Biology subjects

Zhao, X.

Publications and source records attributed to Zhao, X..

At least 523 records · Page 29Linked to original sources

bioRxiv2019

The socioeconomic burden of severe mental disorder in China, 2014-2017: a prevalence study

Mental illness is a chronic disease with high morbidity and mortality rate, resulting in heavy economic burden for family and society, especially the severe ones. Chinese government has taken a series of action on the treatment and management of severe mental disorder (SMD), but the scale of economic burden caused by SMD was still unclear. In this paper, we applied prevalence-based bottom-up approach to estimate the direct and indirect economic burden of SMD in Southwest China from 2014 to 2017. We used the sampled inpatient medical record data of patient with SMD to calculate the total direct cost and estimated the indirect economic burden using human capital approach.The total ecomonic burden of SMD was USD9,733 million and direct burden was contiributed for 7.5% as USD734.5 million in four years total. The growth rate of direct medical cost was declined due to the health policy reform and total cost control policy. The indirect cost was rapidly increased in four years when estimated with DALYs reported in GBD2010 and resulting USD8,998.6 million. We next estimated the indirect burden using sample DALYs and occupation wage cost approach as sensitive analysis. We found that the indirect burden was sensitive to the key variable and the estimation approach, but the estimates share same increasing trend but with different velocity. Our study suggests that SMD in China have posed substantial economic burden at individual and social levels, with the appropriate estimation of total economic burden, our reaserch would attract more attention and be helpful for health resources distribution.

scientific communication and education↗

bioRxiv2019

NON-EQUILIBRIUM BELOUSOV-ZHABOTINSKY REACTION DESCRIBES THE SPONTANEOUS ACTIVITY OF THE BRAIN

Belousov-Zhabotinsky (BZ) reactions describe chemical patterns in terms of non-equilibrium thermodynamics, chaotic evolution of nonlinear oscillators, excitability under the influence of peculiar chemical stimulations. In touch with this chemical model, we hypothesized that the nonlinear brain electric activity at the edge of the chaos could be triggered by neural oscillation equipped with BZ dynamics, and that changes in neural activity might be correlated with the transient occurrence of (either short and long-range) BZ-like reactions in cortical subareas. To prove our hypothesis of neuronal waves driven by BZ-like processes, we evaluated fMRI movies that assess in vivo BOLD resting state activity of the human brain. We found that the spontaneous activity of the brain display features fully overlapping the recently-introduced local circuits based on BZ chemical reaction. Therefore, neuronal paths during spontaneous activity of the brain match BZ dynamics previsions. Our results point towards the brain as crossed by diffusive nonlinear neural oscillations patterns that are predictable. Furthermore, our results suggest that chaotic dynamics arise from nothing else than the network arrangements subtending physical and biological systems.

neuroscience↗

bioRxiv2019

TET1-mediated Oligodendrocyte Homeostasis Regulates Myelination and Synaptic Functions

Ten-eleven translocation (TET) proteins, the dioxygenase for DNA hydroxymethylation, are important players in nervous system development and diseases. However, their role in myelination and remyelination after injury remains elusive. Here, we identify a genome-wide and locus-specific DNA hydroxymethylation landscape shift during differentiation of oligodendrocyte-progenitor cells (OPC). Ablation of Tet1 results in stage-dependent defects in oligodendrocyte (OL) development and myelination in the mouse brain. The mice lacking Tet1 in the oligodendrocyte lineage develop behavioral deficiency. We also show that TET1 is required for remyelination in adulthood. Transcriptomic, genomic occupancy, and DNA hydroxymethylation profiling reveal a critical TET1-regulated epigenetic program for oligodendrocyte differentiation that includes genes associated with myelination, cell division, and calcium transport. Tet1-deficient OPCs exhibit reduced calcium activity, increasing calcium activity rescues the differentiation defects in vitro. Deletion of a TET1-5hmC target gene, Itpr2 impairs the onset of OPC differentiation. Together, our results suggest that stage-specific TET1-mediated epigenetic programming and intracellular signaling are important for proper myelination and remyelination in mice.

neuroscience↗

bioRxiv2019

Protein Quality Control is a Risk Factor and Therapeutic Target in Toxin-Induced Biliary Atresia

