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Original Research

Super-Enhancer-Associated Hub Genes In Chronic Myeloid Leukemia Identified Using Weighted Gene Co-Expression Network Analysis

, , , , , , & show all
Pages 10705-10718 | Published online: 23 Dec 2019

References

  • Groffen J, Stephenson JR, Heisterkamp N, de Klein A, Bartram CR, Grosveld G. Philadelphia chromosomal breakpoints are clustered within a limited region, bcr, on chromosome 22. Cell. 1984;36(1):93–99. doi:10.1016/0092-8674(84)90077-16319012
  • Daley GQ, Baltimore D. Transformation of an interleukin 3-dependent hematopoietic cell line by the chronic myelogenous leukemia-specific P210bcr/abl protein. Proc Natl Acad Sci U S A. 1988;85(23):9312–9316. doi:10.1073/pnas.85.23.93123143116
  • Zhang J, Jiang Y, Han X, et al. Differential expression profiles and functional analysis of plasma miRNAs associated with chronic myeloid leukemia phases. Future Oncol. 2018;15(7):763–776.30501399
  • Arber DA, Orazi A. Update on the pathologic diagnosis of chronic myelomonocytic leukemia. Mod Pathol. 2019. doi:10.1038/s41379-019-0215-y
  • Heidari N, Abroun S, Bertacchini J, Vosoughi T, Rahim F, Saki N. Significance of inactivated genes in leukemia: pathogenesis and prognosis. Cell J. 2017;19(Suppl 1):9–26. doi:10.22074/cellj.2017.490828580304
  • Druker BJ, Tamura S, Buchdunger E, et al. Effects of a selective inhibitor of the Abl tyrosine kinase on the growth of Bcr-Abl positive cells. Nat Med. 1996;2(5):561–566. doi:10.1038/nm0596-5618616716
  • Zhao WH, Huang BT, Zhang JY, Zeng QC. Distinct EphB4-mediated mechanisms of apoptotic and resistance to dasatinib in human chronic myeloid leukemia and K562 cell lines. Leuk Res. 2017;63:28–33. doi:10.1016/j.leukres.2017.10.01429096333
  • Xiao X, Jiang K, Xu Y, et al. (-)-Epigallocatechin-3-gallate induces cell apoptosis in chronic myeloid leukaemia by regulating Bcr/Abl-mediated p38-MAPK/JNK and JAK2/STAT3/AKT signalling pathways. Clin Exp Pharmacol Physiol. 2018;46(2):126–136.30251267
  • Corrado C, Saieva L, Raimondo S, Santoro A, De Leo G, Alessandro R. Chronic myelogenous leukaemia exosomes modulate bone marrow microenvironment through activation of epidermal growth factor receptor. J Cell Mol Med. 2016;20(10):1829–1839. doi:10.1111/jcmm.1287327196940
  • Riva B, De Dominici M, Gnemmi I, et al. Celecoxib inhibits proliferation and survival of chronic myelogenous leukemia (CML) cells via AMPK-dependent regulation of beta-catenin and mTORC1/2. Oncotarget. 2016;7(49):81555–81570. doi:10.18632/oncotarget.1314627835591
  • Lakkireddy S, Aula S, Kapley A, et al. Association of Vascular Endothelial Growth Factor A (VEGFA) and its receptor (VEGFR2) gene polymorphisms with risk of chronic myeloid leukemia and influence on clinical outcome. Mol Diagn Ther. 2016;20(1):33–44. doi:10.1007/s40291-015-0173-026476544
  • Weich N, Ferri C, Moiraghi B, et al. TP53 codon 72 polymorphism predicts chronic myeloid leukemia susceptibility and treatment outcome. Blood Cells Mol Dis. 2016;59:129–133. doi:10.1016/j.bcmd.2016.05.00727282582
  • Liu W, Li L, Ye H, Tu W. [Weighted gene co-expression network analysis in biomedicine research]. Sheng Wu Gong Cheng Xue Bao. 2017;33(11):1791–1801. doi:10.13345/j.cjb.17000629202516
  • Langfelder P, Horvath S. Eigengene networks for studying the relationships between co-expression modules. BMC Syst Biol. 2007;1:54. doi:10.1186/1752-0509-1-5418031580
  • Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559. doi:10.1186/1471-2105-9-55919114008
  • Shi T, Chen J, Li J, Yang BY, Zhang QL. Identification of key gene modules and pathways of human glioma through coexpression network. J Cell Physiol. 2019;234(2):1862–1870. doi:10.1002/jcp.2705930067869
  • Liu R, Zhang W, Liu ZQ, Zhou HH. Associating transcriptional modules with colon cancer survival through weighted gene co-expression network analysis. BMC Genomics. 2017;18(1):361. doi:10.1186/s12864-017-3761-z28486948
  • Qiu JJ, Ren ZR, Yan JB. Identification and functional analysis of long non-coding RNAs in human and mouse early embryos based on single-cell transcriptome data. Oncotarget. 2016;7(38):61215–61228. doi:10.18632/oncotarget.1130427542205
  • Luo Z, Liu R, Sun B, et al. Identification of gene modules associated with warfarin dosage by a genome-wide DNA methylation study. Pharmazie. 2018;73(5):288–293. doi:10.1691/ph.2018.731929724296
  • Alaei S, Sadeghi B, Najafi A, Masoudi-Nejad A. LncRNA and mRNA integration network reconstruction reveals novel key regulators in esophageal squamous-cell carcinoma. Genomics. 2019;111(1):76–89. doi:10.1016/j.ygeno.2018.01.00329317304
  • Liu S, Xie F, Xiang X, et al. Identification of differentially expressed genes, lncRNAs and miRNAs which are associated with tumor malignant phenotypes in hepatoblastoma patients. Oncotarget. 2017;8(57):97554–97564. doi:10.18632/oncotarget.2218129228631
  • Shirasaki DI, Greiner ER, Al-Ramahi I, et al. Network organization of the huntingtin proteomic interactome in mammalian brain. Neuron. 2012;75(1):41–57. doi:10.1016/j.neuron.2012.05.02422794259
  • Pei G, Chen L, Zhang W. WGCNA application to proteomic and metabolomic data analysis. Methods Enzymol. 2017;585:135–158.28109426
  • Tong M, Li X, Wegener Parfrey L, et al. A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease. PLoS One. 2013;8(11):e80702. doi:10.1371/journal.pone.008070224260458
  • Chapuy B, McKeown MR, Lin CY, et al. Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma. Cancer Cell. 2013;24(6):777–790. doi:10.1016/j.ccr.2013.11.00324332044
  • Hnisz D, Abraham BJ, Lee TI, et al. Super-enhancers in the control of cell identity and disease. Cell. 2013;155(4):934–947. doi:10.1016/j.cell.2013.09.05324119843
  • Whyte WA, Orlando DA, Hnisz D, et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell. 2013;153(2):307–319. doi:10.1016/j.cell.2013.03.03523582322
  • Khan A, Zhang X. dbSUPER: a database of super-enhancers in mouse and human genome. Nucleic Acids Res. 2016;44(D1):D164–D171. doi:10.1093/nar/gkv100226438538
  • Langfelder P, Zhang B, Horvath S. Defining clusters from a hierarchical cluster tree: the dynamic tree cut package for R. Bioinformatics. 2008;24(5):719–720. doi:10.1093/bioinformatics/btm56318024473
  • Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 2019;10(1):1523. doi:10.1038/s41467-019-09234-630944313
  • Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504. doi:10.1101/gr.123930314597658
  • Robinson JT, Thorvaldsdottir H, Winckler W, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):24–26. doi:10.1038/nbt.175421221095
  • Wang X, Spandidos A, Wang H, Seed B. PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update. Nucleic Acids Res. 2012;40(Database issue):D1144–D1149. doi:10.1093/nar/gkr101322086960
