Exploring the zinc-related transcriptional landscape in Alzheimer's disease

Abstract

Alzheimer's disease (AD) is a progressive neurological disorder, and increasing evidence suggests AD pathology is driven by metabolic dysfunction in the brain. Zinc is the second most abundant trace element found in the human body and is required by all living organisms. Zinc is used extensively in many biological processes, and alterations in zinc levels are implicated in the pathogenesis of numerous diseases, including AD. Since small fluctuations in brain zinc levels appear to effect AD progression, we investigated the zinc-related transcriptional responses in an AD versus non-AD state using microarray and RNA-sequencing (RNA-seq) datasets from cultured cells, mice, and humans. We identified 582 zinc-related differentially expressed genes (DEG) in human dorsolateral prefrontal cortex samples of late-onset AD (LOAD) versus non-AD controls, 146 zinc-related DEG in 5XFAD versus wild-type mice, and 95 zinc-related DEG in lipopolysaccharide (LPS)-stimulated N9 microglia versus unstimulated control cells, with 19 zinc-related DEG common to all three datasets. Of the 19 common DEG, functional enrichment and network analyses identified several biological processes and molecular functions, such as mRNA destabilization and nucleic acid binding, which may be important in neuroinflammation and AD development. Furthermore, therapeutic drugs targeting zinc-related DEG in the human dataset were identified. Taken together, these data provide insights into zinc utilization for gene transcription during AD progression which may further our understanding of AD pathogenesis and could identify new targets for therapeutic strategies targeted towards AD.

Keywords: AD, Alzheimer’s disease; Alzheimer’s disease; Aβ, amyloid-β; BP, biological process; CC, cellular component; CNS, central nervous system; DEG, differentially expressed genes; FC, fold change; FDR, false discovery rate; GO, gene ontology; LOAD, late-onset Alzheimer’s disease; LPS, lipopolysaccharide; MF, molecular function; Microglia; NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells; NLRP3, nod-like receptor family pyrin domain containing 3; Neuroinflammation; RIN, RNA integrity number; RNA-seq, RNA-sequencing; Transcriptome; ZFP, zinc finger proteins; Zinc.

Fig. 1

Differentially expressed zinc-related genes in AD. (A) Scatter plot of zinc-related DEG (FC > 1, FDR-adjusted P-value < 0.05) by RNA-seq in N9 microglia stimulated with LPS (1 µg/ml) for 6 h versus unstimulated control cells. (B) Scatter plot of zinc-related DEG (FC > 1, FDR-adjusted P-value < 0.05) by microarray in microglia isolated from the brains of 5XFAD mice versus wild-type mice (8 months old). (C) Scatter plot of zinc-related DEG (FC > 1, FDR-adjusted P-value < 0.05) by microarray in human dorsolateral prefrontal cortex samples from LOAD versus non-AD controls. For all scatter plots, up-regulated genes are shown in red and down-regulated genes are shown in green. Data are graphed as log₂FC versus –log₁₀ (P-value). (D) Venn diagram demonstrating overlap in zinc-related DEG amongst the N9 cell culture, mouse microarray, and human microarray datasets.

Fig. 2

GO enrichment analysis. Biological function analyses for the 19 zinc-related DEG common to the three datasets was performed using DAVID. Analyses were performed for Biological Process (BP) (A), Cellular Component (CC) (B), and Molecular Function (MF) (C). Pathways are shown in descending order based on –log₁₀P-values. The number of genes associated with each GO term is shown above each bar. Only GO terms with a P-value ≤ 0.05 are shown.

Fig. 3

Zc3h12a expression network analysis. Gene constellations for Zc3h12a were created using ImmGen. (A) Positive expression correlation of genes to Zc3h12a. (B) Negative expression correlation of genes to Zc3h12a. The numbers in parentheses are the expression correlation coefficients.

Fig. 4

Gene-drug interactions. Interactions between therapeutic drugs and the zinc-related DEG in the human dataset. Genes identified with drug interactions are shown and the number of drugs associated with each gene is shown above each bar.