Adenocarcinoma

Epidermal growth factor receptor (EGFR)

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Integration of Liquid Biopsy Assays for the Early Detection of Lung Cancer

2023

Early Detection Research Award

Maximilian Diehn, MD, PhD

Stanford University

Stanford

Lung cancer is the number one cause of cancer-related deaths in the US because it is often found only after it has spread to other organs in the body, decreasing the likelihood of surviving at least 5 years after diagnosis. Only 21% of patients are diagnosed then their lung cancer is early stage, when it is most treatable. The goal of this project is to create a new way to screen for lung cancer using a blood sample that can find early stage disease when patients can still be treated and/or cured. In preliminary work, Dr. Diehn has developed a blood test that can identify tiny amounts of DNA from lung cancer cells and in this study he will improve this test and apply it to patients and healthy controls. If successful, Dr. Diehn’s work has the potential to significantly improve early detection of lung cancer and improve outcomes for patients.

Research Summary

Lung cancer is the number one cause of cancer-related deaths in the U.S. and can affect both smokers and non-smokers. Lung cancer is often deadly because it is usually found after it has spread to other organs like the brain, liver, or bones, at which point it is no longer possible to cure the disease in most patients. But if caught early when the cancer cells are still confined to the lung, it can often be cured with surgery or radiation. Screening for lung cancer in current or former smokers using CT scans has been proven to reduce the number of patients who die from lung cancer by catching the disease early. Although insurance covers it in the U.S., only about 15% of those who qualify actually get screened. Some reasons for this low rate of screening include worries about false positives from CT scans and difficulty accessing radiology facilities. Our goal is to create a new way to screen for lung cancer using a blood sample that can find early stage cancers when they can still be cured. Our method looks for tiny amounts of DNA in the blood that comes from lung cancer cells. We have completed initial tests that show our idea could work. Now, we plan to further improve our test and to apply it to several hundred lung cancer patients and healthy controls. If our experiments are successful, our blood test could eventually be used alongside CT scans to cut down on unnecessary follow-up tests or even replace CT scans as the main way to screen for lung cancer. If so, this work could contribute to saving lives of patients with lung cancer.

Technical Abstract

Lung cancer is the leading cause of cancer in the U.S., with over 238,000 new cases and more than 125,000 deaths expected in 2023. Early detection is crucial for improving prognosis, and low-dose computed tomography (LDCT) scans are recommended for high-risk populations. However, LDCT screening has limitations, including a significant false positive rate and low compliance. New approaches are therefore needed to enhance early detection in high-risk individuals. Liquid biopsy assays that can detect circulating tumor DNA (ctDNA) represent a promising alternative early detection approach. Our group has developed three state-of-the-art liquid biopsy techniques that each have the potential to detect lung cancer noninvasively, including a somatic mutation approach (Lung-CLiP), a methylation-based approach (meCAPP-Seq), and a fragmentomic-based approach (EPIC-Seq). We hypothesize that combining mutation-, methylation-, and fragmentomic-based ctDNA analysis will maximize sensitivity for detecting early stage lung cancers. Our proposal includes three specific aims. In the first aim, we will compare the clinical sensitivity and specificity of meCAPP- Seq, EPIC-Seq, and Lung-CLiP for early lung cancer detection. In the second aim, we will determine the analytical limits of detection for the three methods, which is important for future regulatory considerations. In the third aim, we will develop an integrated liquid biopsy assay that combines meCAPP-Seq, EPIC-Seq, and/or Lung-CLiP. We will test if combining two or all three assays can improve performance over the best- performing single assay. The deliverable of this project will be the identification of the combination of liquid biopsy assays that achieves the best performance for early lung cancer detection. If successful, our work has the potential to significantly improve early lung cancer detection which would lead to improved outcomes for lung cancer patients.

Key words

Biomarker or biomarker testing

Early detection

Liquid biopsy

Squamous cell lung cancer

Risk profile

Screening

Stage I

Stage II

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Role of the RNA Modifier METTL3 in Lung Cancer

2023

Health Equity and Inclusiveness Research Fellow Award

Maria Trovero, PhD

Boston Children's Hospital

Boston

In this project, Dr. Trovero will study the role of METTL3, an RNA modifying protein that is thought to promote tumor initiation and progression. She will evaluate the function of METTL3 by increasing or decreasing its activity in vivo. Results from this study will help establish METTL3 as a possible therapeutic target for lung cancer, and pave the way for understanding the relationship between RNA modifiers and cancer biology.

