Crotonylation and the Risk of Head and Neck Cancer: Insights from a Two-Sample Mendelian Randomization Study

Head and neck cancer (HNC) remains a major global health burden with limited improvement in survival. Crotonylation has been implicated in tumour biology, but its causal contribution to HNC risk is unclear.

We conducted a two-sample Mendelian randomization (MR) study using expression quantitative trait loci (eQTL)-instrumented expression of crotonylation-related genes. Differential expression was assessed in The Cancer Genome Atlas (TCGA). Mediation MR evaluated 1,400 metabolites and 731 immune-cell traits. Single-cell RNA sequencing (scRNA-seq) mapped cell type - specific expression, and quantitative PCR (qPCR) validated expression in tumour versus normal tissues.

MR analysis identified that genetically predicted expression of Glutaryl-CoA Dehydrogenase (GCDH) and Acyl-CoA synthetase, short-chain family member 2 (ACSS2) were causally associated with an increased risk of HNC, and Double PHD fingers 2 (DPF2) and Histone deacetylase 7 (HDAC7) were found to have protective effects against HNC. Moreover, TCGA analysis confirmed a consistent association between GCDH and HNC risk. Mediation MR showed no significant metabolite mediators, although 16α-hydroxy DHEA 3-sulfate levels exhibited a borderline signal. In contrast, two immune-cell traits: CX3CR1 on CD14⁺CD16⁺ monocytes and CD8 on CD39⁺ CD8^br cells partially mediated the effect of GCDH on HNC. scRNA-seq demonstrated lineage-dependent expression of GCDH, and GCDH was enriched in malignant and stromal compartments, with qPCR confirming elevated GCDH expression in tumour samples compared with adjacent normal tissues.

This study suggests a potential causal association between GCDH expression and increased HNC risk, partially mediated by immune-cell traits, pending further validation via colocalization and functional assays. Our findings highlight GCDH as a promising target for further mechanistic studies and potential therapeutic intervention in HNC.

The identification of GCDH as a potential risk factor in HNC opens new avenues for targeted therapies, offering potential improvements in patient outcomes through precision medicine approaches.