Protocadherins: a large family of cadherin-related molecules in central nervous system

Regulation of neural circuit formation by protocadherins

The protocadherins (Pcdhs), which make up the most diverse group within the cadherin superfamily, were first discovered in the early 1990s. Data implicating the Pcdhs, including ~60 proteins encoded by the tandem Pcdha, Pcdhb, and Pcdhg gene clusters and another ~10 non-clustered Pcdhs, in the regulation of neural development have continually accumulated, with a significant expansion of the field over the past decade. Here, we review the many roles played by clustered and non-clustered Pcdhs in multiple steps important for the formation and function of neural circuits, including dendrite arborization, axon outgrowth and targeting, synaptogenesis, and synapse elimination. We further discuss studies implicating mutation or epigenetic dysregulation of Pcdh genes in a variety of human neurodevelopmental and neurological disorders. With recent structural modeling of Pcdh proteins, the prospects for uncovering molecular mechanisms of Pcdh extracellular and intracellular interactions, and their role in normal and disrupted neural circuit formation, are bright.

Genetic variants affecting equivalent protein family positions reflect human diversity

Members of diverse protein families often perform overlapping or redundant functions meaning that different variations within them could reflect differences between individual organisms. We investigated likely functional positions within aligned protein families that contained a significant enrichment of nonsynonymous variants in genomes of healthy individuals. We identified more than a thousand enriched positions across hundreds of family alignments with roles indicative of mammalian individuality, including sensory perception and the immune system. The most significant position is the Arginine from the Olfactory receptor “DRY” motif, which has more variants in healthy individuals than all other positions in the proteome. Odorant binding data suggests that these variants lead to receptor inactivity, and they are mostly mutually exclusive with other loss-of-function (stop/frameshift) variants. Some DRY Arginine variants correlate with smell preferences in sub-populations and all 2,504 humans studied contain a unique spectrum of active and inactive receptors. The many other variant enriched positions, across hundreds of other families might also provide insights into individual differences.

PCDH9 acts as a tumor suppressor inducing tumor cell arrest at G0/G1 phase and is frequently methylated in hepatocellular carcinoma

Tumor suppressor genes (TSGs) are frequently involved in the pathogenesis of hepatocellular carcinoma (HCC). The epigenetic and genetic alterations of a novel TSG‑protocadherin 9 (PCDH9) and its functions in the pathogenesis of HCC were investigated. The methylation status of the PCDH9 promoter was quantitatively analyzed, and the PCDH9 expression was analyzed in HCC cell lines treated with 5‑azacytidine. The effects of PCDH9 re‑expression and knockdown on growth, proliferation and tumorigenic potential were determined. The results indicated that expression of PCDH9 mRNA was restored in hypermethylation HCC cells following treatment with the DNA de‑methylation reagent 5'‑Aza. Methylation of the PCDH9 promoter was observed in 22% primary HCC tissues (24/111 tumors). Among the primary HCC cases, the methylated PCDH9 appeared to be associated with a larger tumor size (≥5 cm; P=0.0139) and a more pronounced intrahepatic dissemination (P=0.0312). In addition, it was observed that restored PCDH9 expression could inhibit tumor cell proliferation and xenograft tumor formation. Furthermore, restored PCDH9 expression could inhibit cell proliferation of HCC cell lines via inducing cell cycle arrest at G0/G1 phase. Thus, it is suggested that PCDH9 may act as a novel tumor suppressor candidate gene in HCC pathogenesis.

Multiple protocadherins are expressed in brain microvascular endothelial cells and might play a role in tight junction protein regulation

Protocadherins (Pcdhs) are a large family of cadherin-related molecules. They play a role in cell adhesion, cellular interactions, and development of the central nervous system. However, their expression and role in endothelial cells has not yet been characterized. Here, we examined the expression of selected clustered Pcdhs in endothelial cells from several vascular beds. We analyzed human and mouse brain microvascular endothelial cell (BMEC) lines and primary cells, mouse myocardial microvascular endothelial cell line, and human umbilical vein endothelial cells. We examined the mRNA and protein expression of selected Pcdhs using RT-PCR, Western blot, and immunostaining. A strong mRNA expression of Pcdhs was observed in all endothelial cells tested. At the protein level, Pcdhs-gamma were detected using an antibody against the conserved C-terminal domain of Pcdhs-gamma or an antibody against PcdhgC3. Deletion of highly expressed PcdhgC3 led to differences in the tight junction protein expression and mRNA expression of Wnt/mTOR (mechanistic target of rapamycin) pathway genes as well as lower transendothelial electrical resistance. Staining of PcdhgC3 showed diffused cytoplasmic localization in mouse BMEC. Our results suggest that Pcdhs may play a critical role in the barrier-stabilizing pathways at the blood-brain barrier.

Identification of distinct molecular subtypes of uterine carcinosarcoma

Uterine carcinosarcoma (UCS) is a rare but lethal neoplasm with high metastasis and recurrence rate, and to date, no molecular classification of UCS has been defined to achieve targeted therapies. In this study, we identified two distinct molecular subtypes of UCS with distinct gene expression patterns and clinicopathologic characteristics. Subtype I UCS recapitulates low-grade UCS, in contrast subtype II UCS represents high-grade UCS with higher tumor invasion rate and tumor weight. Interestingly, subtype I UCS is characterized by cell adhesion and apoptosis pathways, whereas genes over-expressed in subtype II UCS are more involved in myogenesis/muscle development. We also proposed certain potential subtype specific therapeutic targets, such as SYK (spleen tyrosine kinase) for subtype I and cell-cycle proteins for subtype II. Our findings provide a better recognition of UCS molecular subtypes and subtype specific oncogenesis mechanisms, and can help develop more specific targeted treatment options for these tumors.

Models of convergent extension during morphogenesis

Convergent extension (CE) is a fundamental and conserved collective cell movement that forms elongated tissues during embryonic development. Thus far, studies have demonstrated two different mechanistic models of collective cell movements during CE. The first, termed the crawling mode, was discovered in the process of notochord formation in Xenopus laevis embryos, and has been the established model of CE for decades. The second model, known as the contraction mode, was originally reported in studies of germband extension in Drosophila melanogaster embryos and was recently demonstrated to be a conserved mechanism of CE among tissues and stages of development across species. This review summarizes the two modes of CE by focusing on the differences in cytoskeletal behaviors and relative expression of cell adhesion molecules. The upstream molecules regulating these machineries are also discussed. There are abundant studies of notochord formation in X. laevis embryos, as this was one of the pioneering model systems in this field. Therefore, the present review discusses these findings as an approach to the fundamental biological question of collective cell regulation. WIREs Dev Biol 2018, 7:e293. doi: 10.1002/wdev.293

This article is categorized under: 1

Early Embryonic Development > Gastrulation and Neurulation

2

Comparative Development and Evolution > Model Systems

Regulation of Wnt signaling by protocadherins

The ∼70 protocadherins comprise the largest group within the cadherin superfamily. Their diversity, the complexity of the mechanisms through which their genes are regulated, and their many critical functions in nervous system development have engendered a growing interest in elucidating the intracellular signaling pathways through which they act. Recently, multiple protocadherins across several subfamilies have been implicated as modulators of Wnt signaling pathways, and through this as potential tumor suppressors. Here, we review the extant data on the regulation by protocadherins of Wnt signaling pathways and components, and highlight some key unanswered questions that could shape future research.

