Isoform Remodeling Along the Human Monocyte-to-Macrophage Differentiation Axis

Tissue-resident macrophage diversity has been mapped at the gene-expression level, and alternative splicing has been catalogued across immune lineages [1,2]; isoform behavior along the monocyte-to-macrophage differentiation axis remains unexamined. Analyzing a 17-gene immune panel across BLUEPRINT differentiation series and GTEx v8, we identify an MSR1 isoform switch with complete donor-level separation (short-isoform fraction 0.844–0.914 in monocytes versus 0.291–0.541 in six macrophage samples; exact permutation p = 0.024) — a switch from the dominant-negative SR-AIII scavenger-receptor isoform to functional SR-AI/II receptors — with equally supported PTPRC, MYD88, and IRAK1 remodeling, whereas an IL1B canonical-fraction rise is donor-heterogeneous (p = 0.114). LY96 (MD-2) is induced ~17-fold during differentiation, yet the functionally decisive antagonist/agonist isoform ratio is not resolved by standard short-read annotation — a methodological gap for immune isoform studies. CD14/CD163 show dosage regulation without isoform switching: CD163 peaks in LPS-driven M1 macrophages and, in human brain, marks border-associated macrophages rather than microglia. A 62-gene cytoskeletal panel nominates septin-family isoform divergence as a candidate mechanism of the ramified-to-amoeboid morphology spectrum, with PTBP1/hnRNP/SRSF programs as candidate executors of immune-side switching. Differentiation-coupled isoform remodeling is thus a component of macrophage identity.