Identification and expression patterns of members of the protease‐activated receptor (par) gene family during zebrafish development

Protease‐activated receptors (PARs) play critical roles in hemostasis in vertebrates including zebrafish. However, the zebrafish gene classification appears to be complex, and the expression patterns of par genes are not established. Based on analyses of genomic organization, phylogenetics, protein primary structure, and protein internalization, we report the identification of four zebrafish PARs: par1, par2a, par2b, and par3. This classification differs from one reported previously. We also show that these genes have distinct spatiotemporal expression profiles in embryos and larvae, with par1, par2a, and par2b expressed maternally and ubiquitously during gastrula stages and their expression patterns refined at later stages, and par3 expressed only in 3‐day‐old larvae. Notably, the expression patterns of zebrafish par1 and par2b resemble those of their mammalian counterparts, suggesting that receptor function is conserved among vertebrates. This conservation is supported by our findings that Par1 and Par2b are internalized following exposure to thrombin and trypsin, respectively. Developmental Dynamics, 2011. © 2010 Wiley‐Liss, Inc.     

Expression of strawberry notch family genes during zebrafish embryogenesis

Our previous study suggested a possible role for Sbno1, a mouse homologue of strawberry notch gene during brain development. In this report, we cloned the zebrafish homologues of sbno, and examined their expression pattern during embryogenesis by whole‐mount in situ hybridization. Zebrafish have three sbno genes: one Sbno1 homologue and two Sbno2 homologues, sbno2a and sbno2b. We observed that the expression of sbno1 and sbno2a was initially ubiquitous and gradually became predominant in the central nervous system as development progressed. The expression of sbno2b was observed in non‐neural tissues in contrast to the other two genes. sbno1 and sbno2a exhibited higher expression in distinct regions within the nervous system of pharyngula‐stage embryos, suggesting possible differing roles for sbno1 and sbno2a during later stages of embryogenesis. Together, the observed gene expression patterns suggest an important role of sbno‐family genes during development of the vertebrate central nervous system. Developmental Dynamics 239:1789–1796, 2010. © 2010 Wiley‐Liss, Inc.     

An ultrastructural and immunohistochemical study of elastofibroma: CD 34, MEF-2, prominin 2 (CD133), and factor XIIIa-positive proliferating fibroblastic stromal cells connected by Cx43-type gap junctions

Elastofibromas have been described as ill-defined tumors, composed of fibroblastic stromal cells and a dense collagenous stroma. A total of 5 elastofibromas from 4 Japanese patients were examined by ultrastructural and immunohistochemical methods. The proliferating fibroblastic stromal cells in the lesion showed Cx43-type gap junctions, isolated cilia, prominent nuclear fibrous laminae, and primitive cellular junctions with incomplete laminae. The active proliferating fibroblastic cells showed positive staining for vimentin, CD34, factor XIIIa, prominin 2 (CD133), and MEF 2. Conspicuous cell-to-matrix interactions were observed with abnormally unique elastins, collagens (type I, III, and IV), laminin, fibronectin, and amorphous extracellular matrix (GAGs; glycosaminoglycans). As for the origin of elastofibromas, the tumors in the present study were suggested to arise from subscapular or periosteal connective tissue, but further revealed some similarities to other tissues, such as human skin dermal tissue, as exemplified by the presence of an abundance of type I and III collagen, CD34/factor XIIIa-expressing stromal fibroblast-like cells, amorphous extracellular matrix, and a unique abnormal elastin. The elastofibromas might have arisen from stromal stem cell candidate populations of stromal fibroblastic cells (CD34⁺, MEF2⁺, prominin 2(CD133)⁺, and factor XIIIa⁺).     

miR‐29b and miR‐125a regulate podoplanin and suppress invasion in glioblastoma

Glioblastoma is the most frequent and malignant brain tumor, characterized by an elevated capacity for cellular proliferation and invasion. Recently, it was demonstrated that podoplanin membrane sialo‐glycoprotein encoded by PDPN gene is over‐expressed and related to cellular invasion in astrocytic tumors; however the mechanisms of regulation are still unknown. MicroRNAs are noncoding RNAs that regulate gene expression and several biological processes and diseases, including cancer. Nevertheless, their roles in invasion, proliferation, and apoptosis of glioblastoma are not completely understood. In this study, we focused on miR‐29b and miR‐125a, which were predicted to regulate PDPN, and demonstrated that these microRNAs directly target the 3′ untranslated region of PDPN and inhibit invasion, apoptosis, and proliferation of glioblastomas. Furthermore, we report that miR‐29b and miR‐125a are downregulated in glioblastomas and also in CD133‐positive cells. Taken together, these results suggest that miR‐29b and miR‐125a represent potential therapeutic targets in glioblastoma. © 2010 Wiley‐Liss, Inc.     

