Ultrastructural localization of ependymins in the endomeninx of the brain of the rainbow trout: possible association with collagen fibrils of the extracellular matrix

How to apply the broad toolbox of correlative light and electron microscopy to address a specific biological question

Correlative light and electron microscopy (CLEM) is an approach that combines the strength of multiple imaging techniques to obtain complementary information about a given specimen. The "toolbox" for CLEM is broad, making it sometimes difficult to choose an appropriate approach for a given biological question. In this chapter, we provide experimental details for three CLEM approaches that can help the interested reader in designing a personalized CLEM strategy for obtaining ultrastructural data by using transmission electron microscopy (TEM). First, we describe chemical fixation of cells grown on a solid support (broadest approach). Second, we apply high-pressure freezing/freeze substitution to describe cellular ultrastructure (cryo-immobilization approach). Third, we give a protocol for a ultrastructural labeling by immuno-electron microscopy (immuno-EM approach). In addition, we also describe how to overlay fluorescence and electron microscopy images, an approach that is applicable to each of the reported different CLEM strategies. Here we provide step-by step descriptions prior to discussing possible technical problems and variations of these three general schemes to suit different models or different biological questions. This chapter is written for electron microscopists that are new to CLEM and unsure how to begin. Therefore, our protocols are meant to provide basic information with further references that should help the reader get started with applying a tailored strategy for a specific CLEM experiment.

Molecular evolution of the ependymin-related gene epdl2 in African weakly electric fish

Gene duplication and subsequent molecular evolution can give rise to taxon-specific gene specializations. In previous work, we found evidence that African weakly electric fish (Mormyridae) may have as many as three copies of the epdl2 gene, and the expression of two epdl2 genes is correlated with electric signal divergence. Epdl2 belongs to the ependymin-related family (EPDR), a functionally diverse family of secretory glycoproteins. In this study, we first describe vertebrate EPDR evolution and then present a detailed evolutionary history of epdl2 in Mormyridae with emphasis on the speciose genus Paramormyrops. Using Sanger sequencing, we confirm three apparently functional epdl2 genes in Paramormyrops kingsleyae. Next, we developed a nanopore-based amplicon sequencing strategy and bioinformatics pipeline to obtain and classify full-length epdl2 gene sequences (N = 34) across Mormyridae. Our phylogenetic analysis proposes three or four epdl2 paralogs dating from early Paramormyrops evolution. Finally, we conducted selection tests which detected positive selection around the duplication events and identified ten sites likely targeted by selection in the resulting paralogs. These sites' locations in our modeled 3D protein structure involve four sites in ligand binding and six sites in homodimer formation. Together, these findings strongly imply an evolutionary mechanism whereby epdl2 genes underwent selection-driven functional specialization after tandem duplications in the rapidly speciating Paramormyrops. Considering previous evidence, we propose that epdl2 may contribute to electric signal diversification in mormyrids, an important aspect of species recognition during mating.

Aging Fibroblasts Adversely Affect Extracellular Matrix Formation via the Senescent Humoral Factor Ependymin-Related Protein 1

Skin senescence is characterized by a decrease in extracellular matrix and the accumulation of senescent fibroblasts in the dermis, and their secretion of humoral factors. Ependymin-related protein 1 (EPDR1) is involved in abnormal fibroblast metabolism and collagen deposition, however, its relation to skin aging is unclear. We investigated whether and how EPDR1 is involved in age-related dermal deterioration. When young dermal fibroblasts and senescent cells were co-cultured in a semipermeable membrane separation system, the young fibroblasts showed decreased gene expression of collagen type I α1 chain (COL1A1) and elastin, and increased expression of matrix metalloproteinase (MMP)1 and MMP3. Senescence marker expression and EPDR1 production were increased in the culture medium of senescent cells. Treatment of young fibroblasts with recombinant EPDR1, enhanced matrix-related gene expression and suppressed COL1A1 expression, whereas EPDR1 knockdown had the opposite effects. EPDR1 gene and protein expression were increased in aged skin, compared to young skin. These results suggest that senescent cells affect nearby fibroblasts, in part through EPDR1 secretion, and exert negative effects on matrix production in the dermis. These results may lead to the discovery of potential candidate targets in the development of skin anti-aging therapies.

