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ISSN Print: 1045-4403
ISSN Online: 2162-6502
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Gene Prioritization and Network Topology Analysis of Targeted Genes for Acquired Taxane Resistance by Meta-Analysis
ABSTRACT
Network topology-based approaches prove to be highly efficient in addressing multifactorial phenomena such as acquired drug resistance in cancer. The aim of this study was to identify differentially expressed genes across multiple microarray datasets (meta-DEGs), to prioritize meta-DEGs to find the most promising genes linked to acquired taxane resistance (ATR), and to analyze the relevant biological networks using topology analysis. A total of 771 meta-DEGs were identified by performing a cross-platform meta-analysis of ATR-related microarray datasets. A gene prioritization method was used to simultaneously identify activated or deactivated genes on a co-expression map and protein−protein interaction (PPI) network. The top 10 prioritized genes in the gene co-expression and the top 1% highly ranked genes in the PPI network were identified. The selected meta-DEGs were used to construct biological networks, and topological analysis was performed using network centrality measures. Using integrative analyses, we identified ATR candidate genes, including several previously unidentified genes that were found to be associated with ATR. From the gene co-expression network, PRSS23 was the highest-ranking gene at local average connectivity measure and ADAM9 was ranked highest in other centralities. In protein interaction network, HSPA1A, ANXA1, and PA2G4 showed highest ranks in network centrality analyses. This study provides a comprehensive overview of the gene expression patterns associated with ATR. Furthermore, it presents a new approach to identification of unveiled candidate genes to ATR, using a gene prioritization method and network analysis.
-
Markman M, Mekhail TM. Paclitaxel in cancer therapy. Expert OpinPharmacother. 2002; 3(6): 75 5-66. Available from: http://www.tandfonline.com/doi/full/10.1517/14656566. 3.6.755.
-
Geney R, Ungureanu L, Li D, Ojima I. Overcoming multidrug resistance in taxane chemotherapy. Clin ChemLab Med. 2002;40(9):918-25. Available from: http://europepmc.org/ article/med/12435109.
-
Mukhtar E, Adhami VM, Mukhtar H. Targeting microtubules by natural agents for cancer therapy. Mol Cancer Ther. 2014;13(2):275-84. Available from: http://mct. aacrjournals.org/content/13/2/275.full.
-
Saraswathy M, Gong S. Different strategies to over-come multidrug resistance in cancer. Biotechnol Adv. 2013;31(8): 1397-407. Available from: http://www.sciencedirect.com/science/article/pii/S0734975013001109.
-
Wang H, Vo T, Hajar A, Li S, Chen X, Parissenti AM, Brindley DN, Wang Z. Multiple mechanisms underlying acquired resistance to taxanes in selected docetaxel-resistant MCF-7 breast cancer cells. BMC Cancer [Internet]. 2014 Jan 22 [cited 2017 Apr 14];14:37. Available from: https://bmccancer.biomedcentral.com/articles/10.1186/ 1471-2407-14-37.
-
Ramasamy A, Mondry A, Holmes CC, Altman DG. Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med [Internet]. 2008 Sep 2 [cited 2016 Aug 17];5(9):e184. Available from: http://dx-.plos.org/10.1371/journal.pmed.0050184.
-
Sherman-Baust CA, Becker KG, Wood WH III, Zhang Y, Morin PJ. Gene expression and pathway analysis of ovarian cancer cells selected for resistance to cisplatin, paclitaxel, or doxorubicin. J Ovarian Res [Internet]. 2011 Dec 5 [cited 2017 Apr 3];4(1):21. Available from: https://ovar-ianresearch.biomedcentral.com/articles/10.1186/1757-2215-4-21.
-
Luo W, Schork NJ, Marschke KB, Ng S-C, Hermann TW, Zhang J, Sanders JM, Tooker P, Malo N, Zapala MA, Dziewanowska ZE, Negro-Vilar A, Meglasson MD. Identification of polymorphisms associated with hypertri-glyceridemia and prolonged survival induced by bexarotene in treating non-small cell lung cancer. Anticancer Res. 2011;31(6):2303-11. Available from: http://ar.iiar-journals.org/content/31/6/2303.long.