  • Luo J, Qu J, Yang R, et al. Phytochemicals mediate the expression and activity of OCTN2 as activators of the PPARgamma/RXRalpha pathway. Front Pharmacol. 2016;7:189. doi:10.3389/fphar.2016.0018927445823
  • Ferreira AF, de Oliveira GL, Tognon R, et al. Apoptosis-related gene expression profile in chronic myeloid leukemia patients after imatinib mesylate and dasatinib therapy. Acta Haematol. 2015;133(4):354–364. doi:10.1159/00036944625721555
  • Ko JY, Oh S, Yoo KH. Functional enhancers as master regulators of tissue-specific gene regulation and cancer development. Mol Cells. 2017;40(3):169–177. doi:10.14348/molcells.2017.003328359147
  • Sengupta S, George RE. Super-enhancer-driven transcriptional dependencies in cancer. Trends Cancer. 2017;3(4):269–281. doi:10.1016/j.trecan.2017.03.00628718439
  • Thandapani P. Super-enhancers in cancer. Pharmacol Ther. 2019. doi:10.1016/j.pharmthera.2019.02.014
  • Huang J, Li K, Cai W, et al. Dissecting super-enhancer hierarchy based on chromatin interactions. Nat Commun. 2018;9(1):943. doi:10.1038/s41467-018-03279-929507293
  • Rodriguez-Rodriguez JA, Lewis C, McKinley KL, et al. Distinct roles of RZZ and Bub1-KNL1 in mitotic checkpoint signaling and kinetochore expansion. Curr Biol. 2018;28(21):3422.e3425–3429.e3425. doi:10.1016/j.cub.2018.10.006
  • Mur P, De Voer RM, Olivera-Salguero R, et al. Germline mutations in the spindle assembly checkpoint genes BUB1 and BUB3 are infrequent in familial colorectal cancer and polyposis. Mol Cancer. 2018;17(1):23. doi:10.1186/s12943-018-0762-829448935
  • de Voer RM, Geurts van Kessel A, Weren RD, et al. Germline mutations in the spindle assembly checkpoint genes BUB1 and BUB3 are risk factors for colorectal cancer. Gastroenterology. 2013;145(3):544–547. doi:10.1053/j.gastro.2013.06.00123747338
  • Zhang L, Huang Y, Ling J, et al. Screening and function analysis of hub genes and pathways in hepatocellular carcinoma via bioinformatics approaches. Cancer Biomark. 2018;22(3):511–521. doi:10.3233/CBM-17116029843214
  • Siemeister G, Mengel A, Fernandez-Montalvan AE, et al. Inhibition of BUB1 kinase by BAY 1816032 sensitizes tumor cells toward taxanes, ATR, and PARP inhibitors in vitro and in vivo. Clin Cancer Res. 2018;5(4):1404–1414.
  • Ritter A, Kreis NN, Louwen F, Wordeman L, Yuan J. Molecular insight into the regulation and function of MCAK. Crit Rev Biochem Mol Biol. 2015;51(4):228–245. doi:10.1080/10409238.2016.117870527146484
  • Bie L, Zhao G, Wang YP, Zhang B. Kinesin family member 2C (KIF2C/MCAK) is a novel marker for prognosis in human gliomas. Clin Neurol Neurosurg. 2012;114(4):356–360.22130050
  • Gu Y, Lu L, Wu L, Chen H, Zhu W, He Y. Identification of prognostic genes in kidney renal clear cell carcinoma by RNAseq data analysis. Mol Med Rep. 2017;15(4):1661–1667. doi:10.3892/mmr.2017.619428260099
  • Duan H, Zhang X, Wang FX, et al. KIF-2C expression is correlated with poor prognosis of operable esophageal squamous cell carcinoma male patients. Oncotarget. 2016;7(49):80493–80507. doi:10.18632/oncotarget.1149227563815
  • Rasmussen RD, Gajjar MK, Tuckova L, et al. BRCA1-regulated RRM2 expression protects glioblastoma cells from endogenous replication stress and promotes tumorigenicity. Nat Commun. 2016;7:13398. doi:10.1038/ncomms1339827845331
  • Luo X, Yu H, Song Y, Sun T. Integration of metabolomic and transcriptomic data reveals metabolic pathway alteration in breast cancer and impact of related signature on survival. J Cell Physiol. 2018;34(8):13021–13031.
