Tumor Biology

, Volume 35, Issue 11, pp 11667–11676 | Cite as

Role of novel and GWAS originated PLCE1 genetic variants in susceptibility and prognosis of esophageal cancer patients in northern Indian population

  • Meenakshi Umar
  • Rohit Upadhyay
  • Shaleen Kumar
  • Uday Chand Ghoshal
  • Balraj Mittal
Research Article


Recent genome-wide association studies (GWAS) have identified variants in phospholipase C epsilon1 (PLCE1) as novel susceptibility markers for esophageal squamous cell carcinoma (ESCC) in Chinese population. Although few studies have replicated this findings in other populations, but results are contradictory. So, we aimed to replicate association of two previously reported non-synonymous polymorphisms (rs2274223A>G and rs3765524C>T) from haplotype block 10 and evaluated a novel variant (rs7922612C>T) from haplotype block 2 of PLCE1 with susceptibility and prognosis of ESCC in northern Indian population. The genotyping of PLCE1 variants were performed in 293 histopathologically confirmed incident ESCC cases (including 177 follow-up cases) and 314 age-, gender-, and ethnicity-matched controls using PCR RFLP. All statistical analyses were performed through SPSS version 15.0. Modeling and functional prediction of two non-synonymous variants were carried out using bioinformatics tools. PLCE1 polymorphisms were not associated with susceptibility to ESCC or its clinical phenotypes (tumor location/lymph node metastasis). No interaction with environmental risk factors was found. In silico analysis suggested negligible effect on structure of PLCE1 protein due to PLCE1 rs2274223 (H1927R) and rs3765524 (T1777I) polymorphisms. Survival analysis showed PLCE1 rs7922612CT + TT genotype conferred adverse outcome to ESCC patients. Our study for the first time suggests that GWAS originated PLCE1 variants do not have independent role in susceptibility of ESCC in northern Indian population; however, a novel haplo-tagging SNP rs7922612 may modify survival outcome of ESCC patients.


Esophageal cancer PLCE1 Polymorphisms Prognosis RFLP 



Fellowship grant support from Indian Council of Medical Research (ICMR), New Delhi, is acknowledged. Funders had no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; and in decision to submit the article for publication. The authors also want to acknowledge scholars from School of Telemedicine and Biomedical Informatics, SGPGIMS, for their help in in silico analysis.

