The NCI Small Cell Lung Cancer (SCLC) Consortium is leading several research projects focused on understanding, screening for, and treating this disease.
The Funding Opportunity Announcement from the National Cancer Institute for these Research Projects can be found here: PAR-19-361. Applications are due in March and November through March 2022.
Optimizing Dual-Targeted and Dual-Armored CAR T Cells for Small Cell Lung Cancer
PI: Renier Brentjens
Organization: Memorial Sloan Kettering
Grant # U01 CA256801
ABSTRACT: A patient’s own T cells can be modified using gene therapy technology to express receptors, termed chimeric antigen receptors or CARs, which allow these immune T cells to recognize proteins on the tumor cell surface, and in turn allow these CAR modified T cells to recognize and kill the patient’s own tumor cells. This approach has been successful in some hematological malignancies, however, it has not been successful to date in solid tumors including small cell lung cancer (SCLC). Two mechanisms by which SCLC may evade T cell-mediated killing are loss of expression of antigens, and suppression of T cell function in the tumor microenvironment. In this proposal, we will attempt to overcome these barriers by designing CAR T cells that target two SCLC antigens simultaneously, and that produce multiple factors (“armors”) that enhance T cell activity in solid tumors. We hypothesize that these dual-armored, dual targeted (DADT) CAR T cells will be more effective against SCLC than previous T cell-mediated and immune therapies. We have previously shown that CAR T cells targeted to either the antigen GD3 or to the antigen DLL3, both of which are expressed on the majority of small cell lung cancers, are capable of killing SCLC cells in preclinical systems. Additionally, we have developed multiple armored CAR T cells that secrete factors such as IL-18, or an antibody-derived single-chain variable fragment (scFv) that blocks the immune checkpoint receptor PD-1, or an scFv blocking the phagocytosis-inhibitory signal CD47 on tumor cells. All of these armors enhance CAR T cell activity in our in vivo model systems through different mechanisms. In Aim 1 of this proposal, we will generate CAR T cells targeting DLL3 and GD3 simultaneously, to overcome antigen heterogeneity and antigen loss in tumors as a means of escape from T cell-mediated killing. Simultaneously, in Aim 2, we will test pairs of armors to identify the pair that is the most effective at enhancing the activity of single antigen-targeted CAR T cells against SCLC in vivo in immunocompetent systems. We then analyze the immune cells in the SCLC tumor microenvironment following CAR T cell treatment to assess changes mediated by the armored CAR T cells. Ultimately, in Aim 3, we will combine these approaches to generate CAR T cells that recognize GD3 and DLL3 and produce multiple armors. These DADT CAR T cells for SCLC may be suitable for further preclinical testing in preparation for clinical trials beyond the scope of this proposal, representing a novel therapeutic approach to SCLC. Given our robust track record in CAR T cell clinical translation, we fully anticipate having new CAR T cells suitable for clinical trials at the conclusion of funding. Additionally, these novel CAR T cells may be used as tools to explore the interactions between T cells and the SCLC microenvironment. The analysis of changes in SCLC tumors induced by the armored CAR T cells proposed here may reveal novel aspects of SCLC biology and illuminate mechanisms of immune escape and treatment failure in SCLC.
Studies of the initiation and progression of Small Cell Lung Cancer using cells derived by differentiation from human pluripotent stem cells
PI: Harold Varmus
Organization: Weill Cornell Medicine
Grant # U01 CA224326
ABSTRACT: Small cell lung cancer (SCLC) is an especially virulent form of lung cancer that is only transiently responsive to therapy and kills about 30,000 Americans each year. Based on a more general interest in understanding why certain kinds of cancers have characteristic genotypes, we are developing methods for studying the initiation of human cancers by genetically modifying cells at discrete stages of differentiation after chemical induction of specific lineages from human embryonic stem cells (hESCs). We have extended recently published methods for inducing hESCs to form parts of the pulmonary lineage by perturbing NOTCH signaling and reducing expression of the RB1 gene (one of the two genes commonly inactivated in SCLC); in this way, we have prepared cultures with high proportions of pulmonary neuroendocrine cells (PNECs), the putative precursors of SCLC. Moreover, by also reducing expression of P53, the other gene commonly inactivated in SCLC, PNEC-containing cultures are able to produce small tumors resembling SCLC when implanted in immune-deficient mice. We now propose to expand our studies of this promising model for studying the origins of SCLC in several ways: by determining the mechanisms by which interference with NOTCH and RB1 generates PNECs; by exploring several possible assays for the SCLC-like phenotype we have recently observed; by defining the similarities between the genetic and physiological features of the SCLCs derived from hESCs and the SCLCs arising in human patients; and by making induced pleuropotent stem cells (iPSCs) from normal and tumor cells from patients with lung cancer, especially SCLC, in an effort to seek genetic risk factors for SCLC. Through these studies, we expect to generate new information and ideas about risk assessment, prevention, diagnosis, and treatment for SCLC.
