Microchimerism in the human brain, quantitative assessment and single nuclei profiling establish cell types and diversity

Abstract Bi-directional maternal-fetal exchange during pregnancy creates a long-term microchimerism (Mc) legacy in both individuals, but its presence and cellular fate in human brain are largely unknown. We studied surgically resected epilepsy brain specimens with targetable maternal polymorphisms using polymorphism-specific quantitative PCR. Maternal Mc was prevalent, detectable in 70% of patients, and often at striking quantities spanning temporal, frontal, parietal, and hippocampal regions. Next, we employed single nucleus RNA profiling using cellector , a genetic demultiplexing tool designed to detect rare allogeneic cells. We identified Mc across major neural and glial populations. Finally, analysis of publicly available snRNA-seq datasets from neurotypical brains from gestation to late adulthood further revealed widespread Mc, persisting into advanced age, and preferentially adopting L2/3 intratelencephalic neuronal or microglial/macrophage-like fates. These data show that naturally acquired Mc is prevalent, diverse, and persistent in human brain, inviting reconsideration of what constitutes “self,” with broad implications for health and disease.