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Research Article

Network-base approaches to identify therapeutic biomarkers in hepatocellular carcinoma and search for drug hunting utilizing molecular dynamics simulations

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Received 10 Nov 2023, Accepted 27 Feb 2024, Published online: 14 Mar 2024

References

  • Akdel, M., Pires, D. E. V., Pardo, E. P., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., LaSKowski, R. A., Pozzati, G., Shenoy, A., Zhu, W., Kundrotas, P., Serra, V. R., Rodrigues, C. H. M., Dunham, A. S., Burke, D., Borkakoti, N., Velankar, S., … Beltrao, P. (2022). A structural biology community assessment of AlphaFold2 applications. Nature Structural & Molecular Biology, 29(11), 1056–1067. https://doi.org/10.1038/s41594-022-00849-w
  • Alter, M. J. (2007). Epidemiology of hepatitis C virus infection. World Journal of Gastroenterology, 13(17), 2436–2441. https://doi.org/10.3748/wjg.v13.i17.2436
  • Arora, D., Chaudhary, R., & Singh, A. (2019). System biology approach to identify potential receptor for targeting cancer and biomolecular interaction studies of indole[2,1-a]isoquinoline derivative as anticancerous drug candidate against it. Interdisciplinary Sciences, Computational Life Sciences, 11(1), 125–134. https://doi.org/10.1007/s12539-017-0249-0
  • Arzumanyan, A., Reis, H. M. G. P. V., & Feitelson, M. A. (2013). Pathogenic mechanisms in HBV- and HCV-associated hepatocellular carcinoma. Nature Reviews Cancer, 13(2), 123–135. https://doi.org/10.1038/nrc3449
  • 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
  • Bowers, K., Chow, E., Xu, H., Dror, R., Eastwood, M., Gregersen, B., Klepeis, J., Kolossváry, I., Moraes, M., Sacerdoti, F., Salmon, J., Shan, Y., & Shaw, D. (2006). Molecular dynamics—Scalable algorithms for molecular dynamics simulations on commodity clusters. Proceedings of the ACM/IEEE SC2006 Conference on High Performance Networking and Computing, November 11–17, 2006, Tampa, FL, USA (pp. 84). https://doi.org/10.1145/1188455.1188544
  • 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
  • Bruix, J., Han, K.-H., Gores, G., Llovet, J. M., & Mazzaferro, V. (2015). Liver cancer: Approaching a personalized care. Journal of Hepatology, 62(Suppl. 1), S144–S156. https://doi.org/10.1016/j.jhep.2015.02.007
  • Carreño, V., Bartolomé, J., Castillo, I., & Quiroga, J. A. (2008). Occult hepatitis B virus and hepatitis C virus infections. Reviews in Medical Virology, 18(3), 139–157. https://doi.org/10.1002/rmv.569
  • Chanpong, A., & Dhawan, A. (2022). Wilson disease in children and young adults—State of the art. Saudi Journal of Gastroenterology, 28(1), 21–31. https://doi.org/10.4103/sjg.sjg_501_21
  • 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
  • Chen, J. E., Huang, C. C., & Ferrin, T. E. (2014). RRDistMaps: A UCSF Chimera tool for viewing and comparing protein distance maps. Bioinformatics (Oxford, England), 31(9), 1484–1486. https://doi.org/10.1093/bioinformatics/btu841
  • Chen, R., Hu, B., Jiang, M., Deng, W., Zheng, P., & Fu, B. (2022). Bioinformatic analysis of the expression and clinical significance of the DNA replication regulator MCM complex in bladder cancer. International Journal of General Medicine, 15, 5465–5485. https://doi.org/10.2147/IJGM.S368573
  • Chidambaranathan-Reghupaty, S., Fisher, P. B., & Sarkar, D. (2021). Hepatocellular carcinoma (HCC): Epidemiology, etiology and molecular classification. Advances in Cancer Research, 149, 1–61. https://doi.org/10.1016/bs.acr.2020.10.001
  • Doerge, R. (2006). Bioinformatics and computational biology solutions using R and Bioconductor Edited by Gentleman, R., Carey, V., Huber, W., Irizarry, R., and Dudoit, S. Biometrics, 62(4), 1270–1271. https://doi.org/10.1111/j.1541-0420.2006.00596_2.x
