Background/Purpose: Mendelian inheritances of highly penetrant single gene variants have been reported as monogenic forms of SLE. To explore novel risk variants, we carried out whole-exome sequencing to identify underlying monogenic causes in two multiplex families that each contains unaffected parents and two sons with pediatric-onset SLE, and assessed candidate rare variants for Mendelian inheritance and functional consequences.

Methods: Whole-exome sequencing, variant calling and annotation were conducted using Illumina Hiseq2000, the Genome Analysis Toolkit GATK and ANNOVAR, respectively. Variants in the gene of interest were confirmed by Sanger sequencing.  Functions of candidate variants were tested using Minigene assay for differential splicing, and CRISPR/Cas9 mediated knock-in (KI) mice for the frameshift variant.

Results: In each family, we identified a putative loss-of-function variant in the SAT1 gene that co-segregated with lupus in an X-linked recessive pattern. This variant is extremely rare in the population (absent in > 200,000 individuals), and is not in previously known SLE-associated genes. In one family, a SAT1 frameshift mutation, which is expected to trigger nonsense-mediated mRNA decay, was transmitted from the mother to the two sons affected with SLE, but not to the unaffected son. Using CRISPR/Cas9, we have 5 founders of frameshift mutation KI mice and are establishing a colony for lupus-like phenotype studies. In the other family, we found a missense variant on exon 2 that was predicted to be deleterious by altering transcript splicing. Using the Minigene assay, we confirmed that the mutant construct resulted in aberrantly spliced transcripts, including ~30% intron 2 containing, ~20% exon 2 skipping and 50% normal transcripts, in transiently transfected 293T or HeLa cell lines. We further extended Sanger sequencing of SAT1 in 566 SLE patients enriched in multiplex male lupus and pediatric patients, found 4 common variants and 12 additional rare variants, but none had robust evidence for functions based on HaploReg v4.1 and Regulome database.

Conclusion: We identified two rare SAT1 loss-of-function variants on the X chromosome that segregate with SLE phenotype in two families that each contained two sons with pediatric-onset SLE. The exon 2 variant disrupted the splice donor site, and the frameshift variant created a premature stop codon. SAT1 encodes spermidine/spermine-N¹-acetyltransferase, a rate-limiting enzyme that regulates polyamine catabolism. The low or absent function of SAT1 might perturb polyamine catabolism, predisposing to SLE, especially in boys.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/does-loss-of-function-variants-in-sat1-cause-x-linked-pediatric-lupus/