TWINNING FOR EXCELLENCE TO STRATEGICALLY ADVANCE RESEARCH IN CARCINOGENESIS AND CANCER

Livrables

A protocol for application of IMC on tumour organoids

A detailed protocol on application of innovative technology IMC on tumor organoids will be created to uncover molecular changes at protein and single-cell level in tumor microenvironment after treatments. The protocol will be conducted by exchange of best practices and scientific knowledge within consortium. Protocol will be written, revised by partners of consortium, and available for consortium partners.

Guidelines - Reaching excellence in project management

The guidelines will be produced for internal and external use by interested members of the public, identifying best practices for specific phases of project management and developing them further in the form of recommendations and guidelines to achieve and maintain project management excellence.

Report on the research trainings and expert exchange

Reports on the research trainings and expert exchange conducted under WP5 will be consistent with Dissemination/twinning/networking activities of the project and will include explanations for any discrepancies. Reports shall include description of all activities within research trainings and expert visits including meetings between partner´ staff, exchange of know-how, hands-on training of researchers, summer schools and workshops.

Progress Report

The progress report as a deliverable at Month 17, will be the basis for the interim review meeting.

A protocol for application of ISS on tumour organoids

A detailed protocol on application of state-of-the art methodology ISS on tumor organoids will be created to uncover molecular changes at gene level in tumor microenvironment after treatments. The protocol will be conducted by exchange of best practices and scientific knowledge within consortium. Protocol will be written, revised by partners of consortium, and available for consortium partners.

Scientific publications

Peer-reviewed scientific publications: Dissemination of project results to the international scientific community will be accomplished through publication of results (2-4 papers ) in high impact scientific journals in the scope of Toxicology, Cancer Research, Oncology, etc. Unless there are specific reasons not to do so, only the Open Access format will be chosen, allowing unrestricted access to the scientific and technical results.

Research strategy: NIB: Access to Excellence and presentation of best practices

In addition to monitoring progress and incorporating lessons learned, the draft strategy will include identifying future collaborations and discussing potential future pathways based on an analysis of SWOT and considering each partner's strategies. By learning from each other, we aim to become better, more recognisable, more social, and explore innovative approaches to increase the visibility and accessibility of cutting-edge research. Particular attention will be paid to shaping the consortium's funding portfolio over the life of the project and beyond, seeking, learning, and implementing synergies at multiple levels. Scientific gaps will be considered first, before gaps in support infrastructure are considered.

A protocol for the assessment of genomic instability in hepatic and lung 3D cell models

A detail protocol for the assessment of genomic instability in hepatic and lung 3D cell models will be prepared as a guideline for testing genotoxic activity of chemicals and nanoparticles. The protocol will contain all the necessary steps and information for the successful performance of the cytokinesis block micronucleus (CBMN) assay on hepatic and lung 3D cell models.

A guideline protocol for big data management

Using advanced platforms for high-throughput analysis such as Metafer and FlowSight, as well as spatial technologies and single-cell analysis, a significant amount of raw data, high-resolution images, and (meta-)data are generated, consuming large amounts of digital storage, thus requiring highly efficient tools for Big Data management. It also generates sensitive patient-related and scientific data. By sharing knowledge and best practices on data management and storage, protocols and documents with partner institutions and expert visits from SWAN, SU and VUmc to NIB, NIB will learn how to handle Big Data management and protect sensitive data through protected internal and external data storage options that ensure secure data storage and analysis. The expert exchange will establish general policy protocols that describe procedures and criteria for optimal data management and storage.

A protocol for the use of advanced platforms for high-throughput analysis of (geno)toxicological outcomes

A detail protocol how to use advanced platforms (e.g., MetaferTM system from MetaSystems and FlowSight imaging cytometry platform from Amnis) for medium and high-throughput automated analysis will be prepared as a guideline for testing genotoxic activity of chemicals and nanoparticles. The protocol will contain all the necessary steps and information how to use advanced platforms for the evaluation of genotoxic activity of chemicals and nanoparticles.

Final report on dissemination, exploitation and communication activities

The final report on dissemination, exploitation and communication activities must be consistent with the DMP (Deliverable 2.1) and include explanations for any discrepancies. The final report shall include all communication and dissemination activities, including samples, and shall represent the activities of each partner and the consortium. A communication, dissemination, and exploitation protocol will be provided at the kick-off event at the beginning of the project and will be consistent with the grant and consortium agreement.

