Biology subjects

Xu, J.

Publications and source records attributed to Xu, J..

At least 721 records · Page 40Linked to original sources

bioRxiv2020

Interaction network of SARS-CoV-2 with host receptome through spike protein

Host cellular receptors are key determinants of virus tropism and pathogenesis. Virus utilizes multiple receptors for attachment, entry, or specific host responses. However, other than ACE2, little is known about SARS-CoV-2 receptors. Furthermore, ACE2 cannot easily interpret the multi-organ tropisms of SARS-CoV-2 nor the clinical differences between SARS-CoV-2 and SARS-CoV. To identify host cell receptors involved in SARS-CoV-2 interactions, we performed genomic receptor profiling to screen almost all human membrane proteins, with SARS-CoV-2 capsid spike (S) protein as the target. Twelve receptors were identified, including ACE2. Most receptors bind at least two domains on S protein, the receptor-binding-domain (RBD) and the N-terminal-domain (NTD), suggesting both are critical for virus-host interaction. Ectopic expression of ASGR1 or KREMEN1 is sufficient to enable entry of SARS-CoV-2, but not SARS-CoV and MERS-CoV. Analyzing single-cell transcriptome profiles from COVID-19 patients revealed that virus susceptibility in airway epithelial ciliated and secretory cells and immune macrophages highly correlates with expression of ACE2, KREMEN1 and ASGR1 respectively, and ACE2/ASGR1/KREMEN1 (ASK) together displayed a much better correlation than any individual receptor. Based on modeling of systemic SARS-CoV-2 host interactions through S receptors, we revealed ASK correlation with SARS-CoV-2 multi-organ tropism and provided potential explanations for various COVID-19 symptoms. Our study identified a panel of SARS-CoV-2 receptors with diverse binding properties, biological functions, and clinical correlations or implications, including ASGR1 and KREMEN1 as the alternative entry receptors, providing insights into critical interactions of SARS-CoV-2 with host, as well as a useful resource and potential drug targets for COVID-19 investigation.

microbiology↗

bioRxiv2020

Whole-brain functional connectivity neuromarkers uncover the cognitive recovery scheme for overt hepatic encephalopathy after liver transplantation

Neurocognitive impairment is present in cirrhosis and may be more severe in cirrhosis with the overt hepatic encephalopathy (OHE). Liver transplantation (LT) may reverse the impaired brain function. MRI of resting-state functional connectivity can help unravel the underlying mechanisms that lead to these cognitive deficits and recovery. Sixty-four cirrhotic patients (28 with OHE; 36 without) and 32 healthy controls were recruited for resting-state fMRI. The patients were scanned before and after LT. We evaluated pre- and postsurgical neurocognitive performance in cirrhotic patients using psychomotor tests, i.e. number connection test (NCT) and digit symbol test (DST). Network-based statistics found significant disrupted connectivity in both groups of cirrhosis with OHE and without compared to controls. However, the presurgical connectivity disruption in patients with OHE was included in a greater number of connections than those without (65 vs. 17). The decrease in FC for both OHE and non-OHE patient groups was reversed to the level of controls after LT. An additional hyperconnected network (i.e., higher than controls) was observed in OHE patients after LT (p=0.009). Regarding the neural-behavior relationship, the functional network that predicted cognitive performance in healthy individuals, showed no correlation in presurgical cirrhotic patients. Such an impaired neural-behavior relationship was re-established after LT for non-OHE patients but not for OHE. OHE patients displayed abnormal hyperconnectivity and persistently impaired neural-behavior relationship after LT. Our results suggest that patients with OHE may undergo a different trajectory of postsurgical neurofunctional recovery in comparison to those without, which needs further clarification in the future study.

neuroscience↗

bioRxiv2020

Weighted RSA: an improved framework on the perception of audio-visual affective speech in left insula and superior temporal gyrus

