Biology subjects

He, D.

Publications and source records attributed to He, D..

At least 55 records · Page 3Linked to original sources

bioRxiv2023

Selenoprotein synthesis is not induced by hepatotoxic drugs

Background and AimsMany of the proteins that contain the amino acid selenocysteine are required for optimal defense against cellular stress. As such, one might expect selenoprotein synthesis to persist or be induced upon cellular insult. Because selenocysteine is incorporated by a complex post-transcriptional mechanism, monitoring the transcription of selenoprotein genes is not adequate to understand the regulation of selenoprotein synthesis. We aimed to determine whether selenoprotein synthesis is regulated by the induction of hepatotoxic stress. MethodsWe used hepatotropic clinically relevant drugs to evaluate the regulation of selenoprotein synthesis in human hepatocarcinoma cells. ResultsWe found that two drugs, benzbromarone and sorafenib, caused significant inhibition of selenoprotein synthesis. However, the loss of selenoprotein expression was not specific as total protein synthesis was similarly down-regulated only by benzbromarone and sorafenib. ConclusionsThese results allow us to conclude that these hepatotoxins do not induce or preserve selenoprotein synthesis as a protective mechanism. HighlightsO_LIThe treatment of liver cells with hepatotoxic and hepatotropic compounds does not result in increased synthesis of selenoproteins. C_LIO_LICompounds that induced the canonical oxidative stress response that features NRF2 activation eliminated selenoprotein synthesis. C_LIO_LIThe downregulation of selenoproteins was accompanied by general inhibition of protein synthesis. C_LI

pharmacology and toxicology↗

bioRxiv2023

Integrating gene mutation spectra from tumors and the general population with gene expression topological networks to identify novel cancer driver genes

BackgroundUnderstanding the genetics underlying cancer development and progression is the most important goal of biomedical research to improve patient survival rates. Recently, researchers have proposed computationally combining the mutational burden with biological networks as a novel means to identify cancer driver genes. However, these approaches treated all mutations as having the same functional impact on genes and incorporated gene-gene interaction networks without considering tissue specificity, which may have hampered our ability to identify novel cancer drivers. MethodsWe have developed a framework, DGAT-cancer that integrates the predicted pathogenicity of somatic mutation in cancers and germline variants in the healthy population, with topological networks of gene expression in tumor tissues, and the gene expression levels in tumor and paracancerous tissues in predicting cancer drivers. These features were filtered by an unsupervised approach, Laplacian selection, and those selected were combined by Hotelling and Box-Cox transformations to score genes. Finally, the scored genes were subjected to Gibbs sampling to determine the probability that a given gene is a cancer driver. ResultsThis method was applied to nine types of cancer, and achieved the best area under the precision-recall curve compared to three commonly used methods, leading to the identification of 571 novel cancer drivers. One of the top genes, EEF1A1 was experimentally confirmed as a cancer driver of glioma. Knockdown of EEF1A1 led to a ~ 41-50% decrease in glioma size and improved the temozolomide sensitivity of glioma cells. ConclusionBy combining the pathogenic status of mutational spectra in tumors alongside the spectrum of variation in the healthy population, with gene expression in both tumors and paracancerous tissues, DGAT-cancer has significantly improved our ability to detect novel cancer driver genes.

bioinformatics↗

bioRxiv2023

simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry

SummaryThe alevin-fry ecosystem provides a robust and growing suite of programs for single-cell data processing. However, as new single-cell technologies are introduced, as the community continues to adjust best practices for data processing, and as the alevin-fry ecosystem itself expands and grows, it is becoming increasingly important to manage the complexity of alevin-frys single-cell preprocessing workflows while retaining the performance and flexibility that make these tools enticing. We introduce simpleaf, a program that simplifies the processing of single-cell data using tools from the alevin-fry ecosystem, and adds new functionality and capabilities, while retaining the flexibility and performance of the underlying tools. Availability and implementationSimpleaf is written in Rust and released under a BSD 3-Clause license. It is freely available from its GitHub repository https://github.com/COMBINE-lab/simpleaf, and via bioconda. Documentation for simpleaf is available at https://simpleaf.readthedocs.io/en/latest/ and tutorials for simpleaf are being developed that can be accessed at https://combine-lab.github.io/alevin-fry-tutorials.

