Merging experimental data andin silicoanalysis: a systems-level approach to autoimmune disease and cancer

Cdh11: Roles in different diseases and potential value in disease diagnosis and treatment

Cadherin is a homophilic, Ca2+-dependent cell adhesion glycoprotein that mediates cell-cell adhesion. Among them, Cadherin-11 (CDH11), as a classical cadherin, participates in and influences many crucial aspects of human growth and development. Furthermore, The involvement of CDH11 has been identified in an increasing number of diseases, primarily including various tumorous diseases, fibrotic diseases, autoimmune diseases, neurodevelopmental disorders, and more. In various tumorous diseases, CDH11 acts not only as a tumor suppressor but can also promote migration and invasion of certain tumors through various mechanisms. Likewise, in non-tumorous diseases, CDH11 remains a pivotal factor in disease progression. In this context, we summarize the specific functionalities and mechanisms of CDH11 in various diseases, aiming to gain a more comprehensive understanding of the potential value of CDH11 in disease diagnosis and treatment. This endeavor seeks to provide more effective diagnostic and therapeutic strategies for clinical management across diverse diseases.

Targeting the genetic landscape of oral potentially malignant disorders has the potential as a preventative strategy in oral cancer

This study reviews the molecular landscape of oral potentially malignant disorders (OPMD). We examine the impact of tumour heterogeneity, the spectrum of driver mutations (TP53, CDKN2A, TERT, NOTCH1, AJUBA, PIK3CA, CASP8) and gene transcription on tumour progression. We comment on how some of these mutations impact cellular senescence, field cancerization and cancer stem cells. We propose that OPMD can be monitored more closely and more dynamically through the use of liquid biopsies using an appropriate biomarker of transformation. We describe new gene interactions through the use of a systems biology approach and we highlight some of the first studies to identify functional genes using CRISPR-Cas9 technology. We believe that this information has translational implications for the use of re-purposed existing drugs and/or new drug development. Further, we argue that the use of digital technology encompassing clinical and laboratory-based data will create relevant datasets for machine learning/artificial intelligence. We believe that therapeutic intervention at an early molecular premalignant stage should be an important preventative strategy to inhibit the development of oral squamous cell carcinoma and that this approach is applicable to other aerodigestive tract cancers.

CDH11 inhibits proliferation and invasion in head and neck cancer

BACKGROUND

In this study, we use a bioinformatics-based strategy to nominate a tumor suppressor gene cadherin-11 (CDH11) and investigate its role in growth and invasion in head and neck squamous cell carcinoma (HNSCC).

METHODS

Using the Oncomine^™ database to compare HNSCC and normal specimens, CDH11 was nominated as having a role in HNSCC. CDH11 expression in HNSCC was evaluated by immunohistochemistry on a tissue microarray (TMA) and immunoblotting and immunofluorescence of cell lines. The functional impact of CDH11 on proliferation and invasion was evaluated after siRNA-mediated knockdown.

RESULTS

In silico analysis suggested that CDH11 is overexpressed in HNSCC compared to normal specimens. HNSCC TMA exhibited a small but significant increase in intensity and proportion of CDH11. By immunoblot analysis, CDH11 was higher in 4/7 HNSCC cell lines compared to normal keratinocytes; CDH11 was highly upregulated in UM-SCC-47 and UM-SCC-74A and detectable in UM-SCC-14A and UM-SCC-29 cell lines. Downregulation of CDH11 in both UM-SCC-29 and UM-SCC-47 using two different siRNAs enhanced proliferation and invasion.

CONCLUSION

CDH11 inhibits cell proliferation and invasion of HNSCC. This suggests that CDH11 functions as a tumor suppressor gene in head and neck cancer. Our findings emphasize the importance of verifying in silico findings with functional studies.

Systems biology approaches to enhance our understanding of drug hypersensitivity reactions

Hypersensitivity drug reactions (HDRs) encompass a wide spectrum of unpredictable clinical entities. They represent an important health problem, affecting people of all ages, and lead to a large strain on the public health system. Here, we summarize experiments that use high-throughput genomics technologies to investigate HDRs. We also introduce the field of systems biology as a relatively recent discipline concerned with the integration and analysis of high-throughput data sets such as DNA microarrays and next-generation sequencing data. We describe previous studies that have applied systems biology techniques to related fields such as allergy and asthma. Finally, we present a number of potential applications of systems biology to the study of HDRs, in order to make the reader aware of the types of analyses that can be performed and the insights that can be gained through their application.

Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps

Cancerogenesis is driven by mutations leading to aberrant functioning of a complex network of molecular interactions and simultaneously affecting multiple cellular functions. Therefore, the successful application of bioinformatics and systems biology methods for analysis of high-throughput data in cancer research heavily depends on availability of global and detailed reconstructions of signalling networks amenable for computational analysis. We present here the Atlas of Cancer Signalling Network (ACSN), an interactive and comprehensive map of molecular mechanisms implicated in cancer. The resource includes tools for map navigation, visualization and analysis of molecular data in the context of signalling network maps. Constructing and updating ACSN involves careful manual curation of molecular biology literature and participation of experts in the corresponding fields. The cancer-oriented content of ACSN is completely original and covers major mechanisms involved in cancer progression, including DNA repair, cell survival, apoptosis, cell cycle, EMT and cell motility. Cell signalling mechanisms are depicted in detail, together creating a seamless ‘geographic-like' map of molecular interactions frequently deregulated in cancer. The map is browsable using NaviCell web interface using the Google Maps engine and semantic zooming principle. The associated web-blog provides a forum for commenting and curating the ACSN content. ACSN allows uploading heterogeneous omics data from users on top of the maps for visualization and performing functional analyses. We suggest several scenarios for ACSN application in cancer research, particularly for visualizing high-throughput data, starting from small interfering RNA-based screening results or mutation frequencies to innovative ways of exploring transcriptomes and phosphoproteomes. Integration and analysis of these data in the context of ACSN may help interpret their biological significance and formulate mechanistic hypotheses. ACSN may also support patient stratification, prediction of treatment response and resistance to cancer drugs, as well as design of novel treatment strategies.

The heparin-binding protein interactome in pancreatic diseases

BACKGROUND

The cellular microenvironment plays an important role in the regulation of homoeostasis and is a source of potential biomarkers and drug targets. In a genome-wide analysis the extracellular proteins that bind to heparin (HBPs) have been shown to form highly modular and interconnected extracellular protein regulatory networks. Using a systems biology approach, we have investigated the role of HBP networks in the normal pancreas and pancreatic digestive diseases.

METHODS

Lists of mRNAs encoding for HBPs associated with the normal pancreas (NP), acute pancreatitis (AP), chronic pancreatitis (CP) and pancreatic ductal adenocarcinoma (PDAC) were obtained using public databases and publications. Networks of the putative protein interactomes derived from mRNA expression data of HBPs were built and analysed using cluster analysis, gene ontology term enrichment and canonical pathways analysis.

RESULTS

The extracellular heparin-binding putative protein interactomes in the pancreas were better connected than their non heparin-binding counterparts, having higher clustering coefficients in the normal pancreas (0.273), acute pancreatitis (0.457), chronic pancreatitis (0.329) and pancreatic ductal adenocarcinoma (0.269). 'Hepatic Fibrosis/Hepatic Stellate Cell Activation' appears to be a significant canonical pathway in pancreatic homoeostasis in health and disease with a large number of important HBPs.

CONCLUSIONS

Our analyses clearly demonstrate that HBPs form disease-specific and highly connected networks that can be explored for potential biomarkers and as collective drug targets via the modification of heparin binding properties.

Desmosomal adhesion and pemphigus vulgaris: the first half of the story

Pemphigus vulgaris (PV) is a paradigm of autoimmune disease affecting intercellular adhesion. The mechanisms that lead to cell-cell detachment (acantholysis) have crucial therapeutic implications and are currently undergoing major scrutiny. The first part of this review focuses on the classical view of the pathogenesis of PV, which is dominated by the cell adhesion molecules of the desmosome, namely desmogleins (Dsgs). Cloning of the DSG3 gene, generation DSG3 knock-out mice and isolation of monoclonal anti-Dsg3 IgG have aided to clarify the pathogenic mechanisms of PV, which are in part dependent on the fate of desmosomal molecules. These include perturbation of the desmosomal network at the transcriptional, translational, and interaction level, kinase activation, proteinase-mediated degradation, and hyper-adhesion. By the use of PV models, translational research has in turn helped shed light into the basic structure, function, and dynamics of assembly of desmosomal cadherins. The combined efforts of basic and applied research has resulted in tremendous advance into the understanding of epidermal adhesion and helped debunk old myths on the supposedly unique role of desmogleins in the mechanisms of cell-cell detachment in PV.