Biology subjects

Stein, J. L.

Publications and source records attributed to Stein, J. L..

At least 19 recordsLinked to original sources

bioRxiv2026

From Abandoned Scripts to FAIR Community Pipelines: Rescuing Orphan Bioinformatics Workflows with nf-core - Lessons from Light-Sheet Fluorescence Microscopy

Background Research software is essential for modern data analysis but is often developed and maintained by a small number of researchers. When developers leave, software may become orphaned, limiting reuse and risking the loss of valuable domain knowledge and computational methods. While the FAIR Principles for Research Software (FAIR4RS) provide an essential foundation for improving the reuse of research software, compliance with these principles alone does not guarantee practical reusability. Here, we investigate whether orphaned scientific software can be systematically rescued and transformed into sustainable, reusable workflows using established software engineering practices and community standards. Findings We re-engineered the abandoned MATLAB-based NuMorph toolkit for large-scale light-sheet microscopy image analysis into nf-core/lsmquant, a Nextflow-based workflow developed according to nf-core community guidelines. The re-engineered workflow preserved the original scientific methods at comparable computational cost while improving the software's FAIRness, portability, and reproducibility. Integration into the nf-core ecosystem provides a community-driven framework that supports software sustainability through distributed maintenance and shared development practices, while the modular workflow architecture simplified adaptation of nf-core/lsmquant to additional light-sheet microscopy datasets beyond the original application Conclusion Our work demonstrates that orphaned scientific software can be successfully rescued through systematic re-engineering guided by FAIR and software sustainability principles. By transforming a legacy codebase into a community-maintained workflow, we preserve valuable domain-specific methods while improving usability, maintainability, and reproducibility. This approach provides a practical strategy for recovering orphan research software and integrating it into modern, reusable research ecosystems. Keywords Light-sheet fluorescence microscopy, Nextflow, nf-core, re-engineering, sustainable software

bioinformatics↗

bioRxiv2026

Connectome-based spatial statistics enabling large-scale population analyses of human connectome across cohorts

Large-scale population analyses of structural connectome organization remain challenging because of cross-subject alignment, pathway interpretability and computational burden. No widely adopted standard exists for systematic evaluation across processing methods. We developed connectome-based spatial statistics (CBSS), a scalable framework for anatomically aligned and functionally informed quantification of white-matter microstructure that yields atlas-defined pathways organized into 13 functional networks. Using data from 56,510 UK Biobank participants together with five independent lifespan cohorts, we evaluated the streamline-, voxel- and network-level measures in the aspects of reliability, heritability, structure-function coupling, cognitive and behavioral prediction, brain aging patterns and lifespan trajectories across cohorts. The systematic evaluation workflow compares population-level white-matter representations across methods, spatial scales, tasks and datasets. The results support CBSS as a common connectome reference for large-scale, cross-cohort diffusion MRI studies.

neuroscience↗

bioRxiv2026

CellPheno: A High-throughput Computational Platform for Quantifying Cellular Resolution Whole Brain Microscopy Images

Advances in tissue clearing and light-sheet microscopy enable cellular resolution whole-brain 3D imaging. However, whole-brain quantification tools do not yet meet demands for efficiency or assess morphometry. Here we present CellPheno, a 3D nuclei instance segmentation framework for high-throughput cellular phenotyping. CellPheno quantifies an entire P4 mouse brain within 15 hours. We showcase whole-brain morphometry, enhanced stitching, and co-localization across multiple cell types in 53 brains.

neuroscience↗

bioRxiv2026

Chd8 haploinsufficiency leads to molecular layer heterotopias and age-dependent cortical expansion

Mutations in the chromatin remodeler CHD8 are associated with autism and macrocephaly. While mouse models of Chd8 haploinsufficiency recapitulate brain overgrowth, the specific cellular mechanisms and developmental timing that lead to these anatomical abnormalities remain poorly understood. Here, we conducted 3D imaging of Chd8V986*/+ mouse brains using magnetic resonance imaging followed by tissue clearing and cellular resolution light-sheet microscopy across embryonic and postnatal developmental stages. We found that brain overgrowth occurs postnatally, driven by an increase in non-neuronal cells prior to volumetric expansion. Unexpectedly, we identified prevalent molecular layer heterotopias (MLH) within the frontal cortex of Chd8V986*/+ mice composed of neurons breaking through the pial surface during embryonic development and persisting throughout life. Increased incidence of MLH, previously identified in individuals with idiopathic autism, was replicated across three independent Chd8+/- mouse models and present across multiple genomic backgrounds, establishing aberrant neuronal migration as a core feature of Chd8 haploinsufficiency.