Research Summary

Lung adenocarcinoma (LUAD) is the leading cause of death from cancer worldwide. The survival rate for lung cancer is only about 18%, highlighting the need for more effective treatments. DNA is encoded in our genomes to make RNA, which encodes proteins. However, RNA can have important functions in our cells independent of making proteins, such as exquisite regulation of gene expression. RNA can also undergo chemical modifications. However, the role of RNA modifications in cancer is still poorly understood. METTL3, a protein that modifies RNA, has emerged as a possible oncogene, a gene that promotes tumor growth. Our collaborator Dr. Richard Gregory discovered that METTL3 activity benefits the growth, survival, and invasion of human cancer cell lines (what we call “in vitro”). I aim to explore the role of METTL3 in LUAD initiation and progression in models that more closely resemble reality (“in vivo”). I will evaluate the function of METTL3 in a LUAD mouse model, by studying the effects of decreasing or increasing METTL3 activity on tumor development. I also want to test how METTL3 impacts early stages of lung cancer. Thus, I will manipulate METTL3 expression in a lung tumor organoid system (a simplified 3-dimensional version of an organ generated from stem cells, that recapitulates in vivo tumor growth). The results of this proposal will help to establish METTL3 as a possible future therapeutic target for lung cancer. This investigation could also pave the way for understanding the links between RNA modifiers and cancer biology.

Technical Abstract

Among mRNA modifications, N6- Methyladenosine (m6A) is the most abundant, catalyzed by a complex that includes methyltransferase-like 3 (METTL3). Although the function of m6A in cancer remains understudied, Gregory’s lab provided functional evidence of METTL3 as an oncogenic protein, promoting translation of oncogenes to promote lung cancer cell growth, survival, and invasion in human cancer cell lines. Lung adenocarcinoma (LUAD) is the most common form of lung cancer, with a survival rate of about 18%, highlighting the need for more effective treatments and understanding LUAD biology.

Our hypothesis: METTL3 is a novel oncogenic factor in lung cancer and plays a key role in tumor initiation and progression. I will test the role of METTL3 in a LUAD mouse model, and in tumor organoid culture system.

Aim 1: Determine the effects of METTL3 manipulation on tumor progression in a LUAD mouse model. Lentivirus will be used to knockdown or overexpress METTL3 simultaneously with activation of oncogenic Kras in the LUAD mouse model for comparison of tumor number, size and histopathological features.

Aim 2: Test the effects of METTL3 on early-stage lung cancer by manipulating METTL3 expression in a tumor organoid model of cancer initiation. Alveolar epithelial (AT2) cells from Kras mice will be infected with Cre and shMETTL3 or METTL3 cDNA to initiate early-stage lung cancer in organoid cultures, to assess organoid size, proliferation and differentiation features.

This proposal could establish METTL3 as a therapeutic target for lung cancer and pave the way for understanding links between epitranscriptome and cancer biology.

Key words

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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

Epidermal growth factor receptor (EGFR)

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Role of KIRs in Regulating Anti-tumor Immunity and Autoimmunity

2023

Career Development Award

Diane Tseng, MD, PhD

University of Washington and Fred Hutchinson Cancer Center

Seattle

Checkpoint immunotherapy has advanced treatment of NSCLC, but the majority of patients do not experience long-term disease control and are at risk for autoimmune-related side effects. In this study, Dr. Tseng will examine specialized cells called CD8+ T that express receptors (KIR+) that suppress autoimmunity to understand how these cells regulate the immune system’s cancer-fighting ability during checkpoint immunotherapy treatment. Insights gained from this study could result in better strategies for improving efficacy while decreasing immune-related side effects.

Research Summary

Checkpoint immunotherapy has greatly advanced the treatment of non-small cell lung cancer, but only a minority of patients experience long-term disease control and all patients are at risk for side effects related to inflammation in normal organs (known as autoimmunity). Notably, patients developing mild autoimmune side effects are reported to have improved response rates to checkpoint immunotherapy compared to patients that do not develop side effects. However, the scientific basis of this relationship between treatment efficacy and toxicity is not well understood. There has been a recent scientific breakthrough shedding light on a novel role of an immune cell subset involved in controlling autoimmunity. These specialized immune cells are CD8 T cells that express killer cell immunoglobulin-like receptors (KIR+ CD8+ T cells) and function to eliminate other immune cells that drive autoimmune disease. This study is examining the idea that KIR+ CD8+ T cells play an important role in controlling autoimmune side effects from checkpoint immunotherapy, but may also impact how well the immune system fights the cancer. The first goal of this study is to understand how the normal functions of KIR+ CD8+ T cells break down when patients develop autoimmune side effects from checkpoint immunotherapy. The second goal of this study is to understand the extent to which KIR+ CD8+ T cells regulates the immune system’s cancer-fighting capabilities. Better understanding the relationship between desirable immune responses against tumor and undesirable autoimmune toxicities can lead to better strategies for improving the effectiveness of immunotherapy and minimizing side effects.

