whole transcriptome sequencing wts  (Spatial Transcriptomics Inc)

Journal: Clinical and Translational Medicine

Article Title: Novel cancer‐associated secretory cells and IL‐1β + macrophages as key players in early lung adenocarcinoma progression in female never‐smokers

doi: 10.1002/ctm2.70433

Figure Lengend Snippet: Cancer‐associated secretory (CAS) cells originated from alveolar type 2 (AT2) cells. (A) Principal component analysis (PCA) plot of alveolar type 1 (AT1), AT2 and CAS cells in the solid component of tumour (S) and ground‐glass component of tumour (GG) regions, with lines representing the inferred trajectories. Each dot represents a single cell and is coloured according to cell type. Lines indicate inferred trajectories, estimated using Slingshot. (B) PCA plots of single‐cell transcriptomes, with cells (dots) coloured by region (GG vs. S) (top) and patient (bottom). (C) Pseudotime analysis depicting the gene expression dynamics of surfactant protein A1 (SFTPA1) (AT2 marker), advanced glycation end‐product specific receptor (AGER) (AT1 marker), secretoglobin family 3A member 2 (SCGB3A2) (CAS marker) and carcinoembryonic antigen‐related cell adhesion molecule 6 (CEACAM6) (CAS marker) along the inferred trajectory. The black line and points represent lineage 1 (AT2 to AT1), while the red line and points represent lineage 2 (AT2 to CAS). (D) Violin plots showing the expression levels of carcinoembryonic antigen‐related cell adhesion molecule 5 (CEACAM5), CEACAM6 and serine peptidase inhibitor Kazal type 1 (SPINK1) across different samples in CAS cell types from single‐cell RNA sequencing (scRNA‐seq). (E) Box plots displaying normalised expression levels of SFTPA1, SCGB3A2, CEACAM5, CEACAM6 and SPINK1 across different components (N, GG and S, n = 7, respectively) in whole‐transcriptome sequencing analysis. The Kruskal–Wallis test was performed. (F) Box plots showing the normalised expression levels of SFTPA1, SCGB3A2, CEACAM5, CEACAM6 and SPINK1 across normal (N, n = 23) and cancer (C, n = 34) tissues from a study by Zhang et al. (2020). Wilcox statistical significance is indicated by p ‐values. PSN, part‐solid nodule; SCGB3A1, secretoglobin family 3A member 1.

Article Snippet: Analyses included whole‐exome sequencing (WES) and whole‐transcriptome sequencing (WTS) ( n = 7), single‐cell RNA sequencing ( n = 4) and spatial transcriptomics ( n = 1, SMC‐19) (Figure ).

Techniques: Gene Expression, Marker, Expressing, RNA Sequencing, Sequencing