Differential Gene Expression Common to Acquired and Intrinsic Resistance to BRAF Inhibitor Revealed by RNA-Seq Analysis |
Ahn, Jun-Ho
(System Toxicology Research Center, Korea Institute of Toxicology)
Hwang, Sung-Hee (Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University) Cho, Hyun-Soo (Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology) Lee, Michael (Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University) |
1 | van Duin, M., Broyl, A., de Knegt, Y., Goldschmidt, H., Richardson, P. G., Hop, W. C., van der Holt, B., Joseph-Pietras, D., Mulligan, G., Neuwirth, R., Sahota, S. S. and Sonneveld, P. (2011) Cancer testis antigens in newly diagnosed and relapse multiple myeloma: prognostic markers and potential targets for immunotherapy. Haematologica 96, 1662-1669. DOI |
2 | Verfaillie, A., Imrichova, H., Atak, Z. K., Dewaele, M., Rambow, F., Hulselmans, G., Christiaens, V., Svetlichnyy, D., Luciani, F., Van den Mooter, L., Claerhout, S., Fiers, M., Journe, F., Ghanem, G. E., Herrmann, C., Halder, G., Marine, J. C. and Aerts, S. (2015) Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state. Nat. Commun. 6, 6683. DOI |
3 | Villanueva, J., Vultur, A., Lee, J. T., Somasundaram, R., Fukunaga-Kalabis, M., Cipolla, A. K., Wubbenhorst, B., Xu, X., Gimotty, P. A., Kee, D., Santiago-Walker, A. E., Letrero, R., D’Andrea, K., Pushparajan, A., Hayden, J. E., Brown, K. D., Laquerre, S., McArthur, G. A., Sosman, J. A., Nathanson, K. L. and Herlyn, M. (2010) Acquired resistance to BRAF inhibitors mediated by a RAF kinase switch in melanoma can be overcome by cotargeting MEK and IGF-1R/PI3K. Cancer Cell 18, 683-695. DOI |
4 | Zhang, C., Spevak, W., Zhang, Y., Burton, E. A., Ma, Y., Habets, G., Zhang, J., Lin, J., Ewing, T., Matusow, B., Tsang, G., Marimuthu, A., Cho, H., Wu, G., Wang, W., Fong, D., Nguyen, H., Shi, S., Womack, P., Nespi, M., Shellooe, R., Carias, H., Powell, B., Light, E., Sanftner, L., Walters, J., Tsai, J., West, B. L., Visor, G., Rezaei, H., Lin, P. S., Nolop, K., Ibrahim, P. N., Hirth, P. and Bollag, G. (2015) RAF inhibitors that evade paradoxical MAPK pathway activation. Nature 526, 583-586. DOI |
5 | Ahn, J. H., Han, B. I. and Lee, M. (2015) Induction of resistance to BRAF inhibitor is associated with the inability of Spry2 to inhibit BRAF-V600E activity in BRAF mutant cells. Biomol. Ther. (Seoul) 23, 320-326. DOI |
6 | Agianian, B. and Gavathiotis, E. (2018) Current insights of BRAF inhibitors in cancer. J. Med. Chem. 61, 5775-5793. DOI |
7 | Ahn, J.-H. and Lee, M. (2013) Autophagy-dependent survival of mutant B-Raf melanoma cells selected for resistance to apoptosis induced by inhibitors against oncogenic B-Raf. Biomol. Ther. (Seoul) 21, 114-120. DOI |
8 | Ahn, J. H., Eum, K. H. and Lee, M. (2009) The enhancement of Raf-1 kinase activity by knockdown of Spry2 is associated with high sensitivity to paclitaxel in v-Ha-ras-transformed NIH 3T3 fibroblasts. Mol. Cell. Biochem. 332, 189-197. DOI |
9 | Arozarena, I. and Wellbrock, C. (2017) Overcoming resistance to BRAF inhibitors. Ann. Transl. Med. 5, 387. DOI |
10 | Ji, Z., Erin Chen, Y., Kumar, R., Taylor, M., Jenny Njauw, C. N., Miao, B., Frederick, D. T., Wargo, J. A., Flaherty, K. T., Jonsson, G. and Tsao, H. (2015) MITF Modulates Therapeutic Resistance through EGFR Signaling. J. Invest. Dermatol. 135, 1863-1872. DOI |
11 | Johannessen, C. M., Boehm, J. S., Kim, S. Y., Thomas, S. R., Wardwell, L., Johnson, L. A., Emery, C. M., Stransky, N., Cogdill, A. P., Barretina, J., Caponigro, G., Hieronymus, H., Murray, R. R., Salehi-Ashtiani, K., Hill, D. E., Vidal, M., Zhao, J. J., Yang, X., Alkan, O., Kim, S., Harris, J. L., Wilson, C. J., Myer, V. E., Finan, P. M., Root, D. E., Roberts, T. M., Golub, T., Flaherty, K. T., Dummer, R., Weber, B. L., Sellers, W. R., Schlegel, R., Wargo, J. A., Hahn, W. C. and Garraway, L. A. (2010) COT drives resistance to RAF inhibition through MAP kinase pathway reactivation. Nature 468, 968-972. DOI |
