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European Liquid Biopsies Academy - Towards widespread clinical application of blood- based diagnostic tools

Periodic Reporting for period 2 - ELBA (European Liquid Biopsies Academy - Towards widespread clinical application of blood-based diagnostic tools)

Reporting period: 2020-01-01 to 2022-09-30

Liquid biopsies have been heralded as a game-changer in cancer management, with blood tests offering a minimally invasive, safe, and sensitive alternative or complementary approach for tissue biopsies. Blood represents a rich source of information through which solid cancers (and their subtypes) can be detected, identified and classified, and matched to a specific therapy. However, despite the potential of individual approaches, the promise of liquid biopsies has not yet materialized in the clinic. Widespread deployment requires creative next-generation researchers with an innovative mind-set with access to a unique toolbox, including medical know-how, molecular diagnostics expertise (from health economics to regulatory), and statistical/bioinformatics proficiency. Currently, there are no comprehensive training programs to address this need. To move the promising liquid biopsy technology out of its infancy, the research program and educational curriculum of the European Liquid Biopsy Academy (ELBA) covers the entire value chain of diagnostics development and integrates all required disciplines and sectors. ELBA educates 15 Early Stage Researchers (ESRs) with the skills to circumvent the obstacles currently hampering effective development and commercialization of liquid biopsy approaches. By creating a sustainable network to foster long-term multidisciplinary relationships and communication networks with various stakeholders we aim to accelerate clinical translation of these blood-based diagnostics. ELBA focuses on the development of blood tests for early lung cancer detection and therapy selection.
The ELBA consortium comprises 9 beneficiaries and 12 partner organizations from 10 European countries. The research core of the ELBA consists of 4 work-packages executed through 15 individual research projects with 13 fellows recruited and hosted by academic beneficiaries and 2 fellows by non-academic beneficiaries. The project is supported by 2 work packages fully dedicated to fellows’ career development training, consortium management, and outreach activities. The ELBA successfully completed the implementation of the project, the recruitment of 15 ESRs, and achieved substantial progress within the project’s research core.
The main objective of the Technological Platform Development-WP1 is to provide technological advancement to extract clinically relevant information out of individual blood-based biosources. WP1 ESRs are investigating new isolation and detection methods to develop a multi-biosource combinatorial liquid biopsy assay. ESRs delivered the first and the second generation of assay protocols and datasheets, as well as a biomarker panel selection and assay specifications. We succeeded in achieving the planned milestone, i.e. the development of individual liquid biopsy lung cancer assays.
To address the need for developing diagnostic tests that will aid clinical decision making, ESRs will validate next-generation liquid biopsy tests using well-defined patient cohorts. WP2 (Standardization) projects resulted in the delivery of a first and second series of lung cancer (NSCLC) blood sample cohorts and the report on the first generation of validated assays. Also here we achieved the planned milestone, i.e. the developed combinatorial NSCLC detection assays.
The Computational Data Analysis work package-WP3 with 3 ESRs is dedicated to developing a customized computational grid and bioinformatics approaches that will enable biomarker discovery, assay validation, and data integration. WP3 ESRs specifically focused on developing tools and computation platforms for total RNA profiling, whole-genome and targeted sequencing data analysis and feature selection for improved biomarker selection. In WP3 we determine the best biomarker candidates using state of the art and novel machine learning methods. We were able to deliver the RNA, DNA, and epitranscriptomics reports as well as the “ELBA-BASE”: computational framework, resulting in finalization of the milestones, i.e. presentation and release of the top biomarker candidates and the integrated computational ELBA grid.
In close collaboration with ERSs from WP1 and WP2, 2 ESRs appointed at our commercial partners are working towards the development of liquid biopsy platforms that can be implemented commercially. Their projects are related to Integration and Implementation (WP4) of standardized assays into diagnostics tests, including a combination of biosources. Therefore, WP4 ESRs focused their current work on optimizing the use of different liquid biopsy sources on two analytical assays platforms. Next, ESRs completed detailed guidelines for assay development and validation with the major milestone achieved on time.
ELBA addresses the challenges in liquid biopsies by training a new generation of researchers that can fast-track the development and clinical validation of these innovative diagnostics. The project itself specifically focuses on comparison and integration of liquid biopsy biosources to develop a diagnostic platform for DETECTION of NSCLC and simultaneous SELECTION of the right treatment. However, the training focuses on the final benchmark of success, which is the translation of the skills and tools developed within ELBA towards other disease indications (cancer and beyond) and applications (e.g. early detection, prognosis). Therefore, the project has both direct and indirect impact for researchers by gaining new insights into the biology of cancer, clinicians by providing novel tools and guidelines for effective cancer management, patients by enhancing quality of care and increasing survival chances, biotechnology companies by providing novel approaches to diagnostics development, pharmaceutical companies by generating novel tools that could be used as companion diagnostics and, healthcare systems by developing cost-effective solutions to combat cancer and increase survival. Research and development efforts regarding liquid biopsy diagnostics are scattered throughout Europe and there is a lack of integration between the different pillars: discovery, development, standardization, clinical validation, and implementation. ELBA is bringing together partners from different backgrounds and technologies to educate the next-generation of researchers that can address this challenge. The assessment of the main and alternative approaches for the development and implementation of liquid biopsies in the clinical settings requires a strongly interdisciplinary effort with a wide range of scientific and technology competencies to lead a radical breakthrough with transformative impact. The ELBA academic partners and the two SMEs present in our consortium each possess innovative and disruptive technological platforms for non-invasive diagnostics tests. We will develop and validate assays in ongoing NSCLC clinical trials sponsored by large pharmaceutical companies and, in addition, in patients that are molecularly tested in routine clinical practice. With the first liquid biopsy test for NSCLC recently FDA approved, our focus will ensure that ESRs enter a highly active environment in terms of development and implementation of liquid biopsy technology. Thus, ELBA aims at delivering liquid biopsy tests for the detection and selection of NSCLC, which will provide a basis for future expansion of the European Liquid Biopsy Academy.