Funded Projects

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

Though the introduction of immune checkpoint inhibitors (ICI) has improved outcomes for patients with stage III non-small-cell lung cancer, most patients do not have robust tumor responses to ICI and real-world patients discontinue ICI due to toxicity at a higher rate than clinical trial populations. There is an unmet need to develop predictive models to identify patients at risk of poor ICI response, high risk of ICI toxicity, and high risk of non-cancer mortality, as these patients are unlikely to benefit from ICI and may require treatment intensification or de-intensification, selection of alternative therapies, or enrollment on clinical trials. In this proposal we seek to leverage the richness and national scale of Veterans Affairs (VA) clinical data to develop statistical models to predict ICI efficacy, toxicity, and non-cancer mortality. We will evaluate specific hypotheses generated from preclinical research and use machine-learning approaches to identify new predictors from high-dimensional VA healthcare data. These models will be integrated into a unified multistate model, allowing prediction of the individualized overall survival benefit of ICI for each patient. Clinical decision-making based on model predictions will be compared to other decision making strategies using decision-curve analysis. This work will identify novel biomarkers of ICI efficacy and toxicity, validate putative ICI effect modifiers from the preclinical literature, and develop the first unified model for ICI clinical benefit. If successful, this tool can be used for patient counseling, physician decision-making, and identification of patients likely to benefit from alternative therapies, treatment de-escalation, or clinical trial enrollment.

Despite recent advances, locally advanced non-small cell lung cancer (LA-NSCLC) continues to have a high degree of morbidity and mortality related to both disease progression and sequelae from treatment. The purpose of this study is to develop and evaluate a more personalized radiation therapy (RT) approach with the potential to reduce time and financial burden to patients and increase tumor control. Patients undergoing fractionated RT with concurrent systemic therapy for LA-NSCLC will be treated to a total dose of 60 Gy with the number of fractions determined by ability to meet key dose constraints resulting in a shorter treatment course and higher biologic effective dose (BED) among those treated with shorter fractionation. To reduce the iterative time to determine fractionation schedule and standardize the"‘isotoxic hypofractionation" approach, we will employ a previously developed automated RT planning technique after delineation of the tumor and organs at risk. Fifty patients will be enrolled in a prospective non-randomized 2-stage trial to test the primary objective of whether isotoxic hypofractionation results in an acceptable rate of grade 2 or higher toxicity. Secondary endpoints will include G3+ toxicity, local control, progression free survival and overall survival. Finally, to better inform future "isotoxic" dosing strategies we will evaluate additional predictors of radiation toxicity using established retrospective cohorts through the Stanford Cancer Institute and the Veteran’s Affairs Information and Computing Infrastructure (VINCI).

Our laboratory has demonstrated the potency of the abscopal effect in studies showing that high-dose radiation therapy delivered to primary tumors in combination with dual immune checkpoint blockade can significantly inhibit the growth of satellite tumors. The implication of such results is that radiation therapy has remote effects which are immune-mediated and that new radiation protocols can be devised to exploit our naturally occurring defenses against cancer. Previous studies have shown that immune-mediated tumoricidal effects can be augmented by combining high-dose radiation therapy delivered to a primary tumor site with low-dose radiotherapy (LDRT) targeting secondary tumors. Tumor response is further enhanced if systemic agents are employed to induce immune-checkpoint blockade (ICB). Such protocols employing conventional LDRT are known to reduce the number of regulatory T cells (Tregs) and to activate natural killer cells, thereby modulating the tumor microenvironment (TME). Our laboratory project seeks to test a modification of LDRT called pulsed low-dose-rate radiotherapy (PLDR). By providing radiation in repeated very low doses, the PLDR regimen may reduce the encasement of tumors with stromal elements, thus removing a barrier to infiltrating immune-reactive cells. We propose to use the immunocompetent lung cancer murine model which we developed for our earlier research combining HDRT with anti-PD1 and anti-CTLA-4 antibodies. HDRT will again be delivered to primary tumors in combination with dual ICB. Additionally, LDRT will be delivered to secondary tumors, both in conventional form and as PLDR. The results will thus test an innovative method for exploiting the emerging synergies of radiation and ICB. A demonstration of the superior therapeutic utility of PLDR in our animal model would be of immediate relevance to clinical trials seeking improved strategies for treating patients with metastatic lung cancer.

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.

Hispanics/LatinX comprise the largest-growing minority group in the United States (U.S.). They account for 18.5% of the total U.S. population1 and are projected to become the largest group in the U.S. by 2045, surpassing NHW. Despite large national representation in the U.S., data demonstrates that this population faces barriers to healthcare access. These barriers are often due, but not limited to socioeconomic status, lack of health insurance, limited medical literacy, language barriers, structural racism, and perceived discrimination. Studies show that Hispanics/LatinX have the highest uninsured rates compared to any other ethnic/racial group, thus limiting their ability to receive equitable health care. This lack of equitable care often leads to Hispanics/LatinX forgoing or delaying medical care, avoiding screening, placing them at elevated risk of an advanced stage of cancer diagnosis. Unlike NHW, cancer remains the most common cause of death in the Hispanic/LatinX population.

