Significance of RNA reference in tumour-related gene expression analyses by cDNA array.
The cDNA array technique is an efficient approach for studying the expression of a large number of genes in a single experiment. The cDNA array analysis indicates the relative level of corresponding gene expression from a specimen and a reference. Our investigation was performed to address the significance of reference RNA on the outcome of the cancer-related gene expression profile obtained from cDNA array analysis. Human head and neck squamous cell carcinoma (HNSCC) biopsies and 5 sources of RNA reference were used for this purpose. In these biopsies, each individual patient expressed a unique set of genes both in normal and tumour tissue. It is important to note that 5 striking patterns of tumour-related gene expression were obtained according to the 5 references used. Significant differences in 60%, 16%, 15% and 15% of the genes expressed were shown when autologous normal matched tissue biopsy references were compared to pooled cell lines, allogenic normal mixed cell types, tumours or allogenic normal matched cell type references, respectively. Thus, theoretically and our study suggested that patient autologous normal cells matching with the tumour type should be the most suitable reference in cDNA array for the identification of individual tumour gene profiles with clinical purpose.
Laytragoon-Lewin
Nongnit
N
Department of Oncology Research Laboratory, Clinical Research Centre, Karolinska University Hospital, Huddinge, Sweden. nongnit.laytragoon-lewin@medhs.ki.se
Lagerlund
Magnus
M
Lundgren
Jan
J
Nordlander
Britt
B
Elmberger
Göran
G
Södergren
Towe
T
Lagerros
Christofer
C
Rutqvist
Lars Erik
LE
Lewin
Freddi
F
D000328:Adult; D000368:Aged; D001706:Biopsy; D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling; D006258:Head and Neck Neoplasms / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D012313:RNA; D014407:Tumor Cells, Cultured
D012313:RNA