Journal Article

Distinguishing between cancer driver and passenger gene alteration candidates via cross-species comparison: a pilot study

Yeatman, Timothy J, Ji, Xinglai, Zhao, Shaying, Busam, Dana, Halberg, Richard, Peña, Maria Marjorette O, Venkataramu, Chinnambally, Tang, Jie, Ferriera, Steve

2010

Overview

Background We are developing a cross-species comparison strategy to distinguish between cancer driver- and passenger gene alteration candidates, by utilizing the difference in genomic location of orthologous genes between the human and other mammals. As an initial test of this strategy, we conducted a pilot study with human colorectal cancer (CRC) and its mouse model C57BL/6J Apc Min/+ , focusing on human 5q22.2 and 18q21.1-q21.2. Methods We first performed bioinformatics analysis on the evolution of 5q22.2 and 18q21.1-q21.2 regions. Then, we performed exon-targeted sequencing, real time quantitative polymerase chain reaction (qPCR), and real time quantitative reverse transcriptase PCR (qRT-PCR) analyses on a number of genes of both regions with both human and mouse colon tumors. Results These two regions (5q22.2 and 18q21.1-q21.2) are frequently deleted in human CRCs and encode genuine colorectal tumor suppressors APC and SMAD4 . They also encode genes such as MCC ( mutated in colorectal cancer ) with their role in CRC etiology unknown. We have discovered that both regions are evolutionarily unstable, resulting in genes that are clustered in each human region being found scattered at several distinct loci in the genome of many other species. For instance, APC and MCC are within 200 kb apart in human 5q22.2 but are 10 Mb apart in the mouse genome. Importantly, our analyses revealed that, while known CRC driver genes APC and SMAD4 were disrupted in both human colorectal tumors and tumors from Apc Min/+ mice, the questionable MCC gene was disrupted in human tumors but appeared to be intact in mouse tumors. Conclusions These results indicate that MCC may not actually play any causative role in early colorectal tumorigenesis. We also hypothesize that its disruption in human CRCs is likely a mere result of its close proximity to APC in the human genome. Expanding this pilot study to the entire genome may identify more questionable genes like MCC , facilitating the discovery of new CRC driver gene candidates.

• Publisher: BioMed Central,BioMed Central Ltd,BMC
• Subject: Animals / Base Sequence / Biomedical and Life Sciences / Biomedicine / Cancer Research / Chromosomes, Human, Pair 18 - genetics / Chromosomes, Human, Pair 5 - genetics / Colorectal cancer / Colorectal Neoplasms - genetics / Colorectal Neoplasms - pathology / Computational Biology / Evolution, Molecular / Gene Expression Regulation, Neoplastic / Genes, APC - physiology / Genes, DCC - physiology / Genes, MCC - physiology / Genetic aspects / Genome, Human / Health Promotion and Disease Prevention / Humans / Medicine/Public Health / Mice / Molecular Sequence Data / Oncology / Pilot Projects / Polymerase chain reaction / Research Article / Risk factors / Smad4 Protein - genetics / Species Specificity / Surgical Oncology