Genome-wide scan identifies a copy number variable region at 3q26 that regulates PPM1L in APC mutation-negative familial colorectal cancer patients

• Published in: Genes chromosomes & cancer Vol. 49; no. 2; pp. 99 - 106
• Main Authors: Thean, L. F., Loi, C., Ho, K. S., Koh, P. K., Eu, K. W., Cheah, P. Y.
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01-02-2010
• Subjects: 3' Untranslated Regions - genetics; Adenomatous Polyposis Coli - genetics; Adenomatous Polyposis Coli Protein - genetics; Adult; Chromosome Mapping; Chromosomes, Human, Pair 3; Chromosomes, Human, Pair 5; Colorectal Neoplasms - genetics; Female; Genetic Variation; Genome-Wide Association Study; Germ-Line Mutation; Humans; Male; Pedigree; Phosphoprotein Phosphatases - genetics; Polymerase Chain Reaction - methods; Sequence Deletion; Transcription, Genetic
• ISSN: 1045-2257; 1098-2264
• DOI: 10.1002/gcc.20724

Familial adenomatous polyposis (FAP) is an autosomal dominantly inherited form of colorectal cancer (CRC) caused by mutation in the adenomatous polyposis coli (APC) gene. However, APC mutations are not detected in 10–50% of FAP patients. We searched for a new cancer gene by performing genome‐wide genotyping on members of an APC mutation‐negative FAP variant family and ethnicity‐matched healthy controls. No common copy number change was found in all affected members using the unaffected members and healthy controls as baseline. A 111 kb copy number variable (CNV) region at 3q26.1 was shown to have copy number loss in all eight polyps compared to matched lymphocytes of two affected members. A common region of loss in all polyps, which are precursors to CRC, is likely to harbor disease‐causing gene in accordance to Knudsen's “two‐hit” hypothesis. There is, however, no gene within the deleted region. A 2‐Mb scan of the genomic region encompassing the deleted region identified PPM1L, coding for a novel serine‐threonine phosphatase in the TGF‐β and BMP signaling pathways. Real‐time PCR analyses indicate that the 3′UTR of PPM1L transcript was down‐regulated more than two‐folds in all six polyps and tumors compared to matched mucosa of the affected member. This down‐regulation was not observed in APC mutation‐positive FAP patients. Our results suggest that the CNV region at 3q26 harbors an element that regulates the expression of an upstream candidate tumor suppressor, PPM1L, thus providing a novel mechanism for colorectal tumorigenesis in APC mutation‐negative familial CRC patients. © 2009 Wiley‐Liss, Inc.