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Akut Lenfoblastik Lösemi ile İlişkilendirilen NUDT15 Genindeki Zararlı SNP’lerin Biyoinformatik Araçlar Kullanılarak Belirlenmesi

Year 2023, Issue: 21 - December, 866 - 880, 05.01.2024
https://doi.org/10.38079/igusabder.1196511

Abstract

Amaç: Akut lenfoblastik lösemide (ALL) tiopurin grubu ilaçlar en temel ilaçlardır ve idame tedavisi başta olmak üzere hemen hemen tüm tedavi protokollerinde yer almaktadır. Tiyoguanin nükleotitlerinin etki mekanizması hücrelerde DNA yapısına girmek, DNA sentezini bozmak ve programlı hücre ölümünü tetiklemektir. Zararlı tek nükleotid polimorfizmlerin (SNP’lerin) ALL ile ilgili nükleotid trifosfat difosfataz proteini üzerindeki etkisi henüz tam olarak anlaşılmamıştır. Bu çalışmada, NUDT15 genindeki yanlış anlamlı varyantların hastalığa yatkınlıkta önemli rol oynayan protein yapısı ve stabilizasyonu üzerine olası zararlı etkilerinin modern biyoinformatik yazılımları kullanılarak belirlenmesi amaçlanmıştır.
Yöntem: NUDT15 genindeki SNP’lere erişmek için Ulusal Biyoteknoloji Bilgi Merkezi (NCBI), Tek Nükleotid Polimorfizm Veritabanı (dbSNP) kullanılmıştır. Bu çalışmada SIFT, PolyPhen-2, PROVEAN, SNAP2, PANTHER, I-Mutant, HOPE ve STRING biyoinformatik araçlarının kullanımı yer almıştır.
Bulgular: Analiz sonuçları, NUDT15 genindeki toplam 6663 SNP’de 6 varyantın ‘zararlı’ olarak tanımlandığını göstermiştir. I-Mutant yazılımına göre 4 zararlı SNP protein stabilitesini azaltırken 2 zararlı SNP protein stabilitesini arttırmıştır. HOPE veri tabanı analizinde E115G, E57G, F52L ve K33N mutant amino asitlerinin yabanıl tip amino asitlere göre daha küçük ve hidrofobik olduğu, G53R ve G145D mutant amino asitlerinin ise daha büyük olduğu tespit edilmiştir. Bu sebeple, tüm varyasyonlar NUDT15 proteini üzerindeki net yükte değişiklikle sonuçlanmıştır.
Sonuç: NUDT15 varyantlarına ilişkin veriler, gelecekteki çalışmalarda hastanın tiopürin ilaçlarına yanıtının tahmin edilmesine, hastanın ilaç etkileşimlerine duyarlılığının daha iyi anlaşılmasına ve nihayetinde prognoz hakkında bilgi edinilmesine katkı sağlayacaktır.

