In this project, we aim to compare the gene expression profile of four sets of pancreatic samples:
- Normal pancreas
- Resectable PDAC
- Metastatic PDAC
- Matched PDAC liver metastasis
The primary goal of this investigation is to delineate the trajectory that a pancreatic cell takes from the earliest stage of malignancy until a distant overt metastasis. Our anticipation would be to find some targets and markers that aid clinicians in recognizing cancer cells at different stages.
To perform this, we gathered publicly available scRNA-seq data from Zhang et al (https://doi.org/10.1038/s41467-023-40727-7) and Chen et al (https://doi.org/10.1186/s12967-023-04051-4). Having aligned the data to the GRCh38 human genome reference using Cell Ranger, the data was preprocessed and integrated using Seurat and Harmony packages.
This is an ongoing project and the results are still under interpretation.
The following figures represent a part of the analyses that have been performed so far:
Figure1- Cellular landscape of all the samples after filtration and cell type assignment:
Figure2- Cellular landscape of all the samples split by the group of samples:
Figure3- Canonical markers used for cell type assignment:
Figure4- Cell ratio of cell types per sample group:
Figure5- Number of cell types per sample group:
Figure6- Cellular landscape of epithelial cells:
Figure7- Cellular landscape of epithelial cells split by sample group:
Figure8- Cell ratio of epithelial cells per sample group:
Figure9- Cellular landscape of epithelial cells grouped by PDAC subtype:
Figure10- Cell ratio of epithelial cells per PDAC subtype:
Figure11- Kaplan-Meier survival analysis of CSC genes (CD24, CD44, PROM1, ALDH1A1, CD9, SLC1A5):
Figure12- CNV analysis of one of the samples using the InferCNV package:
