Biology subjects

Han, S.

Publications and source records attributed to Han, S..

At least 253 records · Page 14Linked to original sources

bioRxiv2019

Fatty acid-induced lipotoxicity inhibits choline metabolism independent of ER stress in mouse primary hepatocytes

Choline is an essential nutrient that is critical component of the membrane phospholipid phosphatidylcholine (PC), the neurotransmitter acetylcholine and the methylation pathway. In the liver specifically, PC is the major membrane constituent and can be synthesized by the CDP-choline or the phosphatidylethanolamine (PE) N-methyltransferase (PEMT) pathway. With the continuing global rise in the rates of obesity and non-alcoholic fatty liver disease, we sought to explore how excess fatty acids (FA), typical of an obesity and hepatic steatosis, affect choline uptake and metabolism in primary hepatocytes. Our results demonstrate that hepatocytes chronically treated with palmitate, but not oleate or a mixture, had decreased choline uptake, which was associated with lower choline incorporation into PC and lower expression of choline transport proteins. Interestingly, a reduction in the rate of degradation spared PC levels in response to palmitate when compared to control. PE synthesis was slightly diminished; however, no compensatory changes in the PEMT pathway were observed. We next hypothesized that ER stress may be a potential mechanism by which palmitate treatment diminished choline. However, when we exposed primary hepatocytes to the common ER stress inducing compound tunicamycin, choline uptake, contrary to our expectation was augmented, concomitant with the transcript expression of choline transporters. Moreover, tunicamycin-induced ER stress divorced the observed increase in choline uptake from CDP-choline pathway flux since ER stress significantly diminished the incorporation and total PC content, similar to PE. Conclusion: Therefore, our results suggest that the altered FA milieu seen in obesity and fatty liver disease progression may adversely affect choline metabolism, but that compensatory mechanisms work to maintain phospholipid homeostasis.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC=\"FIGDIR/small/746750v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (42K):\norg.highwire.dtl.DTLVardef@1090f2aorg.highwire.dtl.DTLVardef@1c28eedorg.highwire.dtl.DTLVardef@35a80eorg.highwire.dtl.DTLVardef@ac5a53_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2019

In vitro hepatitis C virus infection and hepatic choline metabolism

Choline is an essential nutrient required for normal neuronal and muscular development, as well as homeostatic regulation of hepatic metabolism. In the liver, choline is incorporated into the main eukaryotic phospholipid, phosphatidylcholine (PC) and can enter one carbon metabolism via mitochondrial oxidation. Hepatitis C virus (HCV) is a hepatotropic positive-strand RNA virus that similar to other positive-strand RNA viruses can impact phospholipid metabolism. In the current study we sought to interrogate the link between choline transport and early HCV infection. Namely, we aimed to investigate how HCV modulates markers of choline metabolism following in vitro infection, while subsequently assessing how the inhibition of choline uptake and metabolism upon concurrent HCV infection may alter early viral replication. Finally, we assessed whether these parameters were consistent between cells cultured in fetal bovine serum (FBS) or human serum (HS), conditions known to differentially affect in vitro HCV infection. We observed that choline transport in FBS-cultured Huh7.5 cells is facilitated by the intermediate affinity transporter choline transporter-like family (CTL), and that CTL1 expression and the incorporation of choline into PC is diminished in 24 h infected FBS-cultured cells. Reciprocally, limiting the availability of choline for PC synthesis resulted in increased HCV replication at this early stage. In chronically HS-cultured Huh7.5 cells, there were no differences in the expression of choline transporters upon HCV infection or alterations to viral replication when choline transport was inhibited compared to control treatments. However, inhibiting choline uptake and metabolism in this system significantly impaired the production of infectious virions in HS-cultured cells. These results suggest that in addition to a known role of choline kinase, the transport of choline, potentially via CTL1, might also represent an important and regulated process during HCV infection.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC=\"FIGDIR/small/746776v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (56K):\norg.highwire.dtl.DTLVardef@133a652org.highwire.dtl.DTLVardef@1ec8fa8org.highwire.dtl.DTLVardef@1cb7626org.highwire.dtl.DTLVardef@b9bbc2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2019

Atrial fibrillation associated common risk variants in SYNE2 lead to lower expression of nesprin-2α1 and increased nuclear stiffness

