Biology subjects

Xu, H.

Publications and source records attributed to Xu, H..

At least 19 recordsLinked to original sources

bioRxiv2018

Actomyosin-mediated nanostructural remodeling of the presynaptic vesicle pool by cannabinoids induces long-term depression

Endo- and exocannabinoids, such as the psychoactive component of marijuana, exert their effects on brain function by inducing several forms of synaptic plasticity through the modulation of presynaptic vesicle release. However, the molecular mechanisms underlying the widely expressed endocannabinoid-mediated long-term depression (eCB-LTD), are poorly understood. Here, we reveal that eCB-LTD depends on the contractile properties of the pre-synaptic actomyosin cytoskeleton. Preventing this contractility, both directly by inhibiting non-muscle myosin II NMII ATPase and indirectly by inhibiting the upstream Rho-associated kinase ROCK, abolished long-term, but not short-term forms of cannabinoid-induced functional plasticity in both inhibitory hippocampal and excitatory cortico-striatal synapses. Furthermore, using 3D superresolution microscopy, we find an actomyosin contractility-dependent redistribution of synaptic vesicle pools within the presynaptic compartment following cannabinoid receptor activation, leading to vesicle clustering and depletion from the pre-synaptic active zone. These results suggest that cannabinoid-induced functional plasticity is mediated by a nanoscale structural reorganization of the presynaptic compartment produced by actomyosin contraction. By introducing the contractile NMII as an important actin binding/structuring protein in the dynamic regulation of synaptic function, our results open new perspectives in the understanding of mechanisms of synaptic and cognitive function, marijuana intoxication and psychiatric pathogenesis.

neuroscience↗

bioRxiv2018

Proteomic Profile of TGF-β1 treated Lung Fibroblasts identifies Novel Markers of Activated Fibroblasts in the Silica Exposed Rat Lung

We performed liquid chromatography-tandem mass spectrometry (LC-MS/MS) on control and TGF-{beta}1-exposed rat lung fibroblasts to identify proteins differentially expressed between cell populations. A total of 1648 proteins were found to be differentially expressed in response to TGF-{beta}1 treatment and 196 proteins were expressed at [≥] 1.2 fold relative to control. Guided by these results, we next determined whether similar changes in protein expression were detectable in the rat lung after chronic exposure to silica dust. Of the five proteins selected for further analysis, we found that levels of all proteins were markedly increased in the silica-exposed rat lung, including the proteins for the very low density lipoprotein receptor (VLDLR) and the transmembrane (type I) heparin sulfate proteoglycan called syndecan 2 (SDC2). Because VLDLR and SDC2 have not, to our knowledge, been previously linked to the pathobiology of silicosis, we next examined whether knockdown of either gene altered responses to TGF-{beta}1 in MRC-5 lung fibroblasts. Interestingly, we found knockdown of either VLDLR or SDC2 dramatically reduced collagen production to TGF-{beta}1, suggesting that both proteins might play a novel role in myofibroblast biology and pathogenesis of silica-induced pulmonary fibrosis. In summary, our findings suggest that performing LC-MS/MS on TGF-{beta}1 stimulated lung fibroblasts can uncover novel molecular targets of activated myofibroblasts in silica-exposed lung.\n\nHighlightsWe identified 196 proteins differentially expressed between control and TGF-{beta}1 treated fibroblastsby LC-MS/MS.\n\nSeveral proteins identified by LC-MS/MS were also found to be differentially expressed in whole lung tissues and isolated fibroblasts after chronic exposure to silica dust, including the very low density lipoprotein receptor (VLDLR) and the transmembrane type I heparan sulfate proteoglycan called syndecan 2\n\nKnockdown of SDC2 or VLDLR markedly inhibited collagen production in MRC-5 fibroblasts, suggesting a novel pathogenic role for these proteins in myofibroblast biology.

