Single‐Cell Transcriptome Identifies Drug‐Resistance Signature and Immunosuppressive Microenvironment in Metastatic Small Cell Lung Cancer

Abstract

Small cell lung cancer (SCLC) is a deadly neuroendocrine malignancy with high metastasis. However, the heterogeneity of metastatic SCLC at the single‐cell level remains elusive. The single‐cell transcriptome of a total of 24 081 cells in metastatic lymph node samples from seven SCLC patients via endobronchial ultrasound‐guided transbronchial needle aspiration (EBUS‐TBNA) is examined. Genomic alterations are also examined by whole exome sequencing (WES) and the immune infiltration between SCLC and non‐SCLC (NSCLC) is compared using public single‐cell RNA sequencing (scRNA‐seq) data. It is identified that malignant cells in lymph‐node metastatic SCLC have inter‐patient and intra‐tumor heterogeneity characterized by distinct ASCL1 and NEUROD1 expression patterns. High expression of genes such as FZD8 in WNT pathway is associated with drug resistance in malignant cells. Compared to NSCLC, SCLC harbors a unique immunosuppressive tumor microenvironment. Malignant cells exhibit a pattern of attenuated MHC‐I antigen presentation‐related gene expression, which is associated with relatively low proportion of exhausted T cells. Natural killer (NK) cells display impaired antitumor function with high expression of TGFBR2. This work characterizes the inter‐patient and intra‐tumor heterogeneity of metastatic SCLC and uncovers the exhaustion signatures in NK cells, which may pave the way for novel treatments for SCLC including immune checkpoint blockade‐based immunotherapy.

Yin Yang 1 promotes the neuroendocrine differentiation of prostate cancer cells via the non‐canonical WNT pathway (FYN/STAT3)

“…FZD8, a constituent of the frizzled (FZD) protein family, functions as a receptor for WNT ligands. Prior studies indicated that FZD8 is overexpressed in diverse tumours, resulting in bone metastasis and resistance to treatment by activating the canonical Wnt/β‐catenin pathway 51,72,73 . In the current study, we identified FZD8 as a critical downstream gene activated by YY1 via promoter binding.…”

“…Prior studies indicated that FZD8 is overexpressed in diverse tumours, resulting in bone metastasis and resistance to treatment by activating the canonical Wnt/β-catenin pathway. 51,72,73 In the current study, we identified FZD8 as a critical downstream gene activated by YY1 via promoter binding. An enhanced binding effect of FZD8 to Wnt9A after ADT was observed in PCa cell membranes based on IF assay results, thus contributing to PCa cell plasticity by activating a non-canonical Wnt pathway (FZD8/FYN/STAT3).…”

DNA methylation in small cell lung cancer

“…Recently, some groups including us have investigated the single-cell transcriptome of primary and metastatic SCLC tissues. 55,61,62 Although they have been reported in only a few studies on NSCLC, 63,64 single-cell multiomics technologies 65 will uncover genome-wide methylation/hydroxymethylation in SCLC, as well as other useful information, such as transcription, histone modification and chromatin accessibility. Second, circulating cell-free DNA (cfDNA) provides a good resource for liquid biopsy by minimally invasive method because of its stability.…”

“…Therefore, DNA methylation should be revealed at single‐cell resolution as TME comprises a complex of different cell types. Recently, some groups including us have investigated the single‐cell transcriptome of primary and metastatic SCLC tissues 55,61,62 . Although they have been reported in only a few studies on NSCLC, 63,64 single‐cell multiomics technologies 65 will uncover genome‐wide methylation/hydroxymethylation in SCLC, as well as other useful information, such as transcription, histone modification and chromatin accessibility.…”

“…Treatment of SCLC has been benefited from this technical advance since the US FDA approved usage of Atezolizumab with first‐line chemotherapy 54 . Despite T cells, other immune cell types, such as macrophages and NK cells, are also proposed as potential targets for immune therapy, which is recently addressed at single‐cell resolution 55 . Taking advantage of the available SCLC cell lines, SCLC‐CellMiner 16 showed high expression of innate immune response genes in the SCLC‐Y cell lines, which include the effector genes, such as CGAS , STING , HLA‐E and interferon‐inducible genes.…”