Activity A. CloudScreen, a “one-stop-shop” next generation computational platform for drug repurposing

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).

 

Selected Publications

• Bafiti V., Ouzounis S., Siapi E., Grypari I.M., Theofanopoulos A., Panagiotopoulos V., Zolota V., Kardamakis D., Katsila T*. Metabolites, 2023, 13(3):362.
• 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

• CLOUDSCREEN is one out of the five innovative ideas put forward within the Greek Start-up ecosystem selected by Pfizer. The start4health challenge addresses the Digital Health landscape in shaping the future of health.
  
• We were selected to present CLOUDSCREEN: a graph-based drug repurposing platform empowered by machine learning
  
• V. Bafiti, M.T. Matsoukas, V. Zolota, D. Kardamakis, T. Katsila* EMBO Workshop. The DNA damage response, immunity and aging, Singapore, Singapore. 2022
• 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

 

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

We exploit the 3D cell microenvironment via profiling of extracellular vesicles/ exosomes 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. Extracellular vesicles and exosomes also serve as a toolbox for drug resistance and drug-drug interactions.

Selected Outreach & Events

• Highlighted among esteemed colleagues https://www.hupo.org/Humans-of-HUPO/
• Excited to discuss exosomal metabolomics in health and disease
  
• Chalikiopoulou C., Katsila T*. Targeted proteomics: Experimental design and data analysis, EMBO Practical Course (web event). 2021

 

Activity C. 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.

Selected Publications

• Kannavou M., Karali K., Katsila T., Siapi E., Marazioti A., Klepetsanis P., Calogeropoulou T., Charalampopoulos I., Antimisiaris S.G. Development and Comparative In Vitro and In Vivo Study of BNN27 Mucoadhesive Liposomes and Nanoemulsions for Nose-to-Brain Delivery. Pharmaceutics, 2023, 15:419.
• Vachlioti E., Ferikoglou S., Georgiou X., Karampatsis V., Afratis K., Bafiti V., Savard M., Papaioannou D., Katsila T., Gobeil F. Jr, Rassias G. Arch Pharm, 2023, e2200610.
• 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.

 

Selected Outreach & Events

• Participation in 86th Thessaloniki International Fair http://www.eie.gr/nhrf/news/2022/2022_09_05_NHRF_TIF.pdf and https://www.amna.gr/macedonia/article/677271/Ellinoamerikaniki-sunergasia-gia-ti-grigori-anichneusi-antisomaton-tou-neou-koronoiou
• PK/ BIOPHARMACEUTICS WEBINAR, EuroNeuroTrophin Learning Scenarios (web event). 2021
  https://www.euroneurotrophin.eu/results.html
• Pre-validation and ADME-Tox studies of the Photostick immunosensing system. 2021
  https://www.sev.org.gr/members_news/uni-pharma-sars-cov-2-protoporiako-elliniko-foteino-test-antisomaton/

 

Activity D. DeepInhibition

 

Activity Ε. DeepEVision

Activity A. Monitoring of immunomodulatory mechanisms

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

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. J Proteome Res, 2014, 13:3706.

Selected Outreach & Events

• Katsila T. HPC-Europa3, 3rd User Group Meeting (web event). 2021
• Descubren un marcador para monitorizar el cáncer colorrectal con muestras de sangre. EQUIPO DEL VHIO BARCELONA, 30 Oct. (EUROPA PRESS) - Investigadores del Vall d'Hebron Instituto de Oncología (VHIO) han descubierto un marcador que permitirá monitorizar el tratamiento del cáncer colorrectal a través de muestras de sangre, lo que supone un nuevo método práctico y no invasivo.
  https://www.europapress.es/catalunya/noticia-descubren-marcador-monitorizar-cancer-colorrectal-muestras-sangre-20141030110736.html
• La sangre revela si el tratamiento del cáncer de colon es efectivo. Viernes, 31 de octubre del 2014. Científicos del Hospital Vall d'Hebron de Barcelona han descubierto un nuevo marcador que permite comprobar si el tratamiento del cáncer colorrectal que recibe un paciente es efectivo o no mediante un simple análisis de sangre. https://www.elperiodico.com/es/sanidad/20141030/la-sangre-revela-si-el-tratamiento-del-cancer-de-colon-es-efectivo-3649003

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.

