Funded Projects

KRAS mutations are the most common activating mutation in lung cancer and are identified in 25-30% of cases of lung adenocarcinoma. The clinical activity of molecularly targeted therapy in KRAS mutant lung cancer has been limited, as most prior approaches focused on downstream targets of the MAPK pathway, an approach which was largely ineffective. KRAS G12C is the most common subtype of activating KRAS mutation in NSCLC. Identification of a binding pocket of KRAS G12C enabled the development of covalent inhibitors (Ostrem et al. Nature, 2013), which selectively bind to the mutant cysteine and spare wild type or other mutant KRAS proteins (hereafter referred to as G12Ci). These drugs bind only to GDP-bound (i.e. inactive) KRAS G12C and trap the oncoprotein in its inactive state by preventing nucleotide exchange (Lito et al. Science, 2016). Of this new class of agents, two drugs (MRTX849 and AMG510) have demonstrated efficacy in early phase clinical trials, representing a remarkable breakthrough in the management of KRAS G12C mutant lung cancer. Acknowledging the limited number of patients treated thus far, response rates of 40-50% have been reported, demonstrating clinical activity far superior to prior molecularly targeted approaches for the management of KRAS mutant lung cancer. Despite this major advance it is clear that resistance to therapy, both primary and acquired, will remain a challenge and may in part be due to upstream receptor tyrosine kinase (RTK) signaling. Understanding the mechanisms of resistance to this new class of therapy is of paramount importance to improve the efficacy and durability of response, and for identifying rational combinatorial therapies for future clinical trials.

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.

Metastatic non-small cell lung cancer (mNSCLC) is the leading cause of cancer-related death in the United States. Most patients with mNSCLC are treated with systemic agents, which prolong survival and improve symptoms, but are typically not curative. Although recent advancements in immune checkpoint inhibitors have revolutionized the management of mNSCLC lacking targetable driver mutations, only a fraction of mNSCLC patients benefit from immunotherapy. Emerging evidence suggests that ablative radiotherapy can augment immunotherapy responses in metastatic disease; however, strategies to optimize the synergy between local radiation and the immune system are not well defined. We are conducting a randomized phase I/II clinical trial designed to evaluate the safety and efficacy of combination immune checkpoint blockade (ipilimumab + nivolumab) plus multisite ablative radiotherapy as a first-line treatment for patients with mNSCLC. As a secondary analysis of the phase I trial, we propose to investigate biomarkers associated with treatment response. In Aim 1, we propose to compare the diagnostic accuracy of established clinical biomarkers, including PD-L1 immunohistochemistry (IHC), tumor mutational burden, gene expression profiles, and multiplex IHC in predicting response to combination ablative radiotherapy and immunotherapy. In Aim 2, we propose to characterize global transcriptional and genomic changes induced by radiation when given prior to or concurrently with immunotherapy and evaluate whether these changes are associated with treatment response. In addition, in Aim 3, we propose to validate a novel biomarker derived from alternative splicing as a predictor of radio-immunotherapy response. By elucidating the immunomodulatory properties of radiotherapy, we may be able to improve treatment responses and long-term survival in patients with mNSCLC.

Several tyrosine kinase inhibitors (TKIs) are available for the treatment of ALK+ NSCLC, but resistance to all ALK TKIs (including alectinib, brigatinib, lorlatinib) has been reported and occurs through a variety of mechanisms. Once patients develop resistance to available ALK inhibitors, they are typically treated with cytotoxic chemotherapy rather than immunotherapy since response rates to PD-1 pathway inhibitors in this population are very low. However, our work in mouse models of ALK+ NSCLC has demonstrated that a vaccine generated against the rearranged portion of ALK can both prevent the development of ALK+ tumors and also more effectively treat them once they arise. We have also recently found evidence for anti-ALK immune responses in patients, as a subset of them generate spontaneous ALK autoantibodies.

We aim to translate our preclinical findings to a first-in-human clinical trial. Aim 1 will test the safety and efficacy of a novel ALK vaccine + an amphiphilic CpG toll-like receptor 9 agonist adjuvant, administered in combination with an ALK TKI or PD-1 inhibitor in patients with TKI-resistant ALK-positive NSCLC. In Aim 2, using liquid chromatography data-independent acquisition mass spectrometry, we will directly identify antigenic ALK peptides presented by MHC molecules on the surface of cancer cells from tumor biopsies obtained on trial participants. In Aim 3, we will study pre- and post-vaccination anti-ALK T-cell responses among trial participants by analyzing peripheral leukocytes and intratumoral immune cells. The overarching goal is to develop a vaccine that stimulates patients’ immune cells to recognize and eliminate ALK+ tumors.

