A spatially resolved single cell genomic atlas of the adult human breast

Tapsi Kumar, Kevin Nee, Runmin Wei, Siyuan He, Quy H. Nguyen, Shanshan Bai, Kerrigan Blake, Maren Pein, Yanwen Gong, Emi Sei, Min Hu, Anna K. Casasent, Aatish Thennavan, Jianzhuo Li, Tuan Tran, Ken Chen, Benedikt Nilges, Nachiket Kashikar, Oliver Braubach, Bassem Ben Cheikh, Nadya Nikulina, Hui Chen, Mediget Teshome, Brian Menegaz, Huma Javaid, Chandandeep Nagi, Jessica Montalvan, Tatyana Lev, Sharmila Mallya, Delia F. Tifrea, Robert Edwards, Erin Lin, Ritesh Parajuli, Summer Hanson, Sebastian Winocour, Alastair Thompson, Bora Lim, Devon A. Lawson, Kai Kessenbrock, Nicholas Navin

Abstract

The adult human breast is comprised of an intricate network of epithelial ducts and lobules that are embedded in connective and adipose tissue1,2,3. Although most previous studies have focused on the breast epithelial system4,5,6, many of the non-epithelial cell types remain understudied. Here we constructed the comprehensive Human Breast Cell Atlas (HBCA) at single-cell and spatial resolution. Our single-cell transcriptomics study profiled 714,331 cells from 126 women, and 117,346 nuclei from 20 women, identifying 12 major cell types and 58 biological cell states. These data reveal abundant perivascular, endothelial and immune cell populations, and highly diverse luminal epithelial cell states. Spatial mapping using four different technologies revealed an unexpectedly rich ecosystem of tissue-resident immune cells, as well as distinct molecular differences between ductal and lobular regions. Collectively, these data provide a reference of the adult normal breast tissue for studying mammary biology and diseases such as breast cancer.

Datasets

1. scRNA-seq data - all cells
Metadata
mapped_reference_assembly
mapped_reference_annotation
alignment_software
self_reported_ethnicity_ontology_term_id
donor_living_at_sample_collection
donor_menopausal_status
organism_ontology_term_id
sample_preservation_method
tissue_ontology_term_id
development_stage_ontology_term_id
sample_derivation_process
sample_source
suspension_depleted_cell_types
suspension_derivation_process
suspension_dissociation_reagent
suspension_dissociation_time
suspension_type
assay_ontology_term_id
sequencing_platform
cell_type_ontology_term_id
author_cell_type
cell_state
disease_ontology_term_id
sex_ontology_term_id
tissue_location
bmi_group
procedure_group
age_group
broad_cell_type
breast_density
tissue_type
reported_diseases
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
GRCh38714331 cells
Preview
A spatially resolved single cell genomic atlas of the adult human breast
2. snRNA-seq data - all cells
Metadata
mapped_reference_assembly
mapped_reference_annotation
alignment_software
donor_id
self_reported_ethnicity_ontology_term_id
donor_living_at_sample_collection
donor_menopausal_status
organism_ontology_term_id
sample_uuid
sample_preservation_method
tissue_ontology_term_id
development_stage_ontology_term_id
sample_derivation_process
sample_source
suspension_derivation_process
suspension_dissociation_reagent
suspension_uuid
suspension_type
library_uuid
assay_ontology_term_id
library_starting_quantity
sequencing_platform
cell_type_ontology_term_id
author_cell_type
disease_ontology_term_id
sex_ontology_term_id
procedure_group
tissue_location
sample_id
age_group
bmi_group
breast_density
tissue_type
reported_diseases
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
GRCh38117346 cells
Preview
A spatially resolved single cell genomic atlas of the adult human breast

Analyze this study

Source data

https://cellxgene.cziscience.com/collections/4195ab4c-20bd-4cd3-8b3d-65601277e731

Alias names

GSE195665, PMID37380767

Cite this study

Kumar, T., Nee, K., Wei, R., He, S., Nguyen, Q.H., Bai, S., Blake, K., Pein, M., Gong, Y., Sei, E. and Hu, M., 2023. A spatially resolved single-cell genomic atlas of the adult human breast. Nature, 620(7972), pp.181-191. https://doi.org/10.1038/s41586-023-06252-9