Single-Cell Transcriptomic Analysis Reveals MCL1-Dominated Apoptotic Remodeling of the Fibroblast–Myofibroblast Lineage in Idiopathic Pulmonary Fibrosis

Background: Idiopathic pulmonary fibrosis (IPF) is a lethal interstitial lung disease in which apoptosis-resistant fibroblasts drive progressive scarring. Fibrotic mesenchymal cells are functionally “primed for death”, but the transcriptional architecture of apoptotic priming in the human IPF fibroblast lineage—and its dominant anti-apoptotic dependency—remains undefined. Methods: We reanalyzed the 114,396-cell GSE135893 atlas [1], scoring 2,653 fibroblast-lineage cells for pre-specified pro- and anti-apoptotic BCL-2-family modules and a composite Apoptosis Index, with donor-level replication in GSE136831 [2] and cell-level confirmation in two further cohorts. Results: In IPF fibroblasts, the anti-apoptotic (cell-level p = 3.0 × 10⁻²¹; d = 0.66) and caspase modules were elevated and the Apoptosis Index shifted toward survival, with MCL1 the dominant anti-apoptotic transcript (log2FC = +1.84; 91.3% versus 63.0% of cells)—an elevation driven substantially by disease-emergent subtype composition (93.5–100% detection, near-absent in control); depth-matched within-state difference attenuates (65.6% versus 62.1%, ns). Cell-level p-values are descriptive; donor-level analyses are the primary inference. The double-high “primed” fraction was elevated in IPF (25.6% versus 11.6%; cell-level p = 2.6 × 10⁻⁴; nominal at donor level, p = 0.023), concentrated in disease-emergent subsets; threshold-sensitivity and module-arm decoupling showed it is driven by the anti-apoptotic arm alone: the fibroblast pool is survival-protected, not genuinely primed, while pro-apoptotic loading emerged only upon myofibroblast differentiation (p = 1.1 × 10⁻⁸)—a two-stage architecture: protected fibroblasts give rise to primed, death-leaning myofibroblasts. Module-level elevations were donor-level null (p = 0.30–0.43); the supported findings are the donor-level primed-pool expansion (Habermann nominal p = 0.023; GSE136831 nominal p = 0.0068) and the compositional MCL1 elevation, with cell-level confirmation in two further cohorts. Conclusions: Apoptotic priming along the IPF fibroblast–myofibroblast lineage is a two-stage program dissected at single-cell resolution, nominating MCL-1 as an antifibrotic target warranting protein-level and pharmacological validation.