Periodic Reporting for period 1 - FANTOM (Future of ALCL: Novel Therapies, Origins, Bio-Markers and Mechanism of resistance)
Période du rapport: 2023-01-01 au 2024-12-31
The FANTOM Doctoral Network (DN) (https://fantom-project.eu(s’ouvre dans une nouvelle fenêtre)) consists of key members of the European research initiative for ALK related malignancies (ERIA) and the European Intergroup for Childhood Non-Hodgkin Lymphoma (EICNHL), a consortium of clinicians (n=46), pathologists (n=24), biologists (n=22) and trials coordinators (n=5) that collectively conduct research into childhood NHL. Employing these two networks and the significant resources within, the FANTOM DN is training and educating 10 talented researchers. Training, centred on interactions between companies and academic institutions, is taking the form of multiple scientific and clinical disciplines in order to explore the biology of childhood NHL to develop quality-controlled assays for stratification biomarkers and novel therapeutic strategies. In particular, we are focussing on a specific form of NHL, Anaplastic Large Cell Lymphoma (ALCL) which largely affects children and young adults specifically when associated with aberrant expression of anaplastic lymphoma kinase (ALK). Whilst overall survival is relatively high for childhood ALCL, 30% of children relapse, they still suffer the long-term side-effects of therapy and for some children, we are likely over-treating. This situation can only be improved if fundamental and clinical science is performed to identify less-toxic therapies guided by (non-invasive) biomarkers. With this in mind, our integrated programme is pursuing the following objectives:
Objective 1: Increase our understanding of the biological mechanisms, including the role of the immune system in ALCL, to inform on novel, less toxic therapeutic targets
The pathogenesis of ALCL is for the most part poorly elucidated with the mechanisms giving rise to this malignancy being little understood. However, the cell of origin of ALCL is postulated as an early thymic progenitor in which the driving oncogenic event, expression of the t(2;5) breakpoint product facilitates the acquisition of cancer hallmarks to incipient cancer cells. We are investigating this process further with a specific emphasis on the contributory role of the immune system and inflammatory signalling pathways. Employing a variety of model systems ranging from Genetically Engineered Mouse Models (GEMM) through to Patient Derived Xenografts (PDX), organoids, primary patient tumour material and cell lines, together with multiple omics technologies, we are studying the pathways that drive tumour growth, as well as the role of inflammatory cells with the aim of using these data to inform on novel therapeutic strategies and biomarkers for disease monitoring.
Objective 2: Apply our findings from the biology of ALCL to develop biomarkers for clinical translation
Primary patient tumours are being assessed for the status of their genomes, such as the presence of acquired mutations that may contribute to tumour growth using multiple omics technologies at a single cell level. In particular, single cell (sc) RNAseq, spatial transcriptomics, CyTOF, analysis of the epigenome and sc cDNA genotyping is being applied to develop prognostic algorithms. We are also assessing plasma components including exosomal small RNA (sRNA) species, circulating tumour DNA (ctDNA) and circulating antibodies to ALK. These data will be correlated to clinical data in order to identify at least 2 potential biomarkers for further clinical development, as well as to determine therapeutic targets in a personalised genomics approach.
Objective 3: Uncover mechanisms and origins of resistance of ALCL to therapy with tyrosine kinase inhibitors in order to identify novel therapeutic targets and develop a personalised therapeutic strategy
Relapse/refractory (r/r) disease is one of the major clinical problems and occurs both after chemotherapy, and targeted agents are employed in the clinic. To understand the mechanisms of resistance, we are employing scRNAseq, spatial transcriptomics and CRISPR screens towards the development of rescue therapies and/or therapeutic approaches that prevent r/r disease from occurring. Employing a variety of model systems from cell lines rendered resistant to targeted therapeutics through to PDX models of relapse and primary relapse tumour material, posited resistance mechanisms are being validated and assessed.
Objective 1: Increase our understanding of the biological mechanisms, including the role of the immune system in ALCL, to inform on novel, less toxic therapeutic targets
The pathogenesis of ALCL is for the most part poorly elucidated with the mechanisms giving rise to this malignancy being little understood. However, the cell of origin of ALCL is postulated as an early thymic progenitor in which the driving oncogenic event, expression of the t(2;5) breakpoint product facilitates the acquisition of cancer hallmarks to incipient cancer cells. We are investigating this process further with a specific emphasis on the contributory role of the immune system and inflammatory signalling pathways. Employing a variety of model systems ranging from Genetically Engineered Mouse Models (GEMM) through to Patient Derived Xenografts (PDX), organoids, primary patient tumour material and cell lines, together with multiple omics technologies, we are studying the pathways that drive tumour growth, as well as the role of inflammatory cells with the aim of using these data to inform on novel therapeutic strategies and biomarkers for disease monitoring.
