Periodic Reporting for period 1 - CONTEXT (Aneuploidy and Its Impact on Blood Development: Context Matters)
Reporting period: 2022-10-01 to 2025-03-31
Many childhood leukaemias start to develop before birth due to accumulation of mutations during foetal development. It’s well known that having the wrong number of chromosomes is often linked to leukemia. Children with Down's Syndrome have an extra copy of chromosome 21 in their cells and are 500 times more likely than other children of developing leukemia. However, there’s still a lot we don’t understand about how blood cells in foetuses develop, how they change over time, and how these changes lead to leukaemia.
Two key questions will be answered by this proposed research:
1. How does having an extra chromosome (aneuploidy) interfere with the development of blood cells in the foetus?
2. How does it affect the way mutations build up in blood stem cells, and how do these mutations contribute to leukaemia?
To answer these questions, we will be taking a following approach:
1. We will analyze the foetal liver and bone marrow from children with Down’s Syndrome using advanced techniques that allow us to study individual cells. This will provide a detailed picture of how growth of blood cells might be disrupted.
2. We will use powerful whole genome sequencing to catalog all the genetic mutations that occur in the blood stem cells of foetuses with Down’s Syndrome. This will allow us to understand how these muataions might contribute to the development of leukemia.
Importantly, by looking at both the internal factors (like genetic mutations) and the external factors (like how the cells develop in the body) that affect blood cell growth, we will uncover how having an extra chromosome triggers or accelerates the development of leukemia. Ultimately, this research could give us a much better understanding of the early steps that lead to leukemia, not just in children with Down’s Syndrome, but in general. By identifying these early events, we could potentially develop better ways to diagnose, monitor, and treat this devastating disease in the future.
Two key questions will be answered by this proposed research:
1. How does having an extra chromosome (aneuploidy) interfere with the development of blood cells in the foetus?
2. How does it affect the way mutations build up in blood stem cells, and how do these mutations contribute to leukaemia?
To answer these questions, we will be taking a following approach:
1. We will analyze the foetal liver and bone marrow from children with Down’s Syndrome using advanced techniques that allow us to study individual cells. This will provide a detailed picture of how growth of blood cells might be disrupted.
2. We will use powerful whole genome sequencing to catalog all the genetic mutations that occur in the blood stem cells of foetuses with Down’s Syndrome. This will allow us to understand how these muataions might contribute to the development of leukemia.
Importantly, by looking at both the internal factors (like genetic mutations) and the external factors (like how the cells develop in the body) that affect blood cell growth, we will uncover how having an extra chromosome triggers or accelerates the development of leukemia. Ultimately, this research could give us a much better understanding of the early steps that lead to leukemia, not just in children with Down’s Syndrome, but in general. By identifying these early events, we could potentially develop better ways to diagnose, monitor, and treat this devastating disease in the future.
Significant progress has been made in all areas of the project. The key early objective was the single-cell sequencing of large numbers of sorted cells from 15 Down’s Syndrome (DS) and five healthy fetuses, from different blood populations. The sorting and processing of cells have progressed very rapidly (1.1 million cells processed in the first half of the project). Sequencing has produced a large amount of high-quality data, allowing us to proceed with the data analysis. We were able to apply all the computational tools proposed in the application, and even went well beyond what was initially proposed, thus generating the most comprehensive analysis of DS fetal blood to date.
The second major focus of the project was the spatial transcriptomics (STx) analysis of DS and healthy fetal liver. This has proceeded as planned, and we have generated a comprehensive STx dataset of both DS and healthy liver. Two manuscripts have been written based on the data generated and the analysis pipeline we developed. The third strand of the project was the functional validation of the findings from the computational analysis. We have achieved some positive results and are working on further developing experimental pipelines.
The second major focus of the project was the spatial transcriptomics (STx) analysis of DS and healthy fetal liver. This has proceeded as planned, and we have generated a comprehensive STx dataset of both DS and healthy liver. Two manuscripts have been written based on the data generated and the analysis pipeline we developed. The third strand of the project was the functional validation of the findings from the computational analysis. We have achieved some positive results and are working on further developing experimental pipelines.
This programme of work sits at the frontier of discovery science, and promises to deliver transformative insights into the transcriptional and mutational processes, which occur during human foetal blood development and contribute to the development of childhood leukaemia. By sequencing hundreds of thousands of single cells, it is on track to produce the following important results:
(1) A comprehensive atlas of single cell gene expression in Down’s syndrome.
(2) Spatial map of Down’s syndrome foetal liver and the niche in which blood stem cells reside.
(3) Genomic distribution of the mutations in blood stem cells.
The results from this study will reveal how disruption of the delicate balance of gene products in cells perturbs gene regulatory networks and causes distinct phenotypic properties of Down’s syndrome haematopoietic cells. Single-cell transcriptomics and spatial analysis will further uncover the biological impact that aneuploidy has on cells in the context of tissue and cell-type affected by examining relevant cell-cell interactions. The analysis of somatically-acquired mutations in hundreds of Ts21 foetal haematopoietic progenitors collected from liver will reveal intricate details of the mutational processes that are active in Ts21. Understanding the mechanisms that drive aberrant foetal blood production in Ts21 will ultimately provide novel therapies for childhood leukaemia.
(1) A comprehensive atlas of single cell gene expression in Down’s syndrome.
(2) Spatial map of Down’s syndrome foetal liver and the niche in which blood stem cells reside.
(3) Genomic distribution of the mutations in blood stem cells.
The results from this study will reveal how disruption of the delicate balance of gene products in cells perturbs gene regulatory networks and causes distinct phenotypic properties of Down’s syndrome haematopoietic cells. Single-cell transcriptomics and spatial analysis will further uncover the biological impact that aneuploidy has on cells in the context of tissue and cell-type affected by examining relevant cell-cell interactions. The analysis of somatically-acquired mutations in hundreds of Ts21 foetal haematopoietic progenitors collected from liver will reveal intricate details of the mutational processes that are active in Ts21. Understanding the mechanisms that drive aberrant foetal blood production in Ts21 will ultimately provide novel therapies for childhood leukaemia.