With the development of increasingly potent and selective ALK tyrosine kinase inhibitors (TKIs), resistance is commonly mediated by ALK-independent mechanisms, such as bypass pathway activation. As bypass signaling dependencies vary across ALK-rearranged (ALK+) lung cancers, a multipronged approach is needed to broadly suppress potential bypass signals. We have identified MET activation in 20% of ALK+ tumors that are resistant to next-generation ALK TKIs. In preclinical studies, dual ALK/MET blockade re-sensitized MET-amplified ALK+ tumors to lorlatinib. MEK and SHP2 have recently been identified as important effector proteins downstream of several bypass signaling pathways. In ALK+ models harboring diverse bypass signals, pairing an ALK TKI with either a MEK or SHP2 inhibitor demonstrated broad anti-proliferative activity. Based on these findings, we will conduct a clinical trial to evaluate lorlatinib in combination with a MET, MEK, or SHP2 inhibitor for patients with ALK+ lung cancers with ALK-independent resistance. Serial tumor biopsies will be analyzed to characterize molecular determinants of response to combination therapy and identify expression changes induced by treatment. This innovative multi-arm trial will also assess whether dynamics of genetic alterations in plasma can be used to guide intensification of treatment from monotherapy to early combination therapy for patients who have not yet developed resistance to ALK-directed therapy. Collectively, the studies in this grant strive to develop diverse strategies for overcoming ALK-independent resistance, a heterogeneous molecular entity that undermines efficacy of current ALK therapeutics.

The current standard of care for ALK rearranged non-small cell lung cancer (NSCLC) is targeted therapy with ALK tyrosine kinase inhibitors (TKIs) which bind within the kinase domain of ALK. Due to the development of ALK resistance mutations or bypass activation of parallel or downstream signal pathways, patients inevitably relapse. Even with the introduction of second or third generation TKIs, median overall survival has been estimated to be 6.8 years . Recent advances in immunotherapy have demonstrated progress in lung cancer treatment. However, a majority of ALK positive NSCLC patients have yet to realize the benefits from checkpoint inhibitors or CAR-T cell therapies due to primary resistance or toxicity. Therefore, the development of new treatments for ALK-rearranged NSCLC is an area of critical need. We believe that an effective assault on ALK-driven tumors requires the implementation of creative strategies that allow us to expand our arsenal of drugs to target ALK beyond its kinase domain. To meet this challenge, we have developed and employed cysteine druggability mapping (CDM), a method to define the landscape of inhibitor-protein interactions in a cancer cell. CDM identifies cysteines that can bind to covalent drug-like molecules which serve as early prototypes on which to base cancer drug development programs.
Cysteine-reactive covalent inhibitors have already emerged as an effective approach to targeting protein kinases. Osimertinib, a third-generation epidermal growth factor receptor (EGFR) TKI covalent inhibitor, overcomes EGFR T790M resistance mutations following treatment with EGFR TKI, demonstrating significant improvements over standard EGFR TKIs when used as first line therapy. Importantly, targeting cysteines with covalent inhibitors massively expands the number of proteins which are targetable with small molecule inhibitors, including many targets previously considered undruggable.

We will use ALK fusion positive cancer cell lines, together with tumor tissues from patients who developed resistance mechanisms, to generate druggable cysteine profiles by CDM. Druggable proteins specific to ALK fusion positive samples, including EML4-ALK itself, will be prioritized in our screening for protein degraders from a library of over 2,500 advanced cysteine reactive compounds. After screening, we will assess the specificity of the compound hits and validate their anti-tumor activity using ALK fusion positive cell lines and patient derived ALK TKI-resistant cell lines. We consider the use of the novel, cutting-edge cysteine targeting technology to screen for potent therapeutic compounds as a valuable proposition to improve management of patients with ALK positive lung cancer, with the goal of transforming this cancer into a chronic condition.

Immunotherapy has transformed treatment for patients with lung cancer, but most patients still do not respond. Interferon signaling has a dichotomous role—without acute signaling, responses cannot occur, whereas persistent signaling can drive adaptive resistance. Our group recently reported in Cell that delayed administration of a JAK inhibitor in combination with immunotherapy can lead to enhanced treatment responses. We have opened a trial to test this approach, but also aim to improve patient selection and monitoring during immunotherapy by studying key parameters of T-cell exhaustion using peripheral blood flow cytometry. Our group recently showed that one could predict which patients would be most likely to respond to PD-1 blockade in this fashion.

Objective/Hypothesis

We hypothesize that in patients with metastatic non-small cell lung cancer (NSCLC) overexpressing PD-L1 (PD-L1=50%), treatment with pembrolizumab followed by delayed administration of itacitinib will improve the objective response rate. We will also measure the impact of this treatment on key parameters of T cell exhaustion and other biomarkers.

