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Published on: September 25, 2011
[Functional mRNA expression analysis and classification of colonic biopsy samples using overall cDNA microarray
Orsolya Galamb1, Ferenc Sipos, Elek Dinya
1Semmelweis Egyetem, Altalános Orvostudományi Kar II. Belgyógyászati Klinika Budapest. orsg1@yahoo.com
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.
Insights
Gene expression profiling of colon biopsies accurately classifies inflammatory bowel disease, adenomas, and colorectal cancer. This molecular approach aids in diagnosing complex cases, improving patient stratification and treatment strategies.
Area of Science:
- Molecular biology
- Genomics
- Oncology
Context:
- Colon biopsies offer insights into local molecular alterations.
- Gene expression analysis aids in classifying inflammatory and neoplastic diseases.
Purpose:
- To analyze mRNA expression profiles in colon biopsies.
- To classify inflammatory bowel disease (IBD), adenomas, and colorectal adenocarcinoma (CRC) using gene expression data.
Summary:
- Multivariate analysis of gene expression data from 22 colon biopsies (IBD, adenomas, CRC) identified distinct molecular patterns.
- Discriminant analysis using four genes accurately reclassified all samples.
- Specific gene expression signatures were associated with IBD, adenomas, and CRC, with validation by RT-PCR and immunohistochemistry.
Impact:
- Objective classification of histological alterations is achievable through functional, multivariate analysis of cDNA microarrays.
- Disease-specific gene expression patterns can improve diagnostic accuracy, particularly for intermediate or nondescript cases.
