European & Developing Countries Clinical Trials Partnership (EDCTP)
Horizon 2020 "Research and Innovation Actions" DESCA
PI: Dr Dimitrios Vlachakis (AUA, Greece)

Biochemical Adjustments of native EBOV Glycoprotein in Patient Sample to Unmask target-Epitopes for Rapid Diagnostic Testing.

Ebolavirus and Marburgvirus are two genera of the negative sense RNA virus family Filoviridae, order mononegavirales. Filoviruses cause rare but fatal viral hemorrhagic fevers-VHF in equatorial Africa--with potential for regional and international urban spread. Both virus associated VHFs present with a similar prodrome; mimicking several tropical infectious diseases. Early detection is important for mobilizing swift response and control. Existing technologies for filovirus detection are not suited for point of care (POC) use, being expensive, not fast-enough and requiring laboratory facilities absent in many villages where index cases occur. While 2 rapid diagnostic tests (RDTs) have recently emerged detecting EBOV at the point of care (POC), there are no pan-filovirus targeted RDTs. This project could yield the 1st ever prototypes of RDTs for the duo-detection of EBOV and MARV. Pan-filovirus RDTs are required to ensure early detection, response and control of the on-going and future outbreaks. Moreover, the mAbs presented are candidate therapeutics.

IRN - FrontINov

EC "International Research Network" project (Fiche dépôt IRN INSB 2019_13062019)
PI: Dr Dimitrios Vlachakis (AUA, Greece)

Frontiers in Inflammation : Novel technologies to harness innate immune responses

The implication of pathological nucleic acid sensing pathways in human pathologies, ranging from viral infections, malignancies to auto-immune disorder, has emerged over recent years. The canonical pathway involved in detection of pathological nucleic acids relies on the STING adaptor protein, the activation of which promoting the production of inflammatory cytokines, including type I interferons (IFNα and IFNβ). Notwithstanding the discovery of drugs targeting STING, it is as of today difficult to predict the outcome of activating or inhibiting STING in specific pathologies. In this context, we propose to use novel and emerging technologies to investigate nucleic acid immunity from new perspectives. Indeed, taking advantage of state of the art multidisciplinary approaches we ambition to unravel (i) novel regulatory mechanisms that are involved in nucleic acid detection, (ii) novel cell type/tissue specific nucleic sensing routes and (iii) the cross-talk between such pathways. To achieve this goal, several groups from the consortium have already obtained proof of concept for implementation of nanotechnologies in the study of inflammation. To strengthen the interactions between the teams and exchange knowledge and know-hows, the establishment of an International Research Network (IRN) is essential. The network will primarily rely on core interactions between the Laguette team (Molecular Basis of Inflammation, IGH, Montpellier) and the Cigler team (Synthetic Nanochemistry, IOCB, Czech Republic) and their main collaborators. Additional teams that have a strong interest in emerging technologies will be considered for consolidation of the proposed network. We will encourage young researchers (student and post docs) to take an active part in IRN activities by supporting student-organized workshops. Using the proposed combined approaches should allow both the identification of novel therapeutic target and unravel biomarkers that will allow patient stratification to efficiently harness innate immune pathways to the benefit of patients. Thus, the FrontINov IRN will allow break-through discoveries and contribute to the emergence of new avenues to tackle inflammation related pathologies..


European University for Smart Urban Coastal Sustainability (EU‐CONEXUS)
Researcher: Dr Dimitrios Vlachakis

The EU-CONEXUS partner universities share a common vision with regard to a new form of transnational university which issues common European degrees and common European diplomas.

