Recurrent

RET or rearranged during transfection

Read more about Novel Protein Degraders for Treating RET Positive Cancer

Developing new therapeutic approaches for RET-positive cancers

2024

Partner Awards

Grant title (if any)

The Hamoui Foundation/LUNGevity Lung Cancer Research Award Program

Romel Somwar, PhD

Memorial Sloan Kettering Cancer Center

New York

This project aims to develop new therapeutic approaches for RET-positive cancers, focusing on overcoming resistance to currently available RET inhibitors. Dr. Somwar and colleagues will investigate ways to block the growth of lung cancers with altered RET in a pathway called MAPK (mitogen activated kinase), which is involved in many biological processes involving cell growth and survival. MAPK is implicated in developing resistance to RET inhibitors and finding strategies to target this pathway in combination with RET could benefit many patients who have no approved therapy options after tumor reoccurence.

Research Summary

Lung cancers are one of the leading causes of death in the US. Significant progress has been made over the past three decades to understand the biology of lung cancers and to stratify these diseases into subsets of patients who will get the maximum benefit of a given form of therapy. New technologies now allow for each patient to have their tumor DNA sequenced to find genetic causes of their cancer. Many genes that regulate cell growth are altered by mutations that cause the unrestricted growth that lead to cancer. Scientists have developed strategies to take advantage of these aberrant genes by finding chemicals or biological agents that will antagonize the protein products of these genes. One gene that is altered in 2% of lung cancers is called RET and there are two drugs that block the tumorigenic function of this cancer-causing gene (oncogene). Although patients respond very well to these two anti-RET drugs at first, they soon become resistant to the therapeutic effects. Additional genetic changes in RET or other genes in the cancer cells that regulate growth are responsible for the drug resistance. Our goal in this grant proposal is to find ways to block the growth of lung cancers with altered RET that stopped responding to anti-RET inhibitors. The strategy that we will test involves the simultaneous inhibition of RET and other proteins in another growth promoting pathway called the MAPK (mitogen activated kinase) pathway. We believe that this therapeutic strategy can benefit more than 30% of patients who stop responding to current drugs that target lung cancers with RET genetic alterations.

Technical Abstract

RET fusions result from abnormal rearrangements of the kinase domain of RET with other non-essential genes and drive tumorigenesis. These oncogenic chimeric tyrosine kinases are found in approximately 2% of non-small cell lung cancer (NSCLC).Two FDA-approved selective RET inhibitors (selpercatinib and pralsetinib) have shown great response rates in lung cancer patients. However, resistance to RET inhibitors inevitably occurs, limiting therapeutic benefit. Multiple mechanisms of resistance to RET inhibitors have been described, including acquired RET solvent front mutations (G810R/S/C/V), and RET-independent mechanisms of resistance due to amplifications of other receptor tyrosine kinases (RTK) including MET, FGFR1 and ERBB2, and alterations in the RAS-MAPK pathway. Some second-generation RET inhibitors that target secondary RET mutations have been recently developed including vepafestinib (TAS0953/HM06) which is currently being tested in phase I/II clinical trials in the US and Japan for RET fusion positive lung cancer. There is a clinical need to identify mechanisms of resistance to vepafestinib and develop strategies to overcome them.

RET with solvent front mutations, amplification of MET/FGFR1/ERBB2 and RAS-MAPK pathway mutations account for >30% of all resistance mechanisms to first-generation RET drugs, and importantly, all of these alterations are expected to activate the RASMAPK pathway. Therefore, a therapeutic strategy that tackles RAS-MAPK pathway activation is expected to benefit >30% of patients who acquire resistance to first-generation RET drugs. Moreover, given that RET fusions, like all tumors arising from activated RTKs engage the RAS-MPAK pathway for oncogenesis, we believe that many treatment-naïve patients may also benefit from a therapeutic strategy that targets RET and the RAS-MAPK pathway.

