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Determination of Deleterious SNPs in APH1A Gene Related to Alzheimer’s Disease by In Silico Methods

Yıl 2019, , 472 - 480, 25.08.2019
https://doi.org/10.19113/sdufenbed.522738

Öz

Alzheimer's
disease (AD) is a progressive neurodegenerative disease characterized by
pathological accumulation of β-amyloid (Aβ) senile plaques and neurofibrillary
tangles. γ-secretase produces the amyloid β peptide (Aβ), which causes AD.
γ-secretase is a macromolecular complex and the protein encoded by the APH1A
gene is located in this complex. In this study, it was aimed to determine the
possible deleterious effects of missense single nucleotide polymorphisms (SNPs)
in APH1A gene on the protein structure and stabilization via in silico methods. PolyPhen-2 and SIFT
were used to predict deleterious SNPs, I-Mutant 2.0 software was used to detect
protein stabilization changes and Project HOPE software tool was used to make
three-dimensional modeling of wild and mutant type proteins. The results showed
that 257 SNPs among a total of 3567 SNPs in the APH1A gene were missense SNPs.
According to the in silico analysis
of the 257 SNPs it has been determined that rs11548266, rs74126634,
rs145324799, rs199961673, rs370361277, rs370719475 and rs376071112
polymorphisms may have deleterious effects. The results of in silico analysis provide data for genotyping of SNPs which have
deleterious effects on protein structure and stabilization rather than
genotyping of entire 3567 SNPs in the APH1A gene associated with Alzheimer's
disease. Therefore, deleterious SNPs may be used in the selection of SNPs and
experimental design which are the most important stages of genotyping studies.
Thus, we envisaged that the obtained results will contribute to the further
studies either experimental or in silico
on Alzheimer's disease.

