Mapping the Immune Architecture of a High-Evolution MSS Colorectal Cancer Subtype: The Role of Plasma Cells

Background

Microsatellite stable (MSS) colon cancers (CCs) typically resist immunotherapy due to limited immune infiltration, unlike microsatellite instability (MSI) tumors. We previously identified a high-evolution MSS (HE-MSS) subtype marked by pronounced B/plasma cell infiltration and elevated mutational divergence between diagnosis and relapse (Martín-Arana et al., 2025). Spatial transcriptomics offers a powerful approach to map the spatial architecture and immune dynamics of the tumor microenvironment in this subset of patients.

Methods

We analyzed 14 primary CC tumors (9 MSS and 5 MSI) using 10x Genomics Visium HD. Tumor evolution was quantified based on genomic similarity between baseline and matched relapse plasma samples, stratifying MSS cases into HE-MSS (n=4) and low-evolution MSS (LE-MSS) (n=5). Data were processed with spaceranger v3.1.2. Cell segmentation on tissue images and 2×2 μm bin-to-cell assignment followed the ENACT pipeline. Cell types were annotated with CellTypist. Downstream analyses were conducted in Python using Squidpy, decoupler (for pathway activity), and stLearn (for ligand–receptor interactions).

Results

Compared to LE-MSS, HE-MSS tumor cells showed increased EGFR/MAPK and PI3K signaling, reduced oxidative stress response activity, and were surrounded by heightened peritumoral inflammation—a profile consistent with elevated genomic instability. Immune infiltrates were more prominent and partially resembled those in MSI tumors—most notably with increased IgG⁺ plasma cells that exhibited greater spatial co-localization than in LE-MSS tumors. B cells and IgG⁺, but not IgA⁺, plasma cells increased with tumor evolution, pointing to a role for reactive rather than resident immune activity. In HE-MSS tumors, IgG⁺ plasma cells engaged in enriched ligand–receptor interactions via integrin signaling and the MIF–CD74 and THBS2–CD47 axes, implying roles in spatial localization, tumor support, and immune suppression, respectively.

Conclusion

A subset of high-evolution MSS CCs displays enriched, spatially organized IgG⁺ plasma cell infiltrates and MSI-like immune features, supporting spatial profiling as a tool for immunotherapy stratification.