Phenotype interactions in SCLC Development and detection
PI: Alissa Weaver and Christine Lovly
Organization: Vanderbilt University
Grant #: U01 CA224276
ABSTRACT: Small Cell Lung Carcinoma (SCLC) is an aggressive neuroendocrine subtype of lung cancer. SCLC patients have a very low 5-year survival, in part because SCLC tumors are often detected at a late stage when the tumors have already metastasized and treatment outcomes are worse. Thus, early detection becomes critical to achieve better treatment results. Emerging evidence supports the idea that, while SCLC tumors seem homogeneous when examined under a microscope, these tumors contain a significant level of intra-tumoral heterogeneity. Indeed, recent observations by our group and others have identified distinct cellular phenotypes in SCLC, including in primary human tumors, in cell lines derived from human tumors, and in tumors from genetically-engineered mouse models. Importantly, data from our group indicate that these cellular phenotypes contribute to SCLC development. The specific goal of this proposal is to elucidate how different cellular subpopulations within SCLC tumors drive early SCLC development, dynamics, and growth and to leverage this mechanistic information to identify biomarkers for early detection and prevention of SCLC. We have previously identified tumor-propagating cells (TPCs) in SCLC tumors and found that these cells are neuroendocrine and strongly tumorigenic. We have also characterized cell populations derived from these TPCs with distinct phenotypes, including non-neuroendocrine NOTCH+ and CD44+ subpopulations, that promote the growth and survival of the neuroendocrine TPCs. Leveraging these findings as well as our unique genetic mouse models that allow dissection of SCLC phenotype evolution, we will investigate how cell-cell interactions of these distinct SCLC cell phenotypes contribute to tumor development and growth, in relationship with the tumor microenvironment. We will also elucidate the role of secretory factors released by these SCLC subpopulations in driving survival, growth, and phenotype composition of SCLC tumors. Finally, we will perform analysis of cfDNA and proteins (including on exosomes) present in SCLC patient plasma for identification of related markers of SCLC development and early detection. We will also follow up on intriguing findings that germline mutations in NOTCH are present in a large fraction of SCLC patients, suggesting a potential risk marker beyond smoking. This interdisciplinary basic-translational project will elucidate fundamental mechanisms of SCLC development and may lead to novel methods for early detection and/or prevention of SCLC
Targeting BCAT1 and branched-chain amino acid metabolism for the detection and prevention of SCLC
PI: Kwon-Sik Park
Organization: University of Virginia
Grant #: U01 CA224293
ABSTRACT: The high mortality of small cell lung cancer (SCLC) is largely due to its invariable resistance to current cytotoxic therapies. Chemoprevention has been considered as an alternative to existing therapeutics on the basis of long tumor latency and the well-defined high-risk population (e.g. smokers). Identification of tractable targets for prevention and early detection requires an understanding of molecular changes underlying early- stage tumor development. We found that enhanced ribosome biogenesis and protein synthesis are critical for MYC family-driven transformation of precancerous precursors (preSC) into fully tumorigenic cells. Both human and mouse SCLC cells are extremely sensitive to a specific inhibitor of ribosome biogenesis that has also been shown to reduce tumor growth in a genetically engineered mouse model. Analysis of the MYC-driven oncogenic gene signature revealed branched-chain aminotransferase 1 (BCAT1) as a potential modulator of both metabolic adaptation and related stress response to promote cellular homeostasis. BCAT1 is an enzyme that catalyzes transfer of the α-amino nitrogen from branched-chain amino acids (BCAAs including leucine) to α-ketoglutarate to produce branched-chain α-keto acids (BCKAs) and glutamate. This