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.


eNIOS was awarded the 1st prize of Pfizer’s accelerator Start4Health

eNIOS was awarded the 1st prize of Start4Health, an accelerator organized by Pfizer’s Center of Digital Innovation.

Start4Health focused on Digital Health and targeted startup companies that develop solutions that can tackle challenges of the health industry, improve the digital experience of patients and promote wellness through technology. eNIOS worked closely with the programme’s experts and presented its technology for acceleration of Precision Medicine, which aims to individualize therapeutic management in a broad spectrum of diseases.

We would like to thank the CDI team and partners involved in the realization of this exciteful programme and congratulate all finalist participants for their exciting and inspiring digital healthtech ventures.


Regulated IRE1α-dependent decay (RIDD)-mediated reprograming of lipid metabolism in cancer (Nature Communications)

Our new paper in Nature Communications, involving functional transcriptomic analysis with the e-NIOS BioInfoMiner platform. BioInfoMiner enables an automated data, but also biology-driven interpretation of omic data, making evident which are the crucial genes driving the phenotypes and how they are interacting.


Almanza A, Mnich K, Blomme A, Robinson CM, Rodriguez-Blanco G, Kierszniowska S, McGrath EP, Le Gallo M, Pilalis E, Swinnen JV, Chatziioannou A, Chevet E, Gorman AM, Samali A. Regulated IRE1α-dependent decay (RIDD)-mediated reprograming of lipid metabolism in cancer. Nat Commun. 2022 May 6;13(1):2493. doi: 10.1038/s41467-022-30159-0. PMID: 35524156; PMCID: PMC9076827.

Integration of Raman spectra with transcriptome data in glioblastoma multiforme defines tumour subtypes and predicts patient outcome

Glioblastoma Multiforme is the most aggressive form of primary brain tumors.

Raman spectroscopy is an imaging technique that has been applied to assess molecular compositions of living cells to characterize cell types and states. However, owing to the diverse molecular species in cells and challenges of assigning peaks to specific molecules, it had not yet been clear how to interpret cellular Raman spectra.

In our new publication in the Journal of Cellular and Molecular Medicine we provide firm evidence that cellular Raman spectra and transcriptomic profiles of glioblastoma can be computationally connected and thus interpreted.

From these analyses, we extract a minimal gene expression signature associated with specific RS profiles and predictive of disease outcome.

This study provides the first association between gene expression and Raman profiles associated with tumor phenotypes (e.g. immune infiltrate). The approach presented in this study could therefore pave the way for near real-time intraoperative tumor characterization and could represent a relevant tool for helping in patient management at a very early stage.

Read the publication here.


e-NIOS is a partner of the international INNOCENT project, with the aim to develop an innovative multifunctional nano-pharmaceutical to overcome the low efficacy and frequent relapses in breast cancer treatment. The use of nano-based delivery systems, together with the benefits of a new generation of epi-drugs and the emergence of robust biomarker data, will help to advance personalized-targeted therapy and the efficacy of treatment for breast and other cancers. The proposed nano-drug will integrate the diagnostic and therapeutic functions within a single nanostructure.

A new paper is publicly accessible here: https://www.mdpi.com/2072-6694/12/12/3622/htm

Announcement of BioS Online Seminars: Digital Skills on Computational Biology for Health Professionals, 15-16 October 2020

Within the framework of the Erasmus days, the BioS project offers further online seminars on modules 1 to 3 to deepen and apply the knowledge acquired in the course. We would like to invite you to join us.


To participate in the BioS Online Seminar, please register under:


After registration, you receive the direct link to the online seminar.

The BioS project offers three online seminars on the topics:


The online seminars give you the opportunity to acquire valuable knowledge for your professional career, to discuss live with experts highly topical issues and to connect with peer learners all around Europe.