Technical Abstract

Checkpoint immunotherapy has advanced the treatment paradigm for non-small cell lung cancer (NSCLC), but only some patients respond to treatment and many patients experience immune related adverse events (irAE). Understanding the distinct and overlapping mechanisms regulating anti-tumor immunity and autoimmunity due to checkpoint immunotherapy is critical for developing more effective and less toxic therapies. A subset of CD8+ T cells expressing killer cell immunoglobulin-like receptors (KIR) have recently been shown to suppress autoimmunity without impairing anti-viral immunity by eliminating autoreactive T cells. We reason that KIR+ CD8+ T cells may also play an important role in regulating autoimmunity arising from checkpoint immunotherapy. Furthermore, we reason that KIR+ CD8+ T cells may also regulate the activity of tumor-reactive T cells to varying degrees, since tumor-reactive T cells are a specialized type of autoreactive T cells. This study examines the hypothesis that KIR+ CD8+ T cells dampen autoimmunity and anti-tumor immunity during checkpoint immunotherapy treatment. To test this hypothesis, we will first interrogate the activity of KIR+ CD8+ T cells during the development of irAE after immune checkpoint blockade (specific aim 1). Next, we will evaluate the impact of KIR+ CD8+ T cells on anti-tumor immunity in NSCLC (specific aim 2). This study may shed light on the biological mechanisms regulating autoimmunity and anti-tumor immunity in lung cancer patients undergoing checkpoint immunotherapy. Insights gained from this study may pave the way toward clinical strategies for improving immunotherapy efficacy while minimizing irAEs.

Key words

Immune checkpoint inhibitors

Immunotherapy

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The Germline-Somatic Interaction in Young-Onset Lung Cancer

2023

Career Development Award

This grant was funded in part by Lung Cancer Initiative

Jaclyn LoPiccolo, MD, PhD

Dana-Farber Cancer Institute

Boston

Although the average age at diagnosis is 70, thousands of new patients under 45 are diagnosed with lung cancer every year, most of whom have never smoked. Dr. LoPiccolo hypothesizes that these patients may share inherited genetic changes that predispose them to developing lung cancer at a younger age. In a preliminary analysis of young-onset lung cancer patients, Dr. LoPiccolo has found that approximately 30% of these patients carry rare mutations in known cancer-associated genes. In this study, Dr. LoPiccolo will investigate whether these mutations affect response to targeted or immune-based therapies. This insight is likely to identify risk factors among young lung cancer patients, which could lead to improved screening and treatment options for this population.

Research Summary

Lung cancer is the most common cause of cancer death in both men and women. Although the average age at lung cancer diagnosis is 70, thousands of new lung cancers occur in patients under 45 years old, most of whom have never smoked. There have been few efforts to analyze potential causes of young-onset lung cancer, particularly looking for inherited genetic changes, which are present in all cells in the body, that are shared among these patients and might predispose to developing lung cancer at a young age. To investigate whether inherited genes cause lung cancer in young patients, we collected blood samples from more than 350 lung cancer patients aged 45 and under at diagnosis and sequenced their genomes. In a preliminary analysis of 243 patients, we found that roughly 30% of young lung cancer patients carry rare, harmful inherited mutations in known cancer-associated genes, higher than many cancers known to have a strong genetic component. In addition to predicting cancer risk, inherited mutations that are present in every cell may influence how a tumor behaves and responds to treatment. We hypothesize that understanding the inherited contribution to tumor development may affect the response of cancer to targeted or immune-based therapies. Additionally, finding genetic risk factors could identify a group of people eligible for yearly CT screening and early detection of lung cancer (currently only used only for patients over 50 years old with heavy smoking histories), and/or guide therapies for lung cancer patients in the future.

