This groundbreaking research combines genetically engineered human forebrain assembloids with polymeric nanofiber scaffolds to create an advanced model system for studying interneuron migration disorders. These disorders are associated with various neurodevelopmental conditions including epilepsy, autism spectrum disorder, and schizophrenia.
As the lead computational analyst, I conducted comprehensive RNA-seq analysis, protein-protein interaction network analysis, and pan-tissue analysis to understand the molecular mechanisms underlying interneuron migration defects. This multiscale approach provides unprecedented insights into how genetic mutations affect brain development at the cellular and molecular levels.
Analysis of sophisticated forebrain assembloids that recapitulate human brain development
Comprehensive RNA-seq analysis revealing molecular signatures of migration disorders
Protein interaction networks uncovering disease mechanisms and therapeutic targets
Pan-tissue expression analysis revealing tissue-specific disease signatures
Interneuron migration is a critical process during brain development where inhibitory neurons born in the ventral forebrain migrate long distances to reach their final positions in the cortex. Disruptions in this process lead to an imbalance between excitation and inhibition, contributing to various neurological and psychiatric disorders.
These are fusion organoids that combine dorsal (cortical) and ventral (subcortical) brain regions, allowing researchers to study interneuron migration in a human-relevant 3D model system. They provide unique insights into human-specific aspects of brain development that cannot be studied in animal models.
The integration of polymeric nanofiber scaffolds provides physical guidance cues that influence cell migration patterns. This biomaterial interface allows for controlled studies of how physical and molecular cues interact to guide neuron migration.
Understanding interneuron migration disorders is crucial for developing therapies for epilepsy, autism, and schizophrenia. This model system provides a platform for drug screening and testing potential therapeutic interventions.
Processed bulk RNA-seq data from assembloids at multiple developmental time points. Implemented quality control, read alignment, and quantification pipelines to ensure accurate gene expression measurements across samples.
Identified genes differentially expressed between control and disease model assembloids. Applied statistical methods to account for biological variability and technical factors, revealing key molecular signatures of migration defects.
Conducted comprehensive pathway analysis using GO, KEGG, and custom neurodevelopmental gene sets. This revealed disrupted biological processes including axon guidance, cell adhesion, and neurotransmitter signaling.
Built protein-protein interaction networks integrating expression data with known interactions. Identified hub genes and network modules associated with interneuron migration, revealing potential therapeutic targets.
Compared expression patterns across multiple human tissues to understand tissue-specific effects of identified genes. This analysis helped distinguish brain-specific pathology from systemic effects.
Identified molecular signatures specific to interneuron migration defects, including dysregulation of cell adhesion molecules, cytoskeletal regulators, and guidance receptors critical for proper neuronal positioning.
Revealed disrupted protein interaction networks centered on key migration regulators. These network perturbations explain how single gene mutations can lead to widespread developmental abnormalities.
Discovered previously uncharacterized genes involved in interneuron migration through integrative analysis. These genes represent new candidates for genetic screening in neurodevelopmental disorders.
Identified druggable pathways and proteins that could be targeted to rescue migration defects. Several FDA-approved drugs were found to potentially modulate these pathways.
This research has significant implications for understanding and treating neurodevelopmental disorders affecting millions of individuals worldwide.
The assembloid system provides a human-relevant platform for modeling neurodevelopmental disorders, allowing researchers to study disease mechanisms that cannot be fully recapitulated in animal models or 2D cell cultures.
This system can be used for high-throughput screening of potential therapeutic compounds. The identified molecular signatures serve as readouts for assessing drug efficacy in rescuing migration defects.
Patient-derived assembloids can be generated to study individual-specific disease mechanisms and test personalized therapeutic strategies, advancing precision medicine approaches for neurodevelopmental disorders.
The molecular signatures identified could serve as biomarkers for early diagnosis or treatment monitoring, potentially enabling earlier intervention in at-risk individuals.
This interdisciplinary project brings together experts in neuroscience, bioengineering, computational biology, and clinical medicine to tackle complex questions in brain development.
Lead PI: Dr. Debojyoti Chakraborty, IGIB CSIR
Collaborators: Neuroscientists, Bioengineers, and Clinical Researchers
Computational Lead: Vishal Bharti - RNA-seq, Network Analysis, and Data Integration
Duration: 2023 - Present
Status: Under revision at Stem Cell Reports
Under revision at Stem Cell Reports (2024)
Abstract: Interneuron migration disorders contribute to various neurodevelopmental conditions including epilepsy and autism spectrum disorder. Here, we present an innovative platform combining genetically engineered human forebrain assembloids with polymeric nanofiber scaffolds to model and analyze these disorders at multiple scales. Through comprehensive transcriptomic profiling and network analysis, we identify key molecular signatures of migration defects and potential therapeutic targets. Our findings reveal disrupted cell adhesion, cytoskeletal regulation, and guidance signaling in disease models. The integration of nanofiber scaffolds provides controlled physical cues that modulate migration patterns, offering insights into mechanobiological aspects of neuronal migration. This platform enables drug screening and personalized medicine approaches for neurodevelopmental disorders, bridging the gap between basic research and clinical applications.
Expanding analysis to single-cell RNA sequencing to understand cell-type-specific effects and heterogeneity in migration disorders. This will reveal rare cell populations and transitional states during migration.
Implementing spatial transcriptomics to map gene expression patterns in 3D within assembloids, providing insights into how spatial organization affects interneuron migration and integration.
Developing automated screening platforms using the molecular signatures as readouts to identify compounds that can rescue migration defects, accelerating therapeutic development.
Validating findings in patient samples and developing diagnostic tools based on the identified biomarkers, moving towards clinical implementation of assembloid-based personalized medicine.
If you're interested in collaborating on brain organoid research, computational neuroscience, or neurodevelopmental disorders, I'd be happy to discuss potential opportunities.