ANKLE1 N6-Methyladenosine-related variant is associated with colorectal cancer risk by maintaining the genomic stability

The N-6-Methyladenosine (m(6)A) modification plays an important role in many biological processes, especially tumor development. However, little is still known about how it affects colorectal cancer (CRC) carcinogenesis. Here, we first systematically investigate the association of variants related to m(6)A modification with the CRC risk in 1,062 CRC cases and 2,184 controls by using our exome-wide association data and followed by two replication sets including 7,341 CRC cases and 7,902 controls. The variant rs8100241 located in ANKLE1 was significantly associated with CRC risk (odds ratio = 0.88, 95% confidence interval = 0.84-0.92, p = 4.85x10(-8)) in 8,403 cases and 10,086 controls. This variant was previously identified to be associated with the susceptibility of breast cancer with BRCA1 mutation triple negative breast cancer. Further functional analysis indicated that overexpression of the rs8100241[A] allele significantly increased the ANKLE1 m(6)A level and facilitated the ANKLE1 protein expression compared to that of rs8100241[G] allele. We further found the ANKLE1 m(6)A modification was catalyzed by the writer complex (METTL3, METTL14, or WTAP) and recognized by the reader YTHDF1. Mechanistically, we found that the ANKLE1 functions as a potential tumor suppressor that inhibits cell proliferation and facilitates the genomic stability. An elevated frequency of micronucleated cells, increased cell proliferation, and colony formation ability were observed when ANKLE1 knockdown. Our study illustrated that the germline missense variant can increase CRC risk by influencing ANKLE1 m(6)A level, highlighting a clinical potential of variants-associated m(6)A modification as a risk marker for CRC prevention. What's new? Variations in cancer-associated genes potentially affect RNA and protein modification, thereby altering tumor-protective or tumor-promoting cell functions. Of particular interest in this regard are variations affecting the N-6-Methyladenosine (m(6)A) RNA modification, which supports numerous biological processes. In this investigation of m(6)A-related variants in colorectal cancer (CRC), a germline missense variant in ANKLE1, an active player in the DNA damage response, was associated with reduced CRC risk. The variant increased ANKLE1 m(6)A modification and ANKLE protein levels. Overexpression of the missense allele was further associated with reduced CRC cell proliferation, revealing a possible tumor-suppressive role for ANKLE1 in CRC development.