-
Landen CN, Goodman B, Katre AA, Steg AD, Nick AM, Stone RL, Miller LD, Mejia PV, Jennings NB, Gershenson DM, Bast RC Jr, Coleman RL, Lopez-Ber- estein G, Sood AK. Targeting aldehyde dehydrogenase cancer stem cells in ovarian cancer. Mol Cancer Ther. 2010;9(12):3186-99. Available from: http://mct.aacrjournals.org/cgi/pmidlookup?view=long&pmid=20889728.
-
Marin-Aguilera M, Codony-Servat J, Kalko SG, Fernandez PL, Bermudo R, Buxo E, Ribal MJ, Gascon P, Mellado B. Identification of docetaxel resistance genes in castration-resistant prostate cancer. Mol Cancer Ther. 2012;11(2):329-39. Available from: http://mct.aacrjournals.org/content/11/2/329.long.
-
Domingo-Domenech J, Vidal SJ, Rodriguez-Bravo V, Castillo-Martin M, Quinn SA, Rodriguez-Barrueco R, Bonal DM, Charytonowicz E, Gladoun N, Iglecia-Vicente J, Petrylak DP, Benson BC, Silva JM, Cordon-Cardo C. Suppression of acquired docetaxel resistance in prostate cancer through depletion of Notch- and Hedgehog-dependent tumor-initiating cells. Cancer Cell. 2012;22(3):373-88. Available from: http://www.sciencedirect.com/science/article/pii/S153561081200308X.
-
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001;29:365-71.
-
Breitling R, Armengaud P, Amtmann A, Herzyk P. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett. 2004;573(1-3):83-92.
-
Adewoye AB, Kyriacou CP, Tauber E. Identification and functional analysis of early gene expression induced by circadian light-resetting in Drosophila. BMC Genomics [Internet]. 2015 [cited 2017 Jun 7];16:570. Available from: https://bmcgenomics.biomedcentral.com/articles/10.1186/ s12864-015-1787-7.
-
Hounkpe BW, Fiusa MML, Colella MP, Nilkenes Gomes da Costa L, Benatti R de O, Olalla Saad ST, Costa FF, Nunes dos Santos MN, De Paula EV. Role of innate immunity-triggered pathways in the pathogenesis of sickle cell disease: a meta-analysis of gene expression studies. Sci Rep [Internet]. 2016 Nov 9 [cited 2017 Jun 7];5(1): 17822. Available from: http://www.nature.com/ articles/srep17822.
-
Tranchevent LC, Capdevila FB, Nitsch D, de Moor B, de Causmaecker P, Moreau Y. A guide to web tools to prioritize candidate genes. Brief Bioinform. 2011;12(1):22-32.
-
Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration. The sequence read archive. Nucleic Acids Res. 2011 Jan;39:D19-21. doi: 10.1093/nar/gkq1019.
-
Gillis J, Pavlidis P. The impact of multifunctional genes on guilt "by association" analysis. PLoS One. 2011;6(2):e17258.
-
van Dam S, Cordeiro R, Craig T, van Dam J, Wood S, de Magalhaes JP. GeneFriends: an online co-expression analysis tool to identify novel gene targets for aging and complex diseases. BMC Genomics. 2012;13(1):535.
-
Garcia-Garcia J, Guney E, Aragues R, Planas-Iglesias J, Oliva B. Biana: a software framework for compiling biological interactions and analyzing networks. BMC Bio-informatics [Internet]. 2010;11(1):56. Available from: https://bmcbioinformatics.biomedcentral.com/articles/10. 1186/1471-2105-11-56.
-
Guney E, Oliva B. Exploiting protein-protein interaction networks for genome-wide disease-gene prioritization. PLoS One [Internet]. Public Library of Science; 2012 [cited 2017 Feb 8];7(9):e43557. Available from: http:// dx.plos.org/10.1371/journal.pone.0043557.
-
Judson N, Mekalanos JJ. TnAraOut, a transposon-based approach to identify and characterize essential bacterial genes. Nat Biotechnol. 2000;18(7):740-5. Available from: http://www.nature.com/doifinder/10.1038/77305.
-
Acencio ML, Lemke N. Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information. BMC Bioinformatics [Internet]. 2009 [cited 2016 Aug 18];10(1):290. Available from: http://www.biomedcentral. com/1471-2105/10/290.
-
Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian K, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kotter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang C, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 2002;418(6896):387-91. Available from: http://www.nature.com/doifinder/10.1038/nature00935.