bioinformatics↗

bioRxiv2023

The mechanosensitive ion channel Piezo1 contributes to ultrasound neuromodulation

Transcranial low-intensity ultrasound is a promising neuromodulation modality, with the advantages of non-invasiveness, deep penetration, and high spatiotemporal accuracy. However, the underlying biological mechanism of ultrasonic neuromodulation remains unclear, hindering the development of efficacious treatments. Here, the well-known Piezo1, was studied through a conditional knockout mouse model as a major molecule for ultrasound neuromodulation ex vivo and in vivo. We showed that Piezo1 knockout in the right motor cortex of mice significantly reduced ultrasound-induced neuronal calcium responses, limb movement and muscle EMG responses. We also detected higher Piezo1 in the central amygdala (CEA) which were found more sensitive to ultrasound stimulation than that of cortex. Knocking out the Piezo1 in CEA neurons showed a significant reduction of response under ultrasound stimulation while knocking out astrocytic Piezo1 showed no obvious changes in neuronal responses. Additionally, we excluded an auditory confound by monitoring auditory cortical activation and using smooth waveform ultrasound with randomized parameters to stimulate P1KO ipsilateral and contralateral regions of the same brain and recording evoked movement in the corresponding limb. Thus, we demonstrate that Piezo1 is functionally expressed in different brain regions, and that it is an important mediator of ultrasound neuromodulation in the brain, laying the ground for further mechanistic studies of ultrasound.

neuroscience↗

bioRxiv2023

Understanding and evaluating ambiguity in single-cell and single-nucleus RNA-sequencing

Recently, a new modification has been proposed by Hjorleifsson and Sullivan et al. to the model used to classify the splicing status of reads (as spliced (mature), unspliced (nascent), or ambiguous) in single-cell and single-nucleus RNA-seq data. Here, we evaluate both the theoretical basis and practical implementation of the proposed method. The proposed method is highly-conservative, and therefore, unlikely to mischaracterize reads as spliced (mature) or unspliced (nascent) when they are not. However, we find that it leaves a large fraction of reads classified as ambiguous, and, in practice, allocates these ambiguous reads in an all-or-nothing manner, and differently between single-cell and single-nucleus RNA-seq data. Further, as implemented in practice, the ambiguous classification is implicit and based on the index against which the reads are mapped, which leads to several drawbacks compared to methods that consider both spliced (mature) and unspliced (nascent) mapping targets simultaneously -- for example, the ability to use confidently assigned reads to rescue ambiguous reads based on shared UMIs and gene targets. Nonetheless, we show that these conservative assignment rules can be obtained directly in existing approaches simply by altering the set of targets that are indexed. To this end, we introduce the spliceu reference and show that its use with alevin-fry recapitulates the more conservative proposed classification. We also observe that, on experimental data, and under the proposed allocation rules for ambiguous UMIs, the difference between the proposed classification scheme and existing conventions appears much smaller than previously reported. We demonstrate the use of the new piscem index for mapping simultaneously against spliced (mature) and unspliced (nascent) targets, allowing classification against the full nascent and mature transcriptome in human or mouse in <3GB of memory. Finally, we discuss the potential of incorporating probabilistic evidence into the inference of splicing status, and suggest that it may provide benefits beyond what can be obtained from discrete classification of UMIs as splicing-ambiguous.

bioinformatics↗

bioRxiv2022

Perception of Rigidity in Three- and Four-Dimensional Spaces

Our brain employs mechanisms to adapt to changing visual conditions. In addition to natural changes in our physiology and those in the environment, our brain is also capable of adapting to "unnatural" changes, such as inverted visual-inputs generated by inverting prisms. In this study, we examined the brains capability to adapt to hyperspaces. We generated four spatial-dimensional stimuli in virtual reality and tested the ability to distinguish between rigid and non-rigid motion. We found that observers are able to differentiate rigid and non-rigid motion of tesseracts (4D) with a performance comparable to that obtained using cubes (3D). Moreover, observers performance improved when they were provided with more immersive 3D experience but remained robust against increasing shape variations. At this juncture, we characterize our findings as "[Formula] perception" since, while we show the ability to extract and use 4D information, we do not have yet evidence of a complete phenomenal 4D experience.

