Periodic Reporting for period 1 - 3DSecret (3D spheroids derived from single cells for discovering stochastic patterns behind metastasis)
Reporting period: 2023-01-01 to 2023-12-31
Metastasis, the spreading of tumours cells to other parts of the body, contributes to up to 9 out of 10 cancer-related deaths. However, some of the mechanisms triggering this process remain elusive and the 3DSecret project set off on a mission to change this. This consortium aims to study metastasis focusing on single cells. By studying individual circulating tumour cells, or CTCs, 3DSecret hopes to uncover hidden patterns that can predict how cancer spreads, with the potential to change how cancer is diagnosed or treated and thus make significant advances in current clinical practice.
To target this challenge, 3DSecret has outlined specific objectives. At the forefront is the development of the ‘3DSecret-chip,’ a sophisticated tool designed to facilitate the controlled creation of 3D cancer cell models from individual cells. This approach promises reproducibility and precision, enhancing the capacity to examine cancer cell behaviour.
Furthermore, 3DSecret is incorporating online ‘SERS metabolomics’- an advanced technology providing continuous insights into the growth kinetics and metabolic profile of these 3D cancer cell models. This dynamic monitoring is crucial for capturing the evolving nature of cancer cells in a controlled environment. Each 3D cancer model with finally be analysed for its genetic profile.
The ultimate aim of 3DSecret extends beyond technological innovation – it seeks to decode metastatic patterns by integrating multi-omics data with artificial intelligence. The convergence of cutting-edge technologies and intelligent computing is a combined effort to decode the intricate complexities in the evolution of metastasis.
The mission of 3DSecret is to analyse single cancer cells in an unprecedented manner, thus uncovering secrets that not only hold the promise of transforming our understanding of cancer, but could also lead to ground-breaking advances in medical sciences.
To target this challenge, 3DSecret has outlined specific objectives. At the forefront is the development of the ‘3DSecret-chip,’ a sophisticated tool designed to facilitate the controlled creation of 3D cancer cell models from individual cells. This approach promises reproducibility and precision, enhancing the capacity to examine cancer cell behaviour.
Furthermore, 3DSecret is incorporating online ‘SERS metabolomics’- an advanced technology providing continuous insights into the growth kinetics and metabolic profile of these 3D cancer cell models. This dynamic monitoring is crucial for capturing the evolving nature of cancer cells in a controlled environment. Each 3D cancer model with finally be analysed for its genetic profile.
The ultimate aim of 3DSecret extends beyond technological innovation – it seeks to decode metastatic patterns by integrating multi-omics data with artificial intelligence. The convergence of cutting-edge technologies and intelligent computing is a combined effort to decode the intricate complexities in the evolution of metastasis.
The mission of 3DSecret is to analyse single cancer cells in an unprecedented manner, thus uncovering secrets that not only hold the promise of transforming our understanding of cancer, but could also lead to ground-breaking advances in medical sciences.
3DSecret intends to leverage novel microfluidic platforms to isolate Circulating Tumour Cells (CTCs) and, following their culture into 3D spheroids, enable their multi-parametric analysis using single-cell omics and an artificial intelligence algorithm to identify and predict the factors associated with a more aggressive metastatic breast cancer. To accomplish it, it is important to use biological samples and clinical data from cancer patients. Therefore, a clinical study needs to be prepared and implemented, following the legal regulations and ethical guidelines, and approved by the competent entities.
During the reporting period, 2CA-Braga requested, to the remaining partners, information of the product under development. 2CA-Braga acquired consultancy services with the clinical team of Hospital de Braga to understand the needs of the patients and of the clinical team, the feasibility and applicability of the product's features, and to establish the requirements of the clinical study. This resulted in the definition of the clinical study design, objectives and data flow.
The clinical study design and data flow were evaluated considering the clinical research legal framework and possible legal, ethical and data protection constrains were identified to be addressed and resolved.
A discussion was conducted between partners and the respective Data Protection Officers (DPOs), and 2CA-Braga supported the definition of the partners and services necessary for the clinical study and their roles (data controllers and data processors).
The data management plan was prepared, which resulted in the Deliverable 1.2.
2CA-Braga also prepared the Joint controllership agreement (JCA) on data protection and the Data Protection Impact Assessment (DPIA) of the clinical study, which was reviewed by the partners involved in the clinical study.
Also, the clinical study was defined, the submission dossier was prepared and submitted to the DPO of Hospital de Braga for approval.
To prepare the submission dossier, it was considered the clinical research legal framework (clinical research regulations ethical guidelines, data protection regulations) as well as the requirements of Hospital de Braga.
The dossier was composed of the documents: Clinical study protocol, Informed Consent Form (ICF), Case Report Form (CRF), Data Protection Impact Assessment (DPIA), Statement of responsibilities, Request for the conduct of the clinical study to the president of the Hospital's Board of Directors, Request for authorization from the Department Service Director, Ethics submission form, Curriculum vitae of all investigators involved in the clinical study, Joint Controllership Agreement on data protection, Statement justifying the need for genomic studies.
