Amplification of repeat-containing transcribed sequences (ARTS): a transcriptome fingerprinting strategy to detect functionally relevant microsatellite mutations in cancer.
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.
Olivero
Martina
M
Laboratory of Cancer Genetics, Department of Oncological Sciences of the University of Torino, SP 142, Km 3.95, 10060 Candiolo, Italy.
Ruggiero
Tina
T
Coltella
Nadia
N
Maffe'
Antonella
A
Calogero
Raffaele
R
Medico
Enzo
E
Di Renzo
Maria Flavia
MF
D000217:Acyltransferases / Q000235:genetics; D001483:Base Sequence; D015179:Colorectal Neoplasms / Q000235:genetics; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D045683:Furin; D015870:Gene Expression; D006023:Glycoproteins; D006801:Humans; D007413:Intestinal Mucosa / Q000378:metabolism; D009154:Mutation; D016133:Polymerase Chain Reaction; D011518:Proto-Oncogene Proteins / Q000235:genetics; D019253:Proto-Oncogene Proteins c-bcl-2; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013381:Subtilisins / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics*; D014407:Tumor Cells, Cultured; D051153:Wnt Proteins; D051028:bcl-2-Associated X Protein
C494826:BAX protein, human; D018076:DNA, Complementary; D006023:Glycoproteins; D011518:Proto-Oncogene Proteins; D019253:Proto-Oncogene Proteins c-bcl-2; D012333:RNA, Messenger; C417262:WNT16 protein, human; D051153:Wnt Proteins; D051028:bcl-2-Associated X Protein; D000217:Acyltransferases; C081007:COOH-terminal signal transamidase; D013381:Subtilisins; D045683:Furin