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Transcriptomic approaches for discovering regenerative and developmental regulatory networks in zebrafish
Zebrafish are capable of fully regenerating organs and tissue such as their caudal fin, which is similar to a human regrowing an arm or a leg. In contrast, most mammals including humans have a greatly reduced capacity for wound healing. The ability of zebrafish to undergo this regenerative process, called epimorphic regeneration, hinges on the capacity to form a blastema at the wound site. The blastema quickly recapitulates the developmental processes involved in complex tissue formation to restore lost or damaged tissue. One key mechanism for inducing blastema formation is global repression of genes involved in tissue differentiation and maintenance.
Induction of repressive factors, such as microRNAs (miRNAs), are involved in reprogramming cells during epimorphic regeneration. The upstream mechanism by which zebrafish undergo epimorphic regeneration remains elusive. Furthermore, while focus is shifting toward regulatory RNAs such as miRNAs, the full complement of their repressive activities is unknown. We took a transcriptomics approach to investigating epimorphic regeneration and fin development. Parallel sequencing of total RNA and small RNA samples was performed on regenerating fin tissue at 1 day post-amputation (dpa). Most miRNAs had increased expression, consistent with global repression of genes involved in cell specialization during de-differentiation. We identified predicted interactions between miRNAs and genes involved in transcriptional regulation, chromatin modification, and developmental signaling. miR-146a and miR-146b are anti-inflammatory miRNAs that were predicted to target eya4, which is involved in chromatin remodeling and innate immunity. miR-132-3p and miR-21 were predicted to cooperate in repression Bone morphogenic protein (BMP) signaling antagonists. Depletion of miR-489 and miR-92b-3p were predicted to be involved in expression of cell cycle regulators mycn and foxm1, as well as other transcription factors associated with regeneration. We also identified Hedgehog and Scatter factor signaling as possibly targets of miRNAs regulation during regeneration.
Next, we performed microarray analysis on tissue exposed to the glucocorticoid beclomethasone diproprionate (BDP). We identified cripto-1 as a highly upregulated gene flowing BDP exposure. Morpholino oligo knockdown of cripto-1 permitted regeneration during BDP exposure. We were able to phenocopy the effects of BDP exposure by exposing zebrafish to an Activin signaling inhibitor, SB431542. Promoter analysis identified binding sites for genes that were differentially expressed in our data. BDP exposure of murine embryonic stem cells confirmed that glucocorticoid-mediated induction of cripto-1 is conserved in mammals.
Finally, we investigated a unique caudal fin duplication, called x-fin, resulting from embryonic exposure an exogenous ligand of the aryl hydrocarbon receptor (AHR), benzo[k]fluoranthene (BkF). We determined that the phenotype is Ahr2-dependent. We also determined that it is independent of hepatic metabolism using a hepatocyte ablation model. RNA seq analysis of trunk tissue at four time points of revealed that BMP and Fibroblast growth factor (FGF) ligands were robustly induced. Enrichment analysis revealed similarities to fin regeneration processes as well as inflammation. Altogether, we leveraged transcriptomics as a useful tool for identifying mechanisms associated with tissue regeneration and development
Sox10 regulates enteric neural crest cell migration in the developing gut
Concurrent Sessions 1: 1.3 - Organs to organisms: Models of Human Diseases: abstract no. 1417th ISDB 2013 cum 72nd Annual Meeting of the Society for Developmental Biology, VII Latin American Society of Developmental Biology Meeting and XI Congreso de la Sociedad Mexicana de Biologia del Desarrollo. The Conference's web site is located at http://www.inb.unam.mx/isdb/Sox10 is a HMG-domain containing transcription factor which plays important roles in neural crest cell survival and differentiation. Mutations of Sox10 have been identified in patients with Waardenburg-Hirschsprung syndrome, who suffer from deafness, pigmentation defects and intestinal aganglionosis. Enteric neural crest cells (ENCCs) with Sox10 mutation undergo premature differentiation and fail to colonize the distal hindgut. It is unclear, however, whether Sox10 plays a role in the migration of ENCCs. To visualize the migration behaviour of mutant ENCCs, we generated a Sox10NGFP mouse model where EGFP is fused to the