PCDH8 inhibits glioma cell proliferation by negatively regulating the AKT/GSK3β/β-catenin signaling pathway

Protocadherin-8 (PCDH8), a member of the protocadherin superfamily of proteins, is frequently lost in numerous types of cancer. However, the role that PCDH8 serves in human glioma, and the molecular mechanisms underlying this, remain unclear. Data from the present study demonstrated that the expression levels of PCDH8 mRNA and protein were significantly decreased in human glioma tissue compared with normal brain tissue. This suggested that PCDH8 is associated with the development of glioma. Thus, the role of PCDH8 in glioma cell proliferation was investigated by silencing and overexpressing PCDH8 in U251 glioma cells. Overexpression of PCDH8 significantly inhibited glioma cell proliferation, while silencing of PCDH8 using small interfering RNA promoted glioma cell proliferation. Restoration of PCDH8 decreased phosphorylated (p)-Rac-α serine/threonine-protein kinase (AKT) [Threonine (T)308/Serine (S)473] and p-glycogen synthase kinase-3β (p-GSK3β) (S9) protein expression, thereby reducing the level of β-catenin when compared with the control. By contrast, silencing of PCDH8 increased levels of p-AKT (T308/S473) and p-GSK3β (S9), thereby increasing the level of β-catenin. In conclusion, the results of the present study suggested that PCDH8 suppressed glioma cell proliferation, and that the loss of PCDH8 may stimulate the proto-oncogene Wnt/β-catenin signaling pathway and therefore promote glioma cell proliferation.

Genetic variations associated with gemcitabine treatment outcome in pancreatic cancer

BACKGROUND

Pancreatic cancer is a rapidly fatal disease with gemcitabine remaining the first-line therapy. We performed a genotype-phenotype association study to identify biomarkers for predicting gemcitabine treatment outcome.

MATERIALS AND METHODS

We selected the top 200 single nucleotide polymorphisms (SNPs) identified from our previous genome-wide association study to associate with overall survival using 400 patients treated with/or without gemcitabine, followed by imputation analysis for regions around the identified SNPs and a replication study using an additional 537 patients by the TaqMan genotyping assay. Functional validation was performed using quantitative reverse transcription-PCR for gemcitabine-induced expression in genotyped lymphoblastoid cell lines and siRNA knockdown for candidate genes in pancreatic cancer cell lines.

RESULTS

Four SNPs in chromosome 1, 3, 9, and 20 showed an interaction with gemcitabine from the discovery cohort of 400 patients (P<0.01). Subsequently, we selected those four genotyped plus four imputed SNPs for SNP×gemcitabine interaction analysis using the secondary validation cohort. Two imputed SNPs in CDH4 and KRT8P35 showed a trend in interaction with gemcitabine treatment. The lymphoblastoid cell lines with the variant sequences showed increased CDH4 expression compared with the wild-type cells after gemcitabine exposure. Knockdown of CDH4 significantly desensitized pancreatic cancer cells to gemcitabine cytotoxicity. The CDH4 SNPs that interacted with treatment are more predictive than prognostic.

CONCLUSION

We identified SNPs with gemcitabine-dependent effects on overall survival. CDH4 might contribute to variations in gemcitabine response. These results might help us to better predict gemcitabine response in pancreatic cancer.

Epigenetic silencing of protocadherin 10 in colorectal cancer

Colorectal cancer (CRC) is one of the most common types of malignant tumor in the world and occurs through a multi-step process resulting from the accumulation of genetic and epigenetic alterations of the genome. Although the molecular mechanisms of the pathogenesis of CRC remain unclear, the inactivation of tumor suppressor genes (TSGs) through promoter methylation serves an important role. Aberrant methylation is a well-defined marker of CRC. At present, the epigenetic silencing of protocadherin 10 (PCDH10) has been identified as an important TSG with key roles in colorectal carcinogenesis, invasion and metastasis as a frequent and early event. Advances in gene methylation detection in tumor tissues and body fluids have led to the development of non-invasive screening methods for CRC. The present study aimed to review the epigenetic alteration of PCDH10 in CRC development, and the potential of PCDH10 to be a non-invasive biomarker for CRC.

Identification and Validation of Novel Subtype-Specific Protein Biomarkers in Pancreatic Ductal Adenocarcinoma

OBJECTIVES

Pancreatic ductal adenocarcinoma (PDAC) has been subclassified into 3 molecular subtypes: classical, quasi-mesenchymal, and exocrine-like. These subtypes exhibit differences in patient survival and drug resistance to conventional therapies. The aim of the current study is to identify novel subtype-specific protein biomarkers facilitating subtype stratification of patients with PDAC and novel therapy development.

METHODS

A set of 12 human patient-derived primary cell lines was used as a starting material for an advanced label-free proteomics approach leading to the identification of novel cell surface and secreted biomarkers. Cell surface protein identification was achieved by in vitro biotinylation, followed by mass spectrometric analysis of purified biotin-tagged proteins. Proteins secreted into a chemically defined serum-free cell culture medium were analyzed by shotgun proteomics.

RESULTS

Of 3288 identified proteins, 2 pan-PDAC (protocadherin-1 and lipocalin-2) and 2 exocrine-like-specific (cadherin-17 and galectin-4) biomarker candidates have been validated. Proximity ligation assay analysis of the 2 exocrine-like biomarkers revealed their co-localization on the surface of exocrine-like cells.

CONCLUSIONS

The study reports the identification and validation of novel PDAC biomarkers relevant for the development of patient stratification tools. In addition, cadherin-17 and galectin-4 may serve as targets for bispecific antibodies as novel therapeutics in PDAC.

Structural determinants of adhesion by Protocadherin-19 and implications for its role in epilepsy

Non-clustered δ-protocadherins are homophilic cell adhesion molecules essential for the development of the vertebrate nervous system, as several are closely linked to neurodevelopmental disorders. Mutations in protocadherin-19 (PCDH19) result in a female-limited, infant-onset form of epilepsy (PCDH19-FE). Over 100 mutations in PCDH19 have been identified in patients with PCDH19-FE, about half of which are missense mutations in the adhesive extracellular domain. Neither the mechanism of homophilic adhesion by PCDH19, nor the biochemical effects of missense mutations are understood. Here we present a crystallographic structure of the minimal adhesive fragment of the zebrafish Pcdh19 extracellular domain. This structure reveals the adhesive interface for Pcdh19, which is broadly relevant to both non-clustered δ and clustered protocadherin subfamilies. In addition, we show that several PCDH19-FE missense mutations localize to the adhesive interface and abolish Pcdh19 adhesion in in vitro assays, thus revealing the biochemical basis of their pathogenic effects during brain development.

DOI:http://dx.doi.org/10.7554/eLife.18529.001

As the brain develops, its basic building blocks – cells called neurons – need to form the correct connections with one another in order to give rise to neural circuits. A mistake that leads to the formation of incorrect connections can result in a number of disorders or brain abnormalities.

Proteins called cadherins that are present on the surface of neurons enable them to stick to their correct partners like Velcro. One of these proteins is called Protocadherin-19. However, it was not fully understood how this protein forms an adhesive bond with other Protocadherin-19 molecules, or how some of the proteins within the cadherin family are able to distinguish between one another.

Cooper et al. used X-ray crystallography to visualize the molecular structure of Protocadherin-19 taken from zebrafish in order to better understand the adhesive bond that these proteins form with each other. In addition, the new structure showed the sites of the mutations that cause a form of epilepsy in infant females. From this, Cooper et al. could predict how the mutations would disrupt Protocadherin-19’s shape and function.

