pubmed.ncbi.nlm.nih.gov

Unraveling intratumoral complexity in metastatic dermatofibrosarcoma protuberans through single-cell RNA sequencing analysis - PubMed

Unraveling intratumoral complexity in metastatic dermatofibrosarcoma protuberans through single-cell RNA sequencing analysis

Ling-Ling Ge et al. Cancer Immunol Immunother. 2023 Dec.

Abstract

Dermatofibrosarcoma protuberans (DFSP) stands as a rare and locally aggressive soft tissue tumor, characterized by intricated molecular alterations. The imperative to unravel the complexities of intratumor heterogeneity underscores effective clinical management. Herein, we harnessed single-cell RNA sequencing (scRNA-seq) to conduct a comprehensive analysis encompassing samples from primary sites, satellite foci, and lymph node metastases. Rigorous preprocessing of raw scRNA-seq data ensued, and employing t-distributed stochastic neighbor embedding (tSNE) analysis, we unveiled seven major cell populations and fifteen distinct subpopulations. Malignant cell subpopulations were delineated using infercnv for copy number variation calculations. Functional and metabolic variations of diverse malignant cell populations across samples were deciphered utilizing GSVA and the scMetabolism R packages. Additionally, the exploration of differentiation trajectories within diverse fibroblast subpopulations was orchestrated through pseudotime trajectory analyses employing CytoTRACE and Monocle2, and further bolstered by GO analyses to elucidate the functional disparities across distinct differentiation states. In parallel, we segmented the cellular components of the immune microenvironment and verified the presence of SPP1+ macrophage, which constituted the major constituent in lymph node metastases. Remarkably, the CellChat facilitated a comprehensive intercellular communication analysis. This study culminates in an all-encompassing single-cell transcriptome atlas, propounding novel insights into the multifaceted nature of intratumor heterogeneity and fundamental molecular mechanisms propelling metastatic DFSP.

Keywords: Dermatofibrosarcoma protuberans; Intratumoral heterogeneity; Metastasis; Single-cell RNA sequencing analysis.

© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.

PubMed Disclaimer

Conflict of interest statement

The authors state no conflict of interest.

Figures

Fig. 1
Fig. 1

Diagram illustrating the course of disease advancement and the treatment journey in the context of a metastatic case of dermatofibrosarcoma protuberans (DFSPs)

Fig. 2
Fig. 2

Description of the detailed clinical information. a Demonstration of the patient’s right supraclavicular primary tumor, chest wall satellite metastases, and lymph node metastases (internal) lesion sites. *: the approximate location of 3 tumor samples; b CT imaging for diagnosis of multisite tumor lesions; c Pathologic findings including Hematoxylin–Eosin (HE) staining and immunohistochemistry for diagnosis of DFSP at different sites

Fig. 3
Fig. 3

Single-cell transcriptional atlas of DFSP. a Flowchart of single-cell transcriptome analysis of 3 DFSP samples; b Visualization of the 7 predominant cell types in metastatic DFSP lesions using a t-distributed stochastic neighbor embedding (t-SNE) plot; c Dot plot illustrating the top 5 differentially expressed genes (DEGs) for 7 major cell clusters; d Feature plot revealing cell-specific characteristics across 7 distinct subgroups; e Stacked bar graph depicting cell proportions across 3 tumor samples

Fig. 4
Fig. 4

Distinct subpopulations of tumor cells in metastatic DFSPs. a t-SNE plot illustrating the presence of 6 subclusters within malignant cells. Fan charts representing the relative proportions of distinct malignant cell groups within 3 tumor samples; b Dot plot for the visualization of the top 5 DEGs across various subpopulations of tumor cells; (c-f) The hierarchical heatmaps show significant copy number variations (CNVs) within different tumor lesions (primary tumor, satellite tumor, lymph node metastasis tumor, all samples merged)

