Germline <i>SH2B3</i> pathogenic variant associated with myelodysplastic syndrome/myeloproliferative neoplasm with ring sideroblasts and thrombocytosis
Authors: Giacomo Coltro, Terra L. Lasho, Christy M. Finke, Naseema Gangat, Animesh Pardanani, Ayalew Tefferi, Dragan Jevremovic, Jessica K. Altman, Mrinal M. Patnaik
Journal: American Journal of Hematology (2019)

The SH2B adaptor protein 3 (SH2B3) gene, located on chromosome 12q24.12, codes for the LNK (lymphocyte adaptor) protein, a negative regulator of cytokine-receptor mediated JAK2/STAT5 signaling.1 The LNK family of proteins is characterized by a conserved NH2-terminal domain which has putative proline motifs for binding to SH3 domains, a pleckstrin homology domain and a COOH-terminal SH2 protein binding domain.2 In genetically engineered mouse models, lnk was found to negatively regulate erythropoietin and thrombopoietin receptor signaling by attenuating Jak2 activation.3 Subsequently, SH2B3 mutations have been described in 5% to 7% of patients with myeloproliferative neoplasms (MPN); including blast-transformed cases, in patients with idiopathic erythrocytosis (IE) with subnormal erythropoietin levels and in myelodysplastic syndrome (MDS)/MPN overlap syndromes such as chronic myelomonocytic leukemia (Table S1).4-6 Germline sequence variants/polymorphisms in JAK2V617F (GGCC-46/1 haplotype), TERT, SH2B3, MECOM, HBS1L-MYB, TET2, ATM, CHECK2, and LINC-PNT have been shown to predispose toward MPN, whereas germline duplications involving ATG2B and GSK1 and mutations involving RBBP6 (5%) and SH2B3 (2%) have been associated with familial MPN.7 MDS/MPN-ring sideroblasts-thrombocytosis (RS-T) is an MDS/MPN overlap syndrome characterized by anemia with erythroid lineage dysplasia, ≥15% RS, <1% peripheral blood (PB) blasts and <5% bone marrow (BM) blasts, persistent thrombocytosis (platelet count ≥450 × 109/L), presence of SF3B1 mutations and no preceding history of MPN or MDS/MPN overlap syndromes.8 While in MDS-RS, a related myeloid neoplasm without proliferative features, the 2016 iteration of the World Health Organization (WHO) classification reduced the requisite BM RS % to >5% in the presence of SF3B1 mutations, for unclear reasons this exception was not extended to MDS/MPN-RS-T.8 The median age of presentation for MDS/MPN-RS-T ranges between 71 and 75 years; 80% have no clonal cytogenetic abnormalities and gene mutations commonly encountered include, SF3B1 (~85%), JAK2V617F (~50%), TET2 (~25%), ASXL1 (~20%), DNMT3A (~15%), and SETBP1 (~10%).9 Apart from JAK2V617F, other MPN-associated driver mutations such as MPL and CALR are extremely infrequent (<5%) and till date, SH2B3 mutations have not been described in these patients.9, 10 We describe a patient in his early 60s who presented with a 2 year history of progressive anemia, macrocytosis, and thrombocytosis, who was found to have BM morphological features of a MDS/MPN-overlap syndrome with RS and thrombocytosis (Figure 1A-D). The BM blasts were <5% and the RS were estimated at 10%. The cytogenetics were normal and next generation sequencing identified pathogenic variants involving SH2B3 c.1198G>A, p.E400K (variant allele frequency [VAF]—48%) and SF3B1 c.1866G>C, p.E622D (VAF—34%). Given atypical features, such as the younger age at presentation, presence of a SH2B3 variant in the context of MDS/MPN-RS-T and the fact that the SH2B3 variant had a higher VAF than the SF3B1 variant (Figure S1A), we obtained germline DNA from a buccal swab and carried out Sanger sequencing for both variants. On the buccal swab DNA only the SH2B3 c.1198G>A, p.E400K variant was identified (Figure S1B). The patient is currently on aspirin and is being clinically observed. He does not have a family history of myeloid neoplasms and his family is currently being counseled about genetic screening possibilities. The SH2B3 E400K variant results in a missense change in exon 6 of the gene, substituting glutamate at position 400 with lysine, impacting the SH2 domain of the LNK protein (Figure S1E). The SH2 domain allows the LNK protein to dock to phosphorylated tyrosine residues on other proteins. The mutational allele frequency of this variant across multiple ethnic groups in the population is <0.001% (gnomeAD and other databases), making it very unlikely to be a single nucleotide polymorphism. This particular variant has been reported in patients with PMF, IE, and polycythemia vera, along with a single citation in catalogue of somatic mutations in cancer (COSMIC) in a patient with glioma.7 In addition, in silico analysis using MutationTaster, Sorting Intolerant from Tolerant, and Protein Variation Effect Analyzer, among others, predict this variant to be deleterious to the LNK protein structure and function (Table 1). While the WHO criteria for MDS/MPN-RS-T require the presence of ≥15% BM RS, we along with others have demonstrated the prognostic irrelevance of RS%, especially in the presence of SF3B1 mutations.9 In addition, as mentioned above, the WHO criteria for MDS-RS only require >5% BM RS in the presence of SF3B1 mutations.8 Hence, although the BM RS% in our patient was 10%, we operationally feel that the PB and BM morphology were consistent with a diagnosis of MDS/MPN-RS-T. With the help of this instructive case, we describe the first patient with MDS/MPN-RS-T who developed early onset disease in the context of a germline SH2B3 pathogenic variant. This is an important finding, given the fact that unlike in MPN, neither germline nor somatic SH2B3 pathogenic variants have been described in MDS/MPN-RS-T. In addition, while in most patients with MDS/MPN-RS-T, there is usually an antecedent MDS-RS (90% with SF3B1 mutations), followed by the development of thrombocytosis due to the acquisition of a signal pathway mutation (usually JAK2V617F), based on germline testing and mutational VAF, we for the first time infer the antecedent occurrence of a signal pathway variant (SH2B3), followed by a splicing abnormality (SF3B1) giving rise to a MDS/MPN-RS-T phenotype. Informed consent from the patient was obtained to share relevant data as outlined in the manuscript, including genetic information. Current publication is supported in part by grants from the "The Henry J. Predolin Foundation for Research in Leukemia, Mayo Clinic, Rochester, MN, USA." This publication was supported by CTSA Grant Number KL2 TR000136 from the National Center for Advancing Translational Science (NCATS). 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