Expanding the Role of SH2B3: T Cell Large Granular Lymphocytosis (LGL) and Common Variable Immune Deficiency in the Setting of Biallelic SH2B3 Mutations

SH2B3 encodes a lymphocyte adaptor protein (LNK) involved in the negative regulation of multiple signaling pathways including hematopoiesis, with mutations reported in myeloproliferative neoplasms and B cell acute lymphoblastic lymphoma. Variants are also associated with coronary artery disease and autoimmune conditions. We report a 41-year-old male of European descent with history of immune thrombocytopenia (ITP), common variable immunodeficiency (CVID), and coronary artery disease who was found to have T cell Large Granular Lymphocytosis (LGL) in the setting of biallelic SH2B3 mutations.

The patient presented with thrombocytopenia in adulthood and was diagnosed with ITP given improvement with corticosteroids. Following this diagnosis he suffered several ITP relapses which responded to corticosteroids, but subsequently developed recurrent upper respiratory infections. Additional workup revealed hypogammaglobulinemia, poor vaccine responses, and imaging concerning for granulomatous lymphocytic interstitial lung disease (GLILD) and he was diagnosed with CVID. He was a healthy child, apart from mild short stature and brachydactyly, but suffered vitiligo and frequent cutaneous fungal infections as an adult. Family history revealed early onset coronary artery disease in both parents, rheumatoid arthritis (mother), and splenectomy for unknown reasons (sister). Several years later he developed diffuse lymphadenopathy and splenomegaly with lymph node biopsy showing follicular hyperplasia. Worsening abdominal pain prompted splenectomy.

Splenic and bone marrow pathology, B cell immunophenotyping, lymphocyte subsets, molecular testing including mutation panels and B and T cell clonality were processed as routine clinical specimens. Fibroblasts from patient skin biopsy were cultured and sequenced. Long read sequencing (LRS) on Oxford Nanopore (ONT) PromethION was done using R10.4.1 flow cells and LSK114 ligation kit and on a ONT P2 solo in duplicate library preps and combined for data analysis. Targeted sequencing of the parents and high resolution immunophenotyping by flow cytometry are planned.

Splenic pathology showed white pulp expansion though workup for lymphoproliferative disorders was negative. Sustained post splenectomy thrombocytosis prompted a bone marrow biopsy, which showed myeloid and megakaryocyte hyperplasia, mild atypia in erythroids and megakaryocytes, and an atypical lymphoid infiltrate. Heme gene panel revealed two missense variants in SH2B3, one pathogenic (c.1183G>A, p.E395K, VAF 48%) and one of uncertain significance (VUS) (c.232G>A, p.E78K, VAF 52%). Peripheral blood flow revealed a clonal population of CD8+ large granular lymphocytes (T-LGL). STAT3 and STAT5B somatic genetic testing was negative. Total B and T cells were increased (total B+T 20.3 K/mm3). CD4/CD8 ratio was reduced (0.85). B cell immunophenotyping was consistent with CVID, including increased immature B cells, CD21-low anergic activated B cells, and virtual absence of class-switched memory B cells. Both SH2B3 variants were identified in fibroblast-derived DNA, supporting germline inheritance. Analysis of phased LRS data from fibroblast derived-DNA confirmed the variants are in trans configuration.

This case represents several novel associations between SH2B3 variants and disease states (CVID, and T-LGL). The c.1183G>A pathogenic variant is associated with primary familial polycythemia, thrombocythemia, and erythrocytosis. The c.232G>A VUS has been reported in the setting of idiopathic erythrocytosis and we suspect together they explain his MPN-like phenotype and are related to his significant coronary disease. History of CVID may also be related, as monogenic drivers including STAT3 gain of function are increasingly recognized and loss of LNK likely results in increased JAK/STAT signaling which may create an analogous immune milieu. Similarly, T-LGL is postulated to arise from dysregulated apoptosis, with increased JAK-STAT signaling as an initial step. Further research is needed to examine the functional implications of these variants on the development of CVID and T-LGL.

Miller:Oxford Nanopore Technologies: Membership on an entity's Board of Directors or advisory committees, Other: travel expense, Research Funding; MyOme: Current holder of stock options in a privately-held company. Panch:Sanofi: Consultancy; Sobi: Consultancy.