Driver gene alterations profiling of Chinese non-small cell lung cancer and the effects of co-occurring alterations on immunotherapy

Prognosis of early-stage lung adenocarcinoma in young patients

Lung adenocarcinoma (LUAD) is a familiar lung cancer with a poor prognosis. This study was meant to determine whether there are differences in survival between younger and older patients with early-stage LUAD because of the rise in the incidence of LUAD in young individuals over the previous few decades. We analysed the clinical, therapeutic and prognostic features of a cohort (2012-2013) of 831 consecutive patients with stage I/II LUAD who underwent curative surgical resection at Shanghai Pulmonary Hospital. Propensity score matching (PSM) was performed for age, sex, tumour size, tumour stage and therapy in a 2:1 ratio between the two groups without taking gender, illness stage at operation or decisive treatment into account. Following PSM analysis to create a 2:1 match for comparison, the final survival study included 163 patients with early-stage LUAD <50 years and 326 patients ≥50 years. Surprisingly, younger patients were overwhelmingly female (65.6%) and never smokers (85.9%). There were no statistical differences between the two groups in terms of the overall survival rate (P = 0.067) or time to advancement (P = 0.76). In conclusion, no significant differences stood out between older and younger patients with stage I/II LUAD regarding overall and disease-free survival rates. Younger patients with early-stage LUAD were more likely to be female and never smokers, which suggests that risk factors other than active smoking may be responsible for lung carcinogenesis in these patients.

Synchronous driver gene alterations (EGFR L858R, T790M, and ROS1) rearrangements in a patient with early-stage lung adenocarcinoma

Concurrent EGFR mutation and ROS1 rearrangement is a rare event in early-stage non-small-cell lung cancer. In addition, a co-occurring de novo EGFR T790M mutation in such a case is extremely rare. We encountered a 72-year-old woman who developed 3 early-stage lung lesions synchronously, one each harboring EGFR L858R, ROS1 rearrangement, and EGFR L858R and de novo T790M. These three nodules were pathologically time-matched lepidic predominant adenocarcinoma with small invasive lesions, which may reflect the concept of field cancerization with driver mutations.

Analytical and clinical validation of a custom 15-gene next-generation sequencing panel for the evaluation of circulating tumor DNA mutations in patients with advanced non-small-cell lung cancer

BACKGROUND

This is a pilot proof-of-concept study to evaluate the utility of a custom 15-gene circulating tumor DNA (ctDNA) panel as a potential companion molecular next-generation sequencing (NGS) assay for identifying somatic single nucleotide variants and indels in non-small-cell lung cancer (NSCLC) patients. The custom panel covers the hotspot mutations in EGFR, KRAS, NRAS, BRAF, PIK3CA, ERBB2, MET, KIT, PDGFRA, ALK, ROS1, RET, NTRK1, NTRK2 and NTRK3 genes which serve as biomarkers for guiding treatment decisions in NSCLC patients.

METHOD

The custom 15-gene ctDNA NGS panel was designed using ArcherDX Assay Designer. A total of 20 ng or 50 ng input ctDNA was used to construct the libraries. The analytical performance was evaluated using reference standards at different allellic frequencies (0.1%, 1%, 5% and parental). The clinical performance was evaluated using plasma samples collected from 10 treatment naïve advanced stage III or IV NSCLC patients who were tested for tissue EGFR mutations. The bioinformatics analysis was performed using the proprietary Archer Analysis Software.

RESULTS

For the analytical validation, we achieved 100% sensitivity and specificity for the detection of known mutations in the reference standards. The limit of detection was 1% allelic frequency. Clinical validation showed that the clinical sensitivity and specificity of the assay for detecting EGFR mutation were 83.3% and 100% respectively. In addition, the NGS panel also detected other mutations of uncertain significance in 6 out of 10 patients.

CONCLUSION

This preliminary analysis showed that the custom 15-gene ctDNA NGS panel demonstrated good analytical and clinical performances for the EGFR mutation. Further studies incorporating the validation of other candidate gene mutations are warranted.

Driver gene alterations profiling of Chinese non-small cell lung cancer and the effects of co-occurring alterations on immunotherapy

Background

Molecular testing for alterations in oncogenic driver genes and targeted therapies have become standard procedures for non‐small cell lung cancer (NSCLC) patients. However, little evidence has shed light on the pattern of co‐existence of driver genes in NSCLC, and whether they may have different tumor features affecting immunotherapy is still unclarified.

Methods

Genomic alterations in 14 lung cancer‐related genes were conducted in 3440 Chinese NSCLC patients using next‐generation sequencing. Meanwhile, tumor mutational burden and immunotherapy dataset from the Memorial sloan kettering cancer center (MSKCC) and lung adenocarcinoma dataset from The Cancer Genome Atlas (TCGA) were utilized for analyzing the impact of the co‐occurring alterations on patients’ survival following immunotherapy.

Results

In this cohort, 90.17% of patients had at least one somatic alteration in the 14 genes, including 51% of co‐occurring alterations. TP53 and epidermal growth factor receptor (EGFR) were the most prevalent genes (54.74% and 53.55%, respectively), followed by KRAS, ERBB2, ALK, PIK3CA, ROS1, RET, MET, BRAF, KIT, FGFR1, PDGFRA, and NRAS. The prevalence of TP53, EGFR, and ERBB2 in our cohort were significantly higher than that from the TCGA database, whereas KRAS, BRAF, and PDGFRA were significantly lower than the latter. Furthermore, the patients who harbored multiple alterations (8.86%, 31/350) in eight driver genes survived longer and have a higher tumor mutation burden compared to the patients with a single alteration. Similar result was found between the patients with co‐occurring alteration of EGFR and other driver genes and the patients with single EGFR alteration. Meanwhile, we found a distinct immune cell infiltration feature between patients with single and multiple driver gene alterations, as well as between patients with only EGFR alteration and co‐occurring groups.

Conclusion

This study identified a unique driver gene feature and found patients harboring co‐occurring alterations of EGFR and other driver genes may benefit from immunotherapy, which may provide more therapeutic selections for EGFR‐mutated NSCLC patients and merit additional investigation.