Periodic Reporting for period 1 - ONCO-COMP (Oncogenic competence during development – When, Where and Why?)
Okres sprawozdawczy: 2023-09-01 do 2026-02-28
Childhood cancers are believed to be rooted in aberrant development, a notion supported by their (i) generally low mutational burden, (ii) high prevalence of single (often epigenetic) driver events and (iii) occurrence during confined developmental periods. Yet, the exact origins of developmental tumours remain one of the principal enigmas of pediatric oncology. A prime example are malignant rhabdoid tumours (MRTs): they are astoundingly genomically simple but extremely deadly childhood cancers that arise almost exclusively in the first two years of life, and are driven by biallelic inactivation of the SWI/SNF chromatin remodelling complex subunit SMARCB1 (>95% of cases). We still do not know what determines oncogenic competence upon SMARCB1 loss. In particular we wonder: (1) What are the cell(s)-of-origin of rhabdoid tumours and what is their normal differentiation potential? (2) What is the molecular framework that facilitates oncogenic transformation upon SMARCB1 loss? (3) What is the contribution of the niche (local and systemic) to the acquisition of oncogenic competence? And, considering the epigenetic nature of the oncogenic event, (4) is the oncogenic MRT state reversible, and how? To answer these questions, we will combine state-of-the-art lineage-barcoded single-cell genomics, spatial transcriptomic, single-cell resolution wholemount imaging, CRISPR/Cas9 and epigenomic approaches, as well as integrative computational analyses, using transgenic mouse, induced pluripotent stem cell and patient-derived xenograft rhabdoid tumour models. This project will provide fundamental insights into the cell autonomous and non-autonomous determinants of oncogenic competence upon SMARCB1 loss. Based on our findings we hope to unlock targeted treatments for MRT patients. Importantly, the conceptual and experimental framework we establish will open up new investigative opportunities for a multitude of developmental cancers.
The period of ONCO-COMP was dedicated to obtaining, implementing and fully establishing a variety of model systems required for the success of this project. This included obtaining and crossing a variety of transgenic mouse lines, establishing the dose and timing required for successful oncogenic conversion, and the generation of a tissue-bank from these animals, containing tissues of interest from tumour-bearing and control animals. In addition, we have generated genome-engineered versions of both hiPSCs and patient-derived cells which will enable us to tightly regulate desired genomic modifications related to the induction or reversion of the oncogenic event.
Main achievements:
1. Crossing of a mouse model which will enable us to accurately trace the ATRT origins in order to understand the determinants of oncogenic competence upon Smarcb1-loss, one of the main objectives of this project.
2. Generation of tissue bank from the generated transgenic animals, which will be used for both molecular and multi-marker histopathological characterisation of Smarcb1-null and their Smarcb1-expressing equivalents during the next project period.
3. Characterisation of the earliest molecular events adjacent to malignant conversion. Indeed, we observe molecular similarities between pre-malignant cells and the full-blown disease.
4. Genomic engineering of in vitro tools to tightly modulate the oncogenic event.
Overall, we are happy to report that we have successfully set up all the complex model systems required to carry out this ambitious project. Molecular and functional characterisations are ongoing.
Main achievements:
1. Crossing of a mouse model which will enable us to accurately trace the ATRT origins in order to understand the determinants of oncogenic competence upon Smarcb1-loss, one of the main objectives of this project.
2. Generation of tissue bank from the generated transgenic animals, which will be used for both molecular and multi-marker histopathological characterisation of Smarcb1-null and their Smarcb1-expressing equivalents during the next project period.
3. Characterisation of the earliest molecular events adjacent to malignant conversion. Indeed, we observe molecular similarities between pre-malignant cells and the full-blown disease.
4. Genomic engineering of in vitro tools to tightly modulate the oncogenic event.
Overall, we are happy to report that we have successfully set up all the complex model systems required to carry out this ambitious project. Molecular and functional characterisations are ongoing.
The first two years of ONCO-COMP were dedicated to setting up the critical and novel model systems which will be key for the success of the project. Indeed, first preliminary molecular characterisations anchored in these newly generated models have given us a glimpse into the suitability of the generated models for addressing the questions set out in ONCO-COMP, as well as a first glimpse into the wealth of insight that the second period of the project will bring. We are looking forward to delving deeper into the functional and biological results that ONCO-COMP is bringing about. We believe that our approach of combining of these new models with lineage tracing technologies will unveil the origin and dynamics of malignant conversion, and is truly beyond the state of the art.