This molecular case report describes a 77-year-old woman who underwent surgical resection for a mismatch repair–proficient (pMMR), microsatellite-stable (MSS) colorectal cancer (CRC) that exhibited a low tumor mutational burden and a synchronous adenoma. The authors set out to determine whether prominent T‑cell infiltration in an MSS, low‑mutational‑burden tumor reflected effective anti-tumor immunity or instead indicated a functionally constrained immune ecosystem.
Whole-exome sequencing (WES) was performed on the tumor, the synchronous adenoma, and adjacent normal tissue. Within the sensitivity of the WES analysis reported, no shared high-confidence somatic mutations were detected between the tumor and the adenoma. WES identified tumor‑specific alterations, including canonical CRC-associated changes in APC, KRAS, and TP53. The tumor was characterized as low in mutational burden, consistent with the MSS/pMMR phenotype described.
Single-cell RNA sequencing of the tumor yielded 7,569 cells. T-lineage populations comprised 83.5% of the sequenced cells, indicating a T‑cell–rich tumor microenvironment. This high relative abundance of T cells provided an opportunity to examine T‑cell states at single‑cell resolution to determine whether numerical infiltration corresponded to functional anti-tumor activity.
Analysis of T‑lineage cells revealed heterogeneous transcriptional programs across major T‑cell subsets. Cytotoxic T cells concurrently exhibited markers of cytolytic activity and signatures associated with dysfunction, indicating coexisting effector and impaired states within the same compartment. Regulatory T cells (Tregs) demonstrated transcriptional evidence of suppressive remodeling, consistent with an immunoregulatory influence within the microenvironment. Th17-lineage cells displayed inflammatory and profibrotic programs, suggesting they may contribute to a stromal environment that modulates immune responses. Together, these patterns indicate that although T cells were abundant, key subsets expressed programs that could limit effective anti-tumor immunity.
Intercellular signaling inference using CellChat highlighted stromal interactions that could influence T‑cell behavior. Notably, stromal MIF/FN1–CD74/CD44 ligand–receptor pairs were nominated, implicating macrophage migration inhibitory factor (MIF) and fibronectin (FN1) signaling to CD74 and CD44 on immune cells. The analysis also emphasized extracellular‑matrix communication between cancer‑associated fibroblasts and T‑cell compartments. These stromal-to-immune signaling axes provide candidate mechanisms by which the tumor stroma and extracellular matrix could constrain T-cell function in an MSS CRC context.
The integrated genomic and single‑cell transcriptomic data from this single‑patient case indicate an important dissociation: high T‑cell abundance does not necessarily equate to effective anti-tumor immunity in MSS CRC. Despite a dominant T‑cell presence, cytotoxic T cells carried dysfunction-associated signatures, Tregs showed suppressive remodeling, and Th17 programs pointed to inflammatory and profibrotic stromal remodeling. CellChat‑nominated stromal signals such as MIF and FN1 interacting with CD74/CD44 receptors suggest mechanistic pathways through which the microenvironment could enforce immune constraint.
This case report documents a functionally constrained immune ecosystem in a mismatch repair–proficient, microsatellite‑stable colorectal cancer that was resolved by combining whole‑exome sequencing with single‑cell RNA sequencing. Tumor‑specific APC, KRAS, and TP53 alterations were identified by WES, and single‑cell profiling of 7,569 cells revealed that T‑lineage populations represented the majority of cells (83.5%). However, transcriptional states and inferred stromal signaling indicated immune dysfunction and suppression despite abundant T cells. The authors conclude that in MSS CRC, T‑cell richness can be uncoupled from immune effectiveness, and they highlight stromal MIF/FN1–CD74/CD44 and extracellular‑matrix communication as candidate contributors to that constraint.
Note: This summary reflects the data and interpretations reported in the source case report. Details such as experimental parameters, statistical measures, and additional molecular findings beyond those explicitly described in the source were not reported in the provided abstract and are therefore not included here.