RationaleAtrial fibrillation (AF) genome-wide association studies (GWAS) identified significant associations for rs1152591 and linked variants in the SYNE2 gene encoding the nesprin-2 protein that connects the nuclear membrane with the cytoskeleton\n\nObjectiveDetermine the effects of the AF-associated rs1152591 and rs1152595, two linked intronic single nucleotide polymorphisms (SNPs), on SYNE2 expression and investigate the mechanisms for their association with AF.\n\nMethods and ResultsRNA sequencing of human left atrial appendage (LAA) tissues indicated that rs1152591 and rs1152595 were significantly associated with the expressions of SYNE21, a short mRNA isoform, without an effect on the expression of the full-length SYNE2 mRNA. SYNE21 mRNA uses an alternative transcription start site and encodes an N-terminal deleted 62 kDa nesprin-21 isoform, which can act as a dominant-negative on nuclear-cytoskeleton connectivity. Western blot and qPCR assays confirmed that AF risk alleles of both SNPs were associated with lower expression of nesprin-21 in human LAA tissues. Reporter gene transfections demonstrated that the risk vs. reference alleles of rs1152591 and rs1152595 had decreased enhancer activity. SYNE2 siRNA knockdown (KD) or nesprin-21 overexpression studies in human stem cell-derived induced cardiomyocytes (iCMs) resulted in ~12.5 % increases in the nuclear area compared to controls (p<0.001). Atomic force microscopy demonstrated that SYNE2 KD or nesprin-21 overexpression led to 57.5% or 33.2% decreases, respectively, in nuclear stiffness compared to controls (p< 0.0001).\n\nConclusionsAF-associated SNPs rs1152591 and rs1152595 downregulate the expression of SYNE21, increasing nuclear-cytoskeletal connectivity and nuclear stiffness. The resulting increase in mechanical stress may play a role in the development of AF.

genomics↗

bioRxiv2019

Developing a primary Paralichthys olivaceus gill epithelial cells as an in vitro model for propagation of VHSV show a corresponding increase in cell viability with increase in protein concentration in growth media

BackgroundViral Hemorrhagic Septicemia Virus (VHSV) is a rhabdovirus that causes high mortalities linked to high economic losses in aquaculture. It has been grouped in four genotypes of which some do not easily propagate on continuous cell lines. As an alternative, the objectives of this study was to develop a primary gill epithelial cell (GEC) model from olive flounder (Paralichthys olivaceus) as an in vitro model for the propagation of VHSV. ResultsOur findings show that the primary GECs developed herein are highly permissive to replication of the JF-09 genotype IVa strain leading to high cytopathic effect observed within 96 hours post virus inoculation. Our findings also show that the viability GECs produced herein corresponded with increase in the concentration fetal bovine serum in growth medium. We envision that GECs produced herein will heighten our understanding of immune mechanisms associated with virus entry on gill mucosal surfaces in flounder.

pathology↗

bioRxiv2019

Liquid-liquid phase separation and fibrillization of tau are independent processes with overlapping conditions

Amyloid aggregation of the microtubule binding protein tau is a hallmark of Alzheimers disease and many other neurodegenerative diseases. Recently, tau has been found to undergo liquid-liquid phase separation (LLPS) near physiological conditions. Although LLPS and aggregation have been shown to simultaneously occur under certain common conditions, it remains to be seen whether tau LLPS promotes aggregation, or if they are two independent processes. In this study, we address this question by combining multiple biochemical and biophysical assays in vitro. We investigated the impacts of LLPS on tau aggregation at three stages: conformation of tau, kinetics of aggregation and fibril quantity. We showed that none of these properties are influenced directly by LLPS, while amyloid aggregation propensity of tau can be altered without affecting its LLPS behavior. LLPS and amyloid aggregation of tau occur under overlapping conditions of enhanced intermolecular interactions and localization, but are two independent processes.

biophysics↗

bioRxiv2019

Shared and Distinct Dysfunction of Dynamic Connectivity Networks across Schizophrenia, Bipolar Disorder and Major Depression Disorder

Dynamic functional connectivity (DFC) analysis can capture time-varying properties of connectivity and may provide further information about transdiagnostic psychopathology across major psychiatric disorders. In this study, we used resting state functional MRI and a sliding-window method to study DFC in 150 schizophrenia (SZ), 100 bipolar disorder(BD), 150 major depressive disorder (MDD), and 210 healthy controls (HC). DFC were clustered into two functional connectivity states. Significant 4-group differences in DFC were found only in state 2. Post hoc analyses showed that transdiagnostic dysconnectivity among there disorders featured decreased connectivity within visual, somatomotor, salience and frontoparietal networks. Our results suggest that decreased connectivity within both lower-order (visual and somatomotor) and higher-order (salience and frontoparietal) networks may serve as transdiagnostic marker of these disorders, and that these dysconnectivity is state-dependent. Targeting these dysconnectivity may improve assessment and treatment for patients that having more than one of these disorders at the same time.