Of note that in the protocol, it is defined the scope, the objectives, the endpoints, the study design, the population of study, eligibility criteria, the procedures for collection and storage of clinical data and samples, statistical analysis, timetable, expected impact, ethical and data protection considerations, and funding of the study, as well as conditions related to the property of the data and publishing of results.
The patient recruitment procedure was defined as well as the clinical study population. The study population are adult women with metastatic breast cancer, who are followed by the medical physicians and investigators at the Oncology Department of HB, during standard clinical practice within the scope of Senology and Oncology group consultation. The eligibility criteria (inclusion and exclusion criteria) of the study were defined together with the clinical team. The study is divided into two phases and 20 participants will be recruited for the first phase and 100 participants for the second phase of the study. The tasks described above were reported in Deliverable 5.1.
During the reporting period, 2CA-Braga requested, to the remaining partners, information of the product under development. 2CA-Braga acquired consultancy services with the clinical team of Hospital de Braga to understand the needs of the patients and of the clinical team, the feasibility and applicability of the product's features, and to establish the requirements of the clinical study. This resulted in the definition of the clinical study design, objectives and data flow.
The clinical study design and data flow were evaluated considering the clinical research legal framework and possible legal, ethical and data protection constrains were identified to be addressed and resolved.
A discussion was conducted between partners and the respective Data Protection Officers (DPOs), and 2CA-Braga supported the definition of the partners and services necessary for the clinical study and their roles (data controllers and data processors).
The data management plan was prepared, which resulted in the Deliverable 1.2.
2CA-Braga also prepared the Joint controllership agreement (JCA) on data protection and the Data Protection Impact Assessment (DPIA) of the clinical study, which was reviewed by the partners involved in the clinical study.
Also, the clinical study was defined, the submission dossier was prepared and submitted to the DPO of Hospital de Braga for approval.
To prepare the submission dossier, it was considered the clinical research legal framework (clinical research regulations ethical guidelines, data protection regulations) as well as the requirements of Hospital de Braga.
The dossier was composed of the documents: Clinical study protocol, Informed Consent Form (ICF), Case Report Form (CRF), Data Protection Impact Assessment (DPIA), Statement of responsibilities, Request for the conduct of the clinical study to the president of the Hospital's Board of Directors, Request for authorization from the Department Service Director, Ethics submission form, Curriculum vitae of all investigators involved in the clinical study, Joint Controllership Agreement on data protection, Statement justifying the need for genomic studies.
Of note that in the protocol, it is defined the scope, the objectives, the endpoints, the study design, the population of study, eligibility criteria, the procedures for collection and storage of clinical data and samples, statistical analysis, timetable, expected impact, ethical and data protection considerations, and funding of the study, as well as conditions related to the property of the data and publishing of results.
The patient recruitment procedure was defined as well as the clinical study population. The study population are adult women with metastatic breast cancer, who are followed by the medical physicians and investigators at the Oncology Department of HB, during standard clinical practice within the scope of Senology and Oncology group consultation. The eligibility criteria (inclusion and exclusion criteria) of the study were defined together with the clinical team. The study is divided into two phases and 20 participants will be recruited for the first phase and 100 participants for the second phase of the study. The tasks described above were reported in Deliverable 5.1.
The clinical study that will be performed under the scope of the 3DSecret project will allow the optimization of the procedeures of CTCs recivery and isolation, proliferation of individual CTCs into microdroplets, monitoring of growth kinetics and extracellular metabolic activity and extraction of genetic material for genomic and transcriptomic analysis. Once the procedures are optimized, the clinical study will allow the identification of factors associated with greater aggressiveness in CTCs from metastatic breast cancer patient through the development of Artificial Intelligence algorithms using the patient clinical data and the results of the CTCs analysis (growth kinetics, metabolomic, genomic and transcriptomic data).
During these reporting period the data flow was defined and the data management plan was prepared. In addition, all the documents of the clinical study submission dossier (Clinical study protocol, Informed Consent Form (ICF), Case Report Form (CRF), Data Protection Impact Assessment (DPIA), Statement of responsibilities, Request for the conduct of the clinical study to the president of the Hospital's Board of Directors, Request for authorization from the Department Service Director, Ethics submission form, Curriculum vitae of all investigators involved in the clinical study, Joint Controllership Agreement on data protection, Statement justifying the need for genomic studies) were prepared and submitted for approval from the Data Protection Officer of Hospital de Braga.
During these reporting period the data flow was defined and the data management plan was prepared. In addition, all the documents of the clinical study submission dossier (Clinical study protocol, Informed Consent Form (ICF), Case Report Form (CRF), Data Protection Impact Assessment (DPIA), Statement of responsibilities, Request for the conduct of the clinical study to the president of the Hospital's Board of Directors, Request for authorization from the Department Service Director, Ethics submission form, Curriculum vitae of all investigators involved in the clinical study, Joint Controllership Agreement on data protection, Statement justifying the need for genomic studies) were prepared and submitted for approval from the Data Protection Officer of Hospital de Braga.