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Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

Abstract

To compare lung adenocarcinoma (ADC) and lung squamous cell carcinoma (SqCC) and to identify new drivers of lung carcinogenesis, we examined the exome sequences and copy number profiles of 660 lung ADC and 484 lung SqCC tumor–normal pairs. Recurrent alterations in lung SqCCs were more similar to those of other squamous carcinomas than to alterations in lung ADCs. New significantly mutated genes included PPP3CA, DOT1L, and FTSJD1 in lung ADC, RASA1 in lung SqCC, and KLF5, EP300, and CREBBP in both tumor types. New amplification peaks encompassed MIR21 in lung ADC, MIR205 in lung SqCC, and MAPK1 in both. Lung ADCs lacking receptor tyrosine kinase–Ras–Raf pathway alterations had mutations in SOS1, VAV1, RASA1, and ARHGAP35. Regarding neoantigens, 47% of the lung ADC and 53% of the lung SqCC tumors had at least five predicted neoepitopes. Although targeted therapies for lung ADC and SqCC are largely distinct, immunotherapies may aid in treatment for both subtypes.

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Figure 1: Distinct somatic alterations in lung ADC and lung SqCC.
Figure 2: Comparison of mutational signatures in lung cancer.
Figure 3: Significantly mutated genes in lung cancer as compared to other cancer types.
Figure 4: New significantly mutated genes in lung cancer.
Figure 5: Significant amplifications in lung cancer.
Figure 6: Fusions involving MET and NTRK2.
Figure 7: New alterations in the RTK–Rho/Ras–Raf pathway in lung ADC.
Figure 8: Neoepitope load in lung cancer.

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Acknowledgements

This work was supported by grants from the National Cancer Institute as part of The Cancer Genome Atlas project: U24CA126546, U24CA143867, U24CA143845, U24CA126544, and U24CA143883. Additionally, this work was funded by National Cancer Institute grant K08CA163677 (P.S.H.), grant 074-U01 from the government of the Russian Federation (A.A.), US Department of Defense contract W81XWH-12-1-0269 (M.M.), the American Cancer Society Research Professor Award (M.M.), and National Cancer Institute grant R35CA197568 (M.M.).

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J.D.C. performed sample quality control, mutation calling and review, ABSOLUTE analysis of tumors from the cohort of Imielinski et al., identification and comparison of recurrently altered genes, mutational signature identification and characterization, identification of EGFR complex indels, and manuscript writing. A.A., M.N.A., and R.S. generated neoantigen calls. J.K. contributed to mutational signature analyses. J.W. contributed to EGFR complex indel characterization. A.H.B. contributed to oncogene-negative analysis and manuscript preparation. C.S.P. generated the pan-lung portal. A.N.B. identified MET exon 14 skipping events using RNA-seq. X.H. and R.G.W.V. generated fusion calls. S.L. and R.A. performed batch effect analyses. G. Guo contributed to MET exon 14 complex indel identification. M.R., M.I., M.S.L., and G. Getz contributed algorithms for mutation calling and analyses. B.A.M. and A.D.C. contributed to copy number and ABSOLUTE analyses. S.A.S. and C.J.W. performed HLA genotyping. C.C. contributed to sample coordination and quality control. A.R., A.D.C., E.A.C., J.N.W., P.S.H., and D.J.K. contributed to manuscript preparation. R.G. and M.M. conceived and designed the study and wrote the manuscript.

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Correspondence to Ramaswamy Govindan or Matthew Meyerson.

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Some authors received research support from Bayer Pharmaceuticals (C.S.P., B.A.M., A.D.C., and M.M.).

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Campbell, J., Alexandrov, A., Kim, J. et al. Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Nat Genet 48, 607–616 (2016). https://doi.org/10.1038/ng.3564

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