References

  • 1. Inaba H, Greaves M, Mullighan CG. Acute lymphoblastic leukaemia. Lancet. 2013;381(9881):1943-1955. DOI:10.1016/S0140-6736(12)62187-4
  • 2. Belson M, Kingsley B, Holmes A. Risk factors for acute leukemia in children: a review. Environ Health Perspect. 2007;115(1),138-145. DOI:10.1289/ehp.9023
  • 3. Mazur B, Szczepański T, Karpe J, Sońta-Jakimczyk D, Bubała H, Torbus M. Decreased numbers of CD4+ T lymphocytes in peripheral blood after treatment of childhood acute lymphoblastic leukemia. Leuk Res. 2006;30(1):33-36. DOI:10. 1016/j.leukres.2005.05.024
  • 4. Lee DK, Chang VY, Kee T, Ho CM, Ho D. Optimizing Combination Therapy for Acute Lymphoblastic Leukemia Using a Phenotypic Personalized Medicine Digital Health Platform: Retrospective Optimization Individualizes Patient Regimens to Maximize Efficacy and Safety. SLAS Technology. 2017; 22(3):276-288. DOI:10.1177/2211068216681979.
  • 5. Nishii R, Moriyama T, Janke LJ, Yang W, Suiter CC, Lin TN, et al. Preclinical evaluation of NUDT15-guided thiopurine therapy and its effects on toxicity and antileukemic efficacy. Blood. 2018;131(22):2466-2474. DOI:10.1182/blood-2017-11-815506
  • 6. Moriyama T, Nishii R, Perez-Andreu V, Yang W, Klussmann FA, Zhao X, et al. NUDT15 polymorphisms alter thiopurine metabolism and hematopoietic toxicity. Nat Genet. 2016;48(4):367-373. DOI:10.1038/ng.3508
  • 7. Peregud-Pogorzelski J, Tetera-Rudnicka E, Kurzawski M, Brodkiewicz A, Adrianowska N, Mlynarski W, et al. Thiopurine S-methyltransferase (TPMT) polymorphisms in children with acute lymphoblastic leukemia, and the need for reduction or cessation of 6-mercaptopurine doses during maintenance therapy: the Polish multicenter analysis. Pediatr Blood Cancer. 2011; 57(4) :578-582. DOI:10.1002/pbc.23013
  • 8. Evans WE, Hon YY, Bomgaars L, Coutre S, Holdsworth M, Janco R, et al. Preponderance of thiopurine S-methyltransferase deficiency and heterozygosity among patients intolerant to mercaptopurine or azathioprine. J Clin Oncol. 2001; 19(8):2293-2301. DOI:10.1200/JCO.2001.
  • 9. McLeod HL, Krynetski EY, Relling MV, Evans WE. Genetic polymorphism of thiopurine methyltransferase and its clinical relevance for childhood acute lymphoblastic leukemia. Leukemia. 2000;14(4):567-572. DOI:10.1038/sj.leu.2401723
  • 10. Yang JJ, Landier W, Yang W, Liu C, Hageman L, Cheng C, et al. Inherited NUDT15 variant is a genetic determinant of mercaptopurine intolerance in children with acute lymphoblastic leukemia. J Clin Oncol. 2015;33(11):1235-1242. DOI:10.1200/JCO. 2014.59.4671
  • 11. KEGG: Kyoto Encyclopedia of Genes and Genomes. Accessed [15 August 2022]. https://www.genome.jp/entry/R09832
  • 12. Matsuoka K. NUDT15 gene variants and thiopurine-induced leukopenia in patients with inflammatory bowel disease. Intest Res. 2020;18:275-281. DOI:10.5217/ir.2020. 00002
  • 13. Mlakar V, Huezo-Diaz Curtis P, Satyanarayana Uppugunduri CR, Krajinovic M, Ansari M. Pharmacogenomics in Pediatric Oncology: Review of Gene-Drug Associations for Clinical Use. Int J Mol Sci. 2016;17(9):1502. DOI:10.3390 /ijms17091502
  • 14. Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31(13):3812-3814. DOI:10.1093/nar/gkg509.
  • 15. Choi Y, Chan AP. PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics. 2015;31:2745-2747
  • 16. Venselaar H, te Beek TA, Kuipers RK, Maarten L Hekkelman ML, Vriend G. Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinformatics. 2010;11:548. DOI:10. 1186/1471-2105-11-548
  • 17. Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, et al. The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 2021;49(D1):D605-D612. DOI:10.1093/nar/gkaa1074. Erratum in: Nucleic Acids Res. 2021;49(18):10800
  • 18. Peleg O, Choi JM, Shakhnovich EI. Evolution of specificity in protein-protein interactions. Biophys J. 2014; 107(7):1686-96. DOI:10.1016/j.bpj.2014.08.004
  • 19. Xu Y, Wang H, Nussinov R, Ma B. Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome. Proteomics. 2013;13(8):1339-1351. DOI:10.1002/pmic.201100540
  • 20. Rotimi SO, Peter O, Oguntade O, Rotimi OA. In silico analysis of the functional non-synonymous single nucleotide polymorphisms in the human CYP27B1 gene. EJMHG. 2018;19:367-378. DOI:10.1016/j.ejmhg.2018.03.001
  • 21. Houndonougbo Y, Pugh B, VanWormer K, April C, Burgis N. Structural dynamics of inosine triphosphate pyrophosphatase (ITPA) protein and two clinically relevant mutants: molecular dynamics simulations. J Biomol Struct Dyn. 2021;39(4):1236-1247. DOI:10.1080/07391102.2020.1727363
  • 22. Boonyawat B, Monsereenusorn C, Photia A, Lertvivatpong N, Kaewchaivijit V, Jindatanmanusan P, Rujkijyanont P. ITPA:c.94C>A and NUDT15:c.415C>T Polymorphisms and Their Relation to Mercaptopurine-Related Myelotoxicity in Childhood Leukemia in Thailand. Appl Clin Genet. 2021;14:341-351. DOI:10.2147/TACG.S318912
  • 23. Wahlund M, Nilsson A, Kahlin AZ, Broliden K, Myrberg IH, Appell ML, Berggren A. The Role of TPMT, ITPA, and NUDT15 Variants during Mercaptopurine Treatment of Swedish Pediatric Patients with Acute Lymphoblastic Leukemia. J Pediatr. 2020;216:150-1577.e1. DOI:10.1016/j.jpeds.2019.09.024
  • 24. Wang DS, Yu CH, Lin CY, Chang YH, Lin KH, Lin DT, et al. Childhood acute lymphoblastic leukemia mercaptopurine intolerance is associated with NUDT15 variants. Pediatr Res. 2021;89(1):217-222. DOI:10.1038/s41390-020-0868-8
  • 25. Chiengthong K, Ittiwut C, Muensri S, Sophonphan J, Sosothikul D, Seksan P, et al. NUDT15 c.415C>T increases risk of 6-mercaptopurine induced myelosuppression during maintenance therapy in children with acute lymphoblastic leukemia. Haematologica. 2016; 101(1):e24-26. DOI:10.3324/haematol.2015.134775
  • 26. Moriyama T, Nishii R, Perez-Andreu V, Yang W, Klussmann FA, Zhao X, et al. (2016). NUDT15 polymorphisms alter thiopurine metabolism and hematopoietic toxicity. Nature Genetics. 48(4):367-373. DOI:10.1038/ng.3508.
  • 27. Zhu Y, Yin D, Su Y, Xia X, Moriyama T, Nishii R, et al. Combination of common and novel rare NUDT15 variants improves predictive sensitivity of thiopurine-induced leukopenia in children with acute lymphoblastic leukemia. Haematologica. 2018;103(7):e293-e295. DOI:10.3324/haematol.2018.187658
  • 28. Ince EÜ, Ertem M. Pharmacogenetics in Acute Lymphoblastic Leukemia, Turkish Pediatric Hematology. 2008 2:6-16.