Technical Abstract

Lung cancer is the most common cause of cancer-related mortality in North America. Although the average age at diagnosis is 70, thousands of new lung cancers are diagnosed each year in patients under 45 years over 45 years old (median age of diagnosis = 67). The work proposed here will further define this difference in a larger cohort, and address whether the identified variants or genes affect tumor evolution and treatment outcomes. The aims of our study are to identify a population of young lung cancer patients with elevated germline risk, and to investigate the mechanism of the germline-somatic interaction in young lung cancer. The young lung cancer population also provides a lens through which to better understand oncogene-driven lung cancer that occurs in non-smokers – increasingly important as global smoking rates decline.old, most of whom have never smoked. Given that younger patients develop lung cancer decades earlier and without known environmental insults, we hypothesized that underlying germline genetic variation predisposes to developing lung cancer at a young age. Here, we assembled a cohort of over 350 patients diagnosed with lung cancer at age 45 or younger and performed germline whole-genome sequencing (WGS). Preliminary data from 243 patients with median diagnosis age of 37 showed at least 30% of patients carry clinically actionable pathogenic germline alterations in cancer-associated genes, at rates exceeding those seen in many other cancer types – with key age-specific differences when compared to ancestry-matched lung cancer patients from The Cancer Genome Atlas diagnosed over 45 years old (median age of diagnosis = 67). The work proposed here will further define this difference in a larger cohort, and address whether the identified variants or genes affect tumor evolution and treatment outcomes. The aims of our study are to identify a population of young lung cancer patients with elevated germline risk, and to investigate the mechanism of the germline-somatic interaction in young lung cancer. The young lung cancer population also provides a lens through which to better understand oncogene-driven lung cancer that occurs in non-smokers – increasingly important as global smoking rates decline.

Key words

Early detection

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Gilteritinib for lorlatinib-resistant ALK NSCLC

2022

Partner Awards

Grant title (if any)

ALK Positive/LUNGevity Lung Cancer Research Awards

Angel Qin, MD

University of Michigan

Ann Arbor

Lorlatinib is currently the only approved treatment for patients with ALK-positive NSCLC whose cancers have progressed on prior ALK drugs, and for those whose tumors develop resistance, there is a lack of other treatment options other than chemotherapy. In this study, Dr. Qin will evaluate a novel drug called gilteritinib as a treatment in patients with ALK-positive NSCLC whose tumors have developed a resistance to lorlatinib.

Research Summary

Lorlatinib is the only approved ALK-targeted drug for patients with ALK-positive non-small cell lung cancer (ALK NSCLC) who progressed on prior ALK drugs. The average duration of benefit from lorlatinib is seven months before resistance develops. There are currently no approved ALK-directed therapies after lorlatinib.

Our understanding of lorlatinib resistance mechanisms remains limited. However, we know that 1) cancer cells can develop two ALK mutations that block lorlatinib action and 2) cancer cells can activate other pathways so that cancers no longer exclusively rely on ALK.

This proposal addresses ALK resistance directly, with the goal of opening a clinical trial using a novel drug called gilteritinib. Preliminary tests show gilteritinib prevents ALK NSCLC from using alternative pathways to overcome ALK inhibition. First, we propose to obtain tumor-containing samples from patients who are progressing on lorlatinib and perform in-depth sequencing of these cancer cells to thoroughly describe resistance mechanisms in all detectable cancer clones. Next, we will perform drug sensitivity testing on these cancer cells using approved and experimental drugs, including gilteritinib. Finally, we will open a clinical trial using gilteritinib, already approved for treatment of a blood cancer (FLT3+ acute myeloid leukemia). In multiple pre-clinical studies, gilteritinib was able to kill lorlatinib-resistant cells, but this drug has not been given to patients with ALK NSCLC. Our proposal focuses on bringing knowledge obtained from patients’ cancer cells through extensive analysis directly into a clinical trial with a novel drug, maximizing the impact to patients.

Technical Abstract

Lorlatinib is currently the only approved ALK TKI (tyrosine kinase inhibitor) for patients with ALK NSCLC that have progressed on prior lines of therapy. The clinical benefit of lorlatinib is modest in previously-treated patients with a median PFS of 7 months (1). Mechanisms of lorlatinib resistance are diverse and include novel ALK mutations, compound ALK mutations, and activation of bypass pathways including AXL. Gilteritinib is a dual inhibitor of FLT3/AXL that is approved for relapsed/refractory FLT3+ acute myeloid leukemia (AML). Pre-clinical work using ALK fusion positive cell lines (including those containing compound mutations), patient-derived tumor cells, and in vivo mouse studies all demonstrate the anti-tumor activity of gilteritinib specifically against lorlatinib-resistant ALK NSCLC.