Our first goal in this proposal is to simultaneously address resistance due to RAS-MAPK pathway alterations and extending the benefit of first-generation RET drugs by developing a combination therapy strategy involving RET and pan-RAS, MEK1/2 or ERK1/2 inhibitors. Our second goal is to decipher mechanisms by which the transcription factor capicua (CIC) regulate RET-driven tumorigenesis and resistance to RET inhibitors. We will perform transcriptomic, epigenic and proteomic profiling to gain insights into RET-ERK-CIC interaction. Our third goal is to identify and target resistance mechanisms to vepafestinib, so that a therapeutic strategy will be in place for when patients being treated with this drug develop resistance.

Our team includes leaders in the field of lung cancer clinical and translation research who have been at the forefront of lung cancer genomics and therapy, developing state of the art therapeutic strategies. We are well positioned to translate the findings from this study to the clinic within two years. These studies have the potential to benefit more than 30% of lung cancer patients with RET fusions.

Key words

RET or rearranged during transfection

Tyrosine kinase inhibitors (TKIs)

Read more about Developing new therapeutic approaches for RET-positive cancers

Immunogenic peptide priming of dendritic cells for RET+ NSCLC

2024

Partner Awards

Grant title (if any)

The Hamoui Foundation/LUNGevity Lung Cancer Research Award Program

Amy Cummings, MD, PhD

University of California, Los Angeles

Los Angeles

This project will explore the use of neoantigens to evaluate immunogenic priming of dendritic cells (DC) in RET+ NSCLC. Neoantigens are short protein fragments present only in cancer cells that bind to genetically encoded proteins known as human leukocyte antigens (HLA). Dr. Cummings will use features of HLA to predict which cancer-specific protein fragments best match an individual’s immune system, utilizing a biobank of RET-rearranged NSCLC biospecimens. This approach could help identify optimal immunogenic targets, that could be translated into a pathway for clinical use of personalized DC vaccines.

Research Summary

RET-rearranged non-small cell lung cancer (NSCLC) is a rare subtype of lung cancer that is driven by growth signals triggered by RET activation. RET-specific inhibitors are effective initially, but most benefit from this treatment for only 1-2 years before additional treatment is needed. Chemotherapy is a widely-available option but typically provides less than six months of benefit, and it is unclear whether immunotherapy alone or in combination with chemotherapy is a better option. Findings from other gene-rearranged NSCLC studies, particularly those on ALK-rearranged NSCLC, suggest that immunotherapy works better when the immune system is better exposed to abnormalities created by the gene-rearrangement. These are neoantigens, or short protein fragments present only in cancer cells that bind to human leukocyte antigen (HLA), a scaffold that displays these protein fragments to the immune system. One issue with this approach is that these fragments have to be specifically matched to the immune system of an individual, and even the most common forms of HLA are only found in 20% of people. This means that these types of approaches would be applicable to at most 1 out of 5 people with RET-rearranged NSCLC. Our techniques broaden this approach by using features of HLA to predict which cancer-specific protein fragments best match an individual’s immune system (motif neoepitopes), including neoantigens from RET rearrangements and those predicted from the individual’s tumor. We propose to use our biobank of RET-rearranged NSCLC biospecimens, which have not been previously analyzed, to determine whether we can detect and elicit enhanced immune responses with motif neoepitopes, neoantigens related to RET-rearrangements, or other predicted neoantigens. We can then offer this approach in a currently open clinical trial investigating immune system optimization through an application to the FDA.

Technical Abstract

RET-rearranged non-small cell lung cancer (NSCLC) presents challenges in management following progression on selective tyrosine kinase inhibitors (TKIs). Platinum-based chemotherapy and docetaxel are available options but are without durable benefit. Real world data with single-agent and combination chemo-immunotherapy suggests modest benefit and possible efficacy if immunotherapy-based approaches are appropriately optimized. For the past decade, our group has meticulously curated hundreds of NSCLC biospecimens including matched tissue and blood from multiple timepoints, including 7 RET-rearranged NSCLC cases that have not previously been analyzed. We have extensive expertise in neoepitope prediction and personalized immunotherapy through dendritic cell (DC)-based vaccination. Our most recent collaboration enabled functional assessments of T-cells through nanovial-based affinity repertoires, further enhancing our ability to predict and translate immunogenic peptides through a personalized vaccine-based program. We propose to use our RET-rearranged NSCLC biospecimens to systematically study T-cell-specific responses to identify optimal immunogenic peptide targets, an approach that could be translated in our currently open and approved DC vaccination trial (NCT03546361) through single patient exemptions.

