research proposal lung cancer

Lung Cancer Research Results and Study Updates

See Advances in Lung Cancer Research for an overview of recent findings and progress, plus ongoing projects supported by NCI.

On August 11, the Food and Drug Administration (FDA) gave accelerated approval to trastuzumab deruxtecan (Enhertu) for adults with non-small cell lung cancer (NSCLC) that has a specific mutation in the HER2 gene. Around 3% of people with NSCLC have this kind of HER2 mutation.

Giving people with early-stage lung cancer the immunotherapy drug nivolumab (Opdivo) and chemotherapy before surgery can substantially delay the progression or return of their cancer, a large clinical trial found.

Atezolizumab (Tecentriq) is now the first immunotherapy approved by FDA for use as an additional, or adjuvant, treatment for some patients with non-small cell lung cancer. The approval was based on results of a clinical trial called IMpower010.

Quitting smoking after a diagnosis of early-stage lung cancer may help people live longer, a new study finds. The study, which included more than 500 patients, also found that quitting smoking delayed the cancer from returning or getting worse.

NCI scientists and their international collaborators have found that the majority of lung cancers in never smokers arise when mutations caused by natural processes in the body accumulate. They also identified three subtypes of lung cancer these individuals.

FDA has approved the first KRAS-blocking drug, sotorasib (Lumakras). The approval, which covers the use of sotorasib to treat some patients with advanced lung cancer, sets the stage for other KRAS inhibitors already in development, researchers said.

Combining the chemotherapy drug topotecan and the investigational drug berzosertib shrank tumors in some patients with small cell lung cancer, results from an NCI-supported phase 1 clinical trial show. Two phase 2 trials of the combination are planned.

Mortality rates from the most common lung cancer, non-small cell lung cancer (NSCLC), have fallen sharply in the United States in recent years, due primarily to recent advances in treatment, an NCI study shows.

In a study of more than 50,000 veterans with lung cancer, those with mental illness who received mental health treatment—including for substance use—lived substantially longer than those who didn’t participate in such programs.

FDA has granted accelerated approval for selpercatinib (Retevmo) to treat certain patients with thyroid cancer or non-small cell lung cancer whose tumors have RET gene alterations. The drug, which works by blocking the activity of RET proteins, was approved based on the results of the LIBRETTO-001 trial.

Osimertinib (Tagrisso) improves survival in people with non-small cell lung cancer with EGFR mutations, updated clinical trial results show. People treated with osimertinib lived longer than those treated with earlier-generation EGFR-targeted drugs.

A large clinical trial showed that adding the immunotherapy drug durvalumab (Imfinzi) to standard chemotherapy can prolong survival in some people with previously untreated advanced small cell lung cancer.

The investigational drug selpercatinib may benefit patients with lung cancer whose tumors have alterations in the RET gene, including fusions with other genes, according to results from a small clinical trial.

FDA has approved entrectinib (Rozlytrek) for the treatment of children and adults with tumors bearing an NTRK gene fusion. The approval also covers adults with non-small cell lung cancer harboring a ROS1 gene fusion.

Clinical recommendations on who should be screened for lung cancer may need to be reviewed when it comes to African Americans who smoke, findings from a new study suggest.

Use of a multipronged approach within hospitals, including community centers, not only eliminated treatment disparities among black and white patients with early-stage lung cancer, it also improved treatment rates for all patients, results from a new study show.

In everyday medical care, there may be more complications from invasive diagnostic procedures performed after lung cancer screening than has been reported in large studies.

The Lung Cancer Master Protocol, or Lung-MAP, is a precision medicine research study for people with advanced non-small cell lung cancer that has continued to grow after treatment. Patients are assigned to different study drug combinations based on the results of genomic profiling of their tumors.

On December 6, 2018, the Food and Drug Administration (FDA) approved atezolizumab (Tecentriq) in combination with a standard three-drug regimen as an initial treatment for advanced lung cancer that does not have EGFR or ALK mutations.

