Here, we analyze and discuss the contribution of the molecular machines operating in the early secretory pathway in the biogenesis of SARS-CoV-2 and their relevance for potential antiviral targeting. The fact that these molecular machines are conserved throughout evolution, together with the redundancy and tissue specificity of their components, provides opportunities in the search for unique proteins essential for SARS-CoV-2 biology that could also be targeted with therapeutic objectives. Finally, we provide an overview of recent evidence implicating proteins of the early secretory pathway as potential antiviral targets with effective therapeutic applications.
RA-map is a fully annotated, expert validated, state-of-the-art knowledge base for RA in the form of a molecular map. BioInfoMiner was used for topological, functional and pharmacogenomic analysis.
The publication is accessible at:
Vidisha Singh, George D Kalliolias, Marek Ostaszewski, Maëva Veyssiere, Eleftherios Pilalis, Piotr Gawron, Alexander Mazein, Eric Bonnet, Elisabeth Petit-Teixeira, Anna Niarakis, RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis, Database, Volume 2020, 2020, baaa017, https://doi.org/10.1093/database/baaa017
In this publication, we introduce PepSimili, an integrated workflow tool, which performs mapping of massive peptide repertoires on whole proteomes and delivers a streamlined, systems-level biological interpretation.
Collaborative publication with DKFZ, ACCC and NHRF on Radiogenomics and Colorectal Cancer towards Precision Medicine
This is a new e-NIOS’ collaborative work on composite biomarker signatures, combining genomics with positron emission tomography (PET) measurements.
The Athens Comprehensive Cancer Center (ACCC) was founded in 2017, in partnership with the German Cancer Research Center (DKFZ) (Heidelberg, Germany) and aims to position itself as the first comprehensive cancer center in Greece based on innovative strategies for precision oncology.
Cambridge, Mass. and Athens, Greece., Sept 11, 2018. Seven Bridges, the leading biomedical data platform and analytics company, and e-NIOS, a biological knowledge discovery start-up, announced a strategic partnership towards data-driven discovery of biomarker signatures. Derivation of robust biomarkers from next generation sequencing and multi-omic data is currently a major bottleneck in precision medicine initiatives. This bottleneck continues to limit the transformation of genomic information into biomedical insights that will improve clinical outcomes through more efficient drug target discovery and more effective patient stratification.
Together, we are leveraging machine learning and physiology to improve and partially automate interpretation of potential biomarkers. Currently, interpretation is largely performed manually, relying on expert decisions. Human experts are both costly and inconsistent. Our partnership will develop efficient and standardized interpretation frameworks which harness the inherent complexity of molecular networks. This partnership has the potential to shift from listing all statistical correlations towards focusing on a smaller set of causal associations.
e-NIOS’ innovative technology enables unsupervised, intelligent translation of -omics data through BioInfoMiner, a cloud platform that resolves biological complexity and derives molecular signatures suitable for data-driven interpretation in different conditions, physiological states and datasets. Additionally, it allows the integration of different -omic layers (genomic, epigenomic, transcriptomic, proteomic, variants). BioInfoMiner can also drive discovery in studies related to plant and microbial systems.
According to e-NIOS’ co-founder Aristotelis Chatziioannou (CEO), “e-NIOS and Seven Bridges share the same vision for data-driven, streamlined computational genomics, integrating all steps from raw data to actionable biological interpretation. The Seven Bridges Platform is a valuable, high-performance cloud environment for the deployment of complex workflows and streamlined processing of massive, genomic datasets. Seven Bridges has been an excellent technological partner for our company as we work together to enable innovative, automated, data-driven biomarker industrial services and applications in the area of precision medicine.”
As Brandi Davis-Dusenbery, CEO of Seven Bridges, explained, “e-NIOS’ technology has the unique ability to combine biological network information with data-driven models. Here we bring together the technical and scientific strengths of both companies to provide a complete solution for the prediction of biomarker associations from raw data. Our strategic partnership supports Seven Bridges’ mission to connect the world’s biomedical information and rapidly transform it into actionable information.”
