Applications of Machine Learning to Predict Cisplatin Resistance in Lung Cancer

References

• Herbst RS, Morgensztern D, Boshoff C. The biology and management of non-small cell lung cancer. Nature. 2018;553(7689):446–454. doi:10.1038/nature25183
   PubMed Web of Science ®Google Scholar
• Torre LA, Siegel RL, Ward EM, Jemal A. Global cancer incidence and mortality rates and trends–an update. Cancer Epidemiol Biomarkers Prev. 2016;25(1):16–27. doi:10.1158/1055-9965.EPI-15-0578
   PubMed Web of Science ®Google Scholar
• Scagliotti G, von Pawel J, Novello S, et al. Phase III multinational, randomized, double-blind, placebo-controlled study of tivantinib (ARQ 197) plus erlotinib versus erlotinib alone in previously treated patients with locally advanced or metastatic nonsquamous non-small-cell lung cancer. J Clin Oncol. 2015;33(24):2667. doi:10.1200/JCO.2014.60.7317
   PubMed Web of Science ®Google Scholar
• Sabari JK, Lok BH, Laird JH, Poirier JT, Rudin CM. Unravelling the biology of SCLC: implications for therapy. Nat Rev Clin Oncol. 2017;14(9):549–561. doi:10.1038/nrclinonc.2017.71
   PubMed Web of Science ®Google Scholar
• Farago AF, Keane FK. Current standards for clinical management of small cell lung cancer. Transl Lung Cancer Res. 2018;7(1):69–79. doi:10.21037/tlcr.2018.01.16
   PubMed Web of Science ®Google Scholar
• Pignon J-P, Tribodet H, Scagliotti GV, et al. Lung adjuvant cisplatin evaluation: a pooled analysis by the LACE collaborative group. J Clin Oncol. 2008;26(21):3552–3559. doi:10.1200/JCO.2007.13.9030
   PubMed Web of Science ®Google Scholar
• Strauss GM, Herndon JE, Maddaus MA, et al. Adjuvant paclitaxel plus carboplatin compared with observation in stage IB non-small-cell lung cancer: CALGB 9633 with the cancer and leukemia group B, radiation therapy oncology group, and north central cancer treatment group study groups. J Clin Oncol. 2008;26(31):5043–5051. doi:10.1200/JCO.2008.16.4855
   PubMed Web of Science ®Google Scholar
• Le Chevalier T, Arriagada R, Le Pechoux C, et al. Cisplatin-based adjuvant chemotherapy in patients with completely resected non-small-cell lung cancer. New Eng J Med. 2004;350(4):351–360.
   PubMed Web of Science ®Google Scholar
• Li G, Ma Y, Yu M, et al. Identification of hub genes and small molecule drugs associated with acquired resistance to gefitinib in non-small cell lung cancer. J Cancer. 2021;12(17):5286–5295. doi:10.7150/jca.56506
   PubMed Web of Science ®Google Scholar
• Iorio F, Knijnenburg TA, Vis DJ, et al. A landscape of pharmacogenomic interactions in cancer. Cell. 2016;166(3):740–754. doi:10.1016/j.cell.2016.06.017
   PubMed Web of Science ®Google Scholar
• Barretina J, Caponigro G, Stransky N, et al. Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2019;565(7738):E5–E6. doi:10.1038/s41586-018-0722-x
   PubMed Web of Science ®Google Scholar
• Basu A, Bodycombe NE, Cheah JH, et al. An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell. 2013;154(5):1151–1161. doi:10.1016/j.cell.2013.08.003
   PubMed Web of Science ®Google Scholar
• Dempster JM, Pacini C, Pantel S, et al. Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets. Nat Commun. 2019;10. doi:10.1038/s41467-019-13805-y
   PubMed Web of Science ®Google Scholar
• Seashore-Ludlow B, Rees MG, Cheah JH, et al. Harnessing connectivity in a large-scale small-molecule sensitivity dataset. Cancer Discov. 2015;5(11):1210–1223. doi:10.1158/2159-8290.CD-15-0235
   PubMed Web of Science ®Google Scholar
• Chabner BA. NCI-60 cell line screening: a radical departure in its time. J Natl Cancer Inst. 2016;108(5):djv388. doi:10.1093/jnci/djv388
   PubMedGoogle Scholar
