Epidermal growth factor receptor (EGFR)

Immunotherapy

Recurrent

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

Eliminating Drug-Tolerant Persister Cells Through T-cell Engineering

2023

Partner Awards

Grant title (if any)

EGFR Resisters/LUNGevity Lung Cancer Research Award

Alexandre Reuben, PhD

University of Texas MD Anderson Cancer Center

Houston

In this project, Dr. Reuben and colleagues aim to develop a novel therapeutic strategy harnessing immune response in EGFR-mutant NSCLC. He will use engineered T cells with receptors targeting EGFR antigens to eradicate drug-tolerant persister (DTP) cells, preventing the emergence of resistance following treatment by osimertinib. This work lays the foundation for use of TCR-engineered T cells in treating patients with EGFR mutations.

Research Summary

Although targeted therapies are extremely effective in destroying tumors, they inevitably leave behind a few cancer cells which persist. These are the cells which eventually become resistant to therapy and lead to the death of patients. Although checkpoint blockade immunotherapy has been largely unsuccessful in EGFR-mutant tumors, immunotherapy via cell therapy may offer promise in this setting. EGFR mutations can give rise to short peptides at the surface of tumor cells, called antigens, which allow the immune system to distinguish tumors from their normal counterparts and to specifically destroy them. Importantly, we have identified several antigens that are found solely on or enriched within EGFR-mutant tumors persisting following treatment with EGFR targeted therapies such as osimertinib/Tagrisso. As a result, we have developed a library of receptors which can be engineered into immune cells to allow their direct recognition and destruction of persisting EGFR-mutant cancer cells on the basis of the unique antigens they display. Here, we propose to test a novel approach to eradicate these EGFR-mutant drug persister cells by treating them with engineered immune cells to eliminate the last remaining persister cell and prevent the emergence of resistance following exposure to osimertinib. Our proposal includes two aims: Aim 1 will focus on determining the impact of EGFR-mutant persister cells on the function of immune cells and on their ability to recognize and kill tumor cells. Aim 2 will focus on assessing the ability of receptor- engineered immune cells to eliminate EGFR persister cells when combined with EGFR targeted therapy in vitro and in vivo.
Together, these aims will allow us to determine the therapeutic potential of this novel treatment strategy approach. Our proposal is highly translational, as we have entered into a partnership with Alaunos Therapeutics, a cellular therapy company performing a clinical trial using engineered immune cells at MD Anderson which could facilitate our ability to move these findings into the clinic. Due to the prevalence of the antigens we are targeting (one of which is found in ~90% of lung cancer patients), our approach could extend to almost all patients harboring EGFR mutations.

Technical Abstract

EGFR mutations render lung cancer tumors resistant to immunotherapy via checkpoint blockade. Fortunately, the development of EGFR tyrosine kinase inhibitors (EGFRi) such as Osimertinib has provided impressive clinical responses in a majority of patients. However, many of these patients eventually recur. Studies by our group and others have identified some of the mechanisms associated with resistance to EGFRi. Although EGFRi eliminate the overwhelming proportion of tumor cells, a limited number of cells persist and have thus been termed DTPCs (drug-tolerant persister cells). Importantly, it is these DTPCs which eventually become resistant and are to blame for patient recurrence, highlighting the importance of eradicating these cells before they become fully resistant. Resistance to EGFR TKIs can emerge via two main mechanisms: oncogene-dependent and independent. While oncogene-dependent mechanisms include accumulation of additional mutations in EGFR such as T790M and C797S, oncogene-independent mechanisms include epithelial to mesenchymal transition (EMT) and small cell transformation. Despite their lack of responsiveness to EGFRi at this juncture, each of these mechanisms offers a unique opportunity to leverage cellular immunotherapy to eradicate EGFR mutant DTPCs before they become resistant, thereby improving clinical outcomes. Over the last few years, we have built a library of T cell receptors (TCRs) which confer the ability to recognize epitopes derived from common EGFR mutations including L858R, T790M, and C797S, as well as from the tumor-associated antigen (TAA) FOXM1 which is overexpressed in tumors, and upregulated upon resistance to EGFRi through EMT and small cell transformation. Therefore, we hypothesize that engineering T cells with receptors targeting these EGFR- and FOXM1-derived antigens allows the destruction of DTPCs following treatment with EGFRi, thereby preventing the emergence of resistance. We propose the following specific aims: Aim 1. Assess the impact of drug-tolerant persister cells on CD8 T cell phenotype and function. In this aim, we will identify immune suppressive mechanisms deployed by DTPCs to inhibit T cell response and function. Aim 2. Evaluate the potential of T cell engineering to eliminate DTPCs. In this aim, we will test the ability of TCR-engineered T cells recognizing epitopes derived from EGFR(L858R) and EGFR(T790M) and from the FOXM1 TAA to eradicate DTPCs in vitro and in vivo. Overall, our proposal aims to demonstrate for the first time that TCR engineering can be used in combination with EGFRi to eradicate EGFR-mutant DTPCs. As a result, this work lays the foundation for use of TCR-engineered T cells in this treatment setting. Most importantly, MD Anderson is currently running a clinical trial employing TCR engineering for the treatment of lung cancer with Alaunos Therapeutics which could provide a clear pathway towards the clinic.

Key words

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Targeting CD74 to Overcome Resistance to EGFR Inhibitors in Lung Cancer

2023

Partner Awards

Grant title (if any)

EGFR Resisters/LUNGevity Lung Cancer Research Award

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.

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

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Combination checkpoint blockade plus VEGF inhibitor in EGFR-mutated NSCLC

2022

Career Development Award

This grant was funded in part by The Huff Project

Joshua Reuss, MD

Georgetown University

Washington

Osimertinib is the standard of care for treating non-small cell lung cancer with EGFR mutations. Unfortunately, the tumors inevitably develop resistance to osimertinib. Currently, very few treatment options exist for patients whose cancers have become resistant to osimertinib. Dr. Reuss is conducting a phase 2 clinical trial to test whether two immunotherapy drugs, atezolizumab and tiragolumab, given with a VEGF inhibitor, bevacizumab, are effective in controlling EGFR-positive NSCLC that has become resistant to osimertinib.

Research Summary

The targeted-therapy (TT) osimertinib has become the frontline standard-of-care for patients with advanced non-small cell lung cancer (NSCLC) who have a mutation in the epidermal growth factor receptor (EGFR) gene, which causes the cancer to grow. Despite this, most people experience progression of the cancer, at which point effective treatments are limited. Immunotherapy targeting the programmed death-1 (PD-1) pathway, while revolutionary for patients without such a mutation, has shown limited benefit in patients with EGFR-mutated NSCLC. Therapies targeting additional immune barriers, as well as a molecule called vascular endothelial growth factor (VEGF), may change this. VEGF suppresses important immune cells and pathways that help make immunotherapy work, and high levels have been found in EGFR-mutated NSCLC. Crucially, several clinical studies have shown promise by combining therapies targeting VEGF with immunotherapy and chemotherapy in EGFR-mutated NSCLC. This suggests that treatments targeting VEGF may help immunotherapy work better in these patients, but how that happens is unclear. It is also unknown if these therapies can be combined without chemotherapy, or if additional immunotherapies can magnify this benefit. To address these questions, we are conducting a phase 2 clinical trial evaluating a novel immunotherapy drug tiragolumab (targeting a molecule called TIGIT) together with the PD-L1-targeting antibody atezolizumab and VEGF-targeting antibody bevacizumab in advanced TT-refractory EGFR-mutated NSCLC. Critically, tumor biopsies and blood samples will be obtained from patients pre- and on-treatment to examine what properties in EGFR-mutated NSCLC make it resistant to immunotherapy, and determine how the tumor and immune system change during treatment. By doing this, we aim to show how therapy targeting VEGF works together with immunotherapy to provide benefit. Knowledge gained from this could help unlock the power of immunotherapy for EGFR-mutant NSCLC, and provide a novel treatment for patients afflicted with this sub-type of NSCLC.

Technical Abstract

The targeted-therapy (TT) osimertinib is frontline standard-of-care for patients with advanced non-small cell lung cancer (NSCLC) harboring mutations in the epidermal growth factor receptor (EGFR) gene. However, nearly all patients develop resistance, at which point treatments are limited. While revolutionary for many cancers, anti-PD-(L)1 immune checkpoint blockade (ICB) has been ineffective in EGFR-mutated(m) NSCLC. Targeting angiogenesis, and specifically vascular endothelial growth factor (VEGF), may be key to changing this. VEGF promotes immunosuppression through multiple mechanisms including inhibition of cytotoxic T-cell trafficking and promotion of regulatory T-cell proliferation. Pre-clinical and clinical evidence has revealed activated EGFR to be a dominant regulator of angiogenesis in EGFRm NSCLC, with increased expression of VEGF and hypoxia inducible factor-1α observed in EGFRm compared to wild-type NSCLC. Clinically, combination chemotherapy with anti-PD-L1 and VEGF blockade has shown efficacy signals in EGFRm NSCLC. However, whether upregulated VEGF potentiates the uninflamed tumor immune microenvironment (TIME), and underlies the observed synergy of these therapies in EGFRm NSCLC, remains unexplored. It is further unknown if VEGF inhibition can be combined with PD-1 blockade to promote benefit in the absence of chemotherapy, or whether blockade of additional checkpoints can further expand anti-tumor immune populations, specifically NK cells, which appear to be upregulated in EGFRm NSCLC responsive to ICB. To address these impactful questions, we have designed a single-arm translationally-focused phase 2 clinical trial assessing the efficacy of tiragolumab (anti-TIGIT) plus atezolizumab (anti-PD-L1) and bevacizumab (anti-VEGF) in advanced TT-refractory, ICB-naïve, EGFRm NSCLC. Critically, the proposed analyses detailed herein of tumor and blood samples obtained pre- and on-treatment will focus on (1) immunopathologic features of ICB resistance in EGFRm-NSCLC and (2) TIME infiltration and immunologic reprogramming imparted by these therapies. The findings from this study will help to define the innate barriers preventing induction of durable anti-tumor immunity by ICB in EGFRm NSCLC, and identify strategies to overcome them.

Key words

Immune checkpoint inhibitors

Immunotherapy

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MET and EGFR as biomarkers for amivantamab in overcoming RET TKI resistance

2022

Partner Awards

Grant title (if any)

The Hamoui Foundation/LUNGevity Lung Cancer Research Award Program

Tejas Patil, MD

University of Colorado Denver, AMC and DC

Denver

Two possible pathways that seem to be important for resistance to RET inhibitors are the EGFR and MET signaling pathways. Conventional methods of detecting EGFR or MET resistance may not identify many cases where both pathways are involved. In this study, Dr. Patil will use several different laboratory techniques to better detect and define EGFR and MET resistance. He anticipates that the EGFR and MET pathways can be blocked by a newer drug called amivantamab, which is a bi-specific antibody that specifically targets both EGFR and MET.

Research Summary

Improved understanding of the genetics of non-small cell lung cancer (NSCLC) has led to the recognition that certain mutations in NSCLC can be effectively treated with targeted therapy. Unlike chemotherapy, targeted therapy interferes with how a cancer grows and spreads by blocking a specific mutation that a cancer cell needs to survive. An important mutation in NSCLC is the RET gene rearrangement. There have been several targeted treatments (such as selpercatinib and pralsetinib) that are highly effective in controlling RET+ NSCLC. While we can achieve durable long-term control with these RET targeted therapies, ultimately resistance is inevitable. An important category of resistance is called bypass signaling. This is when the cancer activates and recruits a different pathway to grow and survive in the presence of a RET inhibitor. Two possible pathways that seem to be important for resistance are the EGFR and MET pathways. Our main hypothesis is that EGFR and MET pathways are recruited by RET+ cancer cells in the presence of a RET inhibitor as a way for the cancer to survive and escape the effects of the targeted treatment. We suspect that the conventional methods of detecting EGFR or MET resistance may not identify many cases where both pathways are involved. In this proposal, we will attempt to use several different laboratory techniques to better detect and define EGFR and MET resistance. We anticipate that the EGFR and MET pathways can be blocked by a newer drug called amivantamab, which is a bi-specific antibody that specifically targets both EGFR and MET. I wrote an investigator initiated clinical trial that has been approved and funded by Janssen. In this clinical trial, we will have a dedicated cohort for RET+ patients and combine amivantamab with their prior RET targeted therapy. We hope this study will provide insights into the nature of EGFR and MET signaling as resistance mechanisms.

