Collections / Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer

Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer

Prostate cancer treatment resistance is a significant challenge facing the field. Genomic and transcriptomic profiling have partially elucidated the mechanisms through which cancer cells escape treatment, but their relation toward the tumor microenvironment (TME) remains elusive. Here we present a comprehensive transcriptomic landscape of the prostate TME at multiple points in the standard treatment timeline employing single-cell RNA-sequencing and spatial transcriptomics data from 120 patients. We identify club-like cells as a key epithelial cell subtype that acts as an interface between the prostate and the immune system. Tissue areas enriched with club-like cells have depleted androgen signaling and upregulated expression of luminal progenitor cell markers. Club-like cells display a senescence-associated secretory phenotype and their presence is linked to increased polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) activity. Our results indicate that club-like cells are associated with myeloid inflammation previously linked to androgen deprivation therapy resistance, providing a rationale for their therapeutic targeting.

Datasets52
Size~1.6 GB
AssayVisium
Samplehuman · prostate gland
KindComparison
PMID:39550375 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse278936")
coll.ordered_artifacts.df()                 # the 52 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
Human prostate gland
GSM8558012
human prostate gland prostate cancer 25 MB 2,071 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size25 MB
Obs2,071
Magnificationother · 4.058 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558005
human prostate gland prostate cancer 51 MB 4,470 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size51 MB
Obs4,470
Magnificationother · 7.038 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558020
human prostate gland prostate cancer 16 MB 1,395 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size16 MB
Obs1,395
Magnificationother · 4.018 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557999
human prostate gland prostate cancer 46 MB 4,572 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size46 MB
Obs4,572
Magnificationother · 5.539 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557982
human prostate gland prostate cancer 51 MB 3,391 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size51 MB
Obs3,391
Magnificationother · 5.520 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558003
human prostate gland prostate cancer 52 MB 4,828 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size52 MB
Obs4,828
Magnificationother · 4.015 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558008
human prostate gland prostate cancer 23 MB 2,296 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size23 MB
Obs2,296
Magnificationother · 4.059 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557990
human prostate gland prostate cancer 58 MB 4,517 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size58 MB
Obs4,517
Magnificationother · 7.027 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558026
human prostate gland prostate cancer 13 MB 2,255 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size13 MB
Obs2,255
Magnificationother · 4.358 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557988
human prostate gland prostate cancer 20 MB 1,617 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size20 MB
Obs1,617
Magnificationother · 3.364 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557976
human prostate gland benign prostatic hyperplasia 45 MB 4,199 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionbenign prostatic hyperplasia
Size45 MB
Obs4,199
Magnificationother · 4.356 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557991
human prostate gland prostate cancer 21 MB 1,096 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size21 MB
Obs1,096
Magnificationother · 3.683 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558009
human prostate gland prostate cancer 27 MB 1,802 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size27 MB
Obs1,802
Magnificationother · 4.061 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558018
human prostate gland prostate cancer 29 MB 2,247 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size29 MB
Obs2,247
Magnificationother · 4.060 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558017
human prostate gland prostate cancer 22 MB 1,748 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size22 MB
Obs1,748
Magnificationother · 4.059 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557993
human prostate gland prostate cancer 28 MB 2,254 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size28 MB
Obs2,254
Magnificationother · 4.517 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557989
human prostate gland prostate cancer 15 MB 1,190 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size15 MB
Obs1,190
Magnificationother · 4.021 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558002
human prostate gland prostate cancer 35 MB 3,906 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size35 MB
Obs3,906
Magnificationother · 5.528 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558022
human prostate gland prostate cancer 21 MB 1,586 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size21 MB
Obs1,586
Magnificationother · 6.032 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558024
human prostate gland prostate cancer 9.3 MB 2,190 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size9.3 MB
Obs2,190
Magnificationother · 4.022 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558023
human prostate gland prostate cancer 13 MB 945 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size13 MB
Obs945
Magnificationother · 4.017 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558021
human prostate gland prostate cancer 29 MB 1,818 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size29 MB
Obs1,818