Online Seminar 1:
Systemic interpretation of data from different –omic layers and derivation of diagnostic, personalized signatures of molecular biomarkers, assisting medical decision.

e-nios, module 1, Thursday 15th of October, 13.00 – 15.00 CEST

In this online seminar the audience is introduced to the secrets of multi-omic analysis and robust systemic interpretation. This process manages to reveal those active, functional, molecular modules, providing consistent, mechanistic understanding of the myriad of interactions occurring, and enables in-silico extraction of signatures of molecular biomarkers, for a more accurate and robust clinical diagnosis/prognosis. The interpretation of the various types of omics data streams is effected through the web platform BioInfoMiner of e-NIOS, integrating the results of diverse analytic workflows showcasing how to extract predictive signatures for several diseases, without requiring advanced programming skills. Two examples of the data-driven interpretation and extraction of diagnostic signatures both at the gene and variant level will be performed on case studies including data from patients suffering from different cancer types.

Online Seminar 2:

BGU, module 2, Friday, 16th of October,
10.00 – 12.00 CEST

In this online seminar, the theoretical material taught during the BioS course is transformed into practical and applicable skills by working with contemporary examples. You will learn how to use predictive methods, such as COVID19 PCR tests, how to interpret results, and how evidence affects the test credibility.

Online Seminar 3:

GOC, module 3, Friday, 16th of October,
13.00 – 15.00 CEST

In this online seminar, the role of tumor genetic profiling, molecular imaging and targeted therapies in the treatment of non-small cell lung cancer will be presented.


To participate in the BioS Online Seminar, please register under:


After registration, you receive the direct link to the online seminar.

BioInfoMiner elucidates the role of the early secretory pathway in SARS-CoV-2 infection


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.

The journeys of CoV-2 in the host cell. Coronavirus infection starts with the binding of the spike protein to cognate receptors. This drives conformational changes that promote fusion of the viral particle with the host cell’s plasma membrane. Once in the cytoplasm, viral particles are uncoated, and the viral RNA genome is translated, producing two polyproteins (pp1a and pp1ab). These polypeptides are proteolytically processed by host and viral proteases, generating nonstructural proteins (nsps). nsps assemble to form the replicase (R), which together with pp1a/pp1ab produces the replicase–polymerase complex. Replicase polymerase complex is responsible for the replication of the viral genome and for the production of subgenomic RNAs. The latter are translated to form structural proteins nucleocapsid (N), spike (S), membrane (M), and envelope (E). In addition to these genomic elements shared by other CoVs, the SARS-CoV-2 genome also contains eight ORFs coding for accessory proteins. Structural proteins are subjected to diverse posttranslational modifications in the ER and Golgi compartments, including disulfide bond and formation N- and O-glycosylation. Structural proteins concentrate in the ERGIC, where they assemble around the genome–nucleocapsid complexes. Mature virions are packed and budded in smooth-walled vesicles and then transported along downstream organelles of the exocytic pathway.

RA-map: a state-of-the-art interactive knowledge base for rheumatoid arthritis

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

New publication on bioinformatic analysis of phage display experiments

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.


Find our new paper here.

The molecular mechanisms underlying inflammatory bowel diseases remain currently not completely understood, and therapeutic options are scarce.

Herein, we have identified that a normally endoplasmic reticulum resident protein, AGR2, exhibits tightly regulated secretion mechanisms that are perturbed in Crohn’s disease. We demonstrate that the extracellular release of AGR2 leads to the chemoattraction of monocytes, thereby suggesting extracellular AGR2’s pro‐inflammatory functions, that can be blocked using specific antibodies.

As a consequence, this discovery could represent an appealing therapeutic approach to attenuate the inflammatory burden in Crohn’s disease.

Join us at Bio-IT World 2019 Boston

e-NIOS is excited to participate in Bio-IT World, 16-18 April 2019, Boston. Join us at Seven Bridges’ booth #332 in the Exhibit Hall, for a demonstration of signature-based interpretation on the Seven Bridges Platform with BioInfoMiner!