INSTITUTE OF CHEMICAL BIOLOGY
 
  Drug Discovery
  Molecular Analysis
  Organic and Organometallic Chemistry
  Medicinal Chemistry
  Synthetic Medicinal Chemistry and Chemical Biology
  Identification & validation of novel therapeutic targets - Biological evaluation of bioactive small molecules and drugs
  Structural Biology & Chemistry
  Molecular Endocrinology
  Signal Mediated Gene Expression
  Molecular & Cellular Ageing
  Biomedical Applications
  Holistic Approaches in Health
  Environment and Health
  Metabolic Engineering-Bioinformatics
  Biomarker Discovery & Translational Research
  Biotechnology
  Enzyme and Synthetic Biotechnology
  Biomimetics & Nanobiotechnology
  Conjugated Polymers for Healthcare, Bioelectronics and Bioimaging

 

Biomarker Discovery & Translational Research
Dr. Theodora Katsila | Associate Researcher, Group Leader

 

 

We translate information growth to knowledge growth

Craving for brain teasers, our strategic steps towards goal achievement are bulletproof.
Translational biomarkers represent a key strategy for innovation and knowledge creation.

Vision

  • Translate information growth to knowledge growth
  • Map inter-individual variability upon xenobiotics profiling
  • (Drug) repurposing exosomes

Mission

  • Next-gen life science breakthroughs
  • Empower biomedical innovation
  • Disruptive healthcare solutions

Roadmap

  • Better-informed decision-making
  • Content- and data-driven analyses
  • Acceleration of impactful innovations

Toolbox

  • Proteomics-based multi-omics
  • ADME-Tox in 3D
  • 3D cell models & cheminformatics
  • ML, DL & computational statistics

Based on their experience and expertise, the team supports fit for purpose to full compliance. The team advises on study design, analytical methodology and pull through from non-clinical to clinical use plus companion diagnostics regulatory submissions.

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Current objectives

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Major outcomes & achievements

(Drug) repurposing exosomes

Activity A. Proteogenomics profiling of the 3D cell microenvironment for drug repurposing

We exploit the 3D cell microenvironment via exosomal profiling as the means to define the druggable key-players as well as identify and validate candidate companion biomarkers. For this, LC-MSn and high-resolution particle-by-particle 3D fluorescent microscopy measurements are coupled. Exosomes also serve as a toolbox for drug resistance and drug-drug interactions.

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Outreach & Events

Chalikiopoulou C., Katsila T*. Targeted proteomics: Experimental design and data analysis, EMBO Practical Course (web event). 2021

 

Activity B. ADME-Tox in 3D assays and services in a 3-tier strategy; in silico, in vitro, in vivo (EMA CHMP, FDA Guidance for Industy)

Funded by private funders, industry.

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Selected Publications

  • T. Rogdakis, D. Charou, A. Latorrata, E. Papadimitriou, A. Tsengenes, C. Athanasiou, M. Papadopoulou, C. Chalikiopoulou, T. Katsila, I. Ramos, K. C. Prousis, R. C. Wade, K. Sidiropoulou, T. Calogeropoulou, A. Gravanis, I. Charalampopoulos. Biomedicines, 2022, 10(3):614.
  • C. Yilmaz, T. Rogdakis, A. Latorrata, E. Thanou, E. Papadimitriou, E. Siapi, K.W. Li, T. Katsila, T. Calogeropoulou, I. Charalampopoulos, V.I. Alexaki. Biomolecules, 2022, 12(3):424.

Outreach & Events

 

Activity C. CloudScreen, our “one-stop-shop” next generation computational platform for drug repurposing goes beyond existing strategies, as it (a) is not limited to 1D data, but curates/ integrates/ analyzes/ interprets 1D and 3D data coming from molecular design and computational chemistry outputs; (b) minimizes confounding in data mining/ integration/ analysis and promotes unbiased decision-making via the synergy of human and machine (artificial intelligence) reasoning capabilities (i) data mining services, ii) collaboration support services, and iii) decision making services; (c) provides dynamic update capabilities and extends text data services (patents, ethics); and (d) serves as an “one-stop shop” tool for predicting and evaluating the efficacy and toxicity of repurposed biomolecules via ADME-Tox profiling in 3D. This research is supported by the European Regional Development Fund of the European Union and Greek national funds through the Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH-CREATE-INNOVATE (project code: T2EDK-03153).

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Selected Publications

  • Katsila T*, Chasapi SA, Gomez Tamayo JC, Chalikiopoulou C, Siapi E, Moros G, Zoumpoulakis P, Spyroulias GA, Kardamakis D. Cancers, 2021, 13(12):2877.