neuroscience↗

bioRxiv2019

The rhg1-a (Rhg1 low-copy) nematode resistance source harbors a copia-family retrotransposon within the Rhg1-encoded α-SNAP gene

Soybean growers widely use the Resistance to Heterodera glycines 1 (Rhg1) locus to reduce yield losses caused by soybean cyst nematode (SCN). Rhg1 is a tandemly repeated four gene block. Two classes of SCN resistance-conferring Rhg1 haplotypes are recognized: rhg1-a (\"Peking-type\", low copy number, 3 or fewer Rhg1 repeats) and rhg1-b (\"PI 88788-type\", high copy number, 4 or more Rhg1 repeats). The rhg1-a and rhg1-b haplotypes encode -SNAP (alpha-Soluble NSF Attachment Protein) variants -SNAPRhg1LC and -SNAPRhg1HC respectively, with differing atypical C-terminal domains, that contribute to SCN-resistance. Here we report that rhg1-a soybean accessions harbor a copia retrotransposon within their Rhg1 Glyma.18G022500 (-SNAP-encoding) gene. We termed this retrotransposon \"RAC\", for Rhg1 alpha-SNAP copia. Soybean carries multiple RAC-like retrotransposon sequences. The Rhg1 RAC insertion is in the Glyma.18G022500 genes of all true rhg1-a haplotypes we tested and was not detected in any examined rhg1-b or Rhg1WT (single-copy) soybeans. RAC is an intact element residing within intron 1, anti-sense to the rhg1-a -SNAP open reading frame. RAC has intrinsic promoter activities, but overt impacts of RAC on transgenic -SNAPRhg1LC mRNA and protein abundance were not detected. From the native rhg1-a RAC+ genomic context, elevated -SNAPRhg1LC protein abundance was observed in syncytium cells, as was previously observed for -SNAPRhg1HC (whose rhg1-b does not carry RAC). Using a SoySNP50K SNP corresponding with RAC presence, just [~]42% of USDA accessions bearing previously identified rhg1-a SoySNP50K SNP signatures harbor the RAC insertion. Subsequent analysis of several of these putative rhg1-a accessions lacking RAC revealed that none encoded -SNAPRhg1LC, and thus they are not rhg1-a. rhg1-a haplotypes are of rising interest, with Rhg4, for combating SCN populations that exhibit increased virulence against the widely used rhg1-b resistance. The present study reveals another unexpected structural feature of many Rhg1 loci, and a selectable feature that is predictive of rhg1-a haplotypes.

plant biology↗

bioRxiv2019

Functional divergence of Plexin B structural motifs in distinct steps of Drosophila olfactory circuit assembly

Plexins exhibit multitudinous, evolutionarily conserved functions in the development of nervous systems. However, how Plexins employ their diverse structural motifs in vivo to perform distinct roles in the stepwise assembly of neural circuits is unclear. Here, we systematically mutagenized structural motifs of Drosophila Plexin B (PlexB) and examined the function of these variants at multiple PlexB-mediated neurodevelopmental processes in olfactory receptor neurons: axon fasciculation, trajectory choice, and synaptic partner selection. We found that the extracellular Sema domain is essential for all three processes, the catalytic site of the intracellular RapGAP is engaged in none, and the intracellular GTPase-binding motifs are essential for trajectory choice and synaptic partner selection, but are dispensable for fasciculation. Moreover, extracellular PlexB cleavage serves as a regulatory mechanism of PlexB signaling. Thus, PlexB structural motifs have divergent roles in distinct steps of neural development, altogether contributing to the functional versatility of PlexB in neural circuit assembly.

neuroscience↗

bioRxiv2019

Structural basis for the transport mechanism of the human glutamine transporter SLC1A5 (ASCT2)