Objective 2: Apply our findings from the biology of ALCL to develop biomarkers for clinical translation
Primary patient tumours are being assessed for the status of their genomes, such as the presence of acquired mutations that may contribute to tumour growth using multiple omics technologies at a single cell level. In particular, single cell (sc) RNAseq, spatial transcriptomics, CyTOF, analysis of the epigenome and sc cDNA genotyping is being applied to develop prognostic algorithms. We are also assessing plasma components including exosomal small RNA (sRNA) species, circulating tumour DNA (ctDNA) and circulating antibodies to ALK. These data will be correlated to clinical data in order to identify at least 2 potential biomarkers for further clinical development, as well as to determine therapeutic targets in a personalised genomics approach.
Objective 3: Uncover mechanisms and origins of resistance of ALCL to therapy with tyrosine kinase inhibitors in order to identify novel therapeutic targets and develop a personalised therapeutic strategy
Relapse/refractory (r/r) disease is one of the major clinical problems and occurs both after chemotherapy, and targeted agents are employed in the clinic. To understand the mechanisms of resistance, we are employing scRNAseq, spatial transcriptomics and CRISPR screens towards the development of rescue therapies and/or therapeutic approaches that prevent r/r disease from occurring. Employing a variety of model systems from cell lines rendered resistant to targeted therapeutics through to PDX models of relapse and primary relapse tumour material, posited resistance mechanisms are being validated and assessed.
We have recruited 10 students from across the globe who are now registered to undertake PhD programmes in the EU. The students are all embedded in research labs at internationally renowned institutes, hospitals and universities and are undertaking secondments in both academia and industry. All network members have met and had initial conversations concerning their projects at a kick-off meeting that was held in Vienna in December 2023. This was the first time all the recruited students and network partners got together to discuss projects and the overall management of the network. At this meeting all procedures and processes for the successful management of the programme were put in place with committees necessary for monitoring training, research, progress and outreach established. Students received training in genomic technologies including analysis of data at the first network-wide meeting held in Czechia and green issues including activities to reflect on sustainable lab practices. At the second network-wide event in Turin, students received training in public outreach, dissemination and communication from the world-renowned Cambridge-based Naked Scientists and Open Science based in Vienna. They also each gave an oral presentation to update the network on the research progress, to discuss data and receive peer feedback.
Work is ongoing with regards to the scientific aspects of the programme whereby many of the model systems required for the successful implementation of the project have now been developed. These include genetically modified cell lines and mouse models which will enable us to dissect apart the biology of this childhood lymphoma towards improved treatment outcomes. Work will now progress using these models to understand why and how this cancer develops in children. At the same time, a collection of patient samples and specimens has been collected and analysis has commenced to understand the unique genetics of these tumours. We are already developing hypotheses as to why some tumours are resistant to treatment and how this might be overcome in the future. This will be facilitated by the assays that are under development that will allow us to develop better prognostic biomarkers which can also be used to stratify children towards the best treatment approach for them. Ongoing work is now developing and validating these biomarker assays.
Work is ongoing with regards to the scientific aspects of the programme whereby many of the model systems required for the successful implementation of the project have now been developed. These include genetically modified cell lines and mouse models which will enable us to dissect apart the biology of this childhood lymphoma towards improved treatment outcomes. Work will now progress using these models to understand why and how this cancer develops in children. At the same time, a collection of patient samples and specimens has been collected and analysis has commenced to understand the unique genetics of these tumours. We are already developing hypotheses as to why some tumours are resistant to treatment and how this might be overcome in the future. This will be facilitated by the assays that are under development that will allow us to develop better prognostic biomarkers which can also be used to stratify children towards the best treatment approach for them. Ongoing work is now developing and validating these biomarker assays.
At present, we have not produced results that are ready to have impact. As mentioned above, the model systems and assays are being developed that will allow us to address the objectives of the programme.