Selected Outreach & Events

  • Chalikiopoulou C and Katsila T*. EACR 2022 Congress - Innovative Cancer Science: Translating Biology to Medicine, Seville, Spain. 2022
  • V. Bafiti, V. Panagiotopoulos, M.T. Matsoukas, V. Zolota, D. Kardamakis, T. Katsila*. EACR 2022 Congress - Innovative Cancer Science: Translating Biology to Medicine, Seville, Spain. 2022
  • Chalikiopoulou C., Katsila T*. Targeted proteomics: Experimental design and data analysis, EMBO Practical Course (web event). 2021
  • V. Bafiti, M.T. Matsoukas, V. Zolota, D. Kardamakis*, T. Katsila* First ESN-ISN School “From Neurodegeneration to Neural Carcinogenesis: Mechanisms and Common Biologies” [Scholarship to Ms. Bafiti], Athens, Greece. 2021
  • V. Bafiti, M.T. Matsoukas, V. Zolota, D. Kardamakis*, T. Katsila* 10th International Conference of the Hellenic Crystallographic Association, Athens, Greece. 2021
Monitoring of immunomodulatory mechanisms

We employ multi-omics (LC-MSn) and high-resolution particle-by-particle 3D fluorescent microscopy (exosomes; nature, number, cargos). The secretome and membrane proteome may add an extra information layer.

BiomarkerDiscovery_TranslationalResearch_01

Selected Publications

  • T. Katsila, M. Juliachs, J. Gregori, T. Macarulla, L. Villarreal, A. Bardelli, C. Torrance, E. Elez, J. Tabernero, J. Villanueva. Clin Cancer Res, 2014, 20: 6346.
  • Gregori J, Méndez O, Katsila T, Pujals M, Salvans C, Villarreal L, Arribas J, Tabernero J, Sánchez A, Villanueva J. 2014. J Proteome Res, 13:3706.

Outreach & Events

Patent

Fundacio Privada Institut d’Investigacio Oncologica de Vall Hebron, 2014. A method for monitoring the treatment of patients with tumors expressing EGFR. EU WO2015/189106, issued December 17, 2015.

Bioenergetics & Oncometabolism

The accumulation of cell biomass is associated with dramatically increased bioenergetic and biosynthetic demand. Metabolic reprogramming, once thought as an epiphenomenon, currently, relates to tumorigenesis and metastasis, often in response to extracellular fate-decisive signals.

BiomarkerDiscovery_TranslationalResearch_01

Selected Publications

  • A. Poulaki, T. Katsila, S. Giannouli, J.C. Gomez Tamayo, I. Stergiou, A.G. Tzioufas, M. Voulgarelis. Leuk Res, 2021, 108 (suppl1): 106681
  • Poulaki A¥, Katsila T¥, Stergiou IE, Giannouli S, Gόmez-Tamayo JC, Piperaki ET, Kambas K, Dimitrakopoulou A, Patrinos GP, Tzioufas AG, Voulgarelis M. Cancers, 2020, 12(12):3520. ¥1st authorship shared

Outreach & Events

  • V. Bafiti, V. Panagiotopoulos, M.T. Matsoukas, V. Zolota, D. Kardamakis, T. Katsila* EACR 2022 Congress - Innovative Cancer Science: Translating Biology to Medicine, Seville, Spain. 2022
  • V. Bafiti, M.T. Matsoukas, V. Zolota, D. Kardamakis*, T. Katsila* First ESN-ISN School “From Neurodegeneration to Neural Carcinogenesis: Mechanisms and Common Biologies” [Scholarship to Ms. Bafiti], Athens, Greece. 2021
  • Poulaki A, Katsila T, Giannouli S, Gomez-Tamayo JC, Stergiou IE, Tzioufas AG, Voulgarelis M. 16th International Congress on Myelodysplastic Syndromes (web event). 2021
  • Poulaki A, Katsila T, Stergiou IE, Giannouli S, Gomez-Tamayo JC, Kambas K, Patrinos GP, Voulgarelis M. European Hematology Association (EHA) (web event). 2020
  • Katsila T, Poulaki A, Stergiou IE, Giannouli S, Gomez-Tamayo JC, Kambas K, Patrinos GP, Tzioufas AG, Voulgarelis M. 16th Annual Conference, Metabolomics 2020 (web event)
Biomarkers to the Rescue

In-house capabilities are coupled with strategic networks and partnerships for discovery, validation and clinical development of biomarkers.