The evolution of ependymin-related proteins

Background

Ependymins were originally defined as fish-specific secreted glycoproteins involved in central nervous system plasticity and memory formation. Subsequent research revealed that these proteins represent a fish-specific lineage of a larger ependymin-related protein family (EPDRs). EPDRs have now been identified in a number of bilaterian animals and have been implicated in diverse non-neural functions. The recent discoveries of putative EPDRs in unicellular holozoans and an expanded EPDR family with potential roles in conspecific communication in crown-of-thorns starfish suggest that the distribution and diversity of EPDRs is significantly broader than currently understood.

Results

We undertook a systematic survey to determine the distribution and evolution of EPDRs in eukaryotes. In addition to Bilateria, EPDR genes were identified in Cnidaria, Placozoa, Porifera, Choanoflagellatea, Filasterea, Apusozoa, Amoebozoa, Charophyta and Percolozoa, and tentatively in Cercozoa and the orphan group Malawimonadidae. EPDRs appear to be absent from prokaryotes and many eukaryote groups including ecdysozoans, fungi, stramenopiles, alveolates, haptistans and cryptistans. The EPDR family can be divided into two major clades and has undergone lineage-specific expansions in a number of metazoan lineages, including in poriferans, molluscs and cephalochordates. Variation in a core set of conserved residues in EPDRs reveals the presence of three distinct protein types; however, 3D modelling predicts overall protein structures to be similar.

Conclusions

Our results reveal an early eukaryotic origin of the EPDR gene family and a dynamic pattern of gene duplication and gene loss in animals. This research provides a phylogenetic framework for the analysis of the functional evolution of this gene family.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1306-y) contains supplementary material, which is available to authorized users.

Labeling of ultrathin resin sections for correlative light and electron microscopy

Correlative microscopy combines the versatility of the light microscope with the excellent spatial resolution of the electron microscope. Here, we describe fast and simple methods for correlative immunofluorescence and immunogold labeling on the very same ultrathin section. The protocols are demonstrated on sections of tissue samples embedded in the methacrylate Lowicryl K4M. Ultrathin sections are mounted on electron microscopy (EM) grids and stained simultaneously with fluorescent and gold markers. For the detection of primary antibodies, we applied either protein A gold or immunoglobulin G (IgG) gold in combination with secondary antibodies coupled to Alexa488 or Alexa555. Alternatively, the correlative marker FluoroNanogold was used, followed by silver enhancement. The samples have to be analyzed first at the light microscope and then in the transmission electron microscope (TEM), because the fluorescence is bleached by the electron beam. Labeled structures selected at the fluorescence microscope can be identified in the TEM and analyzed at high resolution. This way, fluorescent signals can be directly correlated to the corresponding subcellular structures in the area of interest.

Migration and site selection of Ornithodiplostomum ptychocheilus (Trematoda: Digenea) metacercariae in the brain of fathead minnows (Pimephales promelas)

The migration of subadult parasites to preferred sites within final hosts is well characterized. In contrast, the migration of larval stages of trematodes to specific sites within their second intermediate hosts is poorly understood. We used a serial necropsy approach to characterize the migration of Ornithodiplostomum ptychocheilus diplostomules from the point of cercarial penetration, to encystment within the outermost tissues of the brain of fathead minnows. Diplostomules utilized peripheral nerves to access the central nerve cord, or they used specific cranial nerves to directly access the brain. Within 3 h of exposure to cercariae, 46% of all diplostomules were observed within the medulla of the brain. Diplostomules subsequently utilized specific neural tracts to reach lateral regions of the outermost tissue layer of the optic lobes, the stratum marginale. Diplostomules remained in this layer during their 4-week growth phase, then shifted site to the adjacent meninges for encystment. Characterization of a habitat shift for developing versus encysted metacercariae helps explain the results of previous ecological studies that document transient changes in the effects of metacercariae on the surivival, behaviour, and anti-parasite defences of infected fish.

