Multi-omics “upstream analysis” of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer

EuPA Open Proteomics - Tập 13 - Trang 1-13 - 2016
Alexander E. Kel1,2,3, Philip Stegmaier3, Tagir Valeev2,4, Jeannette Koschmann3, Vladimir Poroikov5, Olga V. Kel-Margoulis3, Edgar Wingender3,6
1Institute of Chemical Biology and Fundamental Medicine, SBRAS, Novosibirsk, Russia
2Biosoft.ru, Ltd, Novosibirsk, Russia
3GeneXplain GmbH, D-38302 Wolfenbüttel, Germany
4A.P. Ershov Institute of Informatics Systems SB RAS, Novosibirsk, Russia
5Institute of Biomedical Chemistry, Moscow, Russia
6Institute of Bioinformatics, University Medical Center Göttingen, D-37077 Göttingen, Germany

Tài liệu tham khảo

Osborn, 1958, Inhibition of dihydrofolic reductase by aminopterin and amethopterin, Proc. Soc. Exp. Blot. Med., 97, 429, 10.3181/00379727-97-23764 Morales, 2005, Genetic determinants of methotrexate responsiveness and resistance in colon cancer cells, Oncogene, 24, 6842, 10.1038/sj.onc.1208834 De Anta, 2002, Unmasking the mechanisms of colon cancer cell resistance to methotrexate: cell drug sensitivity is dependent on a transiently adaptive mechanism, Gastroentérologie Clinique et Biologique, 26, 399 Fischer, 2015, Epithelial-to-mesenchymal transition is not required for lung metastasis but contributes to chemoresistance, Nature, 527, 472, 10.1038/nature15748 Kolesnikov, 2015, ArrayExpress update—simplifying data submissions, Nucleic Acids Res., 43, D1113, 10.1093/nar/gku1057 Barrett, 2013, NCBI GEO. archive for functional genomics data sets–update, Nucleic Acids Res., 41, D991, 10.1093/nar/gks1193 Petryszak, 2014, Expression atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments, Nucleic Acids Res., 42, D926, 10.1093/nar/gkt1270 Smith, 2014, The mouse gene expression database (GXD): 2014 update, Nucleic Acids Res., 42, D818, 10.1093/nar/gkt954 Subramanian, 2005, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc. Natl. Acad. Sci. U. S. A., 102, 15545, 10.1073/pnas.0506580102 Kanehisa, 2012, KEGG for integration and interpretation of large-scale molecular data sets, Nucleic Acids Res., 40, D109, 10.1093/nar/gkr988 Kel, 2006, Beyond microarrays: find key transcription factors controlling signal transduction pathways, BMC Bioinf., 7, S13, 10.1186/1471-2105-7-S2-S13 Michael, 2008, Building a knowledge base for systems pathology, Brief. Bioinform., 9, 518, 10.1093/bib/bbn038 Stegmaier, 2011, Advanced computational biology methods identify molecular switches for malignancy in an EGF mouse model of liver cancer, PLoS One, 6, e17738, 10.1371/journal.pone.0017738 Wingender, 2008, The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation, Brief. Bioinform., 9, 326, 10.1093/bib/bbn016 Kel, 2003, MATCH: a tool for searching transcription factor binding sites in DNA sequences, Nucleic Acids Res., 31, 3576, 10.1093/nar/gkg585 Waleev, 2006, Composite module analyst: identification of transcription factor binding site combinations using genetic algorithm, Nucleic Acids Res., 34, W541, 10.1093/nar/gkl342 Krull, 2006, TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations, Nucleic Acids Res., 34, D546, 10.1093/nar/gkj107 Koschmann, 2015, Upstream analysis: an integrated promoter-pathway analysis approach to causal interpretation of microarray data, Microarrays, 4, 270, 10.3390/microarrays4020270 2010 Tropsha, 2010, QSAR in drug discovery, 151, 10.1017/CBO9780511730412.012 Filimonov, 1999, Chemical similarity assessment through multilevel neighborhoods of atoms: definition and comparison with the other descriptors, J. Chem. Inf. Comput. Sci, 39, 666, 10.1021/ci980335o Filimonov, 2008, 182 Demo workflows. Available online: http://www.genexplain.com/demo-workflows. Selga, 2008, Role of caveolin 1, E-cadherin, Enolase 2 and PKCalpha on resistance to methotrexate in human HT29 colon cancer cells, BMC Med. Genomics, 1, 35, 10.1186/1755-8794-1-35 Smyth, 2005, Limma: linear models for microarray data, 397 McMahon, 2012, Characterization of changes in the proteome in different regions of 3D multicell tumor spheroids, J. Proteome Res., 11, 2863, 10.1021/pr2012472 Allen, 2015, The Mediator complex: a central integrator of transcription, Nat. Rev. Mol. Cell Biol., 16, 155, 10.1038/nrm3951 Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25 Zhang, 2008, Model-based