neuroscience↗

bioRxiv2022

Structural basis for intrinsic transcription termination

Efficient and accurate termination is required for gene transcription in all living organisms. Cellular RNA polymerases (RNAP) in both bacteria and eukaryotes can terminate their transcription through a factor-independent termination pathway (called intrinsic termination transcription in bacteria), in which RNAP recognizes terminator sequences, stops nucleotide addition, and releases nascent RNA spontaneously. Here we report a set of single-particle cryo-EM structures of E. coli transcription intrinsic termination complexes representing key intermediate states of the event. The structures show how RNAP pauses at terminator sequences, how the terminator RNA hairpin folds inside RNAP, and how RNAP rewinds the transcription bubble to release RNA and then DNA. These macromolecular snapshots define a structural mechanism for bacterial intrinsic termination and a pathway for RNA release and DNA collapse relevant for factor-independent termination by all RNA polymerases.

molecular biology↗

bioRxiv2022

Cryo-EM complex structure of active GPR75 with a nanobody

Although there has been enormous progress in the last half-century in the drug discovery targeting obesity and associated co-morbidities, the clinical treatment of obesity remains tremendously challenging. GPR75 is an orphan receptor and is suggested to be a potential novel target for the control of obesity and related metabolic disorders. Inhibition of the GPR75 signaling pathway by small molecules, antibodies, or genetic manipulations may provide a therapeutic strategy for obesity. Here, we report the active-like Cryo-EM structure of human GPR75 with an intracellular nanobody, which reveals the receptor activation mechanism. The extensive interaction network required to achieve the active structure helps explain the allosteric coupling between the orthosteric pocket and the G-protein coupling domain. The well-defined orthosteric ligand binding pocket of human GPR75 provides a structural basis for anti-obesity drug discovery.

biophysics↗

bioRxiv2021

Spinal reconsolidation engages non-ionotropic NMDA receptor signaling to reverse pain hypersensitivity

Reconsolidation enables the activity-dependent modification of memory traces and has been used to reverse addiction, fear memory, and pain hypersensitivity in animal models. We demonstrate that non-ionotropic NMDA receptor signalling in the spinal dorsal horn is sufficient to reverse pain hypersensitivity and necessary for pain modulation by spinal reconsolidation. These findings reveal a key process by which reconsolidation disrupts memory traces that may be exploited in the treatment of pain and other disorders.

neuroscience↗

bioRxiv2021

Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data

The rapid growth of high-throughput single-cell and single-nucleus RNA sequencing technologies has produced a wealth of data over the past few years. The available technologies continue to evolve and experiments continue to increase in both number and scale. The size, volume, and distinctive characteristics of these data necessitate the development of new software and associated computational methods to accurately and efficiently quantify single-cell and single-nucleus RNA-seq data into count matrices that constitute the input to downstream analyses. We introduce the alevin-fry framework for quantifying single-cell and single-nucleus RNA-seq data. Despite being faster and more memory frugal than other accurate and scalable quantification approaches, alevin-fry does not suffer from the false positive expression or memory scalability issues that are exhibited by other lightweight tools. We demonstrate how alevin-fry can be effectively used to quantify single-cell and single-nucleus RNA-seq data, and also how the spliced and unspliced molecule quantification required as input for RNA velocity analyses can be seamlessly extracted from the same pre-processed data used to generate regular gene expression count matrices.

bioinformatics↗

bioRxiv2021

The cardiac STAT3 intercalated disc specific expression in tail suspension rat

BackgroundThe cardiovascular system is significantly agitated by loss of gravity. In microgravity, the body fluids shift toward the thoracic cavity, induced the heart becomes more spherical. This further increased the cardiac preload with an increasing of transmural central venous pressure, affects the right heart ventricles to tolerating the enhanced preload on the right ventricular wall. MethodIn this study we investigated the rat right ventricle remodeling in simulating persistent microgravity by using tail-suspension model, examined the remolding of the heart and the specific STAT3 expression in right heart myocardium. ResultThe results indicated that microgravity induced heart remodeling included a significant increasing of the ventricular weight in the left. However, the right ventricle was not increased significantly in the microgravity simulation rats. The histological study demonstrated that the outstanding development on right ventricular wall which included the gap junction remodeling and STAT3 signaling protein specific accumulation in the right ventricles. ConclusionThe results existed that the right cardiac ventricle has a distinctive remodeling process during microgravity simulation which was not the muscular hypertrophy and relative weight increasing, but manifested the STAT3 accumulation and the electrical gap junction remodeling. The effect of microgravity induced right ventricle remodeling and the STAT3 specific accumulation can be used for multi-purpose research.

