Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Abstract

To explore the distinct genotypic and phenotypic states of melanoma tumors we applied single-cell RNA-seq to 4,645 single cells isolated from 19 patients, profiling malignant, immune, stromal and endothelial cells. Malignant cells within the same tumor displayed transcriptional heterogeneity associated with the cell cycle, spatial context, and a drug resistance program. In particular, all tumors harbored malignant cells from two distinct transcriptional cell states, such that “MITF-high” tumors also contained “AXL-high” tumor cells. Single-cell analyses suggested distinct tumor micro-environmental patterns, including cell-to-cell interactions. Analysis of tumor-infiltrating T cells revealed exhaustion programs, their connection to T cell activation and to clonal expansion, and their variability across patients. Overall, we begin to unravel the cellular ecosystem of tumors and how single cell genomics offers insights with implications for both targeted and immune therapies.

Immunophenotyping and Transcriptomic Outcomes in PDX-Derived TNBC Tissue

“…6C). A group of genes known to be related to drug resistance in melanoma (46) showed significant upregulation on average in this pool as well (Fig. 7B), which is consistent with the notion that drug resistance is frequently associated with less proliferative cells and may point further to an important role of this subpopulation.…”

“…B, Differential regulation of the AXL kinase gene set (38) between CD184 lo and CD184 hi cells (see Supplementary Table S2 for list of genes on the x axis). (46), is significantly higher in CD184 lo cells, adding a further facet to this picture.…”

The Human Cell Atlas: from vision to reality

“…New cell types have been found in the brain [3][4][5][6][7] , gut 8 , retina 9 and immune system 10 , and these discoveries have yielded new insight -into how the immune system 11 functions, for example, and into the dynamics of tumour ecosystems 12 . Yet, to take the next step -to build a human cell atlas that is truly useful -requires taking the long view and addressing various systemic and organizational challenges, as well as technical and scientific ones.…”

A B cell-derived gene expression signature associates with an immunologically active tumor microenvironment and response to immune checkpoint blockade therapy

“…To provide context to these findings, we performed a series of analyses to compare the response and survival associations of the MBL signature to that of other genomic measurements of immune infiltration, including the five other immune signatures calculated using our method, a series of single cell RNAseq-derived immune signatures calculated using ssGSEA 18 , and the inferred immune cell fractions of 22 lymphocytes calculated using CIBERSORT. 19 The MBL signature was the only signature that exhibited a significant association with response to immune checkpoint blockade therapy and post-treatment survival in each of the datasets tested (Supplementary Table S1).…”

“…Additional infiltration scores were calculated using gene expression signatures derived from single cell RNAseq data 18 as well as the LM22 matrix used by CIBERSORT. 19 Infiltration scores using the single cell RNAseq signatures were calculated using single sample gene set enrichment analysis (ssGSEA) from the R GSVA package.…”