A New Method To Detect IDH1 Synonymous SNP 105 C >T rs11554137
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Published:
Nov 12, 2018
Keywords:
IDH, SNP, RFLP, AML, Glioma
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Abstract
Alteration of cellular metabolism is one of the oncogenetic mechanisms. Furthermore, the defect of Isocitrate dehydrogenase (IDH) enzymes lead to abnormal cellular metabolism. Mutation in the IDH1 gene is common in glioblastoma multiforme (GMB), glioma, and acute myeloid leukemia (AML). The IDH1 single nucleotide polymorphism (SNP) in codon 105 C>T (rs11554137) is a prognostic factor in patients with glioma and AML. Currently, the most common technique used for IDH1 SNP 105 C>T detection is the sequencing technique that expensive and time-consuming. We designed a new method through the Restriction fragment length polymorphism (RFLP). Ninty Eight unrelated healthy volunteers comprising of 49 male, and 49 female which was randomly selected. Their ages ranged from 1 to 64 years with a median age of 33 years. Polymerase chain reaction (PCR) and RsaI fragmented IDH1 SNP105 C >T were identified in 16.3% of our cases. So we conclude that we may use the PCR-RFLP assay instead.
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References
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[14] Ali, M.A.M., Ahmed, E.K., Assem, M.M.A. and Helwa, R., 2017. The synonymous isocitrate dehydrogenase 1 315C> T SNP confers an adverse prognosis in Egyptian adult patients with NPM1-/CEBPA-negative acute myeloid leukemia. Indian Journal of Hematology and Blood Transfusion, 34(2), 240-252.
[15] Wang, X.W., Boisselier, B., Rossetto, M., Marie, Y., Idbaih, A., Mokhtari, K., Gousias, K., Hoang-Xuan, K., Delattre, J.Y., Simon, M., Labussière, M. and Sanson, M., 2013. Prognostic impact of the isocitrate dehydrogenase 1 single‐nucleotide polymorphism rs11554137 in malignant gliomas. Cancer, 119(4), 806-813.
[16] Rasmussen, H.B., 2012. Restriction fragment length polymorphism analysis of PCR-amplified fragments (PCR-RFLP) and gel electrophoresis-valuable tool for genotyping and genetic fingerprinting. In S. Magdeldin, ed. Gel electrophoresis. London: InTechOpen, pp. 315–334.
[17] Ho, P.A., Kopecky, K.J., Alonzo, T.A., Gerbing, R.B., Miller, K.L., Kuhn, J., Zeng, R., Ries, R.E., Raimondi, S.C., Hirsch, B.A., Oehler, V., Hurwitz, C.A., Franklin, J.L., Gamis, A.S., Petersdorf, S.H., Anderson, J.E., Godwin, J.E., Reaman, G.H., Willman, C.L., Bernstein, I.D., Radich, J.P., Appelbaum, F.R., Stirewalt, D.L. and Meshinchi, S., 2011. Prognostic implications of the IDH1 synonymous SNP rs11554137 in pediatric and adult AML: a report from the Children’s Oncology Group and SWOG. Blood, 118(17), 4561–4566.
[18] Chao, H.Y., Jia, Z.X., Chen, T., Lu, X.Z., Cen, L., Xiao, R., Jiang, N.K., Ying, J.H., Zhou, M. and Zhang, R., 2012. IDH2 mutations are frequent in Chinese patients with acute myeloid leukemia and associated with NPM1 mutations and FAB‐M2 subtype. International journal of laboratory hematology, 34(5), 502-509.
[19] Cruz, G.R., Oliveira, I.D., Moraes, L., Paniago, M.D.G.P., de Seixas Alves, M.T., Capellano, A.M., Saba-Silva, N., Cavalheiro, S., Cerutti, J.M. and Toledo, S.R., 2014. Analysis of KIAA1549–BRAF fusion gene expression and IDH1/IDH2 mutations in low grade pediatric astrocytomas. Journal of Neuro-Oncology, 117(2), 235-242.
[20] Acquaviva, G., Visani, M., de Biase, D., Marucci, G., Franceschi, E., Tosoni, A., Brandes, A.A., Rhoden, K.J., Pession, A. and Tallini, G., 2018. Prevalence of the single-nucleotide polymorphism rs11554137 (IDH1 105GGT) in brain tumors of a cohort of Italian patients. Scientific reports, 8(1), 4459.
[21] Zou, Y., Zeng, Y., Zhang, D.F., Zou, S.H., Cheng, Y.F. and Yao, Y.G., 2010. IDH1 and IDH2 mutations are frequent in Chinese patients with acute myeloid leukemia but rare in other types of hematological disorders. Biochemical and Biophysical Research Communications, 402(2), 378-383.
