Knockdown of heterochromatin protein 1 binding protein 3 recapitulates phenotypic, cellular, and molecular features of aging [RNA-Seq]

Identifying genetic factors that modify an individual’s susceptibility to cognitive decline in aging is critical to understanding biological processes involved and mitigating risk associated with a number of age-related disorders. Recently, heterochromatin protein 1 binding protein 3 (Hp1bp3) was identified as a mediator of cognitive aging. Here we provide a mechanistic explanation for these findings and show that targeted knockdown of Hp1bp3 in the hippocampus by 50-75% is sufficient to induce cognitive deficits and transcriptional changes reminiscent of those observed in aging and Alzheimer’s disease brains. Specifically, neuroinflammatory-related pathways become activated following Hp1bp3 KD in combination with a robust decrease in genes involved in synaptic activity and neuronal function. To test the hypothesis that Hp1bp3 mediates susceptibility to cognitive deficits via a role in neuronal excitability, we performed slice electrophysiology demonstrate transcriptional changes after Hp1bp3 KD manifest functionally as a reduction in hippocampal neuronal intrinsic excitability and synaptic plasticity. In addition, as Hp1bp3 is a known mediator of miRNA biogenesis, here we profile the miRNA transcriptome and identify mir-223 as a putative regulator of a portion of observed mRNA changes, particularly those that are inflammatory-related. In summary, work here identifies Hp1bp3 as a critical mediator of aging-related changes at the phenotypic, cellular, and molecular level and will help inform the development of therapeutics designed to target either Hp1bp3 or its downstream effectors in order to promote cognitive longevity. Viral vectors encoding either shRNA for Hp1bp3 (AAV9-shRNA-Hp1bp3) or a scrambled control (AAV-scrmb-shRNA) were delivered bilaterally into the hippocampus of adult (3-5 month old) C57BL/6J and DBA/2J mice. Three male mice from each group were used for sequencing. Briefly, each mouse was anesthetized using isoflurane, brains were quickly removed, and the hippocampus immediately dissected and snap-frozen in liquid nitrogen. Samples were kept at -80 until further use. RNA quality was evaluated using a BioAnalyzer, libraries prepared, and sequenced on a Illumina HiSeq 2500. A pairs of mRNA samples given identical barcodes during the initial sequencing. All samples were re-sequenced and where available, fastq files from both runs were concatenated, providing expanded sequencing depth for 10/12 samples.