The structures revealed that Protocadherin-19 molecules from adjacent cells engage in a “forearm handshake” to form the bond that connects neurons. Some of the mutations that cause epilepsy occur in the region responsible for this Protocadherin-19 forearm handshake. Laboratory experiments confirmed that these mutations impair the formation of the adhesive bond, revealing the molecular basis for some of the mutations that underlie Protocadherin-19-female-limited epilepsy.

Other cadherin molecules may interact via a similar forearm handshake; this could be investigated in future experiments. It also remains to be discovered how brain wiring depends on Protocadherin-19 adhesion in animal development, and how altering these proteins can rewire developing brain circuits.

DOI:http://dx.doi.org/10.7554/eLife.18529.002

Protocadherin-1 Localization and Cell-Adhesion Function in Airway Epithelial Cells in Asthma

Background

The asthma gene PCDH1 encodes Protocadherin-1, a putative adhesion molecule of unknown function expressed in the airway epithelium. Here, we characterize the localization, differential expression, homotypic adhesion specificity and function of PCDH1 in airway epithelial cells in asthma.

Methods

We performed confocal fluorescence microscopy to determine subcellular localization of PCDH1 in 16HBE cells and primary bronchial epithelial cells (PBECs) grown at air-liquid interface. Next, to compare PCDH1 expression and localization in asthma and controls we performed qRT-PCR and fluorescence microscopy in PBECs and immunohistochemistry on airway wall biopsies. We examined homotypic adhesion specificity of HEK293T clones overexpressing fluorescently tagged-PCDH1 isoforms. Finally, to evaluate the role for PCDH1 in epithelial barrier formation and repair, we performed siRNA knockdown-studies and measured epithelial resistance.

Results

PCDH1 localized to the cell membrane at cell-cell contact sites, baso-lateral to adherens junctions, with increasing expression during epithelial differentiation. No differences in gene expression or localization of PCDH1 isoforms expressing the extracellular domain were observed in either PBECs or airway wall biopsies between asthma patients and controls. Overexpression of PCDH1 mediated homotypic interaction, whereas downregulation of PCDH1 reduced epithelial barrier formation, and impaired repair after wounding.

Conclusions

In conclusion, PCDH1 is localized to the cell membrane of bronchial epithelial cells baso-lateral to the adherens junction. Expression of PCDH1 is not reduced nor delocalized in asthma even though PCDH1 contributes to homotypic adhesion, epithelial barrier formation and repair.

Characterizing PCDH19 in human induced pluripotent stem cells (iPSCs) and iPSC-derived developing neurons: emerging role of a protein involved in controlling polarity during neurogenesis

PCDH19 (Protocadherin 19), a member of the cadherin superfamily, is involved in the pathogenic mechanism of an X-linked model of neurological disease. The biological function of PCHD19 in human neurons and during neurogenesis is currently unknown. Therefore, we decided to use the model of the induced pluripotent stem cells (iPSCs) to characterize the location and timing of expression of PCDH19 during cortical neuronal differentiation. Our data show that PCDH19 is expressed in pluripotent cells before differentiation in a homogeneous pattern, despite its localization is often limited to one pole of the cell. During neuronal differentiation, positional information on the progenitor cells assumes an important role in acquiring polarization. The proper control of the cell orientation ensures a fine balancing between symmetric (giving rise to two progenitor sister cells) versus asymmetric (giving rise to one progenitor cell and one newborn neuron) division. This process results in the polar organization of the neural tube with a lumen indicating the basal part of the polarized neuronal progenitor cell; in the iPSC model the cells are organized in the ‘neural rosette’ and interestingly, PCDH19 is located at the center of the rosette, with other well-known markers of the lumen (N-cadherin and ZO-1). These data suggest that PCDH19 has a role in instructing the apico-basal polarity of the progenitor cells, thus regulating the development of a properly organized human brain.

Characterization of a Single Genomic Locus Encoding the Clustered Protocadherin Receptor Diversity in Xenopus tropicalis

Clustered protocadherins (cPcdhs) constitute the largest subgroup of the cadherin superfamily, and in mammals are grouped into clusters of α-, β-, and γ-types. Tens of tandemly arranged paralogous Pcdh genes of the Pcdh clusters generate a substantial diversity of receptor isoforms. cPcdhs are known to have important roles in neuronal development, and genetic alterations of cPcdhs have been found to be associated with several neurological diseases. Here, we present a first characterization of cPcdhs in Xenopus tropicalis. We determined and annotated all cPcdh isoforms, revealing that they are present in a single chromosomal locus. We validated a total of 96 isoforms, which we show are organized in three distinct clusters. The X. tropicalis cPcdh locus is composed of one α- and two distinct γ-Pcdh clusters (pcdh-γ1 and pcdh-γ2). Bioinformatics analyses assisted by genomic BAC clone sequencing showed that the X. tropicalis α- and γ-Pcdhs are conserved at the cluster level, but, unlike mammals, X. tropicalis does not contain a β-Pcdh cluster. In contrast, the number of γ-Pcdh isoforms has expanded, possibly due to lineage-specific gene duplications. Interestingly, the number of X. tropicalis α-Pcdhs is identical between X. tropicalis and mouse. Moreover, we find highly conserved as well as novel promoter elements potentially involved in regulating the cluster-specific expression of cPcdh isoforms. This study provides important information for the understanding of the evolutionary history of cPcdh genes and future mechanistic studies. It provides an annotated X. tropicalis cPcdh genomic map and a first molecular characterization essential for functional and comparative studies.

Aberrant expression and functions of protocadherins in human malignant tumors

Protocadherins (PCDHs) are a group of transmembrane proteins belonging to the cadherin superfamily and are subdivided into "clustered" and "non-clustered" groups. PCDHs vary in both structure and interaction partners and thus regulate multiple biological responses in complex and versatile patterns. Previous researches showed that PCDHs regulated the development of brain and were involved in some neuronal diseases. Recently, studies have revealed aberrant expression of PCDHs in various human malignant tumors. The down-regulation or absence of PCDHs in malignant cells has been associated with cancer progression. Further researches suggest that PCDHs may play major functions as tumor suppressor by inhibiting the proliferation and metastasis of cancer cells. In this review, we focus on the altered expression of PCDHs and their roles in the development of cancer progression. We also discuss the potential mechanisms, by which PCDHs are aberrantly expressed, and its implications in regulating cancers.

Specification of synaptic connectivity by cell surface interactions

The molecular diversification of cell surface molecules has long been postulated to impart specific surface identities on neuronal cell types. The existence of unique cell surface identities would allow neurons to distinguish one another and connect with their appropriate target cells. Although progress has been made in identifying cell type-specific surface molecule repertoires and in characterizing their extracellular interactions, determining how this molecular diversity contributes to the precise wiring of neural circuitry has proven challenging. Here, we review the role of the cadherin, neurexin, immunoglobulin and leucine-rich repeat protein superfamilies in the specification of connectivity. The emerging evidence suggests that the concerted actions of these proteins may critically contribute to the assembly of neural circuits.