[22] Chotirat, S., Thongnoppakhun, W., Promsuwicha, O., Boonthimat, C. and Auewarakul, C.U., 2012. Molecular alterations of isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) metabolic genes and additional genetic mutations in newly diagnosed acute myeloid leukemia patients. Journal of Hematology & Oncology, 5(1), 5.
[23] Soyer, N., Kaymaz, B.T., Özkan, M.C., Aktan, Ç., Küçükaslan, A.Ş., Şahin, F., Kosova, B. and Saydam, G., 2017. TET2, ASXL1, IDH1, and IDH2 Single nucleotide polymorphisms in Turkish patients with chronic myeloproliferative neoplasms. Turkish Journal of Hematology, 34(2), 174–178.
[2] Patel, K.P., Barkoh, B.A., Chen, Z., Ma, D., Reddy, N., Medeiros, L.J. and Luthra, R., 2011. Diagnostic testing for IDH1 and IDH2 variants in acute myeloid leukemia: an algorithmic approach using high-resolution melting curve analysis. The Journal of Molecular Diagnostics, 13(6), 678-686.
[3] Ravandi, F., Patel, K., Luthra, R., Faderl, S., Konopleva, M., Kadia, T., Brandt, M., Pierce, S., Kornblau, S., Andreeff, M., Wang, X., Garcia-Manero, G., Cortes, J. and Kantarjian, H., 2012. Prognostic significance of alterations in IDH enzyme isoforms in patients with AML treated with high‐dose cytarabine and idarubicin. Cancer, 118(10), 2665-2673.
[4] Chang, C.M., Xu, K. and Shu, H.K.G., 2011. The role of isocitrate dehydrogenase mutations in glioma brain tumors. In: M. Garami, ed. Molecular Targets of CNS Tumors. London: InTechOpen, pp. 413–436.
[5] Rakheja, D., Konoplev, S., Medeiros, L.J. and Chen, W., 2012. IDH mutations in acute myeloid leukemia. Human Pathology, 43(10), 1541-1551.
[6] Chan, S.M., Thomas, D., Corces-Zimmerman, M.R., Xavy, S., Rastogi, S., Hong, W.J., Zhao, F., Medeiros, B.C., Tyvoll, D.A. and Majeti, R., 2015. Isocitrate dehydrogenase 1 and 2 mutations induce BCL-2 dependence in acute myeloid leukemia. Nature Medicine, 21(2), 178–184.
[7] Balss, J., Thiede, C., Bochtler, T., Okun, J.G., Saadati, M., Benner, A., Pusch, S., Ehninger, G., Schaich, M., Ho, A.D., von Deimling, A., Krämer, A. and Heilig, C.E., 2016. Pretreatment d-2-hydroxyglutarate serum levels negatively impact on outcome in IDH1-mutated acute myeloid leukemia. Leukemia, 30(4), 782–788.
[8] Willander, K., Falk, I.J., Chaireti, R., Paul, E., Hermansson, M., Gréen, H., Lotfi, K. and Söderkvist, P., 2014. Mutations in the isocitrate dehydrogenase 2 gene and IDH1 SNP 105C> T have a prognostic value in acute myeloid leukemia. Biomarker Research, 2(1), 18.
[9] Chotirat, S., Thongnoppakhun, W., Wanachiwanawin, W. and Auewarakul, C.U., 2015. Acquired somatic mutations of isocitrate dehydrogenases 1 and 2 (IDH1 and IDH2) in preleukemic disorders. Blood Cells, Molecules, and Diseases, 54(3), 286-291.
[10] Cleven, A.H.G., Suijker, J., Agrogiannis, G., Briaire-de Bruijn, I.H., Frizzell, N., Hoekstra, A.S., Wijers-Koster, P.M., Cleton-Jansen, A.M. and Bovée, J.V.M.G., 2017. IDH1 or -2 mutations do not predict outcome and do not cause loss of 5-hydroxymethylcytosine or altered histone modifications in central chondrosarcomas. Clinical Sarcoma Research, 7(1), 8.
[11] Du, X., Wan, S., Chen, Y., Qu, P., Huang, X., Yu, X., Yang, H., Zhang, Y. and Xing, J., 2014. Genetic variants in genes of tricarboxylic acid cycle key enzymes predict postsurgical overall survival of patients with hepatocellular carcinoma. Annals of Surgical Oncology, 21(13), 4300-4307.
[12] Fasan, A., Haferlach, C., Eder, C., Alpermann, T., Quante, A., Peters, A., Kern, W., Haferlach, T. and Schnittger, S., 2015. Evaluation of IDH1G105 polymorphism as prognostic marker in intermediate-risk AML. Annals of Hematology, 94(12), 1991-2001.
