Immune checkpoint inhibitors

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.

This project describes a 3-year training program for a career as a physician-scientist with the long term goal of establishing a research program within the field of translational thoracic oncology. The applicant is currently an Instructor of Medicine in the Section of Interventional Pulmonology and Thoracic oncology conducting research in developing biomarkers for the treatment selection and monitoring of patients with lung cancer. The research focus of this proposal is to develop molecular markers to better identify the subgroup of patients that will respond to PD1/PDL1 therapies in order to avoid unnecessary toxicities, reduce costs, and enable more appropriate therapies to be delivered. This goal will be accomplished in two complementary specific aims. In Specific Aim 1, a novel approach to acquire fresh tissue samples for immunophenotyping will be utilized to prospectively determine the ability of deep T cell phenotyping and functional assays to predict response to anti-PD1/PDL1 therapy using multi-parametric flow cytometry. In Specific Aim 2, a newly developed technique that enables the quantitative measurement of circulating PDL1 exosomes will be utilized to determine the association of pretreatment and on-treatment exosomal PDL1 expression levels to predict clinical outcomes in non-small cell lung cancer patients receiving checkpoint blockade. The training component of this proposal includes formal coursework, participation in a rich environment of post-doctoral lectures in thoracic oncology/tumor immunology, acquisition of advanced laboratory techniques, and individual mentoring. This project will take place under the supervision of Dr. Steven Albelda who is the Director of the Thoracic Oncology Laboratory at the University of Pennsylvania and Co-Director of the Abramson Cancer Center’s Translational Center of Excellence for Lung Cancer Immunobiology, and Dr. Anil Vachani who is the Director of Clinical Research for the Section of Interventional Pulmonology and Thoracic Oncology at Penn. Dr. Albelda and Dr. Vachani have mentored over 100 trainees. In addition, an advisory committee of distinguished scientists will provide experimental assistance, intellectual guidance, and career advice throughout the duration of this award.

Immune checkpoint blockade (ICB) has demonstrated profound effects on the anti-tumor immune response and has revolutionized the treatment landscape of non-small cell lung cancer (NSCLC). While chemotherapy has traditionally been viewed as detrimental to the immune system, recent clinical trials have demonstrated an impressive survival benefit when combining checkpoint blockade with chemotherapy (ICB+chemo) relative to chemotherapy alone. Despite this, many NSCLC patients do not achieve clinical benefit from ICB, even when combined with chemotherapy. The role of tumor mutational burden, and specifically T cells targeting neoantigens derived from these mutations, has been demonstrated in several ICB studies, however these factors have yet to be fully explored in chemotherapy-containing ICB treatment regimens. There is thus an urgent need to understand the effects of ICB+chemo on the anti-tumor immune response and to specifically evaluate how chemotherapy perturbs the phenotype and function of anti-tumor T cells. It is of paramount importance that we understand how PD-1 blockade and chemotherapy synergize to promote anti-tumor immunity in order to better stratify patients most likely to benefit from these treatments. We propose herein to perform the first comprehensive evaluation of the phenotype and function of neoantigen-specific T cells and their dynamics before and after treatment with ICB+chemo relative to ICB alone. The findings from this study will provide a detailed atlas of the immune system dynamics following treatment and will result in the development of an immunometabolic signature that will be correlated with clinical outcome. Importantly, the results of the proposed work will deepen our understanding of the immune response to ICB+chemo and will unravel the mechanisms underlying clinical response in NSCLC patients.

Statement of the Problem: Cancer develops in a sequenced manner. Patches of lung cells gain the ability to multiply faster than their neighboring normal cells by acquiring mutations. These patches of cells are called “premalignant lesions" (PMLs). Some of these lesions may eventually become cancer. Knowledge about how some PMLs may develop into lung cancer is central to developing tools for Cancer Interception—interrupting the cancer development process and blocking progression to advanced metastatic disease. However, we lack effective lung cancer interception approaches due to our incomplete understanding of the earliest molecular events associated with the development of lung cancer, as well as the challenge in developing personalized tools for early detection and prevention.

Proposed Solution: The Dream Team will use a holistic approach to understand the genetics, immunology, radiological (imaging) profile, and treatment response of patients who show evidence of abnormal lung tissue that puts them at high risk to develop lung cancer. The Team has access to unique groups of patient populations (adenocarcinoma—ADC and squamous cell carcinoma—SCC) with signs of lung cancer risk, and has assembled a collection of blood and tissue specimens from these individuals. The main objective of the Team is to understand how lung cancer develops and test methods that will block the development of cancer. Their three-pronged approach to solve this problem will include:

• Creation of a molecular pre-cancer genome atlas (PCGA) of the lung with the goal of identifying which types of precancerous lung tissue require aggressive treatment and which treatments will block the development of these abnormal lesions to invasive lung cancer.
• Development of two diagnostic tools that can be directly applied in the clinic for simple, yet accurate, detection of early lung cancer: 1) the use of nasal swabs, blood tests, and imaging to confirm whether lung abnormalities found on chest imaging are lung cancer or benign lung disease. 2) blood tests that can identify patients at the earliest stages of lung cancer recurrence, thus enabling their timely and effective intervention with therapies such as those that boost the immune system.
• Development of tests to identify which individuals are most likely to benefit from a number of treatment strategies to intercept lung cancer, including emerging immunotherapies.