MERP1: a mammalian ependymin-related protein gene differentially expressed in hematopoietic cells

We have utilized differential display polymerase chain reaction to investigate the gene expression of hematopoietic progenitor cells from adult bone marrow and umbilical cord blood. A differentially expressed gene was identified in CD34+ hematopoietic progenitor cells, with low expression in CD34- cells. We have obtained the full coding sequence of this gene which we designated human mammalian ependymin-related protein 1 (MERP1). Expression of MERP1 was found in a variety of normal human tissues, and is 4- and 10-fold higher in adult bone marrow and umbilical cord blood CD34+ cells, respectively, compared to CD34- cells. Additionally, MERP1 expression in a hematopoietic stem cell enriched population was down-regulated with proliferation and differentiation. Conceptual translation of the MERP1 open reading frame reveals significant homology to two families of glycoprotein calcium-dependant cell adhesion molecules: ependymins and protocadherins.

The novel ependymin related gene UCC1 is highly expressed in colorectal tumor cells

Normal cells differ from malignant tumor cells in the transcription levels of many different genes. Two colorectal tumor cell lines were compared with a normal colorectal cell line by differential display reverse transcription PCR to screen for tumor cell specific differentially transcribed genes. By this strategy the upregulation of a novel gene was detected designated as 'upregulated in colorectal cancer gene-1' (UCC1). The UCC1 gene transcript level is increased in cultured tumor cells and in two out of three analyzed colorectal tumor tissue specimens compared to normal cultured cells and to corresponding normal tissue samples. Remarkably, the UCC1 protein shows significant sequence similarity to the highly divergent piscine glycoproteins termed ependymins which are synthesized by leptomeningeal fibroblasts and secreted into the cerebrospinal fluid.

Desmosomal localization of beta-catenin in the skin of plakoglobin null-mutant mice

Plakoglobin, a protein belonging to the Armadillo-repeat gene family, is the only component that adherens junctions and desmosomes have in common. Plakoglobin null-mutant mouse embryos die because of severe heart defects and may exhibit an additional skin phenotype, depending on the genetic background. Lack of plakoglobin affects the number and structure of desmosomes, resulting in visible defects when cells are subjected to increasing mechanical stress, e.g. when embryonic blood starts circulating or during skin differentiation. By analysing plakoglobin-negative embryonic skin differentiation in more detail, we show here that, in the absence of plakoglobin, its closest homologue, beta-catenin, becomes localized to desmosomes and associated with desmoglein. This substitution may account for the relatively late appearance of the developmental defects seen in plakoglobin null-mutant embryos. beta-catenin cannot, however, fully compensate a lack of plakoglobin. In the absence of plakoglobin, there was reduced cell-cell adhesion, resulting in large intercellular spaces between keratinocytes, subcorneal acantholysis and necrosis in the granular layer of the skin. Electron microscopic analysis documented a reduced number of desmosomes, and those present lacked the inner dense plaque and had fewer keratin filaments anchored. Our analysis underlines the central role of plakoglobin for desmosomal assembly and function during embryogenesis.

TGF-beta1 and Ha-Ras collaborate in modulating the phenotypic plasticity and invasiveness of epithelial tumor cells

Metastasis of epithelial tumor cells can be associated with the acquisition of fibroblastoid features and the ability to invade stroma and blood vessels. Using matched in vivo and in vitro culture systems employing fully polarized, mammary epithelial cells, we report here that TGF-beta1 brings about these changes in Ras-transformed cells but not in normal cells. When grown in collagen gels in the absence of TGF-beta, both normal and Ras-transformed mammary epithelial cells form organ-like structures in which the cells maintain their epithelial characteristics. Under these conditions, treatment of normal cells with TGF-beta results in growth arrest. The same treatment renders Ras-transformed epithelial cells fibroblastoid, invasive, and resistant to growth inhibition by TGF-beta. After this epithelial-fibroblastoid conversion, the Ras-transformed cells start to secrete TGF-beta themselves, leading to autocrine maintenance of the invasive phenotype and recruitment of additional cells to become fibroblastoid and invasive. More important, this cooperation of activated Ha-Ras with TGF-beta1 is operative during in vivo tumorigenesis and, as in wound healing processes, is dependent on epithelial-stromal interactions.

