Similarities of developmental gene expression changes in the brain between human and experimental animals: rhesus monkey, mouse, Zebrafish, and Drosophila

Abstract

Aim Experimental animals, such as non-human primates (NHPs), mice, Zebrafish, and Drosophila, are frequently employed as models to gain insights into human physiology and pathology. In developmental neuroscience and related research fields, information about the similarities of developmental gene expression patterns between animal models and humans is vital to choose what animal models to employ. Here, we aimed to statistically compare the similarities of developmental changes of gene expression patterns in the brains of humans with those of animal models frequently used in the neuroscience field. Methods The developmental gene expression datasets that we analyzed consist of the fold-changes and P values of gene expression in the brains of animals of various ages compared with those of the youngest postnatal animals available in the dataset. By employing the running Fisher algorithm in a bioinformatics platform, BaseSpace, we assessed similarities between the developmental changes of gene expression patterns in the human (Homo sapiens) hippocampus with those in the dentate gyrus (DG) of the rhesus monkey (Macaca mulatta), the DG of the mouse (Mus musculus), the whole brain of Zebrafish (Danio rerio), and the whole brain of Drosophila (D. melanogaster). Results Among all possible comparisons of different ages and animals in developmental changes in gene expression patterns within the datasets, those between rhesus monkeys and mice were highly similar to those of humans with significant overlap P-value as assessed by the running Fisher algorithm. There was the highest degree of gene expression similarity between 40–59-year-old humans and 6–12-year-old rhesus monkeys (overlap P-value = 2.1 × 10− 72). The gene expression similarity between 20–39-year-old humans and 29-day-old mice was also significant (overlap P = 1.1 × 10− 44). Moreover, there was a similarity in developmental changes of gene expression patterns between 1–2-year-old Zebrafish and 40–59-year-old humans (Overlap P-value = 1.4 × 10− 6). The overlap P-value of developmental gene expression patterns between Drosophila and humans failed to reach significance (30 days Drosophila and 6–11-year-old humans; overlap P-value = 0.0614). Conclusions These results indicate that the developmental gene expression changes in the brains of the rhesus monkey, mouse, and Zebrafish recapitulate, to a certain degree, those in humans. Our findings support the idea that these animal models are a valid tool for investigating the development of the brain in neurophysiological and neuropsychiatric studies.

Forebrain-specific conditional calcineurin deficiency induces dentate gyrus immaturity and hyper-dopaminergic signaling in mice

“…Genes (or transcripts) with absolute fold change > 1.2 and P‐value < 0.05 (without correction for multiple testing) were imported to the web‐based bioinformatics tool BaseSpace (Illumina, San Diego, CA; https://basespace.illumina.com ) [ 59 ] according to the manufacturer's instructions. Subsequently, the gene expression patterns of the two given gene sets were statistically compared using BaseSpace [ 17 , 60 , 61 ]. Using the bioinformatics tool, similarities were examined using the Running Fisher algorithm, a nonparametric rank‐based statistical method, in which information regarding the rank based on the absolute value of fold change and the direction of gene expression changes within each gene set was considered [ 59 ].…”

Exploitation of In Vivo-Emulated In Vitro System in Advanced Food Science

“…Daily food can bring dual effects, one is essential nutrition, and the other may be acute or chronic toxicity. Various toxicological models have been developed such as mice, rats, monkeys, Caenorhabditis elegans , zebra fish ( Danio rerio ) and Drosophila melanogaster . , These in vivo models are characterized as referable to human, sensitive, specific to some typical functions, genetic modifiable, whereas these models also face the obstacles including ethic approval, long time-consuming, discrepant genetic background, differential homology and complicate experimental operation. IVE systems have been vividly developed and rapidly evolved in recent decade, and they are adopted mainly to detect the possible toxicity of food ingredients, food additives and food pollutions.…”

Decoding morphogen patterning of human neural organoids with a multiplexed single-cell transcriptomic screen

“…Morphogens are secreted from distinct locations in the developing neuroepithelium and govern neural regionalization in part by establishing gradients that instruct compartmentalization into multiple domains on the anteroposterior and dorso-ventral axes [1][2][3] . Current knowledge of CNS regionalization mostly originates from studies using non-human animal models with divergent cytoarchitecture, cell behavior and gene expression patterns compared to humans [4][5][6][7] . Research on human tissue has been hampered by largely unattainable primary samples and ethical considerations, however the advent of stem cellbased neural differentiation methods has enabled the study of human-specific developmental features in vitro [6][7][8][9][10][11][12] .…”