Meta-Analysis of Association of SNP 19 In-del Polymorphism at the CAPN 10 Gene with Type2 Diabetes Mellitus

Kali Charan Mishra

University Department of Zoology, LN Mithila University, Darbhnaga, Bihar, India.

Parul Banerjee *

University Department of Zoology, LN Mithila University, Darbhnaga, Bihar, India.

*Author to whom correspondence should be addressed.


Abstract

The CAPN 10 gene encoding the larger subunit of the ubiquitously expressing calpain protein has been found to play a role in the incidence of Type2 diabetes mellitus (T2DM). Several intronic polymorphisms of the CAPN10 gene and the linked haplotypic combinations have been implicated in T2DM. The SNP 19 locus of the gene lying within intron 6 exhibits an in-del polymorphism and has been found to be associated with T2DM in several studies. However, the results have not been constant.

Keeping this in view, the present work was carried out to understand the association of the intronic SNP 19 in-del polymorphism at the CAPN 10 gene with T2DM through meta-analysis of the case-control studies. All statistical tests based on PRISMA and PROSPERO were performed on R studio (4.2.3). However, the pooled odds ratio (OR) estimates did not reveal any significant association between polymorphism at the SNP 19 locus of CAPN 10 gene and T2DM.

Therefore, it is concluded that polymorphism at the SNP19 locus of CAPN 10 gene alone has no role to play in the etiology of T2DM.

Keywords: T2DM, CAPN 10 gene, SNP polymorphisms, Case-control association studies, SNP 19, in-del polymorphisms


How to Cite

Mishra, K. C., & Banerjee , P. (2024). Meta-Analysis of Association of SNP 19 In-del Polymorphism at the CAPN 10 Gene with Type2 Diabetes Mellitus. UTTAR PRADESH JOURNAL OF ZOOLOGY, 45(9), 8–19. https://doi.org/10.56557/upjoz/2024/v45i94017

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References

GeneCards. GeneCards: The human gene database; 2024.

Retrieved March 12, 202 Available: https://www.genecards.org/cgi-bin/carddisp.pl?gene=CAPN10

Horikawa Y, Oda N, Cox NJ, Li X, Orho-Melander M, Hara M, Hinokio Y, Lindner TH, Mashima, H, Schwarz PEH, del Bosque-Plata L, Horikawa Y, Oda Y, Yoshiuchi I, Colilla S, Polonsky KS, Wei S, Concannon P, Iwasaki N, Schulze J, Baier LJ, Bogardus C, Groop L, Boerwinkle E, Hanis CL, and Bell GI. Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus. Nat Genet. 2000;26(2): 163–175.

Baier LJ, Permana PA, Yang X, Pratley RE, Hanson RL, Shen G-Q, Mott D, Knowler WC, Cox NJ, Horikawa Y, Oda N, Bell GI, Bogardus C. A calpain-10 gene polymorphism is associated with reduced muscle mRNA levels and insulin resistance. Journal of Clinical Investigation. 2000;106(7):R69–R73.

Sreenan SK, Zhou Y-P, Otani K, Hansen PA, Currie KPM, Pan C-Y, Lee J-P, Ostrega DM, Pugh W, Horikawa Y, Cox NJ, Hanis CL, Burant CF, Fox AP, Bell GI, Polonsky KS. Calpains Play a Role in Insulin Secretion and Action. Diabetes. 2001;50(9)2013–2020.

Goll DE, Thompson VF, LI H, Wei W, Cong J. The Calpain System. Physiol Rev. 2003; 83(3):731–801.

Marshall C, Hitman G, Turner M. Calpain-10 regulates insulin secretion. Diabetes. 2003;52:A373.

Marshall C, Hitman GA, Partridge CJ, Clark A, Ma H, Shearer TR, Turner MD. Evidence that an Isoform of Calpain-10 Is a Regulator of Exocytosis in Pancreatic β-Cells. Molecular Endocrinology. 2005; 19(1)213–224.

Hoffstedt J, Rydén M, Löfgren P, Orho-Melander M, Groop L, Arner P. Polymorphism in the Calpain 10 gene influences glucose metabolism in human fat cells. Diabetologia. 2002;45(2);276–282.