neuroscience↗

bioRxiv2025

Parallelized Brightfield and Fluorescence Imaging of Organoids Using a Scalable Multi-Camera Platform

Organoid viability, maturation, and growth is commonly assayed through brightfield and fluorescence microscopy using a single objective lens. However, standard microscopic imaging systems pose significant limitations for high-throughput applications, particularly in large-scale experiments where simultaneous imaging of multiple organoids requires increased throughput. There is a strong need for systems that can capture organoid growth rapidly and consistently while minimizing disturbances to culture conditions. Here, we present a novel multi-camera array scanner (MCAS) that parallelizes imaging through the simultaneous use of 48 objective lenses and sensors, resulting in a 95% reduction in acquisition times compared to commercial high-content imagers. We demonstrate and validate this system in multiple well plate formats, in both 2D and 3D neural cell cultures, and in brightfield and fluorescence. The MCAS improves efficiency for measuring organoid growth rates, assessing responses to morphogens and drugs, and measuring viral transduction efficiency. Together, these findings establish the MCAS as a scalable and versatile imaging platform for rapid phenotyping in organoid research.

neuroscience↗

bioRxiv2025

A single cell multi-omic analysis identifies molecular and gene-regulatory mechanisms dysregulated in the developing Down syndrome neocortex

Down syndrome is the most common genetic cause of intellectual disability, presenting with cognitive, learning, memory, and language deficits. The cellular and molecular mechanisms driving this disorder remain unclear, limited by a lack of systematic studies in the developing human brain. Here, we leveraged single-nucleus multi-omics to profile the mid-gestation neocortex in a cohort of 26 donors. We observed a reduction in neural progenitors and corticothalamic neurons and concomitant increase of intratelencephalic neurons, accompanied by accelerated time to neuronal specification. We uncovered widespread changes in gene expression, chromatin accessibility and cell interaction networks impacting neurogenesis, specification and maturation and gene-regulatory networks directing these processes, including those downstream of transcription factors encoded in chromosome 21. Finally, we identified cell-specific molecular pathways shared with other neurodevelopmental disorders as well as heritability enrichment of GWAS signals in altered chromatin. Together, our data revealed a cascade of molecular dysregulation outlining the earliest steps in Down syndrome, providing a foundation for future therapeutic targets.

genomics↗

bioRxiv2025

Early cell cycle genes in cortical organoid progenitors predict interindividual variability in infant brain growth trajectories

Human induced pluripotent stem cell (iPSC) derived cortical organoids (hCOs) model neurogenesis on an individuals genetic background. The degree to which hCO phenotypes recapitulate the brain growth of the participants from which they were derived is not well established. We generated up to 3 iPSC clones from each of 18 participants in the Infant Brain Imaging Study, who have undergone longitudinal brain imaging during infancy. We identified consistent hCO morphology and cortical cell types across clones from the same participant. hCO cross-sectional area and production of cortical hem cells were associated with in vivo cortical growth rates. Cell cycle associated genes expression in early progenitors at the crux of fate decision trajectories were correlated with cortical growth rate from 6-12 months of age, and were enriched in microcephaly and neurodevelopmental disorder genes. Our data suggest the hCOs capture inter-individual variation in cortical cell types influencing infant cortical surface area expansion.

neuroscience↗

bioRxiv2025

Massively parallel assessment of gene regulatory activity at human cortical structure associated variants

Genetic association studies have identified hundreds of largely non-coding loci associated with inter-individual differences in the structure of the human cortex, though the specific genetic variants that impact regulatory activity are unknown. We implemented a Massively Parallel Reporter Assay (MPRA) to measure the regulatory activity of 9,092 cortical structure associated DNA variants in human neural progenitor cells during Wnt stimulation and at baseline. We identified 918 variants with regulatory potential from 150 cortical structure associated loci (76% of loci studied), of which >50% showed allelic effects. Wnt stimulation modified regulatory activity at a subset of loci that functioned as condition-dependent enhancers. Regulatory activity in MPRA was largely induced by Alu elements that were hypothesized to contribute to cortical expansion. The regionally specific impact of genetic variants that disrupt motifs is likely mediated through the levels of transcription factor expression during development, further clarifying the molecular mechanisms altering cortical structure.

genetics↗

bioRxiv2024

The CECR2 bromodomain displays distinct binding modes to select for acetylated histone proteins versus non-histone ligands.