 

Activity B. 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.

Selected Publications

• Bafiti V., Katsila T.* OMICS, 2022, 26(10): 542-551.
• 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

Selected 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)

 

Activity C. 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

• Swen J.J., van der Wouden C.H., Manson L.E., Abdullah-Koolmees H., Blagec K., Blagus T., Böhringer S., Cambon-Thomsen A., Cecchin E., Cheung K.C., Deneer V.H., Dupui M., Ingelman-Sundberg M., Jonsson S., Joefield-Roka C., Just K.S., Karlsson M.O., Konta L., Koopmann R., Kriek M., Lehr T., Mitropoulou C., Rial-Sebbag E., Rollinson V., Roncato R., Samwald M., Schaeffeler E., Skokou M., Schwab M., Steinberger D., Stingl J.C., Tremmel R., Turner R.M., van Rhenen M.H., Dávila Fajardo C.L., Dolžan V., Patrinos G.P., Pirmohamed M., Sunder-Plassmann G., Toffoli G., Guchelaar H.J.; Ubiquitous Pharmacogenomics Consortium. Lancet, 2023, 401(10374): 347
• 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, 141:1697
• Katsila T, Juliachs M, Gregori J, Macarulla T, Villarreal L, Bardelli A, Torrance C, Elez E, Tabernero J, Villanueva J. Clin Cancer Res, 2014, 20:6346

Selected Outreach & Events

 

Activity D. From genotype-to-phenotype associations toward the clinical interpretome

The 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

• V. Bafiti, S. Ouzounis, C. Chalikiopoulou, E. Grigorakou, I.M. Grypari, G. Gregoriou, A. Theofanopoulos, V. Panagiotopoulos, E. Prodromidi, D. Kavouras, V. Zolota, D. Kardamakis, T. Katsila*. Curr Oncol, 2022, 29(6), 4351
• 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

Selected Outreach & Events

A Robust Machine Learning Framework Built Upon Molecular Representations Predicts CYP450 Inhibition: Toward Precision in Drug Repurposing

Sotiris Ouzounis†, Vasilis Panagiotopoulos, Vivi Bafiti, Panagiotis Zoumpoulakis, Dionisis Cavouras, Ioannis Kalatzis, Minos-Timotheos Matsoukas, and Theodora Katsila
OMICS: A Journal of Integrative Biology 27, no. 7 (July 2023): 305–314
https://doi.org/10.1089/omi.2023.0075

 

 

• CLOUDPHARM PC. NHRF, 2024. Application Number N2039646
• CLOUDPHARM PC. NHRF, 2024. Application Number N2039647
• CLOUDPHARM PC. NHRF, 2024. Application Number N2039645
• CLOUDPHARM PC. NHRF, 2024. Application Number N2039644
• Fundacio Privada Institut d’Investigacio Oncologica de Vall Hebron, 2014. EU WO2015/189106, issued December 17, 2015.

Post-doctoral Research Associates
Dr. Constantina Chalikiopoulou (2020 - 2023)
Dr. Angeliki Balasopoulou. State Scholarships Foundation (IKY) Post-doctoral research fellow (2020 - 2022)
Dr. Despoina Antonakaki (2020 - 2021)

Scientific Associates
Mr. Spyridon Marios Giatro (2024 - 2025)
Ms. Antonia Mera (2024)
Ms. Christina Anna Fragkou (2023 - 2025)

PhD students (Co-supervisor; Committee member; Vocal)
Mr. Lorenzo Tagliazucchi (2024)
Mr. Md Kamal Hossain (2023)
Mr. Santiago Rios Azuara (2017)

MSc students
Ms. Nafsika Rossopoulou, NHRF; NKUA
Ms. Efstathia Mamasioula, NHRF; University of Thessaly (2023)
Ms. Nefeli Platania, NKUA (2022 - 2024)
Ms. Maria Kontothanasopoulou, Hellenic Open University (2022)
Ms. Konstantina Marina Nikolaou, NKUA (2021 - 2023)
Mr. Themistoklis Molochadis, NHRF; University of Thessaly (2021 - 2023)
Ms. Stavroula Giannakopoulou, NKUA (2021 - 2022)
Ms. Apostolia Zarmpala, NHRF; University of Thessaly (2020 - 2021)
Mr. Burhan Waheed, Imperial College London (2020)
Ms. Danae Strantzali, NKUA (2019 - 2022)
Ms. Eirini Manou, NKUA (2019 - 2021
Mr. Antonis Tsintarakis, NKUA (2019 - 2021)
Ms. Paraskevi Bafiti, NHRF; University of Crete (2019 - 2020)

