title: Multigene pathway-based analyses identify nasopharyngeal carcinoma risk associations for cumulative adverse effects of TERT-CLPTM1L and DNA double-strand breaks repair.
abstract: The genetic etiology of nasopharyngeal carcinoma (NPC) and mechanisms for inherited susceptibility remain unclear. To examine genetic risk factors for NPC, we hypothesized that heritable risk is attributable to cumulative effects of multiple common low-risk variants. With the premise that individual SNPs only confer subtle effects for cancer risk, a multigenic pathway-based approach was used to systematically examine associations between NPC genetic susceptibility with SNPs in genes in DNA repair pathways and from previously identified cancer genome-wide association study analyses. This case-control study covers 161 genes/loci and focuses on pathway-based analyses in 2,349 Hong Kong individuals, allowing stratification according to NPC familial status for meaningful association analysis. Three SNPs (rs401681, rs6774494 and rs3757318) corresponding to TERT/CLPTM1L (OR 95% CI = 0.77, 0.68-0.88), MDS1-EVI1 (OR 95% CI=0.79 0.69-0.89) and CCDC170 (OR 95% CI = 0.76, 0.66-0.86) conferred modest protective effects individually for NPC risk by the logistic regression analysis after multiple testing adjustment (p(Bonferroni)  < 0.05). Stratification of NPC according to familial status identified rs2380165 in BLM (OR 95% CI = 1.49, 1.20-1.86, p(Bonferroni)  < 0.05) association with family history-positive NPC (FH+ NPC) patients. Multiple SNPs pathway-based analysis revealed that the combined gene dosage effects for increasing numbers of unfavorable genotypes in TERT-CLPTM1L and double-strand break repair (DSBR) conferred elevated risk in FH+ and sporadic NPC patients (ORs per allele, 95% CIs = 1.37, 1.22-1.55, p(Bonferroni)  = 5.00 × 10(-6); 1.17, 1.09-1.26, p(Bonferroni)  = 4.58 × 10(-4) , respectively, in TERT/NHEJ pathways). Our data suggested cumulative increased NPC risk associations with TERT-CLPTM1L and DSBR pathways contribute to genetic susceptibility to NPC and have potential translational relevance for patient stratification and therapeutics.
authors.affiliation: Department of Clinical Oncology, University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China.
authors.forename: Josephine Mun
authors.initials: JM
authors.lastname: Yee Ko
authors.forename: Wei
authors.initials: W
authors.lastname: Dai
authors.forename: Elibe Hiu
authors.initials: EH
authors.lastname: Wun Wong
authors.forename: Dora
authors.initials: D
authors.lastname: Kwong
authors.forename: Wai
authors.initials: W
authors.lastname: Tong Ng
authors.forename: Anne
authors.initials: A
authors.lastname: Lee
authors.forename: Roger
authors.initials: R
authors.lastname: Kai Cheong Ngan
authors.forename: Chun
authors.initials: C
authors.lastname: Chung Yau
authors.forename: Stewart
authors.initials: S
authors.lastname: Tung
authors.forename: Maria
authors.initials: M
authors.lastname: Li Lung
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D002277:Carcinoma; D016022:Case-Control Studies; D053903:DNA Breaks, Double-Stranded; D004260:DNA Repair / Q000235:genetics*; D005260:Female; D005500:Follow-Up Studies; D020869:Gene Expression Profiling; D005838:Genotype; D006801:Humans; D008297:Male; D008565:Membrane Proteins / Q000235:genetics*; D008875:Middle Aged; D005810:Multigene Family; D000077274:Nasopharyngeal Carcinoma; D009303:Nasopharyngeal Neoplasms / Q000235:genetics*; D009363:Neoplasm Proteins / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011379:Prognosis; D012307:Risk Factors; D015398:Signal Transduction; D019098:Telomerase / Q000235:genetics*
chemical_list: D014408:Biomarkers, Tumor; C422445:CLPTM1L protein, human; D008565:Membrane Proteins; D009363:Neoplasm Proteins; C509186:TERT protein, human; D019098:Telomerase
keywords: BLM; CCDC170; DNA DSB repair; NHEJ; NPC; TERT; familial NPC; genetic susceptibility; pathway associations