The NCI Small Cell Lung Cancer (SCLC) Consortium is leading several research projects focused on understanding, screening for, and treating this disease.
Extracellular vesicles in small cell lung cancer early detection
PI: Patrick Nana-Sinkam and James Lee
Grant #:U01 CA213330
ABSTRACT: Lung cancer is the leading cause of cancer deaths worldwide. While the implementation of lung cancer screening for non-small cell lung cancer (NSCLC) subtypes has brought significant hope to this disease, very limited options exist for the early detection of small cell lung cancer (SCLC) SCLC carries a 5-year survival rate of only 7% and despite the development of novel targeted therapies and early detection for NSCLC, no such advances have been achieved in SCLC. A gap in our current approach to lung cancer detection and treatment has been that informative and reliable biomarkers for the detection and surveillance of lung cancer have remained elusive. MicroRNAs (miRNAs) have emerged as viable biomarkers in body fluids thus, providing an excellent means to achieve non-invasive assays for early cancer detection. Furthermore, miRNA expression in circulation appears to be compartment specific. While the majority of miRNAs are intracellular, a significant number of miRNAs have been observed outside of cells, including in various bodily fluids. The origin, applications and potential functionality of RNAs in circulation are the sources of intriguing questions. Obtaining a detailed RNA spectrum in plasma would shed some light on this matter. We have taken a multidisciplinary approach to the investigation of circulating RNA transcripts that integrates expertise in miRNA biology, nanoengineering, lung cancer and bioinformatics. We have developed a simple tethered Cationic Lipoplex Nanoparticle (tCLN) biochip with pre-loaded molecular beacons (MBs) in the lipoplex nanoparticles as probes to capture and detect targeted miRNAs and mRNAs in human plasma without any need of pre- or post-sample treatment. We have successfully demonstrated the ability to assess both exosomal miRNAs and mRNAs using both Next Generation Sequencing and our tCLN biochip in cohorts of control smokers and patients with early stage NSCLC. Our primary objectives are to extend these novel findings by (1) Test and validate the utility of measurement of ASCL1 and DLL3 in the early detection of SCLC in a retrospective and prospective study with network samples (2) Develop A Panel of Comprehensive EV RNA Candidates using nest generation sequencing and q-RT-PCR (3) Develop an optimized EV nanochip based RNA Classifier for early SCLC detection and (4) Validate the optimized EV RNA Classifier by using the multiplex TLN array biochips in independent, blinded case control studies at the OSU James Cancer Hospital and from the SCLC consortium.
Targeting the transcriptional and epigenetic landscape in chemo-refractory small-cell lung cancer
PI: Kwok Kin Wong and Nathanael Gray
Grant #:U01 CA213333
ABSTRACT: Small cell lung cancer (SCLC) is characterized by aggressive growth, genomic heterogeneity, and rapid development of resistance to chemotherapy. SCLC patients frequently demonstrate initial clinical response to chemotherapy, including the clinical standard of care cisplatin-etoposide regimen, but eventually succumb to chemo-refractory disease. Recent sequencing studies have demonstrated that SCLC is one of the most highly mutated cancers, but these efforts have yet to identify targetable ‘driver’ mutations in both chemo-sensitive and chemo-refractory disease. Using an unbiased, high-throughput cellular screen of a diverse chemical library, we have identified that SCLC chemo-sensitive and chemo-refractory tumor cells are highly sensitive to inhibitors of the general transcription apparatus. In particular, we observed that SCLC tumor cells were highly sensitive to THZ1, a newly identified covalent inhibitor of cyclin-dependent kinase 7 (CDK7) that functions as a co-factor for RNA polymerase II (Pol II). We found that this transcriptional vulnerability is conferred, in part, by the exquisite sensitivity of key super-enhancer (SE) -driven SCLC oncogenes to transcriptional inhibition. We therefore hypothesize that the inhibition of other transcriptional CDKs found at SEs and their associated genes could provide additional therapeutic avenues. For this purpose we have developed