Stage III

RET fusions occur in 2-3% cases of lung cancer and there are currently two FDA-approved RET-specific inhibitors, selpercatinib and pralsetinib, for the treatment of patients with RET fusion positive lung or thyroid cancers. Therapeutic resistance eventually emerges, however, and studies have shown that RET-dependent mechanisms of resistance include acquired resistance mutations that alter drug binding. Further, RET fusions and mutations are heterogeneous and the impact of specific fusion partners and RET variants on drug sensitivity is poorly understood. In a recent publication in Nature, our group reported that for a related driver oncogene, EGFR, both primary and acquired resistance mutations can be classified into distinct structural groups that correlate with drug sensitivity and resistance. This structure-function based classification has important advantages 1) structure-based groups predicted drug response significantly better than standard exon-based approaches, 2) this classification enabled us to match drugs for more than ~99% of atypical mutations where currently less than 50% of mutations have an FDA approved drug. In addition, preliminary preclinical and clinical data suggests that two RET-independent mechanisms of resistance- signal bypass and lineage shift-may also drive resistance even in the presence of effective RET inhibition. Applying methodologies we established for elucidating EGFR inhibitor resistance, we will develop a structure-function based classification which can immediately impact clinical decisions for selecting therapies; comprehensively characterize RET-dependent and -independent mechanisms of resistance and biomarkers to assess them; and develop rational therapeutic strategies to overcome resistance which can guide patient selection for future clinical studies.

On-/off-target resistance mechanisms to RET tyrosine kinase inhibition (TKI) are not identified in ~40% of patients with RET fusion-positive lung cancers. As such, focusing solely on genomic alterations (e.g. mutation/amplification) limits our ability to develop novel therapies for all patients. This project addresses the unmet need of identifying and characterizing alternate resistance mechanisms to selective RET TKI therapy via epigenetic mechanisms leading to altered programs of gene expression. As with other oncogene-TKI pairs, we hypothesize that epigenetic re-programming and lineage plasticity drives resistance to RET TKIs. Serial pre- and post-TKI tumor samples will be interrogated (DEG/GSEA analysis) via complementary methylome (EPIC) and transcriptomic (RNAseq) profiling. Pathologic review and immunohistochemical profiling for markers of squamous (p40, CK5/6), small cell (chromogranin, synaptophysin), and epithelial-mesenchymal (E/N-cadherin, vimentin) transformation will be performed. Candidate resistance pathways will be explored in engineered isogenic overexpression/knockout models and our institutional library of xenografts generated from patients treated with a selective RET TKI on a registrational program or standard of care. Genetic manipulation of targets that we and others have associated with licensing lineage plasticity (e.g. myrAKT, MYC, EZH2, and beta-catenin) in RET fusion-positive models to induce histologic transformation will be performed. These analyses will define strategies to constrain or abrogate therapeutic resistance.

Background: Patients with NSCLC whose tumors harbor a targetable molecular alteration have improved outcomes when they receive targeted therapy. Historically, targetable alterations have been associated with specific patient characteristics such as female gender, young age, non-smokers, and Asians. Given this association, patients with characteristics not commonly associated with targetable mutations do not always receive timely and complete molecular testing. We hypothesize that male gender, age >65, history of smoking, African American race and Hispanic ethnicity will be independently associated with delayed detection and treatment of a targetable alteration. We will evaluate the impact of delayed targeted therapy on overall survival and brain metastasis development.

Methods: We will perform a retrospective cohort study of approximately 2200 patients with EGFR, ALK or ROS1 targetable alterations obtained through multi-institution retrospective chart review. Multivariate logistic regression will be used to evaluate the association of patient characteristics with complete molecular testing prior to first-line therapy, targeted therapy as first-line therapy, and development of brain metastases. Kaplan-Meier methodology will be used to estimate median overall survival. The log rank test will be used to compare median overall survivals. Multivariate Cox Regression will further evaluate interactions between delayed targeted therapy and patient characteristics as well as help control for potential confounders.

Importance: This will be the first study to evaluate the impact of delayed detection and delayed treatment of driver mutations in NSCLC. This information is critical to designing interventions to improve outcomes in patient groups with characteristics not usually associated with driver mutations.

Veterans have significantly greater rates of lung cancer and mortality as compared to civilians. In our prior work, these disparities are partly due to lack of receipt of evidence-based cancer care especially among patients with complex comorbidities, psychosocial concerns, and limited social support, characteristics common among Veteran populations. The overall goal of this research is to overcome structural barriers to ensure delivery of evidence-based lung cancer care among Veterans. In our prior work we identified workforce shortages along with complex psychosocial factors and medical conditions that prevent Veterans from fully engaging in their care. We used community-based participatory research and expert panel methods to develop Engagement of Patients with Advanced Cancer (EPAC) – an intervention that integrates community health workers into care.1 In our randomized trial, EPAC improved evidence-based end-of-life care, Veteran satisfaction and reduced acute care use and total healthcare costs. In this study, with our established Advisory Board comprised of Veterans, caregivers, oncology clinicians, and VA leaders, we will refine EPAC to incorporate evidence-based lung cancer care (Aim 1). We will randomize 60 Veterans newly diagnosed with advanced lung cancer to establish feasibility of the refined EPAC intervention (primary outcome) and secondarily, the effects on evidence-based lung cancer care and Veteran activation (Aim 2). The results will inform a multisite randomized study in the VA.

