A cell-type-resolved directory of human brain reveals microRNAs and tRNA fragments associated with aging and Alzheimer's disease

Abstract

Background: MicroRNAs (miRs) and transfer RNA fragments (tRFs) regulate diverse brain processes, from neurogenesis to neurological disease. While both these small RNA classes have been implicated in cell-type-specific regulation, most studies leaned on bulk measurements, due to technical limitations in detecting small RNAs using single-cell RNA sequencing. Consequently, the cell-type specificity of brain miRs and tRFs remains poorly characterized, limiting functional interpretation. Results: To generate a comprehensive, cell-type-resolved atlas of miRs and tRFs from live human brain tissues, we isolated neurons, astrocytes, microglia, and oligodendrocytes from neurosurgery-derived fresh human brain samples and profiled their small RNAs by RNA-sequencing. This revealed pronounced cell-type-specific differences in miR and tRF levels, identified novel small RNA cell-type markers, and provided insight into the genetic regulation of miR cell-type specificity. Notably, neurons exhibited elevated levels of 5'-tRNA halves compared to glial cells, including enriched fragments derived from glycine, leucine and lysine tRNAs. Finally, our resource enabled assignment of cell-type origins to miRs associated with healthy brain aging and tRFs linked to Alzheimer's disease. Conclusions: Highlighting the importance of cellular context for data interpretation, both human brain miRs and tRFs exhibit pronounced cell-type-specific differences associated with brain aging and neurodegenerative diseases. Combined with an accompanying statistical tool for miR cell-type enrichment analysis, this work provides a publicly available resource for resolving the cell-type origins of small RNAs in the human brain.