physiology↗

bioRxiv2021

CNS antigen-specific control of early B-lineage development in the meninges

The random V(D)J recombination of immunoglobulins (Ig) loci often creates autoreactive B cell progenitors expressing self-recognized B-cell receptors (BCRs)1, which are eliminated or inactivated through an autoantigen-dependent central tolerance checkpoint to prevent autoimmune reactions2,3, a process thought to be restricted to the bone marrow (BM) in the adult mammals4. Here we report that early developing B cells are also present in the meninges of mice at all ages. Single cell RNA-sequencing (scRNA-seq) analysis revealed a consecutive trajectory of meningeal developing B cells in mice and non-human primates (NHPs). Parabiosis together with lineage tracing of hematopoietic stem cells (HSCs) showed that meningeal developing B cells are continuously replenished from the HSC-derived progenitors via a circulationindependent route. Importantly, autoreactive immature B cells which recognize myelin oligodendrocyte glycoprotein (MOG)5, a central nervous system (CNS)-specific antigen, are eliminated from the meninges but not BM. Furthermore, genetic deletion of MOG restored the self-reactive B cells in the meninges. Thus, we propose that meninges function as a unique reservoir for B cell development, allowing in situ negative selection of CNS-antigen-autoreactive B cells to ensure a local non-self-reactive immune repertoire.

immunology↗

bioRxiv2021

Robust Prediction of Patient-Specific Clinical Response to Unseen Drugs From in vitro Screens Using Context-aware Deconfounding Autoencoder

Accurate and robust prediction of patient-specific responses to drug treatments is critical for drug development and personalized medicine. However, patient data are often too scarce to train a generalized machine learning model. Although many methods have been developed to utilize cell line data, few of them can reliably predict individual patient clinical responses to new drugs due to data distribution shift and confounding factors. We develop a novel Context-aware Deconfounding Autoencoder (CODE-AE) that can extract common biological signals masked by context-specific patterns and confounding factors. Extensive studies demonstrate that CODE-AE effectively alleviates the out-of-distribution problem for the model generalization, significantly improves accuracy and robustness over state-of-the-art methods in both predicting patient-specific ex vivo and in vivo drug responses purely from in vitro screens and disentangling intrinsic biological signals from confounding factors. Using CODE-AE, we screened 50 drugs for 9,808 cancer patients and discovered novel personalized anti-cancer therapies and drug-response biomarkers. Contact: lxie@iscb.org

bioinformatics↗

bioRxiv2021

Nonsense Mediated RNA Decay Is a Unique Vulnerability of Cancer Cells with SF3B1 and U2AF1 Mutations

Nonsense-mediated RNA decay (NMD) is well recognized as an RNA surveillance pathway that targets aberrant mRNAs with premature translation termination codons (PTCs) for degradation; however, its molecular mechanisms and roles in health and disease remain incompletely understood. In this study, we developed a novel reporter system that can accurately measure NMD activity in individual cells. By carrying out a genome-wide CRISPR/Cas9 knockout screen using this reporter system, we identified novel NMD-promoting factors, including multiple components of the SF3B complex and other U2 spliceosome factors. Interestingly, we also found that cells with mutations in the U2 spliceosome genes SF3B1 and U2AF1--which are commonly found in myelodysplastic syndrome (MDS) and cancers--have overall attenuated NMD activity. Furthermore, we found that compared to wild type cells, SF3B1 and U2AF1 mutant cells are more sensitive to NMD inhibition, a phenotype that is accompanied by elevated DNA replication obstruction, DNA damage and chromosomal instability. Remarkably, the sensitivity of spliceosome mutant cells to NMD inhibition could be rescued by overexpression of RNase H1, which removes R-loops in the genome. Together, our findings shed new light on the functional interplay between NMD and RNA splicing and suggest a novel strategy for the treatment of MDS and cancers with spliceosome mutations.

