Biology subjects

Li, B.

Publications and source records attributed to Li, B..

At least 523 records · Page 29Linked to original sources

bioRxiv2020

Weight Sensitivity of Temporal SNR Metrics in multi-echo fMRI

PurposeIn multi-echo fMRI (ME-fMRI), various weighting schemes have been proposed for the combination of the data across echoes. Here we introduce a framework that facilitates a deeper understanding of the weight dependence of temporal SNR measures in ME-fMRI. Theory and MethodsWe examine two metrics that have been used to characterize ME-fMRI performance: temporal SNR (tSNR) and multi-echo temporal (metSNR). Both metrics can be described using the generalized Rayleigh quotient (GRQ) and are predicted to be relatively insensitive to the weights when there is a high degree of similarity between a metric-specific matrix in the GRQ numerator and a metricindependent covariance matrix in the GRQ denominator. The application of the GRQ framework to experimental data is demonstrated using a resting-state fMRI dataset acquired with a multi-echo multi-band EPI sequence. ResultsIn the example dataset, similarities between the covariance matrix and the metSNR and tSNR numerator matrices are highest in grey matter (GM) and cerebrospinal fluid (CSF) voxels, respectively. For representative GM and CSF voxels that exhibit high matrix similarity values, the metSNR and tSNR values, respectively, are both within 4% of their optimal values across a range of weighting schemes. However, there is a fundamental tradeoff, with a high degree of weight sensitivity in the tSNR and metSNR metrics for the representative GM and CSF voxels, respectively. Geometric insight into the observed weight dependencies is provided through a graphical interpretation of the GRQ. ConclusionA GRQ framework can provide insight into the factors that determine the weight sensitivity of tSNR and metSNR measures in ME-fMRI.

neuroscience↗

bioRxiv2020

Tocilizumab treatment in severe COVID-19 patients attenuates the inflammatory storm incited by monocyte centric immune interactions revealed by single-cell analysis

ABSTRACTDespite the current devastation of the COVID-19 pandemic, several recent studies have suggested that the immunosuppressive drug Tocilizumab can powerfully treating inflammatory responses that occur in this disease. Here, by employing single-cell analysis of the immune cell composition of severe-stage COVID-19 patients and these same patients in post Tocilizumab-treatment remission, we have identified a monocyte subpopulation specific to severe disease that contributes to inflammatory storms in COVID-19 patients. Although Tocilizumab treatment attenuated the strong inflammatory immune response, we found that immune cells including plasma B cells and CD8+ T cells still exhibited an intense humoral and cell-mediated anti-virus immune response in COVID-19 patients after Tocilizumab treatment. Thus, in addition to providing a rich, very high-resolution data resource about the immune cell distribution at multiple stages of the COVID-19 disease, our work both helps explain Tocilizumab’s powerful therapeutic effects and defines a large number of potential new drug targets related to inflammatory storms.Competing Interest StatementJingwen Fang is the executive officer of HanGen BiotechView Full Text

genomics↗

bioRxiv2020

Single cell profiling of immature human postnatal thymocytes resolves the complexity of intra-thymic lineage differentiation and thymus seeding precursors.

During postnatal life, thymopoiesis depends on the continuous colonization of the thymus by bone marrow derived hematopoietic progenitors that migrate through the bloodstream. In human, the nature of these thymus immigrants has remained unclear. Here, we employ single-cell RNA sequencing on approximately 70.000 CD34+ thymocytes to unravel the heterogeneity of the human immature postnatal thymocytes. Integration of bone marrow and peripheral blood precursors datasets identifies several putative thymus seeding precursors that display heterogeneity for currently used surface markers as revealed by CITEseq. Besides T cell precursors, we discover branches of intrathymic developing dendritic cells with predominantly plasmacytoid DCs. Trough trajectory inference, we delineate the transcriptional dynamics underlying early human T-lineage development from which we predict transcription factor modules that drive stage-specific steps of human T cell development. Thus, our work resolves the heterogeneity of thymus seeding precursors in human and reveals the molecular mechanisms that drive their in vivo cell fate.

