Protein- Protein Interaction network analysis for Discovering Potent Candidate Drugs in Female Infertility

International Journal of Biophotonics and Biomedical Engineering

مقاله 1، دوره 2، شماره 1، دی 2022، صفحه 1-14   

نوع مقاله: Research article

شناسه دیجیتال (DOI): 10.30495/ijbbo.2022.696591

نویسندگان

Parinaz Tabrizi-Nejhadi¹؛ Habib MotieGhader^{* 1}؛ Masoud Maleki^{* 2}

¹Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran

²Department of Basic Science, Biotechnology Research Center, Tabriz Branch, Azad Islamic University, Tabriz, Iran

چکیده

This article is based on studying the effects of some potent candidate drugs for the treatment of female infertility. Statistically, it is one of the most important issues experienced by many female groups with the subdivision consisting of primary and secondary infertility. In this article first, genes of female infertility were taken from the Gene Expression Omnibus database, and used to identify the protein-protein interaction network (PPI). Then, three protein modules from the PPI network that is under consideration, were recognized, and followed by drawing the mRNA-miRNA interaction sub-network for each protein module. According to this study, by considering the three main modules, ten miRNAs genes had the most important effect in female infertility, with the genes, MRPS22, BCLAF1, and LYAR having strong positive impact on female infertility. From this study, eventually a drug-gene interaction network for female infertility was obtained. Based on our findings, it is recommended that young couples, use low-risk therapies instead of the prescribed drugs. Finally, to make a scientific conclusion, further studies of the effects of these genes, miRNAs, and drugs in the infertility treatment is needed.