Moher D, Liberati A, Tetzlaff J, Altman DG. Preferred reporting items for systematic reviews and meta-analyses: The PRISMA statement. International Journal of Surgery. 2010;8(5):336–341.

Sarhangi N, Sharifi F, Hashemian L, Hassani Doabsari M, Heshmatzad K, Rahbaran M, Jamaldini SH, Aghaei Meybodi HR, Hasanzad M. PPARG (Pro12Ala) genetic variant and risk of T2DM: a systematic review and meta-analysis. Sci Rep. 2020;10(1);12764.

Stang A. Critical evaluation of the Newcastle-Ottawa scale for the assessment of the quality of nonrandomized studies in meta-analyses. Eur J Epidemiol. 2010;25(9):603–605.

Mantel N, Haenszel W. Statistical aspects of the analysis of data from retrospective studies of disease. J Natl Cancer Inst. 1959;22(4):719–48.

Higgins JPT. Measuring inconsistency in meta-analyses. BMJ. 2003;327(7414): 557–560.

Galbraith RF. A note on graphical presentation of estimated odds ratios from several clinical trials. Stat Med. 1988;7(8); 889–894.

Morales J, Welter D, Bowler EH, Cerezo M, Harris LW, McMahon AC, Hall P, Junkins HA, Milano A, Hastings E, Malangone C, Buniello A, Burdett T, Flicek P, Parkinson H, Cunningham, F, Hindorff LA, MacArthur JAL. A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog. Genome Biol. 2018;19(1):21.

Egger M, Smith GD, Schneider M, Minder C. Bias in meta-analysis detected by a simple, graphical test. BMJ. 1997; 315(7109):629–634.

Sultana M, Islam MdM, Hossain Md M, Rahman MdA, Das SC, Barman DN, Mitu FS, Gupta S Das. Association of CAPN10 gene (rs3842570) polymorphism with the type 2 diabetes mellitus among the population of Noakhali region in Bangladesh: A case-control study. Genomics Inform. 2023;21(3):e33.

Sarkar P, Chatterjee D, Bandyopadhyay AR. Association of CAPN10 (SNP-19) genetic polymorphism and obesity with T2DM: a study on Bengali Hindu caste population. Int J Diabetes Dev Ctries. 2021;41(1):37–42.

Osman H, Osman M, Alsaidy A. GSTT1, Calpain 10 SNP 19 and indices of glycaemia in type 2 diabetes. Br J Biomed Sci. 2019;76(4);205–207.

Bayramci NS, Acik L, Kalkan Ç, Yetkin İ. Investigation of glucocorticoid receptor and calpain-10 gene polymorphisms in Turkish patients with type 2 diabetes mellitus. Turk J Med Sci. 2017;47:1568–1575.

Picos-Cárdenas VJ, Sáinz-González E, Miliar-García A, Romero-Zazueta A, Quintero-Osuna R, Leal-Ugarte E, Peralta-Leal V, Meza-Espinoza JP. Calpain-10 gene polymorphisms and risk of type 2 diabetes mellitus in Mexican mestizos. Genet Mol Res. 2015;14(1): 2205–2215.

Loya Méndez Y, Reyes Leal G, Sánchez González A, Portillo Reyes V, Reyes Ruvalcaba D, and Bojórquez Rangel G. [SNP-19 genotypic variants of CAPN10 gene and its relation to diabetes mellitus type 2 in a population of Ciudad Juarez, Mexico]. Nutr Hosp. 2014;31(2):744–50.

Arslan E, Acik L, Gunaltili G, Ayvaz G, Altinova AE, Arslan M. The effect of calpain-10 gene polymorphism on the development of type 2 diabetes mellitus in a Turkish population. Endokrynol Pol. 2014;65(2):90–5.

Buraczynska M, Wacinski P, Stec A, Kuczmaszewska A. Calpain-10 gene polymorphisms in type 2 diabetes and its micro- and macrovascular complications. J Diabetes Complications. 2013;27(1):54–58.