Key words

RET or rearranged during transfection

Read more about Immunogenic peptide priming of dendritic cells for RET+ NSCLC

Targeting tumor associated macrophages in immunotherapy resistant NSCLC

2024

Partner Awards

Grant title (if any)

Brown/LUNGevity Award to Understand Mechanisms of Resistance to Immunotherapy

Dwight Owen, MD, MSc

The Ohio State University

Columbus

This project will investigate the role of cells called macrophages, key components of the immune system that have multiple functions, including immune surveillance within a unique communication pathway called hedgehog (Hh). The hedgehog signaling pathway is involved in cell growth and differentiation, as well as maintenance of stem cells and tissue repair. Disruption or inhibition of Hh can create an environment that is less favorable for survival of cancer cells, allowing a patient’s immune system to combat it more effectively. This research has the potential to benefit patients who have been diagnosed with NSCLC, who have not responded to current treatments including immunotherapy by boosting the body’s own defense mechanisms.

Research Summary

Lung cancer remains one of the most lethal types of cancer worldwide, with non-small cell lung cancer (NSCLC) accounting for a majority of cases. The goal of our research is to better understand the relationship between certain immune cells called macrophages and NSCLC, and how this interaction contributes to the cancer's survival and resistance to treatment. The scientific premise of our project lies in investigating a unique communication pathway known as hedgehog signaling within these macrophages and determining how it impacts the immune system's ability to fight lung cancer. If successful, our research has the potential to benefit patients who have been diagnosed with NSCLC, particularly those who have not responded to current treatments including treatment with immune therapies. By disrupting the hedgehog signaling pathway in macrophages, we hope to create a tumor immune environment that is less favorable for cancer cell survival, allowing patients' immune systems to effectively combat the disease. This research can pave the way for innovative therapeutic approaches that boost the body's own defense mechanisms.

Technical Abstract

The prognosis for patients with metastatic non-small cell lung cancer (NSCLC) remains poor despite recent progress in immune checkpoint blockade (ICB) therapy. Thus, there is an urgent need to understand mechanisms for lung cancer immune evasion within the tumor microenvironment (TME) in order to develop more effective and durable strategies for treating lung cancer. Tumor associated macrophages (TAMs), a major component of the tumor stromal mass, generally display an anti-inflammatory phenotype and can facilitate tumor growth by promoting angiogenesis, invasion, and metastasis, as well as immune evasion. However, it remains largely undefined exactly how these TAMs regulate anti-tumor immune responses within the TME. Will test the hypothesis that hedgehog signaling in TAMs interferes with recruitment of CD8+ T cells to the TME through the following specific aims: 1) Investigate the role of Hh inhibition with anti-PD-L1 therapy in non-small cell lung cancer; 2) Study the impact of Hh inhibition on TAMs and changes within the TME. The objective of this project is to understand signals required for functional polarization of TAMs within the TME and its contributions to immune cell dysregulation and cancer progression, and whether combined Hh inhibition and ICB can overcome resistance to immunotherapy.

Key words

Immune checkpoint inhibitors

Read more about Targeting tumor associated macrophages in immunotherapy resistant NSCLC

Developing EGFRxHER3 bispecific CAR-T cells for targeting EGFR TKI DTPCs

2024

Career Development Award

Yan Yang, PhD

MD Anderson Cancer Center

Houston

In patients with EGFR-mutant NSCLC, tyrosine kinase inhibitors (TKIs) have been an effective treatment, but over time these patients develop resistance to TKIs, leading to tumor relapse. Dr. Yang’s project focuses on cancer cells called drug-tolerant persisters (DTPs), which are implicated in TKI resistance. A gene called HER3 is expressed in DTPs, and Dr. Yang will use specially engineered immune cells, called CAR-T cells, to target both HER3 and EGFR simultaneously. If successful, this approach would result in a bi-specific CAR-T cell that can be further evaluated in clinical trials.