structure-inspired approaches for the design of covalent inhibitors targeting various transcriptional CDKs. We further hypothesize that comparative analysis of enhancer landscapes and gene expression profiles from chemo-naïve and chemo- refractory primary tumors will 1) identify transcriptional and epigenetic features specific to chemo-refractory disease, 2) enable grouping into clinically relevant subtypes, and 3) identify transcriptional and epigenetic dependencies specific to chemo-refractory disease that can be ‘drugged’ using transcriptional CDK inhibitors. As changes to tumor oncogene expression and chemo-resistance have been shown to impact the immune compartment, we anticipate that chemo-refractory tumors will also exhibit changes in immune cell activation and infiltration. By extending our classification of clinical subtypes to the tumor microenvironment, we hope to find both tumor and immune cell gene expression programs that amenable to small molecule targeting with the goal of enhancing tumor immune surveillance capabilities. Lastly, as many transcription CDKs are known to transcriptionally regulate key pathways that modulate the response to DNA-damaging agents and immunotherapies we will investigate whether transcriptional CDK inhibitors may also be combined with other investigational SCLC therapies.
Preclinical development of a DLL3-targeted theranostic for small cell lung cancer
PI: JT Poirier
Grant #:U01 CA213359
ABSTRACT: Small cell lung cancer (SCLC) is remarkable for exceptionally high metastatic potential, initial robust response to DNA damaging agents, and near universal development of resistance. This combination of predilection for early metastasis acquired treatment resistance – often times manifested as cross resistance to multiple agents – highlights a critical need for novel systemic therapies operating through a novel mechanism in order to achieve improved patient outcomes. Delta-like ligand 3 (DLL3), has recently been identified as a therapeutic target in SCLC. The highly tumor-selective surface expression of this protein make it an excellent candidate target for an antibody drug conjugate (ADC). Rovalpituzumab tesserine (Rova-T) is one such ADC that is showing encouraging efficacy signals in the clinic. However, despite apparent clinical benefit, this agent has also been associated with some severe adverse events attributable to the presence of the anthracycline PBD warhead. DLL3 targeting approaches are in need of both a real-time, quantitative diagnostic biomarker and a therapeutic approach with reduced toxicity. We propose a theranostic approach comprising on 89Zr immunoPET and a 90Y/177Lu radioimmunotherapeutic. The first Aim improves upon already promising bioconjugation chemistry. We are already able to obtain high-contrast immunoPET images using non-specific amine labeling and site-specific maleimide bioconjugation. We will improve upon this approach by developing more stable thiol-clickable methylsuflone chelators for 89Zr and 90Y/177Lu to minimize kidney dose. The second Aim identifies preclinical dosing parameters and comprehensively optimizes efficacy and toxicity in a traditional cell line xenograft. Our preliminary imaging data is focused on H82, an SCLC cell lined derived from a chemoexperienced patient. This cell line is very resistant to etoposide in vitro and in vivo and will be used to identify a radiotherapy dose that demonstrates efficacy in vivo, while minimizing dose to the kidney. Different dose ranges and schedules will be explored. The final Aim explores radiotherapy in a variety of in vivo contexts including lesion sizes ranging from 0.1 to 10 mm in diameter and representing both chemonaïve and chemoresistant disease. Radioisotopes have different energy deposition depending on the volume of the tumor being targeted. We will evaluate 90Y and 177Lu radioisotopes in different in vivo models of small cell lung cancer for the ability to eradicate lesions of different sizes. A unique resource in the lab is our collection of 10 paired chemonaïve and chemoresistant patient-derived xenograft lines. We will place particular emphasis on establishing efficacy in the context of acquired chemoresistance. Data obtained in this study should provide preclinical evidence in support of clinical translation of a DLL3 targeting theranostic based on rovalpituzumab.