Magnificationother · 4.020 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557992
human prostate gland prostate cancer 32 MB 1,839 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size32 MB
Obs1,839
Magnificationother · 3.685 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557996
human prostate gland prostate cancer 35 MB 4,704 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size35 MB
Obs4,704
Magnificationother · 7.544 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557998
human prostate gland prostate cancer 48 MB 3,143 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size48 MB
Obs3,143
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558025
human prostate gland prostate cancer 36 MB 2,346 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size36 MB
Obs2,346
Magnificationother · 4.516 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558000
human prostate gland prostate cancer 51 MB 4,419 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size51 MB
Obs4,419
Magnificationother · 5.029 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558007
human prostate gland prostate cancer 54 MB 4,401 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size54 MB
Obs4,401
Magnificationother · 5.541 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557994
human prostate gland prostate cancer 17 MB 1,778 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size17 MB
Obs1,778
Magnificationother · 4.017 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557986
human prostate gland prostate cancer 25 MB 2,099 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size25 MB
Obs2,099
Magnificationother · 4.013 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557978
human prostate gland benign prostatic hyperplasia 25 MB 2,030 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionbenign prostatic hyperplasia
Size25 MB
Obs2,030
Magnificationother · 4.019 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558011
human prostate gland prostate cancer 31 MB 2,860 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size31 MB
Obs2,860
Magnificationother · 4.060 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558016
human prostate gland prostate cancer 29 MB 2,093 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size29 MB
Obs2,093
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558015
human prostate gland prostate cancer 18 MB 1,650 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size18 MB
Obs1,650
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557985
human prostate gland prostate cancer 59 MB 4,899 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size59 MB
Obs4,899
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557995
human prostate gland prostate cancer 24 MB 2,738 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size24 MB
Obs2,738
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558014
human prostate gland prostate cancer 15 MB 1,465 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size15 MB
Obs1,465
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557979
human prostate gland benign prostatic hyperplasia 50 MB 3,841 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionbenign prostatic hyperplasia
Size50 MB
Obs3,841
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558013
human prostate gland prostate cancer 18 MB 1,525 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size18 MB
Obs1,525
Magnificationother · 4.059 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558010
human prostate gland prostate cancer 28 MB 2,216 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size28 MB
Obs2,216
Magnificationother · 4.058 µm/px
bronze H&E Open in Vitessce
Visium
Human prostate gland
GSM8557981
human prostate gland prostate cancer 39 MB 2,148 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size39 MB
Obs2,148
bronze H&E
Open in Vitessce
Visium
Human prostate gland
GSM8557987
human prostate gland prostate cancer 18 MB 740 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size18 MB
Obs740
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558019
human prostate gland prostate cancer 11 MB 578 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size11 MB
Obs578
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557980
human prostate gland prostate cancer 47 MB 3,937 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size47 MB
Obs3,937
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8558027
human prostate gland prostate cancer 23 MB 3,162 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size23 MB
Obs3,162
Magnificationother · 4.016 µm/px
bronze H&E Open in Vitessce
Visium
Human prostate gland
GSM8558006
human prostate gland prostate cancer 40 MB 3,602 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size40 MB
Obs3,602
bronze H&E
Open in Vitessce
Visium
Human prostate gland
GSM8557983
human prostate gland prostate cancer 36 MB 2,047 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size36 MB
Obs2,047
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557997
human prostate gland prostate cancer 45 MB 3,082 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size45 MB
Obs3,082
bronze H&E Open in Vitessce
Visium
Human prostate gland
GSM8558004
human prostate gland prostate cancer 35 MB 3,621 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size35 MB
Obs3,621
bronze H&E
Open in Vitessce
Visium
Human prostate gland
GSM8558001
human prostate gland prostate cancer 37 MB 2,845 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size37 MB
Obs2,845
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557977
human prostate gland benign prostatic hyperplasia 17 MB 1,317 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionbenign prostatic hyperplasia
Size17 MB
Obs1,317
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human prostate gland
GSM8557984
human prostate gland prostate cancer 22 MB 991 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueprostate gland
Conditionprostate cancer
Size22 MB
Obs991
bronze H&E Open in Vitessce

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