BACKGROUND and AIMS Extra-hepatic biliary atresia (BA) is a pediatric liver disease with no approved medical therapy. Recent studies using human samples and experimental modeling suggest that glutathione redox metabolism and heterogeneity play a role in disease pathogenesis. We sought to dissect the mechanistic basis of liver redox variation and explore how other stress responses affect cholangiocyte injury in BA.METHODS We performed quantitative in situ hepatic glutathione redox mapping in zebrafish larvae carrying targeted mutations in glutathione metabolism genes and correlated these findings with sensitivity to the plant-derived BA-linked toxin biliatresone. We also determined whether genetic disruption of HSP90 protein quality control pathway genes implicated in human BA altered biliatresone toxicity in zebrafish and human cholangiocytes. An in vivo screen of a known drug library was performed to identify novel modifiers of cholangiocyte injury in the zebrafish experimental BA model with subsequent validation.RESULTS Glutathione metabolism gene mutations caused regionally distinct changes in the redox potential of cholangiocytes that differentially sensitized them to biliatresone. Disruption of human BA-implicated HSP90 pathway genes sensitized zebrafish and human cholangiocytes to biliatresone-induced injury independent of glutathione. Phosphodiesterase-5 inhibitors (PDE5i) and other cGMP signaling activators worked synergistically with the glutathione precursor N- acetylcysteine (NAC) in preventing biliatresone-induced injury in zebrafish and human cholangiocytes. PDE5i enhanced proteasomal degradation and required intact HSP90 chaperone.CONCLUSION Regional variation in glutathione metabolism underlies sensitivity to the biliary toxin biliatresone, and mirrors recently reported BA risk stratification linked to glutathione metabolism gene expression. Human BA can be causatively linked to genetic modulation of protein quality control. Combined treatment with NAC and cGMP signaling enhancers warrants further investigation as therapy for BA.Background and Context Biliary atresia (BA) is an obstructive fibrosing cholangiopathy that is the leading indication for liver transplantation in the pediatric population. There are no known treatments to prevent progressive liver injury after surgical restoration of bile flow.New Findings The authors identify factors that affect susceptibility of cholangiocytes to oxidative injury using a toxin-induced BA model. This information is used to validate genetic risk factors for human BA and identified PDE5i as a potential treatment for biliary atresia, either on its own or in combination with the anti-oxidant N-acetyl-cysteine.Limitations The work done in animal and cell culture models needs further study in human tissue-derived models and a larger cohort of BA patients.Impact The findings from this study provide a rationale for identifying new genetic risk factors that predispose to BA and for an interventional study to prevent progressive liver injury in this enigmatic disease.Short Summary This study uses zebrafish and human cell culture models to identify novel injury mechanisms, genetic risk factors and new therapies for the pediatric liver disease biliary atresia.Competing Interest StatementThe authors have declared no competing interest.Abbreviations17-AAG7-N-allylamino-17-demethoxygeldanamycin;BAbiliary atresia;bilbiliatresone;8-Br-cGMP8-Bromoguanosine 3’,5’-cyclic monophosphate;EHCextrahepatic cholangiocytes;Gclglutamate cysteine ligase;GGAgeranylgeranyl acetate;gsrglutathione reductase;GSHreduced glutathione;GSSGoxidized glutathione;IHCintrahepatic cholangiocytes;NACN-acetylcysteine;PDE5iPhosphodiesterase-5 inhibitors;PQCprotein quality control;WTwild-typeView Full Text

pathology↗

bioRxiv2019

Genome-wide identification of accessible chromatin regions in bumblebee (Bombus terrestris) by ATAC-seq

Bumblebees (Hymenoptera: Apidae) are important pollinating insects that play pivotal roles in crop production and natural ecosystem services. To date, while the protein-coding sequences of bumblebees have been extensively annotated, regulatory elements, such as promoters and enhancers, have been poorly annotated in the bumblebee genome. To achieve a comprehensive profile of accessible chromatin regions and provide clues for all possible regulatory elements in the bumblebee genome, we did ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) for B. terrestris samples derived from its four developmental stages: egg, larva, pupa, and adult, respectively. The sequencing reads of ATAC-seq were mapped to B. terrestris reference genome, and the accessible chromatin regions of bumblebee were identified and characterized by using bioinformatic methods. Our study will provide important resources not only for uncovering regulatory elements in the bumblebee genome, but also for expanding our understanding of bumblebee biology. The ATAC-seq data generated in this study has been deposited in NCBI GEO (accession#: GSE131063).

genomics↗

bioRxiv2019

Systematic identification of A-to-I editing associated regulators from multiple human cancers