  • Ellis, K., Brandt-Sarif, M., Sunny, J., & Koyfman, S. (2022). General hepatitis. Pediatrics in Review, 43(9), 493–506. https://doi.org/10.1542/pir.2021-005279
  • Fan, G., Wei, X., & Xu, X. (2020). Is the era of sorafenib over? A review of the literature. Therapeutic Advances in Medical Oncology, 12, 1758835920927602. https://doi.org/10.1177/1758835920927602
  • Ferreira, L. G., Dos Santos, R. N., Oliva, G., & Andricopulo, A. D. (2015). Molecular docking and structure-based drug design strategies. Molecules (Basel, Switzerland), 20(7), 13384–13421. https://doi.org/10.3390/molecules200713384
  • Forli, S., Huey, R., Pique, M. E., Sanner, M., Goodsell, D. S., & Olson, A. J. (2016). Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nature Protocols, 11(5), 905–919. https://doi.org/10.1038/nprot.2016.051
  • Forner, A., Da Fonseca, L. G., Díaz-González, Á., Sanduzzi-Zamparelli, M., Reig, M., & Bruix, J. (2019). Controversies in the management of hepatocellular carcinoma. JHEP Reports: Innovation in Hepatology, 1(1), 17–29. https://doi.org/10.1016/j.jhepr.2019.02.003
  • Frullanti, E., Colombo, F., Falvella, F. S., Galvan, A., Noci, S., De Cecco, L., Incarbone, M., Alloisio, M., Santambrogio, L., Nosotti, M., Tosi, D., PaSTorino, U., & Dragani, T. A. (2012). Association of lung adenocarcinoma clinical stage with gene expression pattern in noninvolved lung tissue. International Journal of Cancer, 131(5), E643–E648. https://doi.org/10.1002/ijc.27426
  • Galvan, A., Frullanti, E., Anderlini, M., Manenti, G., Noci, S., Dugo, M., Ambrogi, F., De Cecco, L., Spinelli, R., Piazza, R., Pirola, A., Gambacorti-Passerini, C., Incarbone, M., Alloisio, M., Tosi, D., Nosotti, M., Santambrogio, L., Pastorino, U., & Dragani, T. A. (2013). Gene expression signature of non-involved lung tissue associated with survival in lung adenocarcinoma patients. Carcinogenesis, 34(12), 2767–2773. https://doi.org/10.1093/carcin/bgt294
  • Hepatocellular Carcinoma (HCC). (2022). Practice essentials, anatomy, pathophysiology. https://emedicine.medscape.com/article/197319-overview?form=fpf
  • Hildebrand, P. W., Rose, A. S., & Tiemann, J. K. S. (2019). Bringing molecular dynamics simulation data into view. Trends in Biochemical Sciences, 44(11), 902–913. https://doi.org/10.1016/j.tibs.2019.06.004
  • Hu, B., Chang, X., & Liu, X. (2019). Predicting functional modules of liver cancer based on differential network analysis. Interdisciplinary Sciences, Computational Life Sciences, 11(4), 636–644. https://doi.org/10.1007/s12539-018-0314-3
  • Huang, Z., Zhou, J.-K., Peng, Y., He, W., & Huang, C. (2020). The role of long noncoding RNAs in hepatocellular carcinoma. Molecular Cancer, 19(1), 77. https://doi.org/10.1186/s12943-020-01188-4
  • Khan, A., Ali, A., Junaid, M., Liu, C., Kaushik, A. C., Cho, W. C. S., & Wei, D.-Q. (2018). Identification of novel drug targets for diamond-blackfan anemia based on RPS19 gene mutation using protein-protein interaction network. BMC Systems Biology, 12(S4), 39. https://doi.org/10.1186/s12918-018-0563-0
  • Kim, S. T., Smith, S. A., Mortimer, P., Loembé, A.-B., Cho, H., Kim, K.-M., Smith, C., Willis, S., Irurzun-Arana, I., Berges, A., Hong, J. Y., Park, S. H., Park, J. O., Park, Y. S., Lim, H. Y., Kang, W. K., Kozarewa, I., Pierce, A. J., Dean, E., & Lee, J. (2021). Phase I study of Ceralasertib (AZD6738), a novel DNA damage repair agent, in combination with weekly paclitaxel in refractory cancer. Clinical Cancer Research, 27(17), 4700–4709. https://doi.org/10.1158/1078-0432.CCR-21-0251
  • Laskowski, R. A. (2001). PDBsum: Summaries and analyses of PDB structures. Nucleic Acids Research, 29(1), 221–222. https://doi.org/10.1093/nar/29.1.221
  • Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple ligand–protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. https://doi.org/10.1021/ci200227u