Research Summary

In lung cancer patients with a specific genetic mutation in EGFR, certain drugs can be helpful, but over time, the cancer can learn to resist these drugs, making them less effective. We're focusing on a small group of tough cancer cells, called DTPCs, that survive the initial treatment because they might be the key to curing the cancer for good. We've noticed that a gene called HER3 is expressed more in these cells. We also have promising results from CAR-T cell therapy. It is a treatment using T cells, a type of immune cells, engineered with the chimeric antigen receptor (CAR) so they can find and destroy cancer cells. We've found that CAR-T cells targeting EGFR can kill DTPCs. We believe if we use these T cells to attack both HER3 and EGFR at the same time, we might have a better chance of killing off these stubborn cancer cells. To make sure this idea works, we'll first check if HER3 is indeed more expressed in these DTPCs in the lab and samples from patients. Then, we'll test our HER3-targeting CAR-T cells to see if they can kill these DTPCs. If that looks promising, we'll tweak the T cells to target both HER3 and EGFR and see if they work even better. If all goes well, we'll be able to make one of the first effective CAR-T cells to target both HER3 and EGFR and try them out in clinical trials.

Technical Abstract

In NSCLC patients harboring mutant EGFR, treatment with tyrosine kinase inhibitors (TKIs) has demonstrated efficacy. However, the emergence of resistance to EGFR TKIs remains a significant challenge, leading to disease progression. Targeting drug-tolerant persister cells (DTPCs), a rare subpopulation surviving initial treatment, emerges as a more effective strategy than awaiting the development of complete drug resistance, holding potential for curative cancer therapy. Based on our preliminary data on the upregulation of HER3 in DTPCs resistant to EGFR TKIs and the potent antitumor activity of EGFR-targeting chimeric antigen receptor (CAR)-T cells against DTPCs. We propose that HER3 is a promising target expressed on EGFR-TKI DTPCs and that CAR-T cells simultaneously targeting both EGFR and HER3 are an effective approach for targeting DTPCs with improved overall efficacy. In this proposal, we will evaluate HER3 as a therapeutic target for CAR-T cell therapy against EGFR-TKI DTPCs by validating its expression in DTPCs using in vitro cell models, in vivo xenograft and PDX models, and patient tissues. Additionally, we will evaluate the anti-tumor activity of HER3-targeting CAR-T cells against DTPCs. Subsequently, we will develop and characterize EGFRxHER3 bispecific CAR-T cells, evaluating their CAR expression, antigen binding affinity, and anti-tumor activity. We next will assess their anti-tumor efficacy in xenograft and PDX models to guide the selection of the most promising bispecific CAR-T cells for further development. If completed successfully, we will have EGFRxHER3 bispecific CAR-T cells ready for GMP-compliant clinical-grade CAR manufacturing, in preparation for clinical trial evaluation.

Key words

Epidermal growth factor receptor (EGFR)

Read more about Developing EGFRxHER3 bispecific CAR-T cells for targeting EGFR TKI DTPCs

TROP2 Directed CAR T in NSCLC as a Strategy for Eradicating Persister MRD

2023

Health Equity and Inclusiveness Research Fellow Award

Elliott Brea, MD, PhD

Dana-Farber Cancer Institute

Boston

This project proposes to develop novel therapeutic approaches to treat advanced EGFR-mutant NSCLC. CAR-T cell therapy is a type of immunotherapy treatment that uses genetically altered T cells to find and destroy cancer cells more effectively. TROP2 is a protein that is over expressed on the surface of NSCLC and is a target of the antibody-drug conjugate (ADC), sacitizumab-govitecan, which is FDA-approved to treat other solid tumors. Dr. Brea hypothesizes that TROP2-directed CAR-T targeting of EGFR-mutant NSCLC will be superior to standard Osimertinib treatment.