The cat eye syndrome chromosome region candidate 2 (CECR2) protein is an epigenetic regulator involved in chromatin remodeling and transcriptional control. The CECR2 bromodomain (CECR2-BRD) plays a pivotal role in directing the activity of CECR2 through its capacity to recognize and bind acetylated lysine residues on histone proteins. This study elucidates the binding specificity and structural mechanisms of CECR2-BRD interactions with both histone and non-histone ligands, employing techniques such as isothermal titration calorimetry (ITC), nuclear magnetic resonance (NMR) spectroscopy, and a high-throughput peptide assay. The CECR2-BRD selectively binds acetylated histone H3 and H4 ligands, exhibiting a preference for multi-acetylated over mono-acetylated targets. The highest affinity was observed for tetra-acetylated histone H4. Neighboring post-translational modifications, including methylation and phosphorylation, modulate acetyllysine recognition, with significant effects observed for histone H3 ligands. Additionally, this study explored the interaction of the CECR2-BRD with the acetylated RelA subunit of NF-{kappa}B, a pivotal transcription factor in inflammatory signaling. Dysregulated NF-{kappa}B signaling is implicated in numerous pathologies, including cancer progression, with acetylation of RelA at lysine 310 (K310ac) being critical for its transcriptional activity. Recent evidence linking the CECR2-BRD to RelA suggests it plays a role in inflammatory and metastatic pathways, underscoring the need to understand the molecular basis of this interaction. We found the CECR2-BRD binds to acetylated RelA with micromolar affinity, and uses a distinctive binding mode to recognize this non-histone ligand. These results provide new insight on the role of CECR2 in regulating NF-{kappa}B-mediated inflammatory pathways. Functional mutagenesis of critical residues, such as Asn514 and Asp464, highlight their roles in ligand specificity and binding dynamics. Notably, the CECR2-BRD remained monomeric in solution and exhibited differential conformational responses upon ligand binding, suggesting adaptive recognition mechanisms. Furthermore, the CECR2-BRD exclusively interacts with nucleosome substrates containing multi-acetylated histones, emphasizing its role in transcriptional activation within euchromatic regions. These findings position the CECR2-BRD as a key chromatin reader and a promising therapeutic target for modulating transcriptional and inflammatory processes, particularly through the development of selective bromodomain inhibitors. HIGHLIGHTSO_LIThe CECR2 bromodomain recognizes a range of combinatorial PTMs on the histone H3 and H4 N-terminal tails. C_LIO_LIThe CECR2 bromodomain binds to an acetylated RelA ligand with micromolar affinity. C_LIO_LINMR perturbation studies delineate the distinct binding modes driving CECR2-BRD recognition of histone versus non-histone ligands. C_LIO_LISite-directed mutagenesis reveals the specificity determinants of CECR2-BRD ligand binding. C_LIO_LIThe bromodomain of CECR2 exhibits a strong interaction with multi-acetylated nucleosomes. C_LI

biochemistry↗

bioRxiv2024

Probabilistic classification of gene-by-treatment interactions on molecular count phenotypes

