Clinical value of immune checkpoints in pancreatic ductal adenocarcinomaco-overexpressing with CEACAM6

Background: Carcinoembryonic cell adhesion molecule 6 (CEACAM6), a cell adhesion immune checkpoint receptor of the Ig-family is overexpressed in Pancreatic Ductal Adenocarcinoma (PDA). CEACAM6 is a poor prognostic marker and a therapeutic target expressed in all subtypes of PDA (Pandey et al. Sci Rep 2019). We report here single cell analysis of the GEO data for PDA cells and non-cancerous adjacent cells from patients for presence of CEACAM6 and co-occurring immune checkpoint markers. Co-presence of CEACAM6 and unique immune checkpoint markers offers insight to potentially develop combination therapy with a monoclonal antibody targeting CEACAM6 in PDA that we have developed. Methods: scRNA-Seq data was obtained from GSE212966. Seurat V5.4.0 was used to analyze gene-cell data matrices for six adjacent non tumor and six PDA samples from 12 patients with no prior treatment. Expression was log normalized and DE genes (cluster markers) were filtered by log2 fold change >1. Dimensionality reduction method UMAP was used to identify distinct clusters. Specific gene markers were plotted on UMAPs and individual clusters on violin plots to compare cell type expression. SingleR, celldex R packages and celltypist were used for cell type marking. First generation immune checkpoint targets that are approved in the clinic and second-generation targets under development were profiled. String was utilized for profiling interaction partners for the markers. Results: CEACAM6 was found to be expressed in many cell clusters in PDA samples and not expressed in adjacent non-cancerous cells. CEACAM6 was present in many cell types in the tumor microenvironment but significantly enriched to epithelial cells. Comparing adjacent cells to PDA, we focused on immune checkpoint markers that were absent or minimum in adjacent cells but were present or relatively higher in PDA cells. PDL1 is scarce in both adjacent and PDA but CTLA4, LAG3, TIGIT were found in abundance in both adjacent and PDA cells, predominantly in T cells and NK cell type clusters. TIM3 was found sparsely but in both tumor and non-tumor cells. LAIR and VSIR were enriched more in adjacent than PDAC cells. CEACAM1 and CD276 (B7-H3) were found to be expressed more in PDA compared to adjacent non tumor cells. Both are found in epithelial cell types and macrophages similar to CEACAM6 cell type expression. CD276, modulates T cell responses and can be targeted by antibody drug conjugates. CD276 interacts with C80 which binds to CTLA4, an inhibitor and CD28, a co-stimulator. CEACAM1, expressed on multiple immune cell types, cell surface immune checkpoint interacts with CEACAM6 in PDA promoting immune suppression. Conclusion: The immune suppressive tumor microenvironment in PDA is complex and deciphering this landscape provides clinical value in developing novel therapeutic interventions. Co-targeting CEACAM6 and B7-H3 (PDA) and CEACAM1 (T-Reg) provides novel therapeutic opportunities in PDA.