We will recruit patients with ALK NSCLC with progression on lorlatinib and collect patient-derived tumor samples. In addition to surgical, biopsy, or effusion fluid samples, plasma will be collected for isolation of circulating tumor DNA and circulating tumor cells. Whole exome sequencing (WES) will be used to identify molecular alterations that define resistance mechanisms. Ex vivo drug testing will be conducted using our existing platform and will include ALK inhibitors and inhibitors of pathways implicated in resistance such as AXL, MET, mTOR, and MAPK. Results of ex vivo drug testing will be correlated with findings from WES.

Simultaneously, we will open a phase I clinical trial to assess the safety and preliminary efficacy of gilteritinib in patients with lorlatinib-resistant ALK NSCLC. Crucially, clinical endpoints will be correlated with sequencing data and ex vivo drug testing results.

Key words

Anaplastic lymphoma kinase (ALK)

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Development of ALK-specific TCR-T cells for the eradication of ALK+ NSCLC

2022

Partner Awards

Grant title (if any)

ALK Positive/LUNGevity Lung Cancer Research Awards

Roberto Chiarle, MD

Boston Children’s Hospital/Harvard Medical School

Boston

In this project, Dr. Chiarle and his team will generate T cells that have engineered receptors, called TCR receptors (TCR-T cells), that will selectively target and attack the ALK protein that is expressed by tumor cells. Generation of such cells could be a powerful tool to eradicate ALK+ lung cancer cells and form the basis of a TCR-T cell-based clinical trial for patients with TKI-resistant ALK+ NSCLC.

Research Summary

Patients with an ALK-positive lung cancer are typically young. For these patients several oral ALK inhibitors are available as pills, typically alectinib, lorlatinib, and brigatinib. These ALK inhibitors are very effective and well tolerated and most patients respond for long time. However, tumors may progressively develop resistance and start to grow back. In this setting of relapsing disease, few therapeutic options are left because most patients with ALK-positive lung cancer do not respond to existing immunotherapies.

For several years, we have been working to develop immunotherapy tools specifically for patients with ALK-positive lung cancer. In this proposal, the strategy is to re-engineer patients’ naturally occurring immune cells to target ALK selectively expressed by tumor cells. First, we will discover several receptors (TCRs) that T lymphocytes use to recognize ALK and kill tumor cells. Next, we will re-introduce these TCRs into the T lymphocytes to rapidly generate a large pool of killer cells all directed simultaneous against the tumor. The rapid infusion of a large number of TCR-engineered T lymphocytes, called TCR-T cells, will generate a wave of killing toward which the tumor will not have the time to adapt and escape. While the identification of ALK specific TCR might be difficult and elusive, we already discovered a series of very specific TCRs directed against ALK expressed by ALK-positive tumors in mice. Leveraging the discovery of ALK peptides expressed by human tumor cells, we will now discover specific TCRs that recognize ALK in human lung cancer. We will use these TCR-T cells to cure ALK-positive human tumors in combination with ALK inhibitors. We expect that this combination will be extremely powerful to rapidly eradicate tumor cells in the lung as well as in metastatic sites.

Technical Summary

About 5-7% of non-small cell lung cancers (NSCLCs) have a rearrangement of the anaplastic lymphoma kinase (ALK) gene. ALK-rearranged NSCLC is typically treated with ALK tyrosine kinase inhibitors (TKIs), but no effective immunotherapies are available for refractory or relapsed tumors. In previous work, we have shown that ALK is an immunogenic oncoprotein that induces specific T cell responses with potent killing activity against ALK+ tumor cells in the lung and in distant metastatic sites, such as the brain. Thus, the lack of efficacy of standard immunotherapy in ALK+ NSCLC can be bypassed by the development of tools to induce ALK-specific T cell responses. Our central hypothesis is that the generation of T cells engineered to express TCRs (TCR-T cells) that selectively target ALK+ NSCLC will be a powerful tool to completely eradicate ALK+ lung cancer cells.

In preliminary experiments, we have shown the feasibility of the cloning of ALK-specific TCRs against an ALK peptide expressed by a mouse model of ALK+ lung cancer. In Aim 1, we will test the potency, the safety and the in vivo efficacy of ALK-specific TCR-T cells obtained by T cells engineered to express TCRs against ALK in a mouse model of ALK+ lung cancer. TCR-T cells will be tested alone or in combination with ALK TKI. Their efficacy will be compared to natural anti-ALK T cells induced by vaccination in mice. In Aim 2, we will discover and study the activity of ALK-specific TCRs against human ALK peptides. We will leverage ALK peptides we previously identified to be expressed by human ALK+ NSCLC. The killing activity of these human specific TCR-T cells will be tested against human ALK+ NSCLC in vitro and in vivo, alone or in combination with ALK TKIs. We expect to identify potent and specific TCRs as leading candidates for a TCR-T cell-based clinical trial for patients with TKI-resistant ALK+ NSCLC.