  • Translational biomarkers (target, mechanism & disease biomarkers) identify the impact of a chemical entity on organs or tissues before a clinical effect is evident.
  • Diagnostic biomarkers (predictive, prognostic & resistance biomarkers) empower patient stratification and enable clinical decisions for potential combinations and/ or next-line therapies. Diagnostic biomarkers maximize therapeutic effects/ minimize ADRs.
  • Pharmacodynamic biomarkers used in pre- and post-treatment settings may shed light to the extent of target modulation, provide biological proof-of-activity, and inform clinical decision making (dosing amounts and/or schedules).
  • Companion diagnostics are intended for launch with a therapeutic drug and enable clinical decision-making (diagnostic or pharmacodynamic biomarker utility)

Selected Publications

  • Kumuthini J, Zick B, Balasopoulou A, Chalikiopoulou C, Dandara C, El-Kamah G, Findley L, Katsila T, Li R, Maceda EB, Monye H, Rada G, Thong MK, Wanigasekera T, Kennel H, Marimuthu V; G2MC Evidence investigators, Williams MS, Al-Mulla F, Abramowicz M. Hum Genet, 2022.
    https://doi.org/10.1007/s00439-022-02452-x
  • Katsila T, Juliachs M, Gregori J, Macarulla T, Villarreal L, Bardelli A, Torrance C, Elez E, Tabernero J, Villanueva J. 2014. Clin Cancer Res, 20:6346

Outreach & Events

BiomarkerDiscovery_TranslationalResearch_01

 

From genotype-to-phenotype associations toward the clinical interpretome

BiomarkerDiscovery_TranslationalResearch_03The team focus is on contextual data, data reliability and interpretation.
An artificial-human intelligence workspace facilitates data mining and curation to empower data reliability and reproducibility This is an illustration of an active synergistic workspace in which multi-faceted data derived from diverse and distributed sources is mined and interrogated. Interoperability is facilitated by the same synergy of human and artificial intelligence which is also anticipated to diminish biases. Nodes may represent ideas, comments, notes, services, data. Lines represent network interactions; those in light blue are those that exhibit evidence-based dominance, those in red are those that fail, while those in dark blue are the ones to be re-visited. In such a way, contextual data integration results in an evidence-based dominant outcome (node in red). Contextual or out-of- context data are equally re-visited and interrogated, and they will only survive, if evidence-based.

 

 

Selected Publications

  • Jenko Bizjan B, Katsila T, Tesovnik T, Šket R, Debeljak M, Matsoukas MT, Kovač J. Comput Struct Biotechnol J, 2019, 18:83.
  • Katsila and Matsoukas, 2018, Expert Opin Drug Discov, 13:791

 

 

Group Structure and Personnel

Dr. Theodora Katsila, Associate Researcher, Research Assistant Professor
Head of the Laboratory of Biomarker Discovery & Translational Research

Post-doctoral Research Associates
Constantina Chalikiopoulou, PhD

Ph.D. candidates
Vivi Bafiti, MSc
Sotiris Ouzounis, MSc

MSc students
Ms. Stavroula Giannakopoulou, MSc Applications of Biology in Medicine, National & Kapodistrian University of Athens
Ms. Athina Kyriakidou, MSc Oncology: From Oncogenesis to Therapy. NHRF/ICB; University of Crete
Mr. Themistoklis Molochadis, MSc Bioentrepreneurship. NHRF/ICB; University of Thessaly
Ms. Konstantina Marina Nikolaou, MSc Clinical Biochemistry-Molecular Diagnostics, National & Kapodistrian University of Athens
Ms. Danae Strantzali, MSc Applications of Biology in Medicine, National & Kapodistrian University of Athens

 

Laboratory Alumni

Post-doctoral Research Associates
Dr. Angeliki Balasopoulou.  State Scholarships Foundation (IKY) Post-doctoral research fellow (2020 – 2022)
Dr. Despoina Antonakaki (2020 – 2021)

MSc students
Mr. Burhan Waheed, Imperial College London (2020)
Ms. Apostolia Zarmpala, NHRF; University of Thessaly (2020-2021)
Ms. Maria Ioanna Ragkousi, NHRF; University of Crete (2020-2021)
Ms. Eirini Manou, National & Kapodistrian University of Athens (2019-2021)
Mr. Antonis Tsintarakis, National & Kapodistrian University of Athens (2019-2021)

BSc students
Ms. Nefeli Platania, National & Kapodistrian University of Athens (2019-2021)

Internships
Mr. Gregory Gregoriou, ACS Athens (2020)
Ms. Eftychia Grigorakou, University of West Attica (2021)
Ms. Marina Constantina Grigoropoulou, University of West Attica (2021)

 

Collaborations

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Collaborations with private entities

  • ATHROA INNOVATIONS PC
  • CHROMACURE SA
  • CLINIGEN Ltd
  • CloudPharm PC
  • LIFE NLB Ltd
  • PhoreMost Ltd
  • Rontis Hellas SA

 

Funding

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2022. HPC-GRNET. Project title: “Extending 3D Drug Repurposing predictions to the human Variome and extended (AlphaFold) Proteome space”. Role: Principal Investigator.