[13] Wagner, K., Damm, F., Göhring, G., Görlich, K., Heuser, M., Schäfer, I., Ottmann, O., Lübbert, M., Heit, W., Kanz, L., Schlimok, G., Raghavachar, A.A., Fiedler, W., Kirchner, H.H., Brugger, W., Zucknick, M., Schlegelberger, B., Heil, G., Ganser, A. and Krauter, J., 2010. Impact of IDH1 R132 mutations and an IDH1 single nucleotide polymorphism in cytogenetically normal acute myeloid leukemia: SNP rs11554137 is an adverse prognostic factor. Journal of Clinical Oncology, 28(14), 2356-2364.
[14] Ali, M.A.M., Ahmed, E.K., Assem, M.M.A. and Helwa, R., 2017. The synonymous isocitrate dehydrogenase 1 315C> T SNP confers an adverse prognosis in Egyptian adult patients with NPM1-/CEBPA-negative acute myeloid leukemia. Indian Journal of Hematology and Blood Transfusion, 34(2), 240-252.
[15] Wang, X.W., Boisselier, B., Rossetto, M., Marie, Y., Idbaih, A., Mokhtari, K., Gousias, K., Hoang-Xuan, K., Delattre, J.Y., Simon, M., Labussière, M. and Sanson, M., 2013. Prognostic impact of the isocitrate dehydrogenase 1 single‐nucleotide polymorphism rs11554137 in malignant gliomas. Cancer, 119(4), 806-813.
[16] Rasmussen, H.B., 2012. Restriction fragment length polymorphism analysis of PCR-amplified fragments (PCR-RFLP) and gel electrophoresis-valuable tool for genotyping and genetic fingerprinting. In S. Magdeldin, ed. Gel electrophoresis. London: InTechOpen, pp. 315–334.
[17] Ho, P.A., Kopecky, K.J., Alonzo, T.A., Gerbing, R.B., Miller, K.L., Kuhn, J., Zeng, R., Ries, R.E., Raimondi, S.C., Hirsch, B.A., Oehler, V., Hurwitz, C.A., Franklin, J.L., Gamis, A.S., Petersdorf, S.H., Anderson, J.E., Godwin, J.E., Reaman, G.H., Willman, C.L., Bernstein, I.D., Radich, J.P., Appelbaum, F.R., Stirewalt, D.L. and Meshinchi, S., 2011. Prognostic implications of the IDH1 synonymous SNP rs11554137 in pediatric and adult AML: a report from the Children’s Oncology Group and SWOG. Blood, 118(17), 4561–4566.
[18] Chao, H.Y., Jia, Z.X., Chen, T., Lu, X.Z., Cen, L., Xiao, R., Jiang, N.K., Ying, J.H., Zhou, M. and Zhang, R., 2012. IDH2 mutations are frequent in Chinese patients with acute myeloid leukemia and associated with NPM1 mutations and FAB‐M2 subtype. International journal of laboratory hematology, 34(5), 502-509.
[19] Cruz, G.R., Oliveira, I.D., Moraes, L., Paniago, M.D.G.P., de Seixas Alves, M.T., Capellano, A.M., Saba-Silva, N., Cavalheiro, S., Cerutti, J.M. and Toledo, S.R., 2014. Analysis of KIAA1549–BRAF fusion gene expression and IDH1/IDH2 mutations in low grade pediatric astrocytomas. Journal of Neuro-Oncology, 117(2), 235-242.
[20] Acquaviva, G., Visani, M., de Biase, D., Marucci, G., Franceschi, E., Tosoni, A., Brandes, A.A., Rhoden, K.J., Pession, A. and Tallini, G., 2018. Prevalence of the single-nucleotide polymorphism rs11554137 (IDH1 105GGT) in brain tumors of a cohort of Italian patients. Scientific reports, 8(1), 4459.
[21] Zou, Y., Zeng, Y., Zhang, D.F., Zou, S.H., Cheng, Y.F. and Yao, Y.G., 2010. IDH1 and IDH2 mutations are frequent in Chinese patients with acute myeloid leukemia but rare in other types of hematological disorders. Biochemical and Biophysical Research Communications, 402(2), 378-383.
[22] Chotirat, S., Thongnoppakhun, W., Promsuwicha, O., Boonthimat, C. and Auewarakul, C.U., 2012. Molecular alterations of isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) metabolic genes and additional genetic mutations in newly diagnosed acute myeloid leukemia patients. Journal of Hematology & Oncology, 5(1), 5.
[23] Soyer, N., Kaymaz, B.T., Özkan, M.C., Aktan, Ç., Küçükaslan, A.Ş., Şahin, F., Kosova, B. and Saydam, G., 2017. TET2, ASXL1, IDH1, and IDH2 Single nucleotide polymorphisms in Turkish patients with chronic myeloproliferative neoplasms. Turkish Journal of Hematology, 34(2), 174–178.