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Quantitative Proteomic and Metabolomic Profiling Reveals Altered Mitochondrial Metabolism and Folate Biosynthesis Pathways in the Aging Drosophila Eye.

ABSTRACT: Aging is associated with increased risk of ocular disease, suggesting that age-associated molecular changes in the eye increase its vulnerability to damage. Although there are common pathways involved in aging at an organismal level, different tissues and cell types exhibit specific changes in gene expression with advanced age. Drosophila melanogaster is an established model system for studying aging and neurodegenerative disease that also provides a valuable model for studying age-associated ocular disease. Flies, like humans, exhibit decreased visual function and increased risk of retinal degeneration with age. Here, we profiled the aging proteome and metabolome of the Drosophila eye and compared these data with age-associated transcriptomic changes from both eyes and photoreceptors to identify alterations in pathways that could lead to age-related phenotypes in the eye. Of note, the proteomic and metabolomic changes observed in the aging eye are distinct from those observed in the head or whole fly, suggesting that tissue-specific changes in protein abundance and metabolism occur in the aging fly. Our integration of the proteomic, metabolomic, and transcriptomic data reveals that changes in metabolism, potentially due to decreases in availability of B vitamins, together with chronic activation of the immune response, may underpin many of the events observed in the aging Drosophila eye. We propose that targeting these pathways in the genetically tractable Drosophila system may help to identify potential neuroprotective approaches for neurodegenerative and age-related ocular diseases. Data are available via ProteomeXchange with identifier PXD027090.

SUBMITTER: Hall H

PROVIDER: S-EPMC8385154 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Purpose: Identify gene expression changes in whole brains of newborn pups whose mothers were exposed to Cd during pregnancy (50ppm CdCl2) compared to unexposed controls (0ppm CdCl2). Methods: 5- to 7-week-old C57BL/6J (‘B’) and CAST/EiJ (‘C’) females (the F0 generation) were exposed through their drinking water to 0 ppm or 50 ppm Cd in the form of CdCl2 (Sigma-Aldrich, catalog number 202908) for a period of 5 weeks, then mated with a male of the opposite strain. Cd exposure continued throughout pregnancy and was discontinued at litter birth. A hybrid mating scheme (the F1 generation) was employed to enable analyses of allele-specific gene expression and DNA methylation for a separate study (Hudson & Cowley, manuscript in preparation). The genotypes of F1 mice are referred to as ‘BxC’ (B mother x C father). F1 animals were sacrificed and dissected within 24 hours of birth; sample sizes can be found in supplementary tables associated with the publication. F1 mice were dissected within 24 hours of birth. All animal work was approved by the North Carolina State University (NCSU) Institutional Animal Care and Use Committee, under protocol 16-045-B. All experiments were conducted in accordance with the Guiding Principles in the Use of Animals in Toxicology. Frozen whole brains obtained from four 0 ppm and four 50 ppm newborn female BxC pups representing four litters per exposure group were pulverized using a hammer and liquid nitrogen. 7-10 mg of tissue was then used to extract DNA and RNA simultaneously using the AllPrep DNA/RNA/miRNA kit (Qiagen, 80204). RNA was extracted using the recommended protocol for fatty tissues. RNA and DNA were quantified using a Nanodrop 2000. RNA purity and size integrity were determined at the NCSU Genomic Sciences Laboratory (GSL) using an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Chip (Agilent Technologies). Results: We identified 15 significantly differentially expressed genes (DEGs) that aligned to both the B and C genomes. Conclusions: These 15 DEGs (and subsequent confirmatory qRT-PCRs on the 8 samples sequenced here plus an additional Cd dose and samples) suggest altered onset of myelination throughout the whole brain, as well as aberrant Hox gene expression due to maternal Cd exposure.

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Quantitative Proteomic and Metabolomic Profiling Reveals Altered Mitochondrial Metabolism and Folate Biosynthesis Pathways in the Aging Drosophila Eye.

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