LC is the leading cause of cancer-related death for Hispanic/LatinX men and the second most common cause of death for Hispanic/LatinX women. LC carries a 5-year overall survival rate of less than 20%, mainly due to advance stage at diagnosis. Survival rates are even lower for Hispanics/LatinX (13% vs 17%), who are more likely to be diagnosed at advanced stages of LC than their NHW counterparts (59% vs 52%). To increase the rates of early detection, different organizations have supported the use of LDCT as a screening modality in eligible individuals, after results from the NLST showed a 20% mortality reduction in LC with the use of LDCT for screening. Currently, The U.S. Preventive Services Task Force (USPSTF) recommends annual screening for LC in adults 50–80 years of age with at least a 20-pack year smoking history who are current smokers or have quit within the last 15 years. This criterion was extrapolated from the high-risk features in subjects that participated in the NLST that ultimately led to the LC screening recommendations. Unfortunately, the population in the NLST is not an accurate representation of the U.S population, as 95% of the participants were white and only 1.8% were Hispanics. Additionally, studies have shown that LatinX individuals are less aware of LC screening than NHW, but when informed, they are more LatinX interested in pursuing screening (90.7%) compared with non-LatinX (67%).

Besides tobacco use, having a previous malignancy is a risk factor for LC. HNC survivors are at increased
risk of second primary lung cancer compared to the general population, largely due to their heavy smoking history. Patients with tobacco related HNC have up to a 13% risk of developing second primary LC. Currently, the guidelines recommend performing a 3-month post treatment for subjects with head and neck malignancies treated with curative intent. However, NCCN does not advise performing imaging surveillance beyond 6 months in this patient population, unless there are signs and/or symptoms to suggest cancer recurrence. In reference to LC screening, The NCCN recommends annual screening with LDCT for HNC survivors with a smoking history of 20 pack years or more. However, no prospective studies have been performed to assess the risk of second primary LC in this high-risk population. Of the few studies that have been completed, one study completed a post hoc secondary analysis of the NLST to evaluate the incidence of second primary lung cancer in HNC survivors screened with low dose CT (LDCT) versus chest x-ray (CXR). Out of X participants, 171 HNC survivors had undergone screening. Of these, 90.1% identified as White, 4.1% as Black, and 0% as Hispanic or LatinX and lung cancer was identified in 20 (12%) of the HNC survivors screened. A total of 15% (12/82) and 9% (8/89) of the HNC survivors screened with LDCT and CXR, respectively, were diagnosed with LC. The study found a higher LC incidence in HNC survivors compared to participants without head and neck cancer, with an adjusted rate ratio of 2.54 (95% CI, 1.63-3.95). Additionally, the study found an average smoking history of 80 pack years amongst HNC survivors compared to 48 pack years in the rest of the study population.

The study proposed here will fill an important gap and assess the awareness and eligibility of lung cancer
screening in Hispanic/LatinX HNC survivors via a survey questionnaire and understand the barriers to
screening via qualitative interviews. We will create the first lung cancer screening program tailored for and focused exclusively on Hispanic/LatinX HNC survivors.

Despite significant progress in the development of novel biomarkers and therapies for lung cancer, such progress has not equitably benefitted all population groups in the United States (US). Racial and ethnic minorities, low income, uninsured, and underinsured individuals with non-small cell lung cancer (NSCLC) continue to experience disparate access to diagnostics tests and treatments, and experience inferior outcomes. These disparities are, at least, partially driven by social context (i.e., social determinants of health). Patients with NSCLC experience high rates of financial hardship and unmet supportive needs, making them a population likely to have high rates of health-related social needs. The prevalence of social needs in patients with NSCLC and their impact on healthcare utilization, cancer outcomes, and quality of life (QOL) remains unknown. To fill this important knowledge gap, we propose an observational, prospective cohort study of 150 patients with unresectable lung cancer receiving first-line systemic therapy. Our study has two primary goals (Aims): 1) Prospectively quantify the prevalence of social needs and determine the associations between social needs, acute care utilization, and QOL; 2) investigate how patient’s social needs influence oncology providers’ clinical decisions for outpatient cancer care of adults with unresectable NSCLC. To achieve these goals, we will conduct serial survey assessments of 150 patients with unresectable NSCLC and conduct semi-structured interviews with 30 oncology providers. This study is significant as it is the first study longitudinally evaluating social needs during cancer therapy in patients with NSCLC. This study will fill a key knowledge gap and inform interventions focused on identifying and supporting patients at risk of social adversity during cancer treatment.

