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
Cell Ranger count v3.1.0714331 cells HANCESTRO:0568364625 cells HANCESTRO:0005241791 cells HANCESTRO:001447968 cells premenopausal551563 cells postmenopausal103399 cells NCBITaxon:9606714331 cells UBERON:0000310714331 cells HsapDv:0000204714331 cells Baylor College of Medicine483078 cells University of California, Irvine121974 cells MD Anderson Cancer Center109279 cells adipocyte of breast714331 cells mechanical dissociation,enzymatic dissociation,centrifugation714331 cells 1 mg/ml collagenase A648972 cells Illumina NovaSeq 6000625476 cells Illumina HiSeq 400065359 cells Illumina HiSeq 300023496 cells Fibro-prematrix50911 cells Mono-non-classical996 cells Reduction Mammoplasty518684 cells Cancer Mastectomy120412 cells Prophylatic Mastectomy75235 cells breast cancer144285 cells luminal epithelial cell of mammary gland104415 cells vein endothelial cell41460 cells mammary gland epithelial cell34161 cells capillary endothelial cell29272 cells vascular associated smooth muscle cell27928 cells CD4-positive helper T cell24782 cells CD8-positive, alpha-beta memory T cell19213 cells endothelial cell of artery12919 cells alternatively activated macrophage9059 cells endothelial cell of lymphatic vessel8982 cells inflammatory macrophage8853 cells effector memory CD8-positive, alpha-beta T cell7303 cells IgA plasma cell5233 cells CD4-positive, alpha-beta T cell5199 cells effector memory CD4-positive, alpha-beta T cell4883 cells natural killer cell4345 cells classical monocyte4166 cells conventional dendritic cell3985 cells class switched memory B cell3491 cells mature NK T cell2867 cells regulatory T cell2365 cells activated CD4-positive, alpha-beta T cell2123 cells IgG plasma cell1076 cells activated CD8-positive, alpha-beta T cell1032 cells non-classical monocyte996 cells gamma-delta T cell529 cells myeloid dendritic cell455 cells unswitched memory B cell420 cells plasmacytoid dendritic cell148 cells African American364625 cells Hispanic or Latin American47968 cells 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
Cell Ranger count v3.1.0117346 cells HANCESTRO:000548885 cells HANCESTRO:056840020 cells postmenopausal29269 cells NCBITaxon:9606117346 cells b3ff1aad-40fd-45da-a0b5-28aae0f6c8bb13096 cells bc0d8a1f-a89e-427d-b05e-f96ff48f324e11515 cells 339bd4b4-c047-43e5-81bb-84e79abf979e9475 cells 04983012-bb56-448d-9546-e353456dd6eb7161 cells b9c76090-0e23-4189-af33-7d8eb91ad93d7131 cells 27830237-7eeb-489d-a36e-1f941ccbb6925610 cells bc909bba-be16-4283-a055-557e93650e585511 cells 2e7f5621-a367-47aa-97d1-35e7ec6184f05398 cells eb92840f-3326-4c18-b2a1-bb3a492db6ca5123 cells 356014e3-647f-4092-9fc4-da2526e99e2e5109 cells 49beb83c-66a1-48db-84db-94fd5735195d4498 cells 5c2c1129-da40-4d41-91f4-ac969d4155504365 cells bd6e1386-856d-4488-99a3-ef69a28003b84356 cells ca308e50-4131-4c1b-ab8a-4ddd6cc4a6774034 cells d83450ee-cf1e-4511-a68f-73a6e6a414673950 cells c373e949-ee2b-4b7d-85dc-f7b6cc48a8cf3852 cells ab088501-d946-4f5a-a832-10e6f49a68cd3763 cells 59bdb2f5-d952-4a24-bae3-4d36a0cd413c3311 cells c4a63080-974c-4eb1-9c40-7c6f93f65de63220 cells b750a9ca-7521-4563-b5f0-a0516b3be3b62177 cells a2a45245-e029-4c6d-abba-41553e991da11818 cells ad5da643-e351-490c-a765-a9d38b5166691430 cells ffcb240a-223b-44a7-94d8-d73b13ed0f921287 cells e5a686e0-54f4-44cc-af21-16c07b6db82a156 cells UBERON:0000310117346 cells HsapDv:0000204117346 cells Baylor College of Medicine58652 cells MD Anderson Cancer Center42352 cells University of California, Irvine16342 cells mechanical dissociation,detergent solubilization117346 cells 0.2% v/v Nonidet P-4096970 cells afd280f3-5bc7-468a-b6fc-b9982b1cc12613096 cells 46922756-6ba7-4e6d-b88c-7920829be50c11515 cells 6d9b6894-55d4-4b07-aec7-68974fcf77de9475 cells 387f5311-8c7d-4cc2-8a0d-6865252a8e7a7161 cells 34158bd3-2d27-4523-938b-e363da9e083c7131 cells 5c5edac0-4fe8-4c48-864e-e43e86b1c3235610 cells b2f7a307-461c-438e-9aa4-332e857c5c195511 cells 150c165e-d69e-4e7c-a0d6-204e1509b0b15398 cells d3ed0e2e-9c44-47e7-a86a-58d42d63126a5123 cells 6d35bfad-0ffb-4442-9bff-a0b1e48ac5185109 cells d1e2a156-bc53-45d3-a712-ac5398eee0594498 cells 4c8e7a75-3b13-4b9b-a44d-2810faf711584365 cells dc95d0c0-cb94-45b6-a134-40987fb162fa4356 cells 3ccf7843-de31-4e48-b557-7babd29405f54034 cells 61842887-f3d9-405d-aad4-523e4d62fa7d3950 cells 5ff7d807-7b84-4da7-9639-76676686f7483852 cells 0800265a-4ea9-4578-9048-762b490473313763 cells 7f725a92-7dee-41ac-8d2f-eda46871929f3311 cells 280fe094-5fd6-4d01-9170-fa4a3e5b8f413220 cells 254a8d20-dc2a-4e67-91f8-45f8e43bb3142177 cells a84201ef-2535-46d7-97e1-cecfd0dd81ae1818 cells 081ccda8-560d-46d3-9e87-0cdce770dafd1430 cells 4bc2b0e3-aece-4772-9949-6e71beb1b8161287 cells bc3a06fc-d330-4875-bb89-92fccb03654a156 cells ea3b4522-0144-4ad1-9509-301530b2bd7f13096 cells de7e5eff-fd40-42a6-994f-7e4a5e46064311515 cells 5c46bbcd-c39d-4633-b4c3-9ea0fa31910e9475 cells 7783e802-db87-4a7e-9d31-0409ca59c1257161 cells c098399a-0482-4da2-a1e0-98719587670f7131 cells 691e49e2-ffce-4725-9dac-0ebd3987212c5610 cells 8d52cb2a-94f4-49fb-8c90-cc8c6ccb7b805511 cells 83f62ab3-1610-404e-8a77-ccd7b3eeca4b5398 cells 1c440f87-8d30-4c59-8654-90bf07c35bdb5123 cells 4e686887-7507-4ac7-b7cd-6fd52977c4e05109 cells 1a494b68-65b0-4a57-be53-be13dc3a52af4498 cells d3199c29-ed96-4b98-99bf-20f982d925ba4365 cells 01fee896-237e-49b6-94cb-f014a31ba0c44356 cells 2d01af45-7ad9-42f6-9503-f1a97e0644a14034 cells 4d38638c-237b-46ec-8cce-037686726da03950 cells 76938fc3-6aac-4370-9329-f908c0d86cb03852 cells 838805cc-7c26-4032-99b4-84ea080e10593763 cells 147adc7b-54cf-4a07-8cd2-1d969f0e97483311 cells 24236067-3443-4544-91c9-cc0e2604e6fb3220 cells 7a839cc8-31a8-4990-bd21-c4b4fe6a59002177 cells 501e2f11-5d60-41eb-80c7-3f32412d42e41818 cells c74bb84c-6362-4ee2-9c40-ee36f1a559061430 cells b1c8e213-d710-4c52-8d15-4ef93c8c26a81287 cells 4b85488c-eaa9-44c8-8372-7e8643a96f34156 cells 700-1200 nuclei/μl117346 cells Illumina NovaSeq 600096198 cells Illumina HiSeq 400016342 cells Illumina HiSeq 30004806 cells Reduction Mammoplasty81710 cells Cancer Mastectomy25242 cells Prophylatic Mastectomy6542 cells luminal epithelial cell of mammary gland39057 cells adipocyte of breast9780 cells endothelial cell of vascular tree8490 cells endothelial cell of lymphatic vessel4112 cells African American40020 cells Hispanic or Latin American4034 cells 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