Being able to accurately perceive the emotion expressed by the facial or verbal expression from others is critical to successful social interaction. However, only few studies examined the multimodal interactions on speech emotion, and there is no consistence in studies on the speech emotion perception. It remains unclear, how the speech emotion of different valence is perceived on the multimodal stimuli by our human brain. In this paper, we conducted a functional magnetic resonance imaging (fMRI) study with an event-related design, using dynamic facial expressions and emotional speech stimuli to express different emotions, in order to explore the perception mechanism of speech emotion in audio-visual modality. The representational similarity analysis (RSA), whole-brain searchlight analysis, and conjunction analysis of emotion were used to interpret the representation of speech emotion in different aspects. Significantly, a weighted RSA approach was creatively proposed to evaluate the contribution of each candidate model to the best fitted model. The results of weighted RSA indicated that the fitted models were superior to all candidate models and the weights could be used to explain the representation of ROIs. The bilateral amygdala has been shown to be associated with the processing of both positive and negative emotions except neutral emotion. It is indicated that the left posterior insula and the left anterior superior temporal gyrus (STG) play important roles in the perception of multimodal speech emotion.

neuroscience↗

bioRxiv2020

Root growth responses to mechanical impedance are regulated by a network of ROS, ethylene and auxin signalling in Arabidopsis.

O_LIThe growth and development of root systems, essential for plant performance, is influenced by mechanical properties of the substrate in which the plants grow. Mechanical impedance, such as by compacted soil, can reduce root elongation and limit crop productivity. C_LIO_LITo understand better the mechanisms involved in plant root responses to mechanical impedance stress, we investigated changes in the root transcriptome and hormone signalling responses of Arabidopsis to artificial root barrier systems in vitro. C_LIO_LIWe demonstrate that upon encountering a barrier, reduced Arabidopsis root growth and the characteristic step-like growth pattern is due to a reduction in cell elongation associated with changes in signalling gene expression. Data from RNA-sequencing combined with reporter line and mutant studies identified essential roles for reactive oxygen species, ethylene and auxin signalling during the barrier response. C_LIO_LIWe propose a model in which early responses to mechanical impedance include reactive oxygen signalling that is followed by integrated auxin and ethylene responses to mediate root growth changes. Inhibition of ethylene responses allows improved growth in response to root impedance, a result that may inform future crop breeding programmes. C_LI

plant biology↗

bioRxiv2020

Integrative proteomics reveals exceptional diversity and versatility of mammalian humoral immunity

The humoral immune response is essential for the survival of mammals. However, we still lack a systematic understanding of the specific serologic antibody repertoire in response to an antigen. We developed a proteomic strategy to survey, at an unprecedented scale, the landscapes of antigen-engaged, serum-circulating repertoires of camelid heavy-chain antibodies (hcAbs). The sensitivity and robustness of this technology were validated using three antigens spanning orders of magnitude in immune response; thousands of divergent, high-affinity hcAb families were confidently identified and quantified. Using high-throughput structural modeling, cross-linking mass spectrometry, mutagenesis, and deep learning, we mapped and analyzed the epitopes of > 100,000 antigen-antibody complexes. Our results revealed a surprising diversity of high-affinity hcAbs for specific antigen binding on a variety of dominant epitopes. hcAbs perfect both shape and charge complementarity to target challenging antigens specifically; they can rapidly evolve to recognize a conserved, promiscuous cellular protein interaction interface, unraveling the convergent force that drives protein-protein interactions.

bioengineering↗

bioRxiv2020

SARS-CoV-2 Quasispecies provides insight into its genetic dynamics during infection

A novel coronavirus disease (COVID-19) caused by SARS-CoV-2 has been pandemic worldwide. The genetic dynamics of quasispecies afford RNA viruses a great fitness on cell tropism and host range. However, no quasispecies data of SARS-CoV-2 have been reported yet. To explore quasispecies haplotypes and its transmission characteristics, we carried out single-molecule real-time (SMRT) sequencing of the full-length of SARS-CoV-2 spike gene within 14 RNA samples from 2 infection clusters, covering first-to third-generation infected-patients. We observed a special quasispecies structure of SARS-CoV-2 (modeled as One-King): one dominant haplotype (mean abundance ~70.15%) followed by numerous minor haplotypes (mean abundance < 0.10%). We not only discovered a novel dominant haplotype of F1040 but also realized that minor quasispecies were also worthy of attention. Notably, some minor haplotypes (like F1040 and currently pandemic one G614) could potentially reveal adaptive and converse into the dominant one. However, minor haplotypes exhibited a high transmission bottleneck (~6% could be stably transmitted), and the new adaptive/dominant haplotypes were likely originated from genetic variations within a host rather than transmission. The evolutionary rate was estimated as 2.68-3.86 x 10-3 per site per year, which was larger than the estimation at consensus genome level. The One-King model and conversion event expanded our understanding of the genetic dynamics of SARS-CoV-2, and explained the incomprehensible phenomenon at the consensus genome level, such as limited cumulative mutations and low evolutionary rate. Moreover, our findings suggested the epidemic strains may be multi-host origin and future traceability would face huge difficulties.

