A New Pathway Emerges to Interpret Lung Cancer Genomic Alterations

In this issue of Clinical Cancer Research, Zhou and colleagues (1) analyzed targeted next-generation sequencing data (MSK-IMPACT) from 492 surgically resected early stage lung adenocarcinoma samples and correlated their findings with the clinical outcome of disease-free survival (DFS). Rather than focusing on specific genetic alterations, the authors used a pathway-centric approach that they previously defined by analysis of The Cancer Genome Atlas (2) to identify mutation patterns that fit within 10 canonical cancer-related pathways, including: (i) cell cycle, (ii) Hippo, (iii) Myc, (iv) Notch, (v) oxidative stress response/Nrf2, (vi) PI3K, (vii) receptor-tyrosine kinase (RTK)/RAS/MAPK, (viii) TGFβ, (ix) p53, and (x) β-catenin/Wnt. For each tumor they calculated the number of pathways altered (NPA), the tumor mutation burden (TMB), and the fraction of the genome altered (FGA). They found that the NPA correlated with DFS in a multivariate analysis, and that cell cycle, Hippo, TGFβ, and p53 pathway alterations in particular were associated with increased risk of disease recurrence.

Next-generation sequencing through the use of targeted exome panels is a mainstay of clinical testing for advanced lung adenocarcinomas and is critical for the identification of targetable oncogenic driver mutations. The development of EGFR inhibitors in the early 2000s led to the discovery of activating mutations within EGFR as an important predictor of response to EGFR tyrosine kinase inhibitors (TKI), ushering in the era of tumor genetic testing for lung cancer. The success of EGFR testing as a predictive biomarker of response to EGFR TKI treatment led to a hunt for other tumor genetic alterations that may similarly predict targeted therapy responses or identify targets for drug development. This led to a relative explosion of targetable oncogenic alterations in lung adenocarcinoma, including: ALK, ROS1, RET, and NTRK rearrangements, as well as somatic variants in BRAF, MET, and now KRAS. The multitude of targetable oncogenic drivers in lung adenocarcinoma has led to single-gene assays becoming relatively obsolete, with a significant portion of tumor genetic testing now being performed by next-generation sequencing panels. These next-generation sequencing panels typically cover the coding regions of dozens if not hundreds of cancer-related genes, well-beyond the current known targetable alterations. To this point, the importance of nontargetable, so-called “passenger” alterations as predictive or prognostic biomarkers is unknown. New studies are beginning to shed light on the role of these cooccurring genomic alterations.

The clinical significance of cooccurring genomic alterations in 10 cancer-related pathways was assessed in early-stage lung cancer (1). Intriguingly, they found that the NPA present in a tumor was independently associated with DFS, and that alterations in cell cycle, Hippo, TGFβ, and p53 pathways in particular were associated with early relapse of lung adenocarcinoma, suggesting potential avenues for pharmacologic intervention. Notably, the frequency of alterations in known oncogenic drivers, including KRAS, EGFR, and ALK was similar to what would be expected for advanced lung adenocarcinoma, suggesting that genomic alterations identified in early-stage lung cancers are likely to be relevant to patients with advanced disease. In addition, 84% of tumors analyzed harbored genomic alterations in the RAS/RTK pathway confirming that the vast majority of lung adenocarcinomas are driven by oncogenic activation of the RAS/MAPK signaling pathway. Clinically, these alterations can be addressed by many of the targeted therapies that have been developed and have shown clear benefit for patients. However, as the benefits of these therapies are transient and not curative, their utility in early-stage disease is still unproven. Understanding the biological and clinical significance of secondary pathway alterations is critical to devising new strategies to combat both early and advanced stage lung adenocarcinoma.

Many of the pathways associated with decreased DFS in early-stage lung adenocarcinoma have also been shown to correlate with poor response to targeted therapies in advanced stage disease. Genetic alterations in cell-cycle genes correlated with poor response to the third-generation EGFR inhibitor, osimertinib, in a study of cell-free DNA from over 1,000 advanced EGFR-mutant lung cancer cases (3). Whether cell-cycle alterations similarly affect response to other TKIs is unknown, as is the mechanism underlying this effect. The study by Zhou and colleagues, suggests that cell-cycle alterations may promote increased genomic instability and copy-number alterations, which may in turn account for poor DFS in early-stage lung cancer and TKI resistance in advanced stage disease. Whether cell-cycle alterations are the cause of genomic instability, or simply a marker for it, is unclear and further investigation is needed.

Cell-cycle pathway alterations frequently cooccurred with p53 pathway alterations, which were also correlated with decreased DFS in patients with resected lung adenocarcinomas. Both cell-cycle and p53 pathway alterations were associated with an increase in the FGA, which itself correlates with poor DFS in this study (1). This serves as a confirmation of the findings from TRACERx, which showed that elevated copy-number heterogeneity was associated with increased risk of non–small cell lung cancer recurrence or death (4). Lung adenocarcinomas that harbor both cell-cycle and p53 pathway alterations appear to be at high risk for genomic instability, which in turn may promote early recurrence for patients with early-stage disease or resistance to targeted therapy for patients with advanced disease (5).

Genetic alterations in the Hippo and TGFβ pathway were also associated with inferior DFS. Hippo signals primarily through its effectors Yes-Activated Protein and TAZ, whose activities have been implicated in resistance to EGFR- and BRAF-targeted therapies (6) as well in promoting immune evasion through upregulation of Programmed Death-Ligand 1 (PD-L1; ref. 7). Intriguingly, tumors with genetic alterations in the Hippo pathway were also associated with higher TMB (1). Given that PD-L1 expression and TMB have both been shown to be independent predictors of response to immune checkpoint inhibitor (ICI) therapy, these findings suggest that tumors with Hippo pathway alterations may be more likely to respond to ICI and less likely to respond to targeted therapies.

The role of tumor genomics in informing clinical decisions for the treatment of lung adenocarcinomas has evolved from single-gene assays to multi-gene panels and now to broad next-generation sequencing panels that include upwards of several hundred genes. While the primary goal of these assays is to identify single targetable oncogenes in the RTK/RAS pathway, the study by Zhou and colleagues demonstrates that additional prognostic and potentially predictive information may be gleaned by analyzing NPA, FGA, and TMB, as well as which specific pathways are altered (Fig. 1). Clinical trials should be considered to determine whether patients with early-stage lung cancer with elevated NPA or FGA may be more likely to benefit from adjuvant therapy, and whether those with elevated TMB and/or Hippo pathway alterations are more likely to benefit from treatment that includes an ICI. Similarly, clinical trials should be considered for patients with advanced lung adenocarcinomas with a targetable oncogenic driver mutation to determine whether there is clinical benefit to combination therapies that target cooccurring cell cycle (CDK4/6 inhibitor) and/or p53 (MDM2 inhibitor) pathway alterations.

C.M. Blakely is a paid consultant for Revolution Medicines and reports receiving commercial research grants from AstraZeneca, Novartis, Mirati, Spectrum, MedImmune, Roche, and Takeda. No other potential conflicts of interest were disclosed.

C.M. Blakely receives funding from the Damon Runyon Cancer Research Foundation, the Doris Duke Charitable Foundation, and the V Foundation.