Collections / Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs novel combination cancer therapy strategies [visium]

Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs novel combination cancer therapy strategies [visium]

While regulatory T (Treg) cells are traditionally viewed as professional suppressors of antigen presenting and effector T cells in both autoimmunity and cancer, recent findings of distinct Treg functions in tissue maintenance suggest that their regulatory purview extends to a wider range of cells and is broader than previously assumed. To elucidate tumoral Treg “connectivity” to diverse tumor-supporting accessory cell types, we explored immediate early changes in their single cell transcriptomes upon punctual Treg depletion in experimental lung cancer and injury-induced inflammation. Prior to any notable T cell activation and inflammation, fibroblasts, endothelial and myeloid cells exhibited pronounced changes in their gene expression in both cancer and injury settings. Factor analysis revealed shared Treg-dependent gene programs, foremost, prominent upregulation of VEGF signaling-related genes upon Treg deprivation in either setting, as well as in Treg-poor vs Treg-rich human lung adenocarcinomas. Accordingly, punctual Treg depletion combined with short-term VEGF blockade showed markedly improved control of PD-1 blockade-resistant lung adenocarcinoma progression in mice compared to the corresponding monotherapies, highlighting a promising factor-based querying approach to elucidating novel rational combination treatments of solid organ cancers.

Datasets8
Size~361 MB
AssayVisium
Samplemouse · lung
KindComparison
PMID:37127830 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse215361")
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()}
Open in Vitessce
Visium
Mouse lung
GSM6634336
mouse lung lung adenocarcinoma 44 MB 2,947 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuelung
Conditionlung adenocarcinoma
Size44 MB
Obs2,947
Magnificationother · 3.728 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM6634341
mouse lung lung adenocarcinoma 47 MB 3,505 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuelung
Conditionlung adenocarcinoma
Size47 MB
Obs3,505
Magnificationother · 3.730 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM6634339
mouse lung lung adenocarcinoma 49 MB 3,693 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuelung
Conditionlung adenocarcinoma
Size49 MB
Obs3,693
Magnificationother · 3.729 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM6634340
mouse lung lung adenocarcinoma 50 MB 3,788 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuelung
Conditionlung adenocarcinoma
Size50 MB
Obs3,788
Magnificationother · 3.729 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM6634335
mouse lung lung adenocarcinoma 45 MB 3,189 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuelung
Conditionlung adenocarcinoma
Size45 MB
Obs3,189
Magnificationother · 4.145 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM6634342
mouse lung lung adenocarcinoma 42 MB 3,072 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuelung
Conditionlung adenocarcinoma
Size42 MB
Obs3,072
Magnificationother · 4.143 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM6634337
mouse lung lung adenocarcinoma 45 MB 3,503 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuelung
Conditionlung adenocarcinoma
Size45 MB
Obs3,503
Magnificationother · 3.731 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM6634338
mouse lung lung adenocarcinoma 39 MB 2,937 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuelung
Conditionlung adenocarcinoma
Size39 MB
Obs2,937
Magnificationother · 3.729 µm/px
bronze H&E Open in Vitessce

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