Alanine-serine-cysteine transporter 2 (ASCT2, SLC1A5) is the primary transporter of glutamine in cancer cells and regulates the mTORC1 signaling pathway. The SLC1A5 function involves finely tuned orchestration of two domain movements that include the substrate-binding transport domain and the scaffold domain. Here, we present cryo-EM structures of human SLC1A5 and its complex with the substrate, L-glutamine in an outward-facing conformation. These structures reveal insights into the conformation of the critical ECL2a loop which connects the two domains, thus allowing rigid body movement of the transport domain throughout the transport cycle. Furthermore, the structures provide new insights into substrate recognition, which involves conformational changes in the HP2 loop. A putative cholesterol binding site was observed near the domain interface in the outward-facing state. Comparison with the previously determined inward-facing structure of SCL1A5 provides a basis for a more integrated understanding of substrate recognition and transport mechanism in the SLC1 family. Our structures are likely to aid the development of potent and selective SLC1A5 inhibitors for the treatment of cancer and autoimmune disorders.

biophysics↗

bioRxiv2019

LonP1 Orchestrates UPRmt and UPRER and Mitochondrial Dynamics to Regulate Heart Function

Protein quality control is pivotal to cellular homeostasis and integrity of cardiomyocytes for maintenance of normal heart function. The unfolded protein response (UPR) is an adaptive process to modulate protein quality control in the endoplasmic reticulum (ER) and mitochondria, and is accordingly termed UPRER and UPRmt, respectively. Lon protease (LonP1) is a highly conserved mitochondrial protease to modulate UPRmt, which is involved in regulating metabolism, mitophagy, and stress response. However, whether LonP1 regulates UPRER remains elusive. To investigate the regulation of protein quality control in cardiomyocytes, we generated cardiac-specific LonP1 deletion mice. Our findings show that LonP1 deficiency caused impaired mitochondrial respiratory function and fragmentation. Surprisingly, both UPRER and UPRmt is substantially induced in LonP1-deletion heart suggesting of LonP1 as a novel regulator of UPRER; however, the activation of UPRER occurs earlier than UPRmt in response to LonP1 deletion. Consequently, cardiac-specific LonP1 deficiency causes aberrant metabolic reprogramming of cardiomyocytes, pathological heart remodeling, as well as impeded heart function. Thus, we uncovered the novel function of LonP1 as an UPRmt mediator, and reciprocal orchestration of UPRmt and UPRER and mitochondrial dynamics regulated by LonP1 in the cardiomyocytes that is critical to maintain heart function, which offers exciting new insights into the potential therapeutic strategy for heart failure.

cell biology↗

bioRxiv2019

Structure of the human frataxin-bound iron-sulfur cluster assembly complex provides insight into its activation mechanism

Iron-sulfur clusters (ISC) are essential in all life forms and carry out many crucial cellular functions. The core machinery for de novo ISC biosynthesis, located in the mitochondria matrix, is a five-protein complex containing the cysteine desulfurase NFS1 that is activated by frataxin (FXN), scaffold protein ISCU, accessory protein ISD11, and acyl-carrier protein ACP. Deficiency in FXN leads to the loss-of-function neurodegenerative disorder Friedreichs ataxia (FRDA). Recently crystal structures depicting the inactive 3- and 4-way sub-complexes of the ISC biosynthesis machinery, lacking the key activator FXN, have been determined. Here, the 3.2 [A] resolution cryo-electron microscopy structure of the FXN-bound active human complex, containing two copies of the NFS1-ISD11-ACP-ISCU-FXN hetero-pentamer, delineates for the first time in any organism the interactions of FXN with the component proteins. FXN binds at the interface of two NFS1 and one ISCU subunits, modifying the local environment of a bound zinc ion that would otherwise inhibit NFS1 activity in complexes without FXN. Our structure sheds light on how FXN facilitates ISC production through unlocking the zinc inhibition and stabilizing key loop conformations of NFS1 and ISCU at the protein-protein interfaces, and offers an explanation of how FRDA clinical mutations affect complex formation and FXN activation.

biochemistry↗

bioRxiv2019

Remodeling gut microbiota by Streptococcus thermophilus 19 attenuates inflammation in septic mice

Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection and is the leading cause of death in burn patients. Streptococcus thermophilus 19 is a highly effective probiotic, with well-studied health benefits, but its role in protecting viscera against injury caused by sepsis and the underlying mechanism is poorly understood. The goal of this study was to evaluate protection potency of S. thermophilus against inflammation in mice and evaluate the influence of sepsis and S. thermophilus on microbial community. We tested the utility of S. thermophilus 19 in attenuating inflammation in vitro and vivo of LPS-induced sepsis mouse model. We also evaluated the influence of sepsis and S. thermophilus on microbial community. In vitro, S. thermophilus 19 decrease the expression of inflammatory factors. Additionally, in a lipopolysaccharide-induced septic mouse model, mice administered the probiotic 19 was highly resistant to Lps and exhibited decreased expression of inflammatory factors compared to Lps-treated control mice. A MiSeq-based sequence analysis revealed that gut microbiota alterations in mice intraperitoneally injected with 1 mg/ml LPS were mitigated by the administration of oral probiotics 19. Together these findings indicate that S. thermophilus 19 may be a new avenue for interventions against inflammation caused by sepsis and other systemic inflammatory diseases. In an analysis of the gut microbiota of the all group mice, we found that sepsis is associated with gut microbiota and probiotics attenuate the inflammation through remodeling gut microbiota. ImportanceSepsis is life-threatening organ dysfunction which is the leading cause of death in burn patients. Although our understanding of sepsis has increased substantially in recent years, its still reported to be the leading cause of death in seriously ill patients. Evidences showed that gut microbiota play an important role in sepsis. Moreover, probiotics have been used to prevent numbers of gut health disorders and alleviate inflammation associated with some human diseases by promoting changes in the gut microbiota composition. Hence, to investigate the mechanism of probiotics in the treatment of sepsis has emerged. The significance of our research is in identifying the role of gut microbiota in sepsis and found an effective probiotic that reduces inflammation, S. thermophilus 19, and investigating the therapeutic effect and mechanism of S. thermophilus 19 on sepsis, which might be a new avenue for interventions against inflammation caused by sepsis and other systemic inflammatory diseases.

microbiology↗

bioRxiv2019

Molecular mechanism of TRPV2 channel modulation by cannabidiol

Transient receptor potential vanilloid 2 (TRPV2) plays a critical role in neuronal development, cardiac function, immunity, and cancer. Cannabidiol (CBD), the non-psychotropic therapeutically active ingredient of Cannabis sativa, is a potent activator of TRPV2 and also modulates other transient receptor potential (TRP) channels. Here, we determined structures of the full-length TRPV2 channel in a CBD-bound state in detergent and in PI(4,5)P2 enriched nanodiscs by cryo-electron microscopy. CBD interacts with TRPV2 through a hydrophobic pocket located between S5 and S6 helices of adjacent subunits, which differs from known ligand and lipid binding sites in other TRP channels. Comparison between apo- and two CBD-bound TRPV2 structures reveals that the S4-S5 linker plays a critical role in channel gating upon CBD binding. The TRPV2 \"vanilloid\" pocket, which is critical for ligand-dependent gating in other TRPV channels, stays unoccupied by annular lipids, PI(4,5)P2, or CBD. Together these results provide a foundation to further understand TRPV channel gating properties and their divergent physiological functions and to accelerate structure-based drug design.

biophysics↗

bioRxiv2019

Nedd4 E3 ligase and beta-arrestins regulate ubiquitination, trafficking, and stability of the mGlu7 receptor

The metabotropic glutamate receptor 7 (mGlu7) is a class C G protein-coupled receptor (GPCR) that modulates excitatory neurotransmitter release at the presynaptic active zone. Although post-translational modification of cellular proteins with ubiquitin is a key molecular mechanism governing protein degradation and function, mGlu7 ubiquitination and its functional consequences have not been elucidated yet. Here, we report that Nedd4 ubiquitin E3 ligase and {beta}-arrestins regulate ubiquitination of mGlu7 in heterologous cells and neurons. Upon agonist-stimulation, {beta}-arrestins recruit Nedd4 to mGlu7 and facilitate Nedd4-mediated ubiquitination of mGlu7. Nedd4 and {beta}-arrestins regulate constitutive and agonist-induced endocytosis of mGlu7 and are required for mGlu7-dependent MAPK signaling in neurons. In addition, Nedd4-mediated ubiquitination results in the degradation of mGlu7 by both the lysosomal and proteasomal degradation pathways. These findings provide a model in which Nedd4 and {beta}-arrestin act together as a complex to regulate mGlu7 surface expression and function at the presynaptic terminals.

