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Spatial mapping of transcriptomic and lineage plasticity in metastatic pancreatic cancer

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE274557 | GEO | 2025/02/21

REPOSITORIES: GEO

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Project description:Gene expression studies are used to help identify disease-associated genes, by comparing the levels of expressed transcripts between cases and controls, and to identify functional genetic variants known as expression quantitative loci (eQTLs). While many of these studies are performed in blood or lymphoblastoid cell lines due to tissue accessibility, the relevance of expression differences in tissues that are not the primary site of disease is unclear. Further, many eQTLs are tissue specific. Thus, there is a clear and compelling need to conduct gene expression studies in tissues that are specifically relevant to the disease of interest. One major technical concern about using autopsy-derived tissue is how representative it is of physiologic conditions, given the effect of postmortem interval on tissue degradation. In this study, we monitored the gene expression of 13 tissue samples harvested from a rapid autopsy heart (non-failed heart) and 7 from a cardiac explant (failed heart) through 24 hours of autolysis. The 24 hour autopsy simulation design reflects a typical autopsy scenario where a body may begin cooling to ambient temperature for ~12 hours, before transportation and storage in a refrigerated room in a morgue. In addition, we also simulated a scenario wherein the body was left at room temperature for up to 24 hours before being found. RNA from the 20 samples and triplicate from the HeLa cell line were run on the Affymetrix Exon arrays according to the manufacturer's protocol. The expression profiles of 7 cardiac tissue samples from the cardiac transplant operation (explant/failed heart) and 13 from a rapid-autopsy program (autopsy/non-failed heart) were harvested under the cold- and warm-24 hour autolysis conditions. The 7 explant samples include - 2 biological replicates at 0 hr, 1 at 6 hrs, 1 at 12 hrs, 2 biological replicates at 18 hr cold-autolysis condition and 1 at 18 hr warm-autolysis condition. The 13 autopsy samples include - 3 biological replicates at 0 hr (2 from the left and 1 from the right ventricle), 1 at 6 hrs, 2 biological replicates at 12 hrs (1 from the left and 1 from the right ventricle), 3 biological replicates at 18 hr cold-autolysis condition (2 from the left and 1 from the right ventricle), 2 biological replicates at 18 hr warm-autolysis condition ( 1 from the left and 1 from the right ventricle), 1 at 24 hr cold-autolysis condition and 1 at 24 hr warm-autolysis condition. Gene expression profiles of triplicate liver and heart exon array data obtained from Affymetrix were also used as reference .

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Spatial mapping of transcriptomic and lineage plasticity in metastatic pancreatic cancer

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