Periodic Reporting for period 1 - E-CTRL (Engineered control of cellular circuits)
Période du rapport: 2023-05-01 au 2025-10-31
Understanding how memories are formed, stored, and updated in the brain remains a fundamental challenge in neuroscience. Disruptions in these processes contribute to neuropsychiatric disorders like post-traumatic stress disorder (PTSD), where traumatic memories become rigid and uncontrollable. To tackle this, researchers need precise tools to manipulate specific proteins *within* the neurons actively engaged in memory formation, and a deeper understanding of the molecular pathways that enable memories to be flexibly updated.
This project aims to revolutionize our ability to study memory at the molecular level by achieving two interconnected goals:
1. Developing Molecular Tools: We are engineering novel "molecular switches", called conformational integrators, which are genetically encoded modules that can be inserted into specific proteins. Crucially, they act like an "AND gate": the target protein becomes active *only* when the neuron is both illuminated by blue light and experiences the calcium surge associated with neural activity. This provides unprecedented, millisecond-precision control over protein function exclusively in neurons active during defined experiences (e.g. learning). Unlike existing methods, which work slowly at the gene level, our tools directly control protein activity, enabling real-time causal experiments within neural circuits. They also hold potential as ultra-precise "activity recorders" to label these active neurons.
2. Decoding Memory Mechanisms: We are investigating a newly discovered signalling pathway (involving proteins like YTHDC1) that links neuronal activity to changes in gene regulation within the nucleus. Our initial findings revealed that YTHDC1, an RNA-binding protein, plays a critical and unexpected role in memory in excitatory hippocampal neurons. We aim to unravel how this pathway, triggered by neuronal activity, coordinates changes in both RNA processing and chromatin state to allow healthy memory updating.
Expected Impact:
New Research Capabilities: The conformational integrator platform will provide neuroscientists worldwide with a powerful, versatile toolbox to probe the function of any protein in active neurons during behavior with unmatched precision, accelerating discovery across brain research.
Fundamental Insights: Uncovering the YTHDC1 pathway's role in memory offers a completely new molecular explanation for how memories remain adaptable, filling a critical knowledge gap.
Therapeutic Potential: Identifying key molecules like YTHDC1 and its downstream effectors provides novel targets for developing treatments for disorders characterized by maladaptive, inflexible memories, such as PTSD and possibly dementia.
Interdisciplinary Advancements: The work integrates cutting-edge protein engineering, genomics, and behavioral neuroscience, fostering innovation across these fields.
By bridging the gap between precise molecular control and circuit-level memory processes, this research aims to provide fundamental knowledge and powerful new technologies to understand and ultimately treat memory-related brain disorders.
This project aims to revolutionize our ability to study memory at the molecular level by achieving two interconnected goals:
1. Developing Molecular Tools: We are engineering novel "molecular switches", called conformational integrators, which are genetically encoded modules that can be inserted into specific proteins. Crucially, they act like an "AND gate": the target protein becomes active *only* when the neuron is both illuminated by blue light and experiences the calcium surge associated with neural activity. This provides unprecedented, millisecond-precision control over protein function exclusively in neurons active during defined experiences (e.g. learning). Unlike existing methods, which work slowly at the gene level, our tools directly control protein activity, enabling real-time causal experiments within neural circuits. They also hold potential as ultra-precise "activity recorders" to label these active neurons.
2. Decoding Memory Mechanisms: We are investigating a newly discovered signalling pathway (involving proteins like YTHDC1) that links neuronal activity to changes in gene regulation within the nucleus. Our initial findings revealed that YTHDC1, an RNA-binding protein, plays a critical and unexpected role in memory in excitatory hippocampal neurons. We aim to unravel how this pathway, triggered by neuronal activity, coordinates changes in both RNA processing and chromatin state to allow healthy memory updating.
Expected Impact:
New Research Capabilities: The conformational integrator platform will provide neuroscientists worldwide with a powerful, versatile toolbox to probe the function of any protein in active neurons during behavior with unmatched precision, accelerating discovery across brain research.
Fundamental Insights: Uncovering the YTHDC1 pathway's role in memory offers a completely new molecular explanation for how memories remain adaptable, filling a critical knowledge gap.
Therapeutic Potential: Identifying key molecules like YTHDC1 and its downstream effectors provides novel targets for developing treatments for disorders characterized by maladaptive, inflexible memories, such as PTSD and possibly dementia.
Interdisciplinary Advancements: The work integrates cutting-edge protein engineering, genomics, and behavioral neuroscience, fostering innovation across these fields.
By bridging the gap between precise molecular control and circuit-level memory processes, this research aims to provide fundamental knowledge and powerful new technologies to understand and ultimately treat memory-related brain disorders.
This project has made significant strides in developing transformative molecular tools and uncovering fundamental mechanisms of memory. Key achievements include:
1. Breakthrough Molecular Tool Development:
We successfully engineered the first generation of conformational integrators. These tools, inserted into target proteins, require *both* blue light illumination *and* elevated neuronal calcium (indicating activity) to become functional.
Key Milestones:
* Developed functional integrators for two crucial signaling protein kinases, demonstrating the core principle works.
* Overcame initial challenges in transferring the design between proteins through iterative structural optimization, proving the approach is modular.
* Established robust protocols for testing integrator function in cells.
2. Discovery of a Key Memory Update Mechanism:
Using conditional knockout mice lacking the RNA/DNA-binding protein YTHDC1 specifically in excitatory forebrain neurons, we revealed its critical role in memory:
Key Findings:
* By using mice lacking YTHDC1, we showed the role of YTHDC1 in memory, and its relation to PTSD.
* Developed and applied optimized methods (ChIP-seq) to map YTHDC1's binding across the genome in neurons, revealing its unexpected strong association with gene promoter regions, especially after neuronal activation.
