A Novel Non-Coding Variant in DCLRE1C Results in Deregulated Splicing and Induces SCID Through the Generation of a Truncated ARTEMIS Protein That Fails to Support V(D)J Recombination and DNA Damage Repair

Abstract

Severe Combined Immune Deficiency (SCID) is a primary deficiency of the immune system in which opportunistic and recurring infections are often fatal during neonatal or infant life. SCID is caused by an increasing number of genetic defects that induce an abrogation of T lymphocyte development or function in which B and NK cells might be affected as well. Because of the increased availability and usage of next-generation sequencing (NGS), many novel variants in SCID genes are being identified and cause a heterogeneous disease spectrum. However, the molecular and functional implications of these new variants, of which some are non-coding, are often not characterized in detail. Using targeted NGS, we identified a novel homozygous c.465-1G>C splice acceptor site variant in the DCLRE1C gene in a T-B-NK+ SCID patient and fully characterized the molecular and functional impact. By performing a minigene splicing reporter assay, we revealed deregulated splicing of the DCLRE1C transcript since a cryptic splice acceptor in exon 7 was employed. This induced a frameshift and the generation of a p.Arg155Serfs*15 premature termination codon (PTC) within all DCLRE1C splice variants, resulting in the absence of full-length ARTEMIS protein. Consistently, a V(D)J recombination assay and a G0 micronucleus assay demonstrated the inability of the predicted mutant ARTEMIS protein to perform V(D)J recombination and DNA damage repair, respectively. Together, these experiments molecularly and functionally clarify how a newly identified c.465-1G>C variant in the DCLRE1C gene is responsible for inducing SCID. In a clinical context, this demonstrates how the experimental validation of new gene variants, that are identified by NGS, can facilitate the diagnosis of SCID which can be vital for implementing appropriate therapies.

Case report: Rubella virus-induced cutaneous granulomas in a girl with atypical SCID caused by DCLRE1C gene mutations

“…DCLRE1C encodes ARTEMIS, which is essential in the V(D)J recombination of the immunoglobulin and T-cell receptor genes in T- and B-cell development, as well as in DNA repair ( Felgentreff et al, 2015 ). Mutations in the DCLRE1C gene can lead to severe combined immunodeficiency, Omenn syndrome, and radiosensitivity ( Strubbe et al, 2021 ). Severe combined immunodeficiency is an inherited, most severe form of primary immunodeficiency caused by mutations in genes involved in lymphocyte development and function and characterized by the absence or dysfunction of T lymphocytes.…”

Dclre1c-Mutation-Induced Immunocompromised Mice Are a Novel Model for Human Xenograft Research

“…Additionally, the Artemis protein is instrumental in V(D)J recombination, a process that is vital for the development and function of T and B lymphocytes. Consequently, mutations in dclre1c are associated with severe combined immunodeficiency (SCID), a condition characterized by reduced lymphocyte counts and compromised immune functionality [4,5].…”