cell biology↗

bioRxiv2021

BoolSim, a Graphical Interface for Open Access Boolean Network Simulations and Use in Guard Cell CO2 Signaling

Signaling networks are at the heart of almost all biological processes. Most of these networks contain a large number of components and often the connections between these components are either not known, or the rate equations that govern the dynamics of soluble signaling components are not quantified. This uncertainty in network topology and parameters can make it challenging to formulate detailed mathematical models. Boolean networks, in which all components are either on or off, have emerged as viable alternatives to more detailed mathematical models but can be difficult to implement. Therefore, open source format of such models for community use is desirable. Here we present BoolSim, a freely available graphical user interface (GUI) that allows users to easily construct and analyze Boolean networks. BoolSim can be applied to any Boolean network. We demonstrate BoolSims application using a previously published network for abscisic acid-driven stomatal closure in Arabidopsis. We also show how BoolSim can be used to generate testable predictions by extending the network to include CO2 regulation of stomatal movements. Predictions of the model were experimentally tested and the model was iteratively modified based on experiments showing that ABA closes stomata even at near zero CO2 concentrations (1.5 ppm CO2). One Sentence SummaryThis study presents an open-source, graphical interface for the simulation of Boolean networks and applies it to an abscisic acid signaling network in guard cells, extended to include input from CO2.

plant biology↗

bioRxiv2020

Mammalian-unique eIF4E2 maintains GSK3β proline kinase activity to resist senescence against hypoxia

Cellular senescence is a stable state of cell cycle arrest elicited by various stresses. Hypoxia modulates senescence, but its consequences and implications in living organisms remains unknown. Here we identified the eIF4E2-GSK3{beta} pathway regulated by hypoxia to maintain p53 proline-directed phosphorylation (S/T-P) to prevent senescence. We previously knew that GSK3{beta} activates p53 translation through phosphorylation of RBM38 Ser195 (-Pro196). Unexpectedly, eIF4E2 directly binds to GSK3{beta} via a conserved motif, mediating Ser195 phosphorylation. Phosphoproteomics revealed that eIF4E2-GSK3{beta} specifically regulates proline-directed phosphorylation. Peptide e2-I or G3-I that disrupts this pathway dephosphorylates p53 at multiple S/T-P, which accelerate senescence by transcriptional suppressing TOPBP1 and TRX1. Consistently, peptides induce liver senescence that is rescued by TOPBP1 expression, and mediate senescence-dependent tumor regression. Furthermore, hypoxia inhibits eIF4E2-GSK3{beta}. Inspiringly, eIF4E2-GSK3{beta} is unique to mammals, which maintains mice viability and prevents liver senescence against physiological hypoxia. Interestingly, this mammalian eIF4E2 protects heart of zebrafish against hypoxia. Together, we identified a mammalian -unique eIF4E2-GSK3{beta} pathway preventing senescence and guarding against hypoxia in vivo.

cell biology↗

bioRxiv2020

MicroRNA variants and HLA-miRNA interactions are novel rheumatoid arthritis susceptibility factors

