A Bioinformatics Approach to Male Infertility, MicroRNAs, and Targeted Genes

Abstract

Purpose: Infertility affects nearly 12% of couples worldwide, with a male factor being the primary or contributory reason in around 50% of cases. MicroRNAs (miRNAs) are essential post-transcriptional regulators in the spermatogenesis process, and dysregulated miRNAs have been shown to have harmful effects on male fertility. However, it is unclear which miRNAs are associated with infertility-related genes. The aim of this study is, to identify miRNAs that may be involved in the regulation of infertility-related genes using various bioinformatics approaches. Materials and Methods: The study first selected genes associated with infertility from the Male Infertility Knowledge Base (MIK) database. Pathway analysis of the defined genes, protein-protein interaction (PPI), and hub proteins related to these genes were revealed by the Elsevier pathway collection database and Enrichr tool. Following that, miRNAs that can influence infertility-related genes were determined, and the influence of the miRNA-target gene connection on male infertility was established bioinformatically using various in silico tools such as miRPathDB 2.0 tool, StarmiR, and miRNet. Results: 21 male infertility associated genes were selected from the MIK database and 15 miRNAs that are most likely to regulate these genes were identified bioinformatically. 10 hub proteins related to defined male infertility genes were analyzed. Conclusion: Our bioinformatic study results indicate that miR-34a-5p dysregulation may contribute to infertility through CREM, LAMP3, AGBL5, FOXM1 genes and also miR-335-5p may cause infertility via the CFAP65, CFTR, and GAPDHS genes.

Keywords

• Male infertility
• miR-335-5p
• miR-34a-5p

Erkek İnfertilitesi ile İlgili MikroRNA'lara ve Hedef Genlere Biyoinformatik Yaklaşım

Abstract

Amaç: İnfertilite, dünya çapında çiftlerin yaklaşık %12'sini etkileyen bir sağlık sorunudur. İnfertilite oluşumunda erkek kaynaklı sorunların payı yaklaşık %50'dir. Birçok hücresel süreçte rol oynayan mikroRNA (miRNA)'lar, spermatogenez sürecinde de kritik rol üstlenmektedir. Anormal miRNA ifadesinin erkek fertilitesi üzerinde zararlı etkilerinin olduğu gösterilmiştir. İnfertilite ile ilişkili genlerdeki genetik değişikliklerin yanı sıra miRNA'lar gibi gen ekspresyonunu değiştiren epigenetik faktörlerin de infertilite sürecinde kuşkusuz rolü vardır. Bununla birlikte, infertilite ile ilgili genlerle hangi miRNA'ların ilişkili olduğu tam olarak bilinmemektedir. Bu çalışmanın amacı, çeşitli biyoinformatik araçlar kullanılarak infertilite ile ilişkili genlerin düzenlenmesinde rol oynayabilecek miRNA'ları belirlemektir. Araçlar ve Yöntem: Çalışmada ilk önce Erkek İnfertilitesi Bilgi Bankası (MIK) veri tabanından infertilite ile ilişkili genler seçildi. Seçilen genlerin yolak analizi, bu genlerle ilgili protein-protein etkileşimi (PPI) ve hub proteinler, Elsevier pathway veri tabanı ve Enrichr aracı ile ortaya çıkarıldı. Ardından infertilite ile ilişkili genleri etkileyebilecek miRNA'lar belirlendi. Daha sonra miRNA-hedef gen ilişkisinin erkek infertilitesine etkisi miRPathDB 2.0 veritabanı, StarmiR ve miRNet gibi çeşitli in siliko araçlar kullanılmak suretiyle biyoinformatik olarak ortaya çıkarıldı. Bulgular: MIK veri tabanından Erkek infertilitesi ile ilişkili 21 gen seçildi ve bu genlerin ifadesini biyoinformatik olarak düzenlemesi en muhtemel 15 miRNA belirlendi. Aynı zamanda seçilen erkek infertilite genleriyle ilişkili olabilecek 10 hub protein tespit edildi. Sonuç: Biyoinformatik çalışma sonuçlarımız, miR-34a-5p ifade değişiminin CREM, LAMP3, AGBL5, FOXM1 genleri aracılığıyla ayrıca miR-335-5p'nin CFAP65, CFTR ve GAPDHS genleri üzerinden erkek infertilitesine neden olabileceğini göstermektedir.