pharmacology and toxicology↗

bioRxiv2018

The N-end rule E3 ligase UBR2 activates Nlrp1b inflammasomes

Innate immunity relies on the formation of different inflammasomes to initiate immune responses. The recognition of diverse infection and other danger signals by innate immune receptors trigger caspase-1 activation that induces pyroptosis. Anthrax lethal factor (LF) is a secreted bacterial protease that known to potently activate Nlrp1b inflammasomes in mouse macrophages, but the molecular mechanism underlying LF-induced Nlrp1b activation remains unknown. We here carried out both a mouse genome-wide siRNA screen and a CRISPR/Cas9 knockout screen seeking to identify genes that participate in Nlrp1b activation triggered by LF treatment. We found that the N-end rule pathway E3 ligase UBR2 is required for Nlrp1b activation and a ubiquitin conjugating E2 enzyme E2O is also involved in this process via its physically interaction with UBR2. We show that LF triggers activation of Nlrp1b by initiating the degradation of the N-terminal fragment of Nlrp1b itself that produced via an auto-cleavage process. This study deepens our understanding of innate immunity defense against bacterial infection by elucidating the functional role of UBR2-mediated N-end rule pathway in LF-induced Nlrp1b activation.

immunology↗

bioRxiv2018

Metagenomics Analyses of Cellulose and Volatile Fatty Acids Metabolism by Microorganisms in the Cow Rumen

The purpose of this study was to evaluate the effects of different forage-to-concentrate (F:C) ratios (7:3 high-forage, 3:7 high-concentrate) on rumen microflora and fiber degradation mechanism. Compared with the high-concentrate (HC) group, the high-forage(HF) group showed improved fiber degradation and a sustained high level of carboxymethyl cellulose (CMCase), {beta}-glucosidase and {beta}-xylosidase activities, but the total VFAs decreased. Among bacteria at the family level, Lachnospiraceae and Succinivibrionaceae in HF groups were 2-fold and 4-fold more abundant than in the HC group, respectively. A KEGG analysis revealed that succinate-CoA synthetase (EC: 6.2.1.5) and propionate-CoA transferase (EC: 2.8.3.1) leading directly to propionate production were more abundant in HC group. Conversely, butyryl-CoA dehydrogenase (EC: 1.3.8.1) was directly related to butyrate production and was higher in the HF group. A gene expression analysis showed that the relative content of Fibrobacter succinogenes and Butyrivibrio fibrisolvens was higher in the HF group and contributed more to fiber degradation and VFA production. Prevotella ruminicola, Selenomonas ruminantium, and Veillonella alkalescens contributed more to starch degradation and propionate production, which relative content was higher in the HC group. This research gave a further explanation of the fiber degradation parameters and microbiota under different F:C ration. The fiber-degrading bacteria in the roughage group have a high content level, and the corresponding cellulase activity is also high. These results supported the potential of diets for microbial manipulation, which can increase feed digestibility and explored new fibrinolytic bacteria.\n\nIMPORTANCEThe forage of the cows feed occupies a large proportion. The shortage of high-quality forage in cow breeding has become an important factor limiting the Chinas dairy industry. The effective measure is to improve the utilization of low-quality forage. Based on traditional nutrient metabolism, the reasons for the effects of roughage on the growth and metabolism of dairy cows can be explored, but the metabolic mechanism is not well analyzed, and the further utilization of forage is also limited. Metagenomics has proven to be a powerful tool for studying rumen microbial structures and gene function. This experiment used metagenomics to study the metabolism of cellulose and volatile acids in the rumen. Our research showed that different forage-to-concentrate shifted the composition of microorganisms and the activity of enzymes, resulting in different metabolic pathways of volatile fatty acids. This work provides a background for microbial community composition and further use of forage.

microbiology↗

bioRxiv2018

The role of BMP6 in the proliferation and differentiation of chicken cartilage cells

