Characterization of Squamous Cell Lung Cancers from Appalachian Kentucky

Abstract

Background: Lung cancer is the leading cause of cancer mortality in the United States (U.S.). Squamous cell carcinoma (SQCC) represents 22.6% of all lung cancers nationally, and 26.4% in Appalachian Kentucky (AppKY), where death from lung cancer is exceptionally high. The Cancer Genome Atlas (TCGA) characterized genetic alterations in lung SQCC, but this cohort did not focus on AppKY residents.

Methods: Whole-exome sequencing was performed on tumor and normal DNA samples from 51 lung SQCC subjects from AppKY. Somatic genomic alterations were compared between the AppKY and TCGA SQCC cohorts.

Results: From this AppKY cohort, we identified an average of 237 nonsilent mutations per patient and, in comparison with TCGA, we found that PCMTD1 (18%) and IDH1 (12%) were more commonly altered in AppKY versus TCGA. Using IDH1 as a starting point, we identified a mutually exclusive mutational pattern (IDH1, KDM6A, KDM4E, JMJD1C) involving functionally related genes. We also found actionable mutations (10%) and/or intermediate or high-tumor mutation burden (65%), indicating potential therapeutic targets in 65% of subjects.

Conclusions: This study has identified an increased percentage of IDH1 and PCMTD1 mutations in SQCC arising in the AppKY residents versus TCGA, with population-specific implications for the personalized treatment of this disease.

Impact: Our study is the first report to characterize genomic alterations in lung SQCC from AppKY. These findings suggest population differences in the genetics of lung SQCC between AppKY and U.S. populations, highlighting the importance of the relevant population when developing personalized treatment approaches for this disease.

Figure 1.. Significantly mutated genes in lung SQCC.

Significantly mutated genes (FDR<0.2) from whole-exome sequencing of 51 samples from Appalachian Kentucky patients. The number and percentage of samples with mutations in each gene are shown on the left. Samples are displayed as columns, with the overall number of mutations, smoking status, and tumor stage plotted at the top.

Figure 2.. Functional analysis of IDH1 variants.

(A) Segments of multiple sequence alignment for representative IDH1 (upper set) and IDH2 (lower set) orthologs, showing conservation of Arg132, Val178, Ala207, and Leu352. Numbers are provided for a human IDH1 protein. A complete alignment and sequence accession numbers are shown in Supplementary Fig. S7. Positions 132, 178, 307, and 352 are marked and highlighted in yellow, whereas substitutions in these positions are highlighted in blue. For all other positions, residues that are identical to those in the human IDH1 are highlighted in gray. Human, Homo sapiens; Frog, Xenopus tropicalis; Fish, Takifugu rubripes; Nematode, Caenorhabditis elegans, Worm, Saccoglossus kowalevskii; Lancelet, Branchiostoma floridae. (B) Effect of IDH1 variants on enzyme activity. Left: effect of R132H and A307S mutants; Right: effect of V178A and L352P mutants. The two-sample t-test was performed to compare each IDH1 mutant versus the wild type and the Bonferroni correction was used for multiple comparison adjustment. • Statistically significant reductions of NADPH production comparing IDH1 R132H versus wild type; ♦Statistically significant reductions of NADPH production comparing IDH1 L352P versus wild type.

Figure 3.. IDH1 mutations and IDH1 associated pathway analysis.

Variant IDH1 may produce the oncometabolite 2HG that inhibits 2OG-dependent dioxygenases; the 2OG-dependent dioxygenases are highly sensitive to inhibition by 2HG. Mutations in IDH1 and 2OG dependent enzymes are mutually exclusive. The number and percentage of samples with mutations in each gene are shown on the left. Samples are displayed as columns.