Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools

Öz

Apolipoprotein E (APOE) is one of the main proteins responsible for cholesterol transport. It has three major isoforms, APOE2, APOE3, and APOE4. The purpose of this study is to investigate the possible effects of single nucleotide variations (SNVs) in the APOE gene, which cause amino acid substitution, on the function, structure and stabilization of the APOE protein using bioinformatics/s tools. SNVs and protein sequence information were obtained from NCBI and UniProt databases. Bioinformatical analysis was performed using a series of tools such as SIFT, PolyPhen-2, SNPs&GO, Mutation Assessor, PROVEAN, SNAP2, I-Mutant-3, MUPro, and Project HOPE. As a result, 321 missense SNVs were analyzed and rs7412 (R176C), rs769455 (R163C), rs11542029 (R50C), rs121918393 (R154S), rs121918394 (K164Q), rs200703101 (R154P), rs387906567 (R160C), rs11542040 (P102T), rs11542041 (R132S) and rs41382345 (E139V) were predicted to be deleterious/disease related after functional analysis and pathological effect analysis via all of the bioinformatics/s tools. According to the protein stabilization results, it was determined that all SNVs decreased protein stabilization with the MUPro software tool, and two SNVs (rs121918394, rs41382345) increased protein stabilization with the I-Mutant-3 software tool. The models of protein and amino acid properties were obtained via Project HOPE for all high-risk SNVs. We hope our analysis will be valuable for further proteomic, genomic, and clinical research.

Anahtar Kelimeler

• Apolipoprotein E (APOE)
• cholesterol
• in silico
• single nucleotide variation (SNV)

Biyoinformatik araçlar aracılığıyla insan APOE (Apolipoprotein E) genindeki yanlış anlamlı SNV'lerin değerlendirilmesi

Öz

Apolipoprotein E (APOE), kolesterol taşınmasından sorumlu ana proteinlerden biridir. APOE2, APOE3 ve APOE4 olmak üzere üç ana izoformu vardır. Bu çalışmanın amacı, APOE geninde amino asit yer değiştirmesine neden olan tek nükleotid varyantlarının (SNV'ler) APOE proteininin işlevi, yapısı ve stabilizasyonu üzerindeki olası etkilerini biyoinformatik araçlar kullanarak araştırmaktır. SNV'ler ve protein dizi bilgisi, NCBI ve UniProt veritabanlarından elde edilmiştir. Biyoinformatik analiz, SIFT, PolyPhen-2, SNPs&GO, Mutation Assessor, PROVEAN, SNAP2, I-Mutant-3, MUPro ve Project HOPE gibi bir dizi araç kullanılarak yapılmıştır. Sonuç olarak 321 yanlış anlamlı SNV analiz edilmiş ve rs7412 (R176C), rs769455 (R163C), rs11542029 (R50C), rs121918393 (R154S), rs121918394 (K164Q), rs200703101 (R154P), rs387906567 (R160C), 102rsT11542040 rs11542041 (R132S) ve rs41382345 (E139V)'nin tüm biyoinformatik araçları aracılığıyla fonksiyonel analiz ve patolojik etki analizinden sonra zararlı/hastalık ile ilgili olduğu tahmin edilmiştir. Protein stabilizasyon sonuçlarına göre, MUPro yazılım aracı ile tüm SNV'lerin protein stabilizasyonunu azalttığı ve I-Mutant-3 yazılım aracı ile iki SNV'nin (rs121918394, rs41382345) protein stabilizasyonunu arttırdığı belirlenmiştir. Protein ve amino asit özellikleri modelleri, tüm yüksek riskli SNV'ler için Project HOPE aracılığıyla elde edilmiştir. Analizimizin daha fazla proteomik, genomik ve klinik araştırmalar için değerli olacağını umuyoruz.

Anahtar Kelimeler

• Apolipoprotein E (APOE)
• kolesterol
• in silico
• tek nükleotid varyantı (SNV)

Kaynakça

1. Zuo L, van Dyck CH, Luo X, Kranzler HR, Yang BZ, Gelernter J. Variation at APOE and STH loci and Alzheimer’s disease. Behavioral and Brain Functions, 2(1),1-10, (2006).
2. Liu CC, Kanekiyo T, Xu H BG. Apolipoprotein E and Alzheimer disease: risk, mechanisms, and therapy. Nature Reviews Neurology, 9:106–18, (2013).
3. Mahley RW, Huang Y, Rall SC. Pathogenesis of type III hyperlipoproteinemia (dysbetalipoproteinemia): Questions, quandaries, and paradoxes. Journal of lipid research, [Internet];40:1933–49, (1999). Available from: http://dx.doi.org/10.1016/S0022-2275(20)32417-2
4. Gkouskou K, Vasilogiannakopoulou T, Andreakos E, Davanos N, Gazouli M, Sanoudou D, et al. COVID-19 enters the expanding network of apolipoprotein E4-related pathologies. Redox biology, 41, 101938, (2021).
5. Finch CE, Kulminski AM. The ApoE Locus and COVID-19: Are we going where we have been? Journals Gerontol. - The Journals of Gerontology: Series A, 76(2), e1-e3, (2021).
6. Corder EH, Saunders AM, Strittmatter WJ, Schmechel DE, Gaskell PC, Small GW, et al. Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer’s disease in late onset families. Science, 261(5123), 921-923, (1993).
7. Solanas-Barca M, de Castro-Orós I, Mateo-Gallego R, Cofán M, Plana N, Puzo J, et al. Apolipoprotein E gene mutations in subjects with mixed hyperlipidemia and a clinical diagnosis of familial combined hyperlipidemia. Atherosclerosis, [Internet];222:449–55, (2012). Available from: http://dx.doi.org/10.1016/j.atherosclerosis.2012.03.011
8. Masoodi TA, Al Shammari SA, Al-Muammar MN, Alhamdan AA. Screening and evaluation of deleterious SNVs in APOE gene of Alzheimer’s disease. Neurology research international, 2012, (2012).

