Exploring the hub genes and potential drugs involved in Fanconi anemia using microarray datasets and bioinformatics analysis

References

• Ali, A. M., Kirby, M., Jansen, M., Lach, F. P., Schulte, J., Singh, T. R., Batish, S. D., Auerbach, A. D., Williams, D. A., & Meetei, A. R. (2009). Identification and characterization of mutations in FANCL gene: A second case of Fanconi anemia belonging to FA‐L complementation group. Human Mutation, 30(7), E761–E770. https://doi.org/10.1002/humu.21032
   PubMed Web of Science ®Google Scholar
• Alter, B. P., & Giri, N. (2016). Thinking of VACTERL‐H? Rule out Fanconi Anemia according to PHENOS. American Journal of Medical Genetics. Part A, 170(6), 1520–1524. https://doi.org/10.1002/ajmg.a.37637
   PubMed Web of Science ®Google Scholar
• Alter, B. P., & Rosenberg, P. S. (2013). VACTERL-H association and Fanconi anemia. Molecular Syndromology, 4(1-2), 87–93. https://doi.org/10.1159/000346035
   PubMedGoogle Scholar
• Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., & Sherlock, G. (2000). Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics, 25(1), 25–29. https://doi.org/10.1038/75556
   PubMed Web of Science ®Google Scholar
• Barrett, T., Troup, D. B., Wilhite, S. E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I. F., Soboleva, A., Tomashevsky, M., Marshall, K. A., Phillippy, K. H., Sherman, P. M., Muertter, R. N., & Edgar, R. (2009). NCBI GEO: Archive for high-throughput functional genomic data. Nucleic Acids Research, 37(Database issue), D885–D890. https://doi.org/10.1093/nar/gkn764
   PubMedGoogle Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Bhandari, J., Thada, P. K., & Puckett, Y. (2023). Fanconi Anemia. In StatPearls. StatPearls Publishing. http://www.ncbi.nlm.nih.gov/books/NBK559133/
   Google Scholar
• Bierings, M., Bonfim, C., Peffault De Latour, R., Aljurf, M., Mehta, P. A., Knol, C., Boulad, F., Tbakhi, A., Esquirol, A., McQuaker, G., Sucak, G. A., Othman, T. B., Halkes, C. J. M., Carpenter, B., Niederwieser, D., Zecca, M., Kröger, N., Michallet, M., Risitano, A. M., … Dufour, C. (2018). Transplant results in adults with Fanconi anaemia. British Journal of Haematology, 180(1), 100–109. https://doi.org/10.1111/bjh.15006
   PubMed Web of Science ®Google Scholar
• Bluteau, D., Masliah-Planchon, J., Clairmont, C., Rousseau, A., Ceccaldi, R., Dubois d‘Enghien, C., Bluteau, O., Cuccuini, W., Gachet, S., Peffault de Latour, R., Leblanc, T., Socié, G., Baruchel, A., Stoppa-Lyonnet, D., D'Andrea, A. D., & Soulier, J. (2016). Biallelic inactivation of REV7 is associated with Fanconi anemia. The Journal of Clinical Investigation, 126(9), 3580–3584. https://doi.org/10.1172/JCI88010
   PubMed Web of Science ®Google Scholar
• Bp, A. (2014). Fanconi anemia and the development of leukemia. Best Practice & Research. Clinical Haematology, 27(3–4) https://doi.org/10.1016/j.beha.2014.10.002
   Web of Science ®Google Scholar
• Brandes, U., Eiglsperger, M., Herman, I., Himsolt, M., & Marshall, M. S. (2002). GraphML progress report structural layer proposal. In P. Mutzel, M. Jünger, & S. Leipert (Eds.), Graph drawing (pp. 501–512). Springer. https://doi.org/10.1007/3-540-45848-4_59
   Google Scholar
• Brice, A. R., & Dominy, B. N. (2013). Examining electrostatic influences on base-flipping: A comparison of TIP3P and GB solvent models. Communications in Computational Physics, 13(1), Article 1–237. https://doi.org/10.4208/cicp.210711.121011s
   Web of Science ®Google Scholar
