American Association for Cancer Research
00085472can171605-sup-184065_2_supp_4280429_xwkjcx.pdf (408.89 kB)

Supplementary Tables from Genomic Landscape of Atypical Adenomatous Hyperplasia Reveals Divergent Modes to Lung Adenocarcinoma

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journal contribution
posted on 2023-03-31, 01:01 authored by Smruthy Sivakumar, F. Anthony San Lucas, Tina L. McDowell, Wenhua Lang, Li Xu, Junya Fujimoto, Jianjun Zhang, P. Andrew Futreal, Junya Fukuoka, Yasushi Yatabe, Steven M. Dubinett, Avrum E. Spira, Jerry Fowler, Ernest T. Hawk, Ignacio I. Wistuba, Paul Scheet, Humam Kadara

Table S1: Samples analyzed by DNA and RNA sequencing; Table S2: DNA (n=67) and RNA (n=48) sequencing quality metrics for each sample; Table S3: Exonic mutations in known lung adenocarcinoma drivers and other cancer associated genes; Table S4: Genes mutated in atypical adenomatous hyperplasias and lung adenocarcinomas; Table S5: Validation of specific BRAF, KRAS and EGFR mutations using digital PCR; Table S6: Genes differentially expressed among normal lung tissues, atypical adenomatous hyperplasias and lung adenocarcinomas; Table S7: Genes differentially expressed between BRAF-mutant, KRAS-mutant and BRAF/KRAS wild type atypical adenomatous hyperplasias; Table S8: Markers of immune signaling that are aberrantly expressed between normal lung tissues, atypical adenomatous hyperplasias and lung adenocarcinomas.


Cancer Prevention and Research Institute of Texas




There is a dearth of knowledge about the pathogenesis of premalignant lung lesions, especially for atypical adenomatous hyperplasia (AAH), the only known precursor for the major lung cancer subtype adenocarcinoma (LUAD). In this study, we performed deep DNA and RNA sequencing analyses of a set of AAH, LUAD, and normal tissues. Somatic BRAF variants were found in AAHs from 5 of 22 (23%) patients, 4 of 5 of whom had matched LUAD with driver EGFR mutations. KRAS mutations were present in AAHs from 4 of 22 (18%) of patients. KRAS mutations in AAH were only found in ever-smokers and were exclusive to BRAF-mutant cases. Integrative analysis revealed profiles expressed in KRAS-mutant cases (UBE2C, REL) and BRAF-mutant cases (MAX) of AAH, or common to both sets of cases (suppressed AXL). Gene sets associated with suppressed antitumor (Th1; IL12A, GZMB) and elevated protumor (CCR2, CTLA-4) immune signaling were enriched in AAH development and progression. Our results reveal potentially divergent BRAF or KRAS pathways in AAH as well as immune dysregulation in the pathogenesis of this premalignant lung lesion. Cancer Res; 77(22); 6119–30. ©2017 AACR.

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