enzyme routes BCAAs into multiple metabolite pools for biosynthesis and regulates levels of BCAAs, specifically leucine, that stimulate protein synthesis by acting as indicators of nutrient availability. BCAT1 has recently been implicated in multiple types of cancers, including glioblastoma and mouse Kras/p53-driven lung adenocarcinoma. In this application, we will test the hypotheses that enhanced BCAT1 promotes SCLC development by controlling protein synthesis and stress response, and that altered levels of BCAA metabolites inform early BCAT1- dependent SCLC development. To test these hypotheses, we propose the following Aims. Aim 1: To determine the necessity of BCAT1 for SCLC development, we will evaluate the tumor suppressive effects of knocking out Bcat1 and examine the effects of pharmacological inhibition of BCAT1 on SCLC development and long-term survival in vivo. Aim 2: To determine the role of BCAT1 in protein synthesis and stress response during SCLC development, we will manipulate BCAT1 and determine the resulting impact on biochemical interactions among related proteins and pathways that influence proliferation and survival of L-Myc-induced transforming cells, a model of early stage SCLC. We will also determine the significance of BCAA metabolism in tumor development in vivo by setting up variable conditions that mimic different outcomes of the metabolic reaction using a BCAA-defined diet. Aim 3: To test alterations in BCAA metabolites as biomarkers for BCAT1- dependent SCLC development, we will monitor changes in plasma BCAA and BCKA levels during SCLC development in vivo and examine the clinical correlation of plasma levels of these metabolites with a SCLC diagnosis. The expected outcome of this proposal will provide critical insights into novel strategies for targeted prevention using minimally invasive detection methods and intervention using low-toxicity drugs or nutrition.
Molecular mechanisms of SCLC initiation and detection in mice and humans
PI: Mark Krasnow
Organization: Stanford University
Grant #: U01 CA231851
ABSTRACT: Small cell lung carcinoma (SCLC) is one of the deadliest cancers, a “recalcitrant” cancer for which there is no effective treatment except when the disease is diagnosed early. However, only a small fraction of patients are diagnosed early in disease. The greatest challenge to early diagnosis is that SCLC tumor cells typically acquire an exceptional mutation burden and metastasize early, so for most patients disease has spread beyond the lung at the time of diagnosis. The key to developing effective early diagnosis and treatment methods is to elucidate the earliest molecular and cellular events of tumor initiation to uncover ones that can be detected by screening during the premalignant phase of the disease. The goal of this proposal is to define the early, premalignant molecular and cellular events of SCLC, so that they can be detected early and destroyed before they become a deadly, untreatable disease. SCLC is a neuroendocrine cancer. The prominent cell of origin is pulmonary neuroendocrine (NE) cells, neurosensory and neurosecretory epithelial cells that sense and respond to the environment in the lung. Recently, a minor subpopulation of NE cells was found to have stem cell activity, proliferating, dispersing, and replenishing the surrounding bronchial epithelium following severe airway injury. Loss of tumor suppressors Rb and p53 constitutively activates the stem cell program within days of loss of the tumor suppressors, even in the absence of injury. In this proposal, a combination of genetics, cell culture, and single-cell genomics is used to systematically interrogate these stem cells at cellular resolution, both in healthy lungs and in the early, premalignant stage of SCLC. The goal is to define the molecular events immediately following loss of Rb and p53 that constitutively activate the stem cell program and initiate their transformation into cancer stem cells that spread, mutate, and escape immune destruction, and to identify the signals they secrete that might allow the tumors to be detected before they become deadly.
Using patient-derived models to understand drug responses in SCLC
PI: Nicholas Dyson and Anna Farago
Organization: Massachusetts General Hospital
Grant #: U01 CA220323
ABSTRACT: Small cell lung cancer (SCLC) afflicts more than 30,000 patients per year and is rapidly fatal in 95% of cases, with median survival is less than one year. Belying this grim prognosis, treatment-naive SCLC is highly sensitive to chemotherapy, with response rates in excess of 70% for etoposide/platinum. However, relapse is nearly inevitable, and relapsed SCLC presents two obstacles that have been insurmountable for at least 30 years: cross-resistance to chemotherapy, and absence of biomarker-driven targeted therapy. Following relapse, resistance often extends beyond etoposide/platinum, and a disease that was once highly chemosensitive becomes inexorably progressive. However, the molecular determinants of cross-resistance in SCLC remain unclear. Although critically important, cross-resistance is difficult to study experimentally, as it requires a model system that faithfully reproduces clinical outcomes. Topotecan is the only approved second-line therapy, but NCCN guidelines list 10 agents of nearly equivalent efficacy. None are particularly effective in unselected patients, and although there is significant molecular heterogeneity in SCLC, this does not guide patient selection. As novel targets and therapeutic regimens emerge, biomarker discovery will require a model system that recapitulates the molecular features of patient tumors, so that molecular heterogeneity can be parsed into clinically meaningful subgroups. We have generated a panel of 44 SCLC patient-derived xenograft models (PDXs) from biopsy specimens and circulating tumor cells (CTCs). Our panel includes successive models from individual patients at time points before and after specific lines of therapy, with detailed information about the corresponding clinical response. For both standard chemotherapy and experimental agents in clinical trial, these models faithfully mirror patient responses. However, unlike the patient experience, multiple strategies can be compared for identical tumors. We propose to use these models to directly compare standard first and second-line chemotherapy with two experimental regimens that have given promising results in the clinic or in preclinical assays: olaparib plus temozolomide, in a phase I/II trial at MGH, and a combined Mcl-1/Bcl-2 inhibitors. Individually, these PDX population trials are designed to reveal biomarkers of sensitivity and mechanisms of resistance for promising experimental therapies. Collectively, they present a novel opportunity to model cross-resistance through comparative analysis with reference to the clinical histories of each model. The successful completion of this work will establish a large collection of PDX models with comprehensive molecular an functional profiles. In addition, these experiments will investigate the molecular determinants of cross-resistance following chemotherapy, a problem that has beleaguered management of SCLC for over three decades.
Genomic and functional identification of chemotherapy resistance mechanisms in Small Cell Lung Cancer
PI: Ramaswamy Govindan, Trudy Oliver and Obi Griffith
Organization: Washington University in St. Louis and University of Utah
Grant #: U01 CA231844
ABSTRACT: Small cell lung cancer (SCLC) is responsible for over 30,000 deaths each year in the United States alone. SCLC has a two-year survival rate of ~6% and unlike the other major subtypes of lung cancer, there are currently no targeted therapies approved for SCLC. SCLC is initially highly responsive to chemotherapy, but rapidly develops resistance leading to mortality in ~10 months. Clearly, a major unmet need for the treatment of SCLC is the identification of new therapeutic targets and treatment strategies to combat chemo-resistant disease. Our understanding of chemotherapy resistance mechanisms has been hampered by a lack of relapsed human SCLC tissue due to rare surgical resections. In addition, there have been few mouse models of the disease that exhibit short latencies and chemo-sensitivity. To address these challenges, we performed whole exome sequencing on relapsed SCLC from 30 patients. Relapse-specific genomic alterations in the WNT/APC/β-catenin pathway were identified in ~66% of relapsed SCLC suggesting that this pathway promotes chemo-resistance. Second, we developed a novel mouse model of SCLC driven by loss of Rb1, Trp53 and overexpression of Myc—three of the most common genetic alterations in the human disease. Mice develop SCLC within weeks that highly resembles the human disease at the level of histopathology, biomarker expression and chemo-sensitivity followed by relapse. This model will be a useful tool to test candidate chemotherapy resistance mechanisms and identify novel therapeutic targets that inhibit chemo-resistance. The objective of this study is to use this novel mouse model and comprehensive genomic analyses of primary and relapsed human SCLC to identify mechanisms of chemotherapy resistance and novel therapeutic targets to combat chemo-resistant disease. We hypothesize that activation of the WNT/β-catenin pathway promotes chemo-resistance in SCLC and that targeted inhibition of the pathway will inhibit chemo-resistant disease. We predict that expansion of our genomic and transcriptomic profiling will identify additional novel pathways involved in chemo-resistance. To test these hypotheses, we will: 1) identify recurrent pathway alterations in relapsed human and mouse SCLC using whole genome, exome, transcriptome and epigenome sequencing and 2) functionally determine whether canonical WNT/β-catenin signaling and other candidate pathways are necessary and sufficient for chemo-resistance in SCLC in vivo. This approach is innovative because we will employ unbiased comprehensive genomic and epigenomic analyses on relapsed human SCLC and a novel immune-competent mouse model of SCLC that recapitulates key features of the human disease. The WNT/β- catenin pathway is largely unexplored in SCLC. This research is significant because there are currently no targeted therapies approved for SCLC. A better understanding of the critical pathways driving chemo- resistance in SCLC will impact the treatment and survival of patients with this intractable disease.