• Bueren, J. A., Quintana‐Bustamante, O., Almarza, E., Navarro, S., Río, P., Segovia, J. C., & Guenechea, G. (2020). Advances in the gene therapy of monogenic blood cell diseases. Clinical Genetics, 97(1), 89–102. https://doi.org/10.1111/cge.13593
   PubMed Web of Science ®Google Scholar
• Case, D. A., Betz, R. M., Cerutti, D. S., Cheatham, T., Darden, T., Duke, R. E., Giese, T. J., Gohlke, H., Götz, A. W., Homeyer, N., Izadi, S., Janowski, P. A., Kaus, J., Kovalenko, A., Tai-Sung, L., LeGrand, S., Li, P., Lin, C., Luchko, T., … Kollman, P. A. (2016). Amber 16, University of California, San Francisco. University of California, San Francisco, https://doi.org/10.13140/rg.2.2.27958.70729
   Google Scholar
• Che, R., Zhang, J., Nepal, M., Han, B., & Fei, P. (2018). Multifaceted Fanconi anemia signaling. Trends in Genetics: TIG, 34(3), 171–183. https://doi.org/10.1016/j.tig.2017.11.006
   PubMed Web of Science ®Google Scholar
• Chen, E. Y., Tan, C. M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G. V., Clark, N. R., & Ma’ayan, A. (2013). Enrichr: Interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics, 14(1), 128. https://doi.org/10.1186/1471-2105-14-128
   PubMed Web of Science ®Google Scholar
• Chin, C.-H., Chen, S.-H., Wu, H.-H., Ho, C.-W., Ko, M.-T., & Lin, C.-Y. (2014). cytoHubba: Identifying hub objects and sub-networks from complex interactome. BMC Systems Biology, 8(S4), S11. https://doi.org/10.1186/1752-0509-8-S4-S11
   PubMedGoogle Scholar
• Chiravuri, S., & De Jesus, O. (2022). Pancytopenia. In StatPearls. StatPearls Publishing.
   Google Scholar
• Clough, E., & Barrett, T. (2016). The gene expression omnibus database. Methods in Molecular Biology (Clifton, N.J.), 1418, 93–110. https://doi.org/10.1007/978-1-4939-3578-9_5
   PubMedGoogle Scholar
• D’Andrea, A. D., & Grompe, M. (1997). Molecular biology of Fanconi anemia: Implications for diagnosis and therapy. Blood, 90(5), 1725–1736. https://doi.org/10.1182/blood.V90.5.1725
   PubMed Web of Science ®Google Scholar
• Davis, J. (2007). Bioinformatics and computational biology solutions using R and bioconductor, Robert Gentleman, Vincent Carey, Wolfgang Huber, Rafael Irizarry, and Sandrine Dudoit. Journal of the American Statistical Association, 102(477), 388–389. https://doi.org/10.1198/jasa.2007.s179
   Google Scholar
• Dufour, C., & Pierri, F. (2022). Modern management of Fanconi anemia. Hematology. American Society of Hematology. Education Program, 2022(1), 649–657. https://doi.org/10.1182/hematology.2022000393
   PubMedGoogle Scholar
• Ebens, C. L., MacMillan, M. L., & Wagner, J. E. (2017). Hematopoietic cell transplantation in Fanconi anemia: Current evidence, challenges and recommendations. Expert Review of Hematology, 10(1), 81–97. https://doi.org/10.1080/17474086.2016.1268048
   PubMed Web of Science ®Google Scholar
• Fang, C.-B., Wu, H.-T., Zhang, M.-L., Liu, J., & Zhang, G.-J. (2020). Fanconi anemia pathway: Mechanisms of breast cancer predisposition development and potential therapeutic targets. Frontiers in Cell and Developmental Biology, 8, 160. https://doi.org/10.3389/fcell.2020.00160
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), Article 5–461. https://doi.org/10.1517/17460441.2015.1032936
   Web of Science ®Google Scholar
• Győrffy, B., Surowiak, P., Budczies, J., & Lánczky, A. (2013). Online survival analysis software to assess the prognostic value of biomarkers using transcriptomic data in non-small-cell lung cancer. PloS One, 8(12), e82241. https://doi.org/10.1371/journal.pone.0082241
   PubMed Web of Science ®Google Scholar