کلیدواژه‌ها

Female infertility؛ microRNA؛ PPI؛ mRNA-miRNA؛ Drug-gene network؛ POF؛ PCOS

سایر فایل های مرتبط با مقاله

IJBBO-2207-1013 (R1)doi.pdf

مراجع

• Rungsiwiwut, P. Virutamasen, and K. Pruksananonda, "Mesenchymal stem cells for restoring endometrial function: An infertility perspective," Reprod. Med. Biol, vol.20, pp. 13-19, 2021.
• Vander Borght and C. Wyns, "Fertility and infertility: Definition and epidemiology," Clin. Biochem, vol. 62, pp. 2-10, 2018.
• Voulgaris, L. Papanastasiou, G. Piaditis, A. Angelousi, G. Kaltsas, G. Mastorakos, E. Kassi, "Vitamin D and aspects of female fertility," Hormones, vol.16, pp. 5-21, 2017.
• Esfandyari, R.M. Chugh, H. Park, E. Hobeika, M. Ulin, and A. Al-Hendy, "Mesenchymal stem cells as a bio organ for treatment of female infertility," Cells, vol. 9, pp. 2253 (1-37), 2020.
• Sormunen, A. Aanesen, B. Fossum, K. Karlgren, and M. Westerbotn, "Infertility‐related communication and coping strategies among women affected by primary or secondary infertility," J. Clin. Nurs, vol. 27, pp. e335-e344, 2018.
• Cunningham, "Infertility: A primer for primary care providers," JAAPA, vol. 30, pp. 19-25, 2017.
• Starc, M. Trampus, D.P. Jukic, C. Rotim, T. Jukic, T. Jukić, and A. Polona Mivšek, "Infertility and sexual dysfunctions: a systematic literature review," Acta Clin. Croat, vol. 58, pp. 508-515, 2019.
• Sun, X. Rong, Y. Cai, S. Qiu, and M. Farzaneh, "Mini review: The FDA‐approved prescription drugs that induce ovulation in women with ovulatory problems," Drug Dev. Res, vol. 81, pp. 815-822, 2020.
• Hernández-Ochoa, B.N. Karman, and J.A. Flaws, "The role of the aryl hydrocarbon receptor in the female reproductive system," Biochem. Pharmacol, vol. 77, pp. 547-559, 2009.
• Roupa, M. Polikandrioti, P. Sotiropoulou, E. Faros, A. Koulouri, G. Wozniak, and M. Gourni, "Causes of Infertility in Women at Reproductive Age," Health Sci. J, vol. 3, pp. 80-87, 2009.
• Tamura, H. Yoshida, H. Kikuchi, M. Josaki, Y. Mihara, Y. Shirafuta, M. Shinagawa, I. Tamura, T. Taketani, A. Takasaki, and N. Sugino, "The clinical outcome of Dienogest treatment followed by in vitro fertilization and embryo transfer in infertile women with endometriosis," J. Ovarian Res, vol. 12, pp. 1-9, 2019.
• Aghajanova, M.I. Cedars, and H.G. Huddleston, "Platelet-rich plasma in the management of Asherman syndrome: case report," J. Assist. Reprod. Genet, vol. 35, pp. 771-775, 2018.
• J. Walker, "Pre-eclampsia," The Lancet, vol. 356, pp. 1260-1265, 2000.
• Dunkel-Schetter, and M. Lobel, "Psychological reactions to infertility, in Infertility," Springer. pp. 29-57, 1991.
• Klein and R. Rowland, "Hormonal cocktails: Women as test-sites for fertility drugs women as test-sites for fertility drugs," , Women's Stud. Int. Forum. Elsevier, vol. 12, pp. 333-348, 1989.
• A. Yu, X.Y. Lv, K.P. Liu, D.K. Ma, Y.H. Wu, W.J. Dai, and H.C. Jiang, "Fertility drugs associated with thyroid cancer risk: a systematic review and meta-analysis," Biomed Res Int. vol. 2018, pp. 1-7, 2018.
• H.W. Li and E.H.Y. Ng, "Management of anovulatory infertility," Best Pract Res Clin Obstet Gynaecol. vol. 26, pp. 757-768, 2012.
• S. Usadi and K.S. Merriam, "On-label and off-label drug use in the treatment of female infertility," Fertil. Steril. vol. 103, pp. 583-594, 2015.
• Pfeifer, S. Butts, D. Dumesic, G. Fossum, C. Gracia, A. La Barbera, J. Mersereau, R. Odem, R. Paulson, A. Penzias, M. Pisarska, R. Rebar, R. Reindollar, M. Rosen, J. Sandlow, M. Vernon, and E. Widra," Fertility drugs and cancer: a guideline," Fertil. Steril. vol. 106, pp. 1617-1626, 2016.
• Muscogiuri, B. Altieri, C. de Angelis, S. Palomba, R. Pivonello, A. Colao, and F. Orio, "Shedding new light on female fertility: the role of vitamin D." Rev. Endocr. Metab. Disord, vol. 18, pp. 273-283, 2017.