Ependymins: meningeal-derived extracellular matrix proteins at the blood-brain barrier

Ependymins represent regeneration-responsive piscine glycoproteins and in many teleost fish they appear as the predominant cerebrospinal fluid constituents. Thus far, no homologous sequences have been characterized unambiguously in mammals. Sialic acid residues of the N-linked carbohydrate moiety of ependymins are responsible for their calcium-binding capacity. Ependymins from some species bear the L2/HNK-1 epitope typical of many cell adhesion molecules. After their synthesis in fibroblast-like cells of the inner endomeningeal layer, soluble ependymins are widely distributed via the cerebrospinal fluid system. Furthermore, ependymins presumably cross the intermediate endomeningeal barrier layer by way of a transcellular transport phenomenon (transcytosis). A bound form of ependymins is associated with collagen fibrils of the extracellular matrix typically found around cerebral blood vessels. Here, they might modulate the endothelial barrier function. Generally, ependymins are thought to represent a new class of possibly antiadhesive extracellular matrix proteins playing a role in specific cell contact phenomena (e.g., during regeneration).

Cranial meninges of goldfish: age-related changes in morphology of meningeal cells and accumulation of surfactant-like multilamellar bodies

In the optic tectum of goldfish, the outer, middle and inner layers of the endomeninx were evident in animals ranging in age from 1 month to several years. The outer layer in young animals consisted of closely overlapping cells with intertwined processes, whereas in the older animals it contained large extracellular spaces. The intermediate layer cells were always arranged in a single continuous layer, but in young animals they overlapped extensively with one another toward their edges whereas in the oldest animals they became extremely flat and non-overlapping. The inner layer included an outer tier of cells with their bases adhering to the intermediate layer, and an inner tier of cells detached from both the intermediate layer and the basal lamina overlying the brain parenchyma. Inner layer cells contained many large vacuoles that were in continuity with the extracellular space. With age, the extracellular space and the vacuolar system expanded, and the inner layer evolved into a meshwork of attenuated cytoplasmic processes embedded in the granular extracellular matrix. Another age-related feature was the accumulation adjacent to the basal lamina of uniform disc-shaped membranous structures, resembling multilamellar bodies of lung surfactant. These "disc bodies" were apparently generated by the coalescence of vesicles formed at the surface of the inner layer cells, possibly as a by-product of protein secretion by these cells.

Epithelial cell polarity in early Xenopus development

The Xenopus blastula consists of two morphologically distinct cell types. Polarized epithelial cells build up the embryonic surface and fence off an inner non-polarized cell population. We examined the establishment of this early functional cell diversification in the embryo by single cell analysis, in vitro cell culture, and transplantation experiments. Single blastomeres from a 64-cell embryo (1/64 cells) exhibit several features of polarized cells. The plasma membrane of 1/64 cells consists of an apical domain, which is inherited from the original egg membrane, and a basolateral domain derived from newly formed membrane during cleavage. These are inherent, cell-autonomous properties of the blastomeres, as they form and are maintained in blastomeres raised in the absence of any cell interactions in calcium free medium. Upon in vitro culture a single 1/64 cell gives rise to an aggregate of two different cell types. Cells carrying a part of the former egg membrane domain differentiate into polarized epithelial cells, whereas cells lacking this membrane domain are not polarized. These results demonstrate that the inclusion of the egg membrane, rather than external signals related to the position of a cell in the intact embryo, is required for the apical/basolateral differentiation of the surface epithelium. This view is supported by cell transplantation studies. A single 1/64 cell was implanted into the blastocoel of a stage 8 blastula embryo. The progeny of the implanted cell proliferate within the host embryo and split into two morphologically distinct populations with different cell behaviours. Cells incorporating a part of the egg membrane form coherent patches of polarized epithelial cell sheets in the interior of the host embryo. In contrast, cells lacking egg membrane do not exhibit any characteristics of polarized cells and eventually spread into different regions of the host embryo. Our results show that the egg membrane and/or components of the submembrane cortex play a determinative role in the formation of the blastula epithelium.

