Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles.

Area of Science:

• Genetics
• Molecular Biology
• Developmental Biology

Background:

• The KINSSHIP syndrome, characterized by intellectual disability, mesomelic dysplasia, and horseshoe kidney, is linked to de novo variants in the AFF3 gene.
• Previous studies suggested a dominant-negative mechanism for AFF3 variants, where increased AFF3 levels cause pathological effects.

Purpose of the Study:

• To investigate alternative inheritance modes for AFF3-related disorders beyond de novo variants.
• To assess the pathogenicity of various AFF3 variants, including loss-of-function and missense mutations, in individuals with intellectual disability.

Main Methods:

• Screening of intellectual disability cohorts for predicted damaging variants in AFF3.
• Utilizing animal models (zebrafish) and cellular models (fibroblast transcriptomics) to evaluate variant deleteriousness.
• Analyzing gene expression profiles in engineered cell lines with different AFF3 genotypes (wild-type, KINSSHIP, LoF).

Main Results:

• An individual with a KINSSHIP-like phenotype and a partial AFF3 duplication confirmed increased AFF3 levels as pathological.
• Seventeen individuals with milder syndromes carried heterozygous Loss-of-Function (LoF) or biallelic missense variants in AFF3.
• Homozygous LoF and compound heterozygous variants resulted in more severe phenotypes, consistent with semi-dominance. Zebrafish models showed rescue with human AFF3 mRNA, while some missense variants failed to rescue, and overexpression caused developmental defects.

Conclusions:

• Minute alterations in AFF3 gene function are detrimental, leading to a spectrum of disorders.
• Both increased AFF3 levels (as seen in KINSSHIP syndrome) and loss-of-function variants contribute to pathogenicity.
• AFF3 variants exhibit high pleiotropy, affecting diverse pathways including DNA repair, with distinct modulatory effects based on variant type (LoF vs. dominant-negative).