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Targeting CD74 to Overcome Resistance to EGFR Inhibitors in Lung Cancer

2023

EGFR Resisters / LUNGevity Research Award

EGFR Resisters

Susumu Kobayashi, MD, PhD

Beth Israel Deaconess Medical Center

Boston

Tyrosine kinase inhibitors (TKI) are a class of drugs that are used to treat EGFR NSCLC. These drugs eventually stop working and some cancer cells called drug-tolerant persisters (DTPs) are implicated in this resistance. Dr. Kobayashi and his team have found that a protein called CD74 plays a role in developing a resistance to osimertinib. In this project, he will investigate whether CD74-expressing cells allow for the development of DTPs and if inhibition of CD74 by combining an antibody-drug conjugate (CD74-MMAE) with osimertinib, prevents resistance. If successful, this has the potential to significantly impact the survival of EGFR patients by allowing them to stay on osimertinib for a longer duration.

Research Summary

Non-small cell lung cancer (NSCLC) with certain mutations in the EGFR gene at advanced stages can be treated with drugs called EGFR tyrosine kinase inhibitors (TKIs). However, these drugs can eventually stop working as cancer cells develop resistance. Recent evidence suggests that some cancer cells called drug-tolerant persisters (DTPs) are responsible for this resistance. These cells survive and adapt to TKIs during early phases of therapy, and can give rise to resistant cells through various mechanisms. Therefore, targeting DTPs may be a way to prevent resistance to EGFR TKIs. Our research team has found that a protein called CD74 plays a critical role in the drug-tolerant state of cancer cells. We have found that CD74 upregulation signals resistance to a third-generation EGFR TKI called osimertinib, and blocks apoptosis, which allows tumors to grow back. Based on these findings, we hypothesize that elimination of CD74-expressing cells in addition to EGFR inhibition may be a better treatment strategy than EGFR inhibition alone, because it could suppress the emergence of DTPs. In our proposed research, we will investigate whether CD74-expressing cells give rise to DTPs, and how CD74 is upregulated and prevents apoptosis in tumor cells exposed to osimertinib. We will also evaluate the effectiveness of CD74-antibody-drug conjugates (ADCs) alone or in combination with EGFR TKIs using cell culture systems and animal models. CD74-ADCs target and eliminate tumor cells expressing CD74 on the cell surface. Our goal is to better understand the mechanisms underlying resistance to EGFR-TKIs and the emergence of DTPs, and provide preclinical evidence that combined inhibition of CD74 and EGFR is a rational and effective treatment strategy for EGFR-mutated lung cancer.

Technical Abstract

The development of tyrosine kinase inhibitors (TKIs) revolutionized treatment of advanced/metastatic non-small-cell lung cancer with EGFR mutations. Osimertinib is one of several third-generation EGFR TKIs and shows improvement in progression-free survival and overall survival compared to first- and second-generation EGFR TKIs. However, intrinsic or acquired resistance to osimertinib emerges in essentially all patients, which prevents a cure for EGFR-mutated lung cancer. Therefore, it is necessary to develop better strategies to improve clinical outcomes. Recent evidence suggests that drug-tolerant persister (DTP) populations of cancer cells, which survive and adapt to TKIs during early phases of therapy, play an important role in the emergence of resistance to targeted therapies. Such DTP cells give rise to resistant cells via diverse mechanisms and contribute to spatial and temporal heterogeneity of tumors. Therefore, targeting DTP cells may be an efficient strategy to prevent resistance to EGFR TKIs. Using lung cancer cell line models and clinical specimens, we recently identified CD74 as a novel gene that plays a critical role in the drug-tolerant state. In vitro and in vivo experiments demonstrate that CD74 upregulation signals osimertinib resistance and blocks apoptosis, enabling tumor regrowth. Based on preliminary evidence, we hypothesize that CD74 increases tumor cell survival in the presence of TKIs and that elimination of CD74 positive cells by CD74-antibody-drug conjugates (ADCs) may suppress the emergence of DTP cells, which underlie relapse. In this proposal, we will test this hypothesis by: 1) confirming that CD74-positive cells are tolerant to EGFR TKIs; 2) investigating the mechanisms by which osimertinib induces CD74 expression; and 3) evaluating a combination of CD74-ADCs and osimertinib to prevent the emergence of acquired resistance. We will address these questions using cell culture systems and animal models. These experiments should unveil the mechanisms underlying resistance to EGFR-TKIs and the emergence of DTP cells, and provide preclinical evidence that a combination of CD74-ADC and EGFR TKIs is a rational and efficacious treatment strategy for EGFR-mutated lung cancer.

