Boyko AV et al. (2020), The Eupentacta fraudatrix transcriptome provide...

ECB-ART-48609

Sci Rep 2020 Jan 30;101:1522. doi: 10.1038/s41598-020-58470-0.

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The Eupentacta fraudatrix transcriptome provides insights into regulation of cell transdifferentiation.

Boyko AV , Girich AS , Tkacheva ES , Dolmatov IY .

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The holothurian Eupentacta fraudatrix is a unique organism for studying regeneration mechanisms. Moreover, E. fraudatrix can quickly restore parts of its body and entire organ systems, yet at the moment, there is no data on the participation of stem cells in the process. To the contrary, it has been repeatedly confirmed that this process is only due to the transformation of terminally differentiated cells. In this study, we examine changes in gene expression during gut regeneration of the holothurian E. fraudatrix. Transcriptomes of intestinal anlage of the three stages of regeneration, as well as the normal gut, were sequenced with an Illumina sequencer (San Diego, CA, USA). We identified 14,617 sea urchin protein homologs, of which 308 were transcription factors. After analysing the dynamics of gene expression during regeneration and the map of biological processes in which they participate, we identified 11 factors: Ef-EGR1, Ef-ELF, Ef-GATA3, Ef-ID2, Ef-KLF1/2/4, Ef-MSC, Ef-PCGF2, Ef-PRDM9, Ef-SNAI2, Ef-TBX20, and Ef-TCF24. With the exception of TCF24, they are all involved in the regeneration, development, epithelial-mesenchymal transition, and immune response in other animals. We suggest that these transcription factors may also be involved in the transdifferentiation of coelomic epithelial cells into enterocytes in holothurians.

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Genes referenced: elf2 LOC100887844 LOC100888304 LOC115919910 tbx20

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	Figure 1. Structure of gut on different stages of regeneration in holothurian Eupentacta fraudatrix. (A) Connective-tissue thickening on the edge of mesentery on day 3 post-evisceration (first stage). (B) Gut anlage on day 6 post-evisceration (second stage); arrow indicates site of migration of coelomic epithelial cells into connective-tissue thickening, asterisks show clusters inside the intestinal anlage. (C) Digestive tube on day 12 post-evisceration (third stage). bw â body wall, g â digestive tube, ga â gut anlage, gd â gonoduct, il â intestinal lining, m â mesentery.
	Figure 2. Correlation map of all RNA-seq samples (A) and gene expression correlation between RT-qPCR (y-axis) and RNA-seq (x-axis) data. (B) The squared Pearson correlation coefficient, p-value, and linear regression line for 5 genes are indicated on plot. (B) Each point on the plot (B) corresponds to the logarithm (base 2) of the fold change in the second or third stages of regeneration relative to the first stage.
	Figure 3. Venn diagrams for up-regulated and down-regulated DEGs.
	Figure 4. TPM expression values of the most likely candidates for the role of transdifferentiation regulators. All these TFs have a significant peak of expression at second stage of regeneration.
	Figure 5. Network of enrichment biological processes and pathways associated with the most likely candidates for the role of transdifferentiation regulators. Nodes represent biological process (gene set). Edges represent overlap between pair of gene sets. Node size and edge width depend on the number of genes. Node fill represents enrichment scores of terms at the second stage of regeneration relative to the first (right half) and third stages (left half), respectively. The color gradient represents an increase (red color) or decrease (blue color) in the level of expression (depend on the enrichment score) in the second stage, relative to the first or third. A block description is a block number, the number of terms, and the number of all and unique genes in a block. The full version of the network in Cytoscape format is represented in the Supplementary DataÂ S1.

References [+] :

Ahmed, Lung development, regeneration and plasticity: From disease physiopathology to drug design using induced pluripotent stem cells. 2018, Pubmed