Previous studies have indicated that bone morphogenetic protein (BMP) 6 plays an important role in skeletal system development and progression. However, the mechanism underlying the effects of BMP6 in cartilage cell proliferation and differentiation remains unknown. In this study, cartilage cells were isolated from shanks of chicken embryos and treated with different concentrations of GH. Cell proliferation and differentiation potential was assessed using real-time polymerase chain reaction (RT-PCR) and CCK-8 assays in vitro. The results showed that at 48 h, the Collagen II and BMP6 expression levels in 50 ng/l GH-treated cartilage cells were significantly higher than in groups treated with 100 ng/l or 200 ng/l GH. We further observed that knockdown of BMP6 in cartilage cells led to significantly decreased expression levels of Collagen II and Collagen X. Moreover, the suppression of BMP6 expression by a specific siRNA vector led to significantly decreased expression levels of IGF1R, JAK, PKC, PTH, IHH and PTHrP. Taken together, our data suggest that BMP6 may play a critical role in chicken cartilage cell proliferation and differentiation through the regulation of IGF1, JAK2, PKC, PTH, and Ihh-PTHrP signaling pathways.

cell biology↗

bioRxiv2018

New genetic variants associated with major adverse cardiovascular events in patients with acute coronary syndromes and treated with clopidogrel and aspirin

ImportanceAlthough a few studies have reported the effects of several polymorphisms on major adverse cardiovascular events (MACE) in patients with acute coronary syndromes (ACS) and those undergoing percutaneous coronary intervention (PCI), these genotypes account for only a small fraction of the variation and evidence is insufficient. This study aims to identify new genetic variants associated with MACE by large-scale sequencing data.\n\nObjectiveTo identify the genetic variants that caused MACE.\n\nDesignAll patients in this study were allocated to dual antiplatelet therapy for up to 12 months and have the follow-up duration of 18 months.\n\nSettingA two-stage association study was performed.\n\nParticipantsWe evaluated the associations of genetic variants and MACE in 1961 patients with ACS undergoing PCI (2009-2012), including high-depth whole exome sequencing of 168 patients in the discovery cohort and high-depth targeted sequencing of 1793 patients in the replication cohort.\n\nMain Outcomes and MeasureThe primary clinical efficacy endpoint was the major adverse cardiovascular events (MACE) composite endpoint, including cardiovascular death, myocardial infarction (MI), stroke (CT or MR scan confirmed) and repeated revascularization (RR).\n\nResultsWe discovered and confirmed six new genotypes associated with MACE in patients with ACS. Of which, rs17064642 at MYOM2 increased the risk of MACE (hazard ratio [HR] 2.76; P = 2.95 x 10-9) and reached genome-wide significance. The other five suggestive variants were KRTAP10-4 (rs201441480), WDR24 (rs11640115), ECHS1 (rs140410716), AGAP3 (rs75750968) and NECAB1 (rs74569896). Notably, the expressions of MYOM2 and ECHS1 are down-regulated in both animal models and patients with phenotypes related to MACE. Importantly, we developed the first superior classifier for predicting MACE and achieved high predictive accuracy (0.809).\n\nConclusions and RelevanceWe identified six new genotypes associated with MACE and developed a superior classifier for predicting MACE. Our findings shed light on the pathogenesis of cardiovascular outcomes and may help clinician to make decision on the therapeutic intervention for ACS patients.\n\nTrial RegistrationThis study has been registered in the Chinese Clinical Trial Registry (http://www.chictr.org.cn, Registration number: ChiCTR-OCH-11001198).

genetics↗

bioRxiv2018

Transcytosis maintains CFTR apical polarity in the face of constitutive and mutation-induced basolateral missorting

