Collections / Spatial Transcriptomics Reveals Compartment-Specific Cytotoxic T cells Crosstalk with AT2 and Goblet cells in Advanced COPD

Spatial Transcriptomics Reveals Compartment-Specific Cytotoxic T cells Crosstalk with AT2 and Goblet cells in Advanced COPD

Chronic obstructive pulmonary disease (COPD) is characterized by chronic inflammation and structural remodelling across different anatomical structures of the lung, including airways, parenchyma, and pulmonary vessels. However, compartment specific changes in immune cells composition and their communications with underlying structural cells is under investigated. Our study sought to assess the spatially resolved cellular organization of healthy and advanced end-stage COPD lungs using Visium spatial transcriptomics. We generated spatial transcriptomic map that uncovered distinct COPD-associated niches, characterized by increased neutrophils and myofibroblast with pronounced extracellular matrix organization around vessels, and colocalization of cytotoxic T cells and their interaction with alveolar type 2 cells and goblet cells, driving stress-induced cytotoxic response in the parenchyma and epithelial differentiation in the airway, respectively. Overall, our findings provide novel insights into compartment-specific cellular microenvironments that contribute to tissue remodelling processes in COPD.

Datasets8
Size~101 MB
AssayVisium
Samplehuman · lung
KindComparison
PMID:42351239 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse318039")
coll.ordered_artifacts.df()                 # the 8 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]

# …or load each straight into memory as a SpatialData object:
sdatas = {a.key: sd.read_zarr(a.cache()) for a in coll.ordered_artifacts.all()}
Member datasets · 8
Open in Vitessce
Visium
Human lung
GSM9485175
human lung chronic obstructive pulmonary disease 13 MB 2,129 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionchronic obstructive pulmonary disease
Size13 MB
Obs2,129
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM9485176
human lung chronic obstructive pulmonary disease 11 MB 1,872 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionchronic obstructive pulmonary disease
Size11 MB
Obs1,872
Magnificationother · 3.941 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM9485173
human lung 16 MB 2,599 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Size16 MB
Obs2,599
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM9485178
human lung chronic obstructive pulmonary disease 10 MB 1,314 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionchronic obstructive pulmonary disease
Size10 MB
Obs1,314
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM9485179
human lung chronic obstructive pulmonary disease 10 MB 2,867 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionchronic obstructive pulmonary disease
Size10 MB
Obs2,867
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM9485172
human lung 16 MB 3,458 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Size16 MB
Obs3,458
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM9485174
human lung 13 MB 3,604 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Size13 MB
Obs3,604
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM9485177
human lung chronic obstructive pulmonary disease 10 MB 1,945 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionchronic obstructive pulmonary disease
Size10 MB
Obs1,945
bronze H&E Open in Vitessce

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