Technical Abstract

Patients with RET-rearranged non-small cell lung cancer (RET+ NSCLC) demonstrate dramatic responses to RET tyrosine kinase inhibitors (TKIs). An important category of acquired resistance is through bypass signaling that circumvents the RET pathway altogether. When a dominant pathway (such as the RET fusion) is inhibited by a TKI (such as pralsetinib or selpercatinib), recruitment of bypass signaling can allow the cancer cell to sustain critical oncogenic pathways. We have generated RET cancer cell lines resistant to both pralsetinib and selpercatinib, LC-2/ad (CCDC6-RET) and CUTO42 (EML4-RET), that demonstrate sensitivity to afatinib, suggesting that EGFR activation is a possible mechanism of resistance. Similarly, MET amplification has been observed as an important bypass signal, seen in up to 15% of RET resistant cases. However, this is likely an under-estimate of the true spectrum of MET-mediated resistance. First, there is no consensus on what copy number (or gene-to-centromere ratio) defines MET amplification in the acquired resistance setting. Second, MET amplification is likely one of many potential mechanisms of MET-mediated resistance. Finally, the level of MET signaling needed for cancer cells to survive in the presence of a RET TKIs may be different than if MET was a de novo driver oncogene. Our central hypothesis is that MET and EGFR expression are present at baseline to varying degrees among patients with RET+ NSCLC. The use of RET TKIs selects for cancer clones that efficiently and effectively utilize bypass signaling through pre-existing EGFR and MET pathways where both have been described as mechanisms of resistance in oncogene-driven subtypes of lung cancer. Amivantamab (JNJ-61186372) is an EGFR-MET bispecific antibody that has shown synergistic inhibition of tumor growth when combined with EGFR TKIs such as lazertinib. In the ongoing CHRYSALIS Phase 1/2 study of amivantamab with lazertinib, an objective response rate of 29% was seen among 28 patients who had no identifiable mechanism of resistance to EGFR or MET TKIs. One interpretation is that several patients in this analysis had EGFR or MET signaling as a mechanism of resistance that were not being captured through traditional biomarker assays. We anticipate that a similar scenario will be present among patients with RET+ NSCLC progressing on RET TKIs. I have written an investigator-initiated trial (IIT) titled “A phase 1/2, open label, study of amivantamab (JNJ-61186372) among participants with advanced NSCLC harbouring ALK, ROS1, and RET gene fusions progressing on tyrosine kinase inhibitors without identifiable mechanisms of acquired resistance” that has already been approved and funded by Janssen. This trial will have a dedicated RET cohort that will allow us an opportunity to obtain samples pre and post-amivantamab. This infrastructure will allow us to readily test the relevance of MET and

Key words

RET or rearranged during transfection

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Molecular Characterization of Lineage Plasticity

2021

Partner Awards

Grant title (if any)

EGFR Resisters/LUNGevity Lung Cancer Research Award

Helena Yu, MD

Memorial Sloan Kettering Cancer Center

New York

As a mechanism of resistance to EGFR inhibitors, cancers can change histology from adenocarcinoma to small cell or squamous cell lung cancer. Once this happens, EGFR inhibitors are no longer effective treatment; there are no strategies currently available to prevent or reverse transformation after it has occurred. Dr. Yu will use advanced molecular techniques to identify genetic changes that contribute to transformation. Understanding these genetic changes will identify biomarkers that can be utilized to develop treatments to prevent and reverse transformation.

Research Summary

Metastatic EGFR-mutant lung cancer remains an incurable disease despite significant advances in cancer therapeutics. With better EGFR inhibitors, we have identified new mechanisms of resistance that are independent of EGFR signaling, notably small cell and squamous cell histologic transformation. Targeted therapies are ineffective and survival is shortened once transformation has occurred, and no strategies are available to prevent or reverse transformation after it has occurred.