• Maghsoudloo and M.H. Noroozizadeh, "A gene selection approach for Diabetic retinopathy microarray data classification using Ant Colony Optimization," Journal of Ophthalmic and Optometric Sciences, vol. 3, pp: 1-10, 2019.
• Suriyakalaa, R. Ramachandran, J. A. Doulathunnisa, S. B. Aseervatham, D. Sankarganesh, S. Kamalakkannan, B. Kadalmani, J. Angayarkanni, M. A. Akbarsha, and Sh. Achiraman, "Upregulation of Cyp19a1 and PPAR-γ in ovarian steroidogenic pathway by Ficus religiosa: A potential cure for polycystic ovary syndrome," J. Ethnopharmacol, vol. 267, pp. 113540, 2021.
• Körschgen, C. Jäger, K. Tan, M. Buchholz, W. Stöcker, and D. Ramsbeck, "A Primary Evaluation of Potential Small‐Molecule Inhibitors of the Astacin Metalloproteinase Ovastacin, a Novel Drug Target in Female Infertility Treatment," ChemMedChem, vol. 15, pp. 1499-1504, 2020.
• von Mering, M. Huynen, D. Jaeggi, S. Schmidt, P. Bork, and B. Snel, "STRING: a database of predicted functional associations between proteins," Nucleic Acids Res, vol. 31, pp. 258-261, 2003.
• Norouzi, M. Maghsoudloo, M.H. Noroozizadeh, "Collagen Cross-Linking Therapy on Important Functional Genes Involved in Keratoconus Patients," Journal of Ophthalmic and Optometric Sciences. vol. 3, pp. 1-15, 2019.
• O. Consortiu, "The Gene Ontology (GO) database and informatics resource," Nucleic Acids Res. Spec. Publ, vol. 32, pp. D258-D261, 2004.
• Ghorbani, E. Pournoor, and M. Maghsoudloo, "Transcriptomic Analysis of Human Retina Reveals Molecular Mechanisms Underlying Diabetic Retinopathy in Sexually Divergent Manner," Journal of Ophthalmic and Optometric Sciences, vol. 4, pp. 1-12, 2020.
• Clough and T. Barrett, "The gene expression omnibus database, in Statistical genomics," Springer, pp. 93-110, 2016.
• Szklarczyk, J. H. Morris, H. Cook, M. Kuhn, S. Wyder, M. Simonovic, A. Santos, N. T. Doncheva, A. Roth, P. Bork, L.J. Jensen, and Ch. von Mering, "The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible," Nucleic Acids Res. vol. 45, pp. D362–D368, 2016.
• S. Soleimani Zakeri, S. Pashazadeh, and H. MotieGhader, "Drug Repurposing for Alzheimer’s Disease based on Protein-Protein Interaction Network," vol. 2021, pp. 1280237 (1-15), 2021.
• Kohl, S. Wiese, and B. Warscheid, "Cytoscape: software for visualization and analysis of biological networks, in Data mining in proteomics," Springer. vol. 696, pp. 291-303, 2011.
• E. Smoot, K. Ono, J. Ruscheinski, P.L. Wang, and T. Ideker, "Cytoscape 2.8: new features for data integration and network visualization," Bioinformatics, vol. 27, pp. 431-432, 2011.
• W. Huang, B. T. Sherman, Q. Tan, J. Kir, D. Liu, D. Bryant, Y. Guo, R. Stephens, M. W. Baseler, H. C. Lane, and R. A. Lempicki, "DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists," Nucleic Acids Res. vol. 35, pp. W169-W175, 2007.
• J. Lee, V. Kim, D.C. Muth, and K.W. Witwer, "Validated microRNA target databases: an evaluation," Drug Dev. Res, vol. 76, pp. 389-396, 2015.
• Motieghader, M. Kouhsar, A. Najafi, B. Sadeghi, and A. Masoudi-Nejad, "mRNA–miRNA bipartite network reconstruction to predict prognostic module biomarkers in colorectal cancer stage differentiation," Mol. Biosyst, vol. 13, pp. 2168-2180, 2017.
• Li, X. Han, Y. Wan, S. Zhang, Y. Zhao, R. Fan, Q. Cui, and Yuan Zhou, "TAM 2.0: tool for MicroRNA set analysis," Nucleic Acids Res. vol. 46, pp. W180-W185, 2018.
• C Cotto, A. H. Wagner, Y.-Y. Feng, S. Kiwala, A. C. Coffman, G. Spies, A. Wollam, N. C Spies, O. L Griffith, and M. Griffith, "DGIdb 3.0: a redesign and expansion of the drug–gene interaction database," Nucleic Acids Res. vol. 46, pp. D1068-D1073, 2018.