  • Liberati, A., Altman, D. G., Tetzlaff, J., Mulrow, C., Gøtzsche, P. C., Ioannidis, J. P. A., Clarke, M., Devereaux, P. J., Kleijnen, J., & Moher, D. (2009). The PRISMA statement for reporting systematic reviews and meta-analyses of studies that evaluate health care interventions: Explanation and elaboration. Journal of Clinical Epidemiology, 62(10), e1–e34. https://doi.org/10.1016/j.jclinepi.2009.06.006
  • Liu, Y., Tamimi, R. M., Collins, L. C., Schnitt, S. J., Gilmore, H. L., Connolly, J. L., & Colditz, G. A. (2011). The association between vascular endothelial growth factor expression in invasive breast cancer and survival varies with intrinsic subtypes and use of adjuvant systemic therapy: Results from the Nurses’ Health Study. Breast Cancer Research and Treatment, 129(1), 175–184. https://doi.org/10.1007/s10549-011-1432-3
  • Llovet, J. M., Kelley, R. K., Villanueva, A., Singal, A. G., Pikarsky, E., Roayaie, S., Lencioni, R., Koike, K., Zucman-Rossi, J., & Finn, R. S. (2021). Hepatocellular carcinoma. Nature Reviews Disease Primers, 7(1), 6. https://doi.org/10.1038/s41572-020-00240-3
  • Ma, R., Wang, C., Wang, J., Wang, D., & Xu, J. (2016). miRNA-mRNA interaction network in non-small cell lung cancer. Interdisciplinary Sciences, Computational Life Sciences, 8(3), 209–219. https://doi.org/10.1007/s12539-015-0117-8
  • Mantovani, A., & Targher, G. (2017). Type 2 diabetes mellitus and risk of hepatocellular carcinoma: Spotlight on nonalcoholic fatty liver disease. Annals of Translational Medicine, 5(13), 270–270. https://doi.org/10.21037/atm.2017.04.41
  • Menyhárt, O., Nagy, Á., & Győrffy, B. (2018). Determining consistent prognostic biomarkers of overall survival and vascular invasion in hepatocellular carcinoma. Royal Society Open Science, 5(12), 181006. https://doi.org/10.1098/rsos.181006
  • Menyhárt, O., Pongor, L. S., & Győrffy, B. (2019). Mutations defining patient cohorts with elevated PD-L1 expression in gastric cancer. Frontiers in Pharmacology, 9, 1522. https://doi.org/10.3389/fphar.2018.01522
  • Miick, R., Minimo, C., & Bombonati, A. (2022). Hepatocellular Carcinoma Pathology. In C. Doria & J. N. Rogart (Eds.), Hepato-Pancreato-Biliary Malignancies: Diagnosis and Treatment in the 21st Century (pp. 49–86). Springer International Publishing. https://doi.org/10.1007/978-3-030-41683-6_3
  • Mousa, A. B. (2008). Sorafenib in the treatment of advanced hepatocellular carcinoma. Saudi Journal of Gastroenterology, 14(1), 40–42. https://doi.org/10.4103/1319-3767.37808
  • Okuda, H. (2007). Hepatocellular carcinoma development in cirrhosis. Best Practice & Research. Clinical Gastroenterology, 21(1), 161–173. https://doi.org/10.1016/j.bpg.2006.07.002
  • Ozaki, K., Higuchi, S., Kimura, H., & Gabata, T. (2022). Liver metastases: Correlation between imaging features and pathomolecular environments. Radiographics, 42(7), 1994–2013. https://doi.org/10.1148/rg.220056
  • Pai, Y.-Y., Wang, J.-D., Ho, H.-E., Chou, Y.-J., Ho, W.-C., Chan, W.-C., Chu, W.-M., & Tsan, Y.-T. (2022). Risk of fractures, repeated fractures and osteoporotic fractures among patients with Hemophilia in Taiwan: A 14-year population-based cohort study. International Journal of Environmental Research and Public Health, 20(1), 525. https://doi.org/10.3390/ijerph20010525
  • Prado, C. A. D S., Fonseca, D. L. M., Singh, Y., Filgueiras, I. S., Baiocchi, G. C., Plaça, D. R., Marques, A. H. C., Dantas-Komatsu, R. C. S., Usuda, J. N., Freire, P. P., Salgado, R. C., Napoleao, S. M. D S., Ramos, R. N., Rocha, V., Zhou, G., Catar, R., Moll, G., Camara, N. O. S., de MiraNda, G. C., … Cabral-Marques, O. (2023). Integrative systems immunology uncovers molecular networks of the cell cycle that stratify COVID-19 severity. Journal of Medical Virology, 95(2), e28450. https://doi.org/10.1002/jmv.28450
