Feasibility and relevance of global expression profiling of gene transcripts in serum from breast cancer patients using whole genome microarrays and quantitative RT-PCR.
BACKGROUND
Previous studies, by ourselves and others, have indicated that gene transcripts are detectable extracellularly. Advancing on this work, in order to investigate the feasibility of analysing global gene expression profiles and so the possibility in the future of identifying panels of circulating mRNA biomarkers that may be diagnostic, prognostic or predictive for cancer, here we performed the first whole genome microarray analysis of human serum.


METHODS
RNA was isolated from pre-surgery serum and corresponding breast tumour and normal tissue biopsies, and from post-surgery and normal control serum. Specimens were examined using Affymetrix whole genome microarrays and quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR).


RESULTS
Of the 54,675 mRNAs/variants analysed, approximately 8% and 45% were called Present in serum and breast tissue specimens, respectively. Differentially expressed genes were identified for each group of specimens analysed. Analysis, by qRT-PCR, of 3 selected transcripts further indicated that the nucleic acids detected were mRNA, not DNA. mRNAs are apparently present in serum and their global detection and identification can be successfully achieved using microarray technologies.


CONCLUSIONS
The potential implication of this novel finding is that using microarrays it may be possible to identify a panel of extracellular mRNAs that are diagnostic, prognostic and/or predictive of outcome for cancer patients.
O'Driscoll
Lorraine
L
National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland. Lorraine.ODriscoll@dcu.ie
Kenny
Elaine
E
Mehta
Jai Prakash
JP
Doolan
Padraig
P
Joyce
Helena
H
Gammell
Patrick
P
Hill
Arnold
A
O'Daly
Brendan
B
O'Gorman
Donal
D
Clynes
Martin
M
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001943:Breast Neoplasms / Q000097:blood* / Q000235:genetics*; D016000:Cluster Analysis; D004273:DNA, Neoplasm / Q000378:metabolism; D005240:Feasibility Studies; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards; D012333:RNA, Messenger / Q000097:blood*; D012334:RNA, Neoplasm / Q000302:isolation & purification; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction
D004273:DNA, Neoplasm; D012333:RNA, Messenger; D012334:RNA, Neoplasm