Article
Amplification of repeat-containing transcribed sequences (ARTS): a transcriptome fingerprinting strategy to detect functionally relevant microsatellite mutations in cancer

Authors: Calogero R.²; Medico E.¹; Olivero M.; Ruggiero T.; Coltella N.; Maffe’ A.; Di Renzo M.F.

Source: Nucleic Acids Research, Volume 31, Number 7, 1 April 2003 , pp. e33-e33(1)

Publisher: Oxford University Press

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Abstract:

Cancer is a genetic disease caused by mutations in somatic cells. Those that carry advantageous mutations are favoured by natural selection. In most cancers, genetic instability increases mutation rate and facilitates cancer cell evolution. Microsatellite instability (MSI), due to defects of the DNA mismatch repair system, affects in particular repeat sequences (microsatellites) scattered throughout the genome. As mutations in expressed genes are more likely to be functional, we developed a procedure for the systematic identification of mutant repeat-containing expressed sequences (amplification of repeat-containing transcribed sequences, ARTS). The entire cell mRNA was converted into short double-stranded cDNA fragments linked to an adapter at both ends. Repeat-containing cDNA fragments were PCR amplified using the adapter-specific primer in combination with different arbitrary primers including the repeat. ARTS yielded discrete PCR products with lengths that were directly correlated to the lengths of the endogenous repeats. Comparison between ARTS products obtained from control cells and cancer cells with microsatellite instability (MSI+) revealed mRNAs carrying insertions or deletions at repeats. The subsequent sequencing allowed the identification of a series of frameshift-mutated mRNAs in MSI+ cancer cells, including the already described mutant BAX transcript. These data show that ARTS provides an unbiased genome-wide approach to the discovery of functionally relevant genes that could be affected by MSI in cancer.

Document Type: Original article

Affiliations: Laboratory of Cancer Genetics and : 1: Division of Molecular Oncology of the Institute for Cancer Research and Treatment, Department of Oncological Sciences of the University of Torino, SP 142, Km 3.95, 10060 Candiolo (Torino), Italy and 2: Department of Clinical and Biological Sciences of the University of Torino, Az. Osp. S. Luigi, Regione Gonzole 10, 10043 Orbassano (Torino), Italy

Publication date: 2003-04-01

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Nucleic Acids Research (NAR) is a fully Open Access journal, providing rapid publication of leading edge research into the nucleic acids under the following categories: chemistry, computational biology, genomics, molecular biology, nucleic acid enzymes, RNA and structural biology. There is a Survey and Summary section, and methods papers are published
in NAR Methods Online. Each year the first issue is devoted to biological databases, and a later issue to relevant web-based software resources.