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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.

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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.

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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.

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

2022

ALK Positive

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.

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Young lung cancer: psychosocial needs assessment

2022

Health Equity and Inclusiveness Junior Investigator Award

Narjust Florez, MD

Dana-Farber Cancer Institute

Boston

Dr. Florez will study the psychosocial and financial impact of lung cancer in young patients (< 50 years of age). This patient population has seen an increase in incidence in recent years, but little is known about their specific needs. The study will include administration of a survey and focus groups to understand unmet needs of this group of patients. The information gathered from this study will be used to identify challenges unique to this population and develop the first clinical and research program of its kind for young lung cancer patients.

Research Summary

The number of lung cancer cases in young patients (<50 years of age) is increasing across the globe, from Asia to the United States. Young patients with lung cancer are more likely to be women, of Hispanic or Asian descent and be diagnosed with metastatic disease. In this patient population, a lung cancer diagnosis is not age normative and is profoundly disruptive. Young patients often receive more aggressive treatments and face long-term side effects. While we have seen substantial progress in mental health research in recent years, little is known about the psychological needs of young patients with lung cancer, including how they compare to those of older patients, the financial toxicity associated with their cancer treatments, and how their experiences with the healthcare system impact their wellbeing. Most survivorship studies in lung cancer have included small numbers of young patients with lung cancer, with many of these studies preceding newer cancer treatments like targeted therapy and immunotherapy.

We proposed a mixed-method study that will be designed in conjunction with an experienced research team and lung cancer patient advocates. The study will be divided into two phases 1) we plan to administer a survey that explores the psychosocial needs and the financial impact of cancer treatments to a group of young and old patients with lung cancer; this survey could be completed online, in person, or over the phone with trained personnel 2) following the survey completion, information from the survey will be used to create a guide for focus group discussions; we will conduct four focus groups with young patients with lung cancer to expand on the knowledge obtained from the survey. Focus groups are a powerful way to gain a comprehensive understanding of patient experiences by interacting on a personal, exploratory level to hear patient voices and understand their needs. We will also investigate the differences in these needs by gender and race/ethnicity in our two groups. The study results will be shared with the lung cancer patient community via a series of webinars.

The knowledge obtained from this study will be used to create the first clinical program dedicated to young patients with lung cancer in the nation and the creation of an international consortium that will focus on understanding why the number of lung cancer cases is increasing in patients <50 years of age. Most importantly, we will use the information to create interventions to improve this vulnerable population's clinical care and psychosocial support. Our study will be the first of its kind to critically evaluate the psychosocial needs of young patients with lung cancer in a diverse patient population with a secondary focus on their experiences with the healthcare system and the financial impact of a cancer diagnosis and treatments.

Technical Abstract

Background: In recent years, an increasing incidence of lung cancer among young patients (<50 years) has been reported in Europe, Asia, and the United States. Young patients with lung cancer are more likely to be women, of Asian or Hispanic descent, have adenocarcinoma histology, and are more likely to present with distant metastases at diagnosis. Although young patients with lung cancer are more likely to be diagnosed at a disruptive time in their lives and face greater mental health and financial challenges than older patients with lung cancer, we lack data regarding their specific psychosocial needs. The lack of inclusion of young patients in survivorship studies has created a knowledge gap that we propose to remedy with the proposed study.

Aim and Hypothesis: The overarching aim of this study is to define the psychosocial needs of young patients with lung cancer and evaluate important cancer care delivery factors, including financial toxicity, gender and racial differences and study participants’ experiences with the healthcare system. We hypothesize that young patients will have greater unmet psychosocial needs and financial toxicity than older patients with lung cancer.

Methods: This study will utilize an expert, multi-disciplinary research team aligned with patient advocates to deploy an explanatory sequential mixed methods design to understand the needs of young patients with lung cancer. We will conduct a cross-sectional two-arm survey regarding psychosocial distress and financial toxicity among a diverse patient population utilizing two validated questionnaires, the Psychosocial Screen for Cancer (PSSCAN-R) questionnaire and the COmprehensive Score for financial Toxicity (COST) assessment. After the quantitative data collection is completed, we will conduct a preliminary analysis that will guide the discussion in the next phase, where we will conduct four focus groups with young patients with lung cancer to expand and obtain in-depth answers about the issues discovered in the survey portion of the study. The study team will collaborate with experienced biostatisticians and qualitative data researchers to conduct the appropriate statistical analysis.