Research Summary

While advances have been made in treating advanced or metastatic cases of Non-small cell lung cancer (NSCLC) with either targeted therapy or immunotherapy, most patients will progress after these first line therapies and require subsequent treatments which are limited in efficacy. EGFR mutant (EGFRm) lung adenocarcinoma is the most common type of NSCLC in patients without a history of tobacco use. They often respond to first line treatments called EGFR inhibitors (EGFRi) that target or block EGFR but unfortunately this is usually not curative in patients with advanced or metastatic EGFR mutant lung cancer. Chimeric antigen receptor T-cell therapy (CAR-T) works by engineering a patient’s immune fighting cells called T-cells to fight the cancer utilizing a receptor, which is matched to proteins expressed on the cell surface of cancer cells. When the receptor recognizes the cancer- associated proteins, T cells bring their powerful anti-cancer attack directly to the malignant cells. CAR-T has shown significant promise in blood cancers with durable responses observed. TROP2 is a protein present in NSCLC and is the target of FDA approved antibody-drug conjugate (ADC) sacitizumab-govitecan for breast and bladder cancer and is in clinical trials for lung cancer. Our goal is to demonstrate that TROP2 directed CAR-T cell therapy is effective in NSCLC, and can eradicate disease in a more durable fashion when compared to standard therapy with EGFRi. We plan to use the results of this work to translate this to clinical trials evaluating this promising strategy for treating lung cancer.

Technical Abstract

While immunotherapies in cancer have allowed for major advances in the field, most patients with advanced or metastatic solid tumors do not achieve durable responses. While CAR-T cell therapy and bispecific antibody therapies which utilize T-cells as their effector have shown promise and durable responses in hematologic malignancies such as DLBCL and multiple myeloma, the promise of similar responses in solid tumors remains an unmet goal. TROP2, a cell surface protein normally expressed during fetal development and at low levels in some normal adult tissue, is over expressed on a variety of solid tumors including NSCLC, and has emerged as an ideal target. TROP2 is the target of the recently FDA approved ADC sacitizumab-govitecan for breast cancer as well as for patients with locally advanced or metastatic urothelial cancer and is currently being tested in phase II/III trials in NSCLC. However, response in patients and in animal models are not durable, even when targeting minimal residual disease (MRD; defined as the residual disease after effective genotype directed systemic treatment). We propose utilizing TROP2 directed CAR-T to target EGFRm NSCLC at MRD, which we hypothesize when compared to TROP2 directed ADC will demonstrate a more durable response. Our preliminary data support the high activity of TROP2 directed CAR-T against EGFRm NSCLC including in the MRD state after osimertinib treatment. We expect these findings to translate to approaches utilizing CAR-T cellular therapy to target the MRD state after targeted therapy.

Key words

Acquired resistance

Epidermal growth factor receptor (EGFR)

Read more about TROP2 Directed CAR T in NSCLC as a Strategy for Eradicating Persister MRD

Tumor draining lymph node immunomodulation to decrease recurrence in NSCLC

2022

Health Equity and Inclusiveness Junior Investigator Award

Jonathan Villena-Vargas, MD

Weill Medical College of Cornell University

New York

Lymph nodes are small structures that work as filters for foreign substances, such as cancer cells and infections. These nodes contain infection-fighting immune cells that are carried in through the lymph fluid. This project will study the lymph node draining basin, which is involved in the spread of a tumor from the original location site to distant sites, and whether activating cancer-fighting T-cells can decrease recurrence in NSCLC. Dr. Villena-Vargas will use animal models to investigate whether immune checkpoint inhibitors enhance lymph node T-cells memory, which increases their ability to recognize cancer cells in the bod and can prevent metastatic recurrence.