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.

Lung cancer is the leading cause of cancer-related death in the United States and worldwide. Immune checkpoint inhibitors (ICIs) have shown durable responses and improved survival in some patients with advanced non-small cell lung cancer (NSCLC). However, nearly all patients eventually progress on these therapies, and the median survival for patients with metastatic NSCLC remains around one year. Combining immunotherapy with cytotoxic chemotherapy has shown an incremental benefit but at the cost of increased toxicity. Patients who progress on currently available immunotherapies have few effective treatment options. One significant barrier to ICI therapy efficacy is the tumor microenvironment (TME), which contains immunosuppressive cells including myeloid-derived suppressor cells (MDSCs). MDSCs represent an important tumor immune escape mechanism and play a role in the development and progression of lung cancer. Higher levels of MDSCs in the blood are associated with shorter overall survival in patients with NSCLC, and MDSCs are associated with resistance to immune checkpoint inhibitor (ICI) therapy. However, there is significant variation in methods of measurement of MDSCs including 1) the classification of the most common phenotypes, namely CD15+ polymorphonuclear MDSC (PMN-MDSC) and CD14+ monocytic MDSC (M-MDSC), and 2) the functional assessment of MDSCs. There are also significant differences in MDSC function and phenotype in animal models and in patients with cancer. We propose to investigate the role of MDSCs in tumor immune escape, and to target the immunosuppressive impact of MDSCs to improve outcomes of patients with NSCLC treated with ICI. Utilizing mass cytometry and in vitro co-culture assays, we will evaluate MDSC levels and function as well as immune cell subset changes in patients receiving standard of care immunotherapy to identify the cell populations that drive immune responses and resistance. We will then conduct a phase 1b clinical trial of all-trans retinoic acid (ATRA) combined with atezolizumab to test whether this treatment can improve responses and overcome ICI resistance in patients with NSCLC who have progressed on standard therapies. We hypothesize that a decrease in the frequency and immunosuppressive function of circulating MDSCs will be associated with increased clinical benefit in patients with NSCLC, and that modulation of MDSCs through the use of ATRA given in combination with ICIs will be safe, tolerable, and exhibit preliminary efficacy in overcoming resistance to available ICIs. The proposed studies include the first trial of this novel treatment in patients with lung cancer and will examine the potential for targeting MDSCs to overcome resistance and enhance the efficacy of immunotherapy. If successful, these studies may lead to an increased number of patients with advanced NSCLC experiencing durable responses and improved survival.

Patients with non-small cell lung cancers bearing ALK or ROS1 fusions (FD-NSCLC) often experience an initial, marked response to tyrosine kinase inhibitors (TKI). The eventual emergence of TKI resistance in FD-NSCLC can be partially attributed to cancer-cell intrinsic mechanisms, but these do not fully explain the diversity in patient outcomes. Currently, FD-NSCLC is viewed as a “cold” tumor with only a molecular target, and the role of the tumor microenvironment (TME) in these cancers has not been well studied. As patients have limited options after progression on TKIs, there is an urgent need to identify novel drivers of resistance to develop new, more effective therapies. Based on our preliminary data, we believe innate immune cells, monocytes and macrophages (MoMf), within the FD-NSCLC TME shape tumor response to TKI therapy. Using patient derived cell lines, we found marked TKI resistance in multiple FD-NSCLC cell lines when cultured in media conditioned by MoMf. MoMf-driven TKI resistance was associated sustained pERK activity in the cancer cell. In pre-treatment specimens from patients with FD-NSCLC, multispectral tissue imaging demonstrated a range in number of MoMf within the TME. Our preliminary data suggest the presence of MoMf with the FD-NSCLC TME may alter response to therapy. We propose investigating the mechanisms of MoMf-mediated TKI resistance and potential therapeutic approaches with clinically relevant syngeneic and xenograft animal models and patient-derived FD-NSCLC cell lines. Further, we will examine biopsy specimens from patients
Immunotherapy is a treatment approach that leverages the body’s own immune system to destroy cancer cells. In non-small cell lung cancer (NSCLC), the most common type of lung cancer, immunotherapy has opened the door to durable treatment that approaches cure; unfortunately, this outcome is rare, and many NSCLCs are initially or eventually become unresponsive. It was originally thought that unresponsive malignancies had adapted to prevent immune cells from locating and interacting with the tumor. Our research suggests this is not the case: the tumor can remain inflamed and responsive, but the immune response can become exhausted. Therapies that reinvigorate the immune response (including tumor infiltrating lymphocyte [TIL] therapies) may be particularly effective in this context. In fact, our preliminary studies suggest TIL therapy can work in up to a third of treatment-resistant NSCLCs. Capitalizing on these new insights, our proposal seeks to 1) determine pre-treatment features of sensitivity and resistance to TIL therapy in NSCLC and 2) characterize on-treatment patterns of immune response, focusing on the cells that identify and kill NSCLC cells. Accomplishing these aims will fill critical knowledge gaps, identifying characteristics of tumors likely to respond, or that fail to respond, to TIL treatment. These studies will define a roadmap, guiding application of subsequent TIL research for lung cancer. Taken together, these studies will provide crucial insights into novel treatment approaches for patients with few alternatives and an otherwise grim prognosis.

