Pancreatic ductal adenocarcinoma (PDAC) tissue poses a unique challenge for bulk-transcriptomic gene expression, due to their relative stromal density and abundance of inherent ribonuclease enzymes. Spatial transcriptomic (ST) profiling is an established technique to explore the molecular architecture of human cancers. The use of these ST technologies has evolved from their primary development in fresh-frozen tissue, to formalin-fixed paraffin-embedded (FFPE) samples. This has created interest in applying ST to archival PDAC resection specimens.
A selection of archival FFPE samples from surgically resected pancreatic ductal adenocarcinomas underwent 10x Genomics Visium Spatial Gene Expression for FFPE analysis. This selection comprised: 2x classical molecular sub-type, 2x squamous molecular sub-type, 2x treatment naïve, and 2x neoadjuvant treated with chemotherapy. A panel of 18,000 unique gene probes was used i.e Whole Human Transcriptome. Differential gene expression and cluster analysis was performed to characterise the tumour microenvironment and identify immune components. Comparison was made between the ST gene expression and prior bulk-transcriptomics performed on these specimens.
PDAC samples ranged in RNA integrity; no sample had more than 40% of measured RNA fragments > 200 nucleotides in length indicating substantial RNA fragmentation. The mean number of unique genes identified per sample was 17, 871. The mean number of genes identified per 55μm area of tissue was 4,617. Clustering models demonstrated identified distinct cell populations with correlation to histopathological tissue architecture.
These data suggest that ST analysis with Visium can be yield meaningful gene expression information from archival FFPE samples of many variants of PDAC. Applying ST to more PDAC specimens may allow the creation of a spatial atlas of PDAC architecture; as well as an adjunct to bulk and single-cell transcriptomic interrogation. As interest in therapeutic targeting based on transcriptomic subtyping develops, these data provide valuable insight into the heterogeneity of transcriptomic signalling within PDAC.
The authors.
1. Medical Research Council 2. Royal College of Surgeons of Edinburgh 3. Royal College of Physicians and Surgeons of Glasgow.
J. Chell: Financial Interests, Personal, Full or part-time Employment, Dr James Chell is a full-time Research and Development Scientist at Spatial Transcriptomics - Part of 10x Genomics. The work in this abstract was done in collaboration with 10x Genomics R&D Department. All other authors have declared no conflicts of interest.