  • Rasheed, M. A., Iqbal, M. N., Saddick, S., Ali, I., Khan, F. S., Kanwal, S., Ahmed, D., Ibrahim, M., Afzal, U., & Awais, M. (2021). Identification of lead compounds against Scm (fms10) in Enterococcus faecium using computer aided drug designing. Life (Basel, Switzerland), 11(2), 77. https://doi.org/10.3390/life11020077
  • Roerecke, M., Vafaei, A., Hasan, O. S., Chrystoja, B. R., Cruz, M., Lee, R., Neuman, M. G., & Rehm, J. (2019). Alcohol consumption and risk of liver cirrhosis: A systematic review and meta-analysis. The American Journal of Gastroenterology, 114(10), 1574–1586. https://doi.org/10.14309/ajg.0000000000000340
  • Samad, A., Huq, M. A., & Rahman, M. S. (2022). Bioinformatics approaches identified dasatinib and bortezomib inhibit the activity of MCM7 protein as a potential treatment against human cancer. Scientific Reports, 12(1), 1539. https://doi.org/10.1038/s41598-022-05621-0
  • Shen, C., Jiang, X., Li, M., & Luo, Y. (2023). Hepatitis virus and hepatocellular carcinoma: Recent advances. Cancers, 15(2), 533. https://doi.org/10.3390/cancers15020533
  • Shivakumar, D., Williams, J., Wu, Y., Damm, W., Shelley, J., & Sherman, W. (2010). Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. Journal of Chemical Theory and Computation, 6(5), 1509–1519. https://doi.org/10.1021/ct900587b
  • 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
  • Stender, J. D., Kim, K., Charn, T. H., Komm, B., Chang, K. C. N., Kraus, W. L., Benner, C., Glass, C. K., & Katzenellenbogen, B. S. (2010). Genome-wide analysis of estrogen receptor alpha DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation. Molecular and Cellular Biology, 30(16), 3943–3955. https://doi.org/10.1128/MCB.00118-10
  • Su, L., Meng, X., Ma, Q., Bai, T., & Liu, G. (2018). LPRP: A gene-gene interaction network construction algorithm and its application in breast cancer data analysis. Interdisciplinary Sciences, Computational Life Sciences, 10(1), 131–142. https://doi.org/10.1007/s12539-016-0185-4
  • Sun, Y., Cheng, Z., & Liu, S. (2022). MCM2 in human cancer: Functions, mechanisms, and clinical significance. Molecular Medicine, 28(1), 128. https://doi.org/10.1186/s10020-022-00555-9
  • Sung, H., Ferlay, J., Siegel, R. L., Laversanne, M., Soerjomataram, I., Jemal, A., & Bray, F. (2021). Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin, 71(3), 209–249. https://doi.org/10.3322/caac.21660
  • Taibi, C., Vincenzi, L., & D’Offizi, G. (2023). Role of the immune system in hepatocellular carcinoma. In G. M. Ettorre (Ed.), Hepatocellular Carcinoma (pp. 19–26). Springer International Publishing. https://doi.org/10.1007/978-3-031-09371-5_3
  • Tümen, D., Heumann, P., Gülow, K., Demirci, C.-N., Cosma, L.-S., Müller, M., & Kandulski, A. (2022). Pathogenesis and current treatment strategies of hepatocellular carcinoma. Biomedicines, 10(12), 3202. https://doi.org/10.3390/biomedicines10123202
  • Villanueva, A., & Llovet, J. M. (2011). Targeted therapies for hepatocellular carcinoma. Gastroenterology, 140(5), 1410–1426. https://doi.org/10.1053/j.gastro.2011.03.006
  • Vogel, A., Meyer, T., Sapisochin, G., Salem, R., & Saborowski, A. (2022). Hepatocellular carcinoma. Lancet (London, England), 400(10360), 1345–1362. https://doi.org/10.1016/S0140-6736(22)01200-4
  • 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
  • Wu, B., & Xi, S. (2021). Bioinformatics analysis of the transcriptional expression of minichromosome maintenance proteins as potential indicators of survival in patients with cervical cancer. BMC Cancer, 21(1), 928. https://doi.org/10.1186/s12885-021-08674-y
  • 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
  • Yang, J. D., & Roberts, L. R. (2010). Hepatocellular carcinoma: A global view. Nature Reviews. Gastroenterology & Hepatology, 7(8), 448–458. https://doi.org/10.1038/nrgastro.2010.100

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