Kaynakça

  • [1] El Halawany AM, Sayed NSE, Abdallah HM, El Dine RS. 2017. Protective effects of gingerol on streptozotocin-induced sporadic Alzheimer’s disease: emphasis on inhibition of β-amyloid, COX-2, alpha-, beta-secretases and APH1a. Scientific Reports. 7(1):2902.
  • [2] Iqbal K, Grundke-Iqbal I. 2010. Alzheimer's disease, a multifactorial disorder seeking multitherapies. Alzheimer's & Dementia: Elsevier; 420-424.
  • [3] Yonemura Y, Futai E, Yagishita S, Kaether C, Ishiura S. 2016. Specific combinations of presenilins and Aph1s affect the substrate specificity and activity of γ-secretase. Biochemical and biophysical research communications.478(4):1751-1757.
  • [4] De Strooper B. 2003. Aph-1, Pen-2, and nicastrin with presenilin generate an active γ-secretase complex. Neuron. 38(1):9-12.
  • [5] Gertsik N, Chiu D, LI Y. 2015. Complex regulation of gamma-secretase: from obligatory to modulatory subunits. Frontiers in aging neuroscience. 6:342.
  • [6] Hur J-Y, Gertsik N, Johnson D, Li Y-M. 2016. γ-Secretase Inhibitors: From Chemical Probes to Drug Development. Developing Therapeutics for Alzheimer's Disease: Elsevier; 63-76.
  • [7] Lee S-F, Shah S, Li H, Yu C, Han W, Yu G. 2002. Mammalian APH-1 interacts with presenilin and nicastrin and is required for intramembrane proteolysis of amyloid-β precursor protein and Notch. Journal of Biological Chemistry. 277(47):45013-45019.
  • [8] Takasugi N, Tomita T, Hayashi I, et al. 2003. The role of presenilin cofactors in the γ-secretase complex. Nature. 422(6930):438.
  • [9] Haapasalo A, Kovacs DM. 2011. The many substrates of presenilin/γ-secretase. Journal of Alzheimer's disease.25(1):3-28.
  • [10] Mohandas E, Rajmohan V, Raghunath B. 2009. Neurobiology of Alzheimer's disease. Indian journal of psychiatry. 51(1):55.
  • [11] Hemming ML, Selkoe DJ. 2005. Amyloid β-protein is degraded by cellular angiotensin-converting enzyme (ACE) and elevated by an ACE inhibitor. Journal of Biological Chemistry. 280(45):37644-37650.
  • [12] Zhang Y, McLaughlin R, Goodyer C, LeBlanc A. 2002. Selective cytotoxicity of intracellular amyloid β peptide1–42 through p53 and Bax in cultured primary human neurons. The Journal of cell biology. 156(3):519-529.
  • [13] Özkay ÜD, Öztürk Y, Can ÖD. 2011. Yaşlanan dünyanın hastalığı: Alzheimer hastalığı. SDÜ Tıp Fakültesi Dergisi.18(1):35-42.
  • [14] Reddy PH, Beal MF. 2008. Amyloid beta, mitochondrial dysfunction and synaptic damage: implications for cognitive decline in aging and Alzheimer's disease. Trends in molecular medicine.14(2):45-53.
  • [15] Harley, I. and S. Narod, 2009. Single nucleotide polymorphisms–variation on a theme. BJOG: An International Journal of Obstetrics & Gynaecology, 116(12): p. 1556-1557.
  • [16] Ozkan, E., et al., 2015. Genotyping and analysis of rs7501939 polymorphism for prostate cancer. Sigma journal of engineering and natural sciences-Sigma mühendislik ve fen bilimleri dergisi, 6(1): p. 101-107.
  • [17] Poli M, Gatta LB, Archetti S, Padovani A, Albertini A, Finazzi D. 2003. Association analysis between anterior-pharynx defective-1 genes polymorphisms and Alzheimer's disease. Neuroscience letters. 350(2):77-80.
  • [18] Wang Y, Jia J. 2009. Association between promoter polymorphisms in anterior pharynx-defective-1a and sporadic Alzheimer's disease in the North Chinese Han population. Neuroscience letters. 455(2):101-104.
  • [19] Qin W, Jia L, Zhou A, et al. 2011. The− 980C/G polymorphism in APH‐1A promoter confers risk of Alzheimer’s disease. Aging cell.10(4):711-719.
  • [20] Yu H, Zhang H, Yang Y, Li W, Yang G, Lü L. 2015. Association of gene polymorphisms with the susceptibility of schizophrenia in Han Chinese population. Zhonghua yi xue za zhi. 95(47):3803-3807.
  • [21] Çinleti BA, Yardımcı N, Aytürk Z, et al. 2015. The effects and interactions of APOE and APH-1A polymorphisms in Alzheimer disease. Turkish journal of medical sciences. 45(5):1098-1105.
  • [22] Marwa Mohamed Osman, Ahmed Sidahmed Khalifa, Alaa Eldin Yousri Mutasim, et al. 2016. In silico Analysis of Single Nucleotide Polymorphisms (Snps) in Human FTO Gene. JSM Bioinformatics, Genomics and Proteomics.
  • [23] Ng PC, Henikoff S. 2006. Predicting the effects of amino acid substitutions on protein function. Annu. Rev. Genomics Hum. Genet.7:61-80.
  • [24] Kaur T, Thakur K, Singh J, Kamboj SS, Kaur M. 2017. Identification of functional SNPs in human LGALS3 gene by in silico analyses. Egyptian Journal of Medical Human Genetics. 18(4):321–328.
  • [25] Adzhubei IA, Schmidt S, Peshkin L, et al. 2010. A method and server for predicting damaging missense mutations. Nature methods.7(4):248.
  • [26] Capriotti E, Calabrese R, Casadio R. 2006. Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics. 22(22):2729-2734.
  • [27] Ye, Q.-F., et al., 2012. Silencing Notch-1 induces apoptosis and increases the chemosensitivity of prostate cancer cells to docetaxel through Bcl-2 and Bax. Oncology letters, 3(4): p. 879-884.
  • [28] Cargill M, Altshuler D, Ireland J, et al. 1999. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nature genetics. 22(3):231.
  • [29] Teng S, Wang L, Srivastava AK, Schwartz CE, Alexov E. 2010. Structural assessment of the effects of amino acid substitutions on protein stability and protein-protein interaction. International journal of computational biology and drug design. 3(4):334.
  • [30] Dill KA, Fiebig KM, Chan HS. 1993. Cooperativity in protein-folding kinetics. Proceedings of the National Academy of Sciences. 90(5):1942-1946.
  • [31] Wang Z, Moult J. 2001. SNPs, protein structure, and disease. Human mutation. 17(4):263-270.