Associative DNA methylation changes in children with prenatal alcohol exposure

Aim: Prenatal alcohol exposure (PAE) can cause fetal alcohol spectrum disorders (FASD). Previously, we assessed PAE in brain tissue from mouse models, however whether these changes are present in humans remains unknown. Materials & methods: In this report, we show some identical changes in DNA methylation in the buccal swabs of six children with FASD using the 450K array. Results: The changes occur in genes related to protocadherins, glutamatergic synapses, and hippo signaling. The results were found to be similar in another heterogeneous replication group of six FASD children. Conclusion: The replicated results suggest that children born with FASD have unique DNA methylation defects that can be influenced by sex and medication exposure. Ultimately, with future clinical development, assessment of DNA methylation from buccal swabs can provide a novel strategy for the diagnosis of FASD.

Adenosylmethionine decarboxylase 1 (AMD1)-mediated mRNA processing and cell adhesion activated & inhibited transition mechanisms by different comparisons between chimpanzee and human left hemisphere

To understand adenosylmethionine decarboxylase 1 (AMD1)-mediated mRNA processing and cell adhesion activated & inhibited transition mechanisms between chimpanzee and human left hemisphere, AMD1-activated different complete (all no positive correlation, Pearson correlation coefficient < 0.25) and uncomplete (partly no positive correlation except AMD1, Pearson < 0.25) networks were identified in higher human compared with lower chimpanzee left hemisphere from the corresponding AMD1-stimulated (Pearson ≥ 0.25) or inhibited (Pearson ≤ -0.25) overlapping molecules of Pearson and GRNInfer, respectively. This result was verified by the corresponding scatter matrix. As visualized by GO, KEGG, GenMAPP, BioCarta, and disease database integration, we proposed mainly that AMD1-stimulated different complete network was involved in AMD1 activation with cytoplasm ubiquitin specific peptidase (tRNA-guanine transglycosylase) to nucleus paired box-induced mRNA processing, whereas the corresponding inhibited network participated in AMD1 repression with cytoplasm protocadherin gamma and adaptor-related protein complex 3-induced cell adhesion in lower chimpanzee left hemisphere. However, AMD1-stimulated network contained AMD1 activation with plakophilin and phosphodiesterase to SH3 binding glutamic acid-rich protein to dynein and zinc finger-induced cell adhesion, whereas the corresponding inhibited different complete network included AMD1 repression with mitochondrial denine nucleotide translocator, brain protein, and ADH dehydrogenase to ribonucleoprotein-induced mRNA processing in higher human left hemisphere. Our AMD1 different networks were verified by AMD1-activated or -inhibited complete and uncomplete networks within and between chimpanzee left hemisphere or (and) human left hemisphere.

Protocadherin-1 is a glucocorticoid-responsive critical regulator of airway epithelial barrier function

Background

Impaired epithelial barrier function renders the airway vulnerable to environmental triggers associated with the pathogenesis of bronchial asthma. We investigated the influence of protocadherin-1 (PCDH1), a susceptibility gene for bronchial hyperresponsiveness, on airway epithelial barrier function.

Methods

We applied transepithelial electric resistance and dextran permeability testing to evaluate the barrier function of cultured airway epithelial cells. We studied PCDH1 function by siRNA-mediated knockdown and analyzed nasal or bronchial tissues from 16 patients with chronic rhinosinusitis (CRS) and nine patients with bronchial asthma for PCDH1 expression.

Results

PCDH1 was upregulated with the development of epithelial barrier function in cultured airway epithelial cells. Immunocytochemical analysis revealed that PCDH localized to cell-cell contact sites and colocalized with E-cadherin at the apical site of airway epithelial cells. PCDH1 gene knockdown disrupted both tight and adhesion junctions. Immunohistochemical analysis revealed strong PCDH1 expression in nasal and bronchial epithelial cells; however, expression decreased in inflamed tissues sampled from patients with CRS or bronchial asthma. Dexamethasone (Dex) increased the barrier function of airway epithelial cells and increased PCDH1 expression. PCDH1 gene knockdown eradicated the effect of Dex on barrier function.

Conclusion

These results suggest that PCDH1 is important for airway function as a physical barrier, and its dysfunction is involved in the pathogenesis of allergic airway inflammation. We also suggest that glucocorticoids promotes epithelial barrier integrity by inducing PCDH1.

Protocadherin-1 binds to SMAD3 and suppresses TGF-β1-induced gene transcription

Genetic studies have identified Protocadherin-1 (PCDH1) and Mothers against decapentaplegic homolog-3 (SMAD3) as susceptibility genes for asthma. PCDH1 is expressed in bronchial epithelial cells and has been found to interact with SMAD3 in yeast two-hybrid (Y2H) overexpression assays. Here, we test whether PCDH1 and SMAD3 interact at endogenous protein levels in bronchial epithelial cells and evaluate the consequences thereof for transforming growth factor-β1 (TGF-β1)-induced gene transcription. We performed Y2H screens and coimmunoprecipitation (co-IP) experiments of PCDH1 and SMAD3 in HEK293T and 16HBE14o(-) (16HBE) cell lines. Activity of a SMAD3-driven luciferase reporter gene in response to TGF-β1 was measured in BEAS-2B cells transfected with PCDH1 and in 16HBE cells transfected with PCDH1-small-interfering RNA (siRNA). TGF-β1-induced gene expression was quantified in BEAS-2B clones overexpressing PCDH1 and in human primary bronchial epithelial cells (PBECs) transfected with PCDH1-siRNA. We confirm PCDH1 and SMAD3 interactions by Y2H and by co-IP in HEK293T cells overexpressing both proteins, and at endogenous protein levels in 16HBE cells. TGF-β-induced activation of a SMAD3-driven reporter was reduced by exogenous PCDH1 in BEAS2B cells, whereas it was increased by siRNA-mediated knockdown of endogenous PCDH1 in 16HBE cells. Overexpression of PCDH1 suppressed expression of TGF-β target genes in BEAS-2B cells, whereas knockdown of PCDH1 in human PBECs increased TGF-β-induced gene expression. In conclusion, we demonstrate that PCDH1 binds to SMAD3 and regulates its activation by TGF-β signaling in bronchial epithelial cells. We propose that PCDH1 and SMAD3 act in a single pathway in asthma susceptibility that affects sensitivity of the airway epithelium to TGF-β.

Protocadherins and hypothalamic development: do they play an unappreciated role?

Normal brain development requires coordinated cell movements at precise times. It has long been established that cell-cell adhesion proteins of the cadherin superfamily are involved in the adhesion and sorting of cells during tissue morphogenesis. In the present review, we focus on protocadherins, which form the largest subfamily of the cadherin superfamily and mediate homophilic cell-cell adhesion in the developing brain. These molecules are highly expressed during neural development and the exact roles that they play are still emerging. Although, historically, protocadherins were considered to provide mechanical and chemical connections between adjacent cells, recent research suggests that they may also serve as molecular identity markers of neurones to help guide cell recognition and sorting, cell migration, outgrowth of neuronal processes, and synapse formation. This phenomenon of single cell diversity stems, in part, from the vast variation in protein structure, genomic organisation and molecular function of the protocadherins. Although expression profiles and genetic manipulations have provided evidence for the role of protocadherins in the developing brain, we have only begun to construct a complete understanding of protocadherin function. We examine our current understanding of how protocadherins influence brain development and discuss the possible roles for this large superfamily within the hypothalamus. We conclude that further research into these underappreciated but vitally important genes will shed insight into hypothalamic development and perhaps the underlying aetiology of neuroendocrine disorders.

