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Variants in human CD48 lead to impaired T cell immunity and increased inflammation
Samantha Milanesi, Tiziana Lorenzini, Tommaso Marchetti, Diana Tintor, Raquel Planas, Ola Sabet, Lars Malmström, Sudip Acharya, Carson D. Williams, Zoe E. Manning, Jack H. Roser, Angelica C. Ehler, Michael Huber, Seraina Prader, Stefano Vavassori, Cullen M. Dutmer, Jordan K. Abbott, Jana Pachlopnik Schmid
Samantha Milanesi, Tiziana Lorenzini, Tommaso Marchetti, Diana Tintor, Raquel Planas, Ola Sabet, Lars Malmström, Sudip Acharya, Carson D. Williams, Zoe E. Manning, Jack H. Roser, Angelica C. Ehler, Michael Huber, Seraina Prader, Stefano Vavassori, Cullen M. Dutmer, Jordan K. Abbott, Jana Pachlopnik Schmid
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Research Article Immunology Inflammation

Variants in human CD48 lead to impaired T cell immunity and increased inflammation

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Abstract

CD48 is a surface molecule with immunoregulatory functions. Following our initial report of a patient with a de novo heterozygous variant at amino acid S220 in the CD48 gene, we describe a second, unrelated patient with similar features of immune dysregulation and a missense change affecting the same residue. To further elucidate the specific pathogenic mechanisms of the identified variants, we reviewed patient records, analyzed patient-derived cells, and employed complementary in vitro and in vivo model systems, including transfected cell lines and CD48-deficient mice. We demonstrate that the variants are associated with altered distribution of CD48, characterized by diminished CD48 surface expression, intracellular retention, and activation of ER stress signaling. Patient T cells displayed increased susceptibility to apoptosis, reduced antiviral responses, and enhanced inflammation. Both patients exhibited T cell lymphopenia, a restricted T cell receptor repertoire diversity, and oligoclonal expansions consistent with antigen-driven selection. In parallel, virally infected CD48-deficient mice recapitulate key aspects of the human phenotype, including delayed antiviral immune responses, impaired viral clearance, and pronounced inflammation. We conclude that identified variants compromise CD48 cell surface localization, impair T cell survival and function, and predispose to inflammation, thereby highlighting the role of CD48 in immune regulation and the prevention of excessive inflammation.

Authors

Samantha Milanesi, Tiziana Lorenzini, Tommaso Marchetti, Diana Tintor, Raquel Planas, Ola Sabet, Lars Malmström, Sudip Acharya, Carson D. Williams, Zoe E. Manning, Jack H. Roser, Angelica C. Ehler, Michael Huber, Seraina Prader, Stefano Vavassori, Cullen M. Dutmer, Jordan K. Abbott, Jana Pachlopnik Schmid

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Figure 3

Activation-associated intracellular CD48 accumulation in patient T cells correlates with impaired survival and function.

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Activation-associated intracellular CD48 accumulation in patient T cells...
(A) Column graph showing the ratio of intracellular/surface CD48 gMFI in unstimulated (unstim.) and stimulated (stim.) CD4+ and CD8+ T cells, as well as in activated (ICOS+CD25+) stimulated CD4+ and CD8+ T cells from P1 (red), P2 (dark red), and 2 HDs (blue). (B) Volcano plot showing genes involved in type I IFN response, inflammation (*), apoptosis (°), and ER stress (^) differentially expressed between mitogen-stimulated PBMCs from P1 compared with a HD (log2 fold change threshold >1.5; FDR < 0.05). Genes shown in gray are not significantly differentially expressed (ns). (C) Heatmap showing expression levels of genes belonging to the BP category “response to ER stress” in mitogen-stimulated PBMCs from a HD compared with P1. Genes that also belong to the BP categories “ERAD pathway” and “intrinsic apoptosis to ER stress” are shown as blue and black circles, respectively. (D and E) Column graphs showing the fraction of annexin V+/Live-Dead+ cells and the CD4+/CD8+ ratio, respectively, in unstimulated and stimulated single cells from P1 (red), P2 (dark red), and 3 HDs (blue). P1 was analyzed twice in 2 independent experiments, and P2 was analyzed once. In one experiment, P1 was compared with 1 HD; in the other, P1 and P2 were compared with 2 HDs. (F) Column graphs showing the fraction of CFSElo cells in unstimulated and stimulated CD4+ and CD8+ T cells from P1 (red), P2 (dark red), and 2 HDs (blue). (G) Overlaid flow cytometry histograms showing T cell divisions by dilution of CFSE dye in memory (CD45RA–) CD4+ and CD8+ T cells from P1 (red), P2 (dark red), and 7 HDs (blue) stimulated with microbial antigens. Due to the low patient sample size in A and D–G, no statistical analysis was performed.

Copyright © 2026 American Society for Clinical Investigation
ISSN: 0021-9738 (print), 1558-8238 (online)

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