Publications

GUT MICROBIOME IN CANCER: THE NEXT BIG OPPORTUNITY FOR BETTER PATIENT OUTCOMES?

Auteurs: Jure Povšin, Timotej Sotošek, Metka Novak, Barbara Breznik
Publié dans: Slovenian Veterinary Research, Numéro 62, 2025, ISSN 2385-8761
Éditeur: University of Ljubljana
DOI: 10.26873/SVR-2029-2024

Heterogenous mitochondrial ultrastructure and metabolism of human glioblastoma cells: differences between stem-like and differentiated cancer cells in response to chemotherapy

Auteurs: Urban Bogataj, Metka Novak, Simona Katrin Galun, Klementina Fon Tacer, Milos Vittori, Cornelis J.F. Van Noorden, Barbara Breznik
Publié dans: Radiology and Oncology, Numéro 59, 2025, ISSN 1581-3207
Éditeur: Walter de Gruyter GmbH
DOI: 10.2478/RAON-2025-0056

In vitro hepatic 3D cell models and their application in genetic toxicology: A systematic review

Auteurs: Martina Štampar, Bojana Žegura
Publié dans: Mutation Research - Genetic Toxicology and Environmental Mutagenesis, Numéro 900, 2025, ISSN 1383-5718
Éditeur: Elsevier BV
DOI: 10.1016/J.MRGENTOX.2024.503835

Safety of ferrite nanoparticles for biomedical applications: Cyto- and genotoxic effects of MxFe3-xO4 (M = Fe, Zn, Mn) in an Advanced 3D human hepatic in vitro model

Auteurs: Iza Rozman, Alvaro Gallo-Cordova, María del Puerto Morales, Marco A. Morales Ovalle, Gerardo F. Goya, Katja Kološa, Domen Hočevar, Bojana Žegura, Alja Štern
Publié dans: Biomedicine & Pharmacotherapy, Numéro 195, 2026, ISSN 0753-3322
Éditeur: Elsevier BV
DOI: 10.1016/J.BIOPHA.2025.118950

Immune-modulating effects on tumor-draining lymph nodes of neoadjuvant chemoradiotherapy combined with dual immunotherapy in patients with T3-4N0-2 NSCLC

Auteurs: Ezgi B Ulas, Sofie J I Koomen, Anne Vrijmoet, Ilias Houda, H Ibrahim Korkmaz, Chris Dickhoff, Idris Bahce, Suresh Senan, Tanja D de Gruijl, Marieke F Fransen, Teodora Radonic, Febe van Maldegem, Famke L Schneiders
Publié dans: Journal for ImmunoTherapy of Cancer, Numéro 13, 2025, ISSN 2051-1426
Éditeur: BMJ
DOI: 10.1136/JITC-2025-013237

The Slovenian translational platform GlioBank for brain tumor research: Identification of molecular signatures of glioblastoma progression

Auteurs: Metka Novak, Bernarda Majc, Marta Malavolta, Andrej Porčnik, Jernej Mlakar, Matjaž Hren, Anamarija Habič, Mateja Mlinar, Ivana Jovčevska, Neja Šamec, Alja Zottel, Marija Skoblar Vidmar, Tina Vipotnik Vesnaver, Andrej Zupan, Alenka Matjašič, Saša Trkov Bobnar, Dejan Georgiev, Aleksander Sadikov, Roman Bošnjak, Borut Prestor, Radovan Komel, Tamara Lah Turnšek, Barbara Breznik
Publié dans: Neuro-Oncology Advances, Numéro 7, 2025, ISSN 2632-2498
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/NOAJNL/VDAF015

In vitro toxicity assessment of graphene quantum dots using a 3D HepG2 model

Auteurs: Irma Durmišević, Anja Haverić, Sonja Žabkar, Alja Štern, Katja Kološa, Petra Jenuš Belec, Tamara Ćetković Pećar, Maida Hadžić Omanović, Sanjin Gutić, Iza Rozman, Sanin Haverić, Bojana Žegura
Publié dans: Archives of Toxicology, 2026, ISSN 0340-5761
Éditeur: Springer Science and Business Media LLC
DOI: 10.1007/S00204-026-04336-9

Spatial multiplex analysis of lung cancer reveals that regulatory T cells attenuate KRAS-G12C inhibitor–induced immune responses