Determination of Deleterious SNPs in NUDT15 Gene Related to Acute Lymphoblastic Leukemia by using Bioinformatics Tools

Year 2023, Issue: 21 - December, 866 - 880, 05.01.2024
https://doi.org/10.38079/igusabder.1196511

Abstract

Aim: In acute lymphoblastic leukemia (ALL), thiopurine group drugs are the most basic drugs and are included in almost all treatment protocols, especially in maintenance treatment. The mechanism of action of thioguanine nucleotides is to enter the DNA structure in cells, disrupt DNA synthesis, and trigger programmed cell death. The impact of deleterious SNPs on nucleotide triphosphate diphosphatase protein regarding ALL is not yet fully understood. In this study, it was aimed to determine the possible deleterious impacts of missense variants in the NUDT15 gene on protein structure and stabilization that play a significant role in susceptibility to the disease, using modern bioinformatics software.
Method: To access SNPs in the NUDT15, it was used National Center for Biotechnology Information (NCBI), Single Nucleotide Polymorphism Database (dbSNP). In bioinformatics tools used in this study included SIFT, PolyPhen-2, PROVEAN, SNAP2, and PANTHER, followed by I-Mutant, HOPE, and STRING.
Results: The results of the analysis showed that in a total of 6663 SNPs in the NUDT15, 6 variants have been identified as ‘deleterious’. According to the I-Mutant software, 4 deleterious SNPs decreased protein stability while 2 deleterious SNPs increased protein stability. In the HOPE database analysis, E115G, E57G, F52L, and K33N mutant amino acids were found to be smaller and more hydrophobic than wild-type amino acids, while G53R and G145D mutant amino acids were found to be larger. Thus, all variations resulted in alterations in the net charge on the NUDT15 protein.
Conclusion: Data on NUDT15 variants will contribute to the prediction of the patient’s response to thiopurine drugs in future studies, to a better understanding of the patient’s susceptibility to drug interactions, and ultimately to obtaining information about the prognosis.