Novel therapeutic approaches for enhancing anti-tumor immunity in SCLC
PI: John Heymach, Lauren Byers, Julien Sage
Grant #:U01 CA213273
ABSTRACT: Small cell lung cancer (SCLC) is a highly lethal malignancy for which new therapeutic strategies are desperately needed. One promising avenue is the use of immunotherapy (IMT) agents such as PD-1/PD-L1 pathway inhibitors. Despite its high mutation burden, however, data from our group and others indicate that SCLC paradoxically has an immunosuppressed phenotype with relatively low levels of infiltrating T-cells, reduced antigen presentation, and increased levels of CD47, a suppressor of myeloid function. Furthermore, initial clinical testing suggests that most SCLC tumors often express low or very low levels of PD-L1 and fail to respond to PD-1 inhibitor monotherapy; IMT resistance also inevitably emerges in responding tumors by mechanisms that have not yet been characterized. Thus, immunosuppressive mechanisms other than the PD- 1/PD-L1 pathway are likely to play a major role in SCLC, and novel therapeutic approaches and combination therapies are needed to realize the potential of IMT in SCLC. The goal of this proposal is to address this issue by identifying new IMT targets and novel combination regimens, and to rapidly translate them into the clinic. Our team already has promising leads. First, we identified that SCLC is highly vulnerable to drugs targeting DNA damage repair (DDR) including PARP and Chk1 inhibitors, a finding now supported by early clinical results. Our preliminary data further suggest that DDR inhibition may increase PD-L1 expression and, by increasing the production of tumor-associated neoantigens (TAA), may sensitize tumors to IMT. In Aim 1, we will test whether DDR inhibitors can increase the expression of TAAs, and enhance the efficacy of PD-1/PD-L1 inhibitors. Second, we have developed a novel strategy for protecting immune cells from the cytotoxic effects of chemotherapy by using inhibitors of CDK4/6, which can be used to protect immune cells, but not RB-deficient SCLC cells. In Aim 2, we will test whether CDK4/6 inhibition can enhance the anti-tumor effects of immune cells by protecting them from chemotherapy-induced cytotoxicity and enable improved chemotherapy/IMT combinations in SCLC. Third, we have identified the “don’t-eat-me” signal CD47 as a novel IMT target for SCLC; blockade of CD47 effectively promotes the phagocytosis of SCLC cells by macrophages and inhibits tumor growth. In Aim 3, we will test whether targeting this CD47 myeloid checkpoint can enhance antitumor immunity and the efficacy of PD-1/PD-L1 blockade and chemotherapy in vivo in SCLC models. The overall hypothesis tested here is that antitumor immunity can be enhanced in SCLC by targeting all these processes, leading to more effective IMT combination regimens. These studies will be facilitated by novel immune-competent pre-clinical murine SCLC models that we have developed and by a multidisciplinary team including clinical and laboratory investigators, immunologists, pathologists, and others with a record of innovation in SCLC and IMT and a track record of translating laboratory findings into the clinic.