immunology↗

bioRxiv2020

Inhibition of Pten activity promotes IB4 positive sensory neuronal axon growth

Traumatic nerve injuries have become a common clinical problem, and axon regeneration is a critical process in the successful functional recovery of the injured nervous system. In this study, we found that peripheral axotomy reduce total PTEN expression in adult sensory neurons, however, it did not alter the expression level of PTEN in IB4-positive sensory neurons. Additionally, our results indicate that the artificial inhibition of PTEN markedly promotes adult sensory axon regeneration, including IB4-positive neuronal axon growth. Thus, our results provide strong evidence that PTEN is a prominent repressor of adult sensory axon regeneration, especially in IB4-positive neurons.

neuroscience↗

bioRxiv2020

Identification of a common deletion in the spike protein of SARS-CoV-2

Two notable features have been identified in the SARS-CoV-2 genome: (1) the receptor binding domain of SARS-CoV-2; (2) a unique insertion of twelve nucleotide or four amino acids (PRRA) at the S1 and S2 boundary. For the first feature, the similar RBD identified in SARs-like virus from pangolin suggests the RBD in SARS-CoV-2 may already exist in animal host(s) before it transmitted into human. The left puzzle is the history and function of the insertion at S1/S2 boundary, which is uniquely identified in SARS-CoV-2. In this study, we identified two variants from the first Guangdong SARS-CoV-2 cell strain, with deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. More extensive screening indicates the deletion at the flank sites of PRRAR could be detected in 3 of 68 clinical samples and half of 22 in vitro isolated viral strains. These data indicate (1) the deletion of QTQTN, at the flank of polybasic cleavage site, is likely benefit the SARS-CoV-2 replication or infection in vitro but under strong purification selection in vivo since it is rarely identified in clinical samples; (2) there could be a very efficient mechanism for deleting this region from viral genome as the variants losing 23585-23599 is commonly detected after two rounds of cell passage. The mechanistic explanation for this in vitro adaptation and in vivo purification processes (or reverse) that led to such genomic changes in SARS-CoV-2 requires further work. Nonetheless, this study has provided valuable clues to aid further investigation of spike protein function and virus evolution. The deletion mutation identified in vitro isolation should be also noted for current vaccine development.

genetics↗

bioRxiv2020

Risperidone-induced changes in DNA methylation from peripheral blood in first-episode schizophrenia parallel neuroimaging and cognitive phenotype

Today, second generation anti-psychotics such as clozapine and risperidone are the favored treatment for schizophrenia. Yet, the absence of relevant biomarkers that can decode their neurobiological effect shackles our ability to accurately predict and track response to treatment. While researchers have investigated DNA methylation as a biomarker for schizophrenia risk, none have performed a systematic analysis of the effect of antipsychotics upon DNA methylation. We hypothesize that disease-related methylation changes occur before treatment, and that acute antipsychotic treatment may affect DNA methylation. We designed a longitudinal DNA methylation study to estimate risperidones effect on DNA methylation and how changes in DNA methylation might influence risperidones therapeutic effect on behavioral and neuroimaging phenotypes. Thirty-eight patients with first-episode drug-naive schizophrenia (FES) and 38 demographically-matched individuals (healthy controls) participated. We identified brain related pathways enriched in 8,204 FES-associated methylation sites. Risperidone administration altered methylation in 6,143 CpG DNA sites. Post-treatment FES associated with methylation in 6760 CpG sites. Majority of the DNA methylation changes were treatment effect in the overall CpG sites, the FES associated CpG sites, and risperidone associated CpG sites, except for the post-treatment FES associated CpG sites. There were 590 DNA methylation cites normalized by risperidone treatment. The methylation changes of these 590 CpG sites were related to alterations in symptom severity, spontaneous neurophysiological activity, and cognitive function. To our knowledge, this is the first longitudinal methylation study of drug treatment effect and side effect in psychiatric disorders to include parallel studies of neuroimaging and cognitive phenotypes. We identified FES-associated CpG sites not confounded by drug treatment as potential SCZ biomarkers. The normalization effect of risperidone monotherapy suggests that DNA methylation changes may serve as a predictive biomarker for treatment effect. The constructed methylation-phenotype network revealed a relationship between methylation and a wide range of biological and psychological variables.