12 | Kim, J. H., Ahn, J. H. and Lee, M. (2017) Upregulation of microRNA-1246 is associated with BRAF inhibitor resistance in melanoma cells with mutant BRAF. Cancer Res. Treat. 49, 947-959. DOI |
13 | Kim, Y. K., Ahn, S. K. and Lee, M. (2012) Differential sensitivity of melanoma cell lines with differing B-Raf mutational status to the new oncogenic B-Raf kinase inhibitor UI-152. Cancer Lett. 320, 215-224. DOI |
14 | Martin, J. A. and Wang, Z. (2011) Next-generation transcriptome assembly. Nat. Rev. Genet. 12, 671-682. DOI |
15 | 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. and Sherlock, G. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29. |
16 | Bindea, G., Mlecnik, B., Hackl, H., Charoentong, P., Tosolini, M., Kirilovsky, A., Fridman, W. H., Pages, F., Trajanoski, Z. and Galon, J. (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25, 1091-1093. DOI |
17 | Konieczkowski, D. J., Johannessen, C. M., Abudayyeh, O., Kim, J. W., Cooper, Z. A., Piris, A., Frederick, D. T., Barzily-Rokni, M., Straussman, R., Haq, R., Fisher, D. E., Mesirov, J. P., Hahn, W. C., Flaherty, K. T., Wargo, J. A., Tamayo, P. and Garraway, L. A.. (2014) A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors. Cancer Discov. 4, 816-827. DOI |
18 | Lu, H., Tran, L., Park, Y., Chen, I., Lan, J., Xie, Y. and Semenza, G. L. (2018) Reciprocal regulation of DUSP9 and DUSP16 expression by HIF-1 controls ERK and p38 MAP kinase activity and mediates chemotherapy-induced breast cancer stem cell enrichment. Cancer Res. 78, 4191-4202. DOI |
19 | Bollag, G., Hirth, P., Tsai, J., Zhang, J., Ibrahim, P. N., Cho, H., Spevak, W., Zhang, C., Zhang, Y., Habets, G., Burton, E. A., Wong, B., Tsang, G., West, B. L., Powell, B., Shellooe, R., Marimuthu, A., Nguyen, H., Zhang, K. Y., Artis, D. R., Schlessinger, J., Su, F., Higgins, B., Iyer, R., D’Andrea, K., Koehler, A., Stumm, M., Lin, P. S., Lee, R. J., Grippo, J., Puzanov, I., Kim, K. B., Ribas, A., McArthur, G. A., Sosman, J. A., Chapman, P. B., Flaherty, K. T., Xu, X., Nathanson, K. L. and Nolop, K. (2010) Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma. Nature 467, 596-599. DOI |
20 | Cancer Genome Atlas Network. (2015) Genomic classification of cutaneous melanoma. Cell 161, 1681-1696. DOI |
21 | Pattani, K. M., Soudry, E., Glazer, C. A., Ochs, M. F., Wang, H., Schussel, J., Sun, W., Hennessey, P., Mydlarz, W., Loyo, M., Demokan, S., Smith, I. M. and Califano, J. A. (2012) MAGEB2 is activated by promoter demethylation in head and neck squamous cell carcinoma. PLoS ONE 7, e45534. DOI |
22 | Rapino, F., Delaunay, S., Rambow, F., Zhou, Z., Tharun, L., De Tullio, P., Sin, O., Shostak, K., Schmitz, S., Piepers, J., Ghesquiere, B., Karim, L., Charloteaux, B., Jamart, D., Florin, A., Lambert, C., Rorive, A., Jerusalem, G., Leucci, E., Dewaele, M., Vooijs, M., Leidel, S. A., Georges, M., Voz, M., Peers, B., Buttner, R., Marine, J. C., Chariot, A. and Close, P. (2018) Codon-specific translation reprogramming promotes resistance to targeted therapy. Nature 558, 605-609. DOI |
23 | Rizos, H., Menzies, A. M., Pupo, G. M., Carlino, M. S., Fung, C., Hyman, J., Haydu, L. E., Mijatov, B., Becker, T. M., Boyd, S. C., Howle, J., Saw, R., Thompson, J. F., Kefford, R. F., Scolyer, R. A. and Long, G. V. (2014) BRAF inhibitor resistance mechanisms in metastatic melanoma: spectrum and clinical impact. Clin. Cancer Res. 20, 1965-1977. DOI |
