Aristidis Charonis

Implementation of proteomic biomarkers: Making it work

Eur J Clin Invest 2012; 42 (9): 1027–1036

Prox1 Regulates the Notch1-Mediated Inhibition of Neurogenesis

During development of the spinal cord, Prox1 controls the balance between proliferation and differentiation of neural progenitor cells via suppression of Notch1 gene expression.

Altered intestinal tight junctions’ expression in patients with liver cirrhosis: a pathogenetic mechanism of intestinal hyperpermeability

Eur J Clin Invest 2012; 42 (4): 439–446

Altered expression of calreticulin during the development of fibrosis

Tissue damage following injury leads to inflammation and fibrosis. To understand the molecular mechanisms and the proteins involved in the fibrotic process, we used the well‐established unilateral ureteric obstruction rat model and we analyzed the alterations at early and late time intervals using a classical proteomic approach. Data analysis demonstrates a correlation between calreticulin up‐regulation and progression of fibrosis. Calreticulin is involved in Ca++ homeostasis but has not been previously implicated in animal models of fibrosis. Proteomic analysis consistently revealed up‐regulation of calreticulin in both early and late time intervals. These findings were further confirmed by biochemical and morphological approaches. Next, animal models of lung fibrosis (bleomycin‐induced) and heart fibrosis (desmin‐null) were examined. In the lung model, calreticulin expression was up‐regulated from early time intervals, whereas in the heart model no change in the expression of calreticulin was observed. In addition, TGF‐β, a well known major contributing factor in several fibrotic processes, was found to up‐regulate calreticulin in cultured human proximal tubule epithelial cells. The above observations suggest that calreticulin might be involved in fibrotic processes; however the mechanism(s) underlying its possible involvement are yet unresolved.

Enterocytes’ tight junctions: From molecules to diseases

Tight junctions (TJs) are structures between cells where cells appear in the closest possible contact. They are responsible for sealing compartments when epithelial sheets are generated. They regulate the permeability of ions, (macro) molecules and cells via the paracellular pathway. Their structure at the electron microscopic level has been well known since the 1970s; however, only recently has their macromolecular composition been revealed. This review first examines the major macromolecular components of the TJs (occludin, claudins, junctional adhesion molecule and tricellulin) and then the associated macromolecules at the intracellular plaque [zonula occludens (ZO)-1, ZO-2, ZO-3, AF-6, cingulin, 7H6]. Emphasis is given to their interactions in order to begin to understand the mode of assembly of TJs. The functional significance of TJs is detailed and several mechanisms and factors involved are discussed briefly. Emphasis is given to the role of intestinal TJs and the alterations observed or speculated in diverse disease states. Specifically, intestinal TJs may exert a pathogenetic role in intestinal (inflammatory bowel disease, celiac disease) and extraintestinal diseases (diabetes type 1, food allergies, autoimmune diseases). Additionally, intestinal TJs may be secondarily disrupted during the course of diverse diseases, subsequently allowing the bacterial translocation phenomenon and promoting the systemic inflammatory response, which is often associated with clinical deterioration. The major questions in the field are highlighted.

Whole-transcriptome analysis of UUO mouse model of renal fibrosis reveals new molecular players in kidney diseases

Transcriptome analysis by RNA-seq technology allows novel insights into gene expression and regulatory networks in health and disease. To better understand the molecular basis of renal fibrosis, we performed RNA-seq analysis in the Unilateral Ureteric Obstruction (UUO) mouse model. We analysed sham operated, 2- and 8-day post-ligation renal tissues. Thousands of genes with statistical significant changes in their expression were identified and classified into cellular processes and molecular pathways. Many novel protein-coding genes were identified, including critical transcription factors with important regulatory roles in other tissues and diseases. Emphasis was placed on long non-coding RNAs (lncRNAs), a class of molecular regulators of multiple and diverse cellular functions. Selected lncRNA genes were further studied and their transcriptional activity was confirmed. For three of them, their transcripts were also examined in other mouse models of nephropathies and their up- or down-regulation was found similar to the UUO model. In vitro experiments confirmed that one selected lncRNA is independent of TGFβ or IL1b stimulation but can influence the expression of fibrosis-related proteins and the cellular phenotype. These data provide new information about the involvement of protein-coding and lncRNA genes in nephropathies, which can become novel diagnostic and therapeutic targets in the near future.