Bioinformatic-chemical approach to credential molecular targets to combat rapid chemo-radiation resistance in SCLC
PI: Luigi Marchionni, Christine Haan and Phuoc Tran
Organization: Johns Hopkins
Grant #: U01 CA231776
ABSTRACT: Limited stage small cell lung cancer (LS SCLC), the only curable form of SCLC, is remarkably sensitive to etoposide plus cisplatin combined with thoracic radiotherapy with response rates > 70%; however, therapy- refractory recurrence is common. LS SCLC has less than a 25% 5-year overall survival (OS) and ultimately a strategy for improving long-term SCLC outcomes needs to successfully target tumor cell populations that survive standard therapy and give rise to recurrent disease. There is, however, a considerable gap in understanding the specific mechanisms responsible for chemoradiotherapy resistance in SCLC. Our project is unique among the current portfolio of SCLC funded programs in that we have focused on chemoradioresistance to increase cure rates in LS SCLC. Recently, our work has suggested using patient- derived xenograft (PDX) models of SCLC may be an important tool to elucidate mechanisms of therapy resistance. This approach was remarkably successful, identifying a tolerable and strongly synergistic anti- SCLC interaction that led to a CTEP-approved trial based on our preclinical data - (NCI #10070; Study Chair: Hann). In this research program, we will test key hypotheses via three specific aims that will provide more mechanistic insights into the rapidly emergent chemoradiation resistance observed in LS SCLC. One central hypothesis of this proposal is that adaptive gene expression changes mediate rapid emergence of the chemoradiation resistance phenotype in LS SCLC. We have developed a novel chemoradiation treatment regimen with SCLC PDX models to facilitate these studies. Development and characterization of this novel model involves a unique collaboration between medical oncologists, radiation oncologists, bioinformaticians, medical physicists, veterinarians and molecular/cell biologists that is extremely well suited to develop an integrated program dedicated to resolving questions of SCLC chemoradioresistance. Finally, we have already identified novel gene targets that are correlated with SCLC chemoradioresistance. Our research program is organized as follows: Aim #1: Characterize natural history of response of experimental models of SCLC to chemoradiation in vivo. We will determine response rates and recurrence patterns of a panel of SCLC PDXs and transgenic mouse models. Aim #2: Characterization of molecular underpinnings of SCLC chemoradiation resistance. We will reconstruct gene regulatory networks and gene expression profiles associated with chemoradiation resistance and develop small-scale predictive classifiers for therapy response to be validated in follow-up studies. Aim #3: Pharmacologic and genetic validation of candidate genes for SCLC chemoradiation resistance in vitro and in vivo. We will validate our novel gene candidates for conferring chemoradiation resistance using pharmacologic and genetic approach with SCLC PDX-derived organoids and SCLC transgenic mouse models.