pathology↗

bioRxiv2020

rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated tool for Genome-Wide Association Study

Along with the development of high-throughout sequencing technologies, both sample size and number of SNPs are increasing rapidly in Genome-Wide Association Studies (GWAS) and the associated computation is more challenging than ever. Here we present a Memory-efficient, Visualization-enhanced, and Parallel-accelerated R package called "rMVP" to address the need for improved GWAS computation. rMVP can: (1) effectively process large GWAS data; (2) rapidly evaluate population structure; (3) efficiently estimate variance components by EMMAX, FaST-LMM, and HE regression algorithms; (4) implement parallel-accelerated association tests of markers using GLM, MLM, and FarmCPU methods; (5) compute fast with a globally efficient design in the GWAS processes; and (6) generate various visualizations of GWAS related information. Accelerated by block matrix multiplication strategy and multiple threads, the association test methods embedded in rMVP are approximately 5-20 times faster than PLINK, GEMMA, and FarmCPU_pkg. rMVP is freely available at https://github.com/xiaolei-lab/rMVP.

genetics↗

bioRxiv2020

Peptide Antidotes to SARS-CoV-2 (COVID-19)

The design of an immunogenic scaffold that serves a role in treating a pathogen, and can be rapidly and predictively modeled, has remained an elusive feat. Here, we demonstrate that SARS-BLOCK synthetic peptide scaffolds act as antidotes to SARS-CoV-2 spike protein-mediated infection of human ACE2-expressing cells. Critically, SARS-BLOCK peptides are able to potently and competitively inhibit SARS-CoV-2 S1 spike protein receptor binding domain (RBD) binding to ACE2, the main cellular entry pathway for SARS-CoV-2, while also binding to neutralizing antibodies against SARS-CoV-2. In order to create this potential therapeutic antidote-vaccine, we designed, simulated, synthesized, modeled epitopes, predicted peptide folding, and characterized behavior of a novel set of synthetic peptides. The biomimetic technology is modeled off the receptor binding motif of the SARS-CoV-2 coronavirus, and modified to provide enhanced stability and folding versus the truncated wildtype sequence. These novel peptides attain single-micromolar binding affinities for ACE2 and a neutralizing antibody against the SARS-CoV-2 receptor binding domain (RBD), and demonstrate significant reduction of infection in nanomolar doses. We also demonstrate that soluble ACE2 abrogates binding of RBD to neutralizing antibodies, which we posit is an essential immune-evasive mechanism of the virus. SARS-BLOCK is designed to "uncloak" the viral ACE2 coating mechanism, while also binding to neutralizing antibodies with the intention of stimulating a specific neutralizing antibody response. Our peptide scaffolds demonstrate promise for future studies evaluating specificity and sensitivity of immune responses to our antidote-vaccine. In summary, SARS-BLOCK peptides are a promising COVID-19 antidote designed to combine the benefits of a therapeutic and vaccine, effectively creating a new generation of prophylactic and reactive antiviral therapeutics whereby immune responses can be enhanced rather than blunted.

bioengineering↗

bioRxiv2020

Impaired learning and memory ability induced by a bilaterally hippocampal injection of streptozotocin in mice: involved with the adaptive changes of synaptic plasticity