Sharma R, Matharoo K, Kapoor R, Chopra H. Bhanwer A. Ethnic differences in CAPN10 SNP-19 in type 2 diabetes: a North-West Indian case control study and evidence from meta-analysis. Genet Res (Camb). 2013;95(5):146–155.

Danquah I, Othmer T, Frank LK, Bedu-Addo G, Schulze MB, Mockenhaupt FP. The TCF7L2 rs7903146 (T) allele is associated with type 2 diabetes in urban Ghana: a hospital-based case-control study. BMC Med Genet. 2013;14;96.

Plengvidhya N, Chanprasert K, Tangjittipokin W, Thongnoppakhun W, Yenchitsomanus P. Detection of CAPN10 copy number variation in Thai patients with type 2 diabetes by denaturing high performance liquid chromatography and real‐time quantitative polymerase chain reaction. J Diabetes Investig. 2015;6(6): 632–639.

Bodhini D, Radha V, Ghosh S, Sanapala KR, Majumder PP, Rao MRS, Mohan V. Association of calpain 10 gene polymorphisms with type 2 diabetes mellitus in Southern Indians. Metabolism. 2011;60(5):681–688.

Zaharna MM, Abed AA, Sharif FA. Calpain-10 gene polymorphism in type 2 diabetes mellitus patients in the Gaza Strip. Med Princ Pract. 2010;19(6):457–462.

Ezzidi I, Mtiraoui N, Nemr R, Kacem M, Al-Khateeb GM, Mahjoub T, Almawi WY. Variants within the calpain-10 gene and relationships with type 2 diabetes (T2DM) and T2DM-related traits among Tunisian Arabs. Diabetes Metab. 2010;36(5):357–362.

Ezzidi I, Turki A, Messaoudi S, Chaieb M, Kacem M, Al-Khateeb GM, Mahjoub T, Almawi WY, and Mtiraoui N. Common polymorphisms of calpain-10 and the risk of Type 2 Diabetes in a Tunisian Arab population: a case-control study. BMC Med Genet. 2010;11:75.

Alsaraj F, O’Gorman D, McAteer S, McDermott J, Hawi Z, Sreenan S. Haplotype association of calpain 10 gene variants with type 2 diabetes mellitus in an Irish sample. Ir J Med Sci. 2010;179(2): 269–272.

Adak S, Sengupta S, Chowdhury S, Bhattacharyya M. Co-existence of risk and protective haplotypes of Calpain 10 gene to type 2 diabetes in the eastern Indian population. Diab Vasc Dis Res. 2010;7(1): 63–68.

Ouederni TB, Sanchez-Corona J, Skhiri HA, Maiz H Ben Abid HK, Benammar-Elgaaied A. Study of association of the SNP19 polymorphism of calpain 10 gene with type 2 diabetes in ethnic sub-groups of the Tunisian population: Gene-environment interaction. Ann Biol Clin (Paris). 2009;67(2):171–176.

Demirci H, Yurtcu E, Ergun MA, Yazici AC, Karasu C, Yetkin I. Calpain 10 SNP-44 Gene Polymorphism Affects Susceptibility to Type 2 Diabetes Mellitus and Diabetic-Related Conditions. Genet Test. 2008; 12(2):305–309.

Chen S, Lu X, Yan W-L, Huang J, Gu D. Variations in the calpain-10 gene are associated with the risk of type 2 diabetes and hypertension in northern Han Chinese population. Chin Med J (Engl). 2007; 120(24):2218–2223.

Kang ES, Kim HJ, Nam M, Nam CM, Ahn CW, Cha BS, Lee HC. A novel 111/121 diplotype in the Calpain-10 gene is associated with type 2 diabetes. J Hum Genet. 2006;51(7):629–633.

Einarsdottir E, Mayans S, RuikkaK., Escher SA, Lindgren P, Agren A, Eliasson M, Holmberg D. Linkage but not association of calpain-10 to type 2 diabetes replicated in northern Sweden. Diabetes. 2006;55(6):1879–1883.

