Long intergenic non-coding RNA 00511 (LINC00511) genetic variations and haplotype implication for colorectal cancer susceptibility and prognosis

Long intergenic non-coding RNA 00,511 (LINC00511) is considered an oncogene for various cancers. However, the association between LINC00511 single nucleotide polymorphisms (SNPs) and colorectal cancer (CRC) remains unclear. Our study aims to study whether LINC00511 SNPs could predict CRC susceptibility or prognosis, an important step-toward precision-health, based on an Egyptian CRC patient cohort. A total of 200 CRC patients and 200 cancer-free controls were genotyped for three LINC00511 SNPs - rs9906859, rs1558535, and rs17780195 using qRT-PCR. Studied SNPs were in strong linkage disequilibrium and moderately correlated in all groups. Genotype association concerning tumor stage, revealed rs1558535 AT and rs17780195 AG variants correlated significantly with CRC advanced stages (adjusted OR: 3.99 and 2.72), respectively. Logistic regression showed that rs1558535 and rs9906859 genotypes were associated with CRC. Haplotype analysis disclosed that 'T_rs155535A_rs17780195C_rs9906859' mutant-wild-mutant haplotype has 1.5-fold increased CRC risk (OR: 1.46, 95% CI: 1.07-1.99). 'T_rs155535A_rs17780195T_rs9906859' haplotype conferred fivefold lower CRC risk (OR: 0.20, 95% CI: 0.09-0.47). Epistasis analysis showed individuals heterozygote and homozygote or homozygote and heterozygote for rs1558535 and rs9906859 are at high risk for CRC. Both rs1558535 and rs17780195 were associated with late stages of CRC. A strong interaction was observed between rs1558535 and rs9906859 in predicting CRC risk.