The Role of lncRNA Polymorphisms in Digestive System Cancers: A Systematic Review and Meta-Analysis

Background: Gastrointestinal (GI) cancers, particularly colorectal, gastric, and liver cancers, account for a major global burden of incidence and mortality and remain important targets for genetic susceptibility research. Long non-coding RNAs (lncRNAs) can regulate gene expression and are increasingly studied in carcinogenesis. Numerous case–control studies have investigated associations between lncRNA polymorphisms and cancer risk, but findings are inconsistent. This study systematically evaluated the association between lncRNA single nucleotide polymorphisms (SNPs) and GI cancer susceptibility. Methods: A systematic literature search from Embase, Medline, Scopus, and Web of Science databases identified 174 potentially extractable studies. Eligible studies were case–control or cross-sectional studies published up to 8 May 2026; case reports, reviews, and meta-analyses were excluded. After screening for identical cancer type, identical SNP, and sufficient statistical data, only variants supported by at least three independent case–control studies were eligible for meta-analysis. Seven SNPs across six lncRNAs, comprising 23 studies (15,131 cases and 20,969 controls), were selected. Because of the limited number of eligible studies, subgroup analyses could not be performed consistently. Odds ratios (ORs) with 95% confidence intervals (CIs) were assessed under allelic, dominant, and recessive genetic models using fixed- or random-effects models according to heterogeneity. Results: In the primary analyses restricted to homogenous Chinese populations, H19 rs3024270 was significantly associated with hepatocellular carcinoma under allelic (OR = 1.22, 95% CI: 1.05–1.42, p = 0.01) and dominant models (OR = 1.22, 95% CI: 1.03–1.45, p = 0.02). Exploratory analyses including mixed populations identified additional associations, with the strongest observed for MEG3 rs7158663 and colorectal cancer, showing significant risk elevation under allelic (OR = 1.42, 95% CI: 1.25–1.63, p < 0.00001), dominant (OR = 1.42, 95% CI: 1.20–1.68, p < 0.0001), and recessive models (OR = 1.98, 95% CI: 1.46–2.68, p < 0.0001). PRNCR1 rs16901946 showed a significant association with gastric cancer under the dominant model (OR = 1.20, 95% CI: 1.02–1.41, p = 0.03), while GAS5 rs145204276 demonstrated a recessive-model association with gastric cancer (OR = 1.30, 95% CI: 1.16–1.46, p < 0.0001). In contrast, GAS5 rs145204276 in colorectal cancer; H19 rs2839698 and MALAT1 rs619586 in hepatocellular carcinoma yielded heterogeneous or unstable pooled estimates. Findings should be interpreted cautiously due to the limited number of studies, heterogeneity, and potential publication bias. Conclusions: Among the primary analyses, H19 rs3024270 showed the most consistent association with HCC susceptibility. Exploratory analyses identified candidate variants, including MEG3 rs7158663, PRNCR1 rs16901946, and GAS5 rs145204276. Population-specific effects and study heterogeneity remain important limitations. PROSPERO registration number for this study: CRD42023389742.