Research Summary

Approximately 25% of the patients diagnosed with non-small cell lung cancer (NSCLC) exhibit early-stage disease. Patients with early-stage (I/II) NSCLC are routinely treated by surgery, which results in local control. However, systemic relapse (metastasis) occurs in 50% patients within 5 years of surgical intervention even with additional therapy such as chemotherapy and/or radiation. Immune checkpoint inhibitors (ICI) targeting the PD-1/PD-L1 axis have revolutionized the treatment landscape, generating therapeutic efficacy in approximately 25% of patients in early and advanced stages of lung cancer. However, there are currently inconclusive studies as to 1) timing of treatment 2) optimal combination therapy 3) prediction of patient response. In order, to recapitulate early-stage lung cancer treatment and metastatic recurrence, we have established a murine model of resection and recurrence. Our preliminary data has revealed a major immune response at the level of the tumor draining lymph node (TDLN) with PD-1 checkpoint blockade. In addition, this response is primarily responsible for T-cell memory differentiation, proliferation, and survival with subsequent decrease in metastatic recurrence in responding mice. Given these results, we hypothesize that optimal therapy against metastatic recurrence will be dependent on establishment of appropriate T-cell memory “immunosurveillance”. In addition, we have shown that the memory nodal response can be augmented by utilizing a cytokine immunomodulatory combination strategy with cure in over 70% of mice. Importantly, we have characterized that these specific T-cell memory population are uniquely found in the TDLN of early-stage patients (i.e. not in the primary tumor or peripheral blood that is commonly interrogated). In this proposal we will utilize a combination of both novel preclinical mouse models and patient-derived tumor draining lymph node T cells, to dissect molecular and cellular mechanisms of “immune-memory” response or resistance to immunotherapy, the key steps in establishing immunosurveillance for freedom from metastatic recurrence.

Technical Abstract

Anti–PD-1 therapy has transformed the management of NSCLC, but only a subset of patients respond to anti–PD-1 therapy, and responses are rarely curative. Understanding the effects of anti–PD-1 therapy on the composition and functional state of tumor-associated immune subsets can identify mechanisms of response and resistance to anti–PD-1 therapy and provide insights into rational combination strategies to improve upon response rates. Although the effects of anti–PD-1 therapy within the tumor immune microenvironment in preclinical and human subjects have been previously reported, we propose to broadly characterize the effects of anti–PD-1 therapy on the tumor draining lymph nodes (TDLN). Studying the TDLN is particularly valuable because it is the primary sites at which the tumor antigen exposure and the main site of immune T-cell differentiation. To determine the effect of ICI response in the lymph node, we have created an immunocompetent murine model that recapitulates early-stage treatment and outcomes in patients. Additionally, we have characterized TDLN T cells from early-stage cancer patients and have been able to recapitulate our preclinical findings of unique memory T-cell subsets. Our preliminary results of the immune cell type composition, checkpoint expression, and cytokine expression within TDLNs suggest that there are major remodeling events within the TDLN mediated by anti–PD-1 therapy that are critical for conferring effective antitumor long-term immune responses. We demonstrate that unique memory T cell subsets undergo significant activation, expansion, and maturation in response to anti–PD-1 therapy, to shape antitumor programming in TDLNs. Importantly, our proposed study will provide a methodological demonstration in both a murine model and human TDLN that simultaneous uses Flowcytometry, functional immune assays and single cell sequencing that will enable deep interrogation of the immune profile to PD-1 inhibition resistant and responsive patients.

Key words

Immune checkpoint inhibitors

Squamous cell lung cancer

Tumor microenvironment

Read more about Tumor draining lymph node immunomodulation to decrease recurrence in NSCLC

Integrated Blood-Based and Radiographic Interception of Lung Cancer

2017

SU2C-LUNGevity-ALA LC Interception Award

Grant title (if any)

SU2C-LUNGevity Foundation-American Lung Association Lung Cancer Interception Translational Research Team

This grant was co-funded by Stand Up to Cancer, LUNGevity, and the American Lung Association

Lecia Sequist, MD

Massachusetts General Hospital

Boston

Max Diehn, MD

Stanford University

Palo Alto

Tilak Sundaresan, MD

Kaiser Permanente San Francisco

San Francisco

Gad Getz, PhD

Broad Institute

Cambridge

The SU2C-LUNGevity Foundation-American Lung Association Lung Cancer Interception Translational Research Team, headed by LUNGevity Scientific Advisory Board (SAB) member Dr. Lecia Sequist, is developing a lung cancer interception assay (LCIA) that can be used in conjunction with low-dose CT scans. This assay will be based on an integration of several blood-based assays that examine circulating tumor cells and circulating tumor DNA.

