Clinical and genomic landscape of STAT5B mutations in lymphoid and myeloid malignancies

Abstract

Abstract Background: STAT5 is a critical mediator of cytokine signaling downstream of tyrosine kinases. STAT5B activating mutations – especially N642H - have emerged as oncogenic drivers in T-cell lymphoid neoplasms and recent evidence also implicates them in myeloid neoplasms with eosinophilia. However, clinical significance of other STAT5B variants across hematologic malignancies remains underexplored, and they are often labeled as variants of unknown significance (VUS) in next-generation sequencing (NGS) results. Methods:This retrospective study included adult (≥18 years) patients (pts) with myeloid (M) or lymphoid (L) malignancies harboring STAT5B mutations detected by NGS (Jan 2014- Dec 2024) regardless of specimen type or platform. Mutations were stratified into four tiers based on pathogenicity and functional data by two independent precision medicine oncologists: (A) Tier 1: Established Somatic and Activating (B) Tier 2: Likely Somatic and Likely Activating (C) Tier 3: Likely Somatic and Unclear Activity (4) Tier 4: Likely Germline Polymorphisms. Kaplan–Meier method was used to estimate overall survival (OS) and progression-free survival (PFS) censoring at the time of allogenic stem cell transplant (alloHCT). Results Of 76 ptsidentified, 50 had Tier 1-3 mutations along with a definitive M or L neoplasm. Four pts had a M or L malignancy and a concomitant T-cell large granular lymphocyte leukemia (T-LGL) clone and were analyzed separately. Among the remaining 46 pts (L =28, M=18), Tier 1, 2 , and 3 mutations were present in 28, 6, and 12 pts, respectively. Median follow up time was 33.3 months (L= 30.2 M=36.2), and median age was 64.5 yrs (range 16-83); 65% were male. In the L group, T-cell neoplasms predominated (64%); with T-cell prolymphocytic leukemia (T-PLL) (20%) and T-LGL (13.3%) being most common. Most T-cell neoplasms harbored Tier 1-2 variants. The most common B-cell neoplasm was B-acute lymphoblastic leukemia (ALL) (18%). In contrast to T-cell neoplasms, B-cell neoplasms were mainly associated with Tier 3 variants. Among M malignancies, myelodysplastic syndrome (55%) and acute myeloid leukemia (27%) were the most common diagnoses with variants across all 3 tiers. Median Variable allele frequency (VAF) was 16% (range 0.82-84.6). A total of 17 distinct STAT5B variants were identified: Tier 1 (T628S, N642H, Y665F); Tier 2 (E433K, I704L, V712E); Tier 3 (L142P, R200W, D273E, T411I, S434L, P491L, E579K, Y683C, V700L, V227G, V712fs*20). The most common variant was N642H (18 pts; L= 56% M= 44%), followed by T628S (9 pts; L= 78 % M= 22%), V712E (4 pts; L= 25 % M= 75%, VAF consistently >40%) and Y665F (3 pts; all T and NK cell lymphomas). Only two patients had 2 concurrent STAT5B mutations: -T-PLL (N642H, T628S) and T-ALL (T628S, Y665F). L and M cases harboring STAT5B mutations exhibited varying clinical phenotypes. M cases were more likely to have anemia, thrombocytopenia, eosinophilia, and basophilia while L cases were more likely to have lymphocytosis and monocytosis. Eosinophilia and basophilia were only present with N642H or V712E variants and when present in M cohort had a STAT5B VAF > 20 %. Co-mutation analysis revealed frequent alterations of TET2 (11 pts; evenly distributed in L and M); lymphoid-associated mutations included: ATM (11 pts; L= 72% M= 27, NOTCH1 (8 pts, L= 63%, M= 37%), CDKN2A/B (8 pts, L= 87% M=13%), SETD2 and PCLO (6pts, all L). Myeloid-enriched mutations included ASXL1 (9 pts, L = 33% , M= 56%), KMT2D (8 pts, L= 25% M=75%), U2AF1 (7pts, L= 14% M= 86%, only co-occurred with N642H/T628S), SF3B1 (6pts, exclusively M). Survival analysis showed no significant differences in OS or PFS between Tier 1 and Tiers 2+3 in either L or M groups. VAF < 20% was associated with a numerically longer OS in both L (72.5 mo v 35.7 mo) and M (79.7 mo vs 54.1 mo) cases compared to VAF >20% though this was not statistically significant. Conclusions STAT5B mutations define a distinct molecular subset of hematologic malignancies, with N642H as the most frequent variant across lineages, T628S and Y665F more common in L cases and V712E in M. Lineage-specific patterns in mutation distribution and co-mutations support further investigation in a larger cohort for the integration of STAT5B profiling into diagnostic workflows.