approach to clinical oncology: Focus on breast cancer. Proteome Sci., 4, 5.
7. Robison,J.E., Perreard,L. and Bernard,P.S. (2000) State of the science: molecular classifications of breast cancer for clinical diagnostics. Clin. Biochem., 37, 572-578.
8. Dietel,M. and Sers,C. (2006) Personalized medicine and development of targeted therapies: The upcoming challenge for diagnostic molecular pathology. A review. Virchows Arch., 448, 744-755.
9. Werner,M., Chott,A., Fabiano,A. and Battifora,H. (2000) Effect of formalin tissue fixation and processing on immunohistochemistry. Am. J. Surg. Pathol., 24, 1016-1019.
10. Krafft,A.E., Duncan,B.W., Bijwaard,K.E., Taubenberger,J.K. and Lichy,J.H. (1997) Optimization of the isolation and amplification of RNA from formalin-fixed, paraffin-embedded tissue: The armed forces institute of pathology experience and literature review. Mol. Diagn. 2, 217-230.
11. Stanta,G., Bonin,S. and Perin,R. (1998) RNA extraction from formalin-fixed and paraffin-embedded tissues. Methods Mol. Biol., 86, 23-26.
12. Masuda,N., Ohnishi,T., Kawamoto,S., Monden,M. and Okubo,K. (1999) Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. Nucleic Acids Res., 27, 4436-4443.
13. Coombs,N.J., Gough,A.C. and Primrose,J.N. (1999) Optimisation of DNA and RNA extraction from archival formalin-fixed tissue. Nucleic Acids Res., 27, e12.
14. Cronin,M., Pho,M., Dutta,D., Stephans,J.C., Shak,S., Kiefer,M.C., Esteban,J.M. and Baker,J.B. (2004) Measurement of gene expression in archival paraffin-embedded tissues: Development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay. Am. J. Pathol., 164, 35-42.
15. Lehmann,U. and Kreipe,H. (2001) Real-time PCR analysis of DNA and RNA extracted from formalin-fixed and paraffin-embedded biopsies. Methods 25, 409-418.
16. Lewis,F., Maughan,N.J., Smith,V., Hillan,K. and Quirke,P. (2001) Unlocking the archive - gene expression in paraffin-embedded tissue. J. Pathol., 195, 66-71.
17. Relf,B.L., Machaalani,R. and Waters,K.A. (2002) Retrieval of mRNA from paraffin-embedded human infant brain tissue for non-radioactive in situ hybridization using oligonucleotides. J. Neurosci. Methods, 115 129-136.
18. Capodieci,P., Donovan,M., Buchinsky,H., Jeffers,Y., Cordon-Cardo,C., Gerald,W., Edelson,J., Shenoy,S.M. and Singer,R.H. (2005) Gene expression profiling in single cells within tissue. Nat. Methods, 2, 663-665.
19. Paik,S., Kim,C.Y., Song,Y.K. and Kim,W.S. (2005) Technology insight: application of molecular techniques to formalin-fixed paraffin-embedded tissues from breast cancer. Nat. Clin. Pract. Oncol., 2, 246-254.
20. Bibikova,M., Talantov,D., Chudin,E., Yeakley,J.M., Chen,J., Doucet,D., Wickham,E., Atkins,D., Barker,D. et al. (2004) Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays. Am. J. Pathol., 165, 1799-1807.
21. Bibikova,M., Yeakley,J.M., Chudin,E., Chen,J., Wickham,E., Wang-Rodriguez,J. and Fan,J.B. (2004) Gene expression profiles in formalin-fixed, paraffin-embedded tissues obtained with a novel assay for microarray analysis. Clin. Chem., 50, 2384-2386.
22. Ma,X.J., Patel,R., Wang,X., Salunga,J., Desai,R., Tuggle,J. T., Wang,W., Chu,S., Stecker,K. et al. (2006) Molecular classification of human cancers using a 92 real-time quantitative polymerase chain reaction assay. Arch. Pathol. Lab. Med., 130, 465-473.
23. Karsten,S.L., Van Deerlin,V.M., Sabatti,C., Gill,L.H. and Geschwind,D.H. (2002) An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis. Nucleic Acids Res., 30, e4.
24. Klur,S., Toy,K., Williams,M.P. and Certa,U. (2004) Evaluation of procedures for amplification of small-size samples for hybridization on microarrays. Genomics, 83, 508-517.
25. Xiang,C.C., Chen,M., Ma,L., Phan,Q.N., Inman,J.M., Kozhich,O.A. and Brownstein,M.J. (2003) A new strategy to amplify degraded RNA from small tissue samples for microarray studies. Nucleic Acids Res., 31 e53.
26. Wang,J., Hu,L., Hamilton,S.R., Coombes,K.R. and Zhang,W. (2003) RNA amplification strategies for cDNA microarray experiments. Biotechniques, 34, 394-400.
27. Onken,M.D., Worley,L.A., Ehlers,J.P. and Harbour,J.W. (2004) Gene expression profiling in uveal melanoma reveals two molecular classes and predicts metastatic death. Cancer Res., 64, 7205-7209.
28. Chung,C.H., Parker,J.S., Ely,K., Carter,J., Yi,Y., Murphy,B.A., Ang,K.K., El-Naggar,A.K., Zanation,A.M. et al. (2006) Gene expression profiles identify epithelial-to-mesenchymal transition and activation of nuclear factor-(kappa) B signaling as characteristics of a high-risk head and neck squamous cell carcinoma. Cancer Res., 66, 8210-8218.