Apical polarity of cystic fibrosis transmembrane conductance regulator (CFTR) is essential for solute and water transport in secretory epithelia and can be impaired in human diseases. Maintenance of apical polarity in the face of CFTR non-polarized delivery and compromised apical retention of mutant CFTRs lacking PDZ-domain protein (NHERF1) interaction, remains enigmatic. Here we show that basolateral CFTR delivery originates from biosynthetic (~35%) and endocytic (~65%) recycling missorting. Basolateral channels are retrieved via basolateral-to-apical transcytosis, enhancing CFTR apical expression by two-fold and suppressing its degradation. CFTR transcytosis is microtubule-dependent but independent of Myo5B-, Rab11- and NHERF1 binding to its C-terminal DTRL motif in airway epithelia. Increased basolateral delivery due to compromised apical recycling and accelerated internalization upon impaired NHERF1-CFTR association is largely counterbalanced by CFTR efficient basolateral internalization and apical transcytosis. Thus, transcytosis represents a previously unrecognized but indispensable mechanism for maintaining CFTR apical polarity by attenuating its constitutive and mutation-induced basolateral missorting.

cell biology↗

bioRxiv2018

Strategies to improve photosynthetic nitrogen-use efficiency with no yield penalty: lessons from late-sown winter wheat

HighlightOptimal N allocation at several integration levels accounts for improved canopy PNUE while maintaining high grain yield in winter wheat\n\nAbstractImproving canopy photosynthetic nitrogen-use efficiency (PNUE) may maintain or even increase yield with reduced N input. In this study, later-sown winter wheat was studied to reveal the mechanism underlying improved canopy PNUE while maintaining high yield. N allocation at several levels was optimised in late-sown wheat plants. N content per plant increased. Increased N was allocated to the flag leaf and second leaf, and to ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco) in upper leaves. Constant or reduced N was allocated to leaf 3, leaf 4, and Rubisco in lower leaves. The specific green leaf area nitrogen (SLN) of upper leaves increased, while that of lower leaves remained unchanged or decreased. N allocation to the cell wall decreased in all leaves. As a result, the maximum carboxylation rate of upper leaves increased, and that of lower leaves remained constant or decreased. CO2 diffusion capacity was enhanced in all leaves. Outperformance by light-saturated net photosynthetic rate (Pmax) over SLN led to improved PNUE in upper leaves. Enhanced Pmax coupled with unchanged or decreased SLN resulted in improved PNUE in lower leaves. High yield was maintained because enhanced photosynthetic capacity at the leaf and whole plant levels compensated for reduced canopy leaf area.

cell biology↗

bioRxiv2018

Increased GITRL impairs the function of MDSCs and exacerbates primary Sjögren’s syndrome

It is largely unclear how MDSCs contribute to the development of primary Sjogrens syndrome (pSS). In experimental SS (ESS) mice, MDSCs were significantly increased but exhibited gradually diminished suppressive capacity during the disease progression. The ligand for glucocorticoid-induced TNFR family-related protein (GITRL) was increased with the development of pSS, and the increased GITRL was found to down-regulate the function of MDSCs while blocking GITR signal in MDSCs significantly restored their function and ameliorated ESS progression in mice. In pSS patients, expanded MDSCs expressed lower level of arginase were observed in patients with higher SSDAI. Moreover, the increased GITRL in serum was also found to closely correlate with the aberrant function of MDSCs. Together, our studies have demonstrated a critical role of GITRL in modulating the suppressive capacity of MDSCs in pSS, which may facilitate the validation of GITRL as a therapeutic target for the treatment of pSS.

immunology↗

bioRxiv2018

The Subtype Specificity of Genetic Loci Associated with Stroke in 16,664 cases and 32,792 controls

