Gene expression reveals two distinct groups of anal carcinomas with clinical implications

• Published in: British journal of cancer Vol. 98; no. 7; pp. 1264 - 1273
• Main Authors: Bruland, O, Fluge, Ø, Immervoll, H, Balteskard, L, Myklebust, M P, Skarstein, A, Dahl, O
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 08-04-2008; Nature Publishing Group
• Subjects: Anus Neoplasms - genetics; Anus Neoplasms - virology; Biological and medical sciences; Biomedicine; Biopsy; Cancer Research; Cell cycle; Cell Cycle Proteins - analysis; Cluster analysis; Cyclin-dependent kinases; DNA-Binding Proteins - analysis; Drug Resistance; Epidemiology; Gastroenterology. Liver. Pancreas. Abdomen; Gene Expression; Genes, p16; Genomes; Hospitals; Human papillomavirus; Human papillomavirus 16; Human papillomavirus 16 - genetics; Humans; In Situ Hybridization; Kinases; Medical research; Medical sciences; Minichromosome Maintenance Complex Component 7; Molecular Diagnostics; Molecular Medicine; Nuclear Proteins - analysis; Oligonucleotide Array Sequence Analysis; Oncogene Proteins, Viral - analysis; Oncology; Papillomavirus E7 Proteins; Protein Array Analysis; Protein expression; Proteins; Retinoblastoma; RNA, Messenger - analysis; Stomach. Duodenum. Small intestine. Colon. Rectum. Anus; Transcription factors; Tumors; Viral Load; Norway; microarray; CDKN2A (p16); MCM7; anal cancer; gene expression profiling; human papillomavirus; Minichromosome maintenance protein 7; Anal cancer; Anus carcinoma; Papovaviridae; Malignant tumor; Gene expression; CDKN2 gene; Gene expression profile; Infection; Papillomavirus; Virus; Human papillomavirus; Cancerology; Viral disease; Digestive diseases; Intestinal disease; Anorectal disease; Cancer; Tumor suppressor gene
• ISSN: 0007-0920; 1532-1827
• DOI: 10.1038/sj.bjc.6604285

Human papillomavirus (HPV) is a major aetiological agent in anal carcinomas. We here present a study of global gene expression using microarray hybridisation in a collection of anal carcinoma biopsies. Quantitative PCR was used to verify expression of selected genes. All biopsies contained integrated DNA of human papillomavirus subtype 16 (HPV16) and expressed HPV16 E7 mRNA. No other subspecies of HPV were detected in these 13 biopsies as assessed by PCR amplification and DNA sequencing. Unsupervised cluster analysis, based on global mRNA expression, divided the tumour biopsies into two distinct groups. Cluster analysis based on a number of high-risk HPV and/or E2F-regulated genes reproduced this biopsy grouping, suggesting that integrated HPV16 substantially influenced global gene expression in approximately half the biopsies studied. The levels of HPV16 E7 mRNA were significantly different between the two groups, but with considerable overlap. Thus, influence on global gene expression could not be absolutely ascribed to the expression level of HPV16. To investigate whether this distinction in gene expression had prognostic impact, we studied protein expression in an independent cohort of 55 anal carcinomas not included in the microarray study of two differentially expressed candidate genes, minichromosome maintenance complex component 7 (MCM7) and cyclin-dependent kinase inhibitor 2A (CDKN2A or p16). HPV status was assessed by
in situ
hybridisation. There was a significant association between
in situ
staining for HPV E7 mRNA and immunostaining for CDKN2A (p16) and MCM7 protein. CDKN2A (p16) mRNA was found significantly differentially expressed between the two tumour groups. However, cluster analysis on genes directly regulated by CDKN2A (p16) could not reproduce this split of biopsies into two groups, suggesting that the transcriptional regulatory activity of CDKN2A in these biopsies is inhibited. Furthermore, protein expression of CDKN2A (p16) could not be associated with survival. MCM7 is directly regulated by E2F and induced by HPV, and its mRNA was found differentially expressed between the two tumour groups. High level of MCM7 protein was found to be associated with both improved relapse-free survival (RFS,
P
=0.02) and cancer-specific survival (CSS,
P
=0.03) in anal cancer patients treated with radiation with or without additional chemotherapy.