About Seven Bridges
Seven Bridges is the biomedical data analysis company accelerating breakthroughs in genomics research for cancer, drug development, and precision medicine. Thousands of researchers in government, biotech, and academia use Seven Bridges, including leading global pharmaceutical companies and national genomics projects such as the U.S. National Cancer Institute-funded Cancer Genomics Cloud, the Gabriella Miller Kids’ First Data Center, the Million Veteran Program, and the U.S. National Institutes of Health Data Commons Pilot. To find out more, contact us.
e-NIOS Applications P.C. is a spin-off company of the National Hellenic Research Foundation, founded by a multidisciplinary team with expertise in the fields of Bioinformatics, Genomics, Artificial Intelligence, Data Mining, Operational Research and Decision Support Systems. The company participates in many funded EU Horizon 2020 Research & Innovation networks and has developed sustainable international collaborations with partners such as the National University of Ireland, Galway, the French National Institute of Health and Medical Research (INSERM) the German Anticancer Institute Deutsches Krebsforschungszentrum (DKFZ, Heidelberg) and many Universities and research groups across Europe. Research results obtained through e-NIOS technology have been published in high impact journals (EMBO Molecular Medicine, Cell Metabolism, FASEB, Scientific Reports and Nature Communications). e-NIOS recently filed a joint international patent with INSERM, France, entitled “Method of therapy selection for patients suffering from Glioblastoma”, exploiting results generated through BioInfoMiner. To find out more, contact us.
e-NIOS is excited to sponsor and participate in the 7th European Conference on Computational Biology, 8-12 September, 2018, Athens.
ECCB is the main computational biology event in Europe and will welcome scientists working in a variety of disciplines, including bioinformatics, computational biology, biology, medicine, and systems biology.
On Tuesday September 11, 2018 Eleftherios Pilalis, CTO, will present the BioInfominer platform for streamlined genomic interpretation at the Applications track.
The joint project, entitled “Prioritization and pathway Analysis by MachinE LeArning”, between e-NIOS and Genosalut clinical genomics company, was presented at the PERMIDES Final Conference held on June 12, 2018, in Utrecht, The Netherlands, where fourteen of the best projects presented their results.
The project aimed at the development of an innovative precision medicine application, which integrates clinical and computational expertise, as a decision support tool for diagnosis and treatment of complex diseases. More particularly, an integrated workflow was successfully deployed for patient stratification based on BioInfoMiner biomarker signatures derived from Exome-seq data.
PERMIDES is one out of five European INNOSUP-1-2015 – Cluster facilitated projects for new value chains (funded under EC Call for proposal: H2020-INNOSUP-2015-1), promoting innovation in Personalized Medicine as an Emerging Industry in Europe. PERMIDES targets key solutions for the reconfiguration of the biopharmaceutical value chain towards a Health Economy 4.0 with a special focus on oncology.
New paper involving BioInfoMiner analysis validates proteostasis imbalance as a driver of tumor aggressiveness in Glioblastoma (EMBO Mol. Med.)
Proteostasis imbalance is emerging as a major hallmark of cancer, driving tumor aggressiveness. Evidence suggests that the endoplasmic reticulum (ER), a major site for protein folding and quality control, plays a critical role in cancer development. This concept is valid in glioblastoma multiform (GBM), the most lethal primary brain cancer with no effective treatment.
It was previously demonstrated that the ER stress sensor IRE1α (referred to as IRE1) contributes to GBM progression. The new study entitled “Dual IRE1 RNase functions dictate glioblastoma development” published in EMBO Molecular Medicine provides the first demonstration of a dual role of IRE1 downstream signaling in cancer and opens a new therapeutic window to abrogate tumor progression.
BioInfoMiner analysis was employed in order to define specific IRE1‐dependent gene expression signatures that were confronted to human GBM transcriptomes and shed light to the antagonistic roles of XBP1 mRNA splicing and RIDD on tumor outcomes, mainly through selective remodeling of the tumor stroma.
The research was carried out by an international consortium with the participation of e-NIOS, including among others Université de Bordeaux, Université de Rennes 1, University of Ireland Galway, University of Chile, INSERM, CNRS, National Hellenic Research Foundation and Harvard School of Public Health.