Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer’s disease-like mutation inpsen1indicate effects on oxidative phosphorylation, mcm functions, and iron homeostasis

Abstract

Early-onset familial Alzheimer’s disease (EOfAD) is promoted by dominant mutations, enabling the study of Alzheimer’s disease (AD) pathogenic mechanisms through generation of EOfAD-like mutations in animal models. In a previous study, we generated an EOfAD-like mutation, psen1Q96_K97del, in zebrafish and performed a transcriptome analysis comparing entire brains from 6-month-old wild type and heterozygous mutant fish. We identified predicted effects on mitochondrial function and endolysosomal acidification. Here we aimed to determine whether similar effects occur in 7 day post fertilization (dpf) zebrafish larvae that might be exploited in screening of chemical libraries to find ameliorative drugs. We generated clutches of wild type and heterozygous psen1Q96_K97del 7 dpf larvae using a paired-mating strategy to reduce extraneous genetic variation before performing a comparative transcriptome analysis. We identified 228 differentially expressed genes and performed Goseq analysis and gene set enrichment analysis (GSEA). This predicted a significant effect on oxidative phosphorylation, consistent with our earlier observations of predicted effects on ATP synthesis in adult heterozygous psen1Q96_K97del brains. The dysregulation of minichromosome maintenance protein complex (MCM) genes strongly contributed to predicted effects on DNA replication and the cell cycle and may explain earlier observations of genome instability due to PSEN1 mutation. The upregulation of crystallin gene expression may be a response to defective activity of mutant Psen1 protein in endolysosomal acidification. Extracellular matrix (ECM) related genes were downregulated, consistent with previous studies of EOfAD mutant iPSC neurons and postmortem late onset AD brains. Also, changes in expression of genes controlling iron ion transport were observed without identifiable changes in the prevalence of transcripts containing iron responsive elements (IREs) in their 3’ untranslated regions. These changes may, therefore, predispose to the apparent iron dyshomeostasis previously observed in 6-month-old heterozygous psen1Q96_K97del EOfAD-like mutant brains.

Iron Responsive Element (IRE)-mediated responses to iron dyshomeostasis in Alzheimer’s disease

“…Our findings raise the question of how early IRE gene expression changes and iron dyshomeostasis more broadly may start to occur in fAD brains. In a recent analysis of transcriptome data from pools of 7-day-old larvae heterozygous for the fAD-like mutation psen1 Q96_K97del (compared to wild type half-siblings), we have observed over-representation of the GO term “iron ion transport” without significant changes in 3’ IRE or 5’ IRE transcript abundance [59]. This supports that the 3’ IRE transcript abundance signal in 6-month-old brains of this mutant line reflects changes in ferrous iron abundance that develop with age in response to an underlying defect in cellular iron regulation.…”

“…Please refer to ref. [59] (GEO accession: GSE148631) for details on RNA-seq data processing and analysis. In the current work, we used the gene expression counts matrix with limma to perform gene set enrichment analysis.…”

Frameshift and frame-preserving mutations in zebrafishpresenilin 2affect different cellular functions in young adult brains

“…Genes driving the enrichment of this gene set (i.e. the leading edge genes) include the minichromosome maintenance ( mcm ) genes (see Additional File 4 ), which we observed to be significantly dysregulated due to heterozygosity for an EOfAD-like mutation in psen1 in 7 day old zebrafish larvae [42]. Together, these results provide support for the “two-hit hypothesis” of Mark Smith and colleagues [43], which postulates that “cell cycle events” (CCEs) involving inappropriate attempts at cell division by neurons are critical for development of AD.…”

Comparative analysis of Alzheimer’s disease knock-in model brain transcriptomes implies changes to energy metabolism as a causative pathogenic stress

“…Therefore, effects on oxidative phosphorylation are a common, early “signature” of EOfAD. Intriguingly, we previously observed downregulation of the oxidative phosphorylation genes due to heterozygosity for the psen1 Q96_K97del mutation in whole zebrafish larvae at 7 days post fertilisation (dpf) (Dong et al, 2020), suggesting changes to mitochondrial function are a very early cellular stress in AD pathogenesis. All of the mutations studied have also resulted in changes in the levels of transcripts required for ribosome formation and we suggest this may reflect changes in mTOR activity (see Supplementary File 4 ).…”