Genetic variation can modulate response to treatment (GxT) or environmental stimuli (GxE), both of which may be highly consequential in biomedicine. An effective approach to identifying GxT signals and gaining insight into molecular mechanisms is mapping quantitative trait loci (QTL) of molecular count phenotypes, such as gene expression and chromatin accessibility, under multiple treatment conditions, which is termed response molecular QTL mapping. Although standard approaches evaluate the interaction between genetics and treatment conditions, they do not distinguish between meaningful interpretations such as whether a genetic effect is only observed in the treated condition or whether a genetic effect is observed but accentuated in the treated condition. To address this gap, we have developed a downstream method for classifying response molecular QTLs into subclasses with meaningful genetic interpretations. Our method uses Bayesian model selection and assigns posterior probabilities to different types of GxT interactions for a given feature-SNP pair. We compare linear and nonlinear regression of log-scale counts, noting that the latter accounts for an expected biological relationship between the genotype and the molecular count phenotype. Through simulation and application to existing datasets of molecular response QTLs, we show that our method provides an intuitive and well-powered framework to report and interpret GxT interactions. We provide a software package, ClassifyGxT, which is available at https://github.com/yharigaya/classifygxt. Author summaryResponses to treatment, such as drug, therapeutic intervention, and infection, can vary across individuals at least in part due to their genetic backgrounds. This phenomenon can be conceptualized as a manifestation of gene-by-treatment (GxT) or gene-by-environment (GxE) interactions, which refer to non-additive effects of genotype and treatment on traits and phenotypes. An understading of GxT or GxE interactions can potentially improve strategies for prevention and treatment of diseases, for example by selecting treatments for which a patient is most likely to respond given their genetic information, or enhanced screening for individuals most susceptible to environmental exposures. An effective approach to GxT discovery is response quantitative trait loci (QTL) mapping, where the effect of the treatment on the association between the genotype and phenotype is examined using a linear regression model including the genotype, treatment, and GxT interaction terms. Despite its effectiveness in identifying a large number of associations, the response QTL mapping relies on hypothesis testing, which does not provide classification of different types of GxT interactions. Herein, we propose a use of Bayesian model selection to classify the GxT types of response QTLs and provide a software package for this method. In addition to standard linear regression, our package provides an option to use nonlinear regression that is suited for molecular count phenotypes, such as gene expression and chromatin accessibility, measured by sequencing-based techniques. It also provides an option to use mixed effect models to accommodate replicate measurements per donor, which are common in data generated in in-vitro cell systems.

genetics↗

bioRxiv2024

CD388: A universally protective Drug-Fc Conjugate that targets influenza virus neuraminidase

The ability of the influenza virus to elude humoral immunity by rapid antigenic shift presents a sustained and urgent threat to human health. Globally, seasonal influenza causes an estimated 3 - 5 million cases of severe disease and 300,000 - 500,000 deaths annually, with increased potential for mortality during pandemics1. The recent outbreaks of avian H5N1 in bird populations, subsequent spread to cattle and appearance in humans, highlight the need for effective broad-spectrum influenza antivirals for treatment, prophylaxis and pandemic preparedness. The narrow, strain-specific immunity induced by current seasonal vaccines and mismatches between vaccine strains and circulating viruses result in limited vaccine effectiveness (VE) rates2. Furthermore, VE is even lower in immune-compromised and - senescent populations3. Strategies that provide durable, universal influenza protection in healthy and high-risk populations are urgently needed. Here, we describe CD388, a first-in-class antiviral drug-Fc conjugate (DFC) in clinical trials for seasonal influenza prevention (NCT05285137 and NCT05523089). CD388 comprises a multivalent small molecule inhibitor of influenza virus neuraminidase (NA) linked to a CH1-Fc hybrid domain of human IgG1 engineered for extended half-life. CD388 demonstrated potent, universal activity across influenza A and B viruses, including high pathogenicity and NA resistant strains, a low potential for resistance development, and efficacy in lethal mouse infection models. CD388 is the first therapeutic with the potential for universal prevention of influenza A and B in healthy and high-risk populations.

microbiology↗

bioRxiv2023

Tumor microenvironmental determinants of high-risk DCIS progression

ABSTRACT/SUMMARYDuctal carcinoma in situ (DCIS) constitutes an array of morphologically recognized intraductal neoplasms in the mammary ductal tree defined by an increased risk for subsequent invasive carcinomas at or near the site of biopsy detection. However, only 15-45% of untreated DCIS cases progress to invasive cancer, so understanding mechanisms that prevent progression is key to avoid overtreatment and provides a basis for alternative therapies and prevention. This study was designed to characterize the tumor microenvironment and molecular profile of high-risk DCIS that grew to a large size but remained as DCIS. All patients had DCIS lesions >5cm in size with at least one additional high-risk feature: young age (<45 years), high nuclear grade, hormone receptor negativity, HER2 positivity, the presence of comedonecrosis, or a palpable mass. The tumor immune microenvironment was characterized using multiplex immunofluorescence to identify immune cells and their spatial relationships within the ducts and stroma. Gene copy number analysis and whole exome DNA sequencing identified the mutational burden and driver mutations, and quantitative whole-transcriptome/gene expression analyses were performed. There was no association between the percent of the DCIS genome characterized by copy number variants (CNAs) and recurrence events (DCIS or invasive). Mutations, especially missense mutations, in the breast cancer driver genes PIK3CA and TP53 were common in this high-risk DCIS cohort (47% of evaluated lesions). Tumor infiltrating lymphocyte (TIL) density was higher in DCIS lesions with TP53 mutations (p=0.0079) compared to wildtype lesions, but not in lesions with PIK3CA mutations (p=0.44). Immune infiltrates were negatively associated with hormone receptor status and positively associated with HER2 expression. High levels of CD3+CD8-T cells were associated with good outcomes with respect to any subsequent recurrence (DCIS or invasive cancer), whereas high levels of CD3+Foxp3+ Treg cells were associated with poor outcomes. Spatial proximity analyses of immune cells and tumor cells demonstrated that close proximity of T cells with tumor cells was associated with good outcomes with respect to any recurrence as well as invasive recurrences. Interestingly, we found that myoepithelial continuity (distance between myoepithelial cells surrounding the involved ducts) was significantly lower in DCIS lesions compared to normal tissue (p=0.0002) or to atypical ductal hyperplasia (p=0.011). Gene set enrichment analysis identified several immune pathways associated with low myoepithelial continuity and a low myoepithelial continuity score was associated with better outcomes, suggesting that gaps in the myoepithelial layer may allow access/interactions between immune infiltrates and tumor cells. Our study demonstrates the immune microenvironment of DCIS, in particular the spatial proximity of tumor cells and T cells, and myoepithelial continuity are important determinants for progression of disease.