References

  • 1. Inaba H, Greaves M, Mullighan CG. Acute lymphoblastic leukaemia. Lancet. 2013;381(9881):1943-1955. DOI:10.1016/S0140-6736(12)62187-4
  • 2. Belson M, Kingsley B, Holmes A. Risk factors for acute leukemia in children: a review. Environ Health Perspect. 2007;115(1),138-145. DOI:10.1289/ehp.9023
  • 3. Mazur B, Szczepański T, Karpe J, Sońta-Jakimczyk D, Bubała H, Torbus M. Decreased numbers of CD4+ T lymphocytes in peripheral blood after treatment of childhood acute lymphoblastic leukemia. Leuk Res. 2006;30(1):33-36. DOI:10. 1016/j.leukres.2005.05.024
  • 4. Lee DK, Chang VY, Kee T, Ho CM, Ho D. Optimizing Combination Therapy for Acute Lymphoblastic Leukemia Using a Phenotypic Personalized Medicine Digital Health Platform: Retrospective Optimization Individualizes Patient Regimens to Maximize Efficacy and Safety. SLAS Technology. 2017; 22(3):276-288. DOI:10.1177/2211068216681979.
  • 5. Nishii R, Moriyama T, Janke LJ, Yang W, Suiter CC, Lin TN, et al. Preclinical evaluation of NUDT15-guided thiopurine therapy and its effects on toxicity and antileukemic efficacy. Blood. 2018;131(22):2466-2474. DOI:10.1182/blood-2017-11-815506
  • 6. Moriyama T, Nishii R, Perez-Andreu V, Yang W, Klussmann FA, Zhao X, et al. NUDT15 polymorphisms alter thiopurine metabolism and hematopoietic toxicity. Nat Genet. 2016;48(4):367-373. DOI:10.1038/ng.3508
  • 7. Peregud-Pogorzelski J, Tetera-Rudnicka E, Kurzawski M, Brodkiewicz A, Adrianowska N, Mlynarski W, et al. Thiopurine S-methyltransferase (TPMT) polymorphisms in children with acute lymphoblastic leukemia, and the need for reduction or cessation of 6-mercaptopurine doses during maintenance therapy: the Polish multicenter analysis. Pediatr Blood Cancer. 2011; 57(4) :578-582. DOI:10.1002/pbc.23013
  • 8. Evans WE, Hon YY, Bomgaars L, Coutre S, Holdsworth M, Janco R, et al. Preponderance of thiopurine S-methyltransferase deficiency and heterozygosity among patients intolerant to mercaptopurine or azathioprine. J Clin Oncol. 2001; 19(8):2293-2301. DOI:10.1200/JCO.2001.
  • 9. McLeod HL, Krynetski EY, Relling MV, Evans WE. Genetic polymorphism of thiopurine methyltransferase and its clinical relevance for childhood acute lymphoblastic leukemia. Leukemia. 2000;14(4):567-572. DOI:10.1038/sj.leu.2401723
  • 10. Yang JJ, Landier W, Yang W, Liu C, Hageman L, Cheng C, et al. Inherited NUDT15 variant is a genetic determinant of mercaptopurine intolerance in children with acute lymphoblastic leukemia. J Clin Oncol. 2015;33(11):1235-1242. DOI:10.1200/JCO. 2014.59.4671
  • 11. KEGG: Kyoto Encyclopedia of Genes and Genomes. Accessed [15 August 2022]. https://www.genome.jp/entry/R09832
  • 12. Matsuoka K. NUDT15 gene variants and thiopurine-induced leukopenia in patients with inflammatory bowel disease. Intest Res. 2020;18:275-281. DOI:10.5217/ir.2020. 00002
  • 13. Mlakar V, Huezo-Diaz Curtis P, Satyanarayana Uppugunduri CR, Krajinovic M, Ansari M. Pharmacogenomics in Pediatric Oncology: Review of Gene-Drug Associations for Clinical Use. Int J Mol Sci. 2016;17(9):1502. DOI:10.3390 /ijms17091502
  • 14. Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31(13):3812-3814. DOI:10.1093/nar/gkg509.