• Liu, X. Zhang, C. Shi, J. Lin, G. Chen, B. Wu, L. Wu, H. Shi, Y. Yuan, W. Zhou, Zh. Sun, X. Dong and J. Wang, "Altered microRNAs expression profiling in cumulus cells from patients with polycystic ovary syndrome," J. Transl. Med. vol. 13, pp. 1-9, 2015.
• Salmasi, M. Sharifi, and B. Rashidi, "Ovarian stimulation and exogenous progesterone affect the endometrial miR-16-5p, VEGF protein expression, and angiogenesis," Microvascular Research, vol. 133, pp. 104074, 2021.
• G. Da Broi, J. Meola, J. R. Plaça, K. C. Peronni, C. V. Rocha, Jr, W. A. Silva, Jr, R. A. Ferriani, and P. A. Navarro, "Is the profile of transcripts altered in the eutopic endometrium of infertile women with endometriosis during the implantation window?" Hum. Reprod. vol. 34, pp. 2381-2390, 2019.
• Sabit, E. Cevik, H. Tombuloglu, K. Farag, O. AM Said, Sh. E. Abdel-Ghany, A. I Alqosaibi, H. B. Yildiz, F. Serag ElDeen, E. Wagih, and M. El-Zawahri, "miRNA profiling in MCF-7 breast Cancer cells: seeking a new biomarker," J Biomedical Sci, vol. 8, pp. 1-9, 2019.
• Zhang, N. Ding, Sh. Xie, Y. Ding, M. Huang, X. Ding, and L. Jiang, "Identification of important extracellular vesicle RNA molecules related to sperm motility and prostate cancer," Extracellular Vesicles and Circulating Nucleic Acids, vol. 2, pp. 104-126, 2021.
• Szymanska, K. Shrestha, E. Girsh, A. Harlev, I. Eisenberg, T. Imbar, and R. Meidan, "Reduced Endothelin-2 and Hypoxic Signaling Pathways in Granulosa-Lutein Cells of PCOS Women," International Journal of Molecular Sciences, vol. 22, pp. 8216 (1-14), 2021.
• Li, H. Li, Y. Tian, M. Hu, F. Le, L. Wang, X. Liu, and F. Jin, "Differential microRNAs expression in seminal plasma of normospermic patients with different sperm DNA fragmentation indexes," Reprod. Toxicol, vol. 94, pp. 8-12, 2020.
• Vanhie, D. O, D. Peterse, A. Beckers, A. Cuéllar, A. Fassbender, C. Meuleman, P. Mestdagh, and T. D’Hooghe, "Plasma miRNAs as biomarkers for endometriosis," Hum. Reprod,vol. 34, pp. 1650-1660, 2019.
• Dell’Aversana, F. Cuomo, S. Longobardi, T. D’Hooghe, F. Caprio, G. Franci, M. Santonastaso, N. Colacurci, S. Barone, V. Pisaturo, D. Valerio, and L. Altucci, "Age-related miRNome landscape of cumulus oophorus cells during controlled ovarian stimulation protocols in IVF cycles," Hum. Reprod, vol. 36, pp. 1310-1325, 2021.
• Zahra, Identification of novel microRNAs as potential biomarkers for the early diagnosis of ovarian cancer using an in-silico approach, 2019.
• Sedaghat, M. Fathy, M. H. Modarressi, and A. Shojaie, "Identifying functional cancer-specific miRNA–mRNA interactions in testicular germ cell tumor," J. Theor. Biol, vol. 404, pp. 82-96, 2016.
• Aljubran, A. Graham, W. Cui, and W.B. Nothnick, "Increased CXCL12 expression in endometrium of women with abnormal uterine bleeding is post-transcriptionally mediated via miR-23b-3p and is associated with decreased expression of the miR-23b-3p/24-3p/27b-3p cluster: a pilot study," F&S Science, vol.1, pp. 90-97, 2020.
• J. Seifer, D. Su, and H.S. Taylor, "Circulating miRNAs in murine experimental endometriosis: decreased abundance of let-7a," Reprod. Sci, vol. 24, pp. 376-381, 2017.
• Rood, M. Mehedi Hasan, K. Roos, J. Viil, A. Andronowska, O.-P. Smolander, Ü. Jaakma, A. Salumets, A. Fazeli, and A. Velthut-Meikas, "Cellular, extracellular and extracellular vesicular miRNA profiles of pre-ovulatory follicles indicate signaling disturbances in polycystic ovaries," Int. J. Mol. Sci. vol. 21, pp. 9550 (1-23), 2020.
• Chen, D. Tiosano, T. Guran, H. N Baris, Y. Bayram, A. Mory, L. Shapiro-Kulnane, C. A Hodges, Z. C Akdemir, S. Turan, Sh. N Jhangiani, F. van den Akker, Ch. L Hoppel, H. K Salz, J. R Lupski, and D. A Buchner, "Mutations in the mitochondrial ribosomal protein MRPS22 lead to primary ovarian insufficiency," Hum. Mol. Genet, vol. 27, pp. 1913-1926, 2018.
