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Small cell lung cancer (SCLC) is an aggressive, neuroendocrine malignancy that accounts for approximately 15% of lung cancers. Despite recent advances, including the approval of immunotherapy combined with chemotherapy for frontline treatment, the median overall survival for patients with extensive-stage SCLC remains approximately one year. These dismal outcomes are attributable, in part, to the lack of approved biomarkers for SCLC, which, in turn, is due to the dearth of available tissue for molecular analysis. Using transcriptomic data, we have developed a gene signature that defines four distinct molecular subtypes of SCLC – each with unique biology and therapeutic vulnerabilities. These subtypes are driven by the presence (or absence) of three transcription factors (ASCL1 – SCLC-A; NEUROD1 – SCLC-N; POU2F3 – SCLC-P; and a fourth triple-negative subtype “Inflamed” – SCLC-I) that are largely mutually exclusive. Our preliminary data suggests that inter- and intra-tumoral heterogeneity among these subtypes drives response and resistance to standard and novel therapies for SCLC, including classes such as PARP inhibitors (PARPi) and immunotherapy. We propose applying bulk and single-cell molecular approaches to assign and longitudinally monitor subtype among our established cohort of patient-derived xenograft models treated with PARPi, as well as patient tumor biopsies from an investigator-initiated trial assessing a PARPi/immunotherapy combination. Based on our preliminary data, we hypothesize that SCLC-P and SCLC-I will preferentially benefit from PARP inhibitors and immunotherapy, respectively, and that subtype shifts detectable at the single-cell level along with accompanying shifts in the composition of the immune microenvironment, will govern response and resistance.

Side effects of immune checkpoint therapies, termed immune-related adverse effects (irAEs), are unique and generally secondary to inflammatory tissue damage. The onset and duration of irAEs are unpredictable and predisposing factors for individuals to develop irAEs remains unclear. Some irAEs that emerge with immune checkpoint blockade share clinical features of autoimmune conditions. Preexisting auto-reactive antibodies and their contribution to immune side effects with immunotherapy and radiation have not been defined. This maybe particularly relevant to immune related adverse effects, since recent studies suggest almost 8-9% of the US population carries autoimmune diseases and 26% of healthy individuals have strong IgG humoral responses to variety of self-antigens. For the proposed study, we will use a set of longitudinally collected patient blood samples from a clinical trial which evaluates the clinical activity of combination immune checkpoint inhibitor therapy, nivolumab and ipilimumab with or without local consolidative therapy (stereotactic body irradiation) 

We plan to follow preexisting auto-reactive antibodies, baseline T and B cell receptor clonality and their temporal dynamics for combination immune checkpoint therapy with or without radiation therapy and correlate these findings with irAEs and response to therapy.    

An estimated 160,000 patients die each year from non-small cell lung cancer (NSCLC), primarily due to the development of metastatic and treatment-refractory disease. Dr. Byers, Dr. Gibbons, and their group have previously demonstrated that the epithelial-mesenchymal transition (EMT) is a unifying mechanism that drives tumor progression, metastasis, resistance to standard therapies, and immune suppression. Furthermore, their group and others have shown that the receptor tyrosine kinase Axl and PD-L1 are overexpressed on tumor cells in the setting of EMT in NSCLC and that targeting either Axl or PD-L1 results in preclinical efficacy in lung cancer models.

Based on these results, they have initiated the first clinical trials of BGB324 (a first-in-class, selective Axl inhibitor) for lung cancer patients in combination with either erlotinib or chemotherapy. They hypothesize that Axl is a driver of EMT and EMT-associated immune escape. Therefore, in this project they will use pre-clinical cell line and animal models to determine the role of Axl in driving EMT, identify predictive markers of response to Axl inhibition, and investigate the efficacy of combination therapy with an Axl inhibitor and an immune checkpoint inhibitor, anti-PD-L1. The biomarkers identified in their preclinical models will be directly tested in fresh tumor biopsies from their Phase 1/2 clinical trial that combines erlotinib with BGB324.

Although NSCLC is a molecularly heterogeneous disease, EMT is a potential universal mechanism of progression and drug resistance across many molecular subtypes. It is their goal to leverage this finding to develop single agent or combination treatment strategies that can be used across the molecular spectrum.

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-associated deaths worldwide. Given the limited effectiveness of current treatments, there is a significant need to identify new driver genes that participate in lung cancer pathogenesis. Dr. O’Donnell and her group identified PROTOCADHERIN 7 (PCDH7) in a functional screen for genes that promote transformation of human bronchial epithelial cells (HBECs). This is of interest because PCDH7 encodes a poorly characterized cell surface receptor that is frequently overexpressed in NSCLC and high expression strongly associates with poor survival of NSCLC patients. Moreover, the presence of PCDH7 on the cell surface highlights the potential of this molecule as a novel target for future therapeutics.