• Hira, A., Yoshida, K., Sato, K., Okuno, Y., Shiraishi, Y., Chiba, K., Tanaka, H., Miyano, S., Shimamoto, A., Tahara, H., Ito, E., Kojima, S., Kurumizaka, H., Ogawa, S., Takata, M., Yabe, H., & Yabe, M. (2015). Mutations in the gene encoding the E2 conjugating enzyme UBE2T cause Fanconi anemia. American Journal of Human Genetics, 96(6), 1001–1007. https://doi.org/10.1016/j.ajhg.2015.04.022
   PubMed Web of Science ®Google Scholar
• Huber, W., von Heydebreck, A., Sültmann, H., Poustka, A., & Vingron, M. (2002). Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics (Oxford, England), 18 (Suppl. 1), S96–S104. https://doi.org/10.1093/bioinformatics/18.suppl_1.s96
   PubMedGoogle Scholar
• Jiao, X., Sherman, B. T., Huang, D. W., Stephens, R., Baseler, M. W., Lane, H. C., & Lempicki, R. A. (2012). DAVID-WS: A stateful web service to facilitate gene/protein list analysis. Bioinformatics (Oxford, England), 28(13), 1805–1806. https://doi.org/10.1093/bioinformatics/bts251
   PubMed Web of Science ®Google Scholar
• Khan, A., Rehman, Z., Hashmi, H. F., Khan, A. A., Junaid, M., Sayaf, A. M., Ali, S. S., Hassan, F. U., Heng, W., & Wei, D.-Q. (2020). An integrated systems biology and network-based approaches to identify novel biomarkers in breast cancer cell lines using gene expression data. Interdisciplinary Sciences, Computational Life Sciences, 12(2), 155–168. https://doi.org/10.1007/s12539-020-00360-0
   PubMed Web of Science ®Google Scholar
• Ma, L., Huang, Y., Zhu, W., Zhou, S., Zhou, J., Zeng, F., Liu, X., Zhang, Y., & Yu, J. (2011). An integrated analysis of miRNA and mRNA expressions in non-small cell lung cancers. PloS One, 6(10), e26502. https://doi.org/10.1371/journal.pone.0026502
   PubMed Web of Science ®Google Scholar
• Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Meetei, A. R., de Winter, J. P., Medhurst, A. L., Wallisch, M., Waisfisz, Q., van de Vrugt, H. J., Oostra, A. B., Yan, Z., Ling, C., Bishop, C. E., Hoatlin, M. E., Joenje, H., & Wang, W. (2003). A novel ubiquitin ligase is deficient in Fanconi anemia. Nature Genetics, 35(2), 165–170. https://doi.org/10.1038/ng1241
   PubMed Web of Science ®Google Scholar
• Mehta, P. A., Davies, S. M., Leemhuis, T., Myers, K., Kernan, N. A., Prockop, S. E., Scaradavou, A., O'Reilly, R. J., Williams, D. A., Lehmann, L., Guinan, E., Margolis, D., Baker, K. S., Lane, A., & Boulad, F. (2017). Radiation-free, alternative-donor HCT for Fanconi anemia patients: Results from a prospective multi-institutional study. Blood, 129(16), 2308–2315. https://doi.org/10.1182/blood-2016-09-743112
   PubMed Web of Science ®Google Scholar
• Moreno, O. M., Paredes, A. C., Suarez‑Obando, F., & Rojas, A. (2021). An update on Fanconi anemia: Clinical, cytogenetic and molecular approaches (Review). Biomedical Reports, 15(3), 74. https://doi.org/10.3892/br.2021.1450
   PubMed Web of Science ®Google Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Niraj, J., Färkkilä, A., & D'Andrea, A. D. (2019). The Fanconi anemia pathway in cancer. Annual Review of Cancer Biology, 3(1), 457–478. https://doi.org/10.1146/annurev-cancerbio-030617-050422
   PubMedGoogle Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Reyes, P., García-de Teresa, B., Juárez, U., Pérez-Villatoro, F., Fiesco-Roa, M. O., Rodríguez, A., Molina, B., Villarreal-Molina, M. T., Meléndez-Zajgla, J., Carnevale, A., Torres, L., & Frias, S. (2022). Fanconi anemia patients from an indigenous community in Mexico carry a new founder pathogenic variant in FANCG. International Journal of Molecular Sciences, 23(4), 2334. https://doi.org/10.3390/ijms23042334