Students, staff and teaching personnel participate in tailor‐made mobility programmes adapted to their studies and/or their professional development path. Embedded mobilityin every study programme will enhance the language skills and intercultural competences of the students and also reinforce their sense of European identity and citizenship. Integrated bachelor‐, master and PhD programmes will combine the strengths in education, research and innovation of the partners. They will represent a unique point of entry in Europe and the world for studies in the subject area of smart urban coastal sustainability studies. Students will be able to customize their personal study programme across disciplines and following their personal time schedule by using digital means of education. EU-CONEXUS will operatein close relationship with the socio‐economic environment. It will respond to actual needs of relative industries, support the regional innovation and development and foster an entrepreneurial mindset of their students. EU-CONEXUS understands itself as a service‐oriented institution that aims at the inclusion of a diversity of students through personalization and individualization of its study programme. “Smart” and innovative pedagogies (e‐learning, flexible course programme (major/minor approach), virtual/physical mobility, project‐based learning, work‐based experiences…) will create a new form of university open for students from different backgrounds and with divergent interests and needs for education and training. The final goal is to become the global leader in higher education and research in the area of smart urban coastal sustainability, with a perspective of expansion beyond the size of its founding consortium.


Horizon 2020 "Research and Innovation Actions" (No 690140)
Researcher: Dr Dimitrios Vlachakis (WP4 Leader)

FrailSafe aims to better understand frailty and its relation to co-morbidities - Project ended in 2019

FrailSafe is trying to identify quantitative and qualitative measures of frailty through advanced data mining approaches on multiparametric data and use them to predict short and long-term outcome and risk of frailty; to develop real life sensing (physical, cognitive, psychological, social) and intervention (guidelines, real-time feedback, Augmented Reality serious games) platform offering physiological reserve and external challenges; to provide a digital patient model of frailty sensitive to several dynamic parameters, including physiological, behavioural and contextual; this model being the key for developing and testing pharmaceutical and non-pharmaceutical interventions; to create “prevent-frailty” evidence-based recommendations for the elderly; to strengthen the motor, cognitive, and other “anti-frailty” activities through the delivery of personalised treatment programmes, monitoring alerts, guidance and education; and to achieve all with a safe, unobtrusive and acceptable system for the ageing population while reducing the cost of health care systems.

MS Azure for Genomics

Microsoft Cloud-Based Genomics Grant
PI: Dr Dimitrios Vlachakis

A scalable and secure secondary analysis of genomes, starting from raw reads and producing aligned reads and variant calls

Flaviviridae is a family of viruses that infect vertebrates. Distinct viral structures of this family are visible in thin sections of infected tissue. The size of virion has been estimated by filtration. Virions of the flaviviridae family are enveloped and slightly pleomorphic during their life cycle. They are spherical in shape and usually 40-60 nm in diameter. Their nucleocapsids are isometric and sometimes penetrated by stain. The usual size of the nucleocapsids is 25-30 nm in diameter and they have polyhedral symmetry. Virions of the flaviviridae family contain one molecule of linear positive-sense single stranded RNA. The total genome length is 9500-12500 nt. The 5' end of the genome has a cap, or a genome-linked protein (VPg). The 3' end regularly has no poly (A) tract (except some strains of tick-borne encephalitis complex of flaviviruses, which have a poly (A) tract). Their nucleic acid material is fully encapsidated and solely genomic. The genome of flaviviridae features a 5' end that encodes structural proteins, whereas the non-structural proteins including protease, helicase and polymerase, are encoded at the 3' end. To date neither specific antiviral treatments exist nor are there any vaccines available for either infection. Thus there is an urgent need for new therapies. Herein, an effort will be made to shed light to the genetic, evolutionary and structural features of the viral helicase enzymes towards the establishment of a versatile drug design platform of potent antiviral agents. The proposed project will involve full phylogenetic and biostatistical analysis of viral genomes and comparative/homology modeling of helicase enzymes. Eventually a drug design platform will be established and a series of drug-like inhibitors of the viral helicase enzyme will be in silico scored and evaluated.