• A. Prakash, A. Kumaresan, M.K. Sinha, E. Kamaraj, T. Kumar Mohanty, T. Kumar Datta, and J. M. Morrell, "RNA-Seq analysis reveals functionally relevant coding and non-coding RNAs in crossbred bull spermatozoa." Animal reproduction science, vol. 222, pp. 106621 (1-13), 2020.
• Carroll, T. Luu, and B. Robaire, "Null mutation of the transcription factor inhibitor of DNA binding 3 (id3) affects spermatozoal motility parameters and epididymal gene expression in mice," Biol. Reprod, vol. 84, pp. 765-774, 2011.
• Chang and Y. Cao, "Differentially expressed genes SNRPC and PRPF38A are potential biomarkers candidates for osteosarcoma," 2020.
• A. Gustafson and G.M. Wessel, "DEAD-box helicases: posttranslational regulation and function," Biochem. Biophys. Res. Commun, vol. 395, pp. 1-6, 2010.
• W. Ferguson, Composition-Activity Analyses and Nucleic Acid Loading Strategies for Therapeutic Extracellular Vesicles, The State University of New York at Buffalo, 2019.
• R. Infante, D. S. Mendelson, H. A. Burris, J. C. Bendell, A. W. Tolcher, M. S. Gordon, H. H. Gillenwater, Sh. Arastu-Kapur, H. L. Wong, and K. P. Papadopoulos, "A first-in-human dose-escalation study of the oral proteasome inhibitor oprozomib in patients with advanced solid tumors," Investig. New Drugs, vol. 34, pp. 216-224, 2016.
• Hari, J.V. Matous, P. M. Voorhees, K. H. Shain, M. Obreja, J. Frye, H. Fujii, A. J. Jakubowiak, D. Rossi, and P. Sonneveld, "Oprozomib in patients with newly diagnosed multiple myeloma," Blood Cancer J. vol. 9, pp. 1-4, 2019.
• G. Richardson, P. Sonneveld, M.W. Schuster, D. Irwin, E.A. Stadtmauer, T. Facon, J-L. Harousseau, D. Ben-Yehuda, S. Lonial, H. Goldschmidt, D. Reece, J.F. San Miguel, J. Bladé, M. Boccadoro, J. Cavenagh, W. Dalton, A.L. Boral, D.-L. Esseltine, J.B. Porter, D. Schenkein and K.C. Anderson, "Bortezomib or high-dose dexamethasone for relapsed multiple myeloma," New England journal of medicine, vol. 352, pp. 2487-2498, 2005.
• Zuccari, A. Milelli, F. Pastorino, M. Loi, A. Petretto, A. Parise, Ch. Marchetti, A. Minarini, M. Cilli, L. Emionite, D. Di Paolo, Ch. Brignole, F. Piaggio, P. Perri, V. Tumiatti, V. Pistoia, G. Pagnan, and M. Ponzoni, "Tumor vascular targeted liposomal-bortezomib minimizes side effects and increases therapeutic activity in human neuroblastoma," J. Control. Release, vol. 211, pp. 44-52, 2015.
• Field-Smith, G.J. Morgan, and F.E. Davies, "Bortezomib (Velcade™) in the treatment of multiple myeloma." Ther Clin Risk Manag, vol. 2, pp. 271–279, 2006.
• Offidani, L. Corvatta, P. Caraffa, S. Gentili, L. Maracci, and P. Leoni1, "An evidence-based review of ixazomib citrate and its potential in the treatment of newly diagnosed multiple myeloma," Onco Targets Ther. vol. 7, pp. 1793–1800, 2014.
• Martin Kortuem and A. Keith Stewart, "Carfilzomib. Blood," Am. J. Hematol. vol. 121, pp. 893-897, 2013.
• S. Hosseini, Z. Abedi, M. Maghsoudloo, M. A. Sheikh Beig Goharrizi, and A. Shojaei, "Investigation of genes associated with primary open-angle glaucoma (POAG) using expression profile analysis," Journal of Ophthalmic and Optometric Sciences, vol. 3, pp. 37-54, 2019.
• E. Nestler,"Metformin in the treatment of infertility in polycystic ovarian syndrome: an alternative perspective," Elsevier, vol. 90, pp. 14-16, 2008.
• S. Yucebilgin, M. C. Terek, A. Ozsaran, F. Akercan, O. Zekioglu, E. Isik, and Y. Erhan, "Effect of chemotherapy on primordial follicular reserve of rat: an animal model of premature ovarian failure and infertility," Aust N Z J Obstet Gynaecol. vol. 44, pp. 6-9, 2004.