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Title: Single-Cell Transcriptomic Analysis of Tumor-Derived Fibroblasts and Normal Tissue-Resident Fibroblasts Reveals Fibroblast Heterogeneity in Breast Cancer

Abstract

Cancer-associated fibroblasts (CAFs) are a prominent stromal cell type in solid tumors and molecules secreted by CAFs play an important role in tumor progression and metastasis. CAFs coexist as heterogeneous populations with potentially different biological functions. Although CAFs are a major component of the breast cancer stroma, molecular and phenotypic heterogeneity of CAFs in breast cancer is poorly understood. In this study, we investigated CAF heterogeneity in triple-negative breast cancer (TNBC) using a syngeneic mouse model, BALB/c-derived 4T1 mammary tumors. Using single-cell RNA sequencing (scRNA-seq), we identified six CAF subpopulations in 4T1 tumors including: 1) myofibroblastic CAFs, enriched for α-smooth muscle actin and several other contractile proteins; 2) ‘inflammatory’ CAFs with elevated expression of inflammatory cytokines; and 3) a CAF subpopulation expressing major histocompatibility complex (MHC) class II proteins that are generally expressed in antigen-presenting cells. Comparison of 4T1-derived CAFs to CAFs from pancreatic cancer revealed that these three CAF subpopulations exist in both tumor types. Interestingly, cells with inflammatory and MHC class II-expressing CAF profiles were also detected in normal breast/pancreas tissue, suggesting that these phenotypes are not tumor microenvironment-induced. This work enhances our understanding of CAF heterogeneity, and specifically targeting these CAF subpopulations could be an effective therapeuticmore » approach for treating highly aggressive TNBCs.« less

Authors:
ORCiD logo; ORCiD logo; ; ; ORCiD logo; ; ; ; ORCiD logo
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA); USDOE Laboratory Directed Research and Development (LDRD) Program; National Cancer Institute (NCI)
OSTI Identifier:
1630372
Alternate Identifier(s):
OSTI ID: 1662032
Report Number(s):
LLNL-JRNL-807797
Journal ID: ISSN 2072-6694; CANCCT; PII: cancers12051307
Grant/Contract Number:  
LDRD-19-SI-003, LDRD-17-ER-121; AC52-07NA27344; 19-SI-003; 17-ER-121; P30CA093373
Resource Type:
Published Article
Journal Name:
Cancers (Basel)
Additional Journal Information:
Journal Name: Cancers (Basel) Journal Volume: 12 Journal Issue: 5; Journal ID: ISSN 2072-6694
Publisher:
MDPI
Country of Publication:
Switzerland
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; cancer-associated fibroblasts; breast cancer; mammary fat pad; gene expression profiling; scRNA-seq; CAF heterogeneity; normal fibroblasts; myofibroblasts; inflammatory fibroblasts; pancreatic cancer