A new study has identified a potential biomarker of early-stage non–small cell lung cancer (NSCLC). The biomarker, the study’s leaders said, could help diagnose precancerous lung growths and early-stage lung cancers noninvasively and distinguish them from noncancerous growths.

Results from two large clinical trials should cement the value of the drugs brigatinib (Alunbrig) and durvalumab (Imfinzi) in treating non-small cell lung cancer (NSCLC). The trial results, several experts said, confirm that the drugs can improve the outcomes of patients with advanced NSCLC.

Cancer researchers have trained a computer program to scan images of tissue samples to differentiate normal lung tissue from the two most common forms of lung cancer. The program also learned to detect cancer-related genetic mutations in the samples.

In a large clinical trial, the immunotherapy drug atezolizumab (Tecentriq), combined with a standard chemotherapy regimen, modestly increased survival in patients with advanced small cell lung cancer (SCLC). The trial is the first in more than 20 years to show a survival improvement in this cancer.

Results from a large clinical trial show combining an immune checkpoint inhibitor with chemotherapy helped some patients with advanced lung cancer live longer than chemotherapy alone. How will this change the lung cancer treatment landscape?

An analysis of data from a demonstration project led by the Veterans Health Administration may help to better define who is most likely to benefit from lung cancer screening.

Patterns of gene expression may be different in the tumors of some African Americans than in those of whites, a new study has found, and these biological differences may contribute to racial disparities in lung cancer.

FDA has approved alectinib (Alecensa) as a first-line treatment option for patients with advanced non-small cell lung cancer that is ALK positive. Alectinib is the third ALK inhibitor to be approved in this setting.

A collection of material about the ALCHEMIST lung cancer trials that will examine tumor tissue from patients with certain types of early-stage, completely resected non-small cell lung cancer for gene mutations in the EGFR and ALK genes, and assign patients with these gene mutations to treatment trials testing post-surgical use of drugs targeted against these mutations.

FDA approved the combination of dabrafenib (Tafinlar®) and trametinib (Mekinist®) for the treatment of metastatic non-small cell lung cancer (NSCLC) that has an alteration in the BRAF gene called the V600E mutation.

The FDA has approved the targeted therapy ceritinib as an initial treatment for patients with lung cancer that has a mutation in the ALK gene.

FDA approved the immune checkpoint inhibitor pembrolizumab to be used with chemotherapy as a first-line treatment for non-small cell lung cancer.

On April 28, the FDA granted accelerated approval to the targeted therapy brigatinib (Alunbrig™) for patients with metastatic non-small cell lung cancer (NSCLC) and alterations in the ALK gene whose cancer has progressed during their initial therapy.

A demonstration project by the Veterans Health Administration is highlighting some of the complexities and challenges associated with the expansion of lung cancer screening in the United States.

Results from a phase III trial showed that the immune checkpoint inhibitor pembrolizumab (Keytruda®) improved progression-free and overall survival among patients with advanced non-small cell lung cancer compared with chemotherapy.

The FDA has approved atezolizumab and expanded the approval of pembrolizumab for some patients with non-small cell lung cancer.

A new study has identified a potentially critical vulnerability in lung cancers that have mutations in the KRAS gene, and showed that a drug already under study may be able to exploit it.

A blog post on a modeling study from NCI researchers suggesting that individualized, risk-based selection of ever-smokers for lung cancer screening may prevent more lung cancer deaths compared with current screening recommendations.

The FDA has approved uses of the targeted therapy crizotinib (Xalkori®) for patients with advanced lung cancer whose tumors have alterations in the ROS1 gene.

The FDA has approved alectinib to treat patients with metastatic ALK-positive non-small cell lung cancer who have stopped responding to or who are unable to tolerate crizotinib.

The FDA has approved two targeted therapies, osimertinib (Tagrisso™) and necitumumab (Portrazza™), for the treatment of some patients with advanced lung cancer.

Patients with lung cancer are benefiting from the boom in targeted and immune-based therapies. With a series of precision medicine trials, NCI is keeping pace with the rapidly changing treatment landscape for lung cancer.

The FDA has approved the drug pembrolizumab to treat patients with advanced non-small cell lung cancer (NSCLC) whose tumors express a protein called PD-L1.