MSc students (Co-supervisor; Committee member; Vocal)
Ms. Alexandra Delipetrou, NHRF; NKUA (2024)
Mr. Spyridon Marios Giatro, NHRF; NKUA (2024)
Ms. Eleni Thanou, NHRF; National & Kapodistrian University of Athens (2023)
Ms. Vasiliki Karamani, NHRF; University of Crete (2023)
Ms. Aikaterina Kesidou, Hellenic Open University (2023)
Ms. Pinelopi Kavousanou, Hellenic Open University (2023)
Mr. Sotirios Alexiou, NHRF; University of Thessaly (2022)
Mr. Stratos Sarisholis, NHRF; University of Thessaly (2022)
Mr. Anestis Makris, National & Kapodistrian University of Athens (2021)
Ms. Maria Ioanna Ragkousi, NHRF; University of Crete (2020 - 2021)
Ms. Evgenia Kapeni; NHRF; University of Crete (2020 - 2021)

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

Internships
Ms. Stergiani Telliou, Aristotle University of Athens (2024)
Mr. Constantinos Lekkos, University of West Attica (2023)
Ms. Sara Luelmo Moya, University of Porto (2023)
Ms. Pigi Maria Niotopoulou, National & Kapodistrian University of Athens (2023)
Ms. Vasiliki Miliou, ACS Athens (2022)
Ms. Marina Constantina Grigoropoulou, University of West Attica (2021)
Ms. Eftychia Grigorakou, University of West Attica (2021)
Mr. Gregory Gregoriou, ACS Athens (2020)

	Micro & Nano Scientific Society 2025
	Hellenic Society for Extracellular Vesicles 2025
	International Society for Extracellular Vesicles. 2024 - present
	Imaging Mass Spectrometry Society (IMSS) 2023 - present
	Universal Scientific Education & Research Network. 2023 - present
	European Radiation Research Society 2022 - present
	European Society of the History of Oncology 2021 - present
	Females in Mass Spectrometry (FeMS) 2020 - present
	Metabolomics Society 2020 - present
	European Association of Systems Medicine (EAsyM). 2018 - present
	Open Technologies Alliance (GFOSS) 2018 - present
	Human Proteome Organization (HUPO) 2016 - present
	Global Genomic Medicine Collaborative (G2MC). 2016 - present
	European Association for Cancer Research (EACR). 2012 - present
	Association of Greek Chemists. 2011 - present
	Member of A. G. Leventis Foundation Scholars Association Board (Greece). 2007 - 2011
	Full Member of the Hellenic Society of Biochemistry/ Molecular Biology. 2005 - present
	Associate of the Royal College of Science (RCS) Association. 2004 - present
	Member of the Imperial College London Alumni Association. 2004 - present

• 88th Thessaloniki International Fair
  NerveRepack was showcased at the 88th TIF by National Hellenic Research Foundation (NHRF). N. Rossopoulou and Chr. Fragkou, members of the NHRF team led by Dr. Theodora Katsila, presented the project and the role of their team in WP7 (new materials and biocompatibility).
  With more than 1300 exhibitors, 32,000 square meters of exhibition space, Germany as the Honoured Country with 135 enterprises and institutions, 25 international state participations, nine thematic events, and the dynamic presence of the Chambers of Greece with 350 companies from all over Greece under the auspices of the UHC, the 88th TIF conveyed a strong message of development and international cooperation. More about TIF 2024: https://thessalonikifair.gr/en
  https://shorturl.at/olvF3; https://shorturl.at/ewaC2; https://shorturl.at/TQYTh
• Financial Grant in Memory of Miltiadis Empirikos (Empirikeio Foundation)
  https://rb.gy/3uonub
• TRANSCAN December 2024 newsletter
  TRANSCAN-3 network held its 2nd Symposium in Catania, Italy. All participants in projects funded under the JTC 2022 call “Novel translational approaches to tackle the challenges of hard-to-treat cancers from early diagnosis to therapy” were invited to this event, where they had the chance to share their progress and latest results as well as lessons learned in the first months of their joint work. The event counted with the presence (on site and online) of almost 70 participants from over 30 countries. The session was chaired by T. Katsila and Tr. Liloglou, former members of the scientific evaluation committee that evaluated the JTC 2022 projects. The presentations were a great chance for the researchers to learn about each other's projects and to establish new collaborations and allowed funding agencies to gain first-hand insights into the progress of the funded actions. More about TRANSCAN: https://shorturl.at/RXk2
• Annual Rosalind Franklin Society Award in Science
  The 2023 Rosalind Franklin Society (RFS) Awards in Science in partnership with Mary Ann Liebert Inc. recognize outstanding peer-reviewed research by women and underrepresented minorities in STEM. More about 2023 RFS Awards: https://www.rosalindfranklinsociety.org/rfs-awards-in-science-2023; https://shorturl.at/9X4o3; https://rb.gy/j1y316; https://rb.gy/7qco37
• Remarkable HUPO volunteer (Human Proteome Organization)
  HUPO highlights volunteers who lead and support many of HUPO's various Committees, Initiatives and Working Groups. More about HUPO: https://rb.gy/v0e7zd
• Humans of HUPO (Human Proteome Organization)
  HUPO highlights a member of HUPO. This initiative improves visibility of HUPO members, advertise research and enhance the HUPO community. More about HUPO: https://www.hupo.org/Humans-of-HUPO/
• 86th Thessaloniki International Fair
  The Biomarker Discovery & Translational Research Laboratory at NHRF led by Dr. T. Katsila presented NanoSpot.ai. A SARS-CoV-2 IgG/IgM Rapid Test that quickly and reliably detects the presence of antibodies against the receptor binding domain of the viral spike protein (Spike-RBD) of SARS-CoV-2 by hemagglutination. Image processing and data analysis are performed by AI algorithms. NanoSpot.ai™ technology is innovative being an AI-driven point-of-care diagnostic tool. Thanks to the catalytic and close collaboration of the ICHB/NHRF (Biomarker Discovery Laboratory: Translational Research) and ATHROA INNOVATION IKE, Opto (“OPTO IMMUNOSENSORS IKE”, a subsidiary of Uni-Pharma and ATHROA INNOVATION IKE) intends to develop future and more innovative products from inventions of researchers in and outside Greece in the emerging sector of Connected Diagnostics (“Connected Diagnostics”). More about TIF 2022:https://shorturl.at/09Atm; https://shorturl.at/A8Q9v; https://shorturl.at/WJWZ8
• Pre-validation and ADME-Tox studies of the Photostick immunosensing system
  As a concept, the Photostick immunosensing platform was born in an effort to create a versatile and ubiquitous immunodiagnostic point-of-care diagnostic that exploits the analytical power of light, but is not compromised by operational complexity, increased cost and volume. Photostick was based on the need to move the lab to the field and offer affordable but accurate, de-centralized mass-testing. The Biomarker Discovery & Translational Research laboratory participated in a double-blind test study measuring independently and sequentially the same set of samples. More about Photostick: https://shorturl.at/UQAZb
• Interview of the Associate Researcher of the Institute of the Chemical Biology (ICB), Dr. Theodora Katsila Please visit: https://shorturl.at/UQAZb
• Descubren un marcador para monitorizar el cáncer colorrectal con muestras de sangre. EQUIPO DEL VHIO BARCELONA, 30 Oct. (EUROPA PRESS) - Investigadores del Vall d'Hebron Instituto de Oncología (VHIO) han descubierto un marcador que permitirá monitorizar el tratamiento del cáncer colorrectal a través de muestras de sangre, lo que supone un nuevo método práctico y no invasivo. More about CRC biomarker: https://shorturl.at/cQXCv
• La sangre revela si el tratamiento del cáncer de colon es efectivo
  Viernes, 31 de octubre del 2014. Científicos del Hospital Vall d'Hebron de Barcelona han descubierto un nuevo marcador que permite comprobar si el tratamiento del cáncer colorrectal que recibe un paciente es efectivo o no mediante un simple análisis de sangre. More about CRC biomarker: https://shorturl.at/YWieg