Novel NHEJ1 pathogenic variant linked to severe combined immunodeficiency, microcephaly, and abnormal T and B cell receptor repertoires

Abstract

Background: During the process of generating diverse T and B cell receptor (TCR and BCR, respectively) repertoires, double-strand DNA breaks are produced. Subsequently, these breaks are corrected by a complex system led by the non-homologous end-joining (NHEJ). Pathogenic variants in genes involved in this process, such as the NHEJ1 gene, cause severe combined immunodeficiency syndrome (SCID) along with neurodevelopmental disease and sensitivity to ionizing radiation.

Objective: To provide new clinical and immunological insights on NHEJ1 deficiency arising from a newly diagnosed patient with severe immunodeficiency.

Materials and methods: A male infant, born to consanguineous parents, suspected of having primary immunodeficiency underwent immunological and genetic workup. This included a thorough assessment of T cell phenotyping and lymphocyte activation by mitogen stimulation tests, whole-exome sequencing (WES), TCR repertoire Vβ repertoire via flow cytometry analysis, and TCR and BCR repertoire analysis via next-generation sequencing (NGS).

Results: Clinical findings included microcephaly, recurrent pneumonia, and failure to thrive. An immune workup revealed lymphopenia, reduced T cell function, and hypogammaglobulinemia. Skewed TCR Vβ repertoire, TCR gamma (TRG) repertoire, and BCR repertoire were determined in the patient. Genetic analysis identified a novel homozygous missense pathogenic variant in XLF/Cernunnos: c.A580Ins.T; p.M194fs. The patient underwent a successful hematopoietic stem cell transplantation (HSCT).

Conclusion: A novel NHEJ1 pathogenic variant is reported in a patient who presented with SCID phenotype that displayed clonally expanded T and B cells. An adjusted HSCT was safe to ensure full T cell immune reconstitution.

Keywords: NHEJ1; TCR repertoire; XLF/Cernunnos; next-generation sequencing (NGS); severe combined immunodeficiency (SCID).

FIGURE 1

T cell receptor (TCR) Vβ repertoire analyses. Flow cytometry analysis of surface membrane expression of 24 T cell receptor β chain’s variable gene families, in our non-homologous end-joining-1 (NHEJ1) deficient patients (black bars), compared with healthy controls (white bars), before (upper panel), and after (lower panel) the hematopoietic stem cell transplantation (HSCT).

FIGURE 2

Characteristics of the TRG and IGH repertoire determined by NGS. Graphical presentation of the TCR gamma (TRG) repertoire using the Tree map program where each square represents a specific clone and the size of the square represent the frequency of the clone, for TRG (A) and IGH (B) repertoires. A scatter dot plot presenting the unique (C) and total (D) number of sequences for TRG and IGH repertoires. A scatter dot plot presenting the Shannon’s H diversity index (E) and the Simpson’s Index of Unevenness (F) for TRG and IGH repertoires. TRG and IGH repertoire analysis from a total of four controls were compared with our patient’s data.