  • 15. Choi Y, Chan AP. PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics. 2015;31:2745-2747
  • 16. Venselaar H, te Beek TA, Kuipers RK, Maarten L Hekkelman ML, Vriend G. Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinformatics. 2010;11:548. DOI:10. 1186/1471-2105-11-548
  • 17. Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, et al. The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 2021;49(D1):D605-D612. DOI:10.1093/nar/gkaa1074. Erratum in: Nucleic Acids Res. 2021;49(18):10800
  • 18. Peleg O, Choi JM, Shakhnovich EI. Evolution of specificity in protein-protein interactions. Biophys J. 2014; 107(7):1686-96. DOI:10.1016/j.bpj.2014.08.004
  • 19. Xu Y, Wang H, Nussinov R, Ma B. Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome. Proteomics. 2013;13(8):1339-1351. DOI:10.1002/pmic.201100540
  • 20. Rotimi SO, Peter O, Oguntade O, Rotimi OA. In silico analysis of the functional non-synonymous single nucleotide polymorphisms in the human CYP27B1 gene. EJMHG. 2018;19:367-378. DOI:10.1016/j.ejmhg.2018.03.001
  • 21. Houndonougbo Y, Pugh B, VanWormer K, April C, Burgis N. Structural dynamics of inosine triphosphate pyrophosphatase (ITPA) protein and two clinically relevant mutants: molecular dynamics simulations. J Biomol Struct Dyn. 2021;39(4):1236-1247. DOI:10.1080/07391102.2020.1727363
  • 22. Boonyawat B, Monsereenusorn C, Photia A, Lertvivatpong N, Kaewchaivijit V, Jindatanmanusan P, Rujkijyanont P. ITPA:c.94C>A and NUDT15:c.415C>T Polymorphisms and Their Relation to Mercaptopurine-Related Myelotoxicity in Childhood Leukemia in Thailand. Appl Clin Genet. 2021;14:341-351. DOI:10.2147/TACG.S318912
  • 23. Wahlund M, Nilsson A, Kahlin AZ, Broliden K, Myrberg IH, Appell ML, Berggren A. The Role of TPMT, ITPA, and NUDT15 Variants during Mercaptopurine Treatment of Swedish Pediatric Patients with Acute Lymphoblastic Leukemia. J Pediatr. 2020;216:150-1577.e1. DOI:10.1016/j.jpeds.2019.09.024
  • 24. Wang DS, Yu CH, Lin CY, Chang YH, Lin KH, Lin DT, et al. Childhood acute lymphoblastic leukemia mercaptopurine intolerance is associated with NUDT15 variants. Pediatr Res. 2021;89(1):217-222. DOI:10.1038/s41390-020-0868-8
  • 25. Chiengthong K, Ittiwut C, Muensri S, Sophonphan J, Sosothikul D, Seksan P, et al. NUDT15 c.415C>T increases risk of 6-mercaptopurine induced myelosuppression during maintenance therapy in children with acute lymphoblastic leukemia. Haematologica. 2016; 101(1):e24-26. DOI:10.3324/haematol.2015.134775
  • 26. Moriyama T, Nishii R, Perez-Andreu V, Yang W, Klussmann FA, Zhao X, et al. (2016). NUDT15 polymorphisms alter thiopurine metabolism and hematopoietic toxicity. Nature Genetics. 48(4):367-373. DOI:10.1038/ng.3508.
  • 27. Zhu Y, Yin D, Su Y, Xia X, Moriyama T, Nishii R, et al. Combination of common and novel rare NUDT15 variants improves predictive sensitivity of thiopurine-induced leukopenia in children with acute lymphoblastic leukemia. Haematologica. 2018;103(7):e293-e295. DOI:10.3324/haematol.2018.187658
  • 28. Ince EÜ, Ertem M. Pharmacogenetics in Acute Lymphoblastic Leukemia, Turkish Pediatric Hematology. 2008 2:6-16.
There are 28 citations in total.