Protocadherins branch out: Multiple roles in dendrite development

The proper formation of dendritic arbors is a critical step in neural circuit formation, and as such defects in arborization are associated with a variety of neurodevelopmental disorders. Among the best gene candidates are those encoding cell adhesion molecules, including members of the diverse cadherin superfamily characterized by distinctive, repeated adhesive domains in their extracellular regions. Protocadherins (Pcdhs) make up the largest group within this superfamily, encompassing over 80 genes, including the ∼60 genes of the α-, β-, and γ-Pcdh gene clusters and the non-clustered δ-Pcdh genes. An additional group includes the atypical cadherin genes encoding the giant Fat and Dachsous proteins and the 7-transmembrane cadherins. In this review we highlight the many roles that Pcdhs and atypical cadherins have been demonstrated to play in dendritogenesis, dendrite arborization, and dendritic spine regulation. Together, the published studies we discuss implicate these members of the cadherin superfamily as key regulators of dendrite development and function, and as potential therapeutic targets for future interventions in neurodevelopmental disorders.

Emerging roles of protocadherins: from self-avoidance to enhancement of motility

Protocadherins are a group of transmembrane proteins belonging to the cadherin superfamily that are subgrouped into 'clustered' and 'non-clustered' protocadherins. Although cadherin superfamily members are known to regulate various forms of cell-cell interactions, including cell-cell adhesion, the functions of protocadherins have long been elusive. Recent studies are, however, uncovering their unique roles. The clustered protocadherins regulate neuronal survival, as well as dendrite self-avoidance. Combinatorial expression of clustered protocadherin isoforms creates a great diversity of adhesive specificity for cells, and this process is likely to underlie the dendritic self-avoidance. Non-clustered protocadherins promote cell motility rather than the stabilization of cell adhesion, unlike the classic cadherins, and mediate dynamic cellular processes, such as growth cone migration. Protocadherin dysfunction in humans is implicated in neurological disorders, such as epilepsy and mental retardation. This Commentary provides an overview of recent findings regarding protocadherin functions, as well as a discussion of the molecular basis underlying these functions.

Protocadherin-9 involvement in retinal development in Xenopus laevis

Biological roles of most protocadherins (Pcdhs) are a largely unsolved problem. Therefore, we cloned cDNA for Xenopus laevis protocadherin-9 and characterized its properties to elucidate the role. The deduced amino acid sequence was highly homologous to those of mammalian protocadherin-9 s. X. laevis protocadherin-9 expressed from the cDNA in L cells showed basic properties similar to those of mammalian Pcdhs. Expression of X. laevis protocadherin-9 was first detected in stage-31 embryos and increased as the development proceeded. In the later stage embryos and the adults, the retina strongly expressed protocadherin-9, which was mainly localized at the plexiform layers. Injection of morpholino anti-sense oligonucleotide against protocadherin-9 into the fertilized eggs inhibited eye development; and eye growth and formation of the retinal laminar structure were hindered. Moreover, affected retina showed abnormal extension of neurites into the ganglion cell layer. Co-injection of protocadherin-9 mRNA with the morpholino anti-sense oligonucleotide rescued the embryos from the defects. These results suggest that X. laevis protocadherin-9 was involved in the development of retina structure possibly through survival of neurons, formation of the lamina structure and neurite localization.

Protocadherin 9 inhibits epithelial-mesenchymal transition and cell migration through activating GSK-3β in hepatocellular carcinoma

Protocadherin 9 (PCDH9) was found frequently lost in hepatocellular carcinoma (HCC). Here we investigated the role of PCDH9 in the development of HCC. We confirmed that PCDH9 was down-regulated in HCC tissues and cell lines compared with the adjacent non-tumor tissues. PCDH9 downregulation was significantly associated with malignant portal vein invasion of HCC patients. Gain- and loss-of-function studies revealed that downregulation of PCDH9 facilitated tumor cell migration and epithelial-mesenchymal transition (EMT). We identified PCDH9 as a novel regulator of EMT by increasing the activity of GSK-3β and inhibiting Snail1, indicating its potential therapeutic value for reducing metastasis of HCC.

Mouse protocadherin-1 gene expression is regulated by cigarette smoke exposure in vivo

Protocadherin-1 (PCDH1) is a novel susceptibility gene for airway hyperresponsiveness, first identified in families exposed to cigarette smoke and is expressed in bronchial epithelial cells. Here, we asked how mouse Pcdh1 expression is regulated in lung structural cells in vivo under physiological conditions, and in both short-term cigarette smoke exposure models characterized by airway inflammation and hyperresponsiveness and chronic cigarette smoke exposure models. Pcdh1 gene-structure was investigated by Rapid Amplification of cDNA Ends. Pcdh1 mRNA and protein expression was investigated by qRT-PCR, western blotting using isoform-specific antibodies. We observed 87% conservation of the Pcdh1 nucleotide sequence, and 96% conservation of the Pcdh1 protein sequence between men and mice. We identified a novel Pcdh1 isoform encoding only the intracellular signalling motifs. Cigarette smoke exposure for 4 consecutive days markedly reduced Pcdh1 mRNA expression in lung tissue (3 to 4-fold), while neutrophilia and airway hyperresponsiveness was induced. Moreover, Pcdh1 mRNA expression in lung tissue was reduced already 6 hours after an acute cigarette-smoke exposure in mice. Chronic exposure to cigarette smoke induced loss of Pcdh1 protein in lung tissue after 2 months, while Pcdh1 protein levels were no longer reduced after 9 months of cigarette smoke exposure. We conclude that Pcdh1 is highly homologous to human PCDH1, encodes two transmembrane proteins and one intracellular protein, and is regulated by cigarette smoke exposure in vivo.

Spatio-temporally restricted expression of cell adhesion molecules during chicken embryonic development

Differential cell adhesive properties are known to regulate important developmental events like cell sorting and cell migration. Cadherins and protocadherins are known to mediate these cellular properties. Though a large number of such molecules have been predicted, their characterization in terms of interactive properties and cellular roles is far from being comprehensive. To narrow down the tissue context and collect correlative evidence for tissue specific roles of these molecules, we have carried out whole-mount in situ hybridization based RNA expression study for seven cadherins and four protocadherins. In developing chicken embryos (HH stages 18, 22, 26 and 28) cadherins and protocadherins are expressed in tissue restricted manner. This expression study elucidates precise expression domains of cell adhesion molecules in the context of developing embryos. These expression domains provide spatio-temporal context in which the function of these genes can be further explored.

Sorting out a promiscuous superfamily: towards cadherin connectomics

Members of the cadherin superfamily of proteins are involved in diverse biological processes such as morphogenesis, sound transduction, and neuronal connectivity. Key to cadherin function is their extracellular domain containing cadherin repeats, which can mediate interactions involved in adhesion and cell signaling. Recent cellular, biochemical, and structural studies have revealed that physical interaction among cadherins is more complex than originally thought. Here we review work on new cadherin complexes and discuss how the classification of the mammalian family can be used to search for additional cadherin-interacting partners. We also highlight some of the challenges in cadherin research; namely, the characterization of a cadherin connectome in biochemical and structural terms, as well as the elucidation of molecular mechanisms underlying the functional diversity of nonclassical cadherins in vivo.

Beyond E-cadherin: roles of other cadherin superfamily members in cancer

Loss of cadherin 1 (CDH1; also known as epithelial cadherin (E-cadherin)) is used for the diagnosis and prognosis of epithelial cancers. However, it should not be ignored that the superfamily of transmembrane cadherin proteins encompasses more than 100 members in humans, including other classical cadherins, numerous protocadherins and cadherin-related proteins. Elucidation of their roles in suppression versus initiation or progression of various tumour types is a young but fascinating field of molecular cancer research. These cadherins are very diverse in both structure and function, and their mutual interactions seem to influence biological responses in complex and versatile ways.