ObjectiveAlthogh Genome-wide association studies have identified >100 variants for rheumatoid arthritis (RA),the reported genetic variants only explain <40% of RA heritability. We conducted a systemic association study between common East-Asian miRNA SNPs with RA in a large Han Chinese cohort to explain missing heritability and identify miRNA epistatic interactions. Methods4 HLA SNPs (HLA-DRB1, HLA-DRB9, HLA-DQB1 and TNFAIP3) and 225 common SNPs located in miRNA which might influence the miRNA target binding or pre-miRNA stability were genotyped in 1,607 rheumatoid arthritis and 1,580 matched normal individuals. A meta-analysis with previous GWAS studies (4,873 RA cases and 17,642 controls) was performed to discovery another novel miRNA RA-associated SNPs. Results2 novel SNPs including rs1414273 (miR-548ac, OR=0.84, P=8.26x10-4) and rs2620381 (miR-627, OR=0.77, P=2.55x10-3) conferred significant association with RA. Individuals carried 8 risk alleles showed 15.38 (95%CI: 4.69-50.49, P<1.0x10-6) times more risk to be affected by RA. In addition, rs5997893 (miR-3928) showed significant epistasis effect with rs4947332 (HLA-DRB1, OR=4.23, P=0.04) and rs2967897 (miR-5695) with rs7752903 (TNFAIP3, OR=4.43, P=0.03). Finally, we demonstrated targets of the significant miRNAs showed enrichment in immune related genes (P=2.0x10-5) and FDA approved drug target genes (P=0.014). Conclusions6 novel miRNA SNPs including rs1414273 (miR-548ac, P=8.26x10-4), rs2620381 (miR-627, P=2.55x10-3), rs4285314 (miR-3135b, P=1.10x10-13), rs28477407 (miR-4308, P=3.44x10-5), rs5997893 (miR-3928, P=5.9x10-3) and rs45596840 (miR-4482, P=6.6x10-3) were confirmed to be significantly associated with RA in a Chinese population. Our study suggests that miRNAs might be interesting targets to accelerate the understanding of the pathogenesis and drug development for rheumatoid arthritis.

genetics↗

bioRxiv2020

PacC-dependent adaptation and modulation of host cellular pH controls hemibiotrophic invasive growth and disease development by the rice blast fungus

Many of the worlds most serious crop diseases are caused by hemibiotrophic fungi. These pathogens have evolved the ability to colonize living plant cells, suppressing plant immunity responses, before switching to necrotrophic growth, in which host cells die, providing the energy to fuel sporulation and spread of the fungus. How hemibiotrophic pathogens switch between these two lifestyles remains poorly understood. Here, we report that the devastating rice blast fungus, Magnaporthe oryzae, manipulates host cellular pH to regulate hemibiotrophy. During infection by M. oryzae, host plant cells are alkalinized to pH 7.8 during biotrophic growth, but later acidified to pH 6.5 during necrotrophy. Using a forward genetic screen, we identified alkaline-sensitive mutants of M. oryzae that were blocked in biotrophic proliferation and impaired in induction of host cell acidification and necrotrophy. These mutants defined components of the PacC-dependent ambient pH signal transduction pathway in M. oryzae. We report that PacC exists as a full-length repressor, PacC559, and a truncated transcriptional activator, PacC222, which localize to the fungal nucleus during biotrophic growth and to the cytoplasm during necrotrophy. During biotrophy, PacC222 directly activates genes associated with nutrient acquisition and fungal virulence, while PacC559 represses genes associated with saprophytic mycelial growth and sporulation, which are subsequently de-repressed during necrotrophy. When considered together, our results indicate that temporal regulation of hemibiotrophy by M. oryzae requires PacC-dependent sensing and manipulation of host cellular pH. Author SummaryCrop diseases caused by fungi represent some of the most serious threats to global food security. Many fungal pathogens have evolved the ability to invade living plant tissue and suppress host immunity, before switching to a completely different mode of growth, in which they are able to kill host plant cells. This lifestyle- called hemibiotrophy -is exemplified by the blast fungus, Magnaporthe oryzae, which causes devastating diseases of rice, wheat and many other grasses. We found that during infection by M. oryzae, host cells initially have an alkaline pH, when the fungus is growing in living tissue, but pH rapidly becomes acidic, as host tissue is killed. We identified mutants of the blast fungus that were sensitive to alkaline pH and this enabled us to identify the signal transduction pathway by which the fungus responds to changes in ambient pH. We found that mutants in the pH response pathway were blocked in invasive fungal growth and could not cause acidification of host tissue. Consequently, they are unable to cause blast disease. We characterized the central regulator of this pathway, the PacC transcription factor, which unusually can act as both a repressor and an activator of fungal gene expression. During biotrophic invasive growth, PacC activates many genes previously reported to be required for virulence, including several associated with nutrient acquisition, and at the same time represses genes associated with vegetative growth and sporulation. The PacC signaling pathway is therefore necessary for regulating the switch in fungal lifestyle associated with causing blast disease.

microbiology↗