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• Multidisciplinary Symposium — Screening for Cancer: Monday 15 October 2001, 10.20–12.45
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• Published: 05 May 2015

Proposals for lung cancer screening in the UK

• Janet E. Husband 1  

Cancer Imaging volume  2 ,  pages 6–10 ( 2001 ) Cite this article

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Lung cancer is the most frequent cause of cancer death in the Western world. Low dose Spiral CT offers a new approach to lung cancer detection and early results from screening studies are promising. United Kingdom proposals for a randomized controlled trial of lung cancer screening of spiral CT vs. a control arm of no screening is discussed.

Introduction

Lung cancer is now the leading cause of cancer death in the Western world and accounts for more deaths than the total from colon, lung and prostate cancer combined in the United States[ 1 ]. Although mortality from the disease has been declining over recent years, it remains the most common cause of cancer death in men, and in women mortality is second only to that of breast cancer. The vast majority (>90%) of cases are caused by cigarette smoking. Most patients present with advanced disease for which no curative treatment is available and only 8–14% of patients survive 5 years[ 2 , 3 ]. Therefore, novel approaches to the diagnosis and management of lung cancer are urgently required. Non-small cell lung cancer, which accounts for approximately 70% of all lung cancers, may benefit from screening and early detection because surgery for stage I disease results in 5-year survival rates ranging from 55% to over 80%[ 4 , 5 ].

Lung cancer screening

It is widely accepted that the only valid means of demonstrating the effect of lung cancer screening is by means of a randomized controlled trial with mortality from lung cancer as the primary end-point. Four randomized controlled trials of lung cancer screening were performed in the 1970s, all based on chest radiography together with sputum cytology[ 6 – 9 ]. None showed evidence of reduction in lung cancer mortality although none of the trials had sufficient statistical power to exclude a modest effect. The results of these trials formed the basis of the generally accepted view that lung cancer screening is ineffective.

The National Cancer Institute is reassessing the role of chest radiography in a large randomized controlled trial, the Prostate-Lung-Colorectal-Ovarian (PLCO) Trial, which is designed to have sufficient statistical power to identify a reduction in lung cancer mortality of 10%[ 10 ]. While chest radiography may identify lung lesions greater than 1 cm in diameter, Spiral CT can identify pulmonary nodules less than 5 mm in diameter. This has opened the way for the use of Spiral CT in early detection of peripheral lung cancers.

Early results from non-randomized trials in Japan and the United States using Spiral CT for screening lung cancer have shown that approximately four times as many tumours may be detected with Spiral CT than with conventional radiography. Most of these were stage I and are therefore likely to have a good prognosis[ 11 – 14 ]. The United States Early Lung Cancer Action Project (ELCAP) trial reported by Henschke et al .[ 14 ] enrolled 1000 subjects aged 60 years or over, with at least 10 pack years of cigarette smoking. Lung cancer was detected in 27 (2.7%) by CT and in seven (0.7%) by chest radiography; 23 (81%) had stage I disease at diagnosis. No cancers detected on chest radiography were missed on Spiral CT. Annual repeat Spiral CT detected a further seven interval cancers, all stage I[ 14 ]. Other studies from the Mayo Clinic and Germany have shown similar preliminary results. A recent report from Japan of a 3-year mass screening programme has demonstrated detection of nearly 11 times the expected annual number of early lung cancers[ 15 ].

Currently no randomized controlled trials are being conducted for lung cancer screening using Spiral CT as the intervention arm. The major issue regarding the design of randomized controlled trials (RCT) of Spiral CT is whether to use chest radiography or ‘no screening’ in the control arm. The major disadvantage of using chest radiography as the control arm is that the results of such an RCT would be difficult to interpret as the benefit of chest radiography, if any, is currently unknown. Furthermore, the control arm should represent standard practice and in most of the European studies, including the UK, standard clinical practice is ‘no screening’.

