A single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cells

Bhat‐Nakshatri, Poornima; Gao, Hongyu; Liu, Sheng; McGuire, Patrick; Xuei, Xiaoling; Wan, Jun; Liu, Yunlong; Althouse, Sandra K.; Colter, Austyn; Sandusky, George E.; Storniolo, Anna Maria; Nakshatri, Harikrishna

doi:10.1016/j.xcrm.2021.100219

Cited by 74 publications

(83 citation statements)

References 69 publications

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“…Only, Azizi et al performed sorting on CD45 pos immune cells from breast cancer patients undergoing mastectomy before encapsulation ( 18 ). As a consequence, most studies describe the epithelial cell composition in tumorigenic micro-environment ( 19 , 20 ).…”

Section: Discussionmentioning

confidence: 99%

Ductal Macrophages Predominate in the Immune Landscape of the Lactating Mammary Gland

et al. 2021

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The mammary gland is unique in female mammals. Mammary tissue undergoes development and remodeling during lactation, a stage associated with high susceptibility to bacterial infections, inducing an inflammatory condition called mastitis. Although the immune response of the mammary gland has been the subject of intense research to improve prevention and treatment efficacy, the precise definition of its immune composition at this particular physiological stage is still missing. We combined single-cell RNA-Seq, flow cytometry, and three-dimensional confocal microscopy techniques to characterize the immune landscape of lactating murine mammary tissue. Macrophages dominated the immune cell repertoire and could be subdivided into at least two subsets: ductal and stromal macrophages. Ductal macrophages represented approximately 80% of the total CD45pos immune cells and co-expressed F4/80 and CD11c, with high levels of MHC class II molecules. They were strategically poised below the alveolar basal cells in contact with the myoepithelial cell network. Adaptive T and B lymphocytes were remarkably less numerous at this stage, which could explain the limited efficacy of vaccination against mastitis. These results support the view that new strategies to increase mammary immunity and prevent mastitis should be devised.

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Section: Discussionmentioning

confidence: 99%

Ductal Macrophages Predominate in the Immune Landscape of the Lactating Mammary Gland

et al. 2021

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“…Seeking to understand why TAD signatures provided additional discriminative power, we drilled deeper into the breast tissue data. A particular challenge there is distinguishing between progenitor and mature luminal cells: there are some sub-populations of cells that are transcriptionally similar overall, but where Bhat-Nakshatri et al's expert knowledge of relevant marker genes allowed them to distinguish between progenitor and mature luminal cells [51]. We found that TAD signatures were particularly helpful in these ambiguous situations, enabling more accurate distinction between mature luminal cells and progenitor cells (Methods, Figure 5C).…”

Section: Less-differentiated and Cancer Cells Exhibit Greater Clustering Of Expression Into Tadsmentioning

confidence: 76%

“…Applying the Leiden algorithm for cell clustering, we compared the biological accuracy of the clustering results computed from three input representations of scRNA-seq observations: raw RNA-seq data (generated by applying principal component analysis, PCA, on transcript count data); TAD signatures (by applying PCA on log-odds of TAD activation probabilities); and a concatenation of the two. On three large scRNA-seq datasets sourced from the Chan-Zuckerberg Biohub's cellXgene portal [50], covering breast [51], lung [52] and T cells [53], we compared the overlap between the automatically-computed cell clusters and the expertly-annotated cell type labels made available by the original study authors (Figure 5B, Methods). We found that using TAD signatures led to cell clusters that better agreed with expert labels and in all cases, the representation that combined raw RNA-seq and TAD signatures performed at least as well as the RNA-seq-only representation.…”

Section: Less-differentiated and Cancer Cells Exhibit Greater Clustering Of Expression Into Tadsmentioning

confidence: 99%

“…TAD signatures for cell type inference. We acquired single-cell data from the https:// cellxgene.cziscience.com/ portal, obtaining AnnData-formatted [59] datasets from singlecell RNA-seq studies of the human lung (10x sub-study; European Genome-Phenome Archive accession EGAS00001004344; 65,662 cells; [52]), T-cells (GEO accession GSE126030; 51,876 cells; [53]), and breast epithelial cells (GEO accession GSE164898; 31,696 cells; [51]). Cells with fewer than 20 active genes and genes active in less than 10 cells were removed.…”

Section: Designation Of Early Vs Late-stage Cells During Differentiation When Analyzing Tad Usagementioning

confidence: 99%

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Deciphering the species-level structure of topologically associating domains

Singh

Berger

2021

Preprint

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SummaryChromosome conformation capture technologies such as Hi-C have revealed a rich hierarchical structure of chromatin, with topologically associating domains (TADs) as a key organizational unit, but experimentally reported TAD architectures, currently determined separately for each cell type, are lacking for many cell/tissue types. A solution to address this issue is to integrate existing epigenetic data across cells and tissue types to develop a species-level consensus map relating genes to TADs. Here, we introduce the TAD Map, a bag-of-genes representation that we use to infer, or “impute,” TAD architectures for those cells/tissues with limited Hi-C experimental data. The TAD Map enables a systematic analysis of gene coexpression induced by chromatin structure. By overlaying transcriptional data from hundreds of bulk and single-cell assays onto the TAD Map, we assess gene coexpression in TADs and find that expressed genes cluster into fewer TADs than would be expected by chance, and show that time-course and RNA velocity studies further reveal this clustering to be strongest in the early stages of cell differentiation; it is also strong in tumor cells. We provide a probabilistic model to summarize any scRNA-seq transcriptome in terms of its TAD activation profile, which we term a TAD signature, and demonstrate its value for cell type inference, cell fate prediction, and multimodal synthesis. More broadly, our work indicates that the TAD Map’s comprehensive, quantitative integration of chromatin structure and scRNA-seq data should play a key role in epigenetic and transcriptomic analyses.Software availability: https://tadmap.csail.mit.eduGraphical Abstract

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“…This atlas is based on single-cell RNA-seq and is useful to derive breast epithelial cell subcluster-specific gene expression signatures, which can be applied to breast cancer gene expression data to identify putative cell-of-origin. For complete details on the use and execution of this protocol, please refer to Bhat-Nakshatri et al. (2021) .…”

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confidence: 99%

Acquisition, processing, and single-cell analysis of normal human breast tissues from a biobank

et al. 2022

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Summary The Komen Tissue Bank is the only biorepository in the world for normal breast tissues from women. Below we report the acquisition and processing of breast tissue from volunteer donors and describe an experimental and analysis pipeline to generate a single-cell atlas. This atlas is based on single-cell RNA-seq and is useful to derive breast epithelial cell subcluster-specific gene expression signatures, which can be applied to breast cancer gene expression data to identify putative cell-of-origin. For complete details on the use and execution of this protocol, please refer to Bhat-Nakshatri et al. (2021) .

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A single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cells

Abstract: Highlights d Healthy breast contains 23 subclusters of epithelial cells d Breast cancers may originate from 3 luminal mature and 1 progenitor subclusters d TBX3 and PDK4, co-expressed with estrogen receptor (ER), subclassify ER+ breast cancers

Cited by 74 publications

References 69 publications

Ductal Macrophages Predominate in the Immune Landscape of the Lactating Mammary Gland

Ductal Macrophages Predominate in the Immune Landscape of the Lactating Mammary Gland

Deciphering the species-level structure of topologically associating domains

Acquisition, processing, and single-cell analysis of normal human breast tissues from a biobank

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