A-to-I editing is the most common editing type in human that is catalyzed by ADAR family members (ADARs), ADAR1 and ADAR2. Millions of A-to-I editing sites have been discovered recently, however, the regulation mechanisms of the RNA editing process are still not clear. Here we developed a two-step logistic regression model to identify genes that are potentially involved in RNA editing process in four human cancers. The first step by classifying the editing sites into different categories assists the analysis at the second step. In the first step, ADAR1 was identified as the enzyme that associated with the majority of the A-to-I editing sites. Thus, ADAR1 was taken as a control gene in the second step to identify genes that have a stronger effect on editing sites than ADAR1. In addition, the detectable interferons and their receptors were used as covariates in the both steps to account for potential association caused by interferons. Using our advanced method, we successfully found a set of genes that were significantly positively or negatively associated (PA or NA) with specific sets of RNA editing sites. We highlighted two genes, SRSF5 and MIR22HG which were supported by multiple evidences. Most PA and NA genes were unique to each cancer, and only a few shared across two cancers. Pathway enrichment analysis showed that the PA genes from the four cancer types were enriched in Immune System, while the NA genes were enriched in two pathways: Metabolism of RNA, and Metabolism. The functional similarity of the PA and NA genes across all the four cancers indicates that even though most of the editing associated genes were unique to each cancer, they may impact on editing process through common pathways. Interestingly, the PA genes from kidney cancer were enriched for survival-associated genes while the NA genes were depleted of these genes, indicating that the PA genes may play more important roles in kidney cancer development.

bioinformatics↗

bioRxiv2019

Three-dimensional Genome Structure Reveals Distinct Chromatin Signatures of Mouse Female Germline Stem Cells During Development

The three-dimensional configuration of the genome ensures cell-type-specific gene expression profiles by placing genes and regulatory elements in close spatial proximity. Here, we revealed the distinct features of the chromatin architecture in female germline stem cells (FGSCs) by in situ high-throughput chromosome conformation analysis. We also showed that the X chromosome structures were similar in spermatogonial stem cells and FGSCs. Using integrative analysis of the three-dimensional chromatin structure, we observed that the TADs were attenuated in germinal vesicle oocytes and disappeared in metaphase II oocytes during FGSC development. Finally, we identified conserved compartments belonging to the paternal/maternal genomes during early embryonic development, which were related to imprinted genes. These results will provide a valuable resource for studying and further our understanding of the fundamental characteristics of oogenesis and early embryo development.

cell biology↗

bioRxiv2019

Electroacupuncture at Governor Vessel improves neurobehavioral function via reduction of complexin1

Electroacupuncture at Governor Vessel (GV), as a traditional chinese medicine, has been proved that it can reduce scar and promote axon regeneration. However, the underlying mechanism remains unclear. Herein, complexin1 (CPLX1), as a candidate protein, was found using protein chip. Therefore, using a CRISPR/Cas9 knockout approach, we deleted CPLX1 specifically in the SD rats to assess the role of CPLX1 in GV treatment. Additionally, eIF5A1 stimulate the translation of CPLX1 with PPG sequence, we attempt to uncover whether eIF5A1 play a role in the GV treatment. In fact, GV can reduce scar and promote axon regeneration after SCC. CPLX1-/+ SCC rats demonstrated that decreased CPLX1 improved the microenvironment of injured area via reducing the components of fibrotic scar and further enhanced the synaptic plasticity, which benefit the regeneration of axons. And eIF5A1 could regulate the expression of CPLX1 in the process of GV treatment. Therefore, GV contributes to axon regeneration and synapse plasticity via eIF5A1 regulating CPLX1 following SCC, providing a convincible mechanism for improving the therapeutic efficacy of GV for SCC.

neuroscience↗

bioRxiv2019

Automated Spatially Targeted Optical Micro Proteomics (autoSTOMP) to determine protein complexity of subcellular structures