Details

Primary Language English
Subjects Clinical Sciences
Journal Section Articles
Authors

Deniz Aşlar Öner 0000-0002-9515-0073

Early Pub Date January 8, 2024
Publication Date January 5, 2024
Acceptance Date November 28, 2023
Published in Issue Year 2023 Issue: 21 - December

Cite

APA Aşlar Öner, D. (2024). Determination of Deleterious SNPs in NUDT15 Gene Related to Acute Lymphoblastic Leukemia by using Bioinformatics Tools. İstanbul Gelişim Üniversitesi Sağlık Bilimleri Dergisi(21), 866-880. https://doi.org/10.38079/igusabder.1196511
AMA Aşlar Öner D. Determination of Deleterious SNPs in NUDT15 Gene Related to Acute Lymphoblastic Leukemia by using Bioinformatics Tools. IGUSABDER. January 2024;(21):866-880. doi:10.38079/igusabder.1196511
Chicago Aşlar Öner, Deniz. “Determination of Deleterious SNPs in NUDT15 Gene Related to Acute Lymphoblastic Leukemia by Using Bioinformatics Tools”. İstanbul Gelişim Üniversitesi Sağlık Bilimleri Dergisi, no. 21 (January 2024): 866-80. https://doi.org/10.38079/igusabder.1196511.
EndNote Aşlar Öner D (January 1, 2024) Determination of Deleterious SNPs in NUDT15 Gene Related to Acute Lymphoblastic Leukemia by using Bioinformatics Tools. İstanbul Gelişim Üniversitesi Sağlık Bilimleri Dergisi 21 866–880.
IEEE D. Aşlar Öner, “Determination of Deleterious SNPs in NUDT15 Gene Related to Acute Lymphoblastic Leukemia by using Bioinformatics Tools”, IGUSABDER, no. 21, pp. 866–880, January 2024, doi: 10.38079/igusabder.1196511.
ISNAD Aşlar Öner, Deniz. “Determination of Deleterious SNPs in NUDT15 Gene Related to Acute Lymphoblastic Leukemia by Using Bioinformatics Tools”. İstanbul Gelişim Üniversitesi Sağlık Bilimleri Dergisi 21 (January 2024), 866-880. https://doi.org/10.38079/igusabder.1196511.
JAMA Aşlar Öner D. Determination of Deleterious SNPs in NUDT15 Gene Related to Acute Lymphoblastic Leukemia by using Bioinformatics Tools. IGUSABDER. 2024;:866–880.
MLA Aşlar Öner, Deniz. “Determination of Deleterious SNPs in NUDT15 Gene Related to Acute Lymphoblastic Leukemia by Using Bioinformatics Tools”. İstanbul Gelişim Üniversitesi Sağlık Bilimleri Dergisi, no. 21, 2024, pp. 866-80, doi:10.38079/igusabder.1196511.
Vancouver Aşlar Öner D. Determination of Deleterious SNPs in NUDT15 Gene Related to Acute Lymphoblastic Leukemia by using Bioinformatics Tools. IGUSABDER. 2024(21):866-80.

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