Project 3: Targeting LSD1 to augment responses to PD-L1 inhibition in small cell lung cancer

Project Summary/Abstract – Project 3 Small cell lung cancer (SCLC) exhibits exceptionally poor prognosis. Addition of immune checkpoint blockade (ICB) to standard of care improved clinical responses, but few patients achieve durable benefit, in part, because SCLC tends to suppress expression of antigen presentation machinery. This proposal is focused on using a targeted therapy, LSD1 demethylase inhibition, to improve responses to immunotherapy in SCLC. SCLC patients that benefited from ICB exhibited tumors with the following features: 1) suppression of neuroendocrine gene expression 2) activation of NOTCH, and 3) expression of MHC-I. We showed that LSD1 inhibition suppresses neuroendocrine features, activates NOTCH, increases MHC-I on tumor cells, and improves response to PD-1 inhibition in vivo, demonstrating potential for LSD1 inhibition to switch immune cold SCLC to become immune responsive. Mechanisms by which LSD1 inhibition augments immune responses in SCLC, however, remain poorly defined. Beyond effects on tumor cells, LSD1 inhibition has been shown to directly regulate multiple immune populations that contribute to anti-tumor immunity. We will develop a deep understanding of the impact of LSD1 inhibition on tumor cell and immune cell phenotypes, including phenotypes of tumor antigen-specific T cells. Additionally, there is increasing appreciation of biological heterogeneity in SCLC, in part, driven by activation of different transcription factors (i.e. ASLC1, NEUROD1 POU2F3 and REST, a repressor of neuroendocrine state). We need to how SCLC transcriptional subtype impacts responsiveness to LSD1/PD-1 inhibition if we are to better direct this treatment approach to the right population of patients. We will use novel syngeneic models to understand how LSD1 suppression modulates the TME and sensitivity to PD-1 blockade across different transcriptional subtypes of SCLC. We will probe the molecular consequences of LSD1/PD1 inhibition on tumor cells and various immune populations using single cell RNA-seq and ATAC-seq. As LSD1 inhibition activates NOTCH and de-represses MHC-I, (phenotypes linked to increased responsiveness to ICB in SCLC) we will dissect the importance of LSD1 regulation of these pathways for responsiveness to PD-1 blockade. We developed a novel blood-based assay, based on targeted nucleosome profiling of regulatory regions of ctDNA to correlate SCLC phenotypes with patient responses. We will employ this assay to analyze longitudinally collected samples from a Phase II clinical trial to be conducted in the maintenance setting in patients to be randomized to LSD1i/anti-PDL1 vs. anti-PDL1 following initial chemoimmunotherapy. We will phenotype transcriptional subtype using targeted nucleosome profiling and will call exon mutations across cancer-mutated genes at trial entry, during treatment and upon relapse. We hypothesize that LSD1i will increase plasticity, will reduce ASCL1/neuroendocrine SCLC and result in subtype switches away from ASCL1-positive SCLC. We will also identify biological phenotypes that are associated with strong clinical responses.