-
Cullen LM, Arndt GM. Genome-wide screening for gene function using RNAi in mammalian cells. Immunol Cell Biol. 2005;83(3):217-23. Available from: http://www.nature.com/doifinder/10.1111/j.1440-1711.2005.01332.x.
-
Roemer T, Jiang B, Davison J, Ketela T, Veillette K, Breton A, Tandia F, Linteau A, Sillaots S, Marta C, Martel N, Veronneau S, Lemieux S, Kauffman S, Becker J, Storms R, Boone C, Bussey H. Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery. Mol Microbiol. 2003;50(1): 167-81. Available from: http://doi.wiley. com/10.1046/j.1365-2958.2003.03697.x.
-
Jeong H, Mason SP, Barabasi L, Oltvai ZN. Lethality and centrality in protein networks. Nature. 2001;411(6833):41-2.
-
Newman MEJ. Finding community structure in networks using the eigenvectors of matrices. Phys Rev E Stat Nonlinear Soft Matter Phys. 2006;74(3 Pt 2):036104.
-
Tang Y, Li M, Wang J, Pan Y, Wu F-X. CytoNCA: a cytoscape plugin for centrality analysis and evaluation of protein interaction networks. Biosystems. 2015;127:67-72. Available from: http://linkinghub.elsevier.com/retrieve/ pii/S0303264714001944.
-
Freeman LC. A set of measures of centrality based on betweenness. Sociometry. 1977;40(1):35-41. Available from: http://wwwjstor.org/stable/3033543?origin=crossref.
-
Sabidussi G. The centrality index of a graph. Psychometrika. 1966;31(4):581-603. Available from: http://link. springer.com/10.1007/BF02289527.
-
Bonacich P. Power and centrality: a family of measures. Am J Sociol. 1987;92(5):1170-82. Available from: http:// www.journals.uchicago.edu/doi/10.1086/228631.
-
Li M, Wang J, Chen X, Wang H, Pan Y. A local average connectivity-based method for identifying essential proteins from the network level. Comput Biol Chem. 2011;35(3):143-50.
-
Wang J, Li M, Wang H, Pan Y. Identification of essential proteins based on edge clustering coefficient. IEEE/ ACM Trans Comput Biol Bioinform. 2012;9(4):1070-80. Available from: http://ieeexplore.ieee.org/lpdocs/epic03/ wrapper.htm?arnumber=6081844.
-
Zhang Y-C, Ye Q-F, Long Z, He L-Y. Down-regulation of Notch-1 enhances docetaxel-induced mitotic arrest and apoptosis on prostate cancer cells. Translational andrology and urology. Transl Androl Urol. 2012;1(Suppl 1):PC 12. Available from: http://tau.amegroups.com/article/ view/398/449.
-
Ye Q-F, ZhangY-C, Peng X-Q, Long Z, MingY-Z, He L-Y. Silencing Notch-1 induces apoptosis and increases the chemo-sensitivity ofprostate cancer cells to docetaxel through Bcl-2 and Bax. Oncol Lett. 2012;3(4): 879-84. Available from: https://www.spandidos-publications.com/10.3892/ol.2012. 572/.
-
Brunen D, Willems SM, Kellner U, Midgley R, Simon I, Bernards R. TGF-P: an emerging player in drug resistance. Cell Cycle. 2013;12(18):2960-8. Available from: http://www.tandfonline.com/doi/abs/10.4161/cc.26034.
-
Kubiczkova L, Sedlarikova L, Hajek R, Sevcikova S. TGF-P-an excellent servant but a bad master. J Transl Med [Internet]. 2012 [cited 2017 Jun 7];10(1):183. Available from: http://translational-medicine.biomedcentral.com/articles/ 10.1186/1479-5876-10-183.
-
Chan H-S, Chang S-J, Wang T-Y, Ko H-J, Lin Y-C, Lin K-T, Chang K-M, Chuang Y-J. Serine protease PRSS23 is upregulated by estrogen receptor a and associated with proliferation of breast cancer cells. PLoS One [Internet]. 2012 [cited 2016 Sep 7];7(1):e30397. Available from: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030397.
-
Lee YS, Hwang SG, Kim JK, Park TH, Kim YR, Myeong HS, Choi JD, Kwon K, Jang CS, Ro YT, Noh YH, Kim SY. Identification of novel therapeutic target genes in acquired lapatinib-resistant breast cancer by integrative meta-analysis. Tumour Biol. 2016;37(2):2285-97. Available from: http://link.springer.com/10.1007/s13277-015-4033-7.
