Collections / Spatial transcriptomic profiling of human pancreatic ductal adenocarcinoma using 10x Genomics Visium platform

Spatial transcriptomic profiling of human pancreatic ductal adenocarcinoma using 10x Genomics Visium platform

In this study, we performed spatial transcriptomics (ST) to investigate the gene expression features across one normal pancreatic tissue, PC tissue, adjacent tumor tissue, and tumor stroma using 10x Genomics Visium spatial gene expression platform. We generated high-quality spatial gene expression profiles combined with histomorphological information, aiming to reveal the spatial heterogeneity of pancreatic cancer microenvironment and identify spatially restricted gene signatures associated with tumor progression. Sequencing was performed on Illumina NovaSeq 6000 platform, and data processing was conducted using SpaceRanger software with hg38 reference genome. The results revealed that KRT13+FABP5+ malignant cell subpopulation had keratinization characteristics in the tumor tissue. Fibroblasts from adjacent tumor tissue exhibited a tumor-inhibiting role such as “B-cell activation” and “positive regulation of leukocyte activation.” The FGG+CRP+ inflammatory cancer-associated fibroblasts replaced the islets in tumor stroma. During PC progression, the damage to pancreatic structure and function was heavier in the pancreatic exocrine (AMYA2+PRSS1+) than in the endocrine (INS+GCG+). Our results revealed the spatial heterogeneity of dynamic changes and highlighted the significance of impaired exocrine function in PC.

Datasets4
Size~151 MB
AssayVisium
Samplehuman · pancreas
KindComparison
PMID:42100437 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse327056")
coll.ordered_artifacts.df()                 # the 4 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 · 4
Open in Vitessce
Visium
Human pancreas
GSM9647222
human pancreas pancreatic ductal adenocarcinoma 30 MB 4,724 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size30 MB
Obs4,724
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM9647219
human pancreas pancreatic ductal adenocarcinoma 35 MB 4,885 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size35 MB
Obs4,885
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM9647221
human pancreas pancreatic ductal adenocarcinoma 38 MB 4,483 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size38 MB
Obs4,483
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM9647220
human pancreas pancreatic ductal adenocarcinoma 47 MB 3,983 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size47 MB
Obs3,983
bronze H&E Open in Vitessce

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