Conflicts of interest


Supplementary material

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  1. 1.
    Takiar R, Nadayil D, Nandakumar A. Projections of number of cancer cases in India (2010–2020) by cancer groups. Asian Pac J Cancer Prev. 2010;11:1045–9.PubMedGoogle Scholar
  2. 2.
    McCabe ML, Dlamini Z. The molecular mechanisms of oesophageal cancer. Int Immunopharmacol. 2005;5:1113–30.PubMedCrossRefGoogle Scholar
  3. 3.
    Enzinger PC, Mayer RJ. Esophageal cancer. N Engl J Med. 2003;349:2241–52.PubMedCrossRefGoogle Scholar
  4. 4.
    Hiyama T, Yoshihara M, Tanaka S, Chayama K. Genetic polymorphisms and esophageal cancer risk. Int J Cancer. 2007;121:1643–58.PubMedCrossRefGoogle Scholar
  5. 5.
    Chung CC, Magalhaes WC, Gonzalez-Bosquet J, Chanock SJ. Genome-wide association studies in cancer—current and future directions. Carcinogenesis. 2010;31:111–20.PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Wang LD, Zhou FY, Li XM, Sun LD, Song X, Jin Y, et al. Genome-wide association study of esophageal squamous cell carcinoma in Chinese subjects identifies susceptibility loci at PLCE1 and C20orf54. Nat Genet. 2010;42:759–63.PubMedCrossRefGoogle Scholar
  7. 7.
    Abnet CC, Freedman ND, Hu N, Wang Z, Yu K, Shu XO, et al. A shared susceptibility locus in PLCE1 at 10q23 for gastric adenocarcinoma and esophageal squamous cell carcinoma. Nat Genet. 2010;42:764–7.PubMedCentralPubMedCrossRefGoogle Scholar
  8. 8.
    Wu C, Hu Z, He Z, Jia W, Wang F, Zhou Y, et al. Genome-wide association study identifies three new susceptibility loci for esophageal squamous-cell carcinoma in Chinese populations. Nat Genet. 2011;43:679–84.PubMedCrossRefGoogle Scholar
  9. 9.
    Hinkes B, Wiggins RC, Gbadegesin R, Vlangos CN, Seelow D, Nurnberg G, et al. Positional cloning uncovers mutations in PLCE1 responsible for a nephrotic syndrome variant that may be reversible. Nat Genet. 2006;38:1397–405.PubMedCrossRefGoogle Scholar
  10. 10.
    Rhee SG. Regulation of phosphoinositide-specific phospholipase c. Annu Rev Biochem. 2001;70:281–312.PubMedCrossRefGoogle Scholar
  11. 11.
    Bourguignon LY, Gilad E, Brightman A, Diedrich F, Singleton P. Hyaluronan-CD44 interaction with leukemia-associated RhoGEF and epidermal growth factor receptor promotes Rho/Ras co-activation, phospholipase C epsilon-Ca2+ signaling, and cytoskeleton modification in head and neck squamous cell carcinoma cells. J Biol Chem. 2006;281:14026–40.PubMedCrossRefGoogle Scholar
  12. 12.
    Gbadegesin R, Hinkes BG, Hoskins BE, Vlangos CN, Heeringa SF, Liu J, et al. Mutations in PLCE1 are a major cause of isolated diffuse mesangial sclerosis (IDMS). Nephrol Dial Transplant. 2008;23:1291–7.PubMedCrossRefGoogle Scholar
  13. 13.
    Wang X, Zhou C, Qiu G, Yang Y, Yan D, Xing T, et al. Phospholipase C epsilon plays a suppressive role in incidence of colorectal cancer. Med Oncol. 2012;29:1051–8.PubMedCrossRefGoogle Scholar
  14. 14.
    Bai Y, Edamatsu H, Maeda S, Saito H, Suzuki N, Satoh T, et al. Crucial role of phospholipase Cε in chemical carcinogen-induced skin tumor development. Cancer Res. 2004;64:8808–10.PubMedCrossRefGoogle Scholar
  15. 15.
    Li M, Edamatsu H, Kitazawa R, Kitazawa S, Kataoka T. Phospholipase Cε promotes intestinal tumorigenesis of Apc Min/+ mice through augmentation of inflammation and angiogenesis. Carcinogenesis. 2009;30:1424–32.PubMedCrossRefGoogle Scholar
  16. 16.
    Ou L, Guo Y, Luo C, Wu X, Zhao Y, Cai X. RNA interference suppressing PLCE1 gene expression decreases invasive power of human bladder cancer T24 cell line. Cancer Genet Cytogenet. 2010;200:110–9.PubMedCrossRefGoogle Scholar
  17. 17.
    Luo D, Gao Y, Wang S, Wang M, Wu D, Wang W, et al. Genetic variation in PLCE1 is associated with gastric cancer survival in a Chinese population. J Gastroenterol. 2011;46:1260–6.PubMedCrossRefGoogle Scholar
  18. 18.
    Jain M, Kumar S, Lal P, Tiwari A, Ghoshal UC, Mittal B. Association of genetic polymorphisms of N-acetyltransferase 2 and susceptibility to esophageal cancer in north Indian population. Cancer Invest. 2007;25:340–6.PubMedCrossRefGoogle Scholar
  19. 19.
    Miller SA, Dykes DD, Polesky HF. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 1988;16:1215.PubMedCentralPubMedCrossRefGoogle Scholar
  20. 20.
    Gauderman WJ, Morrison JM: Quanto 1.1: A computer program for power and sample size calculations for genetic-epidemiology studies. 2006.
  21. 21.
    Dupont WD, Plummer Jr WD. Power and sample size calculations. A review and computer program. Control Clin Trials. 1990;11:116–28.PubMedCrossRefGoogle Scholar
  22. 22.
    Yoo J, Seo B, Kim Y. SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis. Nucleic Acids Res. 2005;33:W483–8.PubMedCentralPubMedCrossRefGoogle Scholar
  23. 23.