AWS Amazon Cloud

PI: Dr Dimitrios Vlachakis

Teaching Undergraduate students cloud computing for professional development in modern in metagenomics

Statistical analysis of genomic data. Given the rapid advances in genomics and bioinformatics that have taken place in the past few years, there is a growing need for analysing vast amount of data and interpreting their results. Large-scale cancer genome studies have successfully applied some preliminary integration approaches. To this end, we aim to analyse multi-source data using association statistics to estimate pair wise as well as group dependencies in the data. Multivariate analysis and likelihood-based inference will be also employed to estimate data patterns. The ultimate goal is to establish a methodology to integrate different data which measure multiple genomic features and discover or validate findings that would not be discovered by analysing each data independently. Good programming skills are a pre-requisite (e.g. R statistical software, C/C++).


Ereynw - Dimiourgw - Kainotomw
PI: Dr Dimitrios Vlachakis Project Coordinator

Application of high-throughput techniques in combination with comparative genomic analysis of mRNAs, non-coding RNAs, proteins, and small molecules that bind or are encapsulated in secreted lipid membranes (exosomes) in human breast milk

The aim of this project is to develop research infrastructures in academia and the private sector for the comparative analysis of human milk with three locally traded animal milks. These will be sheep and goats (domestic sheep and goats) and cattle from different regions. In particular, a high-quality, quantitative and qualitative study will be conducted for the analysis of the membranes and intracellular composition of the major classes of secreted extracellular vesicles and other microparticle sizes. The long term aim is to establish topological networks of phylogenetic distance across human biopolymers. The proposed multilevel bioinformatics analysis will show which animal milk has the highest phylogenetic affinity for human milk based on specific nucleotide and amino acid sequences, and thus the highest nutritional value for neonates. Application of high-throughput techniques in combination with comparative genomic analysis of mRNAs, non-coding RNAs, proteins, and small molecules that bind or are encapsulated in secreted lipid membranes (exosomes). Exosomes represent packages carrying regulated conserved sets of functionally enriched biopolymers, which if understood will enable the molecular fingerprinting of a large number of animal sources with regards to their similarity to human breast milk. The present study will also examine the comparison of existing milk processing techniques for which it is most nutritionally and medically appropriate, as well as the certification of innovative milk production and maintenance methods. Finally, it will create the necessary scientific and technological bases in the academy for the manufacture and production of specially modified extracellular vesicles (exosomes) as natural breastfeeding medical supplements in animal milk and thereby enhance the specially-prepared high-quality animal milk with immediate beneficial and therapeutic effect for infants, and in particular early infants, or infants suffering from a series of metabolic and developmental syndromes.


ESPA Young Researchers Support / phase B' (No 47 - Life Sciences & Medicine)
PI: Dr Dimitrios Vlachakis for PhD students Eleni Papakonstantinou & Katerina Pierouli

Rational Drug Design of Novel Antiviral Agents against the Helicase Enzyme of the Yellow Fever Virus

The Flaviviridae family of viruses infects vertebrates and it is primarily spread through arthropod vectors. The Yellow Fever virus belongs to the Flaviviridae family. Although, there are very limited data regarding the Yellow Fever virus and its epidemiology, there have been reported few cases Yellow Fever infection in Greece. However, despite the severity of Flaviviridae causing diseases (e.g. Dengue fever, Classical swine fever, Japanese encephalitis), currently there is not any available anti-flaviviridae therapy. Thus, there is a need for the development of effective anti-Yellow Fever viral pharmaceutical strategies. It has been shown that RNA helicases, which are involved in duplex unwinding during viral RNA replication, represent promising antiviral targets. Therefore, the inhibition of the Yellow Fever viral helicase would be an effective approach of interrupting the life cycle of the Yellow Fever virus. The proposed research will be directed towards the computer-aided development of a series of drug-like low molecular weight compounds capable of inhibiting the helicase enzyme of Yellow Fever virus. Results derived from a repertoire of multi-disciplinary bioinformatics and statistical methods would enhance the understanding of the mechanism of action of the Yellow Fever viral helicase enzyme. The ultimate goal is to design a series of novel anti-helicase compounds as drug candidates against the Yellow Fever virus while the inhibitory activity of our novel compounds will be evaluated biologically.


