[Functional mRNA expression analysis and classification of colonic biopsy samples using overall cDNA microarray technique].

Abstract

BACKGROUND:

Overall mRNA expression analysis of colon biopsies can contribute to the understanding of molecular background of the local 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 adenocarcinoma (CRC), and inflammatory bowel diseases (IBDs: 3-3 CD and UC). 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 objectively classified by functional, multivariate analysis using cDNA microarrays. Disease-specific gene expression patterns can assist to avoid the intermediate and nondescript cases in diagnostics, which do not belong to any of the conventional diagnostic groups.

• Authors: Orsolya Galamb, Ferenc Sipos, Elek Dinya, Sándor Spisák, Aron Somorácz, Béla Molnár, Zsolt Tulassay
• Journal: Orvosi hetilap (Orv Hetil) Vol. 149 Issue 5 Pg. 219-32 (Feb 03 2008) ISSN: 0030-6002 [Print] Hungary
• Vernacular Title: Vastagbél-biopszia funkcionális mRNS-expressziós vizsgálata és osztályozása általános cDNS microarray technikával.
• PMID: 18218589 (Publication Type: English Abstract, Journal Article)

Chemical References

• Biomarkers, Tumor
• RNA, Messenger

Topics

• Adenocarcinoma (genetics, pathology)
• Adenoma (genetics, pathology)
• Aged
• Aged, 80 and over
• Biomarkers, Tumor (analysis, genetics)
• Biopsy
• Colorectal Neoplasms (chemistry, genetics, pathology)
• Discriminant Analysis
• Female
• Gene Expression Profiling
• Humans
• Immunohistochemistry
• Inflammatory Bowel Diseases (genetics, pathology)
• Male
• Middle Aged
• Multivariate Analysis
• Oligonucleotide Array Sequence Analysis
• RNA, Messenger (analysis)
• Reverse Transcriptase Polymerase Chain Reaction
• Up-Regulation