Results and Dissemination Plan: The study results will be submitted to an international conference and later be published in a high-impact journal. In addition, we will disseminate the study results to the lung cancer patient community via a series of webinars; these webinars will be recorded and later shared with patient advocacy groups and lung cancer organizations.

Long-term Outcomes: Our data will yield insights to inform the oncology community of the barriers encountered by young patients with lung cancer and will allow us to develop the first clinical and research program for young patients with lung cancer in the nation.

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Improving lung cancer screening adherence among underserved populations

2021

Health Equity and Inclusiveness Research Fellow Award

Eduardo Nunez, MD

Boston University School of Medicine

Boston

Technical Abstract

Lung cancer remains the leading cause of cancer death worldwide and clinical trials show that annual lung cancer screening with low-dose Computed Tomography can reduce lung cancer-related mortality by 20%. Marginalized populations are disproportionately affected by lung cancer and our prior work has shown that these disparities extend to lung cancer screening; in a national cohort of Veterans we found that Black Veterans, those with mental health disorders and lower income were less likely to adhere to lung cancer screening follow-up recommendations. Currently, little is known about how to optimize lung cancer screening in underserved populations and marginalized populations from diverse backgrounds.

This proposed project focuses on identifying barriers and facilitators to lung cancer screening at the patient, provider, facility and community-levels. We plan to use mixed methods to quantitatively explore factors associated with delayed or lack of adherence to lung cancer screening and then perform in-depth qualitative analysis to identify which factors are critical and modifiable. We will use an implementation strategy mapping tool to select evidence-based strategies best suited to address the identified barriers and develop a tailored implementation plan to improve adherence to lung cancer screening, both overall and among underserved populations, at Baystate Health System. This work is critical in achieving equity in lung cancer screening and improving overall lung cancer mortality among patients.

Key words

Early detection

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Overcoming ALK resistance with covalent cysteine-reactive inhibitors

2020

ALK Positive

A. John Iafrate, MD. PhD

Massachusetts General Hospital

Boston

Liron Bar-Peled, PhD

Massachusetts General Hospital and Harvard Medical School

Boston

Research Summary

The treatment of ALK fusion-positive lung cancer has been revolutionized by precision medicines including ALK kinase inhibitors resulting in improved survival for most patients. However, as we learned with crizotinib and with subsequent ALK inhibitors, most patients eventually relapse with treatment resistant tumors. Unfortunately, once resistance to multiple kinase inhibitors develops, there are few effective options available. Here, we propose to address this urgent need by developing novel inhibitors which target ALK-rearranged lung cancer. Using cutting-edge chemical proteomic technologies, we will develop therapeutic inhibitors that bind tightly to the ALK fusion proteins and cause the protein structure to become inactive. We will test the efficacy of these new inhibitors in reliable cell models of ALK tumors to demonstrate that they can induce tumor cell death. If successful, our program should deliver frontier inhibitors for ALK fusions, providing critical knowledge to direct the development of transformative lung cancer therapies with the hope of making ALK-fusion positive lung cancer a chronic disease.

Technical Abstract

The current standard of care for ALK rearranged non-small cell lung cancer (NSCLC) is targeted therapy with ALK tyrosine kinase inhibitors (TKIs) which bind within the kinase domain of ALK. Due to the development of ALK resistance mutations or bypass activation of parallel or downstream signal pathways, patients inevitably relapse. Even with the introduction of second or third generation TKIs, median overall survival has been estimated to be 6.8 years . Recent advances in immunotherapy have demonstrated progress in lung cancer treatment. However, a majority of ALK positive NSCLC patients have yet to realize the benefits from checkpoint inhibitors or CAR-T cell therapies due to primary resistance or toxicity. Therefore, the development of new treatments for ALK-rearranged NSCLC is an area of critical need. We believe that an effective assault on ALK-driven tumors requires the implementation of creative strategies that allow us to expand our arsenal of drugs to target ALK beyond its kinase domain. To meet this challenge, we have developed and employed cysteine druggability mapping (CDM), a method to define the landscape of inhibitor-protein interactions in a cancer cell. CDM identifies cysteines that can bind to covalent drug-like molecules which serve as early prototypes on which to base cancer drug development programs.
Cysteine-reactive covalent inhibitors have already emerged as an effective approach to targeting protein kinases. Osimertinib, a third-generation epidermal growth factor receptor (EGFR) TKI covalent inhibitor, overcomes EGFR T790M resistance mutations following treatment with EGFR TKI, demonstrating significant improvements over standard EGFR TKIs when used as first line therapy. Importantly, targeting cysteines with covalent inhibitors massively expands the number of proteins which are targetable with small molecule inhibitors, including many targets previously considered undruggable.