neuroscience↗

bioRxiv2018

Dual-color volumetric imaging of neural activity of cortical columns

To capture the emergent properties of neural circuits, high-speed volumetric imaging of neural activity at cellular resolution is desirable. But while conventional two-photon calcium imaging is a powerful tool to study population activity in vivo, it is restrained to two-dimensional planes. Expanding it to 3D while maintaining high spatiotemporal resolution appears necessary. Here, we developed a two-photon microscope with dual-color laser excitation that can image neural activity in a 3D volume. We imaged the neuronal activity of primary visual cortex from awake mice, spanning from L2 to L5 with 10 planes, at a rate of 10 vol/sec, and demonstrated volumetric imaging of L1 long-range PFC projections and L2/3 somatas. Using this method, we map visually-evoked neuronal ensembles in 3D, finding a lack of columnar structure in orientation responses and revealing functional correlations between cortical layers which differ from trial to trial and are missed in sequential imaging. We also reveal functional interactions between presynaptic L1 axons and postsynaptic L2/3 neurons. Volumetric two-photon imaging appears an ideal method for functional connectomics of neural circuits.

neuroscience↗

bioRxiv2018

Real-time monitoring of bacterial growth and fast antimicrobial susceptibility tests exploiting multiple light scattering

AbstractAntimicrobial susceptibility test (AST) is widely used to provide the minimum inhibitory concentration of bacteria, and crucial to provide appropriate uses of antibiotics and to address the issue of drug-resistance bacteria. However, ASTs require the time-consuming incubation about 16-20 h for the visual determination of the growth of bacterial colonies, which has been a major obstacle to on-site applications of ASTs. In this study, we propose a rapid and non-invasive method based on laser speckles to evaluate the bacterial growth movements in real time, thus reducing the time for the agar dilution method. With a simple configuration compatible with conventional agar plates, the analysis of laser speckle from samples enables the early detection of the presence of growth as well as its detailed history of the colony-forming movement on agar plates. Using the samples prepared through the same procedure as the agar dilution method, we obtained the AST results at least 4-8 hours earlier than the conventional method without compromising the accuracy. This technique does not require for the use of exogenous agents, but works for most bacteria regardless of their species. Furthermore, the distinctive responses of several species to microbial agents were revealed through the present technique supporting a comprehensive analysis of the effect of the antibiotics. The findings suggest that this new method could be a useful tool for rapid, simple, and low-cost ASTs in addition to providing the historical information of the bacterial growth on agar plates.

microbiology↗

bioRxiv2018

The landscapes of DNA methylation associated with the transcriptomic network in laying hens and broilers get insight to embryonic muscle development in chicken

As DNA methylation is one of the key epigenetic mechanisms involved in embryonic development, elucidating its relationship with non-coding RNA and genes is essential for understanding early development. In this study, we performed single-base-resolution bisulfite sequencing together with RNA-seq to explore the genetic basis of embryonic muscle development in chicken. Comparison of methylome profiles between broilers and laying hens revealed that lower methylation in broilers might contribute to muscle development. Differential methylated region (DMR) analysis between two chicken lines showed that the majority of DMRs were hypo-DMRs for broilers. Differential methylated genes were significantly enriched in muscle development-related terms at E13 and E19. Furthermore, by constructing the network of the lncRNAs, we identified a lncRNA, which we named MYH1-AS, that potentially regulated muscle development. These findings reveal an integrative landscape of late period of embryonic myogenesis in chicken and give rise to a comprehensive understanding of epigenetic and transcriptional regulation, in skeletal muscle development. Our study provides a reliable data resource for further muscle studies.

bioinformatics↗

bioRxiv2018

A machine learning approach to predicting autism risk genes: Validation of known genes and discovery of new candidates

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic basis. The role of de novo mutations in ASD has been well established, but the set of genes implicated to date is still far from complete. The current study employs a machine learning-based approach to predict ASD risk genes using features from spatiotemporal gene expression patterns in human brain, gene-level constraint metrics, and other gene variation features. The genes identified through our prediction model were enriched for independent sets of ASD risk genes, and tended to be differentially expressed in ASD brains, especially in the frontal and parietal cortex. The highest-ranked genes not only included those with strong prior evidence for involvement in ASD (for example, TCF20 and FBOX11), but also indicated potentially novel candidates, such as DOCK3, MYCBP2 and CAND1, which are all involved in neuronal development. Through extensive validations, we also showed that our method outperformed state-of-the-art scoring systems for ranking ASD candidate genes. Gene ontology enrichment analysis of our predicted risk genes revealed biological processes clearly relevant to ASD, including neuronal signaling, neurogenesis, and chromatin remodeling, but also highlighted other potential mechanisms that might underlie ASD, such as regulation of RNA alternative splicing and ubiquitination pathway related to protein degradation. Our study demonstrates that human brain spatiotemporal gene expression patterns and gene-level constraint metrics can help predict ASD risk genes. Our gene ranking system provides a useful resource for prioritizing ASD candidate genes.

genetics↗