Tumour Biol. 2015 Sep;36(10):7569-79. doi: 10.1007/s13277-015-3472-5.

XPD, APE1, and MUTYH polymorphisms increase head and neck cancer risk: effect of gene-gene and gene-environment interactions.

Sambuddha Das1, Aditi Bhowmik1, Abhinandan Bhattacharjee2, Biswadeep Choudhury3, Momota Naiding4, Agniv Kr. Laskar1, Sankar Kumar Ghosh1, and Yashmin Choudhury1

1 Department of Biotechnology, Assam University, Silchar-788011-India.

2 Department of ENT, Silchar Medical College and Hospital, Silchar-788014, India.

3 Department of Biochemistry, Silchar Medical College and Hospital, Silchar-788014, India.

4 Department of Pathology, Silchar Medical College and Hospital, Silchar-788014, India.



In the present study, we investigated the effect of the DNA repair gene polymorphisms XPD Asp312Asn (G>A), APE1 Asp148Glu (T>G), and MUTYH Tyr165Cys (G>A) on the risk for head and neck cancer (HNC) in association with tobacco use in a population of Northeast India. The study subjects comprised of 80 HNC patients and 92 healthy controls. Genotyping was performed using amplification refractory mutation system-PCR (ARMS-PCR) for XPD Asp312Asn (G>A) and PCR using confronting two-pair primers (PCR-CTPP) for APE1 Asp148Glu (T>G) and MUTYH Tyr165Cys (G>A). The XPD Asp/Asn genotype increased the risk for HNC by 2-fold (odds ratio, OR = 2.072; 95 % CI, 1.025-4.190; p < 0.05). Interaction between APE1 Asp/Asp and XPD Asp/Asn as well as MUTYH Tyr/Tyr and XPD Asp/Asn genotypes further increased the risk by 2.9 (OR = 2.97; 95 % CI, 1.16-7.61; p < 0.05) and 2.3 (OR = 2.37; 95 % CI, 1.11-5.10; p < 0.05) folds, respectively. The risk was further increased in heavy smokers with the XPD Asp/Asn genotype and heavy tobacco chewers with XPD Asn/Asn genotype by 7.7-fold (OR = 7.749; 95 % CI, 2.53-23.70; p < 0.05) and 10-fold (OR = 10; 95 % CI, 1.26-79.13; p < 0.05), respectively. We thus conclude that the XPD Asp312Asn and APE1 Asp148Glu polymorphisms increase the risk for HNC in association with smoking and/or tobacco chewing in the population under study.

KEYWORDS: APE1; Head and neck cancer; MUTYH; Polymorphism; XPD

PMID: 25916209



The population of North-East India has been reported to be highly susceptible to head and neck cancer (HNC) with a significant prevalence rate of 54.48% [1]. Various genetic and etiological factors are found to exaggerate the onset and progression of HNC. Polymorphisms in DNA repair genes are found to alter the DNA repair activity of various repair proteins leading to genetic instability and carcinogenesis [2]. This is further intensified among individuals with etiological habits such as tobacco chewing and smoking [3]. We therefore undertook this case-control study in order to assess the risk of HNC among the people of North-East India with reported polymorphisms of the XPD, MUTYH and APE1 genes alone, or upon interaction with the habits of tobacco chewing and smoking.

We isolated genomic DNA from blood samples of 80 histopathologically proven HNC patients as well as 92 unrelated control individuals and genotyped for polymorphism of XPD G>A, MUTYH G>A and APE1 T>G gene using ARMS-PCR and PCR-CTPP. A schematic representation of the genotypes of the three DNA repair genes among HNC patients and controls revealed that for both the XPD and APE1 genes the distribution of the heterozygous and mutant genotypes are higher in cases than controls (Figure 1). It was also observed that the percentage of individuals with the cancer-predisposing GA and AA genotypes of the XPD gene and the habit/s of either smoking or tobacco chewing or both, was higher among the HNC patients in comparison to controls (Figure 2A). A similar trend was also observed for the APE1 T>G polymorphism clearly indicating the interaction of smoking and tobacco chewing with XPD and APE1 polymorphism in increasing the risk for HNC (Figure 2B). However, no such difference was observed among HNC and control individuals for the MUTYH G>A polymorphism (Figure 2C). Our study revealed a 2 and 2.5 fold increase in the risk for HNC for individuals with XPD GA and AA genotype respectively. We did not observe such risk with MUTYH and APE1 polymorphisms alone. However, the combined effect of XPD and APE1 genes were found to increase the risk for HNC to a great extent. On stratifying our data based on smoking and tobacco habits it was found that smoking individuals with XPD and APE1 polymorphisms were found to be at a higher risk for HNC. The results were further validated with non parametric tests like multifactor dimensionality reduction (MDR) and classification and regression tree (CART). In both the tests, interaction among smoking, XPD and APE1 polymorphisms were predicted to be the highest risk factor for HNC. Taken together, our results imply that smoking itself was the single most important risk factor for HNC for the population under study. Among the genetic factors studied, a synergistic interaction between XPD and APE1 polymorphism was found to increase the risk for HNC [2].



Figure 1-jpgFigure 1: Schematic representation and distribution of different genotypes of XPD, MUTYH and APE1 DNA repair genes for each A) HNC patients and B) healthy control individual recruited for this study; off-white color denotes wild type, blue denotes heterozygous and red denotes mutant genotypes respectively.


The hypothesis of our study was that the synergistic effect of polymorphisms in DNA repairs genes with smoking and tobacco chewing increase the risk for HNC. This study was the first to report the association of XPD, MUTYH and APE1 polymorphism with the increased risk for HNC in the North-East Indian population. Besides that the use of multiple statistical approaches like MDR and CART along with the conventional logistic regression method have not only validated our result but have also helped us to study the interactions among various genetic and etiological factors in detail and with higher accuracy. Thus the XPD G>A polymorphism alone as well as its interaction with APE1 T>G polymorphism can be used in future research to develop a cost effective and minimally invasive blood based biomarker for the early detection of HNC risk in this population [2].


Figure 2-jpg

Figure 2: Distribution of HNC patients (cases) and controls (in percentage) with different genotypes of A) XPD B) APE1 and C) MUTYH DNA repair genes, and habits of chewing tobacco and smoking. “Both” represents individuals who reported both habits of smoking and tobacco chewing; “none” represents individuals who reported neither of these habits.



  1. Bhattacharjee, A., A. Chakraborty, and P. Purkaystha, Prevalence of head and neck cancers in the north east-An institutional study. Indian J Otolaryngol Head Neck Surg, 2006. 58(1): p. 15-9.
  2. Das, S., et al., XPD, APE1, and MUTYH polymorphisms increase head and neck cancer risk: effect of gene-gene and gene-environment interactions. Tumour Biol, 2015. 36(10): p. 7569-79.
  3. Bhowmik, A., et al., MDM2 and TP53 Polymorphisms as Predictive Markers for Head and Neck Cancer in Northeast Indian Population: Effect of Gene-Gene and Gene-Environment Interactions. Asian Pac J Cancer Prev, 2015. 16(14): p. 5767-72.



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