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2021. EPIC-XS Grant. EPIC-XS project 371. Project title: “An integrated model to gain mechanistic insights in glioblastoma prognosis”. Budget: 20,532.00 €. Role: Principal Investigator.

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2021-2025. ADME-Tox services. Private funding, Industry. Budget: 12,070.90 €. Role: Principal Investigator.

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2020-2023. National Strategic Reference Framework 2014-2020. General Secretariat of Research and Technology-Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH-CREATE-INNOVATE (project code: T2EDK-03153). Project title: “CLOUDSCREEN”. Total budget: 469,791.88 €. Lab budget: 352,561.98 €. Role: Principal Investigator.
https://cloudscreen.gr/?lang=en

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2020-2023. National Strategic Reference Framework 2014-2020. General Secretariat of Research and Technology – Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH-CREATE-INNOVATE (project code: T2EDK-03847). Project title: “Design and development of a novel food supplement for osteoporosis based on gut microbiome mechanisms. Efficacy and tolerability assessment”. Total budget: 952,080.00 €. Lab budget: 62,760.00 €. Role: Partner.
https://osteome.eu/?page_id=40

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2020-2022. State Scholarships Foundation (IKY). Operational Programme «Human Resources Development, Education and Lifelong Learning» in the context of the project “Reinforcement of Postdoctoral Researchers - 2nd Cycle” (MIS-5033021). Post-doctoral research fellow: Dr. Angeliki Balasopoulou. Total budget: 26,400.00 €. Lab budget: 26,400.00 €. Role: Coordinator.

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2020. HPC-3 Europa Transnational Access Grant.
Project code: HPC17B9U3T. Role: Principal Investigator.

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2016 – 2017. Private funding, Industry.
Budget: 22,000.00 £. Role: Principal Investigator (Dual PI)

 

Selected Publications

  • T. Rogdakis, D. Charou, A. Latorrata, E. Papadimitriou, A. Tsengenes, C. Athanasiou, M. Papadopoulou, C. Chalikiopoulou, T. Katsila, I. Ramos, K. C. Prousis, R. C. Wade, K. Sidiropoulou, T. Calogeropoulou, A. Gravanis, I. Charalampopoulos. Biomedicines, 2022, 10(3):614.
  • C. Yilmaz, T. Rogdakis, A. Latorrata, E. Thanou, E. Papadimitriou, E. Siapi, K.W. Li, T. Katsila, T. Calogeropoulou, I. Charalampopoulos, V.I. Alexaki. Biomolecules, 2022, 12(3):424.
  • Kumuthini J, Zick B, Balasopoulou A, Chalikiopoulou C, Dandara C, El-Kamah G, Findley L, Katsila T, Li R, Maceda EB, Monye H, Rada G, Thong MK, Wanigasekera T, Kennel H, Marimuthu V; G2MC Evidence investigators, Williams MS, Al-Mulla F, Abramowicz M. Hum Genet, 2022.
    https://doi.org/10.1007/s00439-022-02452-x
  • Katsila T*, Chasapi SA, Gomez Tamayo JC, Chalikiopoulou C, Siapi E, Moros G, Zoumpoulakis P, Spyroulias GA, Kardamakis D. Cancers, 2021, 13(12):2877.
  • A. Poulaki, T. Katsila, S. Giannouli, J.C. Gomez Tamayo, I. Stergiou, A.G. Tzioufas, M. Voulgarelis. Leuk Res, 2021, 108 (suppl1): 106681
  • Poulaki A¥, Katsila T¥, Stergiou IE, Giannouli S, Gόmez-Tamayo JC, Piperaki ET, Kambas K, Dimitrakopoulou A, Patrinos GP, Tzioufas AG, Voulgarelis M. Cancers, 2020, 12(12):3520.
    ¥1st authorship shared
  • Jenko Bizjan B, Katsila T, Tesovnik T, Šket R, Debeljak M, Matsoukas MT, Kovač J. Comput Struct Biotechnol J, 2019, 18:83.
  • Katsila and Matsoukas, 2018, Expert Opin Drug Discov, 13:791
  • T. Katsila, M. Juliachs, J. Gregori, T. Macarulla, L. Villarreal, A. Bardelli, C. Torrance, E. Elez, J. Tabernero, J. Villanueva. Clin Cancer Res, 2014, 20: 6346.
  • Gregori J, Méndez O, Katsila T, Pujals M, Salvans C, Villarreal L, Arribas J, Tabernero J, Sánchez A, Villanueva J. 2014. J Proteome Res, 13:3706.

 

file_iconFull list of Publications [pdf]

 

 

 

 


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