• Garnett MJ, Edelman EJ, Heidorn SJ, et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature. 2012;483(7391):570–587. doi:10.1038/nature11005
   PubMed Web of Science ®Google Scholar
• Druker BJ, Guilhot F, O’Brien SG, et al. Five-year follow-up of patients receiving imatinib for chronic myeloid leukemia. New Eng J Med. 2006;355(23):2408–2417. doi:10.1056/NEJMoa062867
   PubMed Web of Science ®Google Scholar
• Chapman PB, Hauschild A, Robert C, et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. New Eng J Med. 2011;364(26):2507–2516. doi:10.1056/NEJMoa1103782
   PubMed Web of Science ®Google Scholar
• Konecny GE, Pegram MD, Venkatesan N, et al. Activity of the dual kinase inhibitor lapatinib (GW572016) against HER-2-overexpressing and trastuzumab-treated breast cancer cells. Cancer Res. 2006;66(3):1630–1639. doi:10.1158/0008-5472.CAN-05-1182
   PubMed Web of Science ®Google Scholar
• Lynch TJ, Bell DW, Sordella R, et al. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. New Eng J Med. 2004;350(21):2129–2139. doi:10.1056/NEJMoa040938
   PubMed Web of Science ®Google Scholar
• Daver N, Wei AH, Pollyea DA, Fathi AT, Vyas P, DiNardo CD. New directions for emerging therapies in acute myeloid leukemia: the next chapter. Blood Cancer J. 2020;10(10). doi:10.1038/s41408-020-00376-1
   Web of Science ®Google Scholar
• Li M, Lin A, Luo P, et al. DNAH10 mutation correlates with cisplatin sensitivity and tumor mutation burden in small-cell lung cancer. Aging. 2020;12(2):1285–1303. doi:10.18632/aging.102683
   PubMedGoogle Scholar
• Qiu Z, Lin A, Li K, et al. A novel mutation panel for predicting etoposide resistance in small-cell lung cancer. Drug Des Devel Ther. 2019;13:2021–2041. doi:10.2147/DDDT.S205633
   PubMed Web of Science ®Google Scholar
• Li R, Liu J, Fang Z, Liang Z, Chen X. Identification of mutations related to cisplatin-resistance and prognosis of patients with lung adenocarcinoma. Front Pharmacol. 2020;11:1705.
   Web of Science ®Google Scholar
• Esteva A, Robicquet A, Ramsundar B, et al. A guide to deep learning in healthcare. Nat Med. 2019;25(1):24–29. doi:10.1038/s41591-018-0316-z
   PubMed Web of Science ®Google Scholar
• Snow O, Lallous N, Ester M, Cherkasov A. Deep learning modeling of androgen receptor responses to prostate cancer therapies. Int J Mol Sci. 2020;21(16):5847. doi:10.3390/ijms21165847
   PubMed Web of Science ®Google Scholar
• Steiner MC, Gibson KM, Crandall KA. Drug resistance prediction using deep learning techniques on HIV-1 sequence data. Viruses. 2020;12(5):560. doi:10.3390/v12050560
   PubMed Web of Science ®Google Scholar
• Kong J, Lee H, Kim D, et al. Network-based machine learning in colorectal and bladder organoid models predicts anti-cancer drug efficacy in patients. Nat Commun. 2020;11(1). doi:10.1038/s41467-020-19313-8
   Web of Science ®Google Scholar
• Sabuncuoglu I, Bayiz M. Job shop scheduling with beam search. Eur J Oper Res. 1999;118(2):390–412. doi:10.1016/S0377-2217(98)00319-1
   Web of Science ®Google Scholar
• Hsu CW, Lin CJ. A comparison of methods for multiclass support vector machines. IEEE Trans Neural Netw. 2002;13(2):415–425. doi:10.1109/72.991427
   PubMed Web of Science ®Google Scholar
• Xu R, Wunsch D. Survey of clustering algorithms. IEEE Trans Neural Netw. 2005;16(3):645–678. doi:10.1109/TNN.2005.845141
   PubMed Web of Science ®Google Scholar
• Higgs RE, Knierman MD, Freeman AB, Gelbert LM, Patil ST, Hale JE. Estimating the statistical significance of peptide identifications from shotgun proteomics experiments. J Proteome Res. 2007;6(5):1758–1767. doi:10.1021/pr0605320
   PubMed Web of Science ®Google Scholar
• Pedregosa F, Varoquaux G, Gramfort A, et al. Scikit-learn: machine learning in python. J Mach Learn Res. 2011;12:2825–2830.
