Aging Rhesus Macaque show tissue and sex-specific balance of drifting and coordinated miRNA programs

Macaque’s research centrality makes it critical to study their molecular aging. We accomplish this for their non-coding transcriptome by sequencing small RNA from 11 organs, with special focus on brain by including 24 brain regions, sampling males and females between ages 3-35 years. Heart, adrenal gland, corpus callosum and caudate putamen showed the most age-deregulated miRNA trajectories. The MIR-154 family, inside the imprinted, rejuvenation-associated Dlk1-Dio3 cluster, was particularly vulnerable. Known age-associated miRNA families LET-7, MIR-29, MIR-17 and MIR-92 were strongly deregulated, with heavy dependence on tissue and sex. MiRNA genomic clusters deregulation was concordant within tissue-sex combinations, implicating upstream regulation rather than random noise. Cross-species comparison with mouse showed ancient miRNAs dominating age-deregulated trajectories. Deregulation direction in tissues-sex was conserved between species at family/cluster levels, but conservation substantially weakened at individual miRNA level. Thus, we mark a decisive step in translating miRNA aging trajectories between two heavily used model organisms. Key Findings Heart, adrenal gland, corpus callosum, caudate putamen are hotspots of miRNA age deregulation, with dramatic influence from sex. Non-brain organs show tissue specific miRNA change, with inconsistent overlap between tissues. Genomic clusters of miRNAs were found to be concordant in their age deregulation direction, dependent on tissue and sex, suggesting upstream regulation. The MIR-154 family, housed inside the heavily imprinted Dlk1-Dio3 cluster and processed from the rejuvenation associated MEG3-MIRG host gene is prominently involved in both non-brain organs and brain regions. Concentration of age deregulation in evolutionarily ancient miRNAs across species implies regulatory program rather than epigenetic drift, involving MIR-154, LET-7, MIR-29, MIR-17 and MIR-92 families. Direction of change conserved between species at the family / genomic cluster level but diminished substantially at individual miRNA level.