UCLA High-Throughput Neuropsychiatric Disorder Phenotyping Center (UCLA HT-NPC) - Project Summary/Abstract Human genetic studies have identified hundreds of genes contributing to Neuropsychiatric and Neurodevelop- mental Disease (NPD) risk. But for most genes, their normal function or the consequences of their absence or reduction on neurodevelopment and neural function are not known. Here, we propose to address the substantial challenges of discerning potential functions of hundreds of NPD genes through the development of a High Throughput Neuropsychiatric Disease Phenotyping Center (UCLA HT-NPC), driven by the activity of 9 highly collaborative investigators (Aharoni, Bhaduri, Damoiseaux, Geschwind, Golshani, Kitai, Luo, Novich, and Wells) and two substantial core facilities (UCLA Molecular Screening Shared Resource and the Human Stem Cell and Genome Engineering Center). Through a tiered approach, we combine high throughput and high value, quantitative phenotyping with stem cell engineering to characterize the functional consequences of NPD gene knockouts (null alleles), a key initial step that will inform our understanding of disease pathways. In the first step, we will rapidly generate null alleles for 250 genes chosen by the Consortium using a rapid, high throughput lentiviral based system in hESCs. Viability and neural induction potential will be assessed, and quantitative phenotyping conducted using RNA-seq on all lines. Those genes passing viability and neural induction tests will be used in the production of clonal null hiPSC lines (male and female) for downstream phenotyping and wider distribution to the community. Subsequently, we will perform high throughput, quantitative, multi-scale phenotyping at the molecular, morphological, and physiological levels in both 2D and 3D hiPSC-based models of human cortical development. We leverage the relative strengths and scalability of each model to enable us to perform both snRNA and bulk RNA-seq, measure the maturation, morphology, and synaptic density of neural cells using automated imaging, including the multiplexed, protein-based CODEX (Phenocycler) platform, and characterize neuronal activity and synchronization through optical recordings using custom-built mini-scope arrays (STIMscope). By using multiple systems (e.g. hESC/hiPSC; gene editing, 2D and 3D cultures), we test biological reproducibility across systems and technical reproducibility through replication. The use of experimentally validated, quantitative phenotypes across multiple scales of analysis facilitates data sharing and comparisons with other SSPsyGene investigators and provides a template for the field more broadly.
