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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 7

Ex vivo NK cell functional impairments and scRNA-seq dynamics in Vκ*MYC model.

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Ex vivo NK cell functional impairments and scRNA-seq dynamics in Vκ*MYC ...
(A) Workflow schematic for ex vivo NK cell functional assays. Spleens and bone marrow (BM) were harvested from Vκ*MYC-bearing (WT, CD48KO, CD48OE) and naive control mice. Single-cell suspensions of NK cells were incubated in high-binding 96-well plates coated with specific antibodies (anti-NK1.1, anti-CD244), isotype control (mIgG2a), or PBS negative controls for 6 hours. After stimulation, NK cell activation and degranulation were assessed by flow cytometry (intracellular IFN-γ, surface CD107a). (B) Representative flow cytometry gating for ex vivo NK activation in spleen and BM. (C–F) Splenic and BM NK cell IFN-γ secretion and CD107a degranulation. Bar graphs show the percentage of IFN-γ+ and CD107a+ NK cells in spleen- and BM-derived NK cells from naive control, Vκ*MYC WT, CD48KO, and CD48OE groups after stimulation with anti-NK1.1, anti-CD244, isotype (mIgG2a), PBS, or PMA/ionomycin (naive, n = 4; tumor-bearing groups, n = 6 per genotype). Pairwise comparisons were performed using pairwise t tests, with P values adjusted using the Benjamini-Hochberg method applied globally across all 30 pairwise comparisons per panel. (G) UMAP projection of scRNA-seq data from Vκ*MYC BM samples (GSE134370). Major hematopoietic cell populations are color-coded and labeled. (H) Split UMAPs showing 4 different subgroups and batch reduction. Control, newly diagnosed (ND), MM, and advanced MM (AMM) samples from the immunocompetent Vκ*MYC model. (I and J) Violin plots of exhaustion and murine orthologs of the HLA-dependent inhibitory AUCell score for individual NK cells in 4 groups: control, ND, MM, and AMM. Pairwise comparisons were performed using Wilcoxon’s rank-sum tests with Benjamini-Hochberg correction. *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001.

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