Investigating CREBBP as a tumor suppressor in Small Cell Lung Cancer
PI: David MacPherson
Organization: Fred Hutchinson Cancer Research Center
Grant #: R01 CA200547
ABSTRACT: Small cell lung cancer (SCLC) is a neuroendocrine cancer of the lung with dismal survival rates. There are no therapies for SCLC directed towards tumors harboring specific driver mutations. Recent genomic analyses and our own preliminary data revealed that CREBBP mutation/deletion is frequent in human SCLC. CREBBP is an acetyltransferase that acetylates histones and other proteins. CREBBP is emerging as a frequently mutated gene in hematopoietic tumors as well as certain solid tumors, but functional evidence of CREBBP tumor suppressor activity in solid tumors is lacking. We have evidence that CREBBP functions as a critical tumor suppressor gene across multiple neuroendocrine tumor types including SCLC. Our aims are to identify the mechanisms through which CREBBP suppresses SCLC and to test a therapeutic approach directed towards CREBBP-mutant SCLC. Specific Aim 1: To characterize effects of CREBBP deletion in a mouse model of small cell lung cancer and in human cell lines. We will inactivate Crebbp using a sensitized mouse model of SCLC that is driven by lung specific deletions in Rb and p53. In this mouse model, tumors arise with long latency, providing an ideal system to test the ability of potential SCLC driver mutations to accelerate tumorigenesis. Specific Aim 2: To identify mechanisms through which CREBBP deletion collaborates with Rb and p53 loss to promote SCLC. We hypothesize that Crebbp loss collaborates with Rb and p53 loss to promote neuroendocrine tumor types through control of gene expression. By integrating transcriptional data from Crebbp wild-type vs. mutant murine neuroendocrine pituitary tumors, thyroid tumors and SCLC, we will identify a common group of Crebbp-controlled genes across multiple Rb/p53-deleted neuroendocrine tumors. Focusing on SCLC, we will also identify genomic sites with reduced histone acetylation and proteins with reduced acetylation upon CREBBP deletion. Functional experiments will interrogate candidate CREBBP effectors for tumor suppressive activity. Specific Aim 3: To determine whether Crebbp-mutant tumors exhibit sensitivity to HDAC inhibition. We hypothesize that CREBBP deficiency will result in sensitivity to histone deacetylase (HDAC) inhibition as this could potentially restore lost histone acetylation. We will determine whether HDAC inhibition will lead to regression of Crebbp-mutant neuroendocrine tumors employing both genetically engineered and patient derived xenograft models. CREBBP is emerging as a frequently mutated gene in many solid tumors and is one of the most frequently mutated genes in SCLC, but there is a poor understanding of how CREBBP functions as a tumor suppressor. Through integrative analyses of genomic data we will identify Crebbp-controlled tumor suppressive signaling networks. We will also determine whether inactivation of Crebbp leads to sensitivity to the HDAC inhibitor romidepsin. As romidepsin is an FDA- approved drug, positive results could rapidly be translated to improving therapies for patients with CREBBP- mutated tumors
Extracellular vesicles in small cell lung cancer early detection
PI: Patrick Nana-Sinkam and James Lee
Organization: Virginia Commonwealth University and Ohio State University
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
Organization: New York University and Dana-Farber Cancer Institute
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
Organization: New York University
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
Organization: The University of Texas MD Anderson Cancer Center and Stanford University
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
Organization: UT Southwestern Medical Center
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
Organization: The University of Texas MD Anderson Cancer Center
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. Additionally, 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.
Exploiting POU2F3 addition in the tuft cell variant of Small Cell Lung Cancer
PI: Christopher Vakoc
Organization: Cold Spring Harbor Laboratory
Grant #:U01 CA242919
ABSTRACT: Small cell lung cancer (SCLC) is the most aggressive form of lung cancer, which is associated with a high mitotic rate, early metastatic spread, and a rapid evolution of chemotherapy resistance. We recently discovered a novel form of SCLC that resembles the tuft cell lineage, which can be distinguished from the classical neuroendocrine form of this disease through immunohistochemical staining of POU2F3. Importantly, we have identified several molecular vulnerabilities that are specific to the variant form of this disease. In this research proposal, we seek to advance personalized therapies that exploit the unique lineage program present in the tuft cell variant of SCLC. Our innovative functional genomics strategy has already uncovered actionable dependencies that are unique to tuft cell variant of SCLC, such as the kinase IGF1R. In addition, we discovered a profound addiction of tuft cell variant SCLC tumors to POU2F3. Here we will investigate the molecular basis of POU2F3 addiction in SCLC, with the explicit intent to develop small molecules that interfere with POU2F3 function. The first Aim of this proposal will build upon the extensive epigenomic analyses we have performed in SCLC, which has defined a unique enhancer landscape sustained by POU2F3 in this disease. We will now employ two independent functional approaches to elucidate the critical POU2F3 binding sites/enhancers in the genome of SCLC cells, which will be leveraged to pinpoint the critical components of the tuft cell lineage circuit that might be targeted therapeutically. The second Aim will evaluate POU2F3 cofactors, which we have already nominated via an innovative ChIP-SICAP-mass spectrometry analysis of endogenous POU2F3 binding sites. We will perform CRISPR exon scanning and biochemical analysis of each cofactor to define the critical POU2F3:cofactor interactions that selectively support this malignancy. The final Aim of this proposal will employ functional genomics to devise drug combinations with the IGF1R inhibitor linsitinib that are rational and exploit synthetic- lethal genetic interactions. We will also employ our latest CRISPR innovation, homolog co-targeting CRISPR screens, to expose redundant kinase vulnerabilities that are linked with neuroendocrine versus tuft cell variants of SCLC. In summary, we estimate that the tuft cell-like variant is present in ~18% of SCLC cases, which corresponds to approximately 5,000 newly diagnosed SCLC cases and approximately 3,500 deaths in the United States alone each year. Hence, the proposed research could lead to a sustained impact that affects a large patient population for which novel medicines are desperately needed.