The KUPKB: a novel Web application to access multiomics data on kidney disease

The information gathered from the large number of omics experiments in renal biology is underexplored, as it is scattered over many publications or held in supplemental data. To address this, we have developed an open‐source Kidney and Urinary Pathway Knowledge Base (KUPKB) that facilitates simple exploration of these omics data. The KUPKB currently comprises 220 data sets (miRNA, mRNA, proteins, and metabolites) extracted from existing publications or databases. Researchers can explore the integrated data using the iKUP browser, and a simple template is provided to submit new omics data sets to the knowledge base. As an example of iKUPs use, we show how we identified, in silico, calreticulin as a protein induced in human interstitial fibrosis and tubular atrophy (IFTA) in chronic kidney transplant rejection; a link that would have been difficult to establish using existing Web‐based tools. Using immunohistochemistry, we validated in vivo this in silico result in human and rat biopsies of IFTA, thus identifying calreticulin as a potential new player in chronic kidney transplant rejection. The KUPKB provides a simple tool that enables users to quickly survey a wide range of omics data sets and has been shown to facilitate rapid hypothesis generation in the context of renal pathophysiology.—Klein, J., Jupp, S., Moulos, P., Fernandez, M., Buffin‐Meyer, B., Casemayou, A., Chaaya, R., Charonis, A., Bascands, J.‐L., Stevens, R., Schanstra, J. P. The KUPKB: a novel Web application to access multiomics data on kidney disease. FASEB J. 26, 2145‐2153 (2012). www.fasebj.org

Renal fibrosis: Insight from proteomics in animal models and human disease

Chronic kidney disease (CKD) is the end‐point of a number of renal and systemic diseases. The high incidence and financial burden of CKD makes it imperative to diagnose CKD at early stages when therapeutic interventions are far more effective. A key component of CKD is the development of renal fibrosis. Renal fibrosis is a complex process, associated with many cell types and pathways, resulting in structural and functional alterations. Identification of specific biomarkers of renal fibrosis may thus not only help us to understand the pathophysiological mechanisms involved in this process, but also improve diagnosis in the clinic. In this review, the existing literature on proteomic approaches to study renal fibrosis is presented and evaluated. The importance of using animal models along with patient material is discussed and future directions, considered key to this field, are proposed.

Intestinal epithelial cell proliferation, apoptosis and expression of tight junction proteins in patients with obstructive jaundice.

Eur J Clin Invest 2011; 41 (2): 117–125

Basement membrane peptides: functional considerations and biomedical applications in autoimmunity.

Basement membranes are specialized extracellular matrices that surround certain cell types (muscle cells, adipose cells, etc) and are present under the basal surface of cells exhibiting polarity (epithelial, endothelial and mesothelial cells). They have a unique macromolecular composition, consisting mainly of type IV collagen isoforms, laminin isoforms, entactin/nidogen, and perlecan. These components self associate and interact with each other to form networks. Other macromolecules may be found in specialized basement membranes. In this short review, the role of selected basement membrane proteins in autoimmune diseases will be highlighted. As an example, Goodpastures syndrome will be presented and the relatively long quest for identification of the antigenic epitope on specific domains of the alpha3(IV)NC1 will be summarized. Chagas disease will be discussed as an example of laminin-mediated autoimmunity, with emphasis on the role of sugar-based antigenic epitope(s) will be presented. Immune-mediated tubulointerstitial nephritis will be introduced and the role of a synthetic peptide in detecting proximal tubule damage in acute renal failure will be discussed. Auto-immune diseases where other basement membrane macromolecules are involved will be mentioned. Finally, the importance of understanding the functions served by domains at close proximity to the antigenic epitope(s) will be highlighted.