Genomic, single-cell, and functional profiling of the CD48-CD244 axis and NK cell dysfunction in multiple myeloma

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Abstract

Multiple myeloma (MM) orchestrates immune evasion by subverting natural killer (NK) cell function. CD48, one of the most abundant NK ligands on MM cells, paradoxically enhances NK cell activation yet is associated with high-risk cytogenetics and poor patient survival. We integrated multiomics (bulk and single-cell RNA-seq, assay for transposase-accessible chromatin using sequencing [ATAC-seq], chromatin immunoprecipitation sequencing [ChIP-seq]), genome-wide CRISPR knockout/activation screens, and machine learning to dissect CD48 regulation and function. In human MM and Vκ*MYC mouse scRNA-seq datasets, NK cells exhibit stepwise increases in inflammatory and exhaustion signatures and loss of cytotoxic potential as disease progresses. In vitro coculture assays show that CD48 overexpression on MM enhances NK cell cytokine secretion, whereas chronic exposure leads to ex vivo NK dysfunction. In vivo, CD48-overexpressing Vκ*MYC tumors progress more slowly and extend host survival, while NK cell depletion accelerates disease. These findings support a context-dependent role for CD48, potentiating acute NK responses while coexisting with chronic NK exhaustion, and suggest strategies to modulate CD48 for therapeutic benefit.

Authors

Bonell Patiño-Escobar, Torsten Steinbrunn, Lucy Perez-Lugo, Sham Rampersaud, Daniel D. Waller, Daniela Ordoñez, Huimin Geng, Fernando Salangsang, Paul Phojanakong, Juan Antonio Camara Serrano, Yan Zeng, Veronica Steri, Oscar A. Aguilar, Constantine S. Mitsiades, Arun P. Wiita