Technical Abstract

Statement of the Problem: Currently, low dose CT (LDCT) screening for lung cancer is recommended for high-risk individuals, defined as current or former smokers (quit within the past 15 years) with a 30-or-more pack-year smoking history, 55 to 74 years of age, and with no evidence of lung cancer. However, uptake of LDCT screening has been impeded by high rates of false-positive results, which in turn add significant physical and emotional stress to patients as well as additional healthcare costs. Since LDCT is now commonly available, lung nodules detected in LDCT scans are plentiful, but imprecise guidelines for care make it a challenge to ensure quality follow-up and expedited diagnoses for those with lung cancer. Furthermore, screening is not available for those who don’t meet the screening criteria (younger age or low smoking history) when they are the exact population among whom lung cancer rates are rising.

Proposed Solution: Leveraging expertise of academic research centers (Massachusetts General Hospital, Broad Institute, and Stanford University) and a non-profit managed-care consortium (Kaiser Permanente), the Dream Team will develop a test called the Lung Cancer Interception Assay (LCIA) to complement LDCT screening.

The proposal is novel in that it will develop complex computational algorithms to combine high-sensitivity/high-accuracy blood-based molecular biomarkers with image-based biomarkers to create the LCIA assay. At the end of the award period, a streamlined product, the LCIA, will be ready to use in population-level definitive trials for the early detection of lung cancer.

Key words

Circulating tumor cells

Circulating tumor DNA

Squamous cell lung cancer

Screening

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Molecular mechanisms of acquired drug resistance in small cell lung cancer

2014

Career Development Award

This grant was funded in part by the American Lung Association

John Poirier, PhD

Memorial Sloan Kettering Cancer Center

New York

Small cell lung cancer is an exceptionally aggressive type of lung cancer. While these tumors are initially responsive to a combination of chemotherapy drugs, tumor recurrence is near universal. Dr. Poirier will develop and study models of drug resistance to identify new strategies to overcome chemotherapy resistance.

Research Summary

Small cell lung cancer (SCLC) is a common, aggressive, and exceptionally lethal type of lung cancer that is not typically discovered or diagnosed until it has already spread throughout the body. Newly diagnosed SCLC is remarkably sensitive to combination therapy with a combination of two drugs, cisplatin and etoposide, even in patients with extensive-stage disease. While many tumors respond to therapy, shrinking significantly in bulk, this treatment is never curative – when these tumors return, they are generally quite resistant to further therapy. Extensive-stage SCLC is uniformly fatal; less than 1% of patients will be alive five years after diagnosis. Remarkably little is known about how or why these tumors become resistant to this therapy. Defining the basis of acquired chemotherapy resistance in SCLC could have clear and important ramifications for clinical management of this disease. Targeting the key determinants of acquired chemoresistance could be integrated into first-line treatment, and/or could drive rational targeted therapeutic studies for recurrent disease. There are now multiple technical approaches that could comprehensively define the genomic and epigenetic changes that drive acquired resistance in SCLC. This research will use two parallel approaches to analyzing acquired resistance in SCLC: studying resistance in patient samples and studying resistance in patient tumors grown in mice.

Technical Abstract

Small cell lung cancer (SCLC) is a common, aggressive, and exceptionally lethal malignancy that is usually metastatic at the time of diagnosis. Newly diagnosed SCLC is remarkably sensitive to chemotherapy, with response rates of over 60% to cisplatin and etoposide even in patients with extensive-stage disease. These chemotherapy responses are often both rapid and deep, but are never curative: extensive-stage disease recurs universally, in most cases within a few months after completion of first-line therapy. Recurrent SCLC is remarkably refractory to treatment. The median overall survival of patients with extensive-stage SCLC is about nine months from the time of initial diagnosis, and the 5-year survival is less than 1%. Defining the basis of acquired chemotherapy resistance in SCLC could have clear and important ramifications for clinical management of this disease. Targeting the key determinants of acquired chemoresistance could be integrated into first-line treatment, and/or could drive rational targeted therapeutic studies for recurrent disease. We now have in hand multiple technical approaches that could comprehensively define the genomic and epigenetic changes that drive acquired resistance in SCLC. In this award application, we propose two parallel approaches to analyzing acquired resistance in SCLC: analysis of primary samples and patient-derived xenografts before and after acquired resistance.