29. Coudry,A.R, Meireles,R.S, Cooper,H.S., Carpino,A., Wang,X., Engstrom,P.F. and Clapper,M.L. (2007) Successful application of microarray technology to microdissected formalin-fixed, paraffin-embedded tissue. J. Mol. Diagn., 9, 70-79.
30. Penland,S.K., Keku,T.O., Torrice,C., He,X., Krishnamurthy,J., Hoadley,K.A., Woosley,J.T., Thomas,N.E., Perou,C.M. et al. (2007) RNA expression analysis of formalin-fixed paraffin-embedded tumors. Lab. Invest. e1-e9.
31. Van Gelder,R.N., von Zastrow,M.E., Yool,A., Dement,W.C., Barchas,J.D. and Eberwine,J.H. (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc. Natl Acad. Sci. USA, 87 1663-1667.
32. Goff,L.A., Bowers,J., Schwalm,J., Howerton,K., Getts,R.C. and Hart,R.P. (2004) Evaluation of sense-strand mRNA amplification by comparative quantitative PCR. BMC Genomics, 5, 76.
33. Belbin,T.J., Bhuvanesh,S., Barber,I., Socci,N., Wenig,B., Smith,R., Prystowsky,M.B. and Childs,G. (2002) Molecular classification of head and neck squamous cell carcinoma using cDNA microarrays. Cancer Res. 62, 1184-1190.
34. Lebeau,A., Unholzer,A., Amann,G., Kronawitter,M., Bauerfeind,I., Sendelhofert,A., Iff,A. and Lohrs,U. (2003) EGFR, HER-2/neu, cyclin D1, p21 and p53 in correlation to cell proliferation and steroid hormone receptor status in ductal carcinoma in-situ of the breast. Breast Cancer Res. Treat., 79, 187-198.
35. Reid,A.H., Taubenberger,J.K. and Fanning,T.G. (2001) The 1918 spanish influenza: Integrating history and Biology. Microbes Infect., 3 81.
36. Stevens,J., Corper,A.L., Basler,C.F., Taubenberger,J.K., Palese,P. and Wilson,I.A. (2004) Structure of the uncleaved human H1 hemagglutinin from the extinct 1918 influenza virus. Science, 303, 1866-1870.
37. Abrahamsen,H.N., Steiniche,T., Nexo,E., Hamilton-Dutoi,S.J. and Sorensen,B.S. (2003) Towards quantitative mRNA analysis in paraffin-embedded tissues using real-time reverse transcriptase-polymerase chain reaction: A methodological study on lymph nodes from melanoma patients. J. Mol. Diagn., 5, 34-41.
38. Antonov,J., Goldstein,D.R., Oberli,A., Baltzer,A., Pirotta,M., Fleischmann,A., Altermatt,H.J. and Jaggi,R. (2005) Reliable expression measurements from degraded RNA by quantitative real-time PCR depend on short amplicons and a proper normalization. Lab. Invest., 85 1040-1050.
39. Schoor,O., Weinschenk,T., Hennenlotter,J., Corvin,S., Stenzl,A., Rammensee,H-G. and Stefanovic,S. (2003) Moderate degradation does not preclude microarray analysis of small amounts of RNA. Biotechniques 35, 1192-1201.
40. Tomlins,S.A., Mehra,R., Rhodes,D.R., Shah,R.B., Rubin,M.A., Bruening,E., Makarov,V. and Chinnaiyan,A.M. (2006) Whole transcriptome amplification for gene expression profiling and development of molecular archives. Neoplasia, 8, 153-162.
41. Scicchitano,M.S., Dalmas,M.A., Bertiaux,M.A., Anderson,S.M., Turner,L.R., Thomas,R.A., Mirable,R and Boyce,R.W. (2006) Preliminary comparison of quantity, quality, and microarray performance of RNA extracted from formalin-fixed, paraffin-embedded, and unfixed frozen tissue samples. J. Histochem. Cytochem., 54, 1229-1237.
42. Diaz,G.A., Rong,M., McAllister,W.T. and Durbin,R.K. (1996) The stability of abortively cycling T7 RNA polymerase complexes depends upon template conformation. Biochemistry, 35, 10837-10843.
43. Lopez,P.J., Guillerez,J., Sousa,R. and Dreyfus,M. (1997) The low processivity of T7 RNA polymerase over the initially transcribed sequence can limit productive initiation in vivo. J. Mol. Biol., 269, 41-51.
44. Gong,P. and Martin,C.T. (2006) Mechanism of instability in abortive cycling by T7 RNA polymerase. J. Biol. Chem., 281, 23533-23544.
45. Edwalds-Gilbert,G., Veraldi,K.L. and Milcarek,C. (1997) Alternative poly(A) site selection in complex transcription units: Means to an end. Nucleic Acids Res., 25, 2547-2561.
46. Hughes,T.A. (2006) Regulation of gene expression by alternative untranslated regions. Trends Genet., 22, 119-122.
47. De Andres,B., del Pozo,V., Gallardo,S., de Arruda-Chaves,E., Cardaba,B., Martin-Orozco,E., Posada,M., Palomino,P. and Lahoz,C. (1995) Improved method for mRNA extraction from paraffin-embedded tissues. Biotechniques, 18, 42-44.