-
Peduto L. ADAM9 as a potential target molecule in cancer. Curr Pharm Des. 2009;15(20):2282-7. Available from: http://www.eurekaselect.com/69546/article.
-
Josson S, Anderson CS, Sung S-Y, Johnstone PAS, Kubo H, Hsieh C-L, Arnold R, Gururajan M, Yates C, Chung LWK. Inhibition of ADAM9 expression induces epithelial phenotypic alterations and sensitizes human prostate cancer cells to radiation and chemotherapy. Prostate. 2011;71(3):232-40. Available from: https://mdanderson. elsevierpure.com/en/publications/inhibition-of-ad-am9-expression-induces-epithelial-phenotypicalte.
-
Kauttu T, Mustonen H, Vainionpaa S, Krogerus L, Ilonen I, Rasanen J, Salo J, Puolakkainen P. Disintegrin and metal-loproteinases (ADAMs) expression in gastroesophageal reflux disease and in esophageal adenocarcinoma. Clin Transl Oncol. 2017;19(1):58-66. Available from: https:// link.springer.com/article/10.1007%2Fs12094-016-1503-3.
-
Luo J, Qi Y. Identification of essential proteins based on a new combination of local interaction density and protein complexes. PLoS One [Internet]. 2015 [cited 2016 Sep 7];10(6):e0131418. Available from: https://journals.plos. org/plosone/article?id=10.1371/journal.pone.0131418.
-
Vargas-Roig LM, Gago FE, Tello O, Aznar JC, Ciocca DR. Heat shock protein expression and drug resistance in breast cancer patients treated with induction chemotherapy. Int J Cancer. 1998;79(5):468-75. Available from: http://doi.wiley.com/10.1002/%28SICI%291097-021 5%2 8 1 998 1 023%2979%3A5%3C468%3A %3AAID-IJC4%3E3.0.CO%3B2-Z.
-
Shu C-W, Huang C-M. HSP70s: from tumor transformation to cancer therapy. Clin Med Oncol. 2008;2:335-45. Available from: https://journals.sagepub.com/ doi/10.4137/CMO.S475.
-
Yu S, Meng Q, Hu H, Zhang M. Correlation of ANXA1 expression with drug resistance and relapse in bladder cancer. Int J Clin Exp Pathol. 2014;7(9):5538-48. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4203166.
-
Bizzarro V, Belvedere R, Milone MR, Pucci B, Lombardi R, Bruzzese F, Popolo A, Parente L, Budillon A, Petrella A. Annexin A1 is involved in the acquisition and maintenance of a stem cell-like/aggressive phenotype in prostate cancer cells with acquired resistance to zoledronic acid. Oncotarget. 2015;6(28):25074-92. Available from: http://www.oncotarget.com/fulltext/4725.
-
Zhang Y, Linn D, Liu Z, Melamed J, Tavora F, Young CY, Burger AM, Hamburger AW. EBP1, an ErbB3-binding protein, is decreased in prostate cancer and implicated in hormone resistance. Mol Cancer Ther. 2008;7(10):3176-86. Available from: https://mct.aacrjournals.org/content/7/10/3176.long.
-
Menezo YJ, Russo G, Tosti E, Mouatassim S El, Benkhalifa M. Expression profile of genes coding for DNA repair in human oocytes using pangenomic microarrays, with a special focus on ROS linked decays. J Assist Reprod Genet. 2007;24(11):513-20. Available from: http://link. springer.com/10.1007/s10815-007-9167-0.
-
Zheng X, Gai X, Ding F, Lu Z, Tu K, Yao Y, Liu Q. Histone acetyltransferase PCAF up-regulated cell apoptosis in hepatocellular carcinoma via acetylating histone H4 and inactivating AKT signaling. Mol Cancer [Internet]. 2013 [cited 2016 Sep 8];12(1):96. Available from: https://molecular-cancer.biomedcentral.com/articles/ 10.1186/1476-4598-12-96.
-
Zeng Qiuhong, Lin Xiaofang, Chen Huadong, Yan Yixin, Wang Xianlong, Multi-time scale transcriptomic analysis on the dynamic process of tamoxifen resistance development in breast cancer cell lines, Breast Cancer, 29, 3, 2022. Crossref