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Genomic, single-cell, and functional profiling of the CD48-CD244 axis and NK cell dysfunction in multiple myeloma
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
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
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Research Article Cell biology Hematology Immunology

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

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Figure 4

Single-cell RNA-seq and CellChat analysis reveal CD48-CD244 signaling between malignant plasma cells and NK cells in myeloma.

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Single-cell RNA-seq and CellChat analysis reveal CD48-CD244 signaling be...
(A) UMAP visualization of cell types identified across healthy donor (HD) and MM samples based on scRNA-seq data (GSE223060). (B) UMAP split by condition (HD vs. MM), showing shared immune populations across disease states. (C) Feature plots showing expression of CD48 and CD244 across all cells. (D) Dot plot showing CD48, CD244, and TNFRSF17 expression in HD (blue) and MM (red). Dot size indicates percentage of expressing cells; color intensity indicates scale average expression. (E) Dot plot of individual ligand-receptor pairs predicted by CellChat to interact with NK cells. Circle size represents statistical significance (permutation test P value), and circle color indicates communication probability. Among these, CD48-CD244 is highlighted as a significant and strong predicted interaction, suggesting that it is one of the dominant NK cell communication axes in MM. (F) Chord diagram generated using CellChat, illustrating CD48 signaling pathway network from plasma cells, monocytes, macrophages, and B cells, predominantly targeting NK cells. (G) Circle plot showing CD48 signaling pathway network depicting directional CD48 signaling interactions, highlighting strong engagement from CD48+ immune and malignant cells to CD244+ NK cells. (H) Heatmaps of outgoing and incoming signaling strength across cell types in MM, as inferred by CellChat. Interaction strength reflects the relative contribution of each signaling pathway to intercellular communication. The CD48-CD244 axis is highlighted within this broader network of significant signaling pathways.

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