Longitudinal proteomic module configurations differ across human monocyte-derived differentiation and polarization conditions

Abstract

Human monocyte differentiation involves changes in multiple protein programs, but comparisons across culture conditions can conflate source variation with differentiation time. We reanalyzed public proteomic measurements arranged in four source blocks across M1-polarizing, M2-polarizing, dendritic-cell and osteoclast conditions at days 2, 4, 6, 8 and 10. The original experiment used three individual-donor preparations and one preparation pooled from 40 donors; these are not four individual donors. Eight predefined protein-module scores formed an 80-observation matrix. A multivariate model tested joint condition and condition-by-time terms beyond source block and categorical time, using 9,999 permutations that preserved complete block-specific culture trajectories. The joint condition terms accounted for an additional 31.37% of total module-score variation (pseudo-F = 4.257567; permutation p = 0.0002). The association persisted after omission of each source block, with incremental R-squared of 0.315-0.390. Secondary day-specific tests detected differences at days 4-10, whereas day 2 did not meet the false-discovery criterion. Descriptive trajectories showed a shared increase in glycolysis/pentose-phosphate scores alongside condition-dependent mitochondrial, redox and proteostasis profiles. At day 10, M2-labelled cultures had the lowest mean mitochondrial score, whereas M1-labelled cultures had the highest three-protein resolution-associated score. All eight module tests survived multiplicity correction, and no single-module omission abolished the multivariate association. These findings describe condition-associated configurations within four heterogeneous source preparations. Equal weighting of source blocks does not estimate a mean across individual donors. The analysis does not establish pathway activity, single-cell trajectories, population-level replication or external biological validation.