Differential expression of neuroligin genes in the nervous system of zebrafish

The establishment and maturation of appropriate synaptic connections is crucial in the development of neuronal circuits. Cellular adhesion is believed to play a central role in this process. Neuroligins are neuronal cell adhesion molecules that are hypothesized to act in the initial formation and maturation of synaptic connections. In order to establish the zebrafish as a model to investigate the in vivo role of Neuroligin proteins in nervous system development, we identified the zebrafish orthologs of neuroligin family members and characterized their expression. Zebrafish possess seven neuroligin genes. Synteny analysis and sequence comparisons show that NLGN2, NLGN3, and NLGN4X are duplicated in zebrafish, but NLGN1 has a single zebrafish ortholog. All seven zebrafish neuroligins are expressed in complex patterns in the developing nervous system and in the adult brain. The spatial and temporal expression patterns of these genes suggest that they occupy a role in nervous system development and maintenance. Developmental Dynamics 239:703–714, 2010. © 2010 Wiley‐Liss, Inc.     

Expression and retinoic acid regulation of the zebrafish nr2f orphan nuclear receptor genes

Background : The vertebrate nuclear receptor subfamily 2, group f (nr2f) genes encode orphan receptors that have the capacity to act as negative regulators of retinoic acid (RA) signaling. Results : We describe embryonic and larval expression of four of the six zebrafish nr2f genes, nr2f1a, nr2f1b, nr2f2, and nr2f5. These genes show highly regulated patterns of expression within the central nervous system, including in the developing hindbrain, as well as in the mesoderm and endoderm. We also investigated the role of RA and fibroblast growth factor (Fgf) signaling in regulating early nr2f gene expression. RA is not required for nr2f expression in the hindbrain; however, exogenous RA can repress this expression. Conversely, we find that RA positively regulates nr2f1a expression in trunk endoderm and mesoderm. Fgf signaling is not required for nr2f expression onset in the hindbrain; however, it may play a role in maintaining rhombomere‐specific expression. Conclusions : We report detailed expression analysis of four nr2f genes in all three germ layers. The onset of nr2f expression in the hindbrain does not require RA or Fgf signals. Our finding that RA positively regulates nr2f1a expression in the trunk supports the possibility that Nr2fs function in a negative feedback loop to modulate RA signaling in this region. Developmental Dynamics 241:1603–1615, 2012. © 2012 Wiley Periodicals, Inc.     

Differential expression,alternative splicing,and adhesive properties of the zebrafish δ1-protocadherins

Protocadherins comprise the largest family within the cadherin superfamily of cell surface receptors. Here, we characterize the δ1-protocadherin subfamily during the development of the zebrafish nervous system. In zebrafish, there are five δ1-protocadherins: pcdh1a, pcdh1b, pcdh7a, pcdh7b, and pcdh9. Each protocadherin gene is highly homologous to its human ortholog. While the expression pattern in the developing CNS is similar for each δ1-protocadherin, with labeling observed in all major subdivisions, the detailed patterns are distinct. In addition, we provide evidence for alternative splicing of the pcdh7b and pcdh9 genes, resulting in variation in their respective cytoplasmic domains. As protocadherins are widely regarded to act as cell adhesion molecules, we used in vitro assays of δ1-pcdh ectodomains to directly test their adhesive properties. We found no evidence for calcium-dependent, homophilic adhesion, contrasting sharply with the behavior of classical cadherins.     

Loss of adenomatous polyposis coli (apc) results in an expanded ciliary marginal zone in the zebrafish eye

The distal region of neural retina (ciliary marginal zone [CMZ]) contains stem cells that produce non‐neural and neuronal progenitors. We provide a detailed gene expression analysis of the eyes of apc mutant zebrafish where the Wnt/β‐catenin pathway is constitutively active. Wnt/β‐catenin signaling leads to an expansion of the CMZ accompanied by a central shift of the retinal identity gene sox2 and the proneural gene atoh7. This suggests an important role for peripheral Wnt/β‐catenin signaling in regulating the expression and localization of neurogenic genes in the central retina. Retinal identity genes rx1 and vsx2, as well as meis1 and pax6a act upstream of Wnt/β‐catenin pathway activation. Peripheral cells that likely contain stem cells can be identified by the expression of follistatin, otx1, and axin2 and the lack of expression of myca and cyclinD1. Our results introduce the zebrafish apc mutation as a new model to study signaling pathways regulating the CMZ. Developmental Dynamics 239:2066–2077, 2010. © 2010 Wiley‐Liss, Inc.     

Dynamic miRNA expression patterns during retinal regeneration in zebrafish: Reduced dicer or miRNA expression suppresses proliferation of Müller Glia‐derived neuronal progenitor cells

Background: Adult zebrafish spontaneously regenerate their retinas after damage. Although a number of genes and signaling pathways involved in regeneration have been identified, the exact mechanisms regulating various aspects of regeneration are unclear. microRNAs (miRNAs) were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration, we knocked down the expression of Dicer in retinas prior to light‐induced damage. Reduced Dicer expression significantly decreased the number of proliferating Müller glia‐derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in neuronal progenitor cell proliferation, we collected retinas at different stages of light damage and performed small RNA high‐throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. We then knocked down five different miRNAs that increased in expression and assessed the effects on retinal regeneration. Reduction of miR‐142b and miR‐146a expression significantly reduced INL proliferation at 51h of light treatment, while knockdown of miR‐7a, miR‐27c, and miR‐31 expression significantly reduced INL proliferation at 72h of constant light. Conclusions: miRNAs exhibit dynamic expression profiles during retinal regeneration and are necessary for neuronal progenitor cell proliferation. Developmental Dynamics 243:1591–1605, 2014. © 2014 The Authors. Developmental Dynamics published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists     

Invasion and EMT-associated genes are up-regulated in B viral hepatocellular carcinoma with high expression of CD133-human and cell culture study

Hepatocellular carcinomas (HCCs) with expression of stem/progenitor cell markers including CD133 have been reported to have more aggressive biological behavior, and epithelial–mesenchymal transition (EMT), closely related invasion, has been suggested to generate cancer stem cells. To elucidate biological characteristics of HCCs expressing CD133, we evaluated migration assay and the mRNA expression levels of CD133, invasion-associated genes [urokinase plasminogen activator receptor (uPAR), villin 2 (VIL2), and MMP1 and MMP2], and EMT regulators (Snail, Slug, Twist, E-cadherin, and N-cadherin) by real-time PCR in HCC cell lines including HepG2, Hep3B, Huh7, PLC/RFP/6, SNU423, SNU449, and SNU475. Same genes and pathological features were also investigated in 49 samples of hepatitis B virus-related human HCCs. In all HCC cell lines studied, CD133-positive cells showed higher cell migration activity and up-regulated invasion- and EMT-associated genes with increased N-cadherin and decreased E-cadherin expressions compared to CD133-negative cells. The human HCCs were divided into the CD133-high group (top 40%) and the CD133-low group (bottom 40%) according to the level of CD133 mRNA. The CD133-high group showed relatively frequent vascular invasion and significantly higher expression of invasion-associated genes [uPAR (p = 0.002), MMP1 (p = 0.01), and MMP2 (p = 0.003)] and EMT regulators [Snail (p = 0.002) and Twist (p = 0.0003)] compared to the CD133-low group. In conclusion, our results suggest that there is a subtype of HCC with high expression of CD133, which might have more invasive characteristics by up-regulation of invasion-associated genes and EMT-associated genes.     

Identification and expression of voltage‐gated calcium channel β subunits in Zebrafish

Voltage‐gated calcium channels (VGCC) play important roles in electrically excitable cells and embryonic development. The VGCC β subunits are essential for membrane localization of the channel and exert modulatory effects on channel functions. In mammals, the VGCC β subunit gene family contains four members. In zebrafish, there appear to be seven VGCC β subunits including the previously identified β1 subunit. cDNAs for six additional VGCC β subunit homologs were identified in zebrafish, their chromosomal locations determined and their expression patterns characterized during embryonic development. These six genes are primarily expressed in the nervous system with cacnb4a also expressed in the developing heart. Sequence homology, genomic synteny and expression patterns suggest that there are three pairs of duplicate genes for β2, β3, and β4 in zebrafish with distinct expression patterns during embryonic development. Developmental Dynamics 237:3842–3852, 2008. © 2008 Wiley‐Liss, Inc.     

Conservation,expression, and knockdown of zebrafish plxnb2a and plxnb2b

In mice lacking Plexin B2, a receptor of the axon guidance molecules Semaphorin 4C and Semaphorin 4D, the closure of the neural tube and structural organization of the cerebellum are severely impaired. We cloned two Plexin B2 orthologs, plxnb2a and plxnb2b, in zebrafish, which is a widely used model for the development of the vertebrate central nervous system (CNS). The predicted proteins, Plexin B2a and Plexin B2b, contain all the conserved and functional domains of the plexin B‐subfamily. During embryonic development, plxnb2a is expressed, e.g., in pharyngeal arches while plxnb2b expression is more confined to neuronal structures like the cerebellum. However, both plxnb2a and plxnb2b are expressed at the midbrain–hindbrain boundary, in the otic vesicles, facial ganglia, and pectoral fins. Knockdown of both plxnb2a and plxnb2b simultaneously (>95% and 45%, respectively) resulted in normal CNS structure, axon guidance and swimming performance of the morphants. Developmental Dynamics 239:2722–2734, 2010. © 2010 Wiley‐Liss, Inc.     

Zebrafish cx30.3: Identification and characterization of a gap junction gene highly expressed in the skin

We have identified and characterized a zebrafish connexin, Cx30.3. Sequence similarity analyses suggested that Cx30.3 was orthologous to both mammalian Cx26 and Cx30, known to play important roles in the skin and inner ear of mammals. Analysis of mRNA expression showed that Cx30.3 was present in early embryos, and was highly abundant in skin, but also detected in other tissues including fins, inner ear, heart, and the retina. Injection of Cx30.3 cRNA into Xenopus oocytes elicited robust intercellular coupling with voltage gating sensitivity similar to mammalian Cx26 and Cx30. The similarities in functional properties and expression patterns suggest that Cx30.3, like mammalian Cx26 and Cx30, may play a significant role in skin development, hearing, and balance in zebrafish. Thus, zebrafish could potentially serve as an excellent model to study disorders of the skin and deafness that result from human connexin mutations. Developmental Dynamics 239:2627–2636, 2010. © 2010 Wiley‐Liss, Inc.