Truncating mutations in SAMD9L cause an early-onset immune-dysregulatory syndrome of neutrophilic panniculitis, interstitial lung disease and cytopenias

LIN, B; MITCHELL ,JT; BURNHAM J,; ROSEN-WOLFF, A; BEZRODNIK, LILIANA; ALLENSPACH, E; ALSALEEM, AA; ROSENZWEIG, S; GOLDBACH-MANSKY, R; CALVO, KR; MARRERO, BERNADETTE; CHAN, A; HEDRICH, CM; SEMINARIO, A. G.; TORGERSON, TROY; HWANG, SJ; BROOKS, STEPHEN; ALMEIDA DE JESUS, A; MONTELAGERE SANCHEZ, GA ; DARE, JASON; STEPANOVSKIY, Y; LEE-KIRSCH, M; CALDIROLA, MARÍA SOLEDAD; FINN, L; SUN KUEHN, H; DENG, Z

Simposio; 2020 CIS Annual meeting; 2020

Background/Purpose: The Sterile Alpha Motif Domain Containing 9 Like protein that is encoded by SAMD9L plays a role in endosome fusion, and deletions (haploinsufficiency) of SAMD9L including loss of the chromosome 7 where SAMD9L is located (monosomy 7) have been associated with myelodysplasia in humans and mice.Missense mutations in SAMD9L were described in patients presenting with ataxiapancytopenia syndrome. Here we describe 6 patients with de novo frameshiftmutations in SAMD9L who present with early-onset systemic inflammation, variable interstitial lung disease and cytopenias. Methods: Whole exome/genome sequencing (WES/WGS) on trios usingIllumina HiSeq 2000 platform were performed. An interferon-responsegene score was assessed using a customized Nanostring assay and RNAseq was performed in patients and healthy controls (HCs). Toll-like receptor (TLR) stimulation assays and STAT phosphorylation assay were performed in patients and HCs, PBMCs, monocytes and T cells. Results: We identified 6 patients with 4 de novo frameshift variants in SAMD9L (c.2626delA, p.I876Lfs*15; c.2633delA, p.K878Sfs*12; c.2658_2659delTT, p.F886Lfs*11; c.2666delT, p.F889Sfs*2). All 4 variants detected were not detected in public databases (gnomAD and 1000G). Somatic reversion restricted to hematopoietic cells was observed in 1 patient. All 6 patients had disease onset between 1 and 7 days of lifewith generalized nodular skin rashes, fever and increased inflammatory markers (ESR and CRP). Skin biopsies from all 6 patients revealed a neutrophilic panniculitis. Four patients had developed severe interstitial lung disease (ILD) triggered by respiratory viral infections in infancy, all 4 developed pancytopenia , low B-cell count and hypogammaglobulinemia, and two of those underwent bone marrow transplant. The other 2 patients developed leukopenia, a low B cell count,hypogammaglobulinemia and recurrent pulmonary infiltrates at the age of 3 and 5 years, respectively. Additionally, brain imaging revealed basal ganglia calcifications and/or demyelinating changes in 5 out of the 6 patients. qRT-PCR of healthy control cell subsets and tissues showed thatSAMD9L mRNA relative expression is high in B and NK lymphocytes moderate in T cells, monocytes, neutrophils, lung and muscle, and low in skin, liver, heart and kidney tissues. Analysis of each individual gene expression level by nanostring in comparison with healthy controls demonstrated significantly higher levels of the following IRGs: DDX60, EPSTI1, GBP1, IFI6, ISG15, LY6E, OAS1, OAS2, OAS3, RSAD2, RTP4 and SOCS1. Whole blood RNA-seq was performed in 3 patients and pathway analysis with the differentially upregulated genes demonstrated an enrichment of intraluminal vesicle formation and negative regulation of apoptotic signaling pathways. Stimulation of PBMCs with the TLR ligands poly I:C, ODN, and LPS induced a 200-fold increase in IFI27 and a 30-fold increase in IFNA1 and IFNB1 transcription compared to baseline. One patient had constitutive upregulation of STAT1 and STAT6 in monocytes and of STAT1 and STAT3 in T cells. Conclusion:We describe a novel immunedysregulatory disease caused byde novo truncating variants in SAMD9L that presents similar to CANDLE with neutrophilic pannicultis and points to an important role of SAMD9L on regulation of adaptive and innate immune responses.