BackgroundAlzheimers disease (AD) is a neurodegenerative disease characterized by progressive cognitive decline, psychiatric symptoms and behavioral disorders, resulting in disability and loss of self-sufficiency. ObjectiveTo establish an AD mice model, investigate the behavioral performance, and explore the potential mechanism. MethodsStreptozotocin (STZ, 3 mg/kg) was microinjected bilaterally into the dorsal hippocampus of C57BL /6 mice to establish the AD model. Behavioral changes (anhedonia and despair, balance and motor coordination, locomotion, and learning and memory) were examined and the serum concentrations of insulin and nesfatin-1 were measured by ELISA. The activation of hippocampal microglia was assessed by immunohistochemistry and the protein expression of several molecular associated with the regulation of synaptic plasticity in the hippocampus and the prefrontal cortex (PFC) was detected via western blotting. ResultsThe STZ model mice showed a slower bodyweight gain and higher serum concentration of insulin and nesfatin-1. Although there was no significant difference between groups with regard to the ability of balance and motor coordination, the model mice presented a decline of spontaneous movement and exploratory behavior, together with an impairment of learning and memory ability. Increased activated microglia was aggregated in the hippocampal dentate gyrus of model mice. Moreover, the protein expression of NMDAR2A, NMDAR2B, SynGAP, PSD95, BDNF, and p-{beta}-catenin/{beta}-catenin were remarkably decreased in the hippocampus and the PFC of model mice, and the expression of p-GSK-3{beta} (ser9)/GSK-3{beta} were reduced in the hippocampus. ConclusionA bilateral hippocampal microinjection of STZ could successfully duplicate an AD mice model, as indicated by the impaired learning and memory and the alternated synaptic plasticity, together with the hyperactive inflammatory response in the hippocampus and the imbalanced abundance of serum insulin and nesfatin-1. Apart from these, the mechanism might be associated with the imbalanced expression of the key proteins of Wnt signaling pathway in the hippocampus and the PFC. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/235481v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@181c9a9org.highwire.dtl.DTLVardef@1deaa4forg.highwire.dtl.DTLVardef@17f3f09org.highwire.dtl.DTLVardef@1037c21_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2020

Fire effect and its legacy modulate soil bacterial and fungal communities in Chinese boreal forests along a chronosequence

Wildfire has increasingly profound and pervasive consequences for forest ecosystems via directly altering soil physicochemical properties and modulating microbial community. In this study, we examined the changes in soil properties and microbial community at different periods after highly severe wildfire events (44 plots, 113 samples) in the Chinese Great Khingan Mountains. We also separated charcoals from burnt soils to establish the relationship between soil microbes and the microbes colonized on the charcoal. Wildfire significantly altered bacterial and fungal community structures across a 29-year chronosequence. The network analysis revealed that from 17 years after fire, the complexity and connectivity of bacterial and fungal communities were significantly increased. Differential abundance analysis suggested that bacterial and fungal OTUs were enriched or depleted only during 0-4 years after fire. In addition, soil factors, including soil pH, total C and N, soil water content, and dissolved C and N, are key determinants of soil bacterial and fungal communities from 17 years after fire. The fire-derived charcoals provided a new and unusual niche for microbial colonization and charcoal microbes had a significantly different community structure from the burnt soil microbes. Our data suggest that soil bacterial and fungal communities changed dramatically during the recovery from fire events in terms of the abundance and co-occurrence networks in the boreal forest ecosystems. ImportancePervious research has reported fire altered soil microbial community composition and function during short-term succession in boreal forests. However, the long-term effect of fire and fire-derived charcoals which are regarded as fire legacy effect on soil bacterial and fungal communities composition and structure have not previously been shown. Understanding how soil microbes particularly the keystone taxa and determinative soil factors, respond to fire and its legacy matter charcoal, is critical for predicting how future fire influences soil nutrient transformations and biological processes. We accessed time chronosequence to examine the effect of fire history on soil microbial abundance and co-occurrence network. These findings suggest that soil microbes can be reshaped by fire and its legacy effect of fire-derived charcoal even in the long periods after fire and provide further insights into fire and its legacy effect.

ecology↗

bioRxiv2020

Genomic insights into the host specific adaptation of the Pneumocystis genus and emergence of the human pathogen Pneumocystis jirovecii

Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals novel insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans.

evolutionary biology↗

bioRxiv2020

Direct medium-chain carboxylic-acid oil separation from a bioreactor by an electrodialysis/phase separation cell

Medium-chain carboxylic acids (MCCAs) are valuable platform chemicals with numerous industrial-scale applications. These MCCAs can be produced from waste biomass sources or syngas fermentation effluent through an anaerobic fermentation process called chain elongation. We have previously demonstrated successful approaches to separate >90%-purity oil with several MCCAs by integrating the anaerobic bioprocess with membrane-based liquid-liquid extraction (pertraction) and membrane electrolysis. However, membrane electrolysis without pertraction was not able to separate MCCA oil. Therefore, we developed an electrodialysis/phase separation cell (ED/PS) and evaluated whether it can function as a stand-alone extraction and separation unit. First, we tested an ED/PS cell, which, when evaluated in series with pertraction, achieved a maximum MCCA-oil flux of 1,665 g d-1 per projected area (m2) (19.3 mL oil d-1) and a MCCA-oil transfer efficiency [100%*moles MCCA-oil moles electrons-1] of 74% at 15 A m-2. This extraction system demonstrated a [~]10 times lower electric-power consumption of 1.05 kWh kg-1 MCCA oil when compared to membrane electrolysis in series with pertration (11.1 kWh kg-1 MCCA oil) at 15 A m-2. Second, we evaluated our ED/PS as a stand-alone unit when integrated with the anaerobic bioprocess (without pertraction), and demonstrated that we can selectively extract and separate MCCA oil directly from chain-elongating bioreactor broth with just an abiotic electrochemical cell. We assumed that such a stand-alone unit would reduce capital and operating costs, but electric-power consumption increased considerably due to the lower MCCA concentrations in the bioreactor broth compared to the pertraction broth. Only a full techno-economic analysis will be able to determine whether the use of the ED/PS cell should be as a stand-alone unit or after pertraction.

bioengineering↗

bioRxiv2020

Virus-free and live-cell visualizing SARS-CoV-2 cell entry for studies of neutralizing antibodies and compound inhibitors

The ongoing COVID-19 pandemic, caused by SARS-CoV-2 infection, has resulted in hundreds of thousands of deaths. Cellular entry of SARS-CoV-2, which is mediated by the viral spike protein and host ACE2 receptor, is an essential target for the development of vaccines, therapeutic antibodies, and drugs. Using a mammalian cell expression system, we generated a recombinant fluorescent protein (Gamillus)-fused SARS-CoV-2 spike trimer (STG) to probe the viral entry process. In ACE2-expressing cells, we found that the STG probe has excellent performance in the live-cell visualization of receptor binding, cellular uptake, and intracellular trafficking of SARS-CoV-2 under virus-free conditions. The new system allows quantitative analyses of the inhibition potentials and detailed influence of COVID-19-convalescent human plasmas, neutralizing antibodies and compounds, providing a versatile tool for high-throughput screening and phenotypic characterization of SARS-CoV-2 entry inhibitors. This approach may also be adapted to develop a viral entry visualization system for other viruses.

microbiology↗

bioRxiv2020

Lineage recording of zebrafish embryogenesis reveals historical and ongoing lineage commitments

It has been challenging to characterize the lineage relationships among cells in vertebrates, which comprise a great number of cells. Fortunately, recent progress has been made by combining the CRISPR barcoding system with single-cell sequencing technologies to provide an unprecedented opportunity to track lineage at single-cell resolution. However, due to errors and/or dropouts introduced by amplification and sequencing, reconstruction of accurate lineage relationships in complex organisms remains a challenge. Thus, improvements in both experimental design and computational analysis are necessary for lineage inference. In this study, we employed single-cell Lineage tracing On Endogenous Scarring Sites (scLOESS), a lineage recording strategy based on the CRISPR-Cas9 system, to trace cell fate commitments for zebrafish larvae. With rigorous quality control, we demonstrated that lineage commitments of complex organisms could be inferred from a limited number of barcoding sites. Together with cell-type characterization, our method could homogenously recover lineage information. In combination with the cell-type and lineage information, we depicted the development histories for germ layers as well as cell types. Furthermore, when combined with trajectory analysis, our methods could capture and resolve the ongoing lineage commitment events to gain further biological insights into later development and differentiation in complex organisms.

