Droplet-mediated scRNA-seq reveals cancer and non-cancer
components of PPB
To fully understand intra-tumoral and inter-tumor heterogeneity of
pleuropulmonary blastoma (PPB), deep transcriptional profiles of the
cancer cell status and gene expression were obtained by droplet-mediated
scRNA-seq platform (10× Genomics Chromium)14 to
observe whether cell diversity existed (Fig.1A). We sequenced 10 007
cells from the individual at an average of 400 M reads. After quality
control filtering to remove cells with low gene detection
(<500 genes) and high mitochondrial gene coverage
(>10%) with the Seurat pipeline, we obtained a rough cell
atlas of this sample, which was clustered into 14 clusters (Fig.1D).
This whole specimen had several classes of cells, including normal
immune cells (cluster 12, PTPRChi), fibroblasts
(cluster 13, TAGLNhi ), endothelial cells
(cluster 14, CLDN5hi ), and tumor cells (cluster
0-11,NCAM1hiDICER1hiIGF1Rhi )4,15(Supporting Information Figure S1) with
differentially expressed genes
(DEGs). To further verify such cell classification,TAGLNhi normal fibroblasts from a healthy adult
lung were used as a reference to analyze the inferring copy number
variation (inferCNV) of all single cells in PPB, because fibroblasts are
derived from mesenchyme. We found coherent chromosomal aberrations in
tumor clusters (clusters 0–11) but not in the other defined non-cancer
cells (clusters 12–14). Tumor clusters contained chromosome 19 gain and
chromosome 1, 5, 6, and 19 loss (Fig.1C)15.
Interestingly, there were both distinct gain and loss in chromosome 19,
which were probably closely connected to tumorigenesis of the chromosome
variation.