KLRB1 (CD161) as a context-dependent prognostic marker in breast cancer: An exploratory analysis of CD4+ memory T cell infiltration: a retrospective multi-cohort study

The prognostic value of KLRB1 ( CD161 ) in breast cancer is debated, and whether CD4 + memory T cell abundance modulates it is unclear. In this retrospective multi-cohort study we integrated The Cancer Genome Atlas Breast Invasive Carcinoma (n = 1088) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) (n = 1980) with investigator-generated single-cell RNA-sequencing from 3 patients, public single-cell RNA-sequencing validation (GSE176078), Xenium spatial transcriptomics (19 samples) and multiplex immunofluorescence of a paired primary tumor and metastatic lymph node. Cox regression tested whether xCell-estimated CD4 + memory T cell abundance modifies the KLRB1 -overall survival association. Higher KLRB1 expression was associated with favorable overall survival (TCGA hazard ratio [HR] = 0.93, P = .001; METABRIC HR = 0.82, P < .001). The CD4 + memory T cell interaction was significant under median dichotomization (TCGA P = .043; METABRIC P = .014) and after adjustment for age and tumor stage in both cohorts (TCGA P = .033; METABRIC P = .026; pooled HR 1.20, P = .0025); full adjustment for grade and subtype preserved significance in METABRIC ( P = .012) but not in TCGA ( P = .205). Across 3 single-cell cases KLRB1 was enriched in CD4 + memory T cells; functional profiling identified a cytotoxicity-effector T/NK signature, and TIGIT+ KLRB1+ cells showed no clear evidence of a classical exhaustion transcriptional signature. In Xenium, KLRB1+ cells proximal to CD4 + memory T cells co-upregulated TIGIT (pooled OR = 2.98) and PRF1 (OR = 1.99); multiplex immunofluorescence showed no spatial mutual exclusion. CD4 + memory T cell abundance is a hypothesis-generating candidate context modifier of KLRB1 -mediated prognosis. This finding requires external validation in a subtype-stratified cohort, and the present data do not support clinical use.