pharmacology and toxicology↗

bioRxiv2020

A Comprehensive Survey of Mutations in Oesophageal Carcinoma Reveals Recurrent Neoantigens as Potential Immunotherapy Targets

This study was aimed to investigate the mutations in Esophageal Carcinoma (EC) for recurrent neoantigen identification. A total of 733 samples with whole exome sequencing (WES) mutation data and 1153 samples with target region sequencing data were obtained from 7 published studies and GENIE database. Common HLA-I and HLA-II genotypes in both TCGA cohort and Chinese were used to predict the probability of public neoantigens in the dataset. Based on the integrated data, we not only obtained the most comprehensive EC mutation landscape so far, but also found 253 mutation sites which could be identified in at least 3 or more patients, including, TP53 p.R248Q, PIK3CA p.E545K, PIK3CA p.E542K, KRAS p.G12D, PIK3CA p.H1047R and TP53 p.C83F. These mutations can be recognized by multiple common HLA molecules (HLA-A11:01, HLA-B57:01, HLA-A03:01, DRB1-0301, DRB1-1202, et al.) in Chinese and TCGA cohort as potential public neoantigens. Overall, our analysis provides some potential targets for EC immunotherapy.

immunology↗

bioRxiv2020

Iatrogenic Iron Promotes Neurodegeneration and Activates Self-protection of Neural Cells against Exogenous Iron Attacks

Metal implants are used worldwide, with millions of metal nails, plates and fixtures grafted during orthopaedic surgeries. Iron is the most common element of these metal implants. As time passes metal elements can be corroded and iron can be released from the implants in the form of ferric (Fe3+) or ferrous (Fe2+). These iron ions can permeate the surrounding tissues and enter circulation; importantly both Fe3+ and Fe2+ freely pass blood brain barrier (BBB). Can iron from implants represent a risk factor for neurological diseases? This remains an unanswered question. In this study, we discovered that the probability of metal implants delivered through orthopaedic surgeries was higher in patients of Parkinsons diseases (PD) or ischemic stroke than in healthy subjects. This finding instigated subsequent study of iron effects on neuronal cells. In experiments in vivo, we found that iron selectively decreased presence of divalent metal transporter 1 (DMT1) in neurones through increasing the expression of Ndfip1, which degrades DMT1 and rarely exists in glial cells. At the same time iron accumulation increased expression of DMT1 in astrocytes and microglial cells and triggered reactive astrogliosis and microglial activation. Facing the attack of excess iron, glial cells act as neuroprotectors to uptake more extracellular iron by up-regulating DMT1, whereas neurones limit iron uptake through decreasing DMT1 operation. Cerebral accumulation of iron was associated with impaired cognition, locomotion and mood. Excess iron thus affects neural cells and could increase the risk of neurodegeneration.

neuroscience↗

bioRxiv2020

CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells

Topologically associating domains (TAD) and insulated neighborhoods (INs) have been proposed to constrain enhancer-promoter communications to enable cell-type specific transcription programs, but recent studies show that disruption of TADs and INs resulted in relatively mild changes in gene expression profiles. To better understand the role of chromatin architecture in dynamic enhancer-promoter contacts and lineage-specific gene expression, we have utilized the auxin-inducible degron system to acutely deplete CTCF, a key factor involved in TADs and IN formation, in mouse embryonic stem cells (mESCs) and examined chromatin architecture and gene regulation during neural differentiation. We find that while CTCF depletion leads to global weakening of TAD boundaries and loss of INs, only a minor fraction of enhancer-promoter contacts are lost, affecting a small subset of genes. The CTCF-dependent enhancer-promoter contacts tend to be long-range, spanning hundreds of kilobases, and are established directly by CTCF binding to promoters. Disruption of CTCF binding at the promoter reduces enhancer-promoter contacts and transcription, while artificial tethering of CTCF to the promoter restores the enhancer-promoter contacts and gene activation. Genome-wide analysis of CTCF binding and gene expression across multiple mouse tissues suggests that CTCF-dependent promoter-enhancer contacts may regulate expression of additional mouse genes, particularly those expressed in the brain. Our results uncover both CTCF-dependent and independent enhancer-promoter contacts, and highlight a distinct role for CTCF in promoting enhancer-promoter contacts and gene activation in addition to its insulator function.

