A 17q25.3 Duplication Defines a New Dosage-Sensitive Congenital Neutropenia Locus and Implicates SOCS3 as a Candidate Gene for Cases Unexplained by ELA2 Mutation.

Abstract We have investigated the etiology of congenital neutropenia in a girl with de novo duplication of chromosome 17q25.3. She presented during the first year of life with neutropenia, episodic hypothermia, failure to thrive, and other congenital abnormalities. Peripheral blood karyotype demonstrated 46,XX,add(17)(q25.3), and molecular cytogenetic studies confirmed interstitial duplication of chr17-derived material. We excluded ELA2 mutation (the most common cause of hereditary neutropenia) and reasoned that the neutropenia and other medical problems most likely were the result of the chromosomal abnormality. In the duplicated 17q25.3 region, SOCS3 emerged as a promising candidate gene responsible for neutropenia, because SOCS3 is a well-characterized negative regulator of G-CSF-receptor signaling and, in murine conditional knockout models, acts as a physiologic negative regulator of granulopoiesis. As we had previously demonstrated that mutations of the Gfi1 transcriptional repressor are a rare cause of human neutropenia, we searched for potential Gfi1 binding sites in the SOCS3 promoter and noted a total of five, and chromatin immunoprecipitation analysis validated occupancy of the SOCS3 promoter by Gfi1 in Jurkat, HL-60, and U937 cells. Thus, several lines of evidence suggested SOCS3 as a plausible neutropenia gene. We confirmed that SOCS3 is indeed duplicated in this patient by both FISH and quantitative genomic PCR. In an effort to identify other patients with SOCS3-related neutropenia, we sequenced both exons of SOCS3 in a total of 66 patients with severe congenital neutropenia (SCN) or cyclic neutropenia (CN) and 94 patients with chronic idiopathic neutropenia of adults (CINA) in whom ELA2 mutations were absent. No coding mutations were detected, but we did identify several variants in the SOCS3 promoter and 5′- and 3′- UTRs, including a single base pair substitution (+1779AtoG) in the 3′-UTR in a SCN patient and deletion of a single G (-1318delG) occurring in a six-G tract immediately adjacent to a predicted STAT binding site in a highly conserved region of the SOCS3 promoter (found in heterozygous and homozygous form in several patients with CN and SCN). The 3′-UTR alteration was absent in 270 control chromosomes and is located within a predicted binding site for miR-449 that is well-conserved across mammalian species. In sum, we have identified a patient with congenital neutropenia and a de novo duplication of 17q25.3 defining a new candidate locus for congenital neutropenia, and the evaluation to date suggests that SOCS3 is a promising dosage sensitive candidate gene in this interval that additionally could be a key target in neutropenia associated with Gfi1 mutations.

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