CircRNAs mediate the effect of chronic lysosomal dysfunction on Alzheimer’s disease pathology

Abstract

AbstractBackgroundCircular RNAs (circRNAs) and microRNAs (miRNAs) are non‐coding RNAs. CircRNAs modulate miRNA levels by sequestration. MiRNAs regulate amyloidogenic pathways, disrupting transcripts including APP, BACE1, and ADAM10. CircRNAs regulate key endolysosomal transcripts. Chronic lysosomal dysfunction (CLD) is linked to Alzheimer’s Disease (AD). However, the role circRNAs downstream of CLD and AD is unclear. Here, we tested whether CLD affects the amyloidogenic pathway in 5xFAD mice through circRNAs.MethodCortical circRNA expression was obtained of 5xFAD, PPT1+/−, 5xFAD: PPT1+/− (P5X), Naglu+/−, 5xFAD: Naglu+/− (N5X) mice. TruSeq Stranded total RNA was extracted with Ribo‐Zero to deplete rRNA and generate stranded‐RNA‐seq. Libraries were sequenced on a NextSeq 500 platform of Illumina and analysis was done with the DESeq2 package with an FRD <0.05. In silico microRNA binging was done using circAtlas 2.0 browser. The insoluble Aβ‐40 and Aβ‐42 were quantified by ELISA in the hippocampal fraction. The Aβ plaque load was quantified in coronal brain sections using immunohistochemistry.ResultThe P5X and N5X mice exhibit increased amyloid plaque load, hippocampal Aβ‐40, and Aβ‐42 levels, and reduced lifespan compared to 5xFAD mice. We detected 1286 cicRNAs in all the groups. 38 from P5X and N5X groups, 37 from PPT1+/−, and 29 from Naglu+/− passed FRD correction compared with 5xFAD mice. Both linear and circRNAs of 4933406I18Rik, Zfp609, Zfp532, and Nnt changed between PPT1+/− and P5X compared to 5xFAD. The levels of circAdam10, circPan3, circMbtd1, circ4930402H24Rik, circSt6gal2, and circCdc14b were reduced, while circZranb1 and circMyo9a were increased in P5X and N5X compared with 5xFAD. CircNlgn1 levels changed only downstream of PPT1+/−. In silico analyses show amyloidogenic‐related microRNAs exhibit circRNAs binding sites. MiR‐361‐3p has binding sites for circZranb1 and circADAM10, as well as miR‐298‐3p, can bind circNlgn1. Both miR‐361‐3p and miR‐298‐3p trap and inhibit BACE1 function and Aβ production, interfering in the amyloidogenic pathway. CircPan3 regulates the autophagy‐related miR‐421. Experimental evidence shows that overexpression of circPan3 suppresses autophagy through a miR‐421/Pink1 pathway.ConclusionCLD (PPT1+/− and Naglu+/−) boosted AD pathology and induced differential changes in circRNAs levels affecting amyloidogenic and autophagy pathways. There is a positive feedback loop between CLD and circRNAs in AD mouse models.