   Web of Science ®Google Scholar
• Chalmers ZR, Connelly CF, Fabrizio D, et al. Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden. Genome Med. 2017;9. doi:10.1186/s13073-017-0424-2
   Web of Science ®Google Scholar
• Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016;32(18):2847–2849. doi:10.1093/bioinformatics/btw313
   PubMed Web of Science ®Google Scholar
• Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545–15550. doi:10.1073/pnas.0506580102
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47–e47. doi:10.1093/nar/gkv007
   PubMed Web of Science ®Google Scholar
• Yu G, Wang L-G, Han Y, He Q-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287. doi:10.1089/omi.2011.0118
   PubMed Web of Science ®Google Scholar
• Supsrisunjai C, Hsu C-K, Michael M, et al. Coagulation factor XIII-A subunit missense mutation in the pathobiology of autosomal dominant multiple dermatofibromas. J Invest Dermatol. 2020;140(3):624. doi:10.1016/j.jid.2019.08.441
   PubMed Web of Science ®Google Scholar
• Balakrishnan A, Penachioni JY, Lamba S, et al. Molecular profiling of the “plexinome” in melanoma and pancreatic cancer. Hum Mutat. 2009;30(8):1167–1174. doi:10.1002/humu.21017
   PubMed Web of Science ®Google Scholar
• Yang L, Zhao J, Lu WQ, et al. KIAA0649, a 1A6/DRIM-interacting protein with the oncogenic potential. Biochem Biophys Res Commun. 2005;334(3):884–890. doi:10.1016/j.bbrc.2005.06.179
   PubMed Web of Science ®Google Scholar
• Sun J, Wang C, Zhang Y, et al. Genomic signatures reveal DNA damage response deficiency in colorectal cancer brain metastases. Nat Commun. 2019;10. doi:10.1038/s41467-019-10987-3
   Web of Science ®Google Scholar
• Wu M, Sun Q, Mo CH, et al. Prospective molecular mechanism of COL5A1 in breast cancer based on a microarray, RNA sequencing and immunohistochemistry. Oncol Rep. 2019;42(1):151–175.
   PubMed Web of Science ®Google Scholar
• Liu W, Wei H, Gao Z, et al. COL5A1 may contribute the metastasis of lung adenocarcinoma. Gene. 2018;665:57–66. doi:10.1016/j.gene.2018.04.066
   PubMed Web of Science ®Google Scholar
• Kelland L. The resurgence of platinum-based cancer chemotherapy. Nat Rev Cancer. 2007;7(8):573–584. doi:10.1038/nrc2167
   PubMed Web of Science ®Google Scholar
• Park S, Lee H, Lee B, et al. DNA damage response and repair pathway alteration and its association with tumor mutation burden and platinum-based chemotherapy in SCLC. J Thorac Oncol. 2019;14(9):1640–1650. doi:10.1016/j.jtho.2019.05.014
   PubMed Web of Science ®Google Scholar
• Plimack ER, Dunbrack RL, Brennan TA, et al. Defects in DNA repair genes predict response to neoadjuvant cisplatin-based chemotherapy in muscle-invasive bladder cancer. Eur Urol. 2015;68(6):959–967. doi:10.1016/j.eururo.2015.07.009
   PubMed Web of Science ®Google Scholar
• Teo MY, Bambury RM, Zabor EC, et al. DNA damage response and repair gene alterations are associated with improved survival in patients with platinum-treated advanced urothelial carcinoma. Clin Cancer Res. 2017;23(14):3610–3618. doi:10.1158/1078-0432.CCR-16-2520
   PubMed Web of Science ®Google Scholar
• Fink D, Aebi S, Howell SB. The role of DNA mismatch repair in drug resistance. Clin Cancer Res. 1998;4(1):1–6.
   PubMed Web of Science ®Google Scholar
• Stewart DJ. Mechanisms of resistance to cisplatin and carboplatin. Crit Rev Oncol Hematol. 2007;63(1):12–31.
   PubMed Web of Science ®Google Scholar
• Wu YL, Lu S, Cheng Y, et al. Nivolumab versus docetaxel in a predominantly Chinese patient population with previously treated advanced NSCLC: checkMate 078 randomized phase III clinical trial. J Thorac Oncol. 2019;14(5):867–875. doi:10.1016/j.jtho.2019.01.006
   PubMed Web of Science ®Google Scholar
• Paul MR, Pan TC, Pant DK, et al. Genomic landscape of metastatic breast cancer identifies preferentially dysregulated pathways and targets. J Clin Invest. 2020;130(8):4252–4265.
   PubMed Web of Science ®Google Scholar
• Li X, Wu WK, Xing R, et al. Distinct subtypes of gastric cancer defined by molecular characterization include novel mutational signatures with prognostic capability. Cancer Res. 2016;76(7):1724–1732. doi:10.1158/0008-5472.CAN-15-2443
   PubMed Web of Science ®Google Scholar
• Rottenberg S, Disler C, Perego P. The rediscovery of platinum-based cancer therapy. Nat Rev Cancer. 2021;21(1):37–50. doi:10.1038/s41568-020-00308-y
   PubMed Web of Science ®Google Scholar
• Perez RP. Cellular and molecular determinants of cisplatin resistance. Eur J Cancer. 1998;34(10):1535–1542. doi:10.1016/S0959-8049(98)00227-5
   PubMed Web of Science ®Google Scholar