Single-nuncleus RNA sequencing for circulating tumor cell-derived xenograft models of non-metastatic non-small cell lung cancer

Circulating tumor cells (CTCs) represent micrometastatic disease and may offer unique insights into future recurrences in lethal malignancies including non-small cell lung cancer (NSCLC). Due to CTC rarity and limited stability, no CTC-derived xenograft (CDX) models from non-metastatic NSCLC patients have been generated. Alternative strategies are needed to molecularly characterize CTCs in this potentially curable patient group. Surgically resected NSCLC primary tumor tissues were implanted in immunodeficient mice to establish ten patient-derived xenografts (PDXs). CTCs from 2/10 PDX models led to generation of two stable CDX models. CTCs from patients, PDX tumors, PDX-CTCs and CDX tumors shared critical molecular characteristics. WGS of matched CDX, PDX and primary tumors showed overlap in genes with known mutations implicated in cancer. Single cell analysis revealed an additional alveolar epithelial type II (AT2) population in CDX tumors, besides a common AT2 cluster in PDX/CDX tumors. This was consistent with an external validation set analysis in metastatic NSCLC tumors. MYC target genes and proteins were differentially expressed between chemoresistant and chemosensitive CDX tumors, while c-MYC inhibition could overcome chemoresistance to carboplatin/paclitaxel.