Severe Combined Immunodeficiency Due to a Novel Missense Mutation in IL-7R that Abolishes Surface Protein Expression

Abstract

Background: Primary immunodeficiency diseases (PIDs) are a group of congenitally inherited heterogeneous disorders that result in depletion or deficiency of one or more components of the immune system. Severe Combined Immunodeficiency Diseases (SCID) are the most severe and life-threatening subgroup of PID as they affect the development and/or function of T cells, predisposing the patients to recurrent infections and autoimmune manifestations at an early age. IL-7R, the cytokine receptor for interleukin- (IL-) 7, is expressed on lymphoid cells and plays an important role in the proliferation, development, homeostasis, and survival of T cells. Defects in IL-7R abolish T cells resulting in T-B+NK+ SCID.

Case Presentation: The patient under investigation is a 1 year-old female born to consanguineous parents. Her clinical history is indicative of decreased T cell counts associated with recurrent severe infections and autoimmune hemolytic anemia since birth. The early onset and severity of the clinical manifestations were suggestive of SCID.

Methods: Peripheral blood mononuclear cells (PBMCs) were isolated on a Ficoll-paque gradient by differential centrifugation. Immunophenotyping of PBMCs, expression of the IL-7R, Regulatory T cell staining, and T cell proliferation were performed by flow cytometry. Genomic DNA (gDNA) was purified and sequenced by Next Generation Sequencing and Sanger sequencing. RNA was extracted using TRI reagent, reverse transcribed to cDNA using RNA reverse transcription kit, and amplified by PCR followed by Sanger sequencing.

Results and discussion: Immunophenotyping of PBMCs revealed a very low T cell count, absent Recent Thymic Immigrants (RTEs) and B cells, and normal to elevated numbers of NK cells. Importantly, the few patient T cells failed to proliferate when stimulated with anti-CD3 monoclonal antibodies (mAb) or Phytohaemagglutinin (PHA). Next Generation Sequencing analysis identified a homozygous missense mutation in IL7R gene (c.379 G>A) that resulted in a Valine to Isoleucine change at position 127 of the protein (p.V127I). The c.379G>A mutation resulted in aberrant RNA splicing and abolished cell surface IL-7R protein expression, as determined by flow cytometry. These results demonstrate that the patient harbors a deleterious mutation in IL-7R resulting in a T-B+NK+ phenotype, thus confirming the clinical diagnosis of SCID. The patient was successfully transplanted at the AUB-MC using her HLA-matched relative as donor. Ten months after transplant, the patient showed significant increase in the percentage of lymphocytes and T cells, reconstitution of T cells that express IL-7R, and restoration of T cell’s proliferative response to mitogens.

Conclusion: Using genetic and functional approaches, we identified a SCID patient with a novel deleterious homozygous mutation in the IL7R gene and studied the effect of the mutation on protein expression and T cell function. The patient was transplanted at AUBMC and we were able to follow the reconstitution and function of donor cells with time. To our knowledge, this represents the first bedside-to-bench and back to bedside project entirely executed on a patient with SCID at AUB and paves the way for more similar studies in the future.