We will use ALK fusion positive cancer cell lines, together with tumor tissues from patients who developed resistance mechanisms, to generate druggable cysteine profiles by CDM. Druggable proteins specific to ALK fusion positive samples, including EML4-ALK itself, will be prioritized in our screening for protein degraders from a library of over 2,500 advanced cysteine reactive compounds. After screening, we will assess the specificity of the compound hits and validate their anti-tumor activity using ALK fusion positive cell lines and patient derived ALK TKI-resistant cell lines. We consider the use of the novel, cutting-edge cysteine targeting technology to screen for potent therapeutic compounds as a valuable proposition to improve management of patients with ALK positive lung cancer, with the goal of transforming this cancer into a chronic condition.

Key words

Acquired resistance

Anaplastic lymphoma kinase (ALK)

Biomarker or biomarker testing

Metastatic

Molecular profile or molecular testing

Mutation profile

Non-small cell lung cancer (NSCLC)

Stage III

Stage IV

Tyrosine kinase inhibitors (TKIs)

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Overcoming bypass signaling to enhance clinical responses in ALK-positive lung cancer

2020

ALK Positive

Ibiayi Dagogo-Jack, MD

Massachusetts General Hospital

Boston

Research Summary

Despite initial sensitivity to treatment with ALK tyrosine kinase inhibitors (TKIs), ALK-rearranged (ALK+) lung cancers invariably develop resistance. The majority of ALK+ lung cancers will eventually acquire ALK-independent survival mechanisms that allow them to escape ALK inhibition. These ALK-independent survival signals can originate from alternative growth receptors (“bypass tracks”). We have recently identified activation of MET signaling resulting from increased copies of the MET gene in approximately 20% of ALK+ tumors that are resistant to next-generation ALK TKIs. In the laboratory, combining lorlatinib with crizotinib (an ALK/MET TKI) overcame resistance caused by MET signaling. Based on these findings, we will conduct a trial to evaluate whether this promising combination can induce durable responses in ALK+ tumors with MET amplification. As many different bypass signals can mediate ALK-independent resistance in the remaining tumors, our trial will also evaluate whether dual targeting of ALK and MEK or SHP2 (proteins that serve as common signaling hubs for many different receptors) can broadly overcome resistance. During the study, serial biopsies will be performed to assess changes in gene and protein expression induced by treatment. This unique trial will also assess feasibility of using plasma findings to select patients with sensitive ALK+ NSCLC who may benefit from an early combination approach. The overarching goal of these studies is to develop multiple promising strategies for overcoming ALK-independent resistance.

Technical Abstract

With the development of increasingly potent and selective ALK tyrosine kinase inhibitors (TKIs), resistance is commonly mediated by ALK-independent mechanisms, such as bypass pathway activation. As bypass signaling dependencies vary across ALK-rearranged (ALK+) lung cancers, a multipronged approach is needed to broadly suppress potential bypass signals. We have identified MET activation in 20% of ALK+ tumors that are resistant to next-generation ALK TKIs. In preclinical studies, dual ALK/MET blockade re-sensitized MET-amplified ALK+ tumors to lorlatinib. MEK and SHP2 have recently been identified as important effector proteins downstream of several bypass signaling pathways. In ALK+ models harboring diverse bypass signals, pairing an ALK TKI with either a MEK or SHP2 inhibitor demonstrated broad anti-proliferative activity. Based on these findings, we will conduct a clinical trial to evaluate lorlatinib in combination with a MET, MEK, or SHP2 inhibitor for patients with ALK+ lung cancers with ALK-independent resistance. Serial tumor biopsies will be analyzed to characterize molecular determinants of response to combination therapy and identify expression changes induced by treatment. This innovative multi-arm trial will also assess whether dynamics of genetic alterations in plasma can be used to guide intensification of treatment from monotherapy to early combination therapy for patients who have not yet developed resistance to ALK-directed therapy. Collectively, the studies in this grant strive to develop diverse strategies for overcoming ALK-independent resistance, a heterogeneous molecular entity that undermines efficacy of current ALK therapeutics.