cancer biology↗

bioRxiv2023

Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis

The function of some genetic variants associated with brain-relevant traits has been explained through colocalization with expression quantitative trait loci (eQTL) conducted in bulk post-mortem adult brain tissue. However, many brain-trait associated loci have unknown cellular or molecular function. These genetic variants may exert context-specific function on different molecular phenotypes including post-transcriptional changes. Here, we identified genetic regulation of RNA-editing and alternative polyadenylation (APA), within a cell-type-specific population of human neural progenitors and neurons. More RNA-editing and isoforms utilizing longer polyadenylation sequences were observed in neurons, likely due to higher expression of genes encoding the proteins mediating these post-transcriptional events. We also detected hundreds of cell-type-specific editing quantitative trait loci (edQTLs) and alternative polyadenylation QTLs (apaQTLs). We found colocalizations of a neuron edQTL in CCDC88A with educational attainment and a progenitor apaQTL in EP300 with schizophrenia, suggesting genetically mediated post-transcriptional regulation during brain development lead to differences in brain function.

genomics↗

bioRxiv2023

Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture

BackgroundReproducibility of human cortical organoid (hCO) phenotypes remains a concern for modeling neurodevelopmental disorders. While guided hCO protocols reproducibly generate cortical cell types in multiple cell lines at one site, variability across sites using a harmonized protocol has not yet been evaluated. We present an hCO cross-site reproducibility study examining multiple phenotypes. MethodsThree independent research groups generated hCOs from one induced pluripotent stem cell (iPSC) line using a harmonized miniaturized spinning bioreactor protocol. scRNA-seq, 3D fluorescent imaging, phase contrast imaging, qPCR, and flow cytometry were used to characterize the 3 month differentiations across sites. ResultsIn all sites, hCOs were mostly cortical progenitor and neuronal cell types in reproducible proportions with moderate to high fidelity to the in vivo brain that were consistently organized in cortical wall-like buds. Cross-site differences were detected in hCO size and morphology. Differential gene expression showed differences in metabolism and cellular stress across sites. Although iPSC culture conditions were consistent and iPSCs remained undifferentiated, primed stem cell marker expression prior to differentiation correlated with cell type proportions in hCOs. ConclusionsWe identified hCO phenotypes that are reproducible across sites using a harmonized differentiation protocol. Previously described limitations of hCO models were also reproduced including off-target differentiations, necrotic cores, and cellular stress. Improving our understanding of how stem cell states influence early hCO cell types may increase reliability of hCO differentiations. Cross-site reproducibility of hCO cell type proportions and organization lays the foundation for future collaborative prospective meta-analytic studies modeling neurodevelopmental disorders in hCOs.

neuroscience↗

bioRxiv2023

WNT activity reveals context-specific genetic effects on gene regulation in neural progenitors