Lung cancer is the leading cause of cancer-related death in US, and lung adenocarcinoma (LUAD) is the most frequent histology. Early diagnosis is crucial. High-resolution CT has increased the discovery of solitary lung lesions, many of which are benign, whereas some progress to invasive cancer; the identification of novel biomarkers to predict the malignant potential of these lesions is of paramount importance. We found that sodium-dependent glucose transporter 2 (SGLT2) is expressed in human pre-malignant and early-stage LADC, and is required for progression of LUAD. SGLT activity can be measured by PET imaging with methyl-4-[18F] fluorodeoxyglucose (Me4FDG). Importantly, we identified SGLT2 activity in FDG-negative, early-stage lesions in mouse models and in human lung nodules.

Specific aims of the study are: 1. To assess the safety and efficacy of Me4FDG in patients with lung cancer, via a pilot study in 60 patients (30 with pathological diagnosis of LUAD, 30 with a clinical diagnosis of benign nodule); 2. To evaluate the prognostic significance of SGLT2 expression in early lung adenocarcinoma, through SGLT2 staining of 674 samples embedded in tissue microarrays.

The proposed research is likely to introduce a novel diagnostic tool for early diagnosis of lung adenocarcinoma, and further define the prognostic role of SGLT2 in lung cancer. If successful, this pilot trial will open the way for larger clinical studies where we will evaluate the ability of Me4FDG PET to predict the malignant behavior of indeterminate subsolid lung nodules. This will improve the early diagnosis of lung cancer.

Lung cancer remains the leading cause of cancer related mortality in the US and globally— responsible for ~1.8 million deaths annually. Randomized trials of low dose CT (LDCT) for lung cancer screening have demonstrated a clear mortality benefit and are recommended by the United States Preventive Services Task Force (USPSTF). However, most individuals currently eligible for screening do not have lung cancer and many at risk populations are not candidates for screening. Additionally, LDCT has a relatively high rate of false positives leading to potentially harmful tests and invasive procedures. Moreover, early experience suggests that LCS outcomes in clinical practice may differ from those observed in randomized trials. Given the concerns with the performance of LDCT, the use of blood and imaging biomarkers to complement the screening process has the potential to enhance its efficacy and effectiveness. Biomarkers could be employed at two different steps of the screening process – as the initial test for cancer screening, to better define the best candidates for screening, or following a positive LDCT scan, to inform lung nodule evaluation and management. While several screening and diagnostic biomarkers have been developed, they have not been formally evaluated in prospective comparative effectiveness trials, nor have they been subjected to cost-effectiveness analyses. More importantly, their impact on lung cancer burden at the population level is still unknown. Our proposed research will inform the following areas of LCS and biomarker discovery: 1) generate a computational framework to estimate and compare the population impact of emerging screening and diagnostic biomarkers, 2) identify the optimal strategy of integrating biomarker tests into LCS, and 3) highlight and identify the characteristics of biomarkers (sensitivity and specificity for histological subtypes, etc.) which are critical for cost-effective biomarker applications.

Activating mutations in KRAS are found in 20 to 40% of lung cancers and not infrequently in combination with additional alterations in genes such as tumor suppressor TP53 or STK11. How activating KRAS mutations and/or co-mutations affect gene expression in both tumor cells and the cells in the surrounding microenvironment is not known. The impact, if any, of these mutations on intra-tumoral heterogeneity in gene expression is not known. Applying single cell RNA sequencing to resected lung adenocarcinoma samples from US Veterans, I will examine and compare the gene expression profiles of tumor cells from lung adenocarcinomas harboring either mutant and wild-type KRAS, and the expression profiles of cells in the surrounding microenvironment, including tumor infiltrating lymphocytes. In addition, I will determine whether KRAS mutational status affects the degree of intra-tumoral heterogeneity in gene expression, a known factor in survival and resistance to treatment. In sum, we hope to identify specific pathways affected by KRAS in both tumor and surrounding non-tumor cells that could be hypothesis-generating and learn use this knowledge to understand how resistance to KRAS specific therapies might be facilitated by pre-existing intra-tumoral heterogeneity.

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:

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

More specifically, our aims are:

1. 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.
2. 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.

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.