Genomic Characterization of Non-Small-Cell Lung Cancer in African Americans by Targeted Massively Parallel Sequencing

Abstract

Purpose: Technologic advances have enabled the comprehensive analysis of genetic perturbations in non-small-cell lung cancer (NSCLC); however, African Americans have often been underrepresented in these studies. This ethnic group has higher lung cancer incidence and mortality rates, and some studies have suggested a lower incidence of epidermal growth factor receptor mutations. Herein, we report the most in-depth molecular profile of NSCLC in African Americans to date.

Methods: A custom panel was designed to cover the coding regions of 81 NSCLC-related genes and 40 ancestry-informative markers. Clinical samples were sequenced on a massively parallel sequencing instrument, and anaplastic lymphoma kinase translocation was evaluated by fluorescent in situ hybridization.

Results: The study cohort included 99 patients (61% males, 94% smokers) comprising 31 squamous and 68 nonsquamous cell carcinomas. We detected 227 nonsilent variants in the coding sequence, including 24 samples with nonoverlapping, classic driver alterations. The frequency of driver mutations was not significantly different from that of whites, and no association was found between genetic ancestry and the presence of somatic mutations. Copy number alteration analysis disclosed distinguishable amplifications in the 3q chromosome arm in squamous cell carcinomas and pointed toward a handful of targetable alterations. We also found frequent SMARCA4 mutations and protein loss, mostly in driver-negative tumors.

Conclusion: Our data suggest that African American ancestry may not be significantly different from European/white background for the presence of somatic driver mutations in NSCLC. Furthermore, we demonstrated that using a comprehensive genotyping approach could identify numerous targetable alterations, with potential impact on therapeutic decisions.

Fig 1.

(A) Most frequently mutated genes in non–small-cell lung cancer (NSCLC) tumors resected from African Americans and (B) percentage according to tumor histology. Each bar represents a cancer gene as labeled in the x-axis, whereas the y-axis indicates the (A) frequency or (B) percentage of patient cases that presented a mutation in each gene. (C) Classic mutations are depicted as pie charts for NSCLC and nonsquamous patient cases. (*) P value < .05.

Fig 2.

(A) Triangular plots of the genomic proportions of African, European, and Amerindian ancestry in 99 patients self-reported as African Americans. Each point represents an individual patient. African Americans present a predominantly African genetic background, along with European admixture. Patient cases harboring canonical (B) EGFR, (C) KRAS, or (D) any driver mutation are considerably sparse within the groups (in gold), suggesting that the genetic ancestry is not associated with the presence of specific somatic mutations.

Fig 3.

(A) Candidate driver genes with higher frequency of mutations in driver-negative versus driver-positive patient cases. (B, C, and D) Ten samples (12.5%) had low SMARCA4 expression by immunohistochemistry (IHC), nine of which occurred in driver-negative patient cases. Four of these patient cases were explained by truncating mutations in SMARCA4, and two nonoverlapping patient cases had truncating mutations in ARID1A. All truncating mutations were associated with low protein expression (P < .001), whereas some missense mutations were found in samples with high expression (score 3). ATP, adenosine triphosphate; HSA, helicase/SANT-associated; QLQ, glutamine-leucine-glutamine; WT, wild type.

Fig 4.

(A) Clustering analysis of copy number alterations. The clinical samples were grouped according to histology (nonsquamous samples on the left, squamous on the right) and sorted by the presence of drivers. The blue arrows on the right side are pointing to the commonly amplified 3q and 8p chromosome arms. (B) PIK3CA, SOX2, and TP63—all in the 3q arm—are more frequently amplified in squamous than in nonsquamous tumors. (C) The segmental origin of PIK3CA, SOX2, and TP63 in the 3q arm and WHSC1L1 and FGFR1 in the 8p arm is supported by an unsupervised correlation analysis. (D) Alterations with higher frequencies in driver-negative patient cases. Amp, amplification; del, deletion.

Fig 5.

(A) Gene alterations in central pathways in non–small-cell lung cancer. Survival/proliferation pathways comprise the receptor tyrosine kinase (RTK), RAS/MAPK/ERK, phosphatidylinositol 3-kinase (PI3K), and some crosstalk with the WNT pathway. The canonical RB1 and TP53 pathways are illustrated controlling cell cycle and apoptosis. (B) Major alterations in oncogenes and cell cycle genes are shown, with a significant pattern of mutual exclusivity. CNAs, copy number alterations.