Table · study · 2026
SMART: A Spatio-Molecular Atlas of Response Trajectories in Triple-Negative Breast Cancer
Listed in NCBI GEO
Triple-negative breast cancer (TNBC) is typically managed with neoadjuvant chemotherapy (NACT), which induces profound but heterogeneous remodelling of the tumour–immune microenvironment, yet the microanatomical determinants of treatment response remain poorly defined.
Description
By tiling whole pre-NACT core biopsies and pathologist curated regions of interest from post-NACT resections, we generated SMART: a Spatio Molecular Atlas of Response Trajectories in TNBC from 89 patients, totalling 129 samples, profiled using the NanoString GeoMx platform.
This atlas comprises 5,096 high quality, manually selected spatial transcriptomic profiles spanning epithelial, immune and stromal compartments. We define the molecular properties of seven epithelial archetypes (EAs) and seven tumour–immune microenvironments (TIMEs) to capture the spatio-molecular properties of epithelial and immune cells in TNBC. We show that prognostically significant B‑cell–rich immune niches preferentially localise with proliferative, chemokine-activated epithelia in responders but with interferon-activated, antigen‑processing and immunosuppressive tumour regions in non-responders.
Read the rest (2 more)
Using topological analysis of tissue-matched images, we correlate epithelial network organisation with molecular signalling and show that proliferative, chromosomally unstable and mesenchymal-like programmes adopt dispersed spatial architectures, whereas genomically stable epithelial-like states form densely clustered neighbourhoods. By integrating expression-similarity and spatial-distance trees, we map how NACT reshapes the alignment between molecularly defined states and their spatial niches.
Collectively, SMART provides a tractable and clinically relevant framework for dissecting spatial–molecular decoupling, identifying actionable microenvironmental vulnerabilities, and informing the development of spatially resolved biomarkers to guide adaptive and immunotherapy‑inclusive treatment strategies for TNBC.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE331nnn/GSE331245 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE331245 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1467552 ncbi.nlm.nih.gov/bioproject/PRJNA1467552 ↗
project · from NCBI GEO
Topics
- Stated by source
- Homo sapiens · Other
- From keywords
- Life Sciences
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE331245 | 14 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[disease].local:disease:cancer | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:other | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:image | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[organism].NCBITaxon:9606 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |