Alteration of gene expression by alcohol exposure at early neurulation.
- Authors
- Zhou, Feng C; Zhao, Qianqian; Liu, Yunlong; Goodlett, Charles R; Liang, Tiebing; McClintick, Jeanette N; Edenberg, Howard J; Li, Lang
- Year
- 2011
- Journal
- BMC genomics
- PMID
- 21338521
- DOI
- 10.1186/1471-2164-12-124
- PMCID
- PMC3056799
BACKGROUND: We have previously demonstrated that alcohol exposure at early neurulation induces growth retardation, neural tube abnormalities, and alteration of DNA methylation. To explore the global gene expression changes which may underline these developmental defects, microarray analyses were performed in a whole embryo mouse culture model that allows control over alcohol and embryonic variables. RESULT: Alcohol caused teratogenesis in brain, heart, forelimb, and optic vesicle; a subset of the embryos also showed cranial neural tube defects. In microarray analysis (accession number GSM9545), adopting hypothesis-driven Gene Set Enrichment Analysis (GSEA) informatics and intersection analysis of two independent experiments, we found that there was a collective reduction in expression of neural specification genes (neurogenin, Sox5, Bhlhe22), neural growth factor genes [Igf1, Efemp1, Klf10 (Tieg), and Edil3], and alteration of genes involved in cell growth, apoptosis, histone variants, eye and heart development. There was also a reduction of retinol binding protein 1 (Rbp1), and de novo expression of aldehyde dehydrogenase 1B1 (Aldh1B1). Remarkably, four key hematopoiesis genes (glycophorin A, adducin 2, beta-2 microglobulin, and ceruloplasmin) were absent after alcohol treatment, and histone variant genes were reduced. The down-regulation of the neurospecification and the neurotrophic genes were further confirmed by quantitative RT-PCR. Furthermore, the gene expression profile demonstrated distinct subgroups which corresponded with two distinct alcohol-related neural tube phenotypes: an open (ALC-NTO) and a closed neural tube (ALC-NTC). Further, the epidermal growth factor signaling pathway and histone variants were specifically altered in ALC-NTO, and a greater number of neurotrophic/growth factor genes were down-regulated in the ALC-NTO than in the ALC-NTC embryos. CONCLUSION: This study revealed a set of genes vulnerable to alcohol exposure and genes that were associated with neural tube defects during early neurulation.
Alcohol causes dysmorphology of growing embryos. Control embryos (a), Alcohol-treated (b-f). There are many dysmorphologies including microencephaly of forebrain (b, c, f), failure of closure of midbrain (mb; c) or hindbrain (hb; f), dysmorphic optical vesicle (optic; d), flex tail (ft; e) in caudal neural tube, delay formation of heart (H) chamber (b) and occasional detachment of epicardium (epic; b and e), neural tube opening at midbrain (mb; c, arrowheads) and hindbrain (hb; f, arrowheads) in the alcohol group. Majority of the brain vesicles in alcohol-treated group were closed (ALC-NTC; b, e). Approximately 30% of the embryos were found with a neural tube opening (ALC-NTO), usually in the head fold. Scale bars: a, b, c, e, f = 0.05mm; d = 0.25 mm.
LLM interpretation
This figure consists of six microscopy images (a-f) comparing the morphology of control embryos to alcohol-treated embryos. The control embryo (a) shows normal development, while alcohol-treated embryos exhibit various dysmorphologies, including microencephaly of the forebrain (fb), failure of neural tube closure at the midbrain (mb) and hindbrain (hb) indicated by arrowheads (c, f), and a flexed tail (ft) (e). Specific labels identify the optic vesicle (optic), heart chamber (H), and epicardium (epic), with scale bars provided for each panel.
The red blood vessels were less distinguishable in the yolk sac (arrow, left) and embryo (arrow, right) in the alcohol-treated group as compared with those of the Control. All embryos examined for red blood vessels had active heart beat at the termination of experiment.
LLM interpretation
This figure consists of microscopy images comparing embryos and yolk sacs from a Control group and an Alcohol-treated group. In the Control group, red blood vessels are visible in the yolk sac and embryo, indicated by light blue arrows. In contrast, the Alcohol-treated group shows a reduction in the visibility and distinguishability of these red blood vessels.
Hierarchical clustering by arrays in Experiment 1 and Experiment 2.
LLM interpretation
This figure presents two hierarchical clustering heatmaps for Experiment 1 and Experiment 2. The heatmaps display gene expression patterns (indicated by red and green colors) across different sample groups, including "CONTROL" and various "ALC/NTC" or "ALC/NTO" conditions. In both experiments, the dendrograms at the top indicate that the control samples cluster together separately from the treated samples.
Illustration of Gene Set Enrichment Analysis (GSEA) informatics with neurotrophic factor related gene set. (Left panel) Profile of the running enrichment score (ES) and positions of a prominent neurotrophic factor related gene set, GO:0040007: Growth, on the rank ordered list GSEA output for the comparison ALC vs. CONTROL. This test is a one-way test, i.e. whether gene expression is higher in control than in ALC. The x-axis lists all the genes ranked based on their associations with phenotype, i.e. the comparison ALC vs. CONTROL. The blue vertical bars indicate candidate genes in the target gene set. The ES profile records the cumulative score of the gene ranks from the target gene set. If a majority of gene ranks from the candidate gene set are high (i.e. toward the start of ranking) compared to the rest of genes, the cumulative ranking score (profile) will have a high peak, suggesting a significant enrichment of this gene set. The statistical significances (p-value) were calculated based on the height of this peak through a permutation test (p-value = 0.010 in Experiment 1 and 0.005 in Experiment 2). (Right panel) The significant genes (enriched in control) are determined by the position of the peak of the profile. There are 21 candidate genes up to this peak position which are claimed as significant. They are plotted in the Heatmap (green means high expression level, and red means low expression level) in Experiment 2.
LLM interpretation
This figure consists of a Gene Set Enrichment Analysis (GSEA) plot (left) and a corresponding heatmap (right) comparing ALC vs. CONTROL groups. The GSEA plot shows a positive enrichment score (ES) profile for the "Growth" gene set (GO:0040007), with blue vertical bars indicating the distribution of candidate genes across the ranked list. The heatmap displays the expression levels of 21 significant genes, where green indicates high expression and red indicates low expression, showing a general trend of higher expression in the CONTROL samples compared to the ALC samples.
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