IKY postdoctoral scholarship (No 18703 - Life Sciences & Medicine)
PI: Dr Dimitrios Vlachakis for PostDoc Dr Stefanos Leptidis

Single-cell small RNA sequencing (small-seq) from early embryonic cardiac progenitor murine cells

The heart, the first organ to be developed during embryogenesis, is an exceptionally complex tissue, comprised from a variety of cell types. Understanding physiological cardiac development and its relationship to the development of pathological cardiac disease, through transcriptional changes reminiscent of a return to the embryonic gene program, require the careful investigation of their related developmental pathways. A highly significant regulatory layer during cellular differentiation is the post-transcriptional regulation via non-coding RNAs and more specifically microRNAs. Post-transcriptional regulation provides a high degree of flexibility and in many cases microRNAs act as a molecular switch in complex cardiac developmental pathways1. Furthermore, due to their small size and their inherent ability to move through the blood stream, microRNAs constitute exceptional therapeutic targets. Our previous studies in the field of microRNA transcriptomics in the heart, although thorough2, were lacking in the identification of their differential expression per cell-type. Since microRNAs can target a large range of mRNAs, identifying their cell-type specific expression is necessary, both to elucidate the intricate cellular interactions and regulatory pathways, as well as the development of targeted therapeutic approaches.
In this study, we are using data from single-cell small RNA sequencing (small-seq) from early embryonic cardiac progenitor murine cells, which have been isolated already. Our aim is the identification of the transcriptional profile of small RNAs and more specifically microRNAs, during cardiac development. Small-seq sequencing is a novel technology which has been developed in the Karolinska Institute in Sweden and allows us to map the transcriptomic profile of small RNAs on a single-cell level3. Unlike single-cell RNA sequencing (scRNAseq), there are no established data analysis methods in the case of small-seq. In addition, in scRNAseq, years of gene research allow the identification of cell-types based solely on the expression levels of their transcripts, while this is not the case in the field of miRNAs. There are no established marker miRNAs that would allow us to distinguish between different cell-types, during the clustering step of data analysis. Thus, we will also develop a methodology for the identification of cell-types using their microRNA profile, coupled to their predicted targets stemming from a variety of miRNA target prediction algorithms. These data will then be cross-referenced with preliminary data from scRNAseq in the same tissue4, with already identified cell-types. Deciphering the transcriptomic landscape of microRNAs during cardiac development, along with identifying cell-types based on the relationship between their RNA and microRNA fingerprint, enables the in-depth study of the intricate regulatory interactions between cells, cell-types and different embryonic days.
Our proposal, based on cutting-edge technologies that offer single-cell resolution and building on existing data which we have already acquired, constitutes a novel approach for the complete mapping of the transcriptomic profile during cardiac development, paving the way for new therapeutic approaches.


COST Action CA15110
MC sub: Dr Dimitrios Vlachakis (Greece)

Harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research

Biotechnology is an enabling technology that alone, or in combination with cognate technologies, provides the capacity to spur huge leaps in the performance and capabilities of numerous sectors, such as healthcare and medicine, agricultural production, and industrial production. In this context, a prerequisite for modern R&D is a high quality of the research data. By enabling re-use of research assets, research is made considerably more efficient and economical. This can only be achieved reliably and efficiently if these data are generated according to standards and Standard Operating Procedures (SOPs). Standardisation and quality management are thus important drivers in the life sciences and biotechnology, as only data generated with minimum quality assurance can be easily implemented into industrial applications. Furthermore, standards assure and ensure that data become easily accessible, shareable and comparable along the value chain. The use of common standards may hence result in improved efficiency and competitiveness of European life-science research. Moreover, standardisation strategies are required or have gained in importance in the assessment of proposals in the new H2020 framework programme. It was logical then that measures were taken by several initiatives and institutions to develop and implement standards in the life sciences: one of these was set up by the International Organisation for Standardisation (ISO), which is seeking comprehensive agreement on standards in the life sciences, particularly in biotechnology and related fields. Under the auspices of the German Institute for Standardisation (DIN), an international committee (ISO/TC 276 Biotechnology) has been created that will endorse necessary standards and - if necessary - encourage the development of new norms and standards in a top-down approach. Unfortunately, current and new efforts remain fragmented and largely disconnected from each other.
The COST Action CHARME aims to bridge and combine the fragmented areas to achieve a breakthrough in standardisation efforts. CHARME will identify needs and gaps, teaming up with other initiatives and organisations to avoid duplication and overlap of standardisation activities. Only through a common, coordinated, long-term strategy, by active involvement of all stakeholders (from research, industry and policy), can standards be succesfully assimilated into the daily work-flow and thus increase efficiency and competitiveness of European life-science research.

ML4microbiome COST Action

COST Action CA18131
MC sub: Dr Dimitrios Vlachakis (Greece)

Automation opportunities for novel development of ML/Statistics methods targeting microbiome data

In recent years, the human microbiome has been characterised in great detail in several large-scale studies as a key player in intestinal and non-intestinal diseases, e.g. inflammatory bowel disease, diabetes and liver cirrhosis, along with brain development and behaviour. As more associations between microbiome and phenotypes are elucidated, research focus is now shifting towards causality and clinical use for diagnostics, prognostics and therapeutics, where some promising applications have recently been showcased. Microbiome data are inherently convoluted, noisy and highly variable, and non-standard analytical methodologies are therefore required to unlock its clinical and scientific potential. While a range of statistical modelling and Machine Learning (ML) methods are now available, sub-optimal implementation often leads to errors, over-fitting and misleading results, due to a lack of good analytical practices and ML expertise in the microbiome community. Thus, this COST Action network will create productive symbiosis between discovery-oriented microbiome researchers and data-driven ML experts, through regular meetings, workshops and training courses. Together, it will first optimise and then standardise the use of said techniques, following the creation of publicly available benchmark datasets. Correct usage of these approaches will allow for better identification of predictive and discriminatory ‘omics’ features, increase study repeatability, and provide mechanistic insights into possible causal or contributing roles of the microbiome. This Action will also investigate automation opportunities and define priority areas for novel development of ML/Statistics methods targeting microbiome data. Thus, this COST Action will open novel and exciting avenues within the fields of both ML/Statistics and microbiome research.


COST Action CA17103
MC sub: Dr Dimitrios Vlachakis (Greece)

Delivery of Antisense RNA Therapeutics

Antisense oligonucleotides (ASOs) are a new class of drugs that, through very specific targeting, could correct genetic defects for rare inherited diseases, modulate autoimmune or neurodegenerative diseases or target tumors or viruses. However, only a few of such drugs are currently in the market and they have been less effective as expected. The main hurdle for their efficacy seems to be their deficient delivery to target tissues but, while translational research on ASO is surging, very little is known about the mechanisms by which ASOs are taken up by different tissues and specific cells. Regarding delivery, the ASO field is fragmented, with researchers in academia and industry working in isolation on specific diseases, generally focusing on therapeutic effects in target tissues. The main aim of the Delivery of Antisense RNA ThERapeutics (DARTER) Action is to use networking and capacity building in the field of nucleic acid therapy delivery to allow RNA-targeting nucleic acid drugs to reach their full potential and become a mainstream therapeutic option. DARTER will act through 3 Working Groups with research objectives (delivery strategies, model systems, safety and toxicology) and one capacity building group (stakeholder communication) with the objective of achieving consensus on protocols and assessment of ASO delivery and toxicology and training new researchers within a cooperative research framework. DARTER COST network will contain participants from COST countries and several international partners, including academics, industrial partners, patient representatives and clinicians and it is open to other interested stakeholders.