Haploinsufficiency in PTPN2 leads to early onset systemic autoimmunity from Evans syndrome to lupus

An exome sequencing strategy employed to identify pathogenic variants in patients with pediatric-onset systemic lupus or Evans syndrome resulted in the discovery of six novel monoallelic mutations in PTPN2. PTPN2 is a phosphatase that acts as an essential negative regulator of the JAK/STAT pathways downstream of several cytokine pathways. All identified mutations led to a loss of PTPN2 regulatory function as evidenced by in vitro cytokine reporter and phosphatase assays, and by hyperproliferation of patients’ T cells stimulated with cytokines. Furthermore, patients exhibited high serum levels of various inflammatory cytokines, mimicking the profile observed in individuals with gain-of-function mutations in various STAT factors. Flow cytometry analysis of patients’ blood cells revealed typical alterations associated with autoimmunity, such as an expansion of CD11c+ B cells and follicular helper T cells, and all patients presented with anti-platelet or other autoantibodies. These findings further supported the notion that a loss of function in negative regulators of cytokine pathways can lead to a broad spectrum of autoimmune manifestations and that PTPN2 along with SOCS1 haploinsufficiency constitute a new group of monogenic autoimmune diseases that can benefit from targeted therapy. The expanded T cells were starved of IL-2 for 24h, plated at cell concentration of 1.106 cells/ ml in Panserin medium only and then were left unstimulated or stimulated with IFN-a (104U/ml, Millipore, #IF007) or IL-2 (104U/ml) during 3h at 37°C. RNA was extracted using RNeasy Mini Kit (Qiagen) and quality was assessed using Fragment Analyzer (Agilent Technologies) with RNA Integrity Number >8 and 28S/18S ratio around 2. Messenger RNA was finally converted to complementary DNA by capture of poly-A+ RNA, amplified and sequenced to a depth of at least 50 million reads using the Illumina technology (Novaseq 6000 sequencer) at the Genomic Plateform of Imagine Institut. A1: Patient with the heterozygous mutation p.F403Lfs*25 in PTPN2 A2: Patient with the heterozygous mutation p.F403Lfs*25 in PTPN2 B1: Patient with the heterozygous mutation p.W98* in PTPN2 C1: Patient with the heterozygous mutation p.W289* in PTPN2 D1: Patient with the heterozygous mutation p.E24Mfs*20 in PTPN2 E1: Patient with the heterozygous mutation p.Y126N in PTPN2 F1: Patient with the heterozygous mutation p.C216S in PTPN2 HC1: Healthy donor, female 28 years old HC2: Healthy donor, female, 35 years old HC3: Healthy donor, male, 29 years old