Immune-targeted agents have generated antitumor responses that are transforming cancer therapeutics in various tumors types including lung cancer. Despite the impressive responses observed, the majority of patients eventually experience therapeutic resistance after an initial response. Considering the increased cost to patients and health systems both financially and in terms of time spent in management of immune-related adverse effects it has become clear that success of immuno-oncology approaches depends on choosing patient populations most likely to benefit. Our proposed research addresses the urgent unmet clinical need to understand the underlying biology of response and develop molecular assays of response and resistance to immune targeted agents. We propose comprehensive genome-wide analyses of tumors and cell-free circulating DNA to examine how cancer genomes change during immune checkpoint blockade. Our approach is focused on discovery of mechanisms of resistance using a multidimensional strategy that combines comprehensive genomic analyses with functional assays of autologous T-cell reactivity. The underlying premise of this proposal is that through our comprehensive molecular analyses, we will identify changes in the genomic landscape of tumors during immune checkpoint blockade that mediate emergence of primary and acquired resistance to these therapies. Unravelling the genomic mechanisms through which cancer adapts to evade anti-tumor immune responses will be critical for future development of tailored cancer immunotherapy strategies. We envision that the results of the proposed research will be used to develop patient-specific immunotherapy approaches in lung cancer and will launch investigator-initiated clinical trials at Hopkins and other institutions.

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.

Melanoma has the highest propensity to metastasize to the brain once the disease has spread, while non-small cell lung cancer (NSCLC) has the highest incidence of brain metastases among all cancers. Approximately 50,000 patients develop brain metastases from these diseases every year. Patients with brain metastases have exceedingly limited therapeutic options since they are typically excluded from clinical trials. Recently a number of new systemic immune therapies, such as nivolumab (BMS-936558) and lambrolizumab (MK-3475), two inhibitors of PD-1 (an immune inhibitory molecule), have led to dramatic responses in metastatic melanoma (MM) and NSCLC. However, these therapies have not been studied in patients with untreated brain metastases.  Little is known about immune cells in the brain, and whether the immune system can be stimulated to reject cancer cells. Moreover, little is known about what tumor characteristics are associated with response to MK-3475 in brain metastases. This proposal includes innovative correlative biomarker studies incorporated into a clinical trial uniquely designed to study the activity of MK-3475 in patients with limited, small brain metastases in MM and NSCLC. This drug carries the hope to provide prolonged responses similar to responses seen in other metastatic sites, and might enable patients to avoid radiation therapy, and improve their outcome. As part of this clinical trial, we will collect brain and other metastatic specimens from patients enrolled and study the expression of immune inhibitory molecules utilizing a novel quantitative assay and algorithms that we have developed in preliminary work. These studies will facilitate selection of patients who are more likely to respond to this class of drugs.

Advanced (stage IV) lung adenocarcinoma is an incurable disease. Treatment mostly consists of chemotherapy, which provides a consistent but small survival benefit. Standard therapy includes a platinum-doublet (pemetrexed or paclitaxel) often in combination with bevacizumab, followed by maintenance bevacizumab or pemetrexed. Programmed death 1 (PD-1) is a T-cell surface receptor that when activated, delivers a negative signal to T cells. This feedback mechanism dampens immune responses when no longer needed, preventing damaging autoimmune reactions. Tumors can co-opt this T-cell control mechanism to escape surveillance and/or rejection by the immune system. Thus, reversing this tumor action can result in antitumor activity worthy of clinical evaluation. Recently it has been demonstrated that inhibition of the PD-1 receptor with an anti-PD-1 monoclonal antibody (nivolumab) has significant clinical activity in lung cancer with an ORR of 26%. As remarkable as this may be, given the heavily pretreated population of lung cancer patients studied, this also indicates that 74% of patients did not respond and remained resistant to this approach. Therefore, going forward it is important to develop combination therapies to improve the efficacy of this approach, and to discover resistance mechanisms that may allow for better patient (and tumor) selection. One potential class of agents to be used in combination with anti-PD-1 is the adenosine A2AR antagonists. Given that A2AR on T cells within the tumor microenvironment contributes to immune escape and therapeutic resistance, the addition of PBF-509 is expected to improve the efficacy of nivolumab.