Periodic Reporting for period 4 - MicroBar (Microsatellite Barcoding: reconstructing the family tree of hematopoietic cells)
Berichtszeitraum: 2023-02-01 bis 2024-07-31
The MicroBar project focuses on understanding how blood cells develop from stem cells, a process known as hematopoiesis, which is essential for maintaining a healthy blood system throughout life. Disruptions in hematopoiesis can lead to serious conditions such as leukemia and other blood disorders. Tracing the development, or lineage, of individual stem cells is crucial for understanding both normal blood cell formation and disease-related hematopoiesis.
Recent advances in single-cell technologies have made it possible to track the fate of individual cells with unprecedented resolution in mice. These studies have revealed that the traditional model of the murine blood cell family tree, as depicted in textbooks, is partially incorrect and is now being revised. Meanwhile, blood cell production in humans has long been assumed to be similar to that in mice, largely due to a lack of methods to study human blood cell development directly. To improve our understanding of human hematopoiesis, new single-cell technologies are needed that can reconstruct the blood cell family tree in humans in vivo.
The MicroBar project aims to develop these innovative methods for both humans and mice. Once established, these technologies will be applied to enhance our knowledge of blood cell formation in healthy hematopoiesis in both species. This new understanding will have significant long-term implications for diseases related to blood cell production, such as leukemia, and in clinical settings like bone marrow transplants.
Recent advances in single-cell technologies have made it possible to track the fate of individual cells with unprecedented resolution in mice. These studies have revealed that the traditional model of the murine blood cell family tree, as depicted in textbooks, is partially incorrect and is now being revised. Meanwhile, blood cell production in humans has long been assumed to be similar to that in mice, largely due to a lack of methods to study human blood cell development directly. To improve our understanding of human hematopoiesis, new single-cell technologies are needed that can reconstruct the blood cell family tree in humans in vivo.
The MicroBar project aims to develop these innovative methods for both humans and mice. Once established, these technologies will be applied to enhance our knowledge of blood cell formation in healthy hematopoiesis in both species. This new understanding will have significant long-term implications for diseases related to blood cell production, such as leukemia, and in clinical settings like bone marrow transplants.
The MicroBar project has made significant advances both methodology and biological understanding of hematopoiesis. The team successfully achieved its main goals: developing new tools for lineage tracing in humans, advancing the study of blood cell formation in mice and human. These efforts have yielded significant scientific discoveries and produced tools that are now available for wider use in research and clinical applications.
The first major goal of the project was to develop a new technological pipeline for single-cell lineage (SCLin) tracing in humans. Initially, we explored using microsatellite data for lineage tracing, but the approach encountered significant limitations due to high levels of missing data. This led to the publication of a methodological paper that outlined these challenges and prompted a shift in strategy. We then focused on using mitochondrial mutations as an alternative approach for lineage tracing. This led to the development of the first statistical method for identifying lineage-informative mitochondrial mutations from single-cell data.
The second major goal was to apply SCLin methods to study blood cell development in mice.
A breakthrough came with the creation of the DRAG mouse model, a genetically modified system that generates lineage barcodes through recombination of artificial gene segments. This allowed us to perform lineage tracing without the need for lentiviral infection or transplantation. Using this system, we uncovered key insights into how hematopoietic stem cells function during aging. Contrary to the long-held belief that stem cells become exhausted with age, we found that in their native environment, older stem cells continue to contribute to blood production without showing signs of functional decline.
Additionally, we identified a critical link between hematopoietic stem cell metabolism and their lineage specification. We discovered that hematopoietic stem cells undergo metabolic changes to support myelopoiesis (the production of some white blood cells), with the pentose phosphate pathway playing a pivotal role in this process. This finding opens potential avenues for using metabolic interventions to influence immune cell production.
The third objective focused on applying the lineage-tracing techniques developed in the project to human samples. Using human bone marrow and cord blood, we successfully traced cell lineages and are currently finalizing our analysis to uncovered new insights into human hematopoiesis.
The results of the MicroBar project have been disseminated through numerous publications in peer reviewed scientific journals, including Nature Genetics, Nature Communications, Blood, and IEEE/ACM, as well as several conference presentations. Several computational tools and bioinformatics pipelines developed during the project have been made available to the wider research community as open access. These include software packages that facilitate the analysis of single-cell lineage data and the identification of lineage-informative mitochondrial mutations.
The innovative methodologies developed through MicroBar have broad applications in both basic and clinical research. The lineage-tracing techniques can be used to study stem cell behavior in various contexts, including normal development and disease progression, and are particularly relevant for understanding diseases like leukemia. The project’s findings and resources are now available for further research, and the tools we developed will continue to be used in future studies to explore hematopoiesis and other stem cell-related processes.
