Causal Effects and Single-Cell Microenvironmental Implications of Germline Variant-Regulated Lactylation-Related...

Colorectal cancer (CRC) is shaped by inherited genetic susceptibility, metabolic reprogramming, epigenetic regulation, and tumor microenvironment (TME) heterogeneity. Lactylation has recently emerged as an epigenetic mechanism that links lactate accumulation to chromatin remodeling and transcriptional regulation. However, the roles of lactylation-related genes in CRC initiation and progression, particularly from the perspective of SNP-based germline genetic variation, remain to be elucidated.

We integrated GWAS analysis and single-cell RNA sequencing to identify lactylation-related pro-oncogenic genes with potential genetic causal relevance and to further characterize their cellular localization and microenvironmental implications in CRC. GWAS uses inherited germline genetic variants, particularly SNPs associated with gene expression, as instrumental variables, thereby reducing confounding and reverse causation compared with conventional tumor expression-based analyses.

GWAS analysis has identified germline variants in AXIN1, FASN, MLH1, and RAD50 that genetically predicted increased CRC risk. Single-cell analysis was subsequently performed to evaluate the cell-type-specific distribution and functional relevance of these GWAS-identified genes within CRC tissues. Among them, AXIN1 exhibited clearer differential expression and cell-type-specific distribution in CRC-associated cell populations. AXIN1-high cell populations were associated with metabolic adaptation, proliferative activity, lactylation-related transcriptional programs, inflammatory responses, immune regulation, extracellular matrix remodeling, and TME adaptation. Besides, FASN was also confirmed as a genetically supported risk gene implicated in CRC metabolic reprogramming. MLH1 and RAD50 were retained as candidate risk genes at the germline causal level.

This study integrates germline variant-based causal inference with single-cell microenvironmental interpretation, highlighting germline variant-regulated lactylation in promoting colorectal cancer risk.