Spatially Targeted Optical Micro Proteomics (STOMP) is a method to study region-specific protein complexity of a biological specimen. STOMP uses a confocal microscope to both visualize structures of interest and to tag the proteins within those structures by a photo-driven crosslinking reaction so that they can be affinity purified and identified by mass spectrometry1. STOMP has the potential to perform discovery proteomics on sub-cellular structures in a wide range of primary cells types and biopsy-scale tissue samples. However, two significant limitations have prevented the broad adoption of this technique by the scientific community. First, STOMP is performed across two software platforms written in different languages, which requires user operation at each field of view. Up to 48 hours of microscope time is necessary to tag sufficient protein ([~]1 g) for mass spectrometry making STOMP prohibitively time and labor-consuming for many researchers. Second, the original STOMP protocol uses a custom photo-crosslinker that limits the accessibility of the technique for some user. To liberate the user, we developed a protocol that automates communication between Zeiss Zen Black imaging software and FIJI image processing software using a customizable code in SikuliX. To fully automate STOMP (autoSTOMP), this protocol includes a tool to make tile array, autofocus and capture images of fields of view across the sample; as well as a method to modify the file that guides photo-tagging so that subsets of the structures of interest can be targeted. To make this protocol broadly accessible, we implemented a commercially available biotin-benzophenone crosslinker as well as a procedure to block endogenous biotin and purify tagged proteins using magnetic streptavidin beads. Here we demonstrate that autoSTOMP can efficiently label, purify and identify proteins that belong to structures measuring 1-2 m in diameter using human foreskin fibroblasts or mouse bone marrow-derived dendritic cells infected with the protozoan parasite Toxoplasma gondii (Tg). The autoSTOMP platform can easily be adapted to address a range of research questions using Zeiss Zen Black microscopy systems and LC-MS protocols that are standard in many institutional research cores.

biochemistry↗

bioRxiv2019

Extraction of genome-wide reads distribution pattern through whole genome sequencing of cell-free DNA for tracking tissue-of-origin in cancer patients

Somatic mosaicism is widespread among tissues and could indicate distinct tissue origins of circulating cell-free DNA (cfDNA), DNA fragments released by lytic cells into the blood. By investigating the alignment patterns of whole genome sequencing reads with the genomic DNA of different tissues, we found that the read distributions formed type-specific patterns in some regions as a result of somatic mosaicism. We then utilized this information to construct a tissue-of-origin mapping model and evaluated its predictive performance on whole genome sequencing data from tissue and cfDNA samples. In total, 1,545 tissue samples associated with 13 cancer types were included, and identification of the tissue of origin achieved a specificity of 82% and a sensitivity of 80%. Furthermore, a total of 30 cfDNA samples from lung cancer and liver cancer patients and healthy controls were analyzed to predict their tissues of origin with a specificity of 87% and a sensitivity of 87%. Our results show that read distribution patterns from whole genome sequencing could be used to identify cfDNA tissues of origin with high accuracy, suggesting the potential application of our model to early cancer detection and diagnosis.

bioinformatics↗

bioRxiv2019

Offspring production of ovarian organoids derived from spermatogonial stem cells by chromatin reorganization

Fate determination of germline stem cells remains poorly understood at the chromatin structure level1,2. Here, we demonstrate successful production of offspring from oocytes transdifferentiated from mouse spermatogonial stem cells (SSCs) with tracking of transplanted SSCs in vivo, single cell whole exome sequencing, and in 3D cell culture reconstitution of the process of oogenesis derived from SSCs. Furthermore, we demonstrate direct induction of germline stem cells (iGSCs) differentiated into functional oocytes by transduction of H19, Stella, and Zfp57 and inactivation of Plzf in SSCs after screening with ovarian organoids. Using high throughput chromosome conformation, we uncovered extensive chromatin reorganization during SSC conversion into iGSCs, which was highly similar to female germline stem cells. We observed that although topologically associating domains were stable during SSC conversion, chromatin interactions changed in a striking manner, altering 35% of inactive and active chromosomal compartments throughout the genome. These findings have important implications in various areas including mammalian gametogenesis, genetic and epigenetic reprogramming, biotechnology, and medicine.

genetics↗

bioRxiv2019

SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme

Synthetic long reads (SLR) with long-range co-barcoding information have been recently developed and widely applied in genomics researches. We proposed a scaffolding model of the co-barcoding information and developed a scaffolding tool with adopting a top-to-bottom scheme to make full use of the complementary information in SLR datasets and a screening algorithm to reduce negative effects from misassembled contigs in an input assembly. In comparison with other available SLR scaffolding tools, our tool obtained the best quality improvement for different input assemblies, especially for those assembled by the next-generation sequencing reads, where the improvement of contiguity is about several hundred-folds.