Key words

Acquired resistance

Anaplastic lymphoma kinase (ALK)

Biomarker or biomarker testing

Circulating tumor DNA

Metastatic

Molecular profile or molecular testing

Mutation profile

Non-small cell lung cancer (NSCLC)

Stage III

Stage IV

Tyrosine kinase inhibitors (TKIs)

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Phase 1 first in-human clinical trial with a therapeutic ALK vaccine in patients with ALK+ NSCLC

2020

ALK Positive

Mark Awad, MD, PhD

Dana-Farber Cancer Institute

Boston

Roberto Chiarle, MD

Harvard University

Cambridge

Research Summary

About 5% of non-small cell lung cancers (NSCLCs) have DNA mutations in the anaplastic lymphoma kinase (ALK) gene, and patients with this “ALK-positive” subtype of lung cancer are typically young and have never, or only lightly, smoked. For ALK-positive NSCLC, there are a number of FDA-approved oral ALK inhibitor pills, including alectinib, lorlatinib, and brigatinib. While these targeted therapies are initially very effective, the benefit of each of these drugs is usually limited to only a few years because ALK-positive lung cancers almost always develop drug resistance through a variety of complex mechanisms. Although PD-1 inhibitors such as pembrolizumab (Keytruda) have revolutionized the treatment of lung cancer in general, particularly in smoking-associated cancers, most patients with ALK-positive lung cancer do not respond to existing immunotherapies.

We developed an ALK vaccine immunotherapy, composed of small pieces of the ALK protein, which is an effective treatment in animal models of ALK-positive lung cancer. We now plan to launch a first-in-human clinical trial to test this ALK vaccine in patients whose cancer is growing despite treatment with an ALK inhibitor. The vaccine will be tested in combination with an approved ALK inhibitor or with an approved immunotherapy (pembrolizumab). We will also study immune cells in the blood and in tumor biopsies both before and after vaccination to ensure that this novel therapy is generating a proper anti-ALK immunologic response as we would expect. Our goal is to develop a safe and potent ALK vaccine to improve outcomes for our patients.

Technical Abstract

Several tyrosine kinase inhibitors (TKIs) are available for the treatment of ALK+ NSCLC, but resistance to all ALK TKIs (including alectinib, brigatinib, lorlatinib) has been reported and occurs through a variety of mechanisms. Once patients develop resistance to available ALK inhibitors, they are typically treated with cytotoxic chemotherapy rather than immunotherapy since response rates to PD-1 pathway inhibitors in this population are very low. However, our work in mouse models of ALK+ NSCLC has demonstrated that a vaccine generated against the rearranged portion of ALK can both prevent the development of ALK+ tumors and also more effectively treat them once they arise. We have also recently found evidence for anti-ALK immune responses in patients, as a subset of them generate spontaneous ALK autoantibodies.

We aim to translate our preclinical findings to a first-in-human clinical trial. Aim 1 will test the safety and efficacy of a novel ALK vaccine + an amphiphilic CpG toll-like receptor 9 agonist adjuvant, administered in combination with an ALK TKI or PD-1 inhibitor in patients with TKI-resistant ALK-positive NSCLC. In Aim 2, using liquid chromatography data-independent acquisition mass spectrometry, we will directly identify antigenic ALK peptides presented by MHC molecules on the surface of cancer cells from tumor biopsies obtained on trial participants. In Aim 3, we will study pre- and post-vaccination anti-ALK T-cell responses among trial participants by analyzing peripheral leukocytes and intratumoral immune cells. The overarching goal is to develop a vaccine that stimulates patients’ immune cells to recognize and eliminate ALK+ tumors.

Key words

Acquired resistance

Anaplastic lymphoma kinase (ALK)

Biomarker or biomarker testing

Immunotherapy

Metastatic

Non-small cell lung cancer (NSCLC)

Stage III

Stage IV

Tumor microenvironment

Tyrosine kinase inhibitors (TKIs)