Protocadherins in neurological diseases

Cadherins were originally isolated as calcium-dependent cell adhesion molecules and are characterized by their cadherin motifs in the extracellular domain. In vertebrates, including humans, there are more than 100 different cadherin-related genes, which constitute the cadherin superfamily. The protocadherin (Pcdh) family comprises a large subgroup within the cadherin superfamily. The Pcdhs are divided into clustered and non-clustered Pcdhs, based on their genomic structure. Almost all the Pcdh genes are expressed widely in the brain and play important roles in brain development and in the regulation of brain function. This chapter presents an overview of Pcdh family members with regard to their functions, knockout mouse phenotypes, and association with neurological diseases and tumors.

Copy number variation findings among 50 children and adolescents with autism spectrum disorder

OBJECTIVES

Autism spectrum disorders (ASDs) are a heterogeneous group of neurodevelopment disorders with a complex genetic aetiology. The aim of this study was to identify copy number variations (CNVs) with a clinical significance for ASD.

MATERIALS AND METHODS

Array-based comparative genomic hybridization was applied to detect CNVs in a clinically well-characterized population of 50 children and adolescents with ASD.

RESULTS

Nine CNVs with predicted clinical significance were identified among eight individuals (detection rate 16%). Three of the CNVs are recurrently associated with ASDs (15q11.2q13.1) or have been identified in ASD populations [3p14.2 and t(8;12)(p23.1;p13.31)]. The remaining regions (15q11.2, 10q21.1, Xp22.2, 16p13.3 and 22q13.1) have not been reported previously as candidate genes for ASD.

CONCLUSION

This study identified five novel CNVs among the individuals. The causal relationship between identified CNVs and the ASD phenotype is not fully established. However, the genes involved are associated with ASD and/or other neuropsychiatric disorders, or implicated in synaptic and neuronal activity, thus suggesting clinical significance. Further identification of ASD-associated CNVs is required, together with a broad clinical characterization of affected individuals to identify genotype-phenotype correlations.

Clustered protocadherins

The majority of vertebrate protocadherin (Pcdh) genes are clustered in a single genomic locus, and this remarkable genomic organization is highly conserved from teleosts to humans. These clustered Pcdhs are differentially expressed in individual neurons, they engage in homophilic trans-interactions as multimers and they are required for diverse neurodevelopmental processes, including neurite self-avoidance. Here, we provide a concise overview of the molecular and cellular biology of clustered Pcdhs, highlighting how they generate single cell diversity in the vertebrate nervous system and how such diversity may be used in neural circuit assembly.

Comparative analysis of protocadherin-11 X-linked expression among postnatal rodents, non-human primates, and songbirds suggests its possible involvement in brain evolution

Background

Protocadherin-11 is a cell adhesion molecule of the cadherin superfamily. Since, only in humans, its paralog is found on the Y chromosome, it is expected that protocadherin-11X/Y plays some role in human brain evolution or sex differences. Recently, a genetic mutation of protocadherin-11X/Y was reported to be associated with a language development disorder. Here, we compared the expression of protocadherin-11 X-linked in developing postnatal brains of mouse (rodent) and common marmoset (non-human primate) to explore its possible involvement in mammalian brain evolution. We also investigated its expression in the Bengalese finch (songbird) to explore a possible function in animal vocalization and human language faculties.

Methodology/Principal Findings

Protocadherin-11 X-linked was strongly expressed in the cerebral cortex, hippocampus, amygdala and brainstem. Comparative analysis between mice and marmosets revealed that in certain areas of marmoset brain, the expression was clearly enriched. In Bengalese finches, protocadherin-11 X-linked was expressed not only in nuclei of regions of the vocal production pathway and the tracheosyringeal hypoglossal nucleus, but also in areas homologous to the mammalian amygdala and hippocampus. In both marmosets and Bengalese finches, its expression in pallial vocal control areas was developmentally regulated, and no clear expression was seen in the dorsal striatum, indicating a similarity between songbirds and non-human primates.

Conclusions/Significance

Our results suggest that the enriched expression of protocadherin-11 X-linked is involved in primate brain evolution and that some similarity exists between songbirds and primates regarding the neural basis for vocalization.

Delta-protocadherins in health and disease

The protocadherin family comprises clustered and nonclustered protocadherin genes. The nonclustered genes encode mainly δ-protocadherins, which deviate markedly from classical cadherins. They can be subdivided phylogenetically into δ0-protocadherins (protocadherin-20), δ1-protocadherins (protocadherin-1, -7, -9, and -11X/Y), and δ2-protocadherins (protocadherin-8, -10, -17, -18, and -19). δ-Protocadherins share a similar gene structure and are expressed as multiple alternative splice forms differing mostly in their cytoplasmic domains (CDs). Some δ-protocadherins reportedly show cell-cell adhesion properties. Individual δ-protocadherins appear to be involved in specific signaling pathways, as they interact with proteins such as TAF1/Set, TAO2β, Nap1, and the Frizzled-7 receptor. The spatiotemporally restricted expression of δ-protocadherins in various tissues and species and their functional analysis suggest that they play multiple, tightly regulated roles in vertebrate development. Furthermore, several δ-protocadherins have been implicated in neurological disorders and in cancers, highlighting the importance of scrutinizing their properties and their dysregulation in various pathologies.

Regulation of cadherin expression in nervous system development

This review addresses our current understanding of the regulatory mechanisms for classical cadherin expression during development of the vertebrate nervous system. The complexity of the spatial and temporal expression patterns is linked to morphogenic and functional roles in the developing nervous system. While the regulatory networks controlling cadherin expression are not well understood, it is likely that the multiple signaling pathways active in the development of particular domains also regulate the specific cadherins expressed at that time and location. With the growing understanding of the broader roles of cadherins in cell-cell adhesion and non-adhesion processes, it is important to understand both the upstream regulation of cadherin expression and the downstream effects of specific cadherins within their cellular context.

Clustered protocadherins and neuronal diversity

Neuronal diversity is a fundamental requirement for complex neuronal networks and brain function. The clustered protocadherin (Pcdh) family possesses several characteristic features that are important for the molecular basis of neuronal diversity. Clustered Pcdhs are expressed predominantly in the central nervous system, in neurites, growth cones, and synapses. They consist of about 60 isoforms, and their expression is stochastically and combinatorially regulated in individual neurons. The multiple clustered Pcdhs expressed in individual neurons form heteromultimeric protein complexes that exhibit homophilic adhesion properties. Theoretically, the clustered Pcdhs could generate more than 3×10(10) possible variations in each neuron and 12,720 types of cis-tetramers per neuron. The clustered Pcdhs are important for normal neuronal development. The clustered Pcdh genes have also attracted attention as a target for epigenetic regulation.