   PubMed Web of Science ®Google Scholar
• Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015). Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research, 43(7), e47–e47. https://doi.org/10.1093/nar/gkv007
   PubMed Web of Science ®Google Scholar
• Rosenberg, P. S., Tamary, H., & Alter, B. P. (2011). How high are carrier frequencies of rare recessive syndromes? Contemporary estimates for Fanconi Anemia in the United States and Israel. American journal of medical genetics Part A, 155(8), 1877–1883. https://doi.org/10.1002/ajmg.a.34087
   Google Scholar
• Schröder, M. S., Culhane, A. C., Quackenbush, J., & Haibe-Kains, B. (2011). survcomp: An R/Bioconductor package for performance assessment and comparison of survival models. Bioinformatics (Oxford, England), 27(22), 3206–3208. https://doi.org/10.1093/bioinformatics/btr511
   PubMed Web of Science ®Google Scholar
• Shaker, B., Ahmad, S., Lee, J., Jung, C., & Na, D. (2021). In silico methods and tools for drug discovery. Computers in biology and medicine, 137, 104851. https://doi.org/10.1016/j.compbiomed.2021.104851
   Google Scholar
• Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), 2498–2504. https://doi.org/10.1101/gr.1239303
   PubMed Web of Science ®Google Scholar
• Sprenger, K. G., Jaeger, V. W., & Pfaendtner, J. (2015). The general AMBER force field (GAFF) can accurately predict thermodynamic and transport properties of many ionic liquids. The Journal of Physical Chemistry. B, 119(18), 5882–5895. https://doi.org/10.1021/acs.jpcb.5b00689
   PubMed Web of Science ®Google Scholar
• Stacklies, W., Redestig, H., Scholz, M., Walther, D., & Selbig, J. (2007). pcaMethods—A bioconductor package providing PCA methods for incomplete data. Bioinformatics (Oxford, England), 23(9), 1164–1167. https://doi.org/10.1093/bioinformatics/btm069
   PubMed Web of Science ®Google Scholar
• Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K. P., Kuhn, M., Bork, P., Jensen, L. J., & von Mering, C. (2015). STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Research, 43(Database issue), D447–D452. https://doi.org/10.1093/nar/gku1003
   PubMed Web of Science ®Google Scholar
• Tipping, A. J., Pearson, T., Morgan, N. V., Gibson, R. A., Kuyt, L. P., Havenga, C., Gluckman, E., Joenje, H., de Ravel, T., Jansen, S. & Mathew, C. G. (2001). Molecular and genealogical evidence for a founder effect in Fanconi anemia families of the Afrikaner population of South Africa. Proceedings of the National Academy of Sciences, 98(10), 5734–5739. https://doi.org/10.1073/pnas.091402398
   Google Scholar
• Wahedi, H. M., Ahmad, S., & Abbasi, S. W. (2021). Stilbene-based natural compounds as promising drug candidates against COVID-19. Journal of Biomolecular Structure and Dynamics, 39(9), 3225-3234. https://doi.org/10.1080/07391102.2020.1762743
   Google Scholar
• Wishart, D. S., Feunang, Y. D., Guo, A. C., Lo, E. J., Marcu, A., Grant, J. R., Sajed, T., Johnson, D., Li, C., Sayeeda, Z., Assempour, N., Iynkkaran, I., Liu, Y., Maciejewski, A., Gale, N., Wilson, A., Chin, L., Cummings, R., Le, D., … Wilson, M. (2018). DrugBank 5.0: A major update to the DrugBank database for 2018. Nucleic Acids Research, 46(D1), D1074–D1082. https://doi.org/10.1093/nar/gkx1037
   PubMed Web of Science ®Google Scholar
• Xia, J., Gill, E. E., & Hancock, R. E. W. (2015). NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data. Nature Protocols, 10(6), 823–844. https://doi.org/10.1038/nprot.2015.052
   PubMed Web of Science ®Google Scholar