Mutations in EGFR, TP53, and RB1 are associated with transformation, but additional genetic or epigenetic changes must occur for transformation to happen. We will use advanced molecular techniques to identify the mutations and cell signaling pathways that drive transformation in order to identify biomarkers that can be utilized to develop treatments to prevent and reverse transformation. Treatments will then be validated in our unique pre-clinical models which can be rapidly translated into clinical trials, providing treatments for these aggressive cancers.

Technical Abstract

EGFR-mutant lung cancers (LC) serve as the prototype oncogene-driven cancer and mechanisms of resistance to EGFR therapy are well-established. Selective pressure of EGFR inhibitors can induce lineage plasticity to escape oncogene-dependence. While we have shown EGFR/TP53/RB1-mutations are necessary but insufficient to induce small cell transformation, no other genomic signatures and transcriptomic/epigenomic effectors that induce transformation have been identified.

Using parallel exome sequencing, bulk RNA sequencing, and bisulfite sequencing, we will characterize the biomarkers of transformation in EGFR/TP53/RB1-mutant LC and mixed adenocarcinoma/squamous cell tumors. We will also utilize single-cell RNA sequencing to identify the transcriptional changes associated with transformation and to identify distinct cell types within a heterogenous tumor. We will reconstruct a phenotypic landscape to identify subclones in a transitional state between histologies. The information obtained from these studies will nominate novel biomarkers of lineage plasticity that will be validated and proposed for study in clinical trials.

Key words

Biomarker or biomarker testing

Molecular profile or molecular testing

Mutation profile

Small cell lung cancer (SCLC)

Squamous cell lung cancer

Tyrosine kinase inhibitors (TKIs)

Tumor microenvironment

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Targeting Drug Tolerant States + DNA Damage to Block Osimertinib Resistance

2021

Partner Awards

Grant title (if any)

EGFR Resisters/LUNGevity Lung Cancer Research Award

Christine Lovly, MD, PhD

Vanderbilt University Medical Center

Nashville

Despite high tumor response rates, patients treated with EGFR targeted therapies, such as osimertinib, inevitably develop disease progression. Mechanisms of drug resistance remain incompletely understood on both a genomic and proteomic level. The objective of Dr. Lovly’s project is to find new targeted treatments and drug combinations that can tackle cancer evolution and osimertinib resistance.

Research Summary

The problem of EGFR TKI resistance has not been solved. Despite the impressive anti-tumor results observed for some lung cancer patients treated with immune checkpoint inhibitors targeting PD-1/PD-L1, these benefits do not seem to extend to patients whose tumors harbor EGFR mutations. As a result, there is an urgent need to optimize and extend the benefit of TKI therapy.

With osimertinib’s utilization in the first-line setting, there are now no FDA-approved targeted therapy options for patients who develop osimertinib resistance. The majority of studies to date have focused on treating osimertinib resistance once the resistance has already developed and the patient has signs of tumor growth. However, our focus is centered upon the development of up-front combination regimens that will block resistance before it emerges, analogous to the use of combination anti-microbials therapies for treatment of patients with TB and HIV.

We focus on analysis of drug-tolerant persistor cells (DTPCs) – the tumor that we can still see on scans in the clinic, even after patients have had a partial response to osimertinib. We seek to take partial shrinkage to complete tumor regression using cutting edge single cell biology techniques. We have assembled a team of expert investigators working collaboratively to tackle this pressing issue and develop new treatments for our patients in a complete bench to bedside manner. We also aim to train the next generation of researchers so that there is a robust and diverse pipeline in place to continue to advance lung cancer studies.

Technical Abstract

Despite high tumor response rates, patients treated with osimertinib inevitably develop disease progression. Mechanisms of both intrinsic, adaptive, and acquired drug resistance remain incompletely understood on a genomic and proteomic level. Our overall objective is to find new targeted treatments and drug combinations that can tackle cancer evolution and drug resistance.

We seek to:

Understand biological determinants of response prior to therapy (poor prognosis features)
Utilize correct combination therapies in the first line to enhance response, based on biological features of subpopulations present at the start
Reprogram cells toward a more drug-sensitive state through understanding network plasticity.

