Introduction: The pathogenesis underlying the variable clinical presentation and outcomes of sarcoidosis remains incompletely understood. Although kinase inhibitors show therapeutic promise in select cases, the signaling pathways that drive the initiation and progression of pulmonary sarcoidosis remain poorly defined.

Objectives: To define the global phosphorylation landscape and infer kinase signaling networks with potential therapeutic relevance.

Materials and Methods: We analyzed Bronchoalveolar lavage (BAL) cells (BAL) from non‑smoking, untreated sarcoidosis cases (n = 30), classified as non‑progressive (NP) or progressive (P), n = 15 each, based on a two‑year follow-up, with healthy volunteers as controls (HC, n = 10). BAL cells were processed for protein extraction, tryptic digestion, and phosphopeptide enrichment using sequential TiO₂ and Fe‑NTA metal oxide affinity chromatography. Peptides were TMT‑labeled and analyzed on an Orbitrap Eclipse mass spectrometer. Phosphopeptides were identified using FragPipe. We used Post-Translational Modification Signature Enrichment Analysis (PTM‑SEA) to estimate signaling pathway activity by identifying enriched patterns of protein modifications. We inferred kinase activity using motif‑based Kinase Substrate Enrichment Analysis (KSEA), which links phosphorylation sites to known kinase target sequences (motifs),

Results: We identified 5957 phosphopeptides. At nominal p ≤ 0.05, 677 had differential abundance between sarcoidosis and healthy controls, and 398 between NP and P sarcoidosis. PTM‑SEA identified ERK/MAPK as the dominant signaling axis, with downstream engagement of CDK and CK2 in the HC vs sarcoidosis comparison. In addition, P vs NP sarcoidosis demonstrated enrichment of AKT, serum‑ and glucocorticoid‑regulated kinases 2 and 3, AMP‑activated protein kinase‑α, and p90 ribosomal S6 kinase, implicating altered control of mTOR signaling. Motif‑based KSEA concordantly demonstrated shared ERK/MAPK and CK2 substrate motifs across disease states, with progression distinguished by additional calcium‑regulated, PAK‑associated, GPCR‑linked, and stress‑adaptive motifs.

Conclusions: These pilot studies demonstrate a novel application of phosphoproteomics in pulmonary sarcoidosis. Improved understanding of kinase signaling pathways provides a framework for identifying biological mechanisms and therapeutic targets