Distribution of protocadherin 9 protein in the developing mouse nervous system

Protocadherin 9 (Pcdh9) is a member of the protocadherin family, which includes many members involved in various phenomena, such as cell-cell adhesion, neural projection, and synapse formation. Here, we identified Pcdh9 protein in the mouse brain and examined its distribution during neural development. Pcdh9, with a molecular weight of approximately 180 kDa, was localized at cell-cell contact sites in COS-1 cells transfected with Pcdh9 cDNA. In cultured neurons, it was detected at the growth cone and at adhesion sites along neurites. In the E13.5 brain, prominent Pcdh9 immunoreactivity was detected in the dorsal thalamus along with other regions including the vestibulocochlear nerve. As development proceeded (E15.5-P1), Pcdh9 immunoreactivity became observable in various brain regions but was restricted to certain fiber tracts and brain nuclei. Interestingly, many Pcdh9-positive brain nuclei and fascicles belonged to the vestibular (e.g. vestibulocochlear nerve, vestibular nuclei, and the vestibulocerebellum) and oculomotor systems (medial longitudinal fascicles, oculomotor nucleus, trochlear nucleus, and interstitial nucleus of Cajal). In addition, we examined the distribution of Pcdh9 protein in the olfactory bulb, retina, spinal cord, and dorsal root ganglion. In these regions, Pcdh9 and OL-protocadherin proteins were differentially distributed, with the difference highlighted in the olfactory bulb, where they were enriched in different subsets of glomeruli. In the mature retina, Pcdh9 immunoreactivity was detected in distinct sublaminae of the inner and outer plexiform layers. In the dorsal root ganglion, only certain subsets of neurons showed Pcdh9 immunoreactivity. These results suggest that Pcdh9 might be involved in formation of specific neural circuits during neural development.

Cadherins in brain morphogenesis and wiring

Cadherins are Ca(2+)-dependent cell-cell adhesion molecules that play critical roles in animal morphogenesis. Various cadherin-related molecules have also been identified, which show diverse functions, not only for the regulation of cell adhesion but also for that of cell proliferation and planar cell polarity. During the past decade, understanding of the roles of these molecules in the nervous system has significantly progressed. They are important not only for the development of the nervous system but also for its functions and, in turn, for neural disorders. In this review, we discuss the roles of cadherins and related molecules in neural development and function in the vertebrate brain.

Protocadherin-1 polymorphisms are associated with eczema in two Dutch birth cohorts

BACKGROUND

  Eczema and asthma share a common genetic background and show linkage to chromosome 5q31-33. Protocadherin-1 (PCDH1) is located in this region and was identified as a susceptibility gene for bronchial hyper-responsiveness (BHR), a hallmark of asthma. PCDH1 encodes an adhesion molecule, expressed in airway and skin epithelium. We determined whether PCDH1 polymorphisms, previously associated with asthma or BHR, also associated with questionnaire and UK Working Party (UKWP) defined eczema.

METHODS

  Four PCDH1 polymorphisms were genotyped in two Dutch birth cohorts, PIAMA (n = 967) and KOALA Birth Cohort Study (n = 1560). Association with eczema was determined by chi-square tests and generalized estimating equations (GEE).

RESULTS

  Insertion deletion IVS3-116 was associated with development of UKWP eczema in PIAMA [age 4, OR = 1.90 (1.14-3.18)] and borderline with questionnaire-reported eczema in PIAMA [GEE, OR = 1.33 (0.98-1.81)]. Furthermore, IVS3-116 was associated with questionnaire-reported eczema in KOALA [age 1, OR = 1.44 (1.00-2.07)]. Pooled analysis of questionnaire-reported eczema of both cohorts resulted in a significant association of IVS3-116 with eczema [OR = 1.26 (1.01-1.58)]. Rs3822357 (A-allele) associated with protection for eczema in PIAMA only [questionnaires, OR = 0.19 (0.06-0.63)].

CONCLUSION

  PCDH1 gene variant IVS3-116 associates with eczema in two independent birth cohorts. Combined with previous observations, this indicates a shared genetic susceptibility to BHR, asthma and eczema.

Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species

Arrangements of genes along chromosomes are a product of evolutionary processes, and we can expect that preferable arrangements will prevail over the span of evolutionary time, often being reflected in the non-random clustering of structurally and/or functionally related genes. Such non-random arrangements can arise by two distinct evolutionary processes: duplications of DNA sequences that give rise to clusters of genes sharing both sequence similarity and common sequence features and the migration together of genes related by function, but not by common descent [1], [2], [3]. To provide a background for distinguishing between the two, which is important for future efforts to unravel the evolutionary processes involved, we here provide a description of the extent to which ancestrally related genes are found in proximity.

Towards this purpose, we combined information from five genomic datasets, InterPro, SCOP, PANTHER, Ensembl protein families, and Ensembl gene paralogs. The results are provided in publicly available datasets (http://cgd.jax.org/datasets/clustering/paraclustering.shtml) describing the extent to which ancestrally related genes are in proximity beyond what is expected by chance (i.e. form paraclusters) in the human and nine other vertebrate genomes, as well as the D. melanogaster, C. elegans, A. thaliana, and S. cerevisiae genomes.

With the exception of Saccharomyces, paraclusters are a common feature of the genomes we examined. In the human genome they are estimated to include at least 22% of all protein coding genes. Paraclusters are far more prevalent among some gene families than others, are highly species or clade specific and can evolve rapidly, sometimes in response to environmental cues. Altogether, they account for a large portion of the functional clustering previously reported in several genomes.

Role of PCDH10 and its hypermethylation in human gastric cancer

Epigenetic changes of genomic DNA are involved in the development and progression of many cancers. Aberrant methylation of CpG islands in the promoter regions of certain tumor-suppressor genes (TSG) is frequently observed in cancer cells. Protocadherin 10 (PCDH10), a member of the cadherin superfamily, is a recently identified putative TSG. PCDH10 is frequently silenced in many solid tumors. However, the role of PCDH10 in gastric cancer is largely unknown. In this study, we examined the expression and methylation status of PCDH10 in gastric cancer cells and tissues by real time PCR and methylation-specific PCR (MSP), and then investigated the biological function of PCDH10. We found that the expression of PCDH10 was markedly reduced in gastric cancer cells and tissues. The reduced expression correlated with hypermethylation of this gene in its promoter region, as demonstrated by MSP and bisulfite genomic sequencing (BGS) analysis. In addition, pharmacological demethylation using 5-Aza restored the expression of PCDH10 in gastric cancer cells. Over-expression of PCDH10 in gastric cancer cells suppressed cell proliferation and migration, but did not cause marked apoptosis. Over-expression of PCDH10 also suppressed growth of xenograft tumors in nude mice. Thus, PCDH10 functions as a TSG in gastric cancer, and might be a useful target for cancer therapy.

Fusobacterium nucleatum adhesin FadA binds vascular endothelial cadherin and alters endothelial integrity

Fusobacterium nucleatum is a Gram-negative oral anaerobe, capable of systemic dissemination causing infections and abscesses, often in mixed-species, at different body sites. We have shown previously that F. nucleatum adheres to and invades host epithelial and endothelial cells via a novel FadA adhesin. In this study, vascular endothelial (VE)-cadherin, a member of the cadherin family and a cell-cell junction molecule, was identified as the endothelial receptor for FadA, required for F. nucleatum binding to the cells. FadA colocalized with VE-cadherin on endothelial cells, causing relocation of VE-cadherin away from the cell-cell junctions. As a result, the endothelial permeability was increased, allowing the bacteria to cross the endothelium through loosened junctions. This crossing mechanism may explain why the organism is able to disseminate systemically to colonize in different body sites and even overcome the placental and blood-brain barriers. Co-incubation of F. nucleatum and Escherichia coli enhanced penetration of the endothelial cells by the latter in the transwell assays, suggesting F. nucleatum may serve as an 'enabler' for other microorganisms to spread systemically. This may explain why F. nucleatum is often found in mixed infections. This study reveals a possible novel dissemination mechanism utilized by pathogens.