Alzheimer Hastalığı ile İlişkilendirilen APH1A Genindeki Zararlı SNP’lerin In Silico Yöntemler ile Belirlenmesi

Yıl 2019, , 472 - 480, 25.08.2019
https://doi.org/10.19113/sdufenbed.522738

Öz

Alzheimer
hastalığı (AH), β-amiloid (Aβ) senil plakların ve nörofibriler yumakların
patolojik birikimi ile karakterize olan ilerleyici bir nörodejeneratif
hastalıktır. γ-sekretaz, AH nedeni olan amiloid β peptidi (Aβ) üretmektedir.
γ-sekretaz makromoleküler bir komplekstir ve APH1A geninin kodladığı protein bu
komplekste yer almaktadır. Bu çalışmada, APH1A genindeki yanlış anlamlı
(missense) tek nükleotid polimorfizmlerinin (SNP) proteinin yapısı ve
stabilizasyonu üzerindeki olası zararlı etkilerinin in silico yöntemler kullanılarak belirlenmesi amaçlanmıştır.
Zararlı SNP’lerin tahmin edilmesi için PolyPhen-2 ve SIFT yazılım araçları,
protein stabilizasyonu değişimlerinin tespit edilmesi için I-Mutant 2.0
yazılımı, yabanıl ve mutant tip proteinlerin üç boyutlu modellemeleri için
Project HOPE yazılım aracı kullanılmıştır. Sonuçlar, APH1A geninde yer alan
toplam 3567 SNP’nin 257 tanesinin yanlış anlamlı SNP olduğunu göstermiştir. 257
SNP’nin in silico analizlerine göre,
rs11548266, rs74126634, rs145324799, rs199961673, rs370361277, rs370719475 ve
rs376071112 polimorfizmlerinin zararlı etkilerinin olabileceği belirlenmiştir.
Çalışmamızda gerçekleştirdiğimiz in
silico
analizler, Alzheimer hastalığı ile ilgili APH1A geninde yer alan
3567 SNP’nin tamamının genotiplenmesi yerine proteinin yapısı ve
stabilizasyonuna zararlı etkisi olabilecek SNP’lerin genotiplenmesine ilişkin
veri sağlamaktadır. Dolayısıyla, zararlı olduğu tespit edilen SNP’ler
genotipleme çalışmalarının en önemli basamağı olan SNP seçiminde ve deney
tasarımında kullanılabilecektir. Bu nedenle, elde ettiğimiz sonuçların
Alzheimer hastalığı ile ilgili gelecekte yapılacak olan hem deneysel hem de in silico çalışmalara katkı sağlayacağı
düşünülmektedir.