The first major goal of the project was to develop a new technological pipeline for single-cell lineage (SCLin) tracing in humans. Initially, we explored using microsatellite data for lineage tracing, but the approach encountered significant limitations due to high levels of missing data. This led to the publication of a methodological paper that outlined these challenges and prompted a shift in strategy. We then focused on using mitochondrial mutations as an alternative approach for lineage tracing. This led to the development of the first statistical method for identifying lineage-informative mitochondrial mutations from single-cell data.
The second major goal was to apply SCLin methods to study blood cell development in mice.
A breakthrough came with the creation of the DRAG mouse model, a genetically modified system that generates lineage barcodes through recombination of artificial gene segments. This allowed us to perform lineage tracing without the need for lentiviral infection or transplantation. Using this system, we uncovered key insights into how hematopoietic stem cells function during aging. Contrary to the long-held belief that stem cells become exhausted with age, we found that in their native environment, older stem cells continue to contribute to blood production without showing signs of functional decline.
Additionally, we identified a critical link between hematopoietic stem cell metabolism and their lineage specification. We discovered that hematopoietic stem cells undergo metabolic changes to support myelopoiesis (the production of some white blood cells), with the pentose phosphate pathway playing a pivotal role in this process. This finding opens potential avenues for using metabolic interventions to influence immune cell production.
The third objective focused on applying the lineage-tracing techniques developed in the project to human samples. Using human bone marrow and cord blood, we successfully traced cell lineages and are currently finalizing our analysis to uncovered new insights into human hematopoiesis.
The results of the MicroBar project have been disseminated through numerous publications in peer reviewed scientific journals, including Nature Genetics, Nature Communications, Blood, and IEEE/ACM, as well as several conference presentations. Several computational tools and bioinformatics pipelines developed during the project have been made available to the wider research community as open access. These include software packages that facilitate the analysis of single-cell lineage data and the identification of lineage-informative mitochondrial mutations.
The innovative methodologies developed through MicroBar have broad applications in both basic and clinical research. The lineage-tracing techniques can be used to study stem cell behavior in various contexts, including normal development and disease progression, and are particularly relevant for understanding diseases like leukemia. The project’s findings and resources are now available for further research, and the tools we developed will continue to be used in future studies to explore hematopoiesis and other stem cell-related processes.
The work performed by MicroBar represents a significant step forward in stem cell biology and offers valuable insights for both research and clinical applications.
To increase our knowledge of human blood cell production, we need new single cell technologies adapted to work in human to reconstruct the family tree of cells in vivo. To this end, the team developed a novel statistical method based on mitochondrial mutations, which showed promise for more efficient lineage tracing in humans. This statistical method represents a significant advancement in the ability to track stem cell development.
In parallel, the project studied the hematopoietic system in mice, which serves as a model for human blood cell formation. The development of the DRAG mouse was a breakthrough and gave important biological insight into murine hematopoiesis. The DRAG mouse allows for lineage tracing without the need for invasive procedures like viral infections or transplantations.
Using this model, we uncovered new insights into how blood production changes with age. Contrary to previous assumptions, older stem cells in their natural environment continue to contribute to blood production without showing signs of exhaustion. Moreover, we also discovered a link between hematopoietic stem cell metabolism and their lineage specification, highlighting the role of metabolic pathways in determining how stem cells develop into white blood cells. This finding opens new possibilities for targeting metabolism to influence immune cell production.
In conclusion, the project made important strides in both technological innovation and biological discovery. The new methods and tools developed during the project significantly advance our ability to trace the development of blood cells, offering new insights into how blood is produced both in normal conditions and in diseases like leukemia. These findings have broad applications for future research and could lead to improved treatments for blood-related diseases by providing deeper insights into how stem cells function and how their activity can be modulated in disease contexts.
To increase our knowledge of human blood cell production, we need new single cell technologies adapted to work in human to reconstruct the family tree of cells in vivo. To this end, the team developed a novel statistical method based on mitochondrial mutations, which showed promise for more efficient lineage tracing in humans. This statistical method represents a significant advancement in the ability to track stem cell development.
In parallel, the project studied the hematopoietic system in mice, which serves as a model for human blood cell formation. The development of the DRAG mouse was a breakthrough and gave important biological insight into murine hematopoiesis. The DRAG mouse allows for lineage tracing without the need for invasive procedures like viral infections or transplantations.
Using this model, we uncovered new insights into how blood production changes with age. Contrary to previous assumptions, older stem cells in their natural environment continue to contribute to blood production without showing signs of exhaustion. Moreover, we also discovered a link between hematopoietic stem cell metabolism and their lineage specification, highlighting the role of metabolic pathways in determining how stem cells develop into white blood cells. This finding opens new possibilities for targeting metabolism to influence immune cell production.
In conclusion, the project made important strides in both technological innovation and biological discovery. The new methods and tools developed during the project significantly advance our ability to trace the development of blood cells, offering new insights into how blood is produced both in normal conditions and in diseases like leukemia. These findings have broad applications for future research and could lead to improved treatments for blood-related diseases by providing deeper insights into how stem cells function and how their activity can be modulated in disease contexts.