Abstract 6291: Integrative single-cell tracking of genome evolution and tumor cell plasticity in small cell lung cancer (SCLC)

Abstract

Abstract SCLC is the deadliest type of lung cancer, which is mostly diagnosed at late stages and accounts for 15% of pulmonary tumors. Even though chemotherapy is initially effective, SCLC patients relapse quickly with therapy resistant tumors. Genome studies revealed universal loss of TP53 and RB1; recent transcriptional studies categorized SCLC tumors based on the expression of 4 lineage transcription factors (TFs). We aimed to dissect how genomic cues impact transcriptional phenotypes, tumor cell plasticity and the dynamics of tumor and immune cell interactions, to thus decipher molecular mechanisms of phenotypic divergence and therapy resistance in SCLC. We performed genome sequencing and single cell transcriptome profiling on 61 SCLC patient tumors, including primary tumors, metastases and paired relapse tumors acquired throughout therapy. Single cell RNA-seq was performed with the 10x Genomics platform for patient tumors to study cancer cells and the tumor micro-environment (TME)(n=17), and on xenograft models to study tumor cell intrinsic heterogeneity (n=44). Single cell and genome sequencing data were processed with an in-house pipeline. To further validate our findings on the transcriptional level, we performed imaging mass cytometry (IMC) of matched tissue samples to delineate the spatial context of cellular subsets. Single cell transcriptome profiles were determined for 211,446 cells from 61 tumors. Transcriptome profiling at single cell levels revealed co-expression of at least two of the lineage TFs ASCL1, NEUROD1 or POU2F3 for each SCLC tumor. Furthermore, tumor subsets without any expression of the four described TFs were found. Instead of distinct subgroups, our data points to a concerted regulation of a multitude of lineage factors and transcriptional programs in each SCLC tumor. To specifically investigate how underlying genetic alterations affect molecular phenotypes, integrative studies across all patients were performed. This revealed shared transcriptional programs in tumors with MYC family member amplifications; trajectory inference for cases with low and high-level copy gains of MYCN pointed to distinct transcriptional states. We performed multi-regional and longitudinal studies of matched patient cases. We reconstructed genomic patterns of clonal evolution from bulk genome sequencing data, and projected genomic subsets to transcriptional trajectories at single cell level, thus analyzing the effect of genome diversity on the transcriptional landscape. Additionally, tumor intrinsic profiles of heterogeneity were mapped to single cell data of patient tumors to elucidate the effects on the TME, focusing on tumor-immune cell interactions. All together our data provides a first comprehensive framework for the study of underlying genetic alterations that shape the transcriptional landscape and phenotypic plasticity in SCLC. Citation Format: Marcel Schmiel, Roman K. Thomas, Julie George. Integrative single-cell tracking of genome evolution and tumor cell plasticity in small cell lung cancer (SCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6291.