* This suggests YTHDC1 acts as a crucial link between synaptic activity and nuclear changes regulating gene expression during memory updating.
3. Progress Towards Understanding Downstream Effectors (Nr4a proteins):
* Work Performed: Successfully generated essential reagents (validated antibodies for Nr4a proteins) and initiated molecular cloning required for the next phase investigating these key activity-regulated transcription factors downstream of YTHDC1.
* Foundation Laid: This sets the stage for future experiments linking the YTHDC1 pathway to Nr4a-mediated gene programs essential for circuit stability.
Overall Scientific Outcomes:
The project has pioneered a revolutionary class of molecular tools (conformational integrators) for neuroscience and uncovered a fundamental new mechanism (involving YTHDC1) explaining how memories are maintained.
1. Breakthrough Molecular Tool Development:
We successfully engineered the first generation of conformational integrators. These tools, inserted into target proteins, require *both* blue light illumination *and* elevated neuronal calcium (indicating activity) to become functional.
Key Milestones:
* Developed functional integrators for two crucial signaling protein kinases, demonstrating the core principle works.
* Overcame initial challenges in transferring the design between proteins through iterative structural optimization, proving the approach is modular.
* Established robust protocols for testing integrator function in cells.
2. Discovery of a Key Memory Update Mechanism:
Using conditional knockout mice lacking the RNA/DNA-binding protein YTHDC1 specifically in excitatory forebrain neurons, we revealed its critical role in memory:
Key Findings:
* By using mice lacking YTHDC1, we showed the role of YTHDC1 in memory, and its relation to PTSD.
* Developed and applied optimized methods (ChIP-seq) to map YTHDC1's binding across the genome in neurons, revealing its unexpected strong association with gene promoter regions, especially after neuronal activation.
* This suggests YTHDC1 acts as a crucial link between synaptic activity and nuclear changes regulating gene expression during memory updating.
3. Progress Towards Understanding Downstream Effectors (Nr4a proteins):
* Work Performed: Successfully generated essential reagents (validated antibodies for Nr4a proteins) and initiated molecular cloning required for the next phase investigating these key activity-regulated transcription factors downstream of YTHDC1.
* Foundation Laid: This sets the stage for future experiments linking the YTHDC1 pathway to Nr4a-mediated gene programs essential for circuit stability.
Overall Scientific Outcomes:
The project has pioneered a revolutionary class of molecular tools (conformational integrators) for neuroscience and uncovered a fundamental new mechanism (involving YTHDC1) explaining how memories are maintained.
This project's transformative outcomes hold significant potential for scientific, therapeutic, and technological advancement, with clear pathways identified for maximizing impact:
1. Conformational Integrator Platform
Potential Impacts:
- Scientific: Enable causal manipulation of any protein in active neurons during behavior with millisecond precision, revolutionizing neuroscience research.
- Technological: Foundation for next-generation neural activity recorders and targeted neuromodulation tools.
- Commercial: High-demand research reagents; potential for gene therapy applications requiring cell-type-specific control.
Key Needs for Uptake & Success:
- Further Research: Optimization for robust in vivo function across diverse protein targets (ion channels, proteases) and brain regions.
- IPR & Commercialisation:** Secure broad patent protection for design architecture; establish licensing agreements with reagent developers (e.g. Addgene distribution) and neurotech companies.
- Standardisation: Develop benchmarking protocols for performance validation across labs.
2. YTHDC1 Pathway in Memory
* Potential Impacts:
- Therapeutic:YTHDC1 and its interactors represent novel, mechanistically distinct drug targets for PTSD, phobias, and disorders of maladaptive memory.
- Diagnostic: Potential biomarkers for memory flexibility deficits.
* Key Needs for Uptake & Success:
- Further Research: Identify druggable nodes within the pathway (e.g. YTHDC1 phosphorylation sites); validate efficacy of modulators in established PTSD animal models.
- Access to Markets/Finance: Secure venture funding or pharma partnerships for preclinical drug development programs targeting this pathway.
- Regulatory Frameworks:Engage early with regulatory bodies (e.g. EMA/FDA) on pathways for CNS-targeted epigenetic/RNA-modifying therapeutics.
1. Conformational Integrator Platform
Potential Impacts:
- Scientific: Enable causal manipulation of any protein in active neurons during behavior with millisecond precision, revolutionizing neuroscience research.
- Technological: Foundation for next-generation neural activity recorders and targeted neuromodulation tools.
- Commercial: High-demand research reagents; potential for gene therapy applications requiring cell-type-specific control.
Key Needs for Uptake & Success:
- Further Research: Optimization for robust in vivo function across diverse protein targets (ion channels, proteases) and brain regions.
- IPR & Commercialisation:** Secure broad patent protection for design architecture; establish licensing agreements with reagent developers (e.g. Addgene distribution) and neurotech companies.
- Standardisation: Develop benchmarking protocols for performance validation across labs.
2. YTHDC1 Pathway in Memory
* Potential Impacts:
- Therapeutic:YTHDC1 and its interactors represent novel, mechanistically distinct drug targets for PTSD, phobias, and disorders of maladaptive memory.
- Diagnostic: Potential biomarkers for memory flexibility deficits.
* Key Needs for Uptake & Success:
- Further Research: Identify druggable nodes within the pathway (e.g. YTHDC1 phosphorylation sites); validate efficacy of modulators in established PTSD animal models.
- Access to Markets/Finance: Secure venture funding or pharma partnerships for preclinical drug development programs targeting this pathway.
- Regulatory Frameworks:Engage early with regulatory bodies (e.g. EMA/FDA) on pathways for CNS-targeted epigenetic/RNA-modifying therapeutics.