Key words

Anaplastic lymphoma kinase (ALK)

Immunotherapy

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Defining and novel therapeutic targeting of ALK fusion protein granules

2022

Partner Awards

Grant title (if any)

ALK Positive/LUNGevity Lung Cancer Research Awards

Trever Bivona, MD, PhD

University of California, San Francisco

San Francisco

Currently available ALK inhibitors are an effective treatment for lung cancer, but tumors can development treatment resistance. In this project, Dr. Bivona will explore a novel way to treat ALK-positive lung cancer by targeting “membraneless cytoplasmic protein granules,” a new mechanism of signaling in ALK-positive lung cancer. His team will use precision medicine approaches that are complementary to current ALK inhibitors and that could improve their efficacy as well as quality of life for patients.

Research Summary

Precision medicines that specifically target anaplastic lymphoma kinase (ALK) gene fusions that drive cancer growth are leading to improved responses and quality of life in many ALK gene fusion positive (i.e., ALK positive) lung cancer patients. While current ALK inhibitors are highly effective, they are not curative in most patients because treatment resistance arises. The studies in this research project focus on the characterization of a new mechanism of oncogenic signaling in cancer that centers on ALK gene fusions in lung cancer. The overall goal we aim to achieve in this project is to create an entirely new approach to treat ALK positive lung cancer by developing a suite of precision therapies that are distinct in their mechanism of action against ALK and that can complement all current conventional ALK inhibitors and even improve their effectiveness, while maintaining safety and quality of life for patients. The work accomplished in this project could yield molecular treatments that better control, or potentially cure, ALK positive lung cancer through improved precision medicine.

Technical Abstract

ALK gene rearrangements (e.g., EML4-ALK fusions) are validated targets in NSCLC and current ALK kinase inhibitors yield impressive responses. Despite this clinical progress drug resistance remains a problem that limits patient survival. Improved therapeutic strategies are critical to identify to improve clinical outcomes. We propose an innovative, multidisciplinary, and collaborative project to hopefully improve the survival of ALK positive NSCLC patients by defining a new mechanism of oncogenic signaling that we uncovered by studying ALK fusion oncoproteins. We aim to capitalize on our discovery of membraneless cytoplasmic protein granules as a distinct mechanism of oncogenic kinase signaling in cancer. Our data suggest a new paradigm in which certain ALK fusion oncoproteins form de novo their own protein-based subcellular compartment devoid of lipid membranes and utilize higher-order protein assembly as distinguishing principles underlying oncogenic output. These properties comprise a mode of oncogenic signaling that is different from that of native receptor tyrosine kinase (RTK) signaling and oncogenic, mutant forms of other RTKs such as EGFR, which both use classical lipid membrane-based signaling. The pathogenic biomolecular condensates formed by ALK fusion oncoproteins locally concentrate the RAS activating complex GRB2/SOS1 and activate RAS in a lipid membrane-independent manner. RTK protein granule formation is critical for oncogenic RAS/MAPK signaling output in cells. We identified a set of protein granule signaling components and established structural rules that define ALK protein granule formation. Our findings reveal membraneless, higher-order cytoplasmic protein assembly as a distinct subcellular platform for organizing oncogenic RTK and RAS signaling. We propose 3 Specific Aims to further unveil key interacting proteins required for ALK fusion protein condensate formation and signaling, characterize compartmentalized protein-protein interactions (PPIs) that drive condensate formation and/or oncogenic signaling, and identify pharmacologic strategies using existing agents to target the key PPIs required for driving this pathogenic biomolecular condensate formation and relaying the oncogenic signaling underlying the biology of ALK-driven NSCLC. The proposed studies could allow for mechanism-based therapeutic strategies to interfere with ALK protein granule assembly per se and that complement current ALK-inhibitors, which are kinase activity inhibitors. The pharmacologic agents we profile include clinical drugs and could be re-purposed and/or chemically optimized readily for clinical translation. This project will provide insight into ALK fusion biology and potential strategies to better control, or even cure, ALK-driven NSCLC.

Key words

Anaplastic lymphoma kinase (ALK)

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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

Immunotherapy

Squamous cell lung cancer

Recurrent