9. Khalil YA, Rabès JP, Boileau C, Varret M. APOE gene variants in primary dyslipidemia. Atherosclerosis, 328:11–22, (2021).
10. Namboori PKK, Vineeth K V., Rohith V, Hassan I, Sekhar L, Sekhar A, et al. The ApoE gene of Alzheimer’s disease (AD). Functional & İntegrative Genomics, 11(4), 519–22, (2011).
11. AA Abdalla A. In Silico Analysis of Single Nucleotide Polymorphisms (SNVS) in Human Abetalipoprotein Epsilon 4 (APOE E4) Gene as a Cause of Alzheimer’s Disease from Genetic Mutation to Functional Predication from Structural Change Patterns. Current Trends in Biomedical Engineering & Biosciences, 5:40–2, (2017).
12. Kaman T, Karasakal ÖF, Özkan Oktay E, Ulucan K, Konuk M. In silico approach to the analysis of SNVs in the human APAF1 gene. Turkish Journal of Biology, 43(6), 371-381, (2019).
13. Özkan Oktay E, Kaman T, Karasakal ÖF, Ulucan K, Konuk M, Tarhan N. Alzheimer Hastalığı ile İlişkilendirilen APH1A Genindeki Zararlı SNV’lerin In Silico Yöntemler ile Belirlenmesi. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 23(2), (2019).
14. Vaser R, Adusumalli S, Leng SN, Sikic M, Ng PC. SIFT missense predictions for genomes. Nature protocols, [Internet]; 11:1–9, (2016). Available from: http://dx.doi.org/10.1038/nprot.2015-123
15. Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Current protocols in human genetics, 76(1), 7-20, (2013).
16. Choi Y, Sims GE, Murphy S, Miller JR, Chan AP. Predicting the Functional Effect of Amino Acid Substitutions and Indels. PLoS One;7, (2012).
17. Reva B, Antipin Y, Sander C. Determinants of protein function revealed by combinatorial entropy optimization. Genome biology, 8(11), 1-15, (2007).
18. Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R. Functional annotations improve the predictive score of human disease-related mutations in proteins. Human mutation, 30:1237–44, (2009).
19. Capriotti E, Calabrese R, Casadio R. Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics, 22:2729–34, (2006).
20. Cheng J, Randall A, Baldi P. Prediction of protein stability changes for single-site mutations using support vector machines. Proteins: Structure, Function, and Bioinformatics, 62:1125–32, (2006).
21. Venselaar H, te Beek TAH, Kuipers RKP, Hekkelman ML, Vriend G. Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinformatics, 11(1), 1-10, (2010).
22. Rasmussen KL, Tybjærg-Hansen A, Nordestgaard BG, Frikke-Schmidt R. APOE and dementia – resequencing and genotyping in 105,597 individuals. Alzheimer's & Dementia, 16:1624–37, (2020).
23. Saeed NAHAAH, Hamzah IH, Ali ANM, Abuderman AA. Prediction of single nucleotide polymorphisms (SNVs) in apolipoprotein E gene and their possible associations with a deleterious effect on the structure and functional properties: an in silico approach. Network Modeling Analysis in Health Informatics and Bioinformatics/s, [Internet]; 7:1–6, (2018). Available from: http://dx.doi.org/10.1007/s13721-018-0178-9
24. Chang M huei, Yesupriya A, Ned RM, Mueller PW, Dowling NF. Genetic variants associated with fasting blood lipids in the U.S. population: Third National Health and Nutrition Examination Survey. BMC Medical Genetic, 11(1), 1-13, (2010).
25. Kulminski AM, Shu L, Loika Y, He L, Nazarian A, Arbeev K, et al. Genetic and regulatory architecture of Alzheimer’s disease in the APOE region. Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring, 12(1), e12008, (2020).
26. Al-Eitan, L. N., Almasri, A. Y., Alnaamneh, A. H., Aman, H. A., Alrabadi, N. N., Khasawneh, R. H., & Alghamdi, M. A. Influence of CYP4F2, ApoE, and CYP2A6 gene polymorphisms on the variability of Warfarin dosage requirements and susceptibility to cardiovascular disease in Jordan. International journal of medical sciences, 18(3), 826, (2021).
27. Ji, H., Zhou, C., Pan, R., Han, L., Chen, W., Xu, X., ... & Duan, S. APOE hypermethylation is significantly associated with coronary heart disease in males. Gene, 689, 84-89, (2019).
28. El-Lebedy, D., Raslan, H. M., & Mohammed, A. M. Apolipoprotein E gene polymorphism and risk of type 2 diabetes and cardiovascular disease. Cardiovascular diabetology, 15(1), 1-11, (2016).
29. Damodharan, L., & Pattabhi, V. Hydropathy analysis to correlate structure and function of proteins. Biochemical and biophysical research communications, 323(3), 996-1002, (2004).
30. Atalay, S. In Silico Analysis of the Structural and Functional Consequences of Polymorphic Amino Acid Substitutions in the Cattle HSF1 Protein. Kafkas Üniversitesi Veteriner Fakültesi Dergisi, 28(3), (2022).
31. Biro, J. C. Amino acid size, charge, hydropathy indices and matrices for protein structure analysis. Theoretical Biology and Medical Modelling, 3(1), 1-12, (2006).