mRNA expression, functional profiling and multivariate classification of colon biopsy specimen by cDNA overall glass microarray.
OBJECTIVE
To understand the local pathophysiological alterations and gene ontology-based functional classification of colonic biopsies into inflammatory and neoplastic diseases.


METHODS
Total RNA was extracted from frozen biopsies and amplified by T7-method. Expression profile was evaluated by Atlas Glass 1K microarrays. After microarray quality control, applicable data were available from 10 adenomas, 6 colorectal adenocarcinomas (CRCs), and 6 inflammatory bowel diseases (IBDs). Multivariate statistical and cell functional analyses were performed. Real-time RT-PCR and immunohistochemistry were used for validation.


RESULTS
Discriminant analysis of selected genes, could correctly reclassify all 22 samples using 4 parameters (heat shock transcription factor-1, bystin-like, calgranulin-A, TRAIL receptor 3). IBD samples were characterized by overregulated chemokine (C-X-C motif) ligand 13, replication protein A1, E74-like factor 2 and downregulated TNF receptor-associated factor 6, BCL2-interacting killer genes. In adenomas upregulation of TNF receptor-associated factor 6, replication protein A1, E74-like factor 2 and underexpression of BCL2-associated X protein, calgranulin-A genes were found. CRC cases had significantly increased epidermal growth factor receptor, topoisomerase-1, v-jun, TNF receptor-associated factor 6 and TRAIL receptor 3, and decreased RAD51 and RAD52 DNA repair gene, protein phosphatase-2A and BCL2-interacting killer mRNA levels. Epidermal growth factor receptor RT-PCR and immunohistochemistry, topoisomerase-1 RT-PCR confirmed the chip results.


CONCLUSIONS
Different histological alterations can be reclassified by functional, multivariate analysis using cDNA microarrays. Further studies with expanded sample number are needed for subclassification of pathological alterations.
Galamb
Orsolya
O
2nd Department of Internal Medicine, University Semmelweis, Budapest, Hungary. orsg1@yahoo.com
Sipos
Ferenc
F
Dinya
Elek
E
Spisak
Sandor
S
Tulassay
Zsolt
Z
Molnar
Bela
B
D000230:Adenocarcinoma / Q000175:diagnosis / Q000235:genetics / Q000378:metabolism; D000368:Aged; D000369:Aged, 80 and over; D000704:Analysis of Variance; D001706:Biopsy; D016000:Cluster Analysis; D003106:Colon / Q000378:metabolism / Q000473:pathology*; D015179:Colorectal Neoplasms / Q000175:diagnosis / Q000235:genetics / Q000378:metabolism; D004247:DNA / Q000235:genetics; D004273:DNA, Neoplasm / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D005819:Genetic Markers; D006801:Humans; D008297:Male; D008875:Middle Aged; D015999:Multivariate Analysis; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D015203:Reproducibility of Results
D004273:DNA, Neoplasm; D005819:Genetic Markers; D012333:RNA, Messenger; D004247:DNA