Kaynakça

  • [1] El Halawany AM, Sayed NSE, Abdallah HM, El Dine RS. 2017. Protective effects of gingerol on streptozotocin-induced sporadic Alzheimer’s disease: emphasis on inhibition of β-amyloid, COX-2, alpha-, beta-secretases and APH1a. Scientific Reports. 7(1):2902.
  • [2] Iqbal K, Grundke-Iqbal I. 2010. Alzheimer's disease, a multifactorial disorder seeking multitherapies. Alzheimer's & Dementia: Elsevier; 420-424.
  • [3] Yonemura Y, Futai E, Yagishita S, Kaether C, Ishiura S. 2016. Specific combinations of presenilins and Aph1s affect the substrate specificity and activity of γ-secretase. Biochemical and biophysical research communications.478(4):1751-1757.
  • [4] De Strooper B. 2003. Aph-1, Pen-2, and nicastrin with presenilin generate an active γ-secretase complex. Neuron. 38(1):9-12.
  • [5] Gertsik N, Chiu D, LI Y. 2015. Complex regulation of gamma-secretase: from obligatory to modulatory subunits. Frontiers in aging neuroscience. 6:342.
  • [6] Hur J-Y, Gertsik N, Johnson D, Li Y-M. 2016. γ-Secretase Inhibitors: From Chemical Probes to Drug Development. Developing Therapeutics for Alzheimer's Disease: Elsevier; 63-76.
  • [7] Lee S-F, Shah S, Li H, Yu C, Han W, Yu G. 2002. Mammalian APH-1 interacts with presenilin and nicastrin and is required for intramembrane proteolysis of amyloid-β precursor protein and Notch. Journal of Biological Chemistry. 277(47):45013-45019.
  • [8] Takasugi N, Tomita T, Hayashi I, et al. 2003. The role of presenilin cofactors in the γ-secretase complex. Nature. 422(6930):438.
  • [9] Haapasalo A, Kovacs DM. 2011. The many substrates of presenilin/γ-secretase. Journal of Alzheimer's disease.25(1):3-28.
  • [10] Mohandas E, Rajmohan V, Raghunath B. 2009. Neurobiology of Alzheimer's disease. Indian journal of psychiatry. 51(1):55.
  • [11] Hemming ML, Selkoe DJ. 2005. Amyloid β-protein is degraded by cellular angiotensin-converting enzyme (ACE) and elevated by an ACE inhibitor. Journal of Biological Chemistry. 280(45):37644-37650.
  • [12] Zhang Y, McLaughlin R, Goodyer C, LeBlanc A. 2002. Selective cytotoxicity of intracellular amyloid β peptide1–42 through p53 and Bax in cultured primary human neurons. The Journal of cell biology. 156(3):519-529.
  • [13] Özkay ÜD, Öztürk Y, Can ÖD. 2011. Yaşlanan dünyanın hastalığı: Alzheimer hastalığı. SDÜ Tıp Fakültesi Dergisi.18(1):35-42.
  • [14] Reddy PH, Beal MF. 2008. Amyloid beta, mitochondrial dysfunction and synaptic damage: implications for cognitive decline in aging and Alzheimer's disease. Trends in molecular medicine.14(2):45-53.
  • [15] Harley, I. and S. Narod, 2009. Single nucleotide polymorphisms–variation on a theme. BJOG: An International Journal of Obstetrics & Gynaecology, 116(12): p. 1556-1557.
  • [16] Ozkan, E., et al., 2015. Genotyping and analysis of rs7501939 polymorphism for prostate cancer. Sigma journal of engineering and natural sciences-Sigma mühendislik ve fen bilimleri dergisi, 6(1): p. 101-107.
  • [17] Poli M, Gatta LB, Archetti S, Padovani A, Albertini A, Finazzi D. 2003. Association analysis between anterior-pharynx defective-1 genes polymorphisms and Alzheimer's disease. Neuroscience letters. 350(2):77-80.
  • [18] Wang Y, Jia J. 2009. Association between promoter polymorphisms in anterior pharynx-defective-1a and sporadic Alzheimer's disease in the North Chinese Han population. Neuroscience letters. 455(2):101-104.
  • [19] Qin W, Jia L, Zhou A, et al. 2011. The− 980C/G polymorphism in APH‐1A promoter confers risk of Alzheimer’s disease. Aging cell.10(4):711-719.
  • [20] Yu H, Zhang H, Yang Y, Li W, Yang G, Lü L. 2015. Association of gene polymorphisms with the susceptibility of schizophrenia in Han Chinese population. Zhonghua yi xue za zhi. 95(47):3803-3807.
  • [21] Çinleti BA, Yardımcı N, Aytürk Z, et al. 2015. The effects and interactions of APOE and APH-1A polymorphisms in Alzheimer disease. Turkish journal of medical sciences. 45(5):1098-1105.
  • [22] Marwa Mohamed Osman, Ahmed Sidahmed Khalifa, Alaa Eldin Yousri Mutasim, et al. 2016. In silico Analysis of Single Nucleotide Polymorphisms (Snps) in Human FTO Gene. JSM Bioinformatics, Genomics and Proteomics.
  • [23] Ng PC, Henikoff S. 2006. Predicting the effects of amino acid substitutions on protein function. Annu. Rev. Genomics Hum. Genet.7:61-80.
  • [24] Kaur T, Thakur K, Singh J, Kamboj SS, Kaur M. 2017. Identification of functional SNPs in human LGALS3 gene by in silico analyses. Egyptian Journal of Medical Human Genetics. 18(4):321–328.
  • [25] Adzhubei IA, Schmidt S, Peshkin L, et al. 2010. A method and server for predicting damaging missense mutations. Nature methods.7(4):248.
  • [26] Capriotti E, Calabrese R, Casadio R. 2006. Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics. 22(22):2729-2734.
  • [27] Ye, Q.-F., et al., 2012. Silencing Notch-1 induces apoptosis and increases the chemosensitivity of prostate cancer cells to docetaxel through Bcl-2 and Bax. Oncology letters, 3(4): p. 879-884.
  • [28] Cargill M, Altshuler D, Ireland J, et al. 1999. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nature genetics. 22(3):231.
  • [29] Teng S, Wang L, Srivastava AK, Schwartz CE, Alexov E. 2010. Structural assessment of the effects of amino acid substitutions on protein stability and protein-protein interaction. International journal of computational biology and drug design. 3(4):334.
  • [30] Dill KA, Fiebig KM, Chan HS. 1993. Cooperativity in protein-folding kinetics. Proceedings of the National Academy of Sciences. 90(5):1942-1946.
  • [31] Wang Z, Moult J. 2001. SNPs, protein structure, and disease. Human mutation. 17(4):263-270.
Toplam 31 adet kaynakça vardır.