Chen Y, Kittles R, Zhou J. Chen G, Adeyemo A, Panguluri RK, Chen W, Amoah A, Opoku V, Acheampong J, Agyenim-Boateng K, Eghan BA, Nyantaki A, Oli J, Okafor G, Ofoegbu E, Osotimehin B. Abbiyesuku F, Johnson T, Fasanmade O, Rufus T, Furbert-Harris P, Daniel HI, Berg KA, Collins FS, Dunston GM, Rotimi CN. Calpain-10 gene polymorphisms and type 2 diabetes in West Africans: the Africa America Diabetes Mellitus (AADM) Study. Ann Epidemiol. 2005;15(2):153–159.

Wu B, Takahashi J, Fu M, Cheng H, Matsumura S, Taniguchi H. Variants of calpain-10 gene and its association with type 2 diabetes mellitus in a Chinese population. Diabetes Res Clin Pract. 2005; 68(2):155–161.

Iwasaki N, Horikawa Y, Tsuchiya T, Kitamura Y, Nakamura T, Tanizawa Y, Oka Y, Hara K, Kadowaki T, Awata T, Honda M, Yamashita K, Oda N, Yu L, Yamada N, Ogata M, Kamatani, N, Iwamoto Y, Bosque-Plata L Del Hayes MG, Cox NJ, Bell GI. Genetic variants in the calpain-10 gene and the development of type 2 diabetes in the Japanese population. J Hum Genet. 2005;50(2):92–98.

del Bosque-Plata L, Aguilar-Salinas CA, Tusié-Luna MT, Ramírez-Jiménez S, Rodríguez-Torres M, Aurón-Gómez M, Ramírez E, Velasco-Pérez ML, Ramírez-Silva A, Gómez-Pérez F, Hanis CL, Tsuchiya T. Yoshiuchi I, Cox NJ, Bell GI. Association of the calpain-10 gene with type 2 diabetes mellitus in a Mexican population. Mol Genet Metab. 2004;81(2): 122–126.

Rasmussen SK, Urhammer SA, Berglund L, Jensen JN, Hansen L, Echwald SM, Borch-Johnsen K, Horikawa Y, Mashima H, Lithell H, Cox NJ, Hansen T, Bell GI, Pedersen O. Variants within the calpain-10 gene on chromosome 2q37 (NIDDM1) and relationships to type 2 diabetes, insulin resistance, and impaired acute insulin secretion among Scandinavian Caucasians. Diabetes. 2002;51(12):3561–3567.

Malecki MT, Moczulski DK, Klupa T, Wanic K, Cyganek K, Frey J, Sieradzki J. Homozygous combination of calpain 10 gene haplotypes is associated with type 2 diabetes mellitus in a Polish population. Eur J Endocrinol. 2002;146(5):695–699.

Fingerlin TE, Erdos MR, Watanabe RM, Wiles KR, Stringham HM, Mohlke KL, Silander K, Valle TT, Buchanan TA, Tuomilehto J, Bergman RN, Boehnke M, Collins FS. Variation in three single nucleotide polymorphisms in the calpain-10 gene not associated with type 2 diabetes in a large Finnish cohort. Diabetes. 2002;51(5):1644–1648.

Tsai HJ, Sun G, Weeks DE, Kaushal R, Wolujewicz M, McGarvey ST, Tufa J, Viali S, Deka R. Type 2 diabetes and three calpain-10 gene polymorphisms in Samoans: no evidence of association. Am J Hum Genet. 2001;69(6):1236–1244.

El-Far SW, Kassem HSh, Embaby AM, Saad AA, Mowafy N, Haroun M. Association of CAPN10 haplotype combinations with type 2 diabetes mellitus and metabolic syndrome among Egyptians: pilot study—genotyping of three CAPN10 variants. Egyptian Journal of Medical Human Genetics. 2022;23(1):26.

Shima Y, Nakanishi K, Odawara M, Kobayashi T, Ohta H. Association of the SNP-19 genotype 22 in the calpain-10 gene with elevated body mass index and hemoglobin A1c levels in Japanese. Clinica Chimica Acta. 2003;336(1–2):89–96.