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.

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.

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

• 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 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).

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

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.

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

• 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.

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

• 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)

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

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

• 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