BackgroundGenome-wide association studies have identified multiple loci associated with stroke. However, the specific stroke subtypes affected, and whether loci influence both ischaemic and haemorrhagic stroke, remains unknown. For loci associated with stroke, we aimed to infer the combination of stroke subtypes likely to be affected, and in doing so assess the extent to which such loci have homogeneous effects across stroke subtypes.\n\nMethodsWe performed Bayesian multinomial regression in 16,664 stroke cases and 32,792 controls of European ancestry to determine the most likely combination of stroke subtypes affected for loci with published genome-wide stroke associations, using model selection. Cases were subtyped under two commonly used stroke classification systems, Trial of Org 10172 Acute Stroke Treatment (TOAST) and Causative Classification of Stroke (CCS). All individuals had genotypes imputed to the Haplotype Reference Consortium 1.1 Panel.\n\nResultsSixteen loci were considered for analysis. Seven loci influenced both haemorrhagic and ischaemic stroke, three of which influenced ischaemic and haemorrhagic subtypes under both TOAST and CCS. Under CCS, 4 loci influenced both small vessel stroke and intracerebral haemorrhage. An EDNRA locus demonstrated opposing effects on ischaemic and haemorrhagic stroke. No loci were predicted to influence all stroke subtypes in the same direction and only one locus (12q24) was predicted to influence all ischaemic stroke subtypes.\n\nConclusionsHeterogeneity in the influence of stroke-associated loci on stroke subtypes is pervasive, reflecting differing causal pathways. However, overlap exists between haemorrhagic and ischaemic stroke, which may reflect shared pathobiology predisposing to small vessel arteriopathy. Stroke is a complex, heterogeneous disorder requiring tailored analytic strategies to decipher genetic mechanisms.

genetics↗

bioRxiv2018

Multiplexed Primer Extension Sequencing Enables High Precision Detection of Rare Splice Isoforms

Targeted RNA-sequencing aims to focus coverage on areas of interest that are inadequately sampled in standard RNA-sequencing experiments. Here we present a novel approach for targeted RNA-sequencing that uses complex pools of reverse transcription primers to enable sequencing enrichment at user-selected locations across the genome. We demonstrate this approach by targeting hundreds to thousands of pre-mRNA splice junctions, revealing high-precision detection of splice isoforms, including rare pre-mRNA splicing intermediates.

molecular biology↗

bioRxiv2018

HIV protease inhibitor Saquinavir inhibits toll-like receptor 4 activation by targeting receptor dimerization

Toll like receptor 4 (TLR4) is crucial in induction of innate immune response through recognition of invading pathogens or endogenous alarming molecules.Ligand-induced dimerization of TLR4 is required for the activation of downstream signaling pathways. TLR4 dimerization induces the activation of NF-kB and IRF3 through MyD88- or TRIF-dependent pathways. Saquinavir (SQV), a FDA-approved HIV protease inhibitor, has been shown to suppress the activation of NF-kB induced by HMGB1 by blocking TLR4-MyD88 association in proteasome-independent pathway. However, it remains nknown whether SQV is a HMGB1-specific and MyD88-dependent TLR4 signaling inhibitor and which precise signaling element of TLR4 is targeted by SQV. Our results showed that SQV inhibits both MyD88- and TRIF-dependent pathways in response to LPS, a critical sepsis inducer and TLR4 agonist, leading to downregulation of NF-kB and IRF3. SQV did not suppress MyD88-dependent pathway triggered by TLR1/2 agonist Pam3csk4. In the only TRIF-dependent pathway, SQV did not attenuate IRF3 activation induced by TLR3 agonist Poly(I:C). Furthermore, dimerization of TLR4 induced by LPS and HMGB1 was decreased by SQV. These results suggest that TLR4 receptor complex is the molecular target of SQV and shed light on that TLR4-mediated inmune responses and consequent risk for uncontrolled inflammation could be modulated by FDA-approved drug SQV.

immunology↗

bioRxiv2018

Automatic Classification of Prostate Cancer Gleason Scores from Digitized Whole Slide Tissue Biopsies