  • Liang WH, Li N, Yuan ZQ, Qian XL, Wang ZH. DSCAM-AS1 promotes tumor growth of breast cancer by reducing miR-204-5p and up-regulating RRM2. Mol Carcinog. 2018;58(4):461–473.30457164
  • Liu R, Guo CX, Zhou HH. Network-based approach to identify prognostic biomarkers for estrogen receptor-positive breast cancer treatment with tamoxifen. Cancer Biol Ther. 2015;16(2):317–324. doi:10.1080/15384047.2014.100236025756514
  • Liu R, Lv QL, Yu J, et al. Correlating transcriptional networks with pathological complete response following neoadjuvant chemotherapy for breast cancer. Breast Cancer Res Treat. 2015;151(3):607–618. doi:10.1007/s10549-015-3428-x25981901
  • He Z, Tang F, Lu Z, et al. Analysis of differentially expressed genes, clinical value and biological pathways in prostate cancer. Am J Transl Res. 2018;10(5):1444–1456.29887958
  • Li J, Pang J, Liu Y, et al. Suppression of RRM2 inhibits cell proliferation, causes cell cycle arrest and promotes the apoptosis of human neuroblastoma cells and in human neuroblastoma RRM2 is suppressed following chemotherapy. Oncol Rep. 2018;40(1):355–360. doi:10.3892/or.2018.642029749541
  • Chang CC, Lin CC, Wang CH, et al. miR-211 regulates the expression of RRM2 in tumoral metastasis and recurrence in colorectal cancer patients with a k-ras gene mutation. Oncol Lett. 2018;15(5):8107–8117. doi:10.3892/ol.2018.829529731918
  • Farrell JJ, Moughan J, Wong JL, et al. Precision medicine and pancreatic cancer: a gemcitabine pathway approach. Pancreas. 2016;45(10):1485–1493. doi:10.1097/MPA.000000000000071027748721
  • He B, Yin J, Gong S, et al. Bioinformatics analysis of key genes and pathways for hepatocellular carcinoma transformed from cirrhosis. Medicine (Baltimore). 2017;96(25):e6938. doi:10.1097/MD.000000000000693828640074
  • Zhang C, Peng L, Zhang Y, et al. The identification of key genes and pathways in hepatocellular carcinoma by bioinformatics analysis of high-throughput data. Med Oncol. 2017;34(6):101. doi:10.1007/s12032-017-0963-928432618
  • Grolmusz VK, Karaszi K, Micsik T, et al. Cell cycle dependent RRM2 may serve as proliferation marker and pharmaceutical target in adrenocortical cancer. Am J Cancer Res. 2016;6(9):2041–2053.27725909
  • Zheng S, Wang X, Weng YH, et al. siRNA knockdown of RRM2 effectively suppressed pancreatic tumor growth alone or synergistically with doxorubicin. Mol Ther Nucleic Acids. 2018;12:805–816. doi:10.1016/j.omtn.2018.08.00330153565
  • Wu Y, Sun J, Li A, Chen D. The promoted delivery of RRM2 siRNA to vascular smooth muscle cells through liposome-polycation-DNA complex conjugated with cell penetrating peptides. Biomed Pharmacother. 2018;103:982–988. doi:10.1016/j.biopha.2018.03.06829710515
  • Chen CW, Li Y, Hu S, et al. DHS (trans-4,4ʹ-dihydroxystilbene) suppresses DNA replication and tumor growth by inhibiting RRM2 (ribonucleotide reductase regulatory subunit M2). Oncogene. 2018;38(13):2364–2379.30518875
  • Fernandez-Cid A, Riera A, Tognetti S, et al. An ORC/Cdc6/MCM2-7 complex is formed in a multistep reaction to serve as a platform for MCM double-hexamer assembly. Mol Cell. 2013;50(4):577–588. doi:10.1016/j.molcel.2013.03.02623603117
  • Diaz-Trivino S, Del Mar Castellano M, de la Paz Sanchez M, Ramirez-Parra E, Desvoyes B, Gutierrez C. The genes encoding arabidopsis ORC subunits are E2F targets and the two ORC1 genes are differently expressed in proliferating and endoreplicating cells. Nucleic Acids Res. 2005;33(17):5404–5414. doi:10.1093/nar/gki85416179646
  • Asano M, Wharton RP. E2F mediates developmental and cell cycle regulation of ORC1 in Drosophila. Embo J. 1999;18(9):2435–2448. doi:10.1093/emboj/18.9.243510228158
  • Chen X, Xiong D, Ye L, et al. Up-regulated lncRNA XIST contributes to progression of cervical cancer via regulating miR-140-5p and ORC1. Cancer Cell Int. 2019;19:45. doi:10.1186/s12935-019-0744-y30858762
  • Saito A, Muro Y, Sugiura K, Ikeno M, Yoda K, Tomita Y. CENP-O, a protein localized at the centromere throughout the cell cycle, is a novel target antigen in systemic sclerosis. J Rheumatol. 2009;36(4):781–786. doi:10.3899/jrheum.08072619286853