Collections / Spatial mapping of transcriptomic and lineage plasticity in metastatic pancreatic cancer

Spatial mapping of transcriptomic and lineage plasticity in metastatic pancreatic cancer

Patients with treatment-refractory pancreatic cancer often succumb to widespread systemic metastases; however, the transcriptomic heterogeneity that underlies recalcitrance to therapy remains understudied, particularly in the spatial context. We constructed high-resolution spatial maps of transcriptional heterogeneity, clonal architecture and lineage plasticity using spatially resolved transcriptomics from 55 individual samples of primary tumour, liver, lung, and peritoneal metastases, collected from 13 patients via a rapid ("warm") autopsy program. Additionally, we validated the lineage composition and spatial distribution using patient-derived xenograft (PDX) models generated from the primary tumours of two patients.

Datasets57
Size~1.5 GB
AssayVisium
Samplehuman · multiple
KindComparison
PMID:40269162 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse274557")
coll.ordered_artifacts.df()                 # the 57 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 · 57
Open in Vitessce
Visium
Human liver
GSM8452876
human liver pancreatic ductal adenocarcinoma 26 MB 2,887 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size26 MB
Obs2,887
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8452883
human pancreas pancreatic ductal adenocarcinoma 26 MB 3,563 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size26 MB
Obs3,563
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
GSM8452873
human liver pancreatic ductal adenocarcinoma 34 MB 2,915 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size34 MB
Obs2,915
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8714180
human pancreas pancreatic ductal adenocarcinoma 15 MB 1,453 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size15 MB
Obs1,453
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8452891
human pancreas pancreatic ductal adenocarcinoma 36 MB 3,073 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size36 MB
Obs3,073
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8714179
human pancreas pancreatic ductal adenocarcinoma 12 MB 1,829 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size12 MB
Obs1,829
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
GSM8452880
human liver pancreatic ductal adenocarcinoma 19 MB 2,686 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size19 MB
Obs2,686
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8452874
human peritoneum pancreatic ductal adenocarcinoma 24 MB 2,327 obs silver H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditionpancreatic ductal adenocarcinoma
Size24 MB
Obs2,327
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
GSM8452872
human liver pancreatic ductal adenocarcinoma 33 MB 2,531 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size33 MB
Obs2,531
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8452865
human peritoneum pancreatic ductal adenocarcinoma 22 MB 2,260 obs silver H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditionpancreatic ductal adenocarcinoma
Size22 MB
Obs2,260
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8714178
human pancreas pancreatic ductal adenocarcinoma 5.8 MB 660 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size5.8 MB
Obs660
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
GSM8452884
human liver pancreatic ductal adenocarcinoma 25 MB 2,741 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size25 MB
Obs2,741
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8452849
human peritoneum pancreatic ductal adenocarcinoma 34 MB 3,047 obs silver H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditionpancreatic ductal adenocarcinoma
Size34 MB
Obs3,047
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8452853
human pancreas pancreatic ductal adenocarcinoma 41 MB 2,999 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size41 MB
Obs2,999
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8452887
human pancreas pancreatic ductal adenocarcinoma 18 MB 2,892 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size18 MB
Obs2,892
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8714181
human pancreas pancreatic ductal adenocarcinoma 8.9 MB 419 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size8.9 MB
Obs419
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8452881
human lung pancreatic ductal adenocarcinoma 17 MB 1,873 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionpancreatic ductal adenocarcinoma
Size17 MB
Obs1,873
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
GSM8452861
human liver pancreatic ductal adenocarcinoma 39 MB 2,772 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size39 MB
Obs2,772
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8452860
human pancreas pancreatic ductal adenocarcinoma 27 MB 2,931 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size27 MB
Obs2,931
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8714177
human pancreas pancreatic ductal adenocarcinoma 11 MB 444 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size11 MB
Obs444
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
GSM8452857
human liver pancreatic ductal adenocarcinoma 32 MB 2,773 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size32 MB
Obs2,773
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8452856
human pancreas pancreatic ductal adenocarcinoma 47 MB 3,155 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size47 MB
Obs3,155
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8452885
human lung pancreatic ductal adenocarcinoma 22 MB 2,635 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionpancreatic ductal adenocarcinoma
Size22 MB
Obs2,635
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8452867
human pancreas pancreatic ductal adenocarcinoma 34 MB 3,954 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size34 MB
Obs3,954
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8452886
human peritoneum pancreatic ductal adenocarcinoma 18 MB 2,845 obs silver H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditionpancreatic ductal adenocarcinoma
Size18 MB
Obs2,845
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8452863
human pancreas pancreatic ductal adenocarcinoma 20 MB 1,758 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size20 MB
Obs1,758
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8452855
human peritoneum pancreatic ductal adenocarcinoma 30 MB 2,537 obs silver H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditionpancreatic ductal adenocarcinoma