bioinformatics↗

bioRxiv2019

Antibody binding epitope Mapping (AbMap) of hundred antibodies in a single run

Epitope mapping is essential for the understanding how an antibody works. Given millions of antibodies short of epitope information, there is an urgent need for high-throughput epitope mapping. Here we combined a commercial phage displayed random peptide library of 109 diversity with next generation sequencing to develop Antibody binding epitope Mapping (AbMap) technology. Over two hundred antibodies were analyzed in a single test and epitopes were determined for >50% of them. Strikingly, the antibodies were able to recognize different proteins from multiple species with similar epitopes. We successfully identified the epitopes of 14 anti-PD-1 antibodies, including Sintilimab (i.e., L128, A129 and P130), and confirmed that the binding epitopes of Nivolumab and Sintilimab are very close to the binding interface of PD-1 and PD-L1. The predicted conformational epitopes of Pembrolizumab and Nivolumab are consistent with their antibody-antigen co-crystal structures. AbMap is the first technology enables high-throughput epitope mapping. HighlightsO_LIThe first technology enables epitope mapping of two hundred antibodies in a single run C_LIO_LILinear epitope was determined for >50% of the antibodies C_LIO_LIDistinct epitopes of 14 anti-PD-1 antibodies, including Sintilimab, were determined C_LIO_LIThe predicted conformational epitopes of Pembrolizumab and Nivolumab are consistent with the known antibody-antigen co-crystal structures C_LI

immunology↗

bioRxiv2019

Map3k2-Regulated Intestinal Stromal Cells (MRISC) Define a Distinct Sub-cryptic Stem Cell Niche for Damage Induced Wnt Agonist R-spondin1 Production

Intestinal stem cell propagation and differentiation are essential for rapid repair of tissue damage in the gut. While intestinal stromal cells were recently identified as key mediators of this process, the cellular and molecular mechanisms by which this diverse population induces tissue repair remains poorly understood. Here we show that Map3k2 has a colon stromal cell specific function critically required for maintenance of Lgr5+ intestinal stem cells and protection against acute intestinal damage. This Map3k2-specific function is mediated by enhancing Wnt agonist R-spondin1 production. We further reveal a unique novel cell population, named Map3k2-regulated intestinal stromal cells (MRISC), as the primary cellular source of R-spondin1 following intestinal injury. Together, our data identify a novel intestinal stem cell niche organized by MRISC, which specifically dependent on the Map3k2-signaling pathway to augment the production of Wnt agonist R-spondin1 and promote regeneration of the acutely damaged intestine.\n\nHighlightsO_LIMap3k2 protects mice from DSS-induced colitis by promoting intestinal stem cell regeneration.\nC_LIO_LIMap3k2-MAPK pathway cross-talks with Wnt signaling pathway via upregulation of R-spondin1.\nC_LIO_LIMap3k2-Regulated Intestinal Stromal Cells (MRISC) marked by co-expression of CD90, CD34 and CD81 defines a novel colonic stem cell niche.\nC_LI

cell biology↗

bioRxiv2019

Functional annotation of rare structural variation in the human brain

Structural variants (SVs) contribute substantially to risk of many brain related disorders including autism and schizophrenia. However, annotating the potential contribution of SVs to disease remains a major challenge. Here, we integrated high resolution SV calling from genome-sequencing in 755 human post-mortem brains with dorsal lateral prefrontal cortex RNA-sequencing from a subset of 629 samples to quantify the dosage and regulatory effects of SVs. We show that genic (p = 5.44x10-9) and regulatory SVs (enhancer p = 3.22x10-23, CTCF p = 3.86x10-18) are present at significantly lower frequencies than intergenic SVs after correcting for SV length. Copy number variants (CNVs)--deletions and duplications--exhibit a significant quantitative and directional relationship between the proportion of genic and regulatory content altered and gene expression, and the size of the effect is inversely correlated with the loss-of-function intolerance of the gene. We trained a joint linear model that leverages genic and regulatory annotations to predict expression effects of rare CNVs in independent samples (R2 = 0.21-0.41). We further developed a regulatory disruption score for each CNV that aggregates the predicted expression across all affected genes weighted by the genes intolerance score and applied it to an independent set of SVs from 14,891 genome-sequenced individuals. Pathogenic deletions implicated in neurodevelopmental disorders by ClinGen had significantly more extreme regulatory disruption scores than the rest of the SVs. Rank ordering based on the most extreme regulatory disruption scores prioritized pathogenic deletions that would not have been prioritized by frequency or length alone. This work points to the deleteriousness of regulatory SVs, particularly those altering CTCF sites. We further provide a simple approach for functionally annotating the regulatory effects of SVs in the human brain that has potential to be useful in larger SV studies and should improve as more regulatory annotation data is generated.

genomics↗

bioRxiv2019

Large-scale GWAS in sorghum reveals common genetic control of grain size among cereals

