Multi‐Omics Profiling Identifies Novel Therapeutic Targets and Pathobiological Mechanisms in Oral Cancer

ABSTRACT

Oral cancer (OC) remains a therapeutic challenge due to limited validated targets. Cis‐pQTLs from the deCODE cohort ( n  = 35,559) were harmonized with OC‐GWAS (3547 cases and 691,466 controls) meta‐data through a two‐sample Mendelian randomization (MR) framework. Robust Validation included replication in the UKB‐PPP dataset, colocalization analysis, SMR (Summary‐based MR), HEIDI (Heterogeneity in Dependent Instruments) tests, and eQTL evidence. Additional analyses encompassed protein–protein interaction (PPI) networks, Kyoto Encyclopedia of Genes and Genomes annotation (KEGG)/Gene Ontology (GO) pathway enrichment, mediation, Druggability and side effects analysis. Oral cancer (OC) remains a therapeutic challenge due to limited validated targets. Cis‐pQTLs from the deCODE cohort ( n  = 35,559) were harmonized with OC‐GWAS (3547 cases and 691,466 controls) meta‐data through a two‐sample Mendelian randomization (MR) framework. Robust Validation included replication in the UKB‐PPP dataset, colocalization analysis, SMR (Summary‐based MR), HEIDI (Heterogeneity in Dependent Instruments) tests, and eQTL evidence. Additional analyses encompassed protein–protein interaction (PPI) networks, Kyoto Encyclopedia of Genes and Genomes annotation (KEGG)/Gene Ontology (GO) pathway enrichment, mediation, Druggability and side effects analysis. To experimentally corroborate the MR findings, the quantitative real‐time PCR (qRT‐PCR) was performed to examine the mRNA expression levels of selected genes in oral squamous cell carcinoma (OSCC) cell lines (SCC‐9 and SCC‐25) and normal human oral epithelial cells (HOEC). Multi‐omics MR identified TNFSF8 ( p  = 2.49 × 10 ⁻⁸ , OR = 1.24) as a Tier 1 target. XXYLT1 ( p  = 1.41 × 10 ⁻⁴ , OR = 1.34) and HSD17B14 ( p  = 0.04, OR = 2.00) achieved Tier 2. eQTLs‐pQTLs Relationship revealed XXYLT1 expression explained 24.65% of risk through elevated plasma protein levels, TNFSF8 eQTLs mediated 72.80% via protein upregulation. Mediation analyses on CD4 on HLA DR+ CD4+ T cells (7.18%) contributed to the risk of OC by upregulating plasma HSD17B14, while daily cigarette consumption (20.63%) and CD8+ T cell percentage leukocytes (12.06%) contributed to the risk of OC by upregulating plasma TNFSF8. Drug safety assessments highlighted systemic TNFSF8 inhibition may elevate skin cancer risk. Multi‐omics MR prioritizes TNFSF8 as a therapeutic target for oral cancer. Multi‐omics MR identified TNFSF8 ( p  = 2.49 × 10 ⁻⁸ , OR = 1.24) as a Tier 1 target. XXYLT1 ( p  = 1.41 × 10 ⁻⁴ , OR = 1.34) and HSD17B14 ( p  = 0.04, OR = 2.00) achieved Tier 2. eQTLs‐pQTLs Relationship revealed XXYLT1 expression explained 24.65% of risk through elevated plasma protein levels, TNFSF8 eQTLs mediated 72.80% via protein upregulation. Mediation analyses on CD4 on HLA DR+ CD4+ T cells (7.18%) contributed to the risk of OC by upregulating plasma HSD17B14, while daily cigarette consumption (20.63%) and CD8+ T cell percentage leukocytes (12.06%) contributed to the risk of OC by upregulating plasma TNFSF8. Drug safety assessments highlighted systemic TNFSF8 inhibition may elevate skin cancer risk. qRT‐PCR confirmed significant upregulation of XXYLT1 and HSD17B14 in both SCC‐9 and SCC‐25 cell lines ( p  < 0.001), which is consistent with MR predictions. TNFSF8 was not reliably detected in these cancer cells, aligning with its proposed immune‐mediated mechanism. Multi‐omics MR prioritizes TNFSF8 as a therapeutic target for oral cancer. qPCR validation confirms the dysregulation of XXYLT1 and HSD17B14, while findings regarding TNFSF8 underscore its immune origin. These findings warrant further functional studies.