analysis of chIP-Seq (MACS), Genome Biol., 9, R137, 10.1186/gb-2008-9-9-r137 Filimonov, 2008, 182 Stegmaier, 2011, Advanced computational biology methods identify molecular switches for malignancy in an EGF mouse model of liver cancer, PLoS One, 6, e17738, 10.1371/journal.pone.0017738 Viemann, 2004, Transcriptional profiling of IKK2/NF-kappa B- and p38 MAP kinase-dependent gene expression in TNF-alpha-stimulated primary human endothelial cells, Blood, 103, 3365, 10.1182/blood-2003-09-3296 Schimke, 1978, Gene amplification and drug resistance in cultured murine cells, Science, 202, 1051, 10.1126/science.715457 Bertino, 1996, Resistance mechanisms to methotrexate in Tumors, Oncologist, 1, 223, 10.1634/theoncologist.1-4-223 Good, 1996, Regulation of dihydrofolate reductase gene expression and E2F components in human diploid fibroblasts during growth and senescence, J. Cell. Physiol., 168, 580, 10.1002/(SICI)1097-4652(199609)168:3<580::AID-JCP10>3.0.CO;2-3 Lin, 1996, Cell cycle-regulated association of E2F1 and Sp1 is related to their functional interaction, Mol. Cell. Biol., 16, 1668, 10.1128/MCB.16.4.1668 Kel-Margoulis, 2002, TRANSCompel: a database on composite regulatory elements in eukaryotic genes, Nucleic Acids Res., 30, 332, 10.1093/nar/30.1.332 Marra, 1998, Mismatch repair deficiency associated with overexpression of the MSH3 gene, Proc. Natl. Acad. Sci. U. S. A., 95, 8568, 10.1073/pnas.95.15.8568 Allen, 2015, The Mediator complex: a central integrator of transcription, Nat. Rev. Mol. Cell Biol., 16, 155, 10.1038/nrm3951 Firestein, 2008, CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity, Nature, 455, 547, 10.1038/nature07179 Zwang, 2012, Consistency test of the cell cycle: roles for p53 and EGR1, Cancer Res., 72, 1051, 10.1158/0008-5472.CAN-11-3382 El-Karim, 2013, Krüppel-like factor 4 regulates genetic stability in mouse embryonic fibroblasts, Mol. Cancer, 10.1186/1476-4598-12-89 Chen, 2002, Discordant protein and mrna expression in lung adenocarcinomas, Mol. Cell. Proteomics, 1, 304, 10.1074/mcp.M200008-MCP200 Goldhoff, 2008, Targeted inhibition of cyclic AMP phosphodiesterase-4 promotes brain tumor regression, Clin. Cancer Res., 14, 7717, 10.1158/1078-0432.CCR-08-0827 Valabrega, 2005, TGFalpha expression impairs trastuzumab-induced HER2 downregulation, Oncogene, 24, 3002, 10.1038/sj.onc.1208478 Mostovich, 2011, Integrin alpha9 (ITGA9) expression and epigenetic silencing in human breast tumors, Cell Adh. Migr., 5, 395, 10.4161/cam.5.5.17949 Hatakeyama, 2009, Effect of insulin-like growth factor 1 receptor inhibitor on sensitization of head and neck cancer cells to cetuximab and methotrexate, J. Clin. Oncol., 10.1200/jco.2009.27.15_suppl.6079 Bug, 2005, Clinical trial of valproic acid and all-trans retinoic acid in patients with poor-risk acute myeloid leukemia, Cancer, 104, 2717, 10.1002/cncr.21589 Coronel, 2011, A double-blind, placebo-controlled, randomized phase III trial of chemotherapy plus epigenetic therapy with hydralazine valproate for advanced cervical cancer. Preliminary results, Med. Oncol., 28, S540, 10.1007/s12032-010-9700-3 Munster, 2009, Clinical and biological effects of valproic acid as a histone deacetylase inhibitor on tumor and surrogate tissues: phase I/II trial of valproic acid and epirubicin/FEC, Clin. Cancer Res., 15, 2488, 10.1158/1078-0432.CCR-08-1930 Sun, 2014, Phosphodiesterase 3/4 inhibitor zardaverine exhibits potent and selective antitumor activity against hepatocellular carcinoma both in vitro and in vivo independently of phosphodiesterase inhibition, PLoS One, 9, e90627, 10.1371/journal.pone.0090627 Moon, 2002, Inhibition of PDE3B augments PDE4 inhibitor-induced apoptosis in a subset of patients with chronic lymphocytic leukemia, Clin. Cancer Res., 8, 589 Horsman, 1987, Radiosensitisation by nicotinamide in vivo: a greater enhancement of tumor damage compared to that of normal tissues, Radiat. Res., 109, 479, 10.2307/3577048 Kjellen, 1991, A therapeutic benefit from combining normobaric carbogen or oxygen with nicotinamide in fractionated X-ray treatments, Radiother. Oncol., 22, 81, 10.1016/0167-8140(91)90002-X A. Kel, Master regulators and transcriptiption factor binding sites found by upstream analysis of multi-omics data on methotrexate resistance of colon cancer. Data in Brief. submitted.