developmental biology↗

bioRxiv2020

SETD2 deficiency impairs β-catenin destruction complex to facilitate renal cell carcinoma formation

Clear cell renal cell carcinoma (ccRCC) is a largely incurable disease that is highly relevant to epigenetic regulation including histone modification and DNA methylation. SET domain-containing 2 (SETD2) is a predominant histone methyltransferase catalyzing the trimethylation of histone H3 Lysine 36 (H3K36me3) and its mutations are highly relevant to clear cell renal cell carcinoma (ccRCC). However, its physiology role in ccRCC remains largely unexplored. Here we report that Setd2 deletion impairs the {beta}-catenin destruction complex to facilitate ccRCC formation in a c-MYC-generated polycystic kidney disease (PKD) model, which can be relieved by an inhibitor of {beta}-catenin-responsive transcription. Clinically, SETD2 loss is widely observed in ccRCC samples, and negatively correlated with expression of some members of {beta}-catenin destruction complex, but positively correlated with the activation of Wnt/{beta}-catenin signaling. Our findings thus highlight a previously unrecognized role of SETD2-mediated H3K36me3 modification in regulation of Wnt/{beta}-catenin pathway in ccRCC. SummaryOur findings for the first time reveal a previously unrecognized role of the SETD2-mediated H3K36me3 modification in regulation of the Wnt/{beta}-catenin pathway in ccRCC and shed light on the molecular mechanisms underlying the formation of renal cell carcinoma with epigenetic disorders.

cancer biology↗

bioRxiv2020

The Histone Methyltransferase SETD2 Modulates Oxidative Stress to Attenuate Colonic Inflammation and Tumorigenesis in Mice

BACKGROUND & AIMSInflammatory bowel disease (IBD) is a complex and relapsing inflammatory disease, and patients with IBD exhibit a higher risk of developing colorectal cancer (CRC). Epithelial barrier disruption is one of the major causes of IBD in which epigenetic modulation is pivotal. However, the epigenetic mechanisms underlying the epithelial barrier integrity regulation remain largely unexplored. Here, we investigated how SETD2, an epigenetic modifier, maintains intestinal epithelial homeostasis and attenuates colonic in[fl]ammation and tumorigenesis. METHODSGEO public database and IBD tissues were used to investigate the clinical relevance of SETD2 in IBD. To define a role of SETD2 in the colitis, we generated mice with epithelium-specific deletion of Setd2 (Setd2Vil-KO mice). Acute colitis was induced by 2% dextran sodium sulfate (DSS), and colitis-associated CRC was induced by injecting azoxymethane (AOM), followed by three cycles of 2% DSS treatments. Colon tissues were collected from mice and analyzed by histology, immunohistochemistry and immunoblots. Organoids were generated from Setd2Vil-KO and control mice, and were stained with 7-AAD to detect apoptosis. A fluorescent probe, 2',7'-dichlorodihydro[fl]uorescein diacetate (H2DCFDA), was used to detect the levels of ROS in intestinal epithelial cells (IECs) isolated from the two types of mice. RNA-seq and H3K36me3 ChIP-seq analyses were performed to identify the mis-regulated genes modulated by SETD2. Results were validated in functional rescue experiments by N-acetyl-l-cysteine (NAC) treatment and transgenes expression in IECs. RESULTSSETD2 expression became decreased in IBD patients and DSS-treated colitis mice. Setd2Vil-KO mice displayed abnormal loss of mucus-producing goblet cells and antimicrobial peptide (AMP)-producing Paneth cells, and exhibited pre-mature intestinal inflammation development. Consistent with the reduced SETD2 expression in IBD patients, Setd2Vil-KO mice showed increased susceptibility to DSS-induced colitis, accompanied by more severe epithelial barrier disruption and markedly increased intestinal permeability that subsequently facilitated in[fl]ammation-associated CRC. Mechanistically, deletion of Setd2 resulted in excess reactive oxygen species (ROS), which led to cellular apoptosis and defects in barrier integrity. NAC treatment in Setd2Vil-KO mice rescued epithelial barrier injury and apoptosis. Importantly, Setd2 depletion led to excess ROS by directly down-regulating antioxidant genes that inhibit ROS reaction. Moreover, overexpression of antioxidant PRDX6 in Setd2Vil-KO IECs largely alleviated the overproductions of ROS and improved the cellular survival. CONCLUSIONSDeficiency of Setd2 specifically in the intestine aggravates epithelial barrier disruption and inflammatory response in colitis via a mechanism dependent on oxidative stress. Thus, our results highlight an epigenetic mechanism by which Setd2 modulates oxidative stress to regulate intestinal epithelial homeostasis. SETD2 might therefore be a pivotal regulator that maintains the homeostasis of the intestinal mucosal barrier.