Ayrıntılar

Birincil Dil Türkçe
Konular Mühendislik
Bölüm Makaleler
Yazarlar

Ebru Özkan Oktay 0000-0002-0395-9845

Tuğba Kaman 0000-0002-5885-0193

Ömer Faruk Karasakal 0000-0001-7803-3249

Korkut Ulucan 0000-0002-1304-9386

Muhsin Konuk 0000-0002-6651-718X

Nevzat Tarhan 0000-0002-6810-7096

Yayımlanma Tarihi 25 Ağustos 2019
Yayımlandığı Sayı Yıl 2019

Kaynak Göster

APA Özkan Oktay, E., Kaman, T., Karasakal, Ö. F., Ulucan, K., vd. (2019). Alzheimer Hastalığı ile İlişkilendirilen APH1A Genindeki Zararlı SNP’lerin In Silico Yöntemler ile Belirlenmesi. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 23(2), 472-480. https://doi.org/10.19113/sdufenbed.522738
AMA Özkan Oktay E, Kaman T, Karasakal ÖF, Ulucan K, Konuk M, Tarhan N. Alzheimer Hastalığı ile İlişkilendirilen APH1A Genindeki Zararlı SNP’lerin In Silico Yöntemler ile Belirlenmesi. Süleyman Demirel Üniv. Fen Bilim. Enst. Derg. Ağustos 2019;23(2):472-480. doi:10.19113/sdufenbed.522738
Chicago Özkan Oktay, Ebru, Tuğba Kaman, Ömer Faruk Karasakal, Korkut Ulucan, Muhsin Konuk, ve Nevzat Tarhan. “Alzheimer Hastalığı Ile İlişkilendirilen APH1A Genindeki Zararlı SNP’lerin In Silico Yöntemler Ile Belirlenmesi”. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi 23, sy. 2 (Ağustos 2019): 472-80. https://doi.org/10.19113/sdufenbed.522738.
EndNote Özkan Oktay E, Kaman T, Karasakal ÖF, Ulucan K, Konuk M, Tarhan N (01 Ağustos 2019) Alzheimer Hastalığı ile İlişkilendirilen APH1A Genindeki Zararlı SNP’lerin In Silico Yöntemler ile Belirlenmesi. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi 23 2 472–480.
IEEE E. Özkan Oktay, T. Kaman, Ö. F. Karasakal, K. Ulucan, M. Konuk, ve N. Tarhan, “Alzheimer Hastalığı ile İlişkilendirilen APH1A Genindeki Zararlı SNP’lerin In Silico Yöntemler ile Belirlenmesi”, Süleyman Demirel Üniv. Fen Bilim. Enst. Derg., c. 23, sy. 2, ss. 472–480, 2019, doi: 10.19113/sdufenbed.522738.
ISNAD Özkan Oktay, Ebru vd. “Alzheimer Hastalığı Ile İlişkilendirilen APH1A Genindeki Zararlı SNP’lerin In Silico Yöntemler Ile Belirlenmesi”. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi 23/2 (Ağustos 2019), 472-480. https://doi.org/10.19113/sdufenbed.522738.
JAMA Özkan Oktay E, Kaman T, Karasakal ÖF, Ulucan K, Konuk M, Tarhan N. Alzheimer Hastalığı ile İlişkilendirilen APH1A Genindeki Zararlı SNP’lerin In Silico Yöntemler ile Belirlenmesi. Süleyman Demirel Üniv. Fen Bilim. Enst. Derg. 2019;23:472–480.
MLA Özkan Oktay, Ebru vd. “Alzheimer Hastalığı Ile İlişkilendirilen APH1A Genindeki Zararlı SNP’lerin In Silico Yöntemler Ile Belirlenmesi”. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi, c. 23, sy. 2, 2019, ss. 472-80, doi:10.19113/sdufenbed.522738.
Vancouver Özkan Oktay E, Kaman T, Karasakal ÖF, Ulucan K, Konuk M, Tarhan N. Alzheimer Hastalığı ile İlişkilendirilen APH1A Genindeki Zararlı SNP’lerin In Silico Yöntemler ile Belirlenmesi. Süleyman Demirel Üniv. Fen Bilim. Enst. Derg. 2019;23(2):472-80.

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