Small cell lung cancer (SCLC) is one of the deadliest cancers with an extremely low five-year survival rate of 6%. Treatment using platinum-based chemotherapy almost always results in rapid relapse and this approach has not changed in 30 years. The key to understanding this rapid relapse is the existence of varying transcriptional subtypes with different sensitivities to chemotherapy. As such, understanding this tumour heterogeneity for subtype-specific treatment is important in the era of personalised oncology.
We acquired eleven fine needle biopsy aspirations of the lymph node and one lung tumour resection from SCLC patients at diagnosis. Biopsy samples from matched healthy “unaffected” and SCLC-metastasised “affected” lymph nodes were interrogated to identify tumour infiltrating immune cells. These samples were processed for single cell RNA-sequencing using CEL-Seq 2.0, allowing us to enrich for tumour (EpCAM+) and immune (CD45+) cell populations.
Upon Harmony-correction and Seurat clustering of all epithelial tumour cells, there were discrete clusters representing the two most common transcriptional subtypes (ASCL1 and NEUROD1). Interestingly, there were clusters containing cells co-expressing both transcription factors. This co-expression observation was validated using a multiplexed immunohistochemistry panel (Opal™, Akoya Biosciences). Current investigations are focused on understanding the underlying transcriptional pathways of these co-expressing cells and their functional importance in therapeutic response. Furthermore, we also identified clusters with low proliferative capacity and high expression of several Yamanaka factors, suggesting the presence of cancer stem cells.
For the immune cell compartment, we integrated CD45-expressing cells from healthy “unaffected” and SCLC-metastasised “affected” lymph node samples collected from an individual patient. We identified immune cells in discrete clusters that were specific to the SCLC-metastasised lymph node. Similarly, clusters that shared immune cells from healthy and SCLC-metastasised lymph node were considered as lymph node-resident. Overall, these findings will enable future investigations therapeutic vulnerabilities of each transcriptional SCLC subtype and aid with immunotherapy approaches to combat SCLC tumourigenesis.