Immunolocalization of exoglycoproteins ("ependymins") in the goldfish brain

Exoglycoproteins (X-GPs) are a group of very abundant soluble glycoproteins in the goldfish brain. Immunostaining with polyclonal antisera to X-GPs revealed consistent perinuclear staining in the cells of the inner and intermediate layers of the leptomeninx, which is homologous to the pia-arachnoid. Immunolabelling was also prominent in the outer wall of capillaries, and in a variable population of 10-12 microns granular cells that appeared mainly near the ventricles and occasionally within the ventricles or under the meninges. In some cases, small and medium-sized lymphocytes were immunostained. Lymphocytes were sometimes associated with the granular cells, which may be hematogenous cells in transit toward the ventricles. The choroid plexus, saccus dorsalis, the roof of the third ventricle and Reissner's fiber showed strong immunostaining. The localization of the X-GPs suggests that they may contribute to maintenance of the blood-brain barrier or to regulation of immune function within the brain.

Ependymins and their potential role in neuroplasticity and regeneration: calcium-binding meningeal glycoproteins of the cerebrospinal fluid and extracellular matrix

1. Ependymins are unique, highly divergent secretory proteins of the fish endomeninx. Thus far, no homologous sequences have been characterized in mammals. 2. Soluble ependymins are the predominant constituents of the cerebrospinal fluid of many teleost fish. A bound form of these glycoproteins is associated with the extracellular matrix probably with collagen fibrils. The latter may be the functional form of ependymins. 3. Ependymins bind Ca2+ via N-linked sialic acid residues leading to a conformational transition. 4. The molecular function of ependymins seems to be related to cell contact phenomena involving the extracellular matrix. For example, adhesive or anti-adhesive interactions may possibly influence ingrowing axons.

Calcium binding to sialic acids and its effect on the conformation of ependymins

Soluble ependymins from the predominant protein constituents in the cerebrospinal fluid from many orders of teleost fish. Furthermore, these glycoproteins also exist in a bound form associated with the extracellular matrix. Ependymins are synthesized in meningeal fibroblasts. In goldfish, their synthesis is increased during the regeneration of the optic nerve and they share several characteristics with molecules involved in cell contact phenomena. In this study, we show by a calcium overlay technique that ependymins from goldfish and rainbow trout are able to bind 45Ca2+. However, nearly all of this Ca(2+)-binding capacity is lost after digestion with sialidase. Furthermore, circular-dichroism spectra from FPLC-purified rainbow trout ependymins have been recorded in the presence and absence of Ca2+. Below 250 nm, the CD spectrum showed a characteristic minimum of ellipticity at 217 nm typical of beta structures. This signal is independent of the Ca2+ concentration. In contrast, the complex signal at 250-310 nm mainly decreased with increasing Ca2+ concentration indicating changes in the environment of aromatic side chains.

Molecular analysis of ependymins from the cerebrospinal fluid of the orders Clupeiformes and Salmoniformes: no indication for the existence of an euteleost infradivision

Ependymins represent the predominant protein constituents in the cerebrospinal fluid of many teleost fish and they are synthesized in meningeal fibroblasts. Here, we present the ependymin sequences from the herring (Clupea harengus) and the pike (Esox lucius). A comparison of ependymin homologous sequences from three different orders of teleost fish (Salmoniformes, Cypriniformes, and Clupeiformes) revealed the highest similarity between Clupeiformes and Cypriniformes. This result is unexpected because it does not reflect current systematics, in which Clupeiformes belong to a separate infradivision (Clupeomorpha) than Salmoniformes and Cypriniformes (Euteleostei). Furthermore, in Salmoniformes the evolutionary rate of ependymins seems to be accelerated mainly on the protein level. However, considering these inconstant rates, neither neighbor-joining trees nor DNA parsimony methods gave any indication that a separate euteleost infradivision exists.