Blood-Based Proteomics for Deeper Insights into Indolent Systemic Mastocytosis: The Pioneer Trial Experience
Authors: Abbas Hussein A. , Nguyen Annie , Wang Bofei , Chen Min , Yang Guang , Lampson Ben , Erlich Rachel L. , Veletic Ivo 
Published: December 2024

Introduction: Aberrant mast cell activity associated with systemic mastocytosis (SM), of which indolent SM (ISM) is the most common subtype, can significantly impact the quality of life of patients. Despite its inflammatory nature, the components driving the inflammation in ISM are not well explored, aside from smaller studies with focused protein panels and heterogenous treatment groups. Herein, we aimed to conduct high throughput profiling of the proteomic inflammatory components from patients enrolled in PIONEER (NCT03731260), a 3-part, randomized, double-blind, placebo-controlled study of avapritinib in ISM, representing the largest and the most comprehensive characterization of inflammation in a homogenously treated cohort of patients with ISM. We hypothesized that analysis of the circulating plasma proteome of patients enrolled in the PIONEER trial, as well as age-matched healthy donors, may identify individual proteins or composite protein profiles of diagnostic, prognostic, and potentially even therapeutic relevance in ISM.
Methods: Baseline plasma samples of 168 patients (available samples from the 212 enrolled on the randomized, placebo-controlled part of the study) from PIONEER and 39 age-matched healthy donors were tested by the Olink® Explore 384 Inflammation (Uppsala, Sweden) plasma protein panel . This panel detects the abundance of 363 plasma proteins, including various inflammation-associated and disease-relevant plasma proteins in peripheral blood samples across a broad detection range (from pg/mL to mg/mL).
Results: The subset of patients enrolled in PIONEER for whom plasma samples were analyzed using the Olink® Explore 384 Inflammation panel had the following characteristics: 75% female, median age of 51.5 years, prior cytoreductive therapy in 12%, median baseline serum tryptase of 43.6 ng/mL, and median baseline KIT D816V VAF in peripheral blood of 0.4%; mirroring the overall PIONEER trial population. Tryptase, known to be elevated in patients with ISM, was included in the Olink® panel and served as an internal control. As expected, tryptase measured by the panel was significantly higher in patients with ISM compared to age-matched healthy controls (two-sample t-test and multiple testing adjustment using the Benjamini-Hochberg method, false discovery rate [FDR]=6.1x10-12). In total, at baseline, 161/363 proteins were significantly different in patients with ISM vs healthy donors (FDR&lt;0.005). Proteins previously highlighted in the literature as increased in ISM were increased in our analysis, including IL-1β (FDR=0.003) and CCL23 (FDR=6.2x10-7). Notably, new proteins of interest were also identified as increased in ISM, including secernin-1 (FDR=3.9x10-25, initially described as a cytosolic protein that regulates exocytosis in mast cells), CXCL3 (FDR=7.4x10-8) and IL-7 (FDR=8.4x10-11). Levels of certain proteins previously linked to mast cell physiology were found to correlate with clinically measured serum tryptase levels in ISM by Spearman correlation, including SIGLEC10 (r=0.39), CCL23 (r=0.56), and mast cell immunoglobulin like receptor 1 (MILR1, r=0.67). Comparing across ISM samples, significant heterogeneity was noted, including the fact that the composite proteomic profile in some patients with ISM co-segregated with healthy donors and in some patients did not. Additional analysis of proteomic profiling is ongoing and will be presented including dimensionality reduction (partial least squares discriminant analysis), comparative analysis of different subgroups, and model performance assessment with concordance index and time-dependent area under the curve.
Conclusion: Patients with ISM have many alterations in the plasma proteome compared to healthy individuals, highlighting the immune dysregulation that is seen with this disease. The heterogenous profile of circulating plasma proteins even within patients with ISM mirrors the clinically heterogenous nature of the disease, and further understanding of the plasma proteins within an individual patient may hold prognostic or therapeutic value. A number of proteins have been identified in patients with ISM which could aid in future understanding of the disease and therapeutic targets for its treatment. Plasma protein analysis provides a new tool with which to understand and characterize ISM.