Citation Formats

Sebastian, Aimy, Hum, Nicholas R., Martin, Kelly A., Gilmore, Sean F., Peran, Ivana, Byers, Stephen W., Wheeler, Elizabeth K., Coleman, Matthew A., and Loots, Gabriela G. Single-Cell Transcriptomic Analysis of Tumor-Derived Fibroblasts and Normal Tissue-Resident Fibroblasts Reveals Fibroblast Heterogeneity in Breast Cancer. Switzerland: N. p., 2020. Web. doi:10.3390/cancers12051307.
Sebastian, Aimy, Hum, Nicholas R., Martin, Kelly A., Gilmore, Sean F., Peran, Ivana, Byers, Stephen W., Wheeler, Elizabeth K., Coleman, Matthew A., & Loots, Gabriela G. Single-Cell Transcriptomic Analysis of Tumor-Derived Fibroblasts and Normal Tissue-Resident Fibroblasts Reveals Fibroblast Heterogeneity in Breast Cancer. Switzerland. doi:https://doi.org/10.3390/cancers12051307
Sebastian, Aimy, Hum, Nicholas R., Martin, Kelly A., Gilmore, Sean F., Peran, Ivana, Byers, Stephen W., Wheeler, Elizabeth K., Coleman, Matthew A., and Loots, Gabriela G. Thu . "Single-Cell Transcriptomic Analysis of Tumor-Derived Fibroblasts and Normal Tissue-Resident Fibroblasts Reveals Fibroblast Heterogeneity in Breast Cancer". Switzerland. doi:https://doi.org/10.3390/cancers12051307.
@article{osti_1630372,
title = {Single-Cell Transcriptomic Analysis of Tumor-Derived Fibroblasts and Normal Tissue-Resident Fibroblasts Reveals Fibroblast Heterogeneity in Breast Cancer},
author = {Sebastian, Aimy and Hum, Nicholas R. and Martin, Kelly A. and Gilmore, Sean F. and Peran, Ivana and Byers, Stephen W. and Wheeler, Elizabeth K. and Coleman, Matthew A. and Loots, Gabriela G.},
abstractNote = {Cancer-associated fibroblasts (CAFs) are a prominent stromal cell type in solid tumors and molecules secreted by CAFs play an important role in tumor progression and metastasis. CAFs coexist as heterogeneous populations with potentially different biological functions. Although CAFs are a major component of the breast cancer stroma, molecular and phenotypic heterogeneity of CAFs in breast cancer is poorly understood. In this study, we investigated CAF heterogeneity in triple-negative breast cancer (TNBC) using a syngeneic mouse model, BALB/c-derived 4T1 mammary tumors. Using single-cell RNA sequencing (scRNA-seq), we identified six CAF subpopulations in 4T1 tumors including: 1) myofibroblastic CAFs, enriched for α-smooth muscle actin and several other contractile proteins; 2) ‘inflammatory’ CAFs with elevated expression of inflammatory cytokines; and 3) a CAF subpopulation expressing major histocompatibility complex (MHC) class II proteins that are generally expressed in antigen-presenting cells. Comparison of 4T1-derived CAFs to CAFs from pancreatic cancer revealed that these three CAF subpopulations exist in both tumor types. Interestingly, cells with inflammatory and MHC class II-expressing CAF profiles were also detected in normal breast/pancreas tissue, suggesting that these phenotypes are not tumor microenvironment-induced. This work enhances our understanding of CAF heterogeneity, and specifically targeting these CAF subpopulations could be an effective therapeutic approach for treating highly aggressive TNBCs.},
doi = {10.3390/cancers12051307},
journal = {Cancers (Basel)},
number = 5,
volume = 12,
place = {Switzerland},
year = {2020},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: https://doi.org/10.3390/cancers12051307

Figures / Tables:

Figure 1 Figure 1: Single cell analysis of 4T1 mouse mammary tumors. (A) Graphical representation of the experimental workflow. 4T1 syngeneic tumors were dissociated into single cells, and two cell fractions were generated: (1) a viable cell fraction (7AAD−) and (2) immune-depleted stromal cell fraction (obtained by depleting CD45+ immune cells andmore » Thy1.1+ cancer cells). Cells from both fractions were subjected to single cell sequencing using the 10x Genomics Chromium platform. (B) Cell clusters from 10x Genomics scRNA-seq analysis visualized by Uniform Manifold Approximation and Projection (UMAP). Colors indicate clusters of various cell types (CAFs in black circle). (C) Dot plot showing the expression of selected markers of various cell types. Dot size represents the fraction of cells expressing a specific marker in a particular cluster and intensity of color indicates the average expression level in that cluster. (D) Heatmap showing high levels of collagens and collagen-processing enzymes in CAFs. (E) Heatmap showing high levels of key proteoglycans and glycoproteins in CAFs. (F) Dot plot showing the expression of a subset of genes enriched in CAFs. Dot size represents the fraction of cells expressing a specific marker in a particular cluster and intensity of color indicates the average expression in that cluster.« less

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