Fig. 5
Fig. 5

Disparities in enrichment pathways and metabolic profiles between 3 samples and 6 clusters of malignant cells. a Heatmap depicting the characteristic pathway terms of enriched Hallmark pathways within each cellular subgroup; b Heatmap depicting the characteristic pathway terms of enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways within each cellular subgroup; c Heatmap illustrating the distinctive pathway terms enriched within each tumor sample according to Hallmark pathways; d Heatmap illustrating the distinctive pathway terms enriched within each tumor sample according to KEGG pathways; e Heatmap demonstrating variations in metabolic profiles across diverse tumor cell clusters; f Heatmap demonstrating variations in metabolic profiles across primary and metastatic tumor samples

Fig. 6
Fig. 6

CytoTRACE and monocle2 analysis reveal the differentiation trajectories and distinctive gene expression patterns within 5 separate subpopulations of tumor fibroblasts. a Cell differentiation level; b Pseudotime trajectory of fibroblasts; c Cell type distribution; d Cell state transition; e Individual trajectories of each fibroblast subcluster; f Expression pattern of representative genes (TWIST1, MMP2, ACTA2)

Fig. 7
Fig. 7

Heterogeneity of immune cell profiles within metastatic DFSP tumors. a t-SNE diagram visualizing different immune cell subpopulations; b Heatmap displaying the top 5 DEGs for the annotations of various immune cell clusters; c Dot plots representing gene expression levels that define unique subclusters of immune cells across 3 tumor samples; d Bar graph depicting the proportions of various immune cell clusters in 3 tumor samples; e Representative immunofluorescence staining of lymph node metastatic tumor tissue at 20 × and 60 × magnifications. DAPI (cyan), SPP1 (green), in individual and merged channels are shown; f Feature plot showing the distribution of exhausted T cell-related genes in different samples

Fig. 8
Fig. 8

Intricate cellular communication between tumor cells and microenvironmental components in DFSP samples. a Overall view of the ability of different cell–cell communication. The lines link to cell types expressing corresponding receptors. The thickness of the lines is proportional to the number of ligands expressed by the recipient cell types; b Detailed perspective of each cell type engaging in ligand-receptor interactions with other cells; c Assessment of the overall intensity of cellular interaction across 3 distinct samples; d Dot plot displaying the intensities of efferent and afferent signals from different cell clusters in 3 tumor samples; e Enriched outgoing signaling pathways involved in the communication within 3 distinct tumor samples and their corresponding predominant cell clusters; f Enriched incoming signaling pathways involved in the communication within 3 distinct tumor samples and their corresponding predominant cell clusters; g Expression patterns of key ligands and receptors within the IL-10 signaling pathway among different cell types across 3 samples; h Dot plot showing the interaction pathways of cancer stem cells with those of other cells across 3 tumor samples

Similar articles

Cited by

References

    1. Mendenhall WM, Zlotecki RA, Scarborough MT. Dermatofibrosarcoma protuberans. Cancer. 2004;101:2503–2508. doi: 10.1002/cncr.20678. - DOI - PubMed
    1. Criscione VD, Weinstock MA. Descriptive epidemiology of dermatofibrosarcoma protuberans in the United States, 1973 to 2002. J Am Acad Dermatol. 2007;56:968–973. doi: 10.1016/j.jaad.2006.09.006. - DOI - PubMed
    1. Mujtaba B, Wang F, Taher A, Aslam R, Madewell JE, Spear R, Nassar S. Dermatofibrosarcoma protuberans: pathological and imaging review. Curr Probl Diagn Radiol. 2021;50:236–240. doi: 10.1067/j.cpradiol.2020.05.011. - DOI - PubMed
    1. Kreicher KL, Kurlander DE, Gittleman HR, Barnholtz-Sloan JS, Bordeaux JS. Incidence and survival of primary dermatofibrosarcoma protuberans in the United States. Dermatol Surg. 2016;42(Suppl 1):S24–31. doi: 10.1097/dss.0000000000000300. - DOI - PubMed
    1. Larbcharoensub N, Kayankarnnavee J, Sanpaphant S, Kiranantawat K, Wirojtananugoon C, Sirikulchayanonta V. Clinicopathological features of dermatofibrosarcoma protuberans. Oncol Lett. 2016;11:661–667. doi: 10.3892/ol.2015.3966. - DOI - PMC - PubMed

MeSH terms