Role of MYC family members in driving chemoresistance in Small Cell Lung Cancer
PI: Eli Grunblatt
Organization: Fred Hutchinson Cancer Research Center
Grant #: F30 CA232475
ABSTRACT: Small cell lung cancer (SCLC) is a highly aggressive, frequently metastatic cancer that accounts for approximately 35,000 new cases annually in the United States alone. While many patients initially respond well to cisplatin-based chemotherapy, relapse within months is nearly universal. Relapsed disease is frequently resistant to chemotherapy, contributing substantially to the poor overall prognosis of SCLC patients. Decades of study have yet to produce an FDA-approved targeted therapy or a detailed understanding of chemoresistance, severely limiting treatment options for patients with relapsed disease. However, recent studies and preliminary data in this proposal suggest that overexpression of MYC family members, such as MYCL and MYCN, may play a role in SCLC chemoresistance. Therefore, detailed investigation of MYC family member overexpression in SCLC could lead to meaningful clinical advances. This proposal seeks to determine how increased levels of MYCL and MYCN contribute to chemoresistance in SCLC tumors. Aim 1 will utilize genetically engineered mouse models of SCLC, an autochthonous system, to study whether and by what mechanism MYCL or MYCN overexpression affects SCLC tumor response to cisplatin and etoposide. Aim 2 will seek to confirm and extend these findings by examining the effect of lentiviral MYCL or MYCN overexpression on response to cisplatin and etoposide in chemonaive patient derived xenograft human tumor models. These studies will deepen our understanding of the mechanisms by which SCLC develops and maintains a chemoresistant phenotype. Ultimately, the results of the experiments in this proposal can inform development of novel therapeutic agents to successfully target SCLC chemoresistance and alleviate suffering of the tens of thousands of patients with this disease.
Understanding the molecular mechanisms of a protein-recycling complex in small cell lung cancer treatment resistance
PI: Benjamin Lok and Brian Raught
Organization: University Health Network, Toronto, CA
Grant #: U01CA253383
ABSTRACT: Small cell lung cancer (SCLC) patients have an initial robust response to combinations of DNA damaging agents (e.g. cisplatin, etoposide, radiotherapy), however, many patients inevitably suffer from relapse and resistant disease. A clear understanding of these resistance mechanisms remains elusive. Consequently, there is a critical need to: (1) understand the mechanisms of therapeutic resistance and (2) develop novel therapeutics. Poly-(ADP)-ribose polymerase enzymes (PARP) protein levels are upregulated in SCLC relative to other lung cancers, and initial studies suggest that this upregulation is associated with increased sensitivity of SCLC to PARP inhibitors (PARPi) in vitro. PARP inhibitors are synthetic lethal with BRCA1/2 mutated homologous recombination (HR) deficient tumors and restoration of HR by BRCA reversion mutations is a known mechanism of PARPi and cisplatin resistance. However, as BRCA1/2 mutations are exceedingly rare in SCLC non-BRCA mechanisms must be operant. We performed a genome-wide CRISPR knockout screen to identify novel mechanisms of PARPi resistance. From subsequent functional validation and clinical genomic correlation, we identified deficiency in an F-box protein coding gene as a putative biomarker of resistance to PARP inhibitors and cisplatin in SCLC that may be present in up to ~20% of relapse patient tumors. Loss of this F-box protein abrogates the function of its corresponding SKP1, CUL1, F-box (SCF) E3 ubiquitin ligase complex. By proximity-dependent biotin identification (BioID) of this F-box protein, we have identified a high confidence interactor with substrate-like behavior for SCF-mediated ubiquitin-proteasomal degradation that is important for regulation of HR and DNA repair. This proposal aims to: (1) determine the mechanism of this specific SCF complex with its substrate to engage the ubiquitin-proteasome pathway; (2) elucidate the impact of this F-box protein on HR, DNA repair, and therapeutic sensitivity to PARPi/cisplatin; and (3) identify synthetic lethal interactions with deficiencies in this F-box protein to provide biologic insight and characterize immediately translatable approaches for relapsed treatment resistant SCLC.
