Center for Alzheimer's and Related Dementias (CARD): iPSC Neurodegenerative Diseases Initiative

National Institute On Aging

Investigators

Linked publications, trials & patents

Abstract

The iPSC Neurodegenerative Disease Initiative (iNDI) represents a comprehensive effort to create a national resource of isogenic induced pluripotent stem cell (iPSC) lines harboring Alzheimer's disease and related dementia (ADRD)-associated genetic variants. This project has successfully generated and characterized a substantial collection of CRISPR-edited iPSC lines, making them publicly available through the JAX repository. The initiative combines cutting-edge cell line generation with multi-omic characterization approaches, including transcriptomics, proteomics, and advanced microscopy to understand disease mechanisms. The project has achieved significant milestones in establishing automated cell culture systems, developing standardized protocols, and generating comprehensive datasets. Through collaboration with multiple research groups and the establishment of a robust distribution network, iNDI is accelerating mechanistic discovery in neurodegeneration research and supporting the development of precision medicine approaches for ADRD. Project Summary Narrative: This project generates a series of iPSC lines that harbor AD/ADRD-associated single nucleotide variants on isogenic cell backgrounds through CRISPR editing. Heterozygous/homozygous/revertant SNV lines, gene knockout and HaloTag lines, and functionalized (C9orf72, NGN2-expressing, hNIL-expressing) lines are being developed and made publicly available at jax.org/ipsc. Characterization of the lines is performed at NIH and includes microscopy, proteomics, transcriptomics, functional genomics, and synthetic lethality screening. The project status indicates that automation systems are operational and the team is actively generating data, with all lines made available through JAX. Teams are currently working to complete larger-scale experiments, including comprehensive single-cell analysis studies. Completed Milestones: - Published prospective manuscript on iNDI goals and objectives (Complete) - Established methods for manual iPSC cell culture with protocols available on protocols.io (Complete) - Developed methods for iPSC-derived neuronal differentiation using piggy-bac vector approaches (Complete) - Implemented methods for large-scale proteomic workflows (Complete) - Completed methods for CRISPR-based gene expression inhibition and survival studies (Complete) - Successfully established distribution center and website through JAX with MTA agreements (Complete) - Made all generated cell lines available through JAX repository (Complete) - Successfully established methods for automated iPSC cell culture maintenance, transfection and neuronal differentiation using liquid handling systems In Progress Deliverables: - Repository of iPSC lines (ongoing expansion) - Open source transcriptomic, proteomic and microscopy datasets on mutant cell lines - Methods for iPSC-derived microglia differentiation using piggy-bac vector approaches - Methods for microscopic detection of organelle changes in mutant iPSCs and derived cell types - Large-scale experiments investigating proteomic, transcriptomic and microscopy changes from subset of mutant cell lines - Complete characterization of remaining mutant iPSC lines and iPSC-derived cell types - Publication on initial 24 characterized lines Sample and Data Inventory: - CARD cell lines: iPSCs housed in Cell Line Inventory (T44 location) - JAX cell lines: Available through https://www.jax.org/jax-mice-and-services/ipsc/cells-collection - Data inventory: In-house iPSC datasets and associated multi-omic data Repository and Data Access: - JAX iPSC Collection: https://www.jax.org/jax-mice-and-services/ipsc/cells-collection - Protocols.io: Methods for manual iPSC cell culture - Cell Line Inventory: T44 facility housing CARD cell lines Project Documentation: - iNDI single cell analysis protocols and datasets (in development) - Google Drive project repository with ongoing experimental documentation - Prospective manuscript on iNDI goals and objectives (published) Ongoing Publications: - Methods manuscript for large-scale iPSC culture, transcriptomic, proteomic and microscopy experiments (in preparation) - Characterization study of initial 24 iPSC lines (in preparation) - CRISPR-based gene expression methods publication (in preparation) Collaborative Networks: - JAX Laboratory: Distribution and repository services - NIH CARD: Collaborative research and data sharing - Multiple external research institutions accessing cell lines through MTA agreements