More specifically, our aims are:

To define the genomic and proteomic characteristics of drug-tolerant persister cells (DTPCs) under dynamic treatment with osimertinib. Our goal is to identify new vulnerabilities in EGFR-mutant tumors which, when therapeutically targeted, can maximize the depth and duration of benefit to first-line osimertinib therapy.
To decipher mechanisms of altered cell cycle progression and osimertinib-induced DNA damage that drive tumor progression.

We have assembled a collaborative, multi-disciplinary team of laboratory scientists and clinical investigators combined with cutting edge technologies to assess genetic and proteomic heterogeneity at the single cell level, access to a robust pipeline of patient samples, and strong preliminary data to support our studies. The proposed aims are expected to define the molecular determinants of tumor heterogeneity and to develop rational therapeutic strategies for delaying / overcoming resistance. These synergistic aims are highly relevant to the current landscape of EGFR-mutant lung cancer.

Key words

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Overcoming heterogeneity and resistance in EGFR-mutant NSCLC

2017

Career Development Award

Zofia Piotrowska, MD

Massachusetts General Hospital

Boston

Targeted therapies have become a mainstay of treatment for non-small cell lung cancer patients whose tumors test positive for a targetable driver mutation. The EGFR mutation is one such targetable mutation. New third-generation EGFR inhibitors have recently entered the clinic and can be very effective therapies for some patients who develop resistance to first- and second-generation EGFR inhibitors. Unfortunately, we are now seeing that cancer cells can also learn how to outsmart these third-generation inhibitors, and new and more effective treatments are needed. Dr. Zofia Piotrowska is studying how lung cancer cells become resistant to third-generation EGFR inhibitors, such as osimertinib, and how the heterogeneity of EGFR-mutant lung cancers can contribute to resistance to drugs like osimertinib. During the period of this award, Dr. Piotrowska will also be conducting a clinical trial testing a novel drug combination developed to prevent or delay the development of drug resistance among patients with EGFR-mutant lung cancer.

Research Summary

EGFR tyrosine kinase inhibitors (TKIs) have led to dramatic improvements in clinical outcomes among patients with EGFR-mutant lung cancer, but patients typically become resistant after about one year. In 50-60% of cases, resistance is driven by the secondary EGFR T790M resistance mutation. There is now growing evidence that resistant cancers are heterogeneous and that this influences resistance to subsequent therapies. In this proposal, we will take a comprehensive approach to study and characterize the heterogeneity of EGFR-mutant lung cancers and its impact on how cancers respond and become resistant to treatment. We will utilize innovative methods to study heterogeneity on multiple levels, including cell-by-cell variations within individual tumors, variations across different sites of cancer within an individual patient, and fluctuations in heterogeneity over time through “liquid biopsy” analysis. Finally, we will test a new combination treatment strategy designed to delay the emergence of resistance, and use the clinical trial to collect patient samples which will facilitate further studies of how resistance and cancer heterogeneity develops. Ultimately, we aim to identify more effective therapies to decrease heterogeneity, induce more durable responses and improve clinical outcomes.

Technical Abstract

Background: Osimertinib and other “third-generation” EGFR TKIs effectively overcome T790M-mediated resistance in EGFR-mutant lung cancer, but our understanding of acquired resistance in this setting remains limited. Importantly, the intrinsic heterogeneity of resistant cancers leads to clinical challenges. We hypothesize that in-depth study of 3rd-generation TKI resistance and the impact of genetic heterogeneity on treatment response will lead to improved therapeutic options and clinical outcomes. Study Design: We will analyze tumor biopsies, ctDNA and autopsy specimens using a variety of techniques such as next-generation sequencing, digital droplet PCR and whole exome sequencing to characterize heterogeneity in resistant cancers. In addition, we will run a prospective clinical trial to test a novel therapeutic combination designed to minimize heterogeneity and delay progression. On-treatment biopsies and ctDNA collection will be used to study how resistance develops. Impact: This project will leverage our broad array of clinical specimens, well-established translational research program and preexisting industry and academic collaborations to characterize the heterogeneity of resistance in EGFR-mutant lung cancer. We hope to illuminate clinical and biologic implications of heterogeneity, with the ultimate goal of identifying more effective therapies for patients.