24 | Halaban, R., Zhang, W., Bacchiocchi, A., Cheng, E., Parisi, F., Ariyan, S., Krauthammer, M., McCusker, J. P., Kluger, Y. and Sznol, M. (2010) PLX4032, a selective BRAF(V600E) kinase inhibitor, activates the ERK pathway and enhances cell migration and proliferation of BRAF melanoma cells. Pigment Cell Melanoma Res. 23, 190-200. DOI |
25 | Davies, H., Bignell, G., Cox, C., Stephens, P., Edkins, S., Clegg, S., Teague, J., Woffendin, H., Garnett, M. J., Bottomley, W., Davis, N., Dicks, E., Ewing, R., Floyd, Y., Gray, K., Hall, S., Hawes, R., Hughes, J., Kosmidou, V., Menzies, A., Mould, C., Parker, A., Stevens, C., Watt, S., Hooper, S., Wilson, R., Jayatilake, H., Gusterson, B. A., Cooper, C., Shipley, J., Hargrave, D., Pritchard-Jones, K., Maitland, N., Chenevix-Trench, G., Riggins, G. J., Bigner, D. D., Palmieri, G., Cossu, A., Flanagan, A., Nicholson, A., Ho, J. W., Leung, S. Y., Yuen, S. T., Weber, B. L., Seigler, H. F., Darrow, T. L., Paterson, H., Marais, R., Marshall, C. J., Wooster, R., Stratton, M. R. and Futreal, P. A. (2002) Mutations of the BRAF gene in human cancer. Nature 417, 949-954. DOI |
26 | Dobbelstein, M. and Moll, U. (2014) Targeting tumour-supportive cellular machineries in anticancer drug development. Nat. Rev. Drug Discov. 13, 179-196. DOI |
27 | Flaherty, K. T., Puzanov, I., Kim, K. B., Ribas, A., McArthur, G. A., Sosman, J. A., O'Dwyer, P. J., Lee, R. J., Grippo, J. F., Nolop, K. and Chapman, P. B. (2010) Inhibition of mutated, activated BRAF in metastatic melanoma. N. Engl. J. Med. 363, 809-819. DOI |
28 | Shi, H., Hugo, W., Kong, X., Hong, A., Koya, R. C., Moriceau, G., Chodon, T., Guo, R., Johnson, D. B., Dahlman, K. B., Kelley, M. C., Kefford, R. F., Chmielowski, B., Glaspy, J. A., Sosman, J. A., van Baren, N., Long, G. V., Ribas, A. and Lo, R. S. (2014) Acquired resistance and clonal evolution in melanoma during BRAF inhibitor therapy. Cancer Discov. 4, 80-93. DOI |
29 | Tripathi, S. C., Fahrmann, J. F., Celiktas, M., Aguilar, M., Marini, K. D., Jolly, M. K., Katayama, H., Wang, H., Murage, E. N., Dennison, J. B., Watkins, D. N., Levine, H., Ostrin, E. J., Taguchi, A. and Hanash, S. M. (2017) MCAM mediates chemoresistance in small-cell lung cancer via the PI3K/AKT/SOX2 signaling pathway. Cancer Res. 77, 4414-4425. DOI |
30 | Hacohen, N., Kramer, S., Sutherland, D., Hiromi, Y. and Krasnow, M. A. (1998) sprouty encodes a novel antagonist of FGF signaling that patterns apical branching of the Drosophila airways. Cell 92, 253-263. DOI |
31 | Hatzivassiliou, G., Song, K., Yen, I., Brandhuber, B. J., Anderson, D. J., Alvarado, R., Ludlam, M. J., Stokoe, D., Gloor, S. L., Vigers, G., Morales, T., Aliagas, I., Liu, B., Sideris, S., Hoeflich, K. P., Jaiswal, B. S., Seshagiri, S., Koeppen, H., Belvin, M., Friedman, L.S. and Malek, S. (2010) RAF inhibitors prime wild-type RAF to activate the MAPK pathway and enhance growth. Nature 464, 431-435. DOI |
32 | Heidorn, S. J., Milagre, C., Whittaker, S., Nourry, A., Niculescu-Duvas, I., Dhomen, N., Hussain, J., Reis-Filho, J. S., Springer, C. J., Pritchard, C. and Marais, R. (2010) Kinase-dead BRAF and oncogenic RAS cooperate to drive tumor progression through CRAF. Cell 140, 209-221. DOI |
33 | Holderfield, M., Deuker, M. M., McCormick, F. and McMahon, M. (2014) Targeting RAF kinases for cancer therapy: BRAF-mutated melanoma and beyond. Nat. Rev. Cancer 14, 455-467. DOI |
34 | Huang, D. W., Sherman, B. T. and Lempicki, R. A. (2009a) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1-13. DOI |
35 | Huang, D. W., Sherman, B. T. and Lempicki, R. A. (2009b) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57. DOI |