Auteurs: Megan Cole, Panayiotis Anastasiou, Claudia Lee, Xiaofei Yu, Andrea de Castro, Jannes Roelink, Chris Moore, Edurne Mugarza, Martin Jones, Karishma Valand, Sareena Rana, Emma Colliver, Mihaela Angelova, Katey S. S. Enfield, Alastair Magness, Asher Mullokandov, Gavin Kelly, Tanja D. de Gruijl, Miriam Molina-Arcas, Charles Swanton, Julian Downward, Febe van Maldegem
Publié dans: Science Advances, Numéro 10, 2024, ISSN 2375-2548
Éditeur: American Association for the Advancement of Science (AAAS)
DOI: 10.1126/SCIADV.ADL6464

Targeting cystatin F activation enhances NK cell cytotoxicity in glioblastoma models

Auteurs: Emanuela Senjor, Anamarija Habič, Urban Švajger, Ana Mitrović, Matic Proj, Andrej Porčnik, Borut Prestor, Miha Jerala, Matic Bošnjak, Stanislav Gobec, Barbara Breznik, Janko Kos, Milica Perišić Nanut
Publié dans: Frontiers in Immunology, Numéro 16, 2025, ISSN 1664-3224
Éditeur: Frontiers Media SA
DOI: 10.3389/FIMMU.2025.1708281

Adverse (geno)toxic effects of bisphenol A and its analogues in hepatic 3D cell model

Auteurs: Sendra Marta; Štampar Martina; Fras Katarina; Novoa Beatriz; Figueras Antonio; Žegura Bojana
Publié dans: Environment International, Numéro Volume 171, January 2023, 107721, 2023, ISSN 0160-4120
Éditeur: New York : Elsevier, 1978
DOI: 10.1016/J.ENVINT.2022.107721

Melanoma antigens in pediatric medulloblastoma contribute to tumor heterogeneity and species-specificity of group 3 tumors

Auteurs: Rebecca R. J. Collins, Rebecca R. Florke Gee, Sima Tozandehjani, Tara Bayat, Maria Camila Hoyos Sanchez, Juan Sebastian Solano Gutierrez, Barbara Breznik, Anna K. Lee, Samuel T. Peters, Jon P. Connelly, Shondra M. Pruett-Miller, Martine F. Roussel, Dinesh Rakheja, Heather S. Tillman, Patrick Ryan Potts, Klementina Fon Tacer
Publié dans: Acta Neuropathologica Communications, Numéro 13, 2025, ISSN 2051-5960
Éditeur: Springer Science and Business Media LLC
DOI: 10.1186/S40478-025-02055-3

Spatial Architecture of Myeloid and T Cells Orchestrates Immune Evasion and Clinical Outcome in Lung Cancer

Auteurs: Enfield KSS, Colliver E, Lee CSY, Magness A, Moore DA, Sivakumar M, Grigoriadis K, Pich O, Karasaki T, Hobson PS, Levi D, Veeriah S, Puttick C, Nye EL, Green M, Dijkstra KK, Shimato M, Akarca AU, Marafioti T, Salgado R, Hackshaw A, Consortium T, Jamal-Han
Publié dans: Cancer Discovery, Numéro 2024 Jun 3; 14(6): 1018–1047, 2024, ISSN 2159-8290
Éditeur: American Association for Cancer Research
DOI: 10.1158/2159-8290.CD-23-1380

Combined Toxic Effects of BPA and Its Two Analogues BPAP and BPC in a 3D HepG2 Cell Model

Auteurs: Štampar Martina; Ravnjak Tim; Domijan Ana-Marija; Žegura Bojana
Publié dans: Molecules, Numéro Vol 28, Iss 7, p 3085 (2023), 2023, ISSN 1420-3049
Éditeur: MDPI
DOI: 10.3390/MOLECULES28073085

Patient-derived tumor organoids mimic treatment-induced DNA damage response in glioblastoma

Auteurs: Bernarda Majc, Anamarija Habič, Marta Malavolta, Miloš Vittori, Andrej Porčnik, Roman Bošnjak, Jernej Mlakar, Alenka Matjašič, Andrej Zupan, Marija Skoblar Vidmar, Tamara Lah Turnšek, Aleksander Sadikov, Barbara Breznik, Metka Novak
Publié dans: iScience, Numéro 27, 2025, ISSN 2589-0042
Éditeur: Elsevier BV
DOI: 10.1016/J.ISCI.2024.110604

