Small cell lung cancer (SCLC)

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.

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.

Small cell lung cancer (SCLC) is an aggressive, neuroendocrine malignancy that accounts for approximately 15% of lung cancers. Despite recent advances, including the approval of immunotherapy combined with chemotherapy for frontline treatment, the median overall survival for patients with extensive-stage SCLC remains approximately one year. These dismal outcomes are attributable, in part, to the lack of approved biomarkers for SCLC, which, in turn, is due to the dearth of available tissue for molecular analysis. Using transcriptomic data, we have developed a gene signature that defines four distinct molecular subtypes of SCLC – each with unique biology and therapeutic vulnerabilities. These subtypes are driven by the presence (or absence) of three transcription factors (ASCL1 – SCLC-A; NEUROD1 – SCLC-N; POU2F3 – SCLC-P; and a fourth triple-negative subtype “Inflamed” – SCLC-I) that are largely mutually exclusive. Our preliminary data suggests that inter- and intra-tumoral heterogeneity among these subtypes drives response and resistance to standard and novel therapies for SCLC, including classes such as PARP inhibitors (PARPi) and immunotherapy. We propose applying bulk and single-cell molecular approaches to assign and longitudinally monitor subtype among our established cohort of patient-derived xenograft models treated with PARPi, as well as patient tumor biopsies from an investigator-initiated trial assessing a PARPi/immunotherapy combination. Based on our preliminary data, we hypothesize that SCLC-P and SCLC-I will preferentially benefit from PARP inhibitors and immunotherapy, respectively, and that subtype shifts detectable at the single-cell level along with accompanying shifts in the composition of the immune microenvironment, will govern response and resistance.

Small cell lung cancer (SCLC) is among the most aggressive and deadly human cancers. It represents approximately 15% of all lung cancers, and it is responsible for over 30,000 deaths in the US and 200,000 deaths worldwide every year. SCLC responds to treatment but recurs frequently and aggressively, with the majority of patients dying within 12 months of diagnosis. No targeted therapies are yet available for SCLC. New strategies are needed to improve outcomes for patients with SCLC. This project will expand upon preliminary data identifying at least two distinct subpopulations of cells in SCLC cell lines and patient-derived xenografts comprising a neuroendocrine (NE) and mesenchymal-like (ML) set of cell line populations. Dr. Lehman and his team will use an innovative approach using mass cytometry, using rare earth antibody conjugates to antibody label more than 30 proteins simultaneously, including phospho and signaling proteins. This technique will establish at a single-cell resolution tumor heterogeneity and signaling in small cell lung carcinoma in multiple primary human samples as well as in patient-derived xenograft samples before and after chemotherapy treatment. This proposal aims to (1) characterize the signaling of subpopulations in human primary SCLCs at a single-cell resolution, (2) identify changes in tumor heterogeneity and in these subpopulations after chemotherapy treatment and relapse, and (3) disrupt and manipulate developmental signaling/ associated subpopulations (prototypically the HH [Hedgehog] and Notch/DLL3 pathways) to reduce tumor burden and lead to targeted rational combination therapy for SCLC.

The overarching goal of the project is to develop a new technology for accurate and cost-effective lung cancer screening in current/former smokers. Lung cancer is curable if detected early. However, there are no robust screening techniques with options such as CT scans fraught with cost, harms, and a high false positive rate. Dr. Backman and his group hope to transform the clinical practice of lung cancer screening by exploiting field carcinogenesis, the concept that the genetic/environmental milieu that results in lung tumor impacts upon the entire aerodigestive mucosa including the buccal mucosa, which was referred to as a “molecular mirror” of lung carcinogenesis.

Their data show that the alteration of nanoscale architecture of buccal cells is exquisitely sensitive to lung field carcinogenesis and may serve as a robust biomarker for lung cancer. These nanoarchitectural changes can be detected in a practical and highly accurate fashion via a new technology, partial wave spectroscopic (PWS) microscopy (‘nanocytology’).

In the proposed study, they will conduct a blinded validation case-control trial to determine the sensitivity and specificity of buccal nanocytology for lung cancer. They will evaluate the ability of the test to identify patients who have lung cancer and how many patients with lung cancer would be missed using this technique. They will perform a subgroup analysis for Stage I lung cancers. They will assess the potential confounding effects of smoking frequency and time of cessation and other aerodigestive malignancies.

This project will provide the requisite data for the future definitive multicenter validation trial followed by FDA submission.