genomics↗

bioRxiv2020

Single-cell transcriptome profiling an adult human cell atlas of 15 major organs

BackgroundAs core units of organ tissues, cells of various types play their harmonious rhythms to maintain the homeostasis of the human body. It is essential to identify the characteristics of cells in human organs and their regulatory networks for understanding the biological mechanisms related to health and disease. However, a systematic and comprehensive single-cell transcriptional profile across multiple organs of a normal human adult is missing. ResultsWe perform single-cell transcriptomes of 84,363 cells derived from 15 tissue organs of one adult donor and generate an adult human cell atlas. The adult human cell atlas depicts 252 subtypes of cells, including major cell types such as T, B, myeloid, epithelial, and stromal cells, as well as novel COCH+ fibroblasts and FibSmo cells, each of which is distinguished by multiple marker genes and transcriptional profiles. These collectively contribute to the heterogeneity of major human organs. Moreover, T cell and B cell receptor repertoire comparisons and trajectory analyses reveal direct clonal sharing of T and B cells with various developmental states among different tissues. Furthermore, novel cell markers, transcription factors and ligand-receptor pairs are identified with potential functional regulations in maintaining the homeostasis of human cells among tissues. ConclusionsThe adult human cell atlas reveals the inter- and intra-organ heterogeneity of cell characteristics and provides a useful resource in uncovering key events during the development of human diseases in the context of the heterogeneity of cells and organs.

cell biology↗

bioRxiv2020

A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress

Eukaryotes have evolved various quality control mechanisms to promote proteostasis in the ER. Selective removal of certain ER domains via autophagy (termed as ER-phagy) has emerged as a major quality control mechanism. However, the degree to which ER-phagy is employed by other branches of ER-quality control remains largely elusive. Here, we identify a cytosolic protein, C53, that is specifically recruited to autophagosomes during ER-stress, in both plant and mammalian cells. C53 interacts with ATG8 via a distinct binding epitope, featuring a shuffled ATG8 interacting motif (sAIM). C53 senses proteotoxic stress in the ER lumen by forming a tripartite receptor complex with the ER-associated ufmylation ligase UFL1 and its membrane adaptor DDRGK1. The C53/UFL1/DDRGK1 receptor complex is activated by stalled ribosomes and induces the degradation of internal or passenger proteins in the ER. Consistently, the C53 receptor complex and ufmylation mutants are highly susceptible to ER stress. Thus, C53 forms an ancient quality control pathway that bridges selective autophagy with ribosome-associated quality control at the ER.

cell biology↗

bioRxiv2020

Assessing the statistical reporting quality in high-impact factor urology journals

BackgroundsObservational studies plays an important role in urology studies, But few studies have paid attention to the statistical reporting quality of observational studies. The purpose of this study was to investigate the frequency and evaluate the reporting quality of statistical methods of the published observational studies in urology. MethodsThe five urology journals were selected according to the 5-year impact factor. A systematic literature search was performed in PubMed for relevant articles. The quality of statistical reporting was assessed according to assessment criteria. ResultsA total of 193 articles were included in this study. The mean statistical reporting score of included articles was 0.42 (SD=0.15), accounting for 42% of total score. The items that must be reported with a reporting rate more than 50% were: alpha level (n=122, 65.2%), confidence intervals (n=134, 69.4%), name of statistical package (n=158, 84.5%) and exact P-values (n=161, 86.1%). The items with a reporting rate less than 50% were: outliers (n=2, 1.0%) and sample size (n=13, 6.7%). For multivariable regression models (liner, logistic and Cox), variables coding (n=27, 40.7%), validation analysis of assumptions (n=58, 40.3%), interaction test (n=43, 30.0%), collinearity diagnostics (n=5, 3.5%) and goodness of fit test (n=6, 5.9%) were reported. Number of authors more than 7(OR=2.06, 95%CI=1.04-4.08) and participation of statistician or epidemiologist (OR=1.73, 95%CI=1.18-3.39) were associated with the superior reporting quality. ConclusionThe statistical reporting quality of published observational studies in 5 high-impact factor urological journals was alarming. We encourage researchers to collaborate with statistician or epidemiologist. The authors, reviewers and editors should increase their knowledge of statistical methods, especially new and complex methods.