Key words

Biomarker or biomarker testing

Circulating tumor DNA

Liquid biopsy

Tyrosine kinase inhibitors (TKIs)

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Axl as a target to reverse EMT, treatment resistance and immunosuppression

2015

Targeted Therapeutics Research Award

Lauren Averett Byers, MD

MD Anderson Cancer Center

Houston

Don Gibbons, Jr., MD, PhD

MD Anderson Cancer Center

Houston

Drs. Byers and Gibbons have discovered that lung cancer cells acquire the ability to hide from the immune system during epithelial-to-mesenchymal transition—a process through which cancer cells develop the ability to spread to other parts of the body (metastasis). The LUNGevity award will help Drs. Byers and Gibbons study the effect of a new drug that can reverse the EMT process and make lung cancer cells more visible to the immune system.

Research Summary

For patients with non-small cell lung cancer (NSCLC), there is an urgent, unmet need for therapies that can overcome resistance to chemotherapy or targeted drugs. Dr. Byers and Dr. Gibbons’ group and others have previously demonstrated that the biological process of “epithelial to mesenchymal transition” (EMT) is a unifying mechanism that drives tumor progression, spread to other parts of the body (metastasis), resistance to standard therapies, and suppression of the anti-tumor immune response. Moreover, they have shown that after EMT occurs: (1) tumor cells overexpress a protein receptor called Axl and immune modulatory proteins (such as PD-L1) that help a cancer cell escape the normal immune system and (2) blocking either Axl or PD-L1 with existing drugs shrinks NSCLC tumors and reduces metastases in mice.

Based on these results, they have developed the first clinical trials of BGB324, an oral drug that inhibits Axl, for lung cancer patients. These will begin patient enrollment this summer. In this project, they will test their hypothesis that Axl drives the EMT process and EMT-mediated immune escape and whether the combination of Axl + PD-L1 inhibitors are more effective than either drug alone (Aim 1); identify biomarkers that predict response to drugs that inhibit Axl (including BGB324) (Aim 2); and test these biomarkers in biopsies from patients treated with BGB324 in the clinical trial (Aim 3).

The ultimate goal of this project is to identify those patients who will benefit the most from drugs that block Axl and to explore whether Axl inhibitors can increase the efficacy of immunotherapy.

Technical Abstract

An estimated 160,000 patients die each year from non-small cell lung cancer (NSCLC), primarily due to the development of metastatic and treatment-refractory disease. Dr. Byers, Dr. Gibbons, and their group have previously demonstrated that the epithelial-mesenchymal transition (EMT) is a unifying mechanism that drives tumor progression, metastasis, resistance to standard therapies, and immune suppression. Furthermore, their group and others have shown that the receptor tyrosine kinase Axl and PD-L1 are overexpressed on tumor cells in the setting of EMT in NSCLC and that targeting either Axl or PD-L1 results in preclinical efficacy in lung cancer models.

Based on these results, they have initiated the first clinical trials of BGB324 (a first-in-class, selective Axl inhibitor) for lung cancer patients in combination with either erlotinib or chemotherapy. They hypothesize that Axl is a driver of EMT and EMT-associated immune escape. Therefore, in this project they will use pre-clinical cell line and animal models to determine the role of Axl in driving EMT, identify predictive markers of response to Axl inhibition, and investigate the efficacy of combination therapy with an Axl inhibitor and an immune checkpoint inhibitor, anti-PD-L1. The biomarkers identified in their preclinical models will be directly tested in fresh tumor biopsies from their Phase 1/2 clinical trial that combines erlotinib with BGB324.

Although NSCLC is a molecularly heterogeneous disease, EMT is a potential universal mechanism of progression and drug resistance across many molecular subtypes. It is their goal to leverage this finding to develop single agent or combination treatment strategies that can be used across the molecular spectrum.

Key words

Biomarker or biomarker testing

Immune checkpoint inhibitors

Immunotherapy