Study Design

This is an optimal three-stage trial of pembrolizumab and itacitinib for first-line treatment of PD-L1=50% metastatic NSCLC. Up to 48 evaluable patients with previously untreated metastatic NSCLC with tumor PD-L1=50% will be enrolled. Beginning with cycle 3 of pembrolizumab, the patient will receive itacitinib for 6 weeks. After 6 weeks of treatment with itacitinib, repeat imaging and tumor biopsy will be performed. Objective response by RECIST 1.1 will be determined based on this scan. Pembrolizumab monotherapy will then be resumed in the absence of progression. Serial blood and tumor samples will be used to monitor established biomarkers and markers of T-cell exhaustion using flow cytometry.

Patients with extensive-stage small cell lung cancer (SCLC) have robust responses to first-line platinum and etoposide; however, most patients suffer rapid and chemoresistant relapse. Even with the recent incorporation of immunotherapy into first-line treatment, the majority of SCLC patients will die of therapeutically resistant disease. This leads to great impetus to develop more effective, mechanism-based treatment strategies in both the initial and subsequent-line treatment settings in patients with this devastating disease.

Our laboratory has previously used multiple patient-derived xenografts (PDXs) to define EZH2-mediated SLFN11 gene silencing as a frequent mechanism of acquired chemoresistance in SCLC. Mechanistically, SLFN11 sensitizes cells to chemotherapy-induced replication stress, therefore enhancing the effects of DNA-damaging agents. We found that EZH2 inhibition could re-express SLFN11 and prevent its silencing, which was able to either maintain or re-sensitize SCLC PDXs to chemotherapy, suggesting a potential combinatorial strategy to enhance the effectiveness of current standard chemotherapy. To better understand how epigenetic changes can reverse chemoresistance in a clinical setting involving recurrent SCLC, we aim to conduct a prospective clinical trial with pre-specified tissue and peripheral blood correlative testing. Specifically, on-treatment biopsies and circulating tumor cells (CTCs) will be used to better understand the expected reversal of chemoresistance with the addition of an EZH2 inhibitor. This project will involve testing this broad array of clinical specimens in the well-established translation research program within our lab as well as through pre-existing industry and academic collaborations. Our ultimate goal is to identify more effective therapies for patients with this deadly disease.

Effective immunotherapy options are lacking for patients with advanced non-small cell lung cancer (NSCLC) and programmed cell death-ligand 1 (PD-L1) expression <50%. One commonly proposed reason for the lack of efficacy of PD-(L)1 agents in these patients is the absence of tumor infiltrating lymphocytes. This leads to the rationale to develop therapies that could recruit T cells to the site of the tumor, such as in situ vaccination with intratumoral (IT) injection of functional antigen presenting cells. One potential approach to IT vaccination, which could convert tumor sites into a lymph node-like environment, is the injection of autologous dendritic cells (DCs) transduced with an adenoviral (Ad) vector expressing chemokine (C-C motif) ligand 21 (CCL21), a chemokine known to (1) facilitate T lymphocyte activation and (2) promote co-localization of T lymphocytes and DCs.

Design

Phase I dose escalation, multi-cohort trial, followed by dose expansion evaluating IT Ad-CCL21-DC plus pembrolizumab. Maximum 24 patients (9-12 escalation + 12 expansion) with stage IV NSCLC will be evaluated who have tumors accessible for IT injection, are treatment naïve, and have PD-L1 expression <50%. Administration of three autologous CCL21-DC IT injections (days 0/21/42) plus pembrolizumab, followed by q3wk pembrolizumab up to 1 year. Dose escalation primary objectives are safety and determination of maximum tolerated dose of IT CCL21-DC when combined with pembrolizumab. Dose expansion primary objective is objective response rate of CCL21-DC plus pembrolizumab. To evaluate the resulting immunological changes (a) mass cytometry (CyTOF) and (b) multiplex immunofluorescence (MIF) will be performed on trial specimens.

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.

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.

The majority of lung cancer patients present with advanced disease that is largely incurable. Efforts to improve the early detection of this disease are critical to decrease lung cancer-related mortality. Low-dose computed tomography (CT) screening in high risk patients has demonstrated reduction in lung cancer related mortality through diagnosis of earlier stage disease at the cost of high false-positive rates and the frequent need for invasive diagnostic testing when indeterminate lung nodules are identified. Detecting tumor specific somatic mutations and/or epigenetic signatures in circulating tumor DNA (ctDNA) represents an attractive non-invasive method for identifying early stage lung cancer. However, to realize this promise for lung cancer screening, where ctDNA from small tumors is miniscule, the development of sensitive, specific, and economical ctDNA based assays is critical. 
The bacterial innate immune system consisting of clustered regularly interspaced short palindromic repeats (CRISPR) and their associated endonucleases (CRISPR-Cas) are specifically adapted to recognize foreign nucleic acids. The recent identification and diagnostic adaptation of certain classes of CRISPR-Cas systems, such as CRISPR-Cas12a and -Cas13a, offer unique platforms on which to develop sensitive, specific, and economical assays for the detection of ctDNA. The goal of the current project is to develop CRISPR-Cas12a and -Cas13a based ctDNA assays that can sensitively detect somatic cancer mutations and aberrant promoter hypermethylation often found in lung cancer patients and to validate these assays in plasma samples of patients with early stage NSCLC and in discriminating between benign and malignant nodules identified by low-dose CT screening studies. 