systems biology↗

bioRxiv2020

DNA methylation is indispensable for leukemia inhibitory factor dependent embryonic stem cells reprogramming

Naive pluripotency can be maintained by the 2i/LIF supplements (CHIR99021, PD0325901 and LIF), which primarily affect canonical WNT, FGF/ERK, and JAK/STAT3 signaling. However, whether one of these tripartite supplements alone is sufficient to maintain naive self-renewal remain unclear. Here we show that LIF alone is sufficient to induce reprogramming of 2i/LIF cultured ESCs (2i/L-ESCs) to ESCs with hypermethylated state (L-ESCs). In vitro, upon withdrawal of 2i, 2i/L-ESCs overcome the epigenetic barrier and DNA hypermethylated, which accompanies transcriptional changes and subsequent establishment of epigenetic memory. Global transcriptome features also show that L-ESCs are close to 2i/L-ESCs and in a stable state between naive and primed pluripotency. Notably, our results demonstrate that DNA methylation was indispensable for LIF-dependent mouse ESCs reprogramming and self-renew. LIF-dependent ESCs reprogramming efficiency is significantly increased in serum treatment and reduced in Dnmt3a or Dnmt3l knockout ESCs. Importantly, unlike epiblast and EpiSCs, L-ESCs contribute to somatic tissues and germ cells in chimaeras. Such simple culture system of ESCs is more conducive to clarify the molecular mechanism of ESCs in vitro culture. SignificanceEmbryonic stem cell (ESCs) exhibit naive pluripotency which reflects their ability to contribute to all embryonic lineages upon injection into blastocyst. ESCs were originally derived by co-culture with feeder cells and fetal calf serum. In this manuscript, we took a detailed approach to dissect the roles of LIF alone in ESC reprogramming of 2i/LIF cultured ESCs (2i/L-ESCs). Here, for the first time, we derived stable hypermethylated pluripotent ESCs under culture of LIF alone (L-ESCs). We further assessed L-ESCs properties both in vitro and in vivo, and provide molecular insights to the mechanism which allows LIF alone to maintain pluripotency and a hypermethylated state. We believe these findings are novel and valuable for future ESCs study.

