Periodic Reporting for period 4 - CellularBiographies (Global views of cell type specification and differentiation)
Periodo di rendicontazione: 2024-07-01 al 2025-12-31
Every cell in your body has a unique history — a record of which genes were active at each point in its life, shaping what kind of cell it ultimately becomes. A central question in biology is: how does a cell go from a naive state to something as specialized as a neuron, a liver cell, or a muscle fiber? Recent breakthroughs in gene editing and the ability to read gene activity in thousands of individual cells at once have made it possible to study this process on a massive scale, one cell at a time.
By tracking both the ancestry of cells (who descended from whom) and the sequence of gene activity changes along the way, we can now build detailed "family trees" of cell development — revealing how the remarkable variety of cell types in our bodies emerges from a single egg, and how cells gradually acquire the specialized functions they need to keep us alive.
With this in mind, we set out to accomplish three things using the zebrafish embryo as our model: first, to catalogue all the different cell types that arise during development and map the gene activity patterns that define them; second, to connect a cell's lineage — its family history — with the changes in gene activity that drive it toward a particular fate; and third, to uncover the step-by-step genetic programs that transform a generic cell into one that can perform a specific physiological job.
Together, these efforts aimed to produce the first complete, bird's-eye view of how a vertebrate animal builds itself from scratch — a resource that could reshape our understanding of development, disease, and regeneration.
By tracking both the ancestry of cells (who descended from whom) and the sequence of gene activity changes along the way, we can now build detailed "family trees" of cell development — revealing how the remarkable variety of cell types in our bodies emerges from a single egg, and how cells gradually acquire the specialized functions they need to keep us alive.
With this in mind, we set out to accomplish three things using the zebrafish embryo as our model: first, to catalogue all the different cell types that arise during development and map the gene activity patterns that define them; second, to connect a cell's lineage — its family history — with the changes in gene activity that drive it toward a particular fate; and third, to uncover the step-by-step genetic programs that transform a generic cell into one that can perform a specific physiological job.
Together, these efforts aimed to produce the first complete, bird's-eye view of how a vertebrate animal builds itself from scratch — a resource that could reshape our understanding of development, disease, and regeneration.
One of the most fundamental mysteries in biology is how a single fertilized egg gives rise to hundreds of different cell types — brain cells, muscle cells, liver cells — each with its own identity and job. We tackled that question using zebrafish embryos and cutting-edge genomic tools, making four major contributions:
1. Mapping the developing brain: We created detailed "census" data for the zebrafish brain at different points in development, cataloguing the many cell types present and identifying the molecular signatures that define each one. We also developed better tools to track which cells are descended from which, essentially reconstructing family trees of brain cells as they diversify.
2. Understanding how cells become specialized: As cells specialize, thousands of genes switch on and off in coordinated waves. We built a computational tool (MIMIR) to identify groups of genes that work together during this process. Applying it to cells that become glands versus cells that produce structural scaffolding revealed both familiar and new biological mechanisms — including how cells manage to secrete very different products while using shared and distinct regulatory mechanisms.
3. Connecting gene regulation to cell specialization: Beyond which genes are active, we examined how genes get turned on — specifically, which regions of DNA are physically "open" and accessible in different cell types. We built an AI model to predict this from DNA sequence alone, and found that surprisingly few master regulator proteins (transcription factors) are responsible for giving each cell type its unique identity. Remarkably, many of these same regulators are borrowed and repurposed from their original roles in organ formation.
4. Seeing gene activity in space and time: We developed a way to measure the activity of hundreds of genes simultaneously across an entire embryo while preserving its physical structure. This allowed us to track not just what genes are active in a cell, but where that cell sits in the embryo and where it came from, capturing how gene activity changes as cells physically move and reorganize during development. The resulting dataset covers over 25,000 genes and is publicly available for other scientists to explore.
Taken together, these tools and discoveries move us from snapshots of individual genes toward a comprehensive "biography" of how every cell in an embryo acquires its identity. Such global views of development will help understand birth defects, regeneration, and ultimately what it means to build a body.
1. Mapping the developing brain: We created detailed "census" data for the zebrafish brain at different points in development, cataloguing the many cell types present and identifying the molecular signatures that define each one. We also developed better tools to track which cells are descended from which, essentially reconstructing family trees of brain cells as they diversify.
2. Understanding how cells become specialized: As cells specialize, thousands of genes switch on and off in coordinated waves. We built a computational tool (MIMIR) to identify groups of genes that work together during this process. Applying it to cells that become glands versus cells that produce structural scaffolding revealed both familiar and new biological mechanisms — including how cells manage to secrete very different products while using shared and distinct regulatory mechanisms.
3. Connecting gene regulation to cell specialization: Beyond which genes are active, we examined how genes get turned on — specifically, which regions of DNA are physically "open" and accessible in different cell types. We built an AI model to predict this from DNA sequence alone, and found that surprisingly few master regulator proteins (transcription factors) are responsible for giving each cell type its unique identity. Remarkably, many of these same regulators are borrowed and repurposed from their original roles in organ formation.
4. Seeing gene activity in space and time: We developed a way to measure the activity of hundreds of genes simultaneously across an entire embryo while preserving its physical structure. This allowed us to track not just what genes are active in a cell, but where that cell sits in the embryo and where it came from, capturing how gene activity changes as cells physically move and reorganize during development. The resulting dataset covers over 25,000 genes and is publicly available for other scientists to explore.
Taken together, these tools and discoveries move us from snapshots of individual genes toward a comprehensive "biography" of how every cell in an embryo acquires its identity. Such global views of development will help understand birth defects, regeneration, and ultimately what it means to build a body.
The projects made both technological and conceptual advances.
- On the technology side, the project developed the first pipeline to detect the expression of hundreds of genes in a whole embryo and provided the first atlas of the developing zebrafish brain. These technologies and atlases moved the field beyond the previous state of the art.
- Conceptually, the project discovered that a flat network of transcription factors can activate the expression of hundreds of genes that lead to the instant differentiation of pluripotent cells into highly specialized and functional cell types. This finding extended the previous state of the art that had portrayed much of development as a cascade of transcription factors regulating differentiation in a stepwise fashion.
- On the technology side, the project developed the first pipeline to detect the expression of hundreds of genes in a whole embryo and provided the first atlas of the developing zebrafish brain. These technologies and atlases moved the field beyond the previous state of the art.
- Conceptually, the project discovered that a flat network of transcription factors can activate the expression of hundreds of genes that lead to the instant differentiation of pluripotent cells into highly specialized and functional cell types. This finding extended the previous state of the art that had portrayed much of development as a cascade of transcription factors regulating differentiation in a stepwise fashion.