Several ALK tyrosine kinase inhibitors (TKIs) are available for the treatment of ALK-rearranged non-small cell lung cancer (NSCLC), but resistance to all ALK TKIs (including crizotinib, ceritinib, alectinib, brigatinib, and lorlatinib) has been reported and occurs through a variety of mechanisms. Once patients develop resistance to available ALK inhibitors, they are typically treated with cytotoxic chemotherapy rather than immunotherapy since response rates to PD-1 pathway inhibitors in this population are very low. However, our work in mouse models of ALK-positive NSCLC has demonstrated that a vaccine generated against the rearranged portion of ALK can both prevent the development of ALK-positive tumors and also more effectively treat them once they arise. In addition, we have recently found evidence of an anti-ALK immune response in patients, as a subset of them generate spontaneous ALK autoantibodies.

To more deeply characterize anti-ALK immunologic responses in patients, we propose (Aim 1) to determine if the presence of anti-ALK antibodies correlates with progression-free and overall survival among patients with ALK-positive NSCLC, and (Aim 2) to directly identify and validate antigenic ALK peptides in different HLA-haplotype backgrounds. Antigenic peptides that are identified through these studies will serve as the basis for a therapeutic ALK peptide vaccine clinical trial, for which funding has been secured independently.

ALK rearrangements define a distinct molecular subset of NSCLC and confer sensitivity to treatment with ALK tyrosine kinase inhibitors (TKIs). These agents have produced dramatic improvements in clinical outcomes among ALK-rearranged (ALK+) patients, yet acquired resistance remains a major challenge. Thus, there is an urgent need for alternative therapeutic approaches for this disease. Recently, immune checkpoint inhibitors targeting negative regulators of the immune response (e.g., PD-1/PD-L1) have emerged as powerful new therapies in NSCLC. In preliminary analyses, we and others have observed that ALK+ lung cancers are generally less responsive to immune checkpoint inhibitors. We hypothesize that distinct immune-based strategies may therefore be needed for ALK+ lung cancers. To inform these strategies, we will investigate 1) tumor-intrinsic factors associated with immunogenicity in ALK+ tumors (e.g., neoantigens, tumor mutation burden), 2) tumor-immune cell interactions (e.g., PD-L1 expression, alternative checkpoint expression, antigen presentation), and 3) endogenous T cell responses against ALK in the peripheral blood. Together, these studies may lay the groundwork for development of biomarkers informing optimal delivery of PD-(L)1 therapy in ALK+ lung cancers, while also promoting the development of novel combinations and approaches, including autologous cellular therapies directed against ALK.

Targeted therapies, such as ALK inhibitors, represent a major advance in the treatment of lung cancer patients with specific oncogenic drivers. However, these patients relapse due to acquired or intrinsic resistance to these agents. While targeting immnoevasive pathways, such as immune checkpoint inhibitors, have shown efficacy in a subset of lung cancer patients who have progressed on other therapies, the response rate in ALK-positive lung cancer to these agents is very low, underscoring the need to identify other potential regulators of the anti-tumor immune response. The complement pathway is a component of the innate immune response, which regulates the adaptive immune system. Complement activation, initiated through multiple pathways, leads to a series of proteolytic cascades that generate inflammatory mediators designated as anaphylatoxins (C3a, C5a).

Our laboratory has employed an immunocompetent orthotopic model of lung cancer progression, where lung cancer cells are implanted into the lungs of syngeneic mice. To study pathways regulating progression of ALK-positive lung cancer, we have developed a panel of murine lung cancer cell lines with the oncogenic driver EML4/ALK. Using both genetic and pharmacological approaches we have demonstrated that while these tumors are resistant to anti-PD-1/anti-PD-L1 therapy, they are strongly inhibited by blocking the complement pathway. This project will define the mechanisms of complement activation, and the cellular and molecular mechanisms whereby complement inhibition blocks ALK-positive tumor progression. Studies will test a panel of complement inhibitors targeting different steps in the complement cascade and validate complement activation in human ALK-positive lung tumors.