Somatic mutations in lymphocytes in patients with immune-mediated aplastic anemia

Sofie Lundgren,Eva Hellström-Lindberg,Jaroslaw P Maciejewski,Neal S Young,Jani Huuhtanen,Michael Clemente,Seishi Ogawa,Satu Mustjoki,Hanna Rajala,Matti Kankainen,Pekka Ellonen,Mikko A I Keränen,Oscar Brück,Sari Hannula,Gunilla Walldin,Cassandra M Kerr,Harri Lähdesmäki,Freja Ebeling,Tiina Hannunen

doi:10.1038/s41375-021-01231-3

Abstract

The prevalence and functional impact of somatic mutations in nonleukemic T cells is not well characterized, although clonal T-cell expansions are common. In immune-mediated aplastic anemia (AA), cytotoxic T-cell expansions are shown to participate in disease pathogenesis. We investigated the mutation profiles of T cells in AA by a custom panel of 2533 genes. We sequenced CD4+ and CD8+ T cells of 24 AA patients and compared the results to 20 healthy controls and whole-exome sequencing of 37 patients with AA. Somatic variants were common both in patients and healthy controls but enriched to AA patients’ CD8+ T cells, which accumulated most mutations on JAK-STAT and MAPK pathways. Mutation burden was associated with CD8+ T-cell clonality, assessed by T-cell receptor beta sequencing. To understand the effect of mutations, we performed single-cell sequencing of AA patients carrying STAT3 or other mutations in CD8+ T cells. STAT3 mutated clone was cytotoxic, clearly distinguishable from other CD8+ T cells, and attenuated by successful immunosuppressive treatment. Our results suggest that somatic mutations in T cells are common, associate with clonality, and can alter T-cell phenotype, warranting further investigation of their role in the pathogenesis of AA.

Highlights

Acquired aplastic anemia (AA) is an immune-mediated bone marrow failure syndrome in which cytotoxic T cells mediate the destruction of hematopoietic stem and10 Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan11 ICAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland progenitor cells (HSPCs) [1,2,3]
Characteristic features of immune-mediated AA are clonal alterations in HSPCs: Xchromosome skewing [4], cytogenetic abnormalities [5, 6], uniparental disomy of the 6p [7], somatic phosphatidylinositol glycan class A gene mutations leading to paroxysmal nocturnal hemoglobinuria [8], and somatic mutations in genes related to clonal hematopoiesis (CH) [9,10,11,12,13,14]
We addressed the key questions of somatic mutations in T cells in patients with immune-mediated AA: in which cell subset they occur, at which state of immune cell development they emerge, which genes and pathways are affected, and correlation with clinical findings

Summary

Introduction

Acquired aplastic anemia (AA) is an immune-mediated bone marrow failure syndrome in which cytotoxic T cells mediate the destruction of hematopoietic stem and10 Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan11 ICAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland progenitor cells (HSPCs) [1,2,3]. T cells in AA patients are known to be aberrantly active [18,19,20], but their antigenic target on HSPC remains unknown. We and others have detected somatic mutations in T cells in patients with various immune-mediated disorders: newly diagnosed rheumatoid arthritis [21], Felty’s syndrome [22], pure red cell aplasia [23], multiple sclerosis [24, 25], chronic graft-versus-host disease [26], and T-cell large granular lymphocytic (T-LGL) leukemia [27,28,29]. In T-LGL leukemia and Felty’s syndrome activating STAT3 mutations in CD8+ T cells are the hallmark of the disease, but STAT3 mutations have been discovered in 11% of AA patients [30]

Methods

Results

Conclusion