cell biology↗

bioRxiv2020

Schistosoma Japonicum infection in Treg-specific USP21 knock-out mice

USP21, an E3 de-ubiquitin enzyme playing vital roles in physiological activities, is important for Treg cells to maintain immune homeostasis and control immune tolerance. To understand its diverse functions and potential mechanism is essential for disease development. We, using the USP21 gene-conditional knock-out mice model of Schistosoma Japonicum infection, found more cercariae developed into adults, and more eggs deposited in the liver in KO mice. However, immunohistochemistry showed the degree and the area of egg granuloma and liver fibrosis were both reduced. This suggested knock-out USP21 did affect the immunoregulation between schistosomes and the host. In KO mice the content of IFN-gamma and IL-4, and the expression of anti-SEA IgG and anti-SWAP IgG both increased in the liver, spleen and blood by flow cytometry, while the content of IL-10, lL-17A, IL-23, IL-9 and the expression of USP21 and anti-SEA IgM decreased. This indicated USP21-knockout-Tregs promoted both Th1-type and Th2-type immunity and inhibited other immunities during schistosomes infection, which disordered the host immunity. This study revealed the immunomodulatory of USP21 and preliminarily suggests it might be essential to regulate the complex immune network between the host and schistosomes. USP21 provides a new possible target for schistosomiasis treatment in the future. Author summarySchistosomiasis is a common neglected tropical disease that affects more than 230 million people worldwide. Therefore, the study on the mechanism of immune interaction between schistosomas and the host is not only helpful for the understanding of immune homeostasis, but also helpful for the further development of the treatment of schistosomiasis. Ubiquitin Specific Protease 21(USP21) has been shown to be involved in the regulation of many biological processes, such as maintaining immune homeostasis and regulating cell growth. Here, we observed that the specific deletion of USP21 led to the decrease of mices ability to resist schistosomes infection and promoted the survival of schistosomes. It was also proved that unstable regulatory T cells would produce polarization phenomenon and promote differentiation to helper T cells, which would lead to disorder of immune response in mice. However, this process reduced the serious immune pathological damage caused by egg granuloma. Our findings reveal that USP21 may be an important molecule regulating immune interaction between Schistosoma japonicum and the host.

immunology↗

bioRxiv2020

Defining Strawberry Uniformity using 3D Imaging and Genetic Mapping

Strawberry uniformity is a complex trait, influenced by multiple genetic and environmental components. To complicate matters further, the phenotypic assessment of strawberry uniformity is confounded by the difficulty of quantifying geometric parameters by eye and variation between assessors. An in-depth genetic analysis of strawberry uniformity has not been undertaken to date, due to the lack of accurate and objective data. Nonetheless, uniformity remains one of the most important fruit quality selection criteria for the development of a new variety. In this study, a 3D-imaging approach was developed to characterise berry uniformity. We show that circularity of the maximum circumference had the closest predictive relationship with the manual uniformity score. Combining five or six automated metrics provided the best predictive model, indicating that human assessment of uniformity is highly complex. Furthermore, visual assessment of strawberry fruit quality in a multi-parental QTL mapping population has allowed the identification of genetic components controlling uniformity. A "regular shape" QTL was identified and found to be associated with three uniformity metrics. The QTL was present across a wide array of germplasm, indicating a strong candidate for marker-assisted breeding. A greater understanding of berry uniformity has been achieved through the study of the relative impact of automated metrics on human perceived uniformity. Furthermore, the comprehensive definition of strawberry uniformity using 3D imaging tools has allowed precision phenotyping, which has improved the accuracy of trait quantification. This tool has allowed us to illustrate the use of advanced image analysis towards the breeding of greater uniformity in strawberry.

bioinformatics↗

bioRxiv2020

Effects of emotion and semantic relatedness on recognition memory: Behavioral and electrophysiological evidence

Some aspects of our memory are enhanced by emotion, whereas other can be unaffected or even hindered. Previous studies report impaired associative memory of emotional content, an effect termed associative "emotional interference". The current study used EEG and an associative recognition paradigm to investigate the cognitive and neural mechanisms associated with this effect. In two experiments, participants studied negative and neutral stimulus-pairs that were either semantically related or unrelated. In Experiment 1 emotions were relevant to the encoding task (valence judgment) whereas in Experiment 2 emotions were irrelevant (familiarity judgment). In a subsequent associative recognition test, EEG was recorded while participants discriminated between intact, rearranged, and new pairs. An associative emotional interference effect was observed in both experiments, but was attenuated for semantically related pairs in Experiment 1, where valence was relevant to the task. Moreover, a modulation of an early associative memory ERP component (300-550 ms) occurred for negative pairs when valence was task-relevant (Experiment 1), but for semantically related pairs when valence was irrelevant (Experiment 2). A later ERP component (550-800 ms) showed a more general pattern, and was observed in all experimental conditions. These results suggest that both valence and semantic relations can act as an organizing principle that promotes associative binding. Their ability to contribute to successful retrieval depends on specific task demands.

neuroscience↗

bioRxiv2020

Predicting changes in protein thermostability upon point mutation with deep 3D convolutional neural networks