Key words

Acquired resistance

Chemotherapy

Small cell lung cancer (SCLC)

Read more about Molecular mechanisms of acquired drug resistance in small cell lung cancer

Molecular predictors of outcome in non-small cell lung cancer

2012

Career Development Award

Christopher A. Maher, PhD

Washington University in St. Louis

St. Louis

Dr. Maher is working to improve on the accuracy and usability of tests that identify lung cancer patients who are likely to relapse. He is using next-generation sequencing techniques to develop a signature set of key genetic changes and convert it to a clinical test that will be able to predict who is at high risk for relapse.

Research Summary

Currently, approximately 30% of non-small cell lung cancer (NSCLC) patients will die from recurrent disease despite undergoing surgery. Therefore, there is a critical need to develop accurate markers to distinguish high-risk patients who are more likely to have recurrent disease from patients who are at a lower risk for recurrent disease. To date several groups have applied high-throughput methods to identify a set of genes, or a “signature,” that will classify patients as high-risk or low-risk. However, there are two limitations to existing approaches. First, technological advances in sequencing technology offer an opportunity to identify additional markers, which would have eluded previous approaches, and therefore could result in a more accurate signature. Second, previous methods for developing a signature were developed on tumor material that is not routinely collected in clinics. This presents a critical need to develop an assay that can effectively apply a predictive signature on samples collected in the clinic. Therefore, our proposal focuses on using newer sequencing technologies to generate a refined signature for predicting which patients have more aggressive disease. We then proposed two goals for adapting this signature into a clinically useful assay. First, we intend to confirm that the predictive signature works on the same sample material collected in a clinic. Second, we intend to test our predictive signature on a completely independent cohort of patients to ensure it accurately stratifies patients with more aggressive disease. Overall, if the proposed aims are met, this research could lead to an improved assay that could be widely adopted in the clinic to stratify high-risk patients for more aggressive therapies and assign less aggressive treatments to patients at low risk for recurrence.

Technical Abstract

Approximately 30% of patients with stage 1 non-small cell lung cancer (NSCLC) will die from recurrent disease despite surgical resection . Currently, there is a lack of reliable molecular predictors being routinely used in the clinic for identifying patients at high risk for developing recurrent disease and therefore may benefit from more aggressive therapies. To date several groups have applied microarray-based methods for global gene expression profiling of frozen tumor tissues in an attempt to identify prognostic ‘signatures’ in patients with early stage NSCLC. Building upon this, through a meta-analysis of seven independent microarray studies Govindan et al. were able to identify a 64-gene signature that is highly predictive of survival in patients with stage I NSCLC. However, recent advances in high-throughput sequencing have enabled an unbiased view of the transcriptome including novel transcriptional events such as gene fusions, splicing variants, and novel transcripts. This offers an opportunity to incorporate additional markers, which may have eluded previous technologies, but could serve for improving a predictive signature of survival in non-small cell lung cancer (NSCLC). However, despite the potential of RNA-Seq to improve existing predictive signatures, we are still faced with the challenge of translating these findings into a platform where they can be reliably applied to formalin fixed paraffin embedded (FFPE) clinical tissue specimens routinely collected in tertiary referral centers. Therefore, this proposal focuses on refining the 64-gene predictive signature using transcriptome sequencing and developing a NanoString nCounter assay to reliably predict survival of patients with resected stage I NSCLC, using RNA derived from FFPE tumor blocks. To accomplish this we have proposed the following specific aims: (1) use transcriptome sequencing to detect molecular predictors of outcome in patients with stage I NSCLC, (2) validate the technical performance of the NanoString nCounter using an RNA-Seq predictive signature across FFPE tumor blocks of resected stage I NSCLC, and (3) clinically validate the prognostic power of the predictive signature across an independent sample set. Overall, if the proposed aims are met, this research could lead to an improved assay that could be translated into future prospective studies for risk-stratifying stage I NSCLC patients.

Key words

Anaplastic lymphoma kinase (ALK)

Biomarker or biomarker testing

KRAS

Molecular profile or molecular testing

Mutation profile