Investigation of sub-Lineages in pulmonary neuroendocrine cells and identification of the cells of origin of small cell lung cancer
PI: Joyce Chen
Organization: University of Chicago
Grant # R00 CA226353
ABSTRACT: Small cell lung cancer (SCLC) remains a major challenge in public health because of its frequency, its lethality, and the paucity of convenient models for exploring its pathogenesis and potential therapeutic strategies. Pulmonary neuroendocrine cells (PNECs) are believed to be the putative precursor of SCLC. However, increasing evidence shows that PNECs contain sub-lineages varying in location, cell size, and physiological functions. In my previous research, I developed a novel experimental approach for studying the biology of PNECs - and the initiation of SCLC - by differentiating human embryonic stem cells (hESCs) into the lung lineage, and subsequently perturbing three tumor suppressor genes that are frequently altered in SCLC. By perturbing NOTCH signaling, the lung progenitor cells can be differentiated into PNECs that further undergo oncogenic transformation and form SCLC-like tumors in mice, when RB and P53 expression are reduced. Single cell RNA (scRNA) profiles demonstrated great similarity between the hESC-derived PNECs and the native PNECs in human and mouse lung. Of particular significance, scRNA analysis further revealed sub-lineages within the hESC-derived PNECs. Among them, one profile demonstrated significant similarity to the RNA profiles of early stage human SCLC tumors and SCLC cell lines. The above findings and recent studies by others, led me to further hypothesize that the PNEC sub-lineages have different oncogenic potential, and among them, one specific population serves as the dominant cell of origin of SCLC. I propose to use this model together with other methods such as scRNA transcriptomics, genetically engineering mouse models, to test this hypothesis and to study the origins of SCLC in several ways. First, I will identify the PNEC sub- lineages in normal human and mouse lung tissues that are similar to the ones in the hESC-derived PNECs. Alternatively, sub-lineages of PNECs in mouse lung will be characterized by scRNA profiling and new cell-fate markers identified from the mouse PNEC sub-lineages will be extrapolated to further delineate the heterogeneous populations in human PNECs. Next, I will purify the sub-populations of hESC-derived PNECs and test their transformative potential in culture and in immunocompromised mice by known oncogenic events in SCLC. Alternatively, the PNEC sub-lineages in mouse lung can be tested for their potential to form tumors by using conditional Rb1/Trp53 knockout mice. Through these studies, I expect to identify a specific sub-lineage of PNECs that are most sensitive to SCLC mutations and capable of transformation, which would implicate them as the cell of origin in SCLC. In the R00 phase, I propose to expand the research to explore mechanisms driving the lineage hierarchies of PNECs and their variant oncogenic potentials. These include studying inter-differentiation among the PNEC sub-lineages, the effects of NOTCH, SOX2 and other single pathways on PNEC fate determination, and using CRISPR screening to explore new molecular events important in maintenance of PNEC hierarchical patterns and the regulation of their specific oncogenic capacity. These studies are expected to not only advance our understanding of carcinogenesis of PNECs, but also provide new opportunities to diagnose, categorize, treat, and possibly even prevent this disease more effectively.