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      Distinct initiating events underpin the immune and metabolic heterogeneity of KRAS-mutant lung adenocarcinoma

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          Abstract

          The KRAS oncoprotein, a critical driver in 33% of lung adenocarcinoma (LUAD), has remained an elusive clinical target due to its perceived undruggable nature. The identification of dependencies borne through common co-occurring mutations are sought to more effectively target KRAS-mutant lung cancer. Approximately 20% of KRAS-mutant LUAD carry loss-of-function mutations in KEAP1, a negative regulator of the antioxidant response transcription factor NFE2L2/NRF2. We demonstrate that Keap1-deficient Kras G12D lung tumors arise from a bronchiolar cell-of-origin, lacking pro-tumorigenic macrophages observed in tumors originating from alveolar cells. Keap1 loss activates the pentose phosphate pathway, inhibition of which, using 6-AN, abrogated tumor growth. These studies highlight alternative therapeutic approaches to specifically target this unique subset of KRAS-mutant LUAD cancers.

          Abstract

          Lung adenocarcinomas frequently harbour KRAS mutations, of which a subset are characterized by co-mutation of KEAP1. Here the authors show, in mice, that Kras G12D mutant tumours are metabolically distinct, with a bronchiolar cell-of-origin.

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          Most cited references36

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.

            The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics.
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              Testing significance relative to a fold-change threshold is a TREAT

              Motivation: Statistical methods are used to test for the differential expression of genes in microarray experiments. The most widely used methods successfully test whether the true differential expression is different from zero, but give no assurance that the differences found are large enough to be biologically meaningful. Results: We present a method, t-tests relative to a threshold (TREAT), that allows researchers to test formally the hypothesis (with associated p-values) that the differential expression in a microarray experiment is greater than a given (biologically meaningful) threshold. We have evaluated the method using simulated data, a dataset from a quality control experiment for microarrays and data from a biological experiment investigating histone deacetylase inhibitors. When the magnitude of differential expression is taken into account, TREAT improves upon the false discovery rate of existing methods and identifies more biologically relevant genes. Availability: R code implementing our methods is contributed to the software package limma available at http://www.bioconductor.org. Contact: smyth@wehi.edu.au
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                Author and article information

                Contributors
                sutherland.k@wehi.edu.au
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                13 September 2019
                13 September 2019
                2019
                : 10
                : 4190
                Affiliations
                [1 ]GRID grid.1042.7, Cancer Biology and Stem Cells Division, , The Walter and Eliza Hall Institute of Medical Research, ; Parkville, VIC 3052 Australia
                [2 ]ISNI 0000 0001 2179 088X, GRID grid.1008.9, Department of Medical Biology, , The University of Melbourne, ; Parkville, VIC 3052 Australia
                [3 ]GRID grid.1042.7, Epigenetics and Development Division, , The Walter and Eliza Hall Institute of Medical Research, ; Parkville, VIC 3052 Australia
                [4 ]GRID grid.430814.a, Division of Experimental Animal Pathology, , The Netherlands Cancer Institute, ; Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
                [5 ]ISNI 0000 0001 0125 2443, GRID grid.8547.e, School of Life Sciences, , Fudan University, ; Shanghai, China
                [6 ]ISNI 0000 0001 2179 088X, GRID grid.1008.9, Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, , The University of Melbourne, ; Parkville, VIC 3052 Australia
                [7 ]ISNI 0000 0001 2314 964X, GRID grid.41156.37, School of Life Sciences, , Nanjing University, ; Nanjing, 210023 China
                [8 ]GRID grid.1042.7, Inflammation Division, , The Walter and Eliza Hall Institute of Medical Research, ; Parkville, VIC 3052 Australia
                [9 ]ISNI 0000 0001 2179 088X, GRID grid.1008.9, Department of Anatomical Pathology, St Vincent’s Hospital, , The University of Melbourne, ; Fitzroy, VIC 3065 Australia
                [10 ]ISNI 0000 0001 2179 088X, GRID grid.1008.9, Department of Surgery, St Vincent’s Hospital, , The University of Melbourne, ; Fitzroy, VIC 3065 Australia
                [11 ]ISNI 0000 0001 2179 088X, GRID grid.1008.9, School of Mathematics and Statistics, , The University of Melbourne, ; Parkville, VIC 3052 Australia
                Author information
                http://orcid.org/0000-0002-4232-9432
                http://orcid.org/0000-0001-5545-3419
                http://orcid.org/0000-0002-7383-0609
                http://orcid.org/0000-0002-7453-3366
                Article
                12164
                10.1038/s41467-019-12164-y
                6744438
                31519898
                00db1013-59f2-4cc3-ba10-db407ac5a572
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 5 June 2019
                : 23 August 2019
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100000925, Department of Health | National Health and Medical Research Council (NHMRC);
                Award ID: 1138275
                Award ID: 1159002
                Award ID: 1138275
                Award ID: 1104924
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100008018, Victorian Cancer Agency (VCA);
                Award ID: 18003
                Award Recipient :
                Funded by: Peter and Julie Alston WEHI Centenary Fellowship
                Categories
                Article
                Custom metadata
                © The Author(s) 2019

                Uncategorized
                cancer metabolism,cancer microenvironment,cancer models,non-small-cell lung cancer

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