cell biology↗

bioRxiv2020

Smoothened Transduces Hedgehog Signals via Activity-Dependent Sequestration of PKA Catalytic Subunits

ABSTRACTThe Hedgehog (Hh) pathway is essential for organ development, homeostasis, and regeneration. Dysfunction of this cascade drives several cancers. To control expression of pathway target genes, the G protein-coupled receptor (GPCR) Smoothened (SMO) activates glioma-associated (GLI) transcription factors via an unknown mechanism. Here we show that, rather than conforming to traditional GPCR signaling paradigms, SMO activates GLI by binding and sequestering protein kinase A (PKA) catalytic subunits at the membrane. This sequestration, triggered by GPCR kinase 2 (GRK2)-mediated phosphorylation of SMO intracellular domains, prevents PKA from phosphorylating soluble substrates, releasing GLI from PKA-mediated inhibition. Our work provides a mechanism directly linking Hh signal transduction at the membrane to GLI transcription in the nucleus. This process is more fundamentally similar between species than prevailing hypotheses suggest. The mechanism described here may apply broadly to other GPCR- and PKA-containing cascades in diverse areas of biology.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biochemistry↗

bioRxiv2020

BBB pathophysiology independent delivery of siRNA in traumatic brain injury

Small interfering RNA (siRNA) represents a powerful strategy to mitigate the long-term sequelae of traumatic brain injury (TBI). However, poor permeability of siRNA across the blood brain barrier (BBB) poses a major hurdle. One approach to overcome this challenge involves treatment administration while the BBB is physically breached post-injury. However, this approach is only applicable to a subset of injuries with substantial BBB breach and can lead to variable therapeutic response due to the heterogeneity of physical breaching of BBB in TBI. Moreover, since physical breaching of BBB is transient, this approach offers a limited window for therapeutic intervention, which is not ideal as repeated dosing beyond the transient window of physically breached BBB might be required. Herein, we report a nanoparticle platform for BBB pathophysiology-independent delivery of siRNA in TBI. We achieved this by combined modulation of surface chemistry and coating density, which maximized the active transport of nanoparticles across BBB. Intravenous injection of engineered nanoparticles, within or outside the window of physically breached BBB in TBI mice resulted in 3-fold higher brain accumulation compared to conventional PEGylated nanoparticles and demonstrated up to 50% gene silencing. To our knowledge, this is the first reported example of BBB pathophysiology-independent drug delivery in TBI, and the first time combined modulation of surface chemistry and coating density has been shown to tune BBB penetration of nanoparticles. Taken together, our approach offers a clinically relevant approach to develop siRNA therapeutics for preventing long-term effects of TBI and deserves further exploration.Competing Interest StatementJMK has been a paid consultant and or equity holder for multiple biotechnology companies (listed here https://www.karplab.net/team/jeff-karp). The interests of JMK were reviewed and are subject to a management plan overseen by his institutions in accordance with its conflict of interest policies. N.J., J.MK., W.L., R.M., J.Q. and R.L. have one unpublished patent based on the nanoparticle work presented in this manuscript. For a list of entities with which R.L. is involved, compensated or uncompensated, see www.dropbox.com/s/yc3xqb5s8s94v7x/Rev%20Langer%20COI.pdf?dl=0.View Full Text

bioengineering↗