Proteomic and phosphoproteomic signatures of disease progression in unmutated IGHV chronic lymphocytic leukemia

Chronic lymphocytic leukemia (CLL) patients with an unmutated (UM) immunoglobulin heavy chain variable region gene (IGHV) typically have poorer prognosis and require earlier treatment compared to those with mutated IGHV. Nevertheless, disease progression among UM-CLL patients is heterogeneous, with some experiencing stable disease and prolonged time to first treatment (TTFT). Because the cellular proteome directly reflects cell function, comprehensive proteomic and phosphoproteomic profiling may improve prediction of progression of UM-CLL and uncover novel biomarkers.

We applied mass spectrometry-based quantitative proteomics and phosphoproteomics to peripheral blood mononuclear cells from 18 UM‑CLL patients, comparing those with a TTFT of ≤ 2 years (progressive disease) to those with TTFT ≥ 4 years (stable disease).

We quantified over 6,300 proteins across all samples. The top 100 differentially expressed proteins clearly distinguished progressive from stable UM-CLL. Phosphoproteomic analysis identified over 15,000 phosphorylation sites across 4,200 proteins, with the top 100 phosphopeptides similarly separating patient groups. Gene set enrichment analysis of proteins up‑regulated in progressive UM‑CLL revealed strong enrichment for RNA processing and ribosome biogenesis, together with mitochondrial translation and oxidative phosphorylation pathways, underscoring dysregulated RNA metabolism and energy production as key features of disease progression.

Specific proteins and phosphopeptides identified here, upon further validation, may serve as biomarkers for early intervention in UM‑CLL. More broadly, our study demonstrates the value of integrated proteomic and phosphoproteomic profiling which may lead to refining risk stratification and advancing understanding of the complex biology underlying CLL progression.