Developing ASCL1 and NEUROD1 lineage oncogene targeted therapy for small cell lung cancer
PI: John Minna
Grant #:U01 CA213338
ABSTRACT: Developing ASCL1 and NEUROD1 lineage oncogene targeted therapy for small cell lung cancer (SCLC) This application focuses on developing new targeted therapy for SCLC focusing on two key lineage oncogenes involved in SCLC pathogenesis and malignant behavior, ASCL1 and NEUROD1. Nearly 90% of SCLCs express ASCL1, NEUROD1 or both. In the preclinical models, including human SCLC lines and xenografts and genetically engineered mouse models (GEMMs) of SCLC, tumors that express either ASCL1 or NEUROD1 appear “addicted” to their expression and function. The presence of ASCL1 or NEUROD1 also are associated with expression of important downstream oncogenes and regulatory genes. If ASCL1/NEUROD1 are removed (through genetic knockdown) SCLCs undergo many logs of tumor cell kill. Using state of the art technology in human preclinical models, we propose to systematically study the dependency of a large number of SCLC lines and xenografts (including patient derived xenografts, PDXs, and circulating tumor cell derived xenografts, CDXs) on ASCL1 and NEUROD1 through genetic knockdown, and systematically test the ability of blocking genetically and pharmacologically downstream potentially “druggable” targets of these two transcription factors to kill SCLCs. We have three specific aims: Aim 1. Determine ASCL1 and NEUROD1 expression patterns and clinical and molecular correlates in preclinical SCLC models and tumor specimens; Aim 2. Determine ASCL1 and NEUROD1 genetic dependency phenotypes, potential molecular biomarkers predicting response, and frequency and mechanisms of resistance in SCLC preclinical models; Aim 3. Determine the role of ASCL1 and NEUROD1 directly regulated “downstream” targets as vulnerabilities that can be exploited for therapeutic effect using in vivo xenograft shRNA mini-library “drop out” screens and selected drugs that inhibit downstream “druggable” targets. As part of these aims we will also determine if resistance to ASCL1 or NEUROD1 targeted therapy in SCLCs develops using CRISPR-CAS9 technology including potential mechanisms of this resistance, and we will explore the possible use of ASCL1 and NEUROD1 expression as SCLC enrollment biomarkers for developing “precision medicine” to predict the response of such targeted therapy in individual SCLCs. We have developed a large amount of preliminary data on which this application is based including 1) assembling the world’s largest collection of clinically and molecularly annotated human SCLC lines and xenografts, as well as important GEMMs of SCLC, 2) generating a comprehensive list of directly regulated downstream targets of ASCL1 and NEUROD1 through ChipSeq/RNASeq and chromatin landscape studies, and 3) developing experimental approaches to systematically study the dependency of SCLCs on ASCL1 and NEUORD1 downstream targets. We have assembled a world class team of investigators, including a patient advocate, with complementary skills to assure the successful completion of this project. The final deliverables will serve as the basis for new ASCL1 and NEUROD1 targeted therapeutics for SCLC.
Development of risk and early detection biomarker for small cell lung cancer
PI: Samir Hanash
Grant #:U01 CA213285
ABSTRACT: The goal of this proposal by a multi-disciplinary team at MD Anderson Cancer Center, the University of Texas Southwestern Cancer Center and the University of Pittsburg Cancer Center is to explore approaches based on circulating protein markers and autoantibodies to develop a blood based marker panel to assess risk of harboring or developing small cell lung cancer (SCLC). There are currently several established SCLC protein markers which individually lack sufficient performance for early detection. Additionally, the applicant group has uncovered several protein marker candidates through integrated analyses of mouse models and human SCLC samples. To assess the potential of established and newly discovered candidate markers to yield a combined panel of markers indicative of risk of harboring or developing SCLC, validation studies will be conducted using plasma samples collected up to 5 years prior to a diagnosis of SCLC, from participants in the large European Prospective Investigation into Cancer and Nutrition (EPIC) and the Singapore Chinese Health Study (SCHS) cohorts. Additonally, plasmas collected at the time of diagnosis of SCLC and post-treatment as well as tissue molecular profiles will be interrogated to establish the biological relevance to candidates to SCLC. Two approaches will be implemented to identify antigenic proteins and peptides that induce autoantibodies that can be mined for SCLC early detection. One consisting of Ig bound proteins in plasmas from SCLC cases and another novel approach consists of interrogating whole genome derived peptide arrays for reactivity with aliquots of SCLC plasmas utilized for validation of circulating proteins. The resulting combination of the most promising markers will be further validated using pre-diagnostic SCLC samples and matched controls from the US Prostate Lung Colon and Ovarian (PLCO) cohort. The applicant group has a substantial track record of collaboration and expertise relevant to project objectives, with rigor in experimental design for discovery and validation studies of lung cancer biomarkers.