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  • br c Department of Zoology P


    c Department of Zoology, P.M.B Gujarati Science College, Indore, India
    Promoter SNP
    Colorectal cancer 
    Different diseases have been associated with PARK2/PACRG overlapping promoter polymorphisms (rs2276201 and rs9347683) in the recent past. However association of these polymorphisms with cancer remains elusive till date. Thus in this study we evaluated association between these polymorphisms and colorectal cancer (CRC) incidences among North Indians. Genomic DNA was isolated using venous blood of 400 unrelated subjects (200 CRC cases and 200 healthy controls) of North Indian origin. Both SNPs were genotyped using PCR-RFLP method. Promoter methylation status in tumor DNA was checked using MS-PCR. Statistical analysis was performed using SPSS-17 software. In-silico predictions for transcription factor binding were performed using “PROMO” a freely available online tool. SNP rs2276201 showed statistically significant difference (P = 0.047) among cases and controls while rs9347683 did not (P = 0.113). The TC genotype (OR: 1.855, 95% CI: 1.021–3.369, P = 0.043),
    1. Introduction
    Colorectal cancer (CRC) is a diverse genetic disease with highly heterogeneous clinical features that influence therapeutic outcomes (Markowitz and Bertagnolli, 2009; Fearon, 2011). In men and women colorectal cancer is the third-most and second-most common cancer, respectively. With both sexes combined, colorectal cancer accounts for 9.7% of all cancers (Ferlay et al., 2015). Worldwide in 2012, 746,000 men (10% of new cancer cases) and 614,000 women (9.2% of all new cancer cases) were diagnosed with colorectal cancer. In the incidence rates there is a geographical difference with more than half of the cases
    of CRC occurring in developed countries. However, 109244-58-8 is higher in the less developed countries that have inadequate resources and health infrastructure. There also, the numbers of patients suffering from CRC are constantly increasing while the survival rate is one of the lowest in the world (Allemani et al., 2015).
    PARK2 and PACRG are shown to possess tumor suppressive prop-erties (Cesari et al., 2003; Poulogiannis et al., 2010). PARK2 shares common overlapping promoter polymorphisms with PACRG (Parkin co-regulated gene protein) and both genes have been shown to be asso-ciated with Leprosy (Mira et al., 2004; Chopra et al., 2013). PACRG is also suggested to be involved in Parkinson's pathogenesis (Taylor et al.,
    Abbreviations: SNP, single nucleotide polymorphism; CRC, colorectal cancer; PARK2, Parkin gene; TSG, tumor suppressor gene; SPSS, Statistical Package of Social Sciences; PCR, polymerase chain reaction; RFLP, restriction fragment length polymorphism; MS, methylation specific; TFBS, transcription factor binding sites; LD, linkage disequilibrium; OR, odds ratio
    Corresponding author at: Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
    E-mail address: [email protected] (M.M. Alam Rizvi). 1 Equal first authors.
    2007). Alterations in PARK2 have been implicated in multiple cancers such as non-small cell lung cancer, cervical cancer and other cancers (Picchio et al., 2004; Mehdi et al., 2011; Xu et al., 2014; Naseem et al., 2017). Promoter methylation of this overlapping region is also shown to be involved in acute lymphoblastic leukemia and chronic myeloid leukemia (Agirre et al., 2006). Single-nucleotide polymorphisms (SNPs) have been described in the Parkin core promoter region identified to possess the majority of transcription regulation (Asakawa et al., 2001; West et al., 2001). Promoter polymorphisms can effect gene expression and has earlier been associated with age-associated diseases (Artiga et al., 1998; Ye, 2000; Chiba-Falek and Nussbaum, 2001; Farrer et al., 2001; Bond et al., 2004; Matsumura et al., 2005; Parsons et al., 2008). Polymorphisms in the PARK2 and PACRG genes have been positively associated with Leprosy, Typhoid and Parkinson's (Ali et al., 2006b; Biswas et al., 2007; Chopra et al., 2013). However the association of PARK2 SNPs with cancer remains elusive. Given the recently explored involvement of PARK2 in cancer we examined if common PARK2/ PACRG promoter SNPs (rs2276201 and rs9347683) influence the sus-ceptibility to colorectal cancer in north Indian population.
    2. Materials and methods
    2.1. Ethics statement
    This study was approved by the Institution Ethics Committee of G B Pant Hospital New Delhi and the Institutional Human Ethical Committee of Jamia Millia Islamia, New Delhi and written informed consent was obtained from each participant.
    2.2. Study subjects and sample collection
    The present hospital-based case control study included a total of 400 genetically distinct subjects of North Indian population comprising 200 colorectal cancer cases and 200 healthy controls. Colorectal cancer subjects were recruited from the Department of GIT, G B Pant Hospital New Delhi. Controls were age, sex and geographical locations matched healthy volunteers to cases and were taken from the people who visited the hospital for routine check-up with no malignancy. All colorectal cancer cases were newly diagnosed and histopathologically confirmed. 5 ml of venous blood sample was collected from each subject and used for DNA extraction and genotyping. Clinical characteristics of the cases and control subjects are provided in Table 1.