While non-randomized controlled trials will provide information on the frequency of detection of malignant nodules with Spiral CT, none are designed to examine lung cancer mortality in a screened group in comparison with lung cancer mortality in a control group. Therefore, they will not answer the primary question ‘does Spiral CT screening for lung cancer reduce lung cancer mortality?’ In the United States there is increasing belief that Spiral CT for early lung cancer detection is likely to be beneficial, even in the absence of proven efficacy, and demand for this service is rapidly increasing. Thus randomized controlled trials of Spiral CT are timely. At the present time it is impossible to estimate the financial implications of screening but if Spiral CT is shown to be worthwhile, it is likely that the health impact would be as great or greater than that of breast cancer screening. Even if screening reduced lung cancer mortality by only 10% of all lung cancers, it would represent more than double the number of lives saved from breast cancer screening. The effect of Spiral CT screening may well be greater than 10%.

Single-channel Spiral CT has been used in most of the low-dose screening studies to date. However, Multichannel CT, now being introduced widely into clinical practice, provides improved fast data acquisition combined with excellent image quality. This new CT technology is unlikely to be superseded by a significant alternative in the foreseeable future and is advocated for all proposed screening trials. It is important to use the most up-to-date technology because randomized controlled trials take many years to complete and advances in technology during the trial period may lead to criticism of the results.

Although the risk of X-radiation exposure is an important consideration, the dose of X-radiation received at Spiral CT screening is likely to be less than 2.5 mSv per scan, irrespective of the type of scanner used. Adopting the same protocol as Henschke et al. [ 14 ] and using a scanner of above-average dose efficiency, the patient dose is 1mSv[ 16 ]. This compares favourably with the average annual environmental exposure in the UK of 2.2 mSv, some regions receive as much as 10 mSv[ 16 , 17 ]. The radiation dose of Spiral CT will be monitored in a quality control programme by the physicist designated to the study.

The ELCAP study showed that 23% of individuals screened with Spiral CT had pulmonary nodules but only 2.7% of screened individuals had lung cancer, indicating a high ratio of benign to malignant nodules. False-positive Spiral CT examinations or false-positive histology/cytology results from biopsy may lead to unnecessary lung resection, introducing the risks of morbidity and mortality associated with thoracic surgery. However, in the ELCAP study no patient with a benign nodule was referred for thoracotomy. Biopsies were performed on 28 nodules and 27 of these were malignant[ 14 ]. Although risks of biopsy are small, they carry important clinical significance in elderly smokers with chronic obstructive pulmonary disease.

Small peripheral lung cancers may be missed on the initial Spiral CT examination although identified on a subsequent scan. Kakinuma et al .[ 13 ] reported that seven of 22 lung cancers were missed on initial screening with Spiral CT but when detected at follow-up, six of these were stage I. Lung cancers arising in the central airways are also likely to be missed on Spiral CT as the technique is insensitive in detecting small endo-bronchial lesions.

The proposed UK Spiral CT Trial

In the UK in 1999 lung cancer was responsible for 34 240 deaths (22% of all cancer deaths). Proposals for a randomized controlled trial have been developed by the UK Cancer Coordinating Committee for Research — Lung (UKCCCR). The primary research objective of the UK trial is to determine whether lung cancer screening using low-dose Spiral CT reduces mortality from lung cancer. To address this issue a randomized controlled trial of Spiral CT vs. no screening in smokers, 60 years and over, is proposed, with lung cancer mortality as the primary end-point. Smoking cessation will be offered to both the screened and unscreened group. Initially a pilot trial of 2000 individuals is planned, the purpose of which is to determine the feasibility, compliance and costs of a large randomized controlled trial. There will be six participating centres in the pilot.

It is anticipated that approximately 40 000 individuals will be required in the full trial conducted over 5 years to demonstrate a reduction in lung cancer mortality of 25%. In the pilot we propose to perform Spiral CT at baseline and then at 1 year. In the full trial Spiral CT would be performed annually for 5 years (Fig. 1 ).

UK Randomized Trial Design — for 5 years. The power to detect a difference of 25% at 5% level of statistical significance is 84% .

