A novel mutation in TRAC in a patient with abnormal newborn screening for severe combined immunodeficiency

Several genetic defects lead to the clinical syndrome of severe combined immunodeficiency (SCID), characterized by profound susceptibility to bacterial, viral, and opportunistic infections, failure to thrive, and death in infancy in the absence of appropriate treatment. SCID is caused by genetic defects that affect the T cell receptor (TCR), T cell differentiation, maturation, survival, or function (Roifman 2019). The TCR is composed of two subunits with discrete functions: (1) an antigen-recognizing heterodimer consisting either α and β chains or γ and δ chains (each with a variable region and constant region), and (2) a signal transduction unit composed of three invariant CD3 dimers (Gouaillard et al. 2001). The TRAC gene encodes for the constant region of the TCR-α chain. The first cases of TCR-α chain deficiency were reported by Morgan et al. (2011) in 2 unrelated children from consanguineous families of Pakistani descent. They presented in infancy with recurrent respiratory infections, otitis media, candidiasis, diarrhea, and failure to thrive. Both patients also had features of immune dysregulation and were treated with hematopoietic stem cell transplantation (HSCT) (Morgan et al. 2011). In a recent case series, Rawat et al. (2021) reported a nonconsanguineous East Indian family in which 3 siblings had an immunodeficiency disorder resulting in death in all patients aged between 12 months and 11 years. Five patients have been so far identified with TCR-α chain deficiency. All carry an identical homozygous G to A transition in exon 3, located in the consensus 5’ splice site, predicting aberrant transcription, skipping of exon 3, and a protein that is lacking significant portions of the transmembrane and cytoplasmic domains of the TCR-α chain.

TCR-α chain deficiency is a rare and relatively new condition that remains ill-defined, and is attributed to mutations in the TRAC gene. We herein report a novel mutation in TRAC resulting in SCID.

The development and implementation of NBS have led to increased early detection of patients with SCID, allowing affected infants to be treated appropriately with HSCT before the onset of complications. As reported previously, X-linked IL2RG SCID is most frequently observed, while other causes of SCID include JAK3 mutations, ADA deficiency, deficiency of RAG1 or RAG2, IL7R deficiency, TCR CD3 δ, ε, and ξ chains deficiencies, Artemis mutations, and syndromic SCID such as Cartilage hair hypoplasia. Despite advanced genetic testing of known SCID genes, up to 10% of infants with SCID remain without a proven genotype. In this regard, homozygous mutations in TRAC resulting in TCR-α chain constant deficiency were not previously reported in the context of positive NBS (Kwan et al. 2014; Dinur et al. 2019; Mandola et al. 2019; Giżewska et al. 2020; Kumrah et al. 2020; Scott et al. 2021).

The first report of mutations in TRAC to cause immunodeficiency was by Morgan et al. in 2011 describing 2 patients. Both patients displayed features of combined immunodeficiency with recurrent bacterial infections, candidiasis, diarrhea, and failure to thrive. One patient also displayed chronic EBV, varicella, and human herpesvirus 6 (HHV6) viremia while the other patient was able to clear varicella at the age of 6 years uneventfully. In addition to immunodeficiency, both patients had evidence of immune dysregulation with hypereosinophilia, low-titer antinuclear antibodies (ANA), vitiligo, and alopecia areata in one patient and hypereosinophilia, eczema, autoimmune hemolytic anemia, anti-TTG antibodies, low-titer ANA in the other patient. Interestingly, humoral immunity against vaccine antigens appeared normal despite T cells abnormalities of abnormal CD3+ cells which expressed TCRαβ at extremely low levels and low PHA stimulation index (<50% of the control). When assessed by flow cytometry, surface staining for TCR-αβ was strongly reduced in patient cells. Functional studies showed that the TRAC mutation resulted in mis-localization of the TCR-α and -β chains. Furthermore, patient cells showed undetectably low expression of both TCR-α or TCR-β polypeptides, suggesting that the TRAC mutation not only resulted in TCR-α deficiency but also reduced TCR-β expression.

An additional recent case series of 3 patients was reported by Rawat et al. in 2021. The patients were 3 siblings born to a non-consanguineous family from Northwest India who all succumbed due to complications of immunodeficiency. All three had similar clinical and immunological features, manifesting as recurrent ear and chest infections, deep seated abscesses, cutaneous warts and lymphadenopathy, however, the youngest child also developed non-Hodgkin’s lymphoma in infancy. Genetic analysis revealed a previously reported variant in the TRAC gene (Rawat et al. 2021).

Clinically, our patient displayed lymphopenia and PHA < 10% of the control, in complete agreement with a diagnosis of T-B+NK+ SCID (Shearer et al. 2015), and has been well for the first months of life with supportive care until he received a HSCT. This patient would likely have presented with recurrent life-threatening infections as described thus far in the literature with low overall survival rate had it not been for the early detection through NBS.

The β chain gene is rearranged before the α chain, and, if productive, the TCR-β chain is initially expressed with pre-T-α, the invariant chain. Functional signaling through this complex must occur for progression of α chain rearrangement to take place (Anderson et al. 1996). Furthermore, defective expression of TCR-α would be expected to impair αβ T cell development beyond β selection because of a failure to deliver positively selecting signals as was shown by Morgan et al. (2011).

Our patient’s variant, a nonsense homozygous variant in exon 3 of the TRAC gene, c.C347G; p.Ser116Ter, results in a premature termination codon in exon 3, predicted to cause truncation of the encoded protein or complete absence. As the TRAC gene encodes for the constant region of the TCR-α chain and is essential for membrane expression of the TCR-αβ heterodimer, we presume that in our patient this probably resulted in a non-functional TCR-α chain, which is essential for T cell development, explaining the T-B+NK+ phenotype as well as the near complete lack of representation of CD4+ and CD8+ Vβ families, respectively.

The current report contributes to the spectrum of mutations in TRAC, both genotypically and phenotypically. Furthermore, to our knowledge, this is the first of case of a mutation in TRAC reported in regard to positive NBS for SCID.