Divergent transcriptomic transition programs in Alzheimer disease: immune priming and synaptic collapse in females versus organelle membrane bifurcation in males

Alzheimers disease (AD) disproportionately affects women, who account for approximately two-thirds of prevalent cases. Despite decades of research, the mechanistic basis for this profound sex disparity remains poorly resolved. Prior transcriptomic studies have predominantly used pooled or female-enriched cohorts, obscuring whether the transition from normal cognition (NCI) to AD follows a common molecular program across sexes or reflects fundamentally divergent biology. Here, we analyzed bulk RNA-sequencing data from the dorsolateral prefrontal cortex of 624 individuals (401 females, 223 males) in the ROSMAP cohort using a transition-aware framework that separates variance instability along the disease axis from mean expression changes. We demonstrate that female and male brains exhibit structurally distinct transcriptomic transition programs. Females display a sequential, multi-tier architecture: interferon and immune variance priming (628 genes) is detectable early at the NCI-to-mild cognitive impairment (MCI) interval, which structurally precedes a massive mean-level synaptic and neuropeptide loss (8,935 genes) in AD. The female NCI-to-MCI interval alone produces 1,249 variance bifurcation events entirely absent in males. Conversely, males exhibit no early immune priming or powered mean-level changes. Instead, they collapse into a single large variance bifurcation pool (8,237 genes) heavily enriched for system-wide organelle membrane fusion, post-translational modification, and intracellular trafficking. These findings reveal that the AD transcriptomic transition is not a unitary program quantitatively modified by sex, but two distinct biological trajectories. This fundamental divergence motivates sex-stratified mechanistic models and independent biomarker development for each sex, cautioning against analytical pooling in transition-stage cohorts.