Silent mutations reveal therapeutic vulnerability in RAS Q61 cancers
Ostrem, JM, Peters, U., Sos, ML, Wells, JA & Shokat, KM K-Ras (G12C) inhibitors allosterically control GTP affinity and effector interactions. Nature 503548–551 (2013).
Canon, J. et al. Clinical KRAS Inhibitor (G12C) AMG 510 stimulates anti-tumor immunity. Nature 575217-223 (2019).
Hallin, J. et al. The KRAS (G12C) inhibitor MRTX849 provides insight into the therapeutic sensitivity of KRAS mutant cancers in mouse models and patients. Discovery of cancer. ten54–71 (2020).
Middleton, G. et al. The National Lung Matrix Trial of personalized therapy in lung cancer. Nature 583807–812 (2020).
Zehir, A. et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat. Med. 23703–713 (2017).
Ramalingam, SS et al. Overall survival with osimertinib in untreated advanced EGFR-mutated NSCLC. N.Engl. J.Med. 38241–50 (2020).
Diederichs, S. et al. The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non-coding RNA and synonymous mutations. EMBO Mol. Med. 8442–457 (2016).
Group, PTC et al. Genomic basis of RNA alterations in cancer. Nature 578129-136 (2020).
Consortium, APG AACR GENIE project: propelling precision medicine through an international consortium. Discovery of cancer. 7818–831 (2017).
Jane, PA et al. Selumetinib plus docetaxel versus docetaxel alone and progression-free survival in patients with kras-advanced mutant non-small cell lung cancer: the SELECT-1 randomized clinical trial. JAMA 3171844–1853 (2017).
Kitai, H. et al. The epithelial-mesenchymal transition defines the feedback activation of receptor tyrosine kinase signaling induced by MEK inhibition in kras– mutant lung cancer. Discovery of cancer. 6754–769 (2016).
Kruspig, B. et al. The ERBB network facilitates KRAS-induced lung tumorigenesis. Science. Transl. Med. teneaao2565 (2018).
Mol, HP et al. Afatinib limits K-RAS-induced lung tumorigenesis. Science. Transl. Med. teneaao2301 (2018).
LaMarche, MJ et al. Identification of TNO155, an allosteric inhibitor of SHP2 for the treatment of cancer. J.Med. Chem. 6313578–13594 (2020).
Hong, DS et al. KRAS (G12C) inhibition with sotorasib in advanced solid tumors. N.Engl. J.Med. 3831207-1217 (2020).
Hunter, JC et al. Biochemical and structural analysis of common KRAS mutations associated with cancer. Mol. Cancer Res. 131325-1335 (2015).
Zhou, ZW et al. KRASQ61H signals preferentially via MAPK in an RAF dimer-dependent manner in non-small cell lung cancer. Cancer Res. 803719–3731 (2020).
Oxnard, GR et al. Evaluation of resistance mechanisms and clinical implications in patients with EGFR T790M positive lung cancer and acquired resistance to osimertinib. JAMA Oncol. 41527-1534 (2018).
Ramalingam, SS et al. Mechanisms of acquired resistance to first-line osimertinib: preliminary data from the phase III FLAURA study. Ann. Oncol 29VIII740 (2018).
Reinert, T. et al. Analysis of plasma cell-free DNA by ultra-deep sequencing in patients with stage I to III colorectal cancer. JAMA Oncol. 51124-1131 (2019).
Chabon, JJ et al. Integration of genomic features for the non-invasive early detection of lung cancer. Nature 580245-251 (2020).
Amendola, CR et al. KRAS4A directly regulates hexokinase 1. Nature 576482–486 (2019).
Cartegni, L., Chew, SL & Krainer, AR Listening to Silence and Understanding Nonsense: Exon Mutations that Affect Splicing. Nat. Reverend Genet. 3285-298 (2002).
Desmet, FO et al. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res. 37e67 (2009).
McVety, S., Li, L., Gordon, PH, Chong, G. & Foulkes, WD Disruption of an exon splicing enhancer in exon 3 of MLH1 is the cause of HNPCC in a Quebec family . J.Med. Broom. 43153-156 (2006).
Khvorova, A. & Watts, JK The chemical evolution of clinically useful oligonucleotide therapies. Nat. Biotechnol. 35238-248 (2017).
Kim, J. et al. Personalized oligonucleotide therapy for a rare genetic disease. N.Engl. J.Med. 3811644-1652 (2019).
Janes, MR et al. Targeting KRAS mutant cancers with a specific covalent G12C inhibitor. Cell 172578–589.e517 (2018).
Brant, R. et al. Clinically viable gene expression assays with potential for predicting the benefits of MEK inhibitors. Clin. Cancer Res. 231471-1480 (2017).
Chang, MT et al. The identification of recurrent mutations in cancer reveals great lineage diversity and mutational specificity. Nat. Biotechnol. 34155-163 (2016).
Zammarchi, F. et al. Antitumorigenic potential of STAT3 alternative splicing modulation. proc. Natl Acad. Science. United States 10817779–17784 (2011).
Ross, SJ et al. Targeting krasdependent with AZD4785, a therapeutic high affinity antisense oligonucleotide inhibitor of kras. Science. Transl. Med. 9eaal5253 (2017).
Amodio, V. et al. Blocking EGFR restores KRAS resistanceG12C inhibition in colorectal cancer. Discovery of cancer. ten1129-1139 (2020).
Klein, AF et al. Peptide-conjugated oligonucleotides evoke long-lasting correction of myotonic dystrophy in patient-derived cells and mice. J. Clin. Invest. 1294739–4744 (2019).
Boisguerin, P. et al. Administration of therapeutic oligonucleotides with cell-penetrating peptides. Adv. Deliver. Tower. 8752–67 (2015).
Imbert, M., Dias-Florencio, G. & Goyenvalle, A. Viral vector-mediated antisense therapy for genetic diseases. Genoa 851 (2017).
Sharma, Y. et al. A pan-cancer analysis of synonymous mutations. Nat. Common. ten2569 (2019).
Cartegni, L., Wang, J., Zhu, Z., Zhang, MQ & Krainer, AR ESEfinder: A web resource for identifying exonic splicing activators. Nucleic Acids Res. 313568-3571 (2003).
Smith, PJ et al. An increased specificity score matrix for the prediction of SF2/ASF-specific exon splicing activators. Hmm. Mol. Broom. 152490-2508 (2006).
Fairbrother, WG et al. RESCUE-ESE identifies candidate exon splicing activators in vertebrate exons. Nucleic Acids Res. 32W187–W190 (2004).
Zhang, XH & Chasin, LA Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev. 181241–1250 (2004).
Hori, S.-i et al. California2+ the enrichment in culture medium potentiates the effect of the oligonucleotides. Nucleic Acids Res. 43e128 (2015).
Garcia, EP et al. Validation of OncoPanel: a next-generation targeted sequencing assay for the detection of somatic variants in cancer. Camber. Pathol. Laboratory. Med. 141751–758 (2017).
Odegaard, JI et al. Validation of a comprehensive plasma-based cancer genotyping test using orthogonal tissue and plasma-based methodologies. Clin. Cancer Res. 243539–3549 (2018).