Immune checkpoint inhibitors have revolutionized the care of patients with metastatic non-small cell lung cancer (NSCLC). Unfortunately, not all patients benefit from this therapy, and rational combinatorial strategies to enhance immune checkpoint inhibitors (ICI) efficacy in therapy non-responders are needed. We and others have shown that patients with liver metastases derive limited clinical benefit from ICI across a wide variety of disease types. In preclinical models, we discovered that liver metastases cause anti-PD-L1 resistance by siphoning tumor-specific T cells from systemic circulation. Within the liver, activated antigen-specific CD8+ T cells undergo apoptosis. Consequently, liver metastases create a systemic immune desert in preclinical models. Similarly, patients with liver metastases have reduced peripheral T cell numbers and diminished tumoral T cell diversity and function. In preclinical models, liver-directed radiotherapy eliminates immunosuppressive hepatic macrophages, increases hepatic T cell survival, and reduces hepatic siphoning of T cells. The central hypothesis of this proposal is that liver SBRT can enhance CPP therapy non-responders in NSCLC patients with liver metastases. In Aim 1, we will conduct a Phase IB clinical trial establishing the feasibility of delivering multi-target liver SBRT following the first cycle of carboplatin, pembrolizumab, and pemetrexed (CPP) in metastatic NSCLC patients with liver metastases. Up to four liver metastases will be targeted. In Aim 2, we will determine whether liver SBRT combined with ipilimumab and nivolumab modulates the hepatic and systemic immune microenvironment in NSCLC patients with liver metastases. The completion of these aims will assess the feasibility of ablating liver metastases with SBRT in combination with chemoimmunotherapy and deepen our understanding of the contribution of hepatic immune tolerance mechanisms in patients. The ultimate goal of this work is to test rationally-developed combinatorial treatment approaches in hopes of improving the care of NSCLC patients.

Activating mutations in KRAS are found in 20 to 40% of lung cancers and not infrequently in combination with additional alterations in genes such as tumor suppressor TP53 or STK11. How activating KRAS mutations and/or co-mutations affect gene expression in both tumor cells and the cells in the surrounding microenvironment is not known. The impact, if any, of these mutations on intra-tumoral heterogeneity in gene expression is not known. Applying single cell RNA sequencing to resected lung adenocarcinoma samples from US Veterans, I will examine and compare the gene expression profiles of tumor cells from lung adenocarcinomas harboring either mutant and wild-type KRAS, and the expression profiles of cells in the surrounding microenvironment, including tumor infiltrating lymphocytes. In addition, I will determine whether KRAS mutational status affects the degree of intra-tumoral heterogeneity in gene expression, a known factor in survival and resistance to treatment. In sum, we hope to identify specific pathways affected by KRAS in both tumor and surrounding non-tumor cells that could be hypothesis-generating and learn use this knowledge to understand how resistance to KRAS specific therapies might be facilitated by pre-existing intra-tumoral heterogeneity.

Lung cancer is the leading cause of cancer-related death in the United States and worldwide. Immune checkpoint inhibitors (ICIs) have shown durable responses and improved survival in some patients with advanced non-small cell lung cancer (NSCLC). However, nearly all patients eventually progress on these therapies, and the median survival for patients with metastatic NSCLC remains around one year. Combining immunotherapy with cytotoxic chemotherapy has shown an incremental benefit but at the cost of increased toxicity. Patients who progress on currently available immunotherapies have few effective treatment options. One significant barrier to ICI therapy efficacy is the tumor microenvironment (TME), which contains immunosuppressive cells including myeloid-derived suppressor cells (MDSCs). MDSCs represent an important tumor immune escape mechanism and play a role in the development and progression of lung cancer. Higher levels of MDSCs in the blood are associated with shorter overall survival in patients with NSCLC, and MDSCs are associated with resistance to immune checkpoint inhibitor (ICI) therapy. However, there is significant variation in methods of measurement of MDSCs including 1) the classification of the most common phenotypes, namely CD15+ polymorphonuclear MDSC (PMN-MDSC) and CD14+ monocytic MDSC (M-MDSC), and 2) the functional assessment of MDSCs. There are also significant differences in MDSC function and phenotype in animal models and in patients with cancer. We propose to investigate the role of MDSCs in tumor immune escape, and to target the immunosuppressive impact of MDSCs to improve outcomes of patients with NSCLC treated with ICI. Utilizing mass cytometry and in vitro co-culture assays, we will evaluate MDSC levels and function as well as immune cell subset changes in patients receiving standard of care immunotherapy to identify the cell populations that drive immune responses and resistance. We will then conduct a phase 1b clinical trial of all-trans retinoic acid (ATRA) combined with atezolizumab to test whether this treatment can improve responses and overcome ICI resistance in patients with NSCLC who have progressed on standard therapies. We hypothesize that a decrease in the frequency and immunosuppressive function of circulating MDSCs will be associated with increased clinical benefit in patients with NSCLC, and that modulation of MDSCs through the use of ATRA given in combination with ICIs will be safe, tolerable, and exhibit preliminary efficacy in overcoming resistance to available ICIs. The proposed studies include the first trial of this novel treatment in patients with lung cancer and will examine the potential for targeting MDSCs to overcome resistance and enhance the efficacy of immunotherapy. If successful, these studies may lead to an increased number of patients with advanced NSCLC experiencing durable responses and improved survival.