They demonstrated that 1) enforced expression of PCDH7 is sufficient to promote transformation of HBECs, 2) PCDH7 cooperates with oncogenic KRAS to promote tumorigenesis, and 3) PCDH7 potently enhances KRAS-mediated activation of the ERK1/2 pathway. They will elucidate the role of this lung cancer driver by testing the following central hypothesis: Overexpression of PCDH7 initiates a signal transduction cascade that potentiates KRAS-induced MAPK-ERK signaling to promote lung tumorigenesis. In Aim 1, they will correlate PCDH7 immunoexpression with clinical features of resected NSCLCs. In Aim 2, they will elucidate the mechanisms through which PCDH7 potentiates MAPK signaling and tumorigenesis. In Aim 3, they will develop and test the therapeutic efficacy of PCDH7 blocking antibodies in patient-derived xenografts.

These experiments will yield insights into the mechanisms of PCDH7-mediated transformation and reveal new opportunities to pursue this cell-surface receptor as a therapeutic target in NSCLC.

Inhibitors of the VEGF pathway, including the VEGF antibody bevacizumab (BV) and multitargeted VEGFR tyrosine kinase inhibitors such as vandetanib, have in some cases improved progression-free survival (PFS) and/or overall survival (OS) in patients with advanced NSCLC. While benefits in the overall NSCLC population have thus far been modest, it is clear that a subset of patients have dramatic benefit, while others may experience no benefit or even life-threatening toxicities. Furthermore, virtually all patients who respond inevitably develop therapeutic resistance. Thus, the development of markers predictive of response or resistance for VEGF inhibitors is critically needed to advance NSCLC treatment. There are currently no validated predictive markers for VEGF inhibitors, and the development of such markers is made more challenging by the impact of both tumor- and host-derived circulating factors on tumor angiogenesis. Useful predictive markers will likely need to reflect factors from both sources. We hypothesize that by comprehensively profiling angiogenesis-related CAFs and other peptides in the blood, as well as germline variations in angiogenesis-related genes, non-invasive predictive markers for identifying which patients benefit from VEGF inhibitors (alone or with chemotherapy) can be developed and validated.

The investigators of this proposal have a longstanding collaboration to develop predictive markers for VEGF inhibitors and, along with other investigators, have identified three promising and potentially complementary approaches using blood-based markers that will be tested in this grant. We have also played leadership roles in major randomized clinical trials of VEGF inhibitors, which have enabled us to leverage a unique set of resources to address these questions.

In Aim 1, we will use multiplexed CAF profiling to identify high-priority candidate predictive markers for differential benefit from VEGF inhibitors with chemotherapy compared to chemotherapy alone using two independent sets of samples from randomized phase II trials: one testing bevacizumab (BV) with chemotherapy (pemetrexed/carboplatin or Pem/C) vs. Pem/C alone (BATTLE-FL) trial, and another testing the VEGFR/EGFR tyrosine kinase inhibitor vandetanib (VAN) plus carboplatin/paclitaxel (VCP) vs. CP, in first-line NSCLC trial. We will also test CAF markers of benefit for VAN vs. standard therapy with erlotinib using specimens from a recently completed randomized phase III trial (ZEST).

In Aim 2, we will use MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectroscopy to develop a serum proteomic classifier for benefit for VEGF inhibitors, using samples from the same trials as in Aim 1. We previously used a similar approach to develop a serum proteomic marker of benefit (Veristrat) for EGFR inhibitors.

Finally, in Aim 3, we will validate a signature of SNPs from three angiogenesis-related genes that were found to be predictive of benefit for BV with CP (BCP) vs. CP in the ECOG4599 trial. This will be tested in the same three trials of VEGF inhibitors. It is worth noting that our interest is not in developing markers for a particular drug, but rather to identify markers and pathways relevant to predicting response or resistance to inhibitors of the VEGF pathway, a validated therapeutic target in NSCLC. Our data thus far suggest there will be overlap in markers for BV and VEGFR TKIs but it will be important to determine whether this is true, particularly as more potent and specific inhibitors are tested.

Impact. This project has the potential to address a critical unmet need in NSCLC by producing validated, non-invasive blood-based predictive markers for identifying patients more likely to benefit from VEGF inhibitors, and can provide critical insights into mechanisms of resistance to guide future combination regimens.