O_LIGrain size is a key yield component of cereal crops and a major quality attribute. It is determined by a genotypes genetic potential and its capacity to fill the grains.\nC_LIO_LIThis study aims to dissect the genetic architecture of grain size in sorghum via an integrated genome wide association study (GWAS) using a diversity panel of 837 individuals and a BC-NAM population of 1,421 individuals.\nC_LIO_LIIn order to isolate genetic effects associated with grain size, rather than the genotypes capacity to fill grain, a field treatment of removing half of the panicle during flowering was imposed. Extensive variation in grain size with high heritability was observed in both populations across 5 field trials. Subsequent GWAS analyses uncovered 92 grain size QTL, which were significantly enriched for orthologues of known grain size genes in rice and maize. Significant overlap between the 92 QTL and grain size QTL in rice and maize was also found, supporting common genetic control of this trait among cereals. Further analysis found grain size genes with opposite effect on grain number were less likely to overlap with the grain size QTL from this study, indicating the treatment facilitated identification of genetic regions related to the genetic potential of grain size rather than the capacity to fill the grain.\nC_LIO_LIThese results enhance understanding of the genetic architecture of grain size in cereal, and pave the way for exploration of underlying molecular mechanisms in cereal crops and manipulation of this trait in breeding practices.\nC_LI

genetics↗

bioRxiv2019

Using Machine Learning to Facilitate Classification of Somatic Variants from Next-Generation Sequencing

BackgroundMolecular profiling has become essential for tumor risk stratification and treatment selection. However, cancer genome complexity and technical artifacts make identification of real variants a challenge. Currently, clinical laboratories rely on manual screening, which is costly, subjective, and not scalable. Here we present a machine learning-based method to distinguish artifacts from bona fide Single Nucleotide Variants (SNVs) detected by NGS from tumor specimens.\n\nMethodsA cohort of 11,278 SNVs identified through clinical sequencing of tumor specimens were collected and divided into training, validation, and test sets. Each SNV was manually inspected and labeled as either real or artifact as part of clinical laboratory workflow. A three-class (real, artifact and uncertain) model was developed on the training set, fine-tuned using the validation set, and then evaluated on the test set. Prediction intervals reflecting the certainty of the classifications were derived during the process to label \"uncertain\" variants.\n\nResultsThe optimized classifier demonstrated 100% specificity and 97% sensitivity over 5,587 SNVs of the test set. 1,252 out of 1,341 true positive variants were identified as real, 4,143 out of 4,246 false positive calls were deemed artifacts, while only 192(3.4%) SNVs were labeled as \"uncertain\" with zero misclassification between the true positives and artifacts in the test set.\n\nConclusionsWe presented a computational classifier to identify variant artifacts detected from tumor sequencing. Overall, 96.6% of the SNVs received a definitive label and thus were exempt from manual review. This framework could improve quality and efficiency of variant review process in clinical labs.

bioinformatics↗

bioRxiv2019

The Eya1 phosphatase mediates Shh-driven symmetric cell division of cerebellar granule cell precursors

During neural development, stem and precursor cells can divide either symmetrically or asymmetrically. The transition between symmetric and asymmetric cell divisions is a major determinant of precursor cell expansion and neural differentiation, but the underlying mechanisms that regulate this transition are not well understood. Here, we identify the Sonic hedgehog (Shh) pathway as a critical determinant regulating the mode of division of cerebellar granule cell precursors (GCPs). Using partial gain and loss of function mutations within the Shh pathway, we show that pathway activation determines spindle orientation of GCPs, and that mitotic spindle orientation directly correlates with the mode of division. Mechanistically, we show that the phosphatase Eya1 is essential for implementing Shh-dependent GCP spindle orientation. We identify atypical protein kinase C (aPKC) as a direct target of Eya1 activity and show that Eya1 dephosphorylates Threonine (T410) in the activation loop of this polarity complex component. Thus, Eya1 inactivates the cell polarity complex, resulting in reduced phosphorylation of Numb and other components that regulate the mode of division. This Eya1-dependent cascade is critical in linking spindle orientation, cell cycle exit and terminal differentiation. Together these findings demonstrate that a Shh-Eya1 regulatory axis selectively promotes symmetric cell divisions during cerebellar development by coordinating spindle orientation and cell fate determinants.\n\nSummary statementBiological responses to Shh signaling are specified by the magnitude of pathway activation and the cellular context. This study shows that potent Shh signaling regulates mitotic orientation and symmetric division of cerebellar granule cell precursors in a process that requires the phosphatase Eya1 and unequal distribution of cell fate determinants to daughter cells.

neuroscience↗