Size30 MB
Obs2,537
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
GSM8452888
human liver pancreatic ductal adenocarcinoma 22 MB 2,123 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size22 MB
Obs2,123
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8452882
human peritoneum pancreatic ductal adenocarcinoma 14 MB 2,008 obs silver H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditionpancreatic ductal adenocarcinoma
Size14 MB
Obs2,008
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8452858
human lung pancreatic ductal adenocarcinoma 38 MB 2,623 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionpancreatic ductal adenocarcinoma
Size38 MB
Obs2,623
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8452852
human peritoneum pancreatic ductal adenocarcinoma 23 MB 2,322 obs silver H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditionpancreatic ductal adenocarcinoma
Size23 MB
Obs2,322
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8452859
human peritoneum pancreatic ductal adenocarcinoma 42 MB 3,493 obs silver H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditionpancreatic ductal adenocarcinoma
Size42 MB
Obs3,493
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8452871
human pancreas pancreatic ductal adenocarcinoma 37 MB 3,952 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size37 MB
Obs3,952
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8452890
human peritoneum pancreatic ductal adenocarcinoma 30 MB 2,696 obs silver H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditionpancreatic ductal adenocarcinoma
Size30 MB
Obs2,696
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8452894
human peritoneum pancreatic ductal adenocarcinoma 35 MB 2,160 obs silver H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditionpancreatic ductal adenocarcinoma
Size35 MB
Obs2,160
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
GSM8452862
human liver pancreatic ductal adenocarcinoma 35 MB 2,397 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size35 MB
Obs2,397
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8452850
human pancreas pancreatic ductal adenocarcinoma 25 MB 2,674 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size25 MB
Obs2,674
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8452879
human pancreas pancreatic ductal adenocarcinoma 14 MB 2,225 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size14 MB
Obs2,225
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
GSM8452864
human liver pancreatic ductal adenocarcinoma 19 MB 2,686 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size19 MB
Obs2,686
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8714183
human pancreas pancreatic ductal adenocarcinoma 59 MB 4,339 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size59 MB
Obs4,339
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
GSM8452848
human liver pancreatic ductal adenocarcinoma 7.8 MB 2,956 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size7.8 MB
Obs2,956
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8452870
human peritoneum pancreatic ductal adenocarcinoma 30 MB 3,226 obs silver H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditionpancreatic ductal adenocarcinoma
Size30 MB
Obs3,226
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8452878
human peritoneum pancreatic ductal adenocarcinoma 12 MB 2,169 obs silver H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditionpancreatic ductal adenocarcinoma
Size12 MB
Obs2,169
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8452895
human peritoneum pancreatic ductal adenocarcinoma 47 MB 2,883 obs silver H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditionpancreatic ductal adenocarcinoma
Size47 MB
Obs2,883
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8452893
human lung pancreatic ductal adenocarcinoma 32 MB 2,622 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionpancreatic ductal adenocarcinoma
Size32 MB
Obs2,622
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8452847
human pancreas pancreatic ductal adenocarcinoma 23 MB 2,753 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size23 MB
Obs2,753
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
GSM8452877
human liver pancreatic ductal adenocarcinoma 20 MB 3,271 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size20 MB
Obs3,271
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
GSM8452868
human liver pancreatic ductal adenocarcinoma 34 MB 3,435 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size34 MB
Obs3,435
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8452851
human lung pancreatic ductal adenocarcinoma 35 MB 2,867 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionpancreatic ductal adenocarcinoma
Size35 MB
Obs2,867
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8452875
human pancreas pancreatic ductal adenocarcinoma 22 MB 3,177 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size22 MB
Obs3,177
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8452866
human peritoneum pancreatic ductal adenocarcinoma 13 MB 2,660 obs silver H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditionpancreatic ductal adenocarcinoma
Size13 MB
Obs2,660
silver H&E Open in Vitessce
Visium
Human pancreas
GSM8714182
human pancreas pancreatic ductal adenocarcinoma 17 MB 1,701 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size17 MB
Obs1,701
silver H&E
Open in Vitessce
Visium
Human liver
GSM8452854
human liver pancreatic ductal adenocarcinoma 17 MB 2,696 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size17 MB
Obs2,696
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8714184
human pancreas pancreatic ductal adenocarcinoma 48 MB 2,108 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size48 MB
Obs2,108
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
GSM8452892
human liver pancreatic ductal adenocarcinoma 27 MB 2,815 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size27 MB
Obs2,815
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8452889
human lung pancreatic ductal adenocarcinoma 31 MB 3,361 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionpancreatic ductal adenocarcinoma
Size31 MB
Obs3,361
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
GSM8452869
human liver pancreatic ductal adenocarcinoma 26 MB 2,731 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionpancreatic ductal adenocarcinoma
Size26 MB
Obs2,731
silver H&E Open in Vitessce

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