Replication timing: a fingerprint for cell identity and pluripotency

Many types of epigenetic profiling have been used to classify stem cells, stages of cellular differentiation, and cancer subtypes. Existing methods focus on local chromatin features such as DNA methylation and histone modifications that require extensive analysis for genome-wide coverage. Replication timing has emerged as a highly stable cell type-specific epigenetic feature that is regulated at the megabase-level and is easily and comprehensively analyzed genome-wide. Here, we describe a cell classification method using 67 individual replication profiles from 34 mouse and human cell lines and stem cell-derived tissues, including new data for mesendoderm, definitive endoderm, mesoderm and smooth muscle. Using a Monte-Carlo approach for selecting features of replication profiles conserved in each cell type, we identify “replication timing fingerprints” unique to each cell type and apply a k nearest neighbor approach to predict known and unknown cell types. Our method correctly classifies 67/67 independent replication-timing profiles, including those derived from closely related intermediate stages. We also apply this method to derive fingerprints for pluripotency in human and mouse cells. Interestingly, the mouse pluripotency fingerprint overlaps almost completely with previously identified genomic segments that switch from early to late replication as pluripotency is lost. Thereafter, replication timing and transcription within these regions become difficult to reprogram back to pluripotency, suggesting these regions highlight an epigenetic barrier to reprogramming. In addition, the major histone cluster Hist1 consistently becomes later replicating in committed cell types, and several histone H1 genes in this cluster are downregulated during differentiation, suggesting a possible instrument for the chromatin compaction observed during differentiation. Finally, we demonstrate that unknown samples can be classified independently using site-specific PCR against fingerprint regions. In sum, replication fingerprints provide a comprehensive means for cell characterization and are a promising tool for identifying regions with cell type-specific organization.

While continued advances in stem cell and cancer biology have uncovered a growing list of clinical applications for stem cell technology, errors in indentifying cell lines have undermined a number of recent studies, highlighting a growing need for improvements in cell typing methods for both basic biological and clinical applications of stem cells. Induced pluripotent stem cells (iPSCs)—adult cells reprogrammed to a pluripotent state—show great promise for patient-specific stem cell treatments, but more efficient derivation of iPSCs depends on a more comprehensive understanding of pluripotency. Here, we describe a method to identify sets of regions that replicate at unique times in any given cell type (replication timing fingerprints) using pluripotent stem cells as an example, and show that genes in the pluripotency fingerprint belong to a class previously shown to be resistant to reprogramming in iPSCs, identifying potential new target genes for more efficient iPSC production. We propose that the order in which DNA is replicated (replication timing) provides a novel means for classifying cell types, and can reveal cell type specific features of genome organization.

Characterization of protocadherin-1 expression in primary bronchial epithelial cells: association with epithelial cell differentiation

Protocadherin-1 (PCDH1) is a novel susceptibility gene for asthma that is expressed in airway epithelium. We aimed to characterize PCDH1 mRNA transcripts and protein expression in primary bronchial epithelial cells and to determine regulation of PCDH1 during mucociliary differentiation. Total RNA and protein were isolated from human primary bronchial epithelial cells. PCDH1 transcripts were characterized by rapid amplification of cDNA ends in bronchial epithelial cells of 4 subjects. PCDH1 expression was quantified by quantitative RT-PCR and Western blotting in bronchial epithelial cells directly ex vivo and after air liquid interface (ALI) or submerged culture. We identified 5 novel exons on the 5' end and 1 exon on the 3' end of PCDH1. Novel transcripts showed major variation in expression of intracellular conserved motifs. Expression levels of PCDH1 transcripts encoding exon 1-2 were 4-fold higher, and transcripts encoding exon 3-4 were 15-fold higher in freshly isolated bronchial epithelial cells than in submerged cultures. PCDH1 mRNA (3- to 8-fold) and protein levels (2- to 3-fold) were strongly up-regulated during mucociliary differentiation of primary bronchial epithelial cells in ALI cultures. In summary, PCDH1 transcripts display remarkable variability in expression of conserved intracellular signaling domains. Enhanced PCDH1 expression levels strongly correlate with differentiation of bronchial epithelial cells.

Spectrum of phenotypes in female patients with epilepsy due to protocadherin 19 mutations

PURPOSE

To describe clinical and neuropsychological features of six consecutive sporadic girls with protocadherin 19 (PCDH19) mutations.

METHODS

Following recent descriptions of PCDH19 mutation in girls with epilepsy, we sequenced this gene in patients with infantile or early childhood seizures onset, either focal or generalized, without an obvious etiology.

KEY FINDINGS

Mean age at the time of the study was 13.5 ± 11 years. Mean age at seizure onset was 15.5 ± 11 months (range 9-38). All patients experienced clusters of either focal or generalized seizures, precipitated during febrile illness in five patients. Attacks were very frequent at onset, but they became less numerous during follow-up. Ictal electroencephalography (EEG) showed temporal lobe involvement in five patients. Periictal EEG showed focal or multifocal epileptiform and slow abnormalities. Cognitive impairment became obvious after seizure onset in three patients and was associated with autistic features in two. Genetic analysis revealed five new and one known de novo PCDH19 mutation that were missense in four and frameshift in two. Variants are clustered in the large exon 1, corresponding to the extracellular domain of the PCDH19 protein.

SIGNIFICANCE

Our findings emphasize that de novo PCDH19 mutations are associated with infantile or early childhood onset of febrile or afebrile seizures often occurring in clusters. Cognitive impairment is not constantly present and autistic features are observed in some patients. Most patients have a "stormy" seizure onset, often related to fever; however, seizure severity does not clearly correlate with the degree of cognitive deficit. PCDH19 is likely a major epilepsy gene; phenotypes associated with mutations of this gene range from epileptic encephalopathies to mild epilepsy, yet large series of patients will be necessary to fully delineate phenotypic spectrum.

Protocadherin-12 cleavage is a regulated process mediated by ADAM10 protein: evidence of shedding up-regulation in pre-eclampsia

Protocadherins are a group of transmembrane proteins with homophilic binding activity, members of the cadherin superfamily. Apart from their role in adhesion, the cellular functions of protocadherins are essentially unknown. Protocadherin (PCDH)12 was previously identified in invasive trophoblasts and endothelial and mesangial cells in the mouse. Invalidation studies revealed that the protein was required for optimal placental development. In this article, we show that its human homolog is abundantly expressed in various trophoblast subtypes of the human placenta and at lower levels in endothelial cells. We demonstrate that PCDH12 is shed at high rates in vitro. The shedding mechanism depends on ADAM10 and results in reduced cellular adhesion in a cell migration assay. PCDH12 is subsequently cleaved by the γ-secretase complex, and its cytoplasmic domain is rapidly degraded by the proteasome. PCDH12 shedding is regulated by interlinked intracellular pathways, including those involving protein kinase C, PI3K, and cAMP, that either increase or inhibit cleavage. In endothelial cells, VEGF, prostaglandin E(2), or histamine regulates PCDH12 shedding. The extracellular domain of PCDH12 was also detected in human serum and urine, thus providing evidence of PCDH12 shedding in vivo. Importantly, we observed an increase in circulating PCDH12 in pregnant women who later developed a pre-eclampsia, a frequent pregnancy syndrome and a major cause of maternal and fetal morbidity and mortality. In conclusion, we speculate that, like in mice, PCDH12 may play an important role in human placental development and that proteolytic cleavage in response to external factors, such as cytokines and pathological settings, regulates its activity.