The success of the pilot will be based upon the ability to identify eligible individuals for the trial, the number recruited, and their return for a second Spiral CT scan after 1 year. This information will be used to determine the size, duration and costs of the full trial, provided the pilot is considered to be successful. In addition, the pilot will indicate the proportion of subjects who have nodules which require further evaluation and the proportion of these that are cancers including observation of nodule growth. The algorithm for evaluating nodules is shown in Fig. 2 .

Algorithm for evaluating lung nodules .

Definition and classification of nodules

A pulmonary nodule is defined as soft tissue or ground glass opacity of rounded shape.

Benign nodules: lesions showing central, rim, uniform or other benign distribution of calcification; fat attenuation within the nodule, clear linear or linear branching densities, or known to be stable size for at least 12 months (for CT, defined as within measurement error of up to ∼ 20%).

Micronodules, i.e. ≤4 mm diameter. The characteristics and locations of all nodules will be documented for purposes of future comparison at annual screening CT.

Indeterminate nodules of 5–10 mm diameter whose growth rate is, as yet, undetermined, which do not fall into Category 1.

Nodules >10 mm diameter which do not fall into the description for benign nodules, or those <10 mm if known to be enlarging on serial CT studies. Nodule characteristics may include round or spiculated margins, and cavitation. Focal areas of ground glass are also included in this category.

All Category 3 nodules will be measured and observed for tumour growth at 3, 6, 9, 12 and 24 months.

Nodule measurement

Soft tissue nodules are be measured (in mm) on standard lung and soft tissue windows, as defined above, using the maximum short axis ( x ) and long axis ( y ) diameters taken at the widest point of the nodule. Tumour volume can be calculated from the 2-dimensional measurements using the prolate eclipse formula (dimension x × dimension y × 0.52).

Recent research using specially designed computer software (Nodview) developed by Dr A Reeves and colleagues[ 18 ] at the Weill Medical College of Cornell University, New York, USA, has shown that tumours are frequently irregular in shape and may also grow asymmetrically. This new software, which is currently still under development, promises to be considerably more accurate for assessing tumour growth.

Lung cancer screening is being investigated throughout the Western world using low-dose Spiral CT and some encouraging results have already been published. A randomized controlled trial is generally accepted as the only method of demonstrating a reduction in disease-specific mortality. However, as yet, no randomized trials of lung cancer screening are being conducted. Proposals for a UK randomized controlled trial of Spiral CT vs. no screening are presented.

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Husband, J.E. Proposals for lung cancer screening in the UK. cancer imaging 2 , 6–10 (2001). https://doi.org/10.1102/1470-7330.2001.006

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Published : 05 May 2015

Issue Date : June 2001

DOI : https://doi.org/10.1102/1470-7330.2001.006

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Call for Proposals: Lung Cancer Research

We are seeking to fund pilot programs focused on preventing, intercepting, or curing lung cancer at early stages. Research teams from across BU are invited to apply.

Pre-proposals are due by Friday, July 30. Projects will be selected by a joint steering committee for funding up to a maximum of $250,000 (inclusive of indirect costs) per year, with the opportunity to renew for a second year.

Research Focus

Proposals should be focused on preventing, intercepting, or curing lung cancer at early stages and should consider the concepts that lung cancer is often caused by chronic exposure to respiratory carcinogens that produce cellular/genomic damage, chronic inflammation, and alterations in innate/adaptive immunity—all may trigger the escape of transformed cells from immune surveillance.

Additionally, proposals of interest could include: orthotopic lung cancer animal models (small and large animals) for investigating treatments, intratumoral injection technologies (e.g., formulation, delivery device, procedure enablers), characterization of immunogenic cell death pathways, as well as the use of analytics to develop algorithms to better predict healthcare outcomes (e.g., risk of disease/recurrence).

Proposals that characterize the biology of premalignant lesions, early (resectable) lung cancers, or that substantially improve the detection and treatment of lung cancer at more curable, early stages will also be prioritized for funding. Proposals that investigate immunological changes to the tumor microenvironment after chemotherapy or radiotherapy in advanced diseased will be considered.