Histological Gleason grading of tumor patterns is one of the most powerful prognostic predictors in prostate cancer. However, manual analysis and grading performed by pathologists are typically subjective and time-consuming. In this paper, we propose an automatic technique for Gleason grading of prostate cancer from H&E stained whole slide biopsy images using a set of novel completed and statistical local bi-nary pattern (CSLBP) descriptors. First the technique divides the whole slide image into a set of small image tiles, where salient tumor tiles with high nuclei densities are selected for analysis. The CSLBP texture features that encode pixel intensity variations from circularly surrounding neighborhoods are then extracted from salient image tiles to characterize different Gleason patterns. Finally, CSLBP texture features computed from all tiles are integrated and utilized by the multi-class support vector machine (SVM) that assigns patient biopsy with different Gleason score of 6, 7 or [≥]8. Experiments have been performed on 312 different patient cases selected from the cancer genome atlas (TCGA) and have achieved more than 79% classification accuracies, which is superior to state-of-the-art textural descriptors for prostate cancer Gleason grading.

bioinformatics↗

bioRxiv2018

Mono-homologous linear DNA recombination by the non-homologous end-joining pathway as a novel and simple gene inactivation method: a proof of concept study in Dietzia sp. DQ12-45-1b

Non-homologous end-joining (NHEJ) is critical for genome stability because of its roles in double-strand break repair. Ku and ligase D (LigD) are the crucial proteins in this process, and strains expressing Ku and LigD can cyclize linear DNA in vivo. Herein, we established a proof-of-concept mono-homologous linear DNA recombination for gene inactivation or genome editing by which cyclization of linear DNA in vivo by NHEJ could be used to generate non-replicable circular DNA and could allow allelic exchanges between the circular DNA and the chromosome. We achieved this approach in Dietzia sp. DQ12-45-1b, which expresses Ku and LigD homologs and presents NHEJ activity. By transforming the strain with a linear DNA mono homolog to the sequence in chromosome, we mutated the genome. This method did not require the screening of suitable plasmids and was easy and time-effective. Bioinformatic analysis showed that more than 20% prokaryotic organisms contain Ku and LigD, suggesting the wide distribution of NHEJ activities. Moreover, the Escherichia coli strain also showed NHEJ activity when the Ku and LigD of Dietzia sp. DQ12-45-1b were introduced and expressed in it. Therefore, this method may be a widely applicable genome editing tool for diverse prokaryotic organisms, especially for non-model microorganisms.\n\nIMPORTANCEThe non-model gram-positive bacteria lack efficient genetic manipulation systems, but they express genes encoding Ku and LigD. The NHEJ pathway in Dietzia sp. DQ12-45-1b was evaluated and was used to successfully knockout eleven genes in the genome. Since bioinformatic studies revealed that the putative genes encoding Ku and LigD ubiquitously exist in phylogenetically diverse bacteria and archaea, the mono-homologous linear DNA recombination by the NHEJ pathway could be a potentially applicable genetic manipulation method for diverse non-model prokaryotic organisms.

microbiology↗

bioRxiv2018

PCPE2 and SR-BI Partner to Impact Accumulation of Fat in Mice

LDL receptor knockout mice (LDLr-/-) were crossed with PCPE2 knockout mice to obtain Ldlr-/-,Pcpe2-/- mice. The rationale of these studies was to examine the effects of an extracellular matrix protein, PCPE2, on fat storage in a dyslipidemic mouse model. Male Ldlr-/-, Pcpe2-/- mice were fed a Western diet for 25 weeks and their plasma triglyceride metabolism and triglyceride storage was examined. Interestingly, visceral but not subcutaneous fat pad were smaller in diet-fed Ldlr-/-,Pcpe2-/- mice compared to controls. There was no difference in the fatty acid distribution in triglyceride and cholesteryl esters (CE) among the genotypes. Ldlr-/-, Pcpe2-/- mice have higher plasma triglyceride levels and reduced lipoprotein lipase activity. Immunoprecipitation of SR-BI from cell extracts co-precipitated PCPE2 suggesting that PCPE2 and SR-BI are tightly associated. This work also showed that in the absence of PCPE2 SR-BI does