Keywords

• Erkek İnfertilitesi
• miR-335-5p
• miR-34a-5p

References

1. 1. Zegers-Hochschild F, Adamson GD, Dyer S, et al. The International Glossary on Infertility and Fertility Care, 2017. Fertil Steril. 2017;108(3):393-406.
2. 2. Sun H, Gong TT, Jiang YT, Zhang S, Zhao YH, Wu QJ. Global, regional, and national prevalence and disability-adjusted life-years for infertility in 195 countries and territories, 1990-2017: results from a global burden of disease study, 2017. Aging (Albany NY). 2019;11(23):10952-10991.
3. 3. Agarwal A, Baskaran S, Parekh N, et al. Male infertility. Lancet. 2021;397(10271):319-333.
4. 4. Khawar MB, Mehmood R, Roohi N. MicroRNAs: Recent insights towards their role in male infertility and reproductive cancers. Bosn J Basic Med Sci. 2019;19(1):31-42.
5. 5. Chen H, Ruan YC, Xu WM, Chen J, Chan HC. Regulation of male fertility by CFTR and implications in male infertility. Hum Reprod Update. 2012;18(6):703-713.
6. 6. Ilaslan E, Kwiatkowska K, Smialek MJ, et al. Distinct Roles of NANOS1 and NANOS3 in the Cell Cycle and NANOS3-PUM1-FOXM1 Axis to Control G2/M Phase in a Human Primordial Germ Cell Model. Int J Mol Sci. 2022;23(12).
7. 7. Margaryan H, Dorosh A, Capkova J, et al. Characterization and possible function of glyceraldehyde-3-phosphate dehydrogenase-spermatogenic protein GAPDHS in mammalian sperm. Reprod Biol Endocrinol. 2015;13(1):15-21.
8. 8. Lambertos A, Ramos-Molina B, López-Contreras AJ, Cremades A, Peñafiel R. New insights of polyamine metabolism in testicular physiology: A role of ornithine decarboxylase antizyme inhibitor 2 (AZIN2) in the modulation of testosterone levels and sperm motility. PLoS One. 2018;13(12):e0209202.

9. 9. Lian J, Zhang X, Tian H, et al. Altered microRNA expression in patients with non-obstructive azoospermia. Reprod Biol Endocrinol. 2009;7(1):13-19.
10. 10. Comazzetto S, Di Giacomo M, Rasmussen KD, et al. Oligoasthenoteratozoospermia and infertility in mice deficient for miR-34b/c and miR-449 loci. PLoS Genet. 2014;10(10):e1004597.
11. 11. Salas-Huetos A, Blanco J, Vidal F, Mercader JM, Garrido N, Anton E. New insights into the expression profile and function of micro-ribonucleic acid in human spermatozoa. Fertil Steril. 2014;102(1):213-222.
12. 12. Abu-Halima M, Hammadeh M, Schmitt J, et al. Altered microRNA expression profiles of human spermatozoa in patients with different spermatogenic impairments. Fertil Steril. 2013;99(5):1249-1255.
13. 13. Salas-Huetos A, Blanco J, Vidal F, et al. Spermatozoa from patients with seminal alterations exhibit a differential micro-ribonucleic acid profile. Fertil Steril. 2015;104(3):591-601.
14. 14. Heidary Z, Zaki-Dizaji M, Saliminejad K, Khorram Khorshid HR. MicroRNA profiling in spermatozoa of men with unexplained asthenozoospermia. Andrologia. 2019;51(6):e13284.
15. 15. Christensen GL, Wooding SP, Ivanov IP, Atkins JF, Carrell DT. Sequencing and haplotype analysis of the activator of CREM in the testis (ACT) gene in populations of fertile and infertile males. Mol Hum Reprod. 2006;12(4):257-262.
16. 16. Krausz C, Sassone-Corsi P. Genetic control of spermiogenesis: insights from the CREM gene and implications for human infertility. Reprod Biomed Online. 2005;10(1):64-71.
17. 17. Liu T, Cheng W, Gao Y, Wang H, Liu Z. Microarray analysis of microRNA expression patterns in the semen of infertile men with semen abnormalities. Mol Med Rep. 2012;6(3):535-542.
18. 18. Xu YW, Ou NJ, Song YX, et al. Seminal plasma miR-210-3p induces spermatogenic cell apoptosis by activating caspase-3 in patients with varicocele. Asian J Androl. 2020;22(5):513-518.
19. 19. Bayraktar R, Van Roosbroeck K. miR-155 in cancer drug resistance and as a target for miRNA-based therapeutics. Cancer Metastasis Rev. 2018;37(1):33-44.
20. 20. Tsatsanis C, Bobjer J, Rastkhani H, et al. Serum miR-155 as a potential biomarker of male fertility. Hum Reprod. 2015;30(4):853-860.
21. 21. Kaya M, Karatas OF. The Relationship Between Larynx Cancer and MicroRNAs. Van Med J. 2020;27(4):535-541.
22. 22. Momeni A, Najafipour R, Hamta A, Jahani S, Moghbelinejad S. Expression and Methylation Pattern of hsa-miR-34 Family in Sperm Samples of Infertile Men. Reprod Sci. 2020;27(1):301-308.
23. 23. Zhou R, Zhang Y, Du G, et al. Down-regulated let-7b-5p represses glycolysis metabolism by targeting AURKB in asthenozoospermia. Gene. 2018;663:83-87.
24. 24. Abhari A, Zarghami N, Shahnazi V, et al. Significance of microRNA targeted estrogen receptor in male fertility. Iran J Basic Med Sci. 2014;17(2):81-86.
25. 25. Joshi M, Andrabi SW, Yadav RK, Sankhwar SN, Gupta G, Rajender S. Qualitative and quantitative assessment of sperm miRNAs identifies hsa-miR-9-3p, hsa-miR-30b-5p and hsa-miR-122-5p as potential biomarkers of male infertility and sperm quality. Reprod Biol Endocrinol. 2022;20(1):122-131.
26. 26. Silva JV, Yoon S, Domingues S, et al. Amyloid precursor protein interaction network in human testis: sentinel proteins for male reproduction. BMC Bioinformatics. 2015;16(1):12-19.
27. 27. Clement TM, Inselman AL, Goulding EH, Willis WD, Eddy EM. Disrupting Cyclin Dependent Kinase 1 in Spermatocytes Causes Late Meiotic Arrest and Infertility in Mice. Biol Reprod. 2015;93(6):137-149.