The following is a summary of “Abnormal biomarkers predict complex FAS or FADD defects missed by exome sequencing,” published in the January 2024 issue of Allergy & Immunology by Rensing-Ehl, et al.
Elevated levels of TCRαβ+CD4–CD8– double-negative T cells (DNT) and specific serum biomarkers aid in the identification of patients with autoimmune lymphoproliferative syndrome (ALPS) who carry mutations in the FAS gene. Nonetheless, in certain cases exhibiting clinical features and biomarker profiles consistent with ALPS, standard exon sequencing fails to detect either germline or somatic FAS mutations, resulting in a classification known as ALPS-undetermined (ALPS-U). For a study, researchers sought to investigate whether complex genetic alterations in the FAS gene or mutations in other genes related to the FAS pathway could account for cases of ALPS that are missed by routine exon sequencing.
Genetic analysis encompassed comprehensive sequencing of the entire FAS gene, evaluation of copy number variations, and sequencing of FAS cDNA and other genes associated with the FAS pathway. The analysis was guided by FAS expression analysis on CD57+DNT cells, which can indicate somatic loss of heterozygosity (sLOH).
Among sixteen patients classified as having ALPS-undetermined (ALPS-U), nine exhibited a lack of FAS expression on CD57+DNT cells, suggesting heterozygous “loss-of-expression” FAS mutations combined with acquired somatic second hits in the FAS gene, primarily enriched in DNT cells. Specifically, seven of the nine analyzed patients harbored deep intronic mutations or large deletions in the FAS gene, along with sLOH detectable in DNT cells. Additionally, one patient exhibited a FAS exon duplication. Among the remaining patients, three showed reduced FAS expression, with two carrying mutations in the FAS promoter that reduced FAS expression in reporter assays. Furthermore, three of the four ALPS-U patients with normal FAS expression carried heterozygous FADD mutations with sLOH.
Combining serum biomarkers and DNT phenotyping is an effective strategy for identifying patients with ALPS who may be missed by routine exome sequencing. The findings highlighted the importance of considering complex genetic alterations and mutations in the FAS pathway in cases of ALPS-undetermined, thus contributing to improved diagnostic accuracy and patient care.
Reference: jacionline.org/article/S0091-6749(23)01462-8/abstract