Metabolic and genetic factors guiding hematopoietic cell fate
Proper organismal development requires precise control over cellular identity, and a wide range of diseases is characterized by altered differentiation states. Understanding the environmental factors that interplay with gene expression networks to regulate cell state holds immense potential for both...
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| Format: | Thesis |
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Massachusetts Institute of Technology
2023
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| Online Access: | https://hdl.handle.net/1721.1/152783 |
| _version_ | 1826205646357266432 |
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| author | Do, Brian Tshao |
| author2 | Vander Heiden, Matthew G. |
| author_facet | Vander Heiden, Matthew G. Do, Brian Tshao |
| author_sort | Do, Brian Tshao |
| collection | MIT |
| description | Proper organismal development requires precise control over cellular identity, and a wide range of diseases is characterized by altered differentiation states. Understanding the environmental factors that interplay with gene expression networks to regulate cell state holds immense potential for both basic scientific understanding and therapeutic advancements to treat cancer and other diseases. Of particular interest is the role of nutrient availability and metabolism in modulating cell states, as metabolites play dual roles as both signaling cues and physical substrates. However, the specific metabolic cues that maintain or alter cell state in physiologically relevant contexts have not been fully characterized. Moreover, we lack a mechanistic understanding of how metabolic perturbations translate into specific context-appropriate decisions across diverse cell types.
In this dissertation, we examine how metabolism influences the acquisition of context-specific cell states in normal and transformed hematopoiesis. Guided by metabolism-focused small molecule screens, we find that nucleotide depletion and imbalance initiate differentiation-related cell state changes specifically by impairing DNA replication, rather than as a general consequence of impaired proliferation or reduced viability. Genetic screens in three cell types reveal that while different cellular contexts have divergent responses to depletion of metabolic enzymes and other pathways, inhibition of nucleotide metabolism and DNA replication are shared paths to differentiated cell states across all three model systems. Surprisingly, checkpoint signaling is not required for these effects. Instead, by tracking early transcriptional and epigenetic changes, we find that DNA replication stress appears to preferentially activate primed regulatory loci with pre-existing chromatin accessibility. In the presence of differentiation blockades, this creates a synthetic cell state where features of the progenitor gene regulatory program are retained even as the maturation program emerges, whereas in untransformed cells we observe the acceleration of an otherwise normal maturation process. Transcriptional and epigenetic changes begin while cells are still in S phase but do not depend on which genomic regions are being actively replicated, suggesting that a previously uncharacterized signaling or sequestration mechanism could enable replication stress to trigger maturation programs in trans; we identify the Mediator kinase module as a potential link. Finally, we catalog additional context-specific metabolic and genetic determinants of differentiation that are specific to replication stress. Together, the studies presented in this dissertation shed light on how nucleotide depletion and DNA replication stress accelerate cell state transitions across multiple hematopoietic cell types, with implications for how such processes may underlie developmental and disease states and be harnessed for therapeutic benefit. |
| first_indexed | 2024-09-23T13:16:24Z |
| format | Thesis |
| id | mit-1721.1/152783 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T13:16:24Z |
| publishDate | 2023 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/1527832023-11-03T03:31:09Z Metabolic and genetic factors guiding hematopoietic cell fate Do, Brian Tshao Vander Heiden, Matthew G. Harvard-MIT Program in Health Sciences and Technology Proper organismal development requires precise control over cellular identity, and a wide range of diseases is characterized by altered differentiation states. Understanding the environmental factors that interplay with gene expression networks to regulate cell state holds immense potential for both basic scientific understanding and therapeutic advancements to treat cancer and other diseases. Of particular interest is the role of nutrient availability and metabolism in modulating cell states, as metabolites play dual roles as both signaling cues and physical substrates. However, the specific metabolic cues that maintain or alter cell state in physiologically relevant contexts have not been fully characterized. Moreover, we lack a mechanistic understanding of how metabolic perturbations translate into specific context-appropriate decisions across diverse cell types. In this dissertation, we examine how metabolism influences the acquisition of context-specific cell states in normal and transformed hematopoiesis. Guided by metabolism-focused small molecule screens, we find that nucleotide depletion and imbalance initiate differentiation-related cell state changes specifically by impairing DNA replication, rather than as a general consequence of impaired proliferation or reduced viability. Genetic screens in three cell types reveal that while different cellular contexts have divergent responses to depletion of metabolic enzymes and other pathways, inhibition of nucleotide metabolism and DNA replication are shared paths to differentiated cell states across all three model systems. Surprisingly, checkpoint signaling is not required for these effects. Instead, by tracking early transcriptional and epigenetic changes, we find that DNA replication stress appears to preferentially activate primed regulatory loci with pre-existing chromatin accessibility. In the presence of differentiation blockades, this creates a synthetic cell state where features of the progenitor gene regulatory program are retained even as the maturation program emerges, whereas in untransformed cells we observe the acceleration of an otherwise normal maturation process. Transcriptional and epigenetic changes begin while cells are still in S phase but do not depend on which genomic regions are being actively replicated, suggesting that a previously uncharacterized signaling or sequestration mechanism could enable replication stress to trigger maturation programs in trans; we identify the Mediator kinase module as a potential link. Finally, we catalog additional context-specific metabolic and genetic determinants of differentiation that are specific to replication stress. Together, the studies presented in this dissertation shed light on how nucleotide depletion and DNA replication stress accelerate cell state transitions across multiple hematopoietic cell types, with implications for how such processes may underlie developmental and disease states and be harnessed for therapeutic benefit. Ph.D. 2023-11-02T20:15:55Z 2023-11-02T20:15:55Z 2023-09 2023-09-07T20:18:42.658Z Thesis https://hdl.handle.net/1721.1/152783 0000-0003-4992-2623 In Copyright - Educational Use Permitted Copyright retained by author(s) https://rightsstatements.org/page/InC-EDU/1.0/ application/pdf application/octet-stream Massachusetts Institute of Technology |
| spellingShingle | Do, Brian Tshao Metabolic and genetic factors guiding hematopoietic cell fate |
| title | Metabolic and genetic factors guiding hematopoietic cell fate |
| title_full | Metabolic and genetic factors guiding hematopoietic cell fate |
| title_fullStr | Metabolic and genetic factors guiding hematopoietic cell fate |
| title_full_unstemmed | Metabolic and genetic factors guiding hematopoietic cell fate |
| title_short | Metabolic and genetic factors guiding hematopoietic cell fate |
| title_sort | metabolic and genetic factors guiding hematopoietic cell fate |
| url | https://hdl.handle.net/1721.1/152783 |
| work_keys_str_mv | AT dobriantshao metabolicandgeneticfactorsguidinghematopoieticcellfate |