Gene regulatory effects in bulk-post mortem brain tissues are undetected at many non-coding brain trait-associated loci. We hypothesized that context-specific genetic variant function during stimulation of a developmental signaling pathway would explain additional regulatory mechanisms. We measured chromatin accessibility and gene expression following activation of the canonical Wnt pathway in primary human neural progenitors from 82 donors. TCF/LEF motifs, brain structure-, and neuropsychiatric disorder-associated variants were enriched within Wnt-responsive regulatory elements (REs). Genetically influenced REs were enriched in genomic regions under positive selection along the human lineage. Stimulation of the Wnt pathway increased the detection of genetically influenced REs/genes by 66.2%/52.7%, and led to the identification of 397 REs primed for effects on gene expression. Context-specific molecular quantitative trait loci increased brain-trait colocalizations by up to 70%, suggesting that genetic variant effects during early neurodevelopmental patterning lead to differences in adult brain and behavioral traits.

genetics↗

bioRxiv2022

Inferring cell-type-specific causal gene regulatory networks during human neurogenesis

BackgroundGenetic variation influences both chromatin accessibility, assessed in chromatin accessibility quantitative trait loci (caQTL) studies, and gene expression, assessed in expression QTL (eQTL) studies. Genetic variants can impact either nearby genes (local eQTLs) or distal genes (trans eQTLs). Colocalization between caQTL and eQTL, or local- and distant-eQTLs suggests that they share causal variants. However, pairwise colocalization between these molecular QTLs does not guarantee a causal relationship. Mediation analysis can be applied to assess the evidence supporting causality versus independence between molecular QTLs. Given that the function of QTLs can be cell-type-specific, we performed mediation analyses to find epigenetic and distal regulatory causal pathways for genes within two major cell types of the developing human cortex, progenitors and neurons. ResultsWe found that expression of 168 and 38 genes were mediated by chromatin accessibility in progenitors and neurons, respectively. We also found that the expression of 781 and 200 downstream genes were mediated by upstream genes in progenitors and neurons. Moreover, we discovered that a genetic locus associated with inter-individual differences in brain structure showed evidence for mediation of SLC26A7 through chromatin accessibility, identifying molecular mechanisms of a common variant association to a brain trait. ConclusionsIn this study, we identified cell-type-specific causal gene regulatory networks whereby the impacts of variants on gene expression were mediated by chromatin accessibility or distal gene expression. Identification of these causal paths will enable identifying and prioritizing actionable regulatory targets perturbing these key processes during neurodevelopment.

genomics↗

bioRxiv2022

MicroRNA-eQTLs in the developing human neocortex link miR-4707-3p expression to brain size

Expression quantitative trait loci (eQTL) data have proven important for linking non-coding loci to protein-coding genes. But eQTL studies rarely measure microRNAs (miRNAs), small non-coding RNAs known to play a role in human brain development and neurogenesis. Here, we performed small-RNA sequencing across 212 mid-gestation human neocortical tissue samples, measured 907 expressed miRNAs, discovering 111 of which were novel, and identified 85 local-miRNA-eQTLs. Colocalization of miRNA-eQTLs with GWAS summary statistics yielded one robust colocalization of miR-4707-3p expression with educational attainment and brain size phenotypes, where the miRNA expression increasing allele was associated with decreased brain size. Exogenous expression of miR-4707-3p in primary human neural progenitor cells decreased expression of predicted targets and increased cell proliferation, indicating miR-4707-3p modulates progenitor gene regulation and cell fate decisions. Integrating miRNA-eQTLs with existing GWAS yielded evidence of a miRNA that may influence human brain size and function via modulation of neocortical brain development.

genetics↗

bioRxiv2022

Cellular genome wide association study identifies common genetic variation influencing lithium induced neural progenitor proliferation

Lithium is used in the treatment of bipolar disorder (BD) and is known to increase neural progenitor cell (NPC) proliferation. Though the mechanism of lithiums therapeutic effect is not understood, evidence suggests that genetic variation influences response to treatment. Here, we used a library of genetically diverse human NPCs to identify common genetic variants that modulate lithium induced proliferation. We identified a locus on chr3p21.1 associated with lithium induced proliferation that colocalizes with BD risk. One lithium responsive gene, GNL3, was detected within the locus. The allele associated with increased baseline and lithium-induced GNL3 expression was also associated with increased lithium-induced NPC proliferation. Experimental manipulation of GNL3 expression using CRISPRa/i in NPCs showed that GNL3 was necessary for lithiums full proliferative effects, and sufficient to induce proliferation without lithium treatment. In all, our data suggest that GNL3 expression sensitizes NPCs for a stronger proliferative response to lithium.

genetics↗