Predicting mutation-induced changes in protein thermodynamic stability ({triangleup}{triangleup}G) is of great interest in protein engineering, variant interpretation, and understanding protein biophysics. We introduce ThermoNet, a deep, 3D-convolutional neural network designed for structure-based prediction of {triangleup}{triangleup}Gs upon point mutation. To leverage the image-processing power inherent in convolutional neural networks, we treat protein structures as if they were multi-channel 3D images. In particular, the inputs to ThermoNet are uniformly constructed as multi-channel voxel grids based on biophysical properties derived from raw atom coordinates. We train and evaluate ThermoNet with a curated data set that accounts for protein homology and is balanced with direct and reverse mutations; this provides a framework for addressing biases that have likely influenced many previous {triangleup}{triangleup}G prediction methods. ThermoNet demonstrates performance comparable to the best available methods on the widely used Ssym test set. However, ThermoNet accurately predicts the effects of both stabilizing and destabilizing mutations, while most other methods exhibit a strong bias towards predicting destabilization. We further show that homology between Ssym and widely used training sets like S2648 and VariBench has likely led to overestimated performance in previous studies. Finally, we demonstrate the practical utility of ThermoNet in predicting the {triangleup}{triangleup}Gs for two clinically relevant proteins, p53 and myoglobin, and for pathogenic and benign missense variants from ClinVar. Overall, our results suggest that 3D convolutional neural networks can model the complex, non-linear interactions perturbed by mutations, directly from biophysical properties of atoms. Author SummaryThe thermodynamic stability of a protein, usually represented as the Gibbs free energy for the biophysical process of protein folding ({triangleup}G), is a fundamental thermodynamic quantity. Predicting mutation-induced changes in protein thermodynamic stability ({triangleup}{triangleup}G) is of great interest in protein engineering, variant interpretation, and understanding protein biophysics. However, predicting {triangleup}{triangleup}Gs in an accurate and unbiased manner has been a long-standing challenge in the field of computational biology. In this work, we introduce ThermoNet, a deep, 3D-convolutional neural network designed for structure-based {triangleup}{triangleup}G prediction. To leverage the image-processing power inherent in convolutional neural networks, we treat protein structures as if they were multi-channel 3D images. ThermoNet demonstrates performance comparable to the best available methods. However, ThermoNet accurately predicts the effects of both stabilizing and destabilizing mutations, while most other methods exhibit a strong bias towards predicting destabilization. We also demonstrate that the presence of homologous proteins in commonly used training and testing sets for {triangleup}{triangleup}G prediction methods has likely influenced previous performance estimates. Finally, we highlight the practical utility of ThermoNet by applying it to predicting the {triangleup}{triangleup}Gs for two clinically relevant proteins, p53 and myoglobin, and for pathogenic and benign missense variants from ClinVar.

bioinformatics↗

bioRxiv2020

3D Epigenomic Characterization Reveals Insights Into Gene Regulation and Lineage Specification During Corticogenesis

Lineage-specific epigenomic changes during human corticogenesis have previously remained elusive due to challenges with tissue heterogeneity and sample availability. Here, we analyze cis-regulatory chromatin interactions, open chromatin regions, and transcriptomes for radial glia, intermediate progenitor cells, excitatory neurons, and interneurons isolated from mid-gestational human brain samples. We show that chromatin looping underlies transcriptional regulation for lineage-specific genes, with transcription factor motifs, families of transposable elements, and disease-associated variants enriched at distal interacting regions in a cell type-specific manner. A subset of promoters exhibit unusually high degrees of chromatin interactivity, which we term super interactive promoters. Super interactive promoters are enriched for critical lineage-specific genes, suggesting that interactions at these loci contribute to the fine-tuning of cell type-specific transcription. Finally, we present CRISPRview, a novel approach for validating distal interacting regions in primary cells. Our study presents the first characterization of cell type-specific 3D epigenomic landscapes during human corticogenesis, advancing our understanding of gene regulation and lineage specification during human brain development.

genomics↗