Proposal Process

This RFP involves a two-stage process for submission and review of applications. Following the initial pre-proposal deadline, the joint steering committee will identify promising pre-proposals to be expanded into full proposals.

View details about the proposal process and download the full RFP and pre-proposal template on the Industry Engagement website (Kerberos log-in required).

Ready to start planning your care?  Call us at 833-347-1665 to make an appointment.

Research projects.

• Specific Aim 1
• Specific Aim 2
• Specific Aim 3

The NCI Small Cell Lung Cancer (SCLC) Consortium is leading several research projects focused on understanding, screening for, and treating this disease.  

PI: Kristin Lastwika and Stanley Riddell

Organization: Fred Hutchinson Cancer Center

Grant #: U01 CA268066-01

ABSTRACT:   Abstract For the last 30 years, the 5-year survival rate of small cell lung cancer (SCLC) has been less than 7% despite the addition of immune checkpoint inhibitors as treatment options. Therapies like immune checkpoint inhibitors that aim to reengage an immune response may not succeed for SCLC as previous studies have shown downregulation of MHC molecules, low PD-L1 expression and limited immune infiltration. However, SCLC is often associated with autoantibody-driven Paraneoplastic Syndromes, providing evidence for the immunogenicity of SCLC. We propose that chimeric antigen receptor T cells (CAR-Ts) as a novel approach for SCLC immunotherapy that overcomes impediments to endogenous immunity. CAR-Ts are synthetically engineered to fuse antibody ligand binding domains with costimulatory components that activate T cells after engagement of cell surface antigens, and have had considerable success in leukemia, lymphoma, and multiple myeloma. The microenvironment of SCLC is phenotypically closer to CAR-T responsive lymphoma than many solid tumors where CAR-Ts have thus far had limited success. A challenge for CAR-T cells in many solid tumors is the identification of target antigens that are tumor-specific. We have identified 13 novel cell surface antigen and here will prioritize 3 with high prevalence in SCLC. Each of these antigens have post-translational modifications that act as neoantigens and lead to autoantibody production in a high percentage of SCLC cases. We will capture these neoantigen-autoantibodies from SCLC patient-derived B cells, sequence the tumor specific binding sequences, and design and test CARs constructed from the single chain variable fragments (scFvs). The benefit of isolating autoantibodies from SCLC patients to detect tumor-specific neoantigens is three-fold: 1. The antigens identified have already proven to be immunogenic; 2. The variable regions of these human autoantibodies can be directly engineered into ligand binding domains of CAR-T cells; and 3. Autoantibodies can be detected in the blood of patients and serve as tissue surrogate biomarkers to guide CAR-T cell target selection. The CAR-T cells we develop will be rigorously tested in multiple preclinical models that address complementary but non-overlapping therapeutic barriers. These include testing CAR-T cell tumor infiltration, efficacy and toxicity in a library of genetically diverse SCLC patient derived xenografts and identifying, then overcoming, immunosuppressive mechanisms in the immune competent Rb/p53 genetically engineered mouse model. Our team of experts in lung cancer, autoantibody biomarkers, immunology and CAR-T cells is well equipped to execute the development of novel immunotherapies that are desperately needed in SCLC.

