Causal Single-Cell Transcriptomic and Splicing Clocks Uncouple Molecular Damage from Protective Adaptation Across Human Aging, Spatial Microenvironments, and Rejuvenation

Single-cell transcriptomic aging clocks predict chronological age with high precision, yet conventional models conflate molecular drivers of degeneration (Damage) with compensatory stress responses preserving viability (Adaptation). This study introduces scCausAge, integrating 51,852 SuSiE fine-mapped expression and LeafCutter RNA-splicing quantitative trait loci (PIP >= 0.001, F >= 10) across 20 human cohorts with correlation-adjusted multi-trait Mendelian Randomization across six longevity and epigenetic aging genome-wide association studies (N > 1,000,000), identifying 3,153 causal aging loci (114 at FDR < 0.10; 404 with colocalization PP.H4 >= 0.50). Intersecting genetic causal directionality with single-cell aging trajectories across 90,683 human cortical nuclei spanning six representative subclass atlases from the 1,392,421-nuclei Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) via nested donor-grouped cross-validation uncouples causal damage (scDamAge) from protective adaptation (scAdaptAge) across 20 cortical lineages and reveals 425 cross-lineage context-flipping genes (ENO1, LIPA, KDM1B, NOVA1). Causally constrained clocks outperform chronological clocks in GABAergic interneurons (r = 0.630 vs. 0.549) and distinguish cognitive resilience from Alzheimer's dementia via preserved endothelial scCausAge (d = -0.778, p = 0.00336, AUROC = 0.690) and scAdaptAge (d = -0.536, p = 0.0262, AUROC = 0.664), as well as lower L5 ET neuronal (d = +0.586, p = 0.0247) and microglial (d = +0.425, p = 0.0384) Net Vulnerability Index. Across 650,459 MERFISH cells from 27 human brains, high-damage glia transmit paracrine damage within 30 um (p = 4.11e-13), whereas high-adaptation glia shield neighboring oligodendrocytes and neurons (p = 9.58e-11). Across external human progeria, radiation senescence, and OSKM reprogramming cohorts, maturation-phase partial reprogramming (Days 16-24) achieves selective rejuvenation (Delta scDamAge = -2.31 yr, p = 0.00965 at Day 16; Delta scDamAge = -1.85 yr, p = 0.00161 and Delta scAdaptAge = +1.23 yr, p = 0.0142 at Day 24), whereas full iPSC pluripotency erases somatic adaptation (Delta scAdaptAge = -5.56 yr, p = 7.57e-5 in Endothelial and -5.37 yr, p = 0.0163 in OPC), and Open Targets/ChEMBL screening prioritizes 16 clinical geroprotectors.