    Upadhyay R, Jain M, Kumar S, Ghoshal UC, Mittal B. Functional polymorphisms of cyclooxygenase-2 (COX-2) gene and risk for esophageal squmaous cell carcinoma. Mutat Res. 2009;663:52–9.PubMedCrossRefGoogle Scholar
  24. 24.
    Carlson JM, Heckerman D, Shani G: Estimating false discovery rates for contingency tables. Microsoft Res. 2009.Google Scholar
  25. 25.
    Sali A, Potterton L, Yuan F, van Vlijmen H, Karplus M. Evaluation of comparative protein modeling by MODELLER. Proteins. 1995;23:318–26.PubMedCrossRefGoogle Scholar
  26. 26.
    Kelley LA, MacCallum RM, Sternberg MJ. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol. 2000;299:499–520.PubMedCrossRefGoogle Scholar
  27. 27.
    Morris AL, MacArthur MW, Hutchinson EG, Thornton JM. Stereochemical quality of protein structure coordinates. Proteins. 1992;12:345–64.PubMedCrossRefGoogle Scholar
  28. 28.
    Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31:3812–4.PubMedCentralPubMedCrossRefGoogle Scholar
  29. 29.
    Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7:248–9.PubMedCentralPubMedCrossRefGoogle Scholar
  30. 30.
    Jain M, Kumar S, Upadhyay R, Lal P, Tiwari A, Ghoshal UC, et al. Influence of apoptosis (BCL2, FAS), cell cycle (CCND1) and growth factor (EGF, EGFR) genetic polymorphisms on survival outcome: an exploratory study in squamous cell esophageal cancer. Cancer Biol Ther. 2007;6:1553–8.PubMedCrossRefGoogle Scholar
  31. 31.
    Bunney TD, Harris R, Gandarillas NL, Josephs MB, Roe SM, Sorli SC, et al. Structural and mechanistic insights into RAS association domains of phospholipase C epsilon. Mol Cell. 2006;21:495–507.PubMedCrossRefGoogle Scholar
  32. 32.
    Hu H, Yang J, Sun Y, Yang Y, Qian J, Jin L, et al. Putatively functional PLCE1 variants and susceptibility to esophageal squamous cell carcinoma (ESCC): a case–control study in eastern Chinese populations. Ann Surg Oncol. 2012;19:2403–10.PubMedCrossRefGoogle Scholar
  33. 33.
    Gu H, Ding G, Zhang W, Liu C, Chen Y, Chen S, et al. Replication study of PLCE1 and C20orf54 polymorphism and risk of esophageal cancer in a Chinese population. Mol Biol Rep. 2012;39:9105–11.PubMedCrossRefGoogle Scholar
  34. 34.
    Zhou RM, Li Y, Wang N, Liu BC, Chen ZF, Zuo LF. PLC-ε1 gene polymorphisms significantly enhance the risk of esophageal squamous cell carcinoma in individuals with a family history of upper gastrointestinal cancers. Arch Med Res. 2012;43:578–84.PubMedCrossRefGoogle Scholar
  35. 35.
    Palmer AJ, Lochhead P, Hold GL, Rabkin CS, Chow WH, Lissowska J, et al. Genetic variation in C20orf54, PLCE1 and MUC1 and the risk of upper gastrointestinal cancers in Caucasian populations. Eur J Cancer Prev. 2012;21:541–4.PubMedCentralPubMedCrossRefGoogle Scholar
  36. 36.
    Bye H, Prescott NJ, Lewis CM, Matejcic M, Moodley L, Robertson B, et al. Distinct genetic association at the PLCE1 locus with oesophageal squamous cell carcinoma in the South African population. Carcinogenesis. 2012;33:2155–61.PubMedCentralPubMedCrossRefGoogle Scholar
  37. 37.
    Umar M, Upadhyay R, Khurana R, Kumar S, Ghoshal UC, Mittal B. Evaluation of MTHFR677C > T polymorphism in prediction and prognosis of esophageal squamous cell carcinoma: a case-control study in a northern Indian population. Nutr Cancer. 2010;62:743–9.PubMedCrossRefGoogle Scholar
  38. 38.
    Upadhyay R, Khurana R, Kumar S, Ghoshal UC, Mittal B. Role of survivin gene promoter polymorphism (−31G>C) in susceptibility and survival of esophageal cancer in northern India. Ann Surg Oncol. 2011;18:880–7.PubMedCrossRefGoogle Scholar
  39. 39.
    Umar M, Upadhyay R, Kumar S, Ghoshal UC, Mittal B. CASP8–652 6N del and CASP8 IVS12–19G>A gene polymorphisms and susceptibility/prognosis of ESCC: a case control study in northern Indian population. J Surg Oncol. 2011;103:716–23.PubMedCrossRefGoogle Scholar
  40. 40.
    van Leeuwen DM, van Agen E, Gottschalk RW, Vlietinck R, Gielen M, van Herwijnen MH, et al. Cigarette smoke-induced differential gene expression in blood cells from monozygotic twin pairs. Carcinogenesis. 2007;28:691–7.PubMedCrossRefGoogle Scholar

Copyright information

© International Society of Oncology and BioMarkers (ISOBM) 2014

Authors and Affiliations

  • Meenakshi Umar
    • 1
    • 4
  • Rohit Upadhyay
    • 1
    • 5
  • Shaleen Kumar
    • 2
  • Uday Chand Ghoshal
    • 3
  • Balraj Mittal
    • 1
  1. 1.Department of GeneticsSanjay Gandhi Postgraduate Institute of Medical SciencesLucknowIndia
  2. 2.Department of RadiotherapySanjay Gandhi Postgraduate Institute of Medical SciencesLucknowIndia
  3. 3.Department of GastroenterologySanjay Gandhi Postgraduate Institute of Medical SciencesLucknowIndia
  4. 4.Division of Endocrinology, Gerontology and MetabolismStanford UniversityStanfordUSA
  5. 5.Department of PharmacologyWeill Cornell Medical College in QatarDohaQatar

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