PI: Mohamed Abazeed

Organization: Northwestern University

Grant #: U01 CA268052

ABSTRACT: Small cell lung carcinoma (SCLC) is one of the most intractable human cancers to cure. It is an aggressive tumor characterized by rapid growth, metastatic progression, and initial response followed by almost invariable resistance to therapy. Studies to date have not resolved the extent that diverse genetic and epigenetic programs drive SCLC and contribute to its lethality. We combined one of the largest and most diverse inventories of patient-derived xenograft models of SCLC globally with an ex vivo culture system that maintains transcriptional fidelity with matched primary SCLC tumor to identify distinct and dynamic phenotypic states that differ in functional attributes within individual tumors. We show that human SCLC tumors display distinctive equilibria in the proportion of cells in various phenotypic (not merely transcriptional) states. We also show that SCLC states are highly regulated by multivalent cellular plasticity and we measure the kinetics of this plasticity at the single cell level. Importantly, standard of care chemotherapies in this disease preferentially kill specific cancer cell states. In this proposal, we posit that understanding the facets of SCLC’s intratumoral heterogeneity will: 1) contribute to our understanding of a poorly characterized aspect of cancer heterogeneity; 2) reveal how stochasticity and/or ecological cues in single-cell behaviors promote phenotypic equilibrium in cancer populations; 3) provide insight into the biological and clinical behavior of SCLC; and 4) advance desperately needed new therapeutic strategies of epigenetic reprogramming in this recalcitrant disease. Our team of investigators have content expertise in several computational, experimental, and translational methods pertinent to this proposal including human-derived in vivo and ex vivo model systems, single-cell RNA sequencing, bulk genetic and expression analysis, single cell fluorescence tracking, and mathematical and statistical modeling. Our integrative approach is poised to formulate and validate a unified model of cellular states and program diversity in SCLC. If successful, the characterization of malignant cell ontogenic programs (SA1), their plasticity (SA2), and the advancement of new therapies designed to combat plasticity by epigenetic reprogramming (SA3) will advance a unique scientific canvas for the study of this highly lethal disease.

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.

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.

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

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

PI: Eli Grunblatt

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.

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.

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.

PI: Lauren Byers, John Heymach, Jianjun Zhang

Organization: MD Anderson Cancer Center

Grant # U01 CA256780-01

ABSTRACT: Small cell lung cancer (SCLC) is an aggressive malignancy for which there is a critical need for improved therapeutic strategies. While targeted and immune-based therapies have demonstrated encouraging results recently, they have shown benefit in only a subset of patients and, thus, have yielded little to no impact on the survival of unselected populations and even these benefits are limited by the rapid onset of resistance. There are currently no standard markers for selecting treatment or evaluating therapeutic resistance, issues made more challenging by the dearth of available tissue for molecular assessment in SCLC. Recent evidence from our group and others suggests that SCLC is a molecularly diverse disease and can be divided into four subtypes largely defined by the differential expression of three transcription factors [ASCL1 (SCLC-A), NEUROD1 (SCLC-N), and POU2F3 (SCLC-P)], and a fourth subtype with high expression of inflammatory and mesenchymal markers [Inflamed, (SCLC-I)]. Each subtype is characterized, in vitro, by distinct therapeutic vulnerabilities. Moreover, we showed that genomic and immune intra-tumoral heterogeneity (ITH) portends poorer survival, while increasing transcriptional ITH may be associated with therapeutic resistance in SCLC. The overarching goal of this proposal is to systematically investigate heterogeneity in SCLC and its association with therapeutic response, and develop tools to evaluate these features in the clinic. More specifically, we hypothesize (1) That SCLC is heterogeneous and can be divided into major subgroups with distinct therapeutic vulnerabilities; and (2) That greater ITH- assessed either at the genomic, immune, or transcriptional level- is associated with therapeutic resistance in SCLC and can be assessed dynamically during treatment in a non-invasive manner using blood-based biomarkers. To address these hypotheses, in Aim 1, we will assess whether these four molecular subtypes can serve as predictive biomarkers in co-clinical trials in vivo and in retrospective patient tissue analyses, while also developing blood-based strategies to identify the subtypes. In Aim 2, we will assess ITH at multiple molecular levels, including genomic, transcriptomic, methylomic, and immunologic, to characterize how baseline ITH influences patient survival. Lastly, in Aim 3, we will assess dynamic changes in transcriptional ITH following treatment, using paired samples from in vivo models and patient samples, to determine if increasing ITH of molecular subtype drives resistance and whether epigenetic modification may prevent or reverse it. The overall hypothesis tested here is that careful initial molecular subtyping of SCLC tumors, paired with strategies aimed at assessing, then limiting/reversing ITH, may better optimize the rate and duration of response to therapy. The studies will be facilitated by a comprehensive library of patient-derived murine models and extensive clinical data sets and executed by a multidisciplinary team of clinical/laboratory investigators, pathologists, computational biologists, and others with a strong track record of innovation in SCLC and translating laboratory findings into the clinic.