N-terminal domain of Sox10. Using time-lapse imaging, we found that ENCCs in Sox10NGFP/+ mutants displays lower migration speed and altered trajectories compared to normal controls. This behaviour was cell-autonomous, as shown by organotypic grafting of Sox10NGFP/+ gut segments onto control guts and vice versa. ENCCs encounter different extracellular matrix (ECM) molecules along the developing gut. We performed gut explant culture on various ECM and found that Sox10NGFP/+ ENCCs tend to form aggregates, particularly on fibronectin. Time-lapse imaging of single cells in gut explant culture indicated that the tightly-packed Sox10 mutant cells failed to exhibit contact inhibition of locomotion. We determined the expression of adhesion molecule families by qPCR analysis, and found integrin expression unaffected while L1-cam and selected cadherins were altered, suggesting that Sox10 mutation affects cell adhesion properties of ENCCs. Our findings identify a de novo role of Sox10 in regulating the migration behaviour of ENCCs, which has important implications for the treatment of Hirschsprung disease.postprin
Analysis of craniofacial defects in Six1/Eya1-associated Branchio-Oto-Renal Syndrome
Poster Session I - Morphogenesis: 205/B10117th ISDB 2013 cum 72nd Annual Meeting of the Society for Developmental Biology, 7th Latin American Society of Developmental Biology Meeting and 11th Congreso de la Sociedad Mexicana de Biologia del Desarrollo.Branchio-Oto-Renal (BOR) syndrome patients exhibit craniofacial and renal anomalies as well as deafness. BOR syndrome is caused by mutations in Six1 or Eya1, both of which regulate cell proliferation and differentiation. The molecular mechanism underlying the craniofacial and branchial arch (BA) defects in BOR syndrome is unclear. We have found that Hoxb3 is up-regulated in the second branchial arch (BA2) of Six1-/- mutants. Moreover, Hoxb3 over-expression in transgenic mice leads to BA abnormalities which are similar to the BA defects in Six1-/- or Eya1-/- mutants, suggesting a regulatory relationship among Six1, Eya1 and Hoxb3 genes. The aim of this study is to investigate the molecular mechanism underlying abnormal BA development in BOR syndrome using Six1 and Eya1 mutant mice. Two potential Six1 binding sites were identified on the Hoxb3 gene. In vitro and in vivo Chromatin IP assays showed that Six1 could directly bind to one of the sites specifically. Furthermore, using a chick in ovo luciferase assay we showed that Six1 could suppress gene expression through one of the specific binding sites. On the other hand, in Six1-/- mutants, we found that the Notch ligand Jag1 was up-regulated in BA2. Similarly, in Hoxb3 transgenic mice, ectopic expression of Jag1 could be also detected in BA2. To investigate the activation of Notch signaling pathway, we found that Notch intracellular domain (NICD), a direct indicator of Notch pathway activation, was up-regulated in BAs of Six1-/-; Eya1-/- double mutants. Our results indicate that Hoxb3 and Notch signaling pathway are involved in mediating the craniofacial defects of Six1/Eya1-associated Branchio-Oto-Renal Syndrome.postprin
Ageing in the zebrafish heart
PhD ThesisWith advancing age there is a progressive decline in the function of the heart. In humans reductions in stroke volume and cardiac output occurs often resulting in cardiac disease and subsequent death. The pathology found in the heart due to advancing age is attributed to a reduction in cardiomyocytes which causes cardiac dysfunction and heart disease, leading to heart failure. Zebrafish are a valuable tool in studying ageing and heart disease. As zebrafish age they gradually senesce. This is similar to humans and other mammals. However the response of the zebrafish heart to ageing has not been explored.
The zebrafish heart changes due to ageing, with increased fibrosis and ventricular wall thickness. I have established new assays to measure proliferation and apoptosis in zebrafish cardiomyocytes using multiplexing of thymidine analogues and cleaved caspase 3, respectively. Using these developed assays it was discovered that these changes may be caused by an observed increase in cardiomyocyte apoptosis. This was coupled with no change in cardiomyocyte proliferation. These changes may be mediated by an increase in natriuretic peptide expression. In response to exercise, cardiomyocyte proliferation increases signalled by increased gata4, nkx2.5, tbx5, and mef2c expression and a reduction of natriuretic peptide expression. In the long term these genetic and cellular changes in the heart in response to exercise may slow some of the pathological changes observed in the heart