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Bioinformatic exploration of MTA1-regulated gene networks in colon cancer |
Chunxiao Li1,Haijuan Wang1,Feng Lin1,Hui Li1,Tao Wen2,Haili Qian1,*(),Qimin Zhan1 |
1. Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, State Key Laboratory of Molecular Oncology, Beijing 100021, China 2. Beijing Chao-Yang Hospital, Capital Medical University, Medical Research Center, Beijing 100020, China |
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Abstract Metastasis-associated gene 1 (MTA1) controls a series of biological processes in tumor progression. Tumor progression is a complex process regulated by a gene network. The global cancer gene regulatory network must be analyzed to determine the position of MTA1 in the molecular network and its cooperative genes by further exploring the biological functions of this gene. We used TCGA data sets and GeneCards database to screen MTA1-related genes. GO and KEGG pathway analyses were conducted with DAVID and gene network analysis via STRING and Cytoscape. Results showed that in the development of colon cancer, MTA1 is linked to certain signal pathways, such as Wnt/Notch/nucleotide excision repair pathways. The findings also suggested that MTA1 demonstrates the closest relationship in a coregulation process with the key molecules AKT1, EP300, CREBBP, SMARCA4, RHOA, and CAD. These results lead MTA1 exploration to an in-depth investigation in different directions, such as Wnt, Notch, and DNA repair.
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Keywords
metastasis-associated gene 1
colon cancer
bioinformatics
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Corresponding Author(s):
Haili Qian
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Just Accepted Date: 17 March 2016
Online First Date: 06 April 2016
Issue Date: 27 May 2016
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1 |
Toh Y, Pencil SD, Nicolson GL. A novel candidate metastasis-associated gene, mta1, differentially expressed in highly metastatic mammary adenocarcinoma cell lines. cDNA cloning, expression, and protein analyses. J Biol Chem 1994; 269(37): 22958–22963
pmid: 8083195
|
2 |
Nicolson GL, Nawa A, Toh Y, Taniguchi S, Nishimori K, Moustafa A. Tumor metastasis-associated human MTA1 gene and its MTA1 protein product: role in epithelial cancer cell invasion, proliferation and nuclear regulation. Clin Exp Metastasis 2003; 20(1): 19–24
https://doi.org/10.1023/A:1022534217769
pmid: 12650603
|
3 |
Toh Y, Oki E, Oda S, Tokunaga E, Ohno S, Maehara Y, Nicolson GL, Sugimachi K. Overexpression of the MTA1 gene in gastrointestinal carcinomas: correlation with invasion and metastasis. Int J Cancer 1997; 74(4): 459–463
https://doi.org/10.1002/(SICI)1097-0215(19970822)74:4<459::AID-IJC18>3.0.CO;2-4
pmid: 9291440
|
4 |
Ghanta KS, Li DQ, Eswaran J, Kumar R. Gene profiling of MTA1 identifies novel gene targets and functions. PLoS ONE 2011; 6(2): e17135
https://doi.org/10.1371/journal.pone.0017135
pmid: 21364872
|
5 |
Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012; 487(7407): 330–337
https://doi.org/10.1038/nature11252
pmid: 22810696
|
6 |
Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, Cerami E, Sander C, Schultz N. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal 2013; 6(269): pl1
https://doi.org/10.1126/scisignal.2004088
pmid: 23550210
|
7 |
Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov 2012; 2(5): 401–404
https://doi.org/10.1158/2159-8290.CD-12-0095
pmid: 22588877
|
8 |
Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D. GeneCards: integrating information about genes, proteins and diseases. Trends Genet 1997; 13(4): 163
https://doi.org/10.1016/S0168-9525(97)01103-7
pmid: 9097728
|
9 |
Huang W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009; 37(1): 1–13
https://doi.org/10.1093/nar/gkn923
pmid: 19033363
|
10 |
Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009; 4(1): 44–57
https://doi.org/10.1038/nprot.2008.211
pmid: 19131956
|
11 |
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 2015; 43(Database issue): D447–D452
https://doi.org/10.1093/nar/gku1003
pmid: 25352553
|
12 |
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003; 13(11): 2498–2504
https://doi.org/10.1101/gr.1239303
pmid: 14597658
|
13 |
Li DQ, Pakala SB, Nair SS, Eswaran J, Kumar R. Metastasis-associated protein 1/nucleosome remodeling and histone deacetylase complex in cancer. Cancer Res 2012; 72(2): 387–394
https://doi.org/10.1158/0008-5472.CAN-11-2345
pmid: 22253283
|
14 |
Liu J, Wang H, Ma F, Xu D, Chang Y, Zhang J, Wang J, Zhao M, Lin C, Huang C, Qian H, Zhan Q. MTA1 regulates higher-order chromatin structure and histone H1-chromatin interaction in-vivo. Mol Oncol 2015; 9(1): 218–235
https://doi.org/10.1016/j.molonc.2014.08.007
pmid: 25205035
|
15 |
Dhar S, Kumar A, Li K, Tzivion G, Levenson AS. Resveratrol regulates PTEN/Akt pathway through inhibition of MTA1/HDAC unit of the NuRD complex in prostate cancer. Biochim Biophys Acta 2015; 1853(2): 265–275
https://doi.org/10.1016/j.bbamcr.2014.11.004
pmid: 25447541
|
16 |
Ohshiro K, Rayala SK, Wigerup C, Pakala SB, Natha RS, Gururaj AE, Molli PR, Månsson SS, Ramezani A, Hawley RG, Landberg G, Lee NH, Kumar R. Acetylation-dependent oncogenic activity of metastasis-associated protein 1 co-regulator. EMBO Rep 2010; 11(9): 691–697
https://doi.org/10.1038/embor.2010.99
pmid: 20651739
|
17 |
Nagaraj SR, Shilpa P, Rachaiah K, Salimath BP. Crosstalk between VEGF and MTA1 signaling pathways contribute to aggressiveness of breast carcinoma. Mol Carcinog 2015; 54(5): 333–350
https://doi.org/10.1002/mc.22104
pmid: 24265228
|
18 |
Yang YM, Liu H, Li WB. Expression of Mta-1 and VEGF and their correlation in the endometrial cancer. Chin J Cell Mol Immunol (Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi) 2010; 26(7): 682–684 (in Chinese)
|
19 |
Esteller M.Epigenetic changes in cancer. F1000 Biol Rep 2011;3:9<DOI OutputMedium="All">1<?Pub Caret1?>0.3410/B3-9</DOI>
pmid: 21655338
|
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