Gene expression profiles associated with carboplatin chemoresistance in high-grade serous ovarian cancer: insights from 2D and 3D models

Auteurs: Vesna Kokondoska Grgič, Nika Marolt, Ajla Kubat, Tamara Dokmanović, Katja Kološa, Ivana Jovčevska, Tea Lanišnik Rižner
Publié dans: Biomedicine & Pharmacotherapy, Numéro 195, 2026, ISSN 0753-3322
Éditeur: Elsevier BV
DOI: 10.1016/J.BIOPHA.2026.119010

Invasive properties of patient-derived glioblastoma cells after reversible electroporation <i>in vitro</i>

Auteurs: Anja Blazic, Bernarda Majc, Metka Novak, Barbara Breznik, Lea Rems
Publié dans: Radiology and Oncology, Numéro 59, 2025, ISSN 1581-3207
Éditeur: Walter de Gruyter GmbH
DOI: 10.2478/RAON-2025-0058

Exploring the genotoxic potential of Bisphenol A and its emerging alternatives in an advanced in vitro 3D zebrafish hepatic cell model

Auteurs: Alja Štern, Katja Kološa, Špela Rozman, Bojana Žegura
Publié dans: Science of The Total Environment, Numéro 1001, 2025, ISSN 0048-9697
Éditeur: Elsevier BV
DOI: 10.1016/J.SCITOTENV.2025.180527

Integrating computational fluid dynamics into organ-on-chip systems: a glioblastoma-centred design and validation framework

Auteurs: Hooman Taleban, Xinzhong Li, Zulfiqur Ali, Karunakaran Kalesh, Jai Prakash, Tugba Bagci-Onder, Barbara Breznik
Publié dans: Frontiers in Bioengineering and Biotechnology, Numéro 13, 2026, ISSN 2296-4185
Éditeur: Frontiers Media SA
DOI: 10.3389/FBIOE.2025.1716813

Anti-Vimentin Nanobody Decreases Glioblastoma Cell Invasion In Vitro and In Vivo

Auteurs: Alja Zottel; Metka Novak; Neja Šamec; Bernarda Majc; Sara Colja; Mojca Katrašnik; Miloš Vittori; Barbara Hrastar; Ana Rotter; Andrej Porčnik; Tamara Lah Turnšek; Radovan Komel; Barbara Breznik; Ivana Jovčevska
Publié dans: Cancers, Numéro Volume 15, Numéro 573 (2023), 2023, ISSN 2072-6694
Éditeur: MDPI
DOI: 10.3390/CANCERS15030573

Exploring the safety of cannabidiol (CBD): A comprehensive in vitro evaluation of the genotoxic and mutagenic potential of a CBD isolate and extract from Cannabis sativa L

Auteurs: Alja Štern; Matjaž Novak; Katja Kološa; Jurij Trontelj; Sonja Žabkar; Tjaša Šentjurc; Metka Filipič; Bojana Žegura
Publié dans: Biomedicine & Pharmacotherapy, 2024, ISSN 1950-6007
Éditeur: Elsevier
DOI: 10.1016/J.BIOPHA.2024.116969

Genotoxicity and heating Performance of VxFe3-xO4 nanoparticles in Health applications

Auteurs: Sanz-Sagué B, Sáenz-Hernández A, Moreno Maldonado AC, Fuentes-García JA, Nuñez JM, Zegura B, Stern A, Kolosa K, Rozman I, Torres TE, Goya GF
Publié dans: Chemico-Biological Interactions, Numéro Volume 394, 1 May 2024, 110977, 2024, ISSN 0009-2797
Éditeur: Elsevier B.V.
DOI: 10.1016/J.CBI.2024.110977

Harnessing the power of an advanced <i>in vitro</i> 3D liver model and error-corrected duplex sequencing for the detection of mutational signatures

Auteurs: Gillian E Conway, Bérénice Chavanel, François Virard, Ume-Kulsoom Shah, Michael J Burgum, Stephen J Evans, Michael Korenjak, Laura E Thomas, Gareth J Jenkins, Jiri Zavadil, Shareen H Doak
Publié dans: Mutagenesis, 2025, ISSN 0267-8357
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/MUTAGE/GEAF015

Livrables

Publications

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