Human Breast Cell Atlas (HBCA)

LASP1

Ontology Term: luminal adaptive secretory precursor cell of mammary glandCL:4033057
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: LASP, LP, alveolar progenitor, AP, LumSec, alveolar cell, luminal progenitor cell, ER-negative luminal alveolar progenitor, AV, luminal progenitor, luminal secretory cell
Category Class of which the cell type is a subclass.: luminal epithelial cell of mammary glandCL:0002326
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: EPCAM, CDH1, KRT17, KIT, ALDH1A3, SLPI, SERPINB3, MUC16, S100A7, SLC34A2, SERPINB4, RARRES1, IGFL1, ADGRF1, C1QL2, LCN2, FDCSP, MGAM2
Canonical Marker Genes: EPCAM, CDH1, KRT17, KIT, ALDH1A3, SLPI, SERPINB3, MUC16
Negative Marker Genes Genes expected to be absent, or expressed at a notably low level, in these cells, and whose absence supports the assignment of this cell annotation.: —
Rationale: EPCAM, CDH1 and KRT17 used to define the epithelial population, further refined by KIT, ALDH1A3 and SLPI to define the luminal adaptive secretory precursor cells of mammary gland (LASP), as supported by literature. Selected specific markers for this cluster (LASP1) are SERPINB3 and MUC16. Differential expression analysis was performed for each of the level2 cell types and here we report the top 10 markers as determined by one-vs-all negative binomial testing (non-redundant).

Inherited from level2

Set of Labels Description: This dataset generates a comprehensive Human Breast Cell Atlas (HBCA) using scRNA-seq of over 800,000 cells from 55 donors, identifying 41 cell subclusters across the epithelial (LASP, LHS, BMYO), immune (T cells, NK, B cells, macrophages), and stromal (fibroblast, endothelial, perivascular) compartments. To capture how key risk-modifying factors alter the homeostatic cellular composition of the breast, we assembled a cohort with broad donor diversity spanning a wide range of ages, parity statuses, and germline mutation backgrounds. By annotating at this resolution we could apply differential abundance testing to detect subcluster-level compositional shifts associated with each risk factor. This annotation set also serves as a standardised reference taxonomy, enabling harmonised cell-type comparisons across existing datasets where nomenclature had been inconsistent.
Annotation Method: manual

LASP1

Ontology Term

luminal adaptive secretory precursor cell of mammary glandCL:4033057

Synonyms

Terms that have the same, or nearly the same, meaning as the selected cell type.

LASP, LP, alveolar progenitor, AP, LumSec, alveolar cell, luminal progenitor cell, ER-negative luminal alveolar progenitor, AV, luminal progenitor, luminal secretory cell

Category

Class of which the cell type is a subclass.

luminal epithelial cell of mammary glandCL:0002326

Ontology Assessment

Disagreements with any aspect of the Cell Ontology.

—

Marker Gene Evidence

Gene markers used by researcher to assign this cell annotation.

EPCAM, CDH1, KRT17, KIT, ALDH1A3, SLPI, SERPINB3, MUC16, S100A7, SLC34A2, SERPINB4, RARRES1, IGFL1, ADGRF1, C1QL2, LCN2, FDCSP, MGAM2

Canonical Marker Genes

EPCAM, CDH1, KRT17, KIT, ALDH1A3, SLPI, SERPINB3, MUC16

Negative Marker Genes

Genes expected to be absent, or expressed at a notably low level, in these cells, and whose absence supports the assignment of this cell annotation.

—

Rationale

EPCAM, CDH1 and KRT17 used to define the epithelial population, further refined by KIT, ALDH1A3 and SLPI to define the luminal adaptive secretory precursor cells of mammary gland (LASP), as supported by literature. Selected specific markers for this cluster (LASP1) are SERPINB3 and MUC16. Differential expression analysis was performed for each of the level2 cell types and here we report the top 10 markers as determined by one-vs-all negative binomial testing (non-redundant).

Inherited from level2

Set of Labels Description

This dataset generates a comprehensive Human Breast Cell Atlas (HBCA) using scRNA-seq of over 800,000 cells from 55 donors, identifying 41 cell subclusters across the epithelial (LASP, LHS, BMYO), immune (T cells, NK, B cells, macrophages), and stromal (fibroblast, endothelial, perivascular) compartments. To capture how key risk-modifying factors alter the homeostatic cellular composition of the breast, we assembled a cohort with broad donor diversity spanning a wide range of ages, parity statuses, and germline mutation backgrounds. By annotating at this resolution we could apply differential abundance testing to detect subcluster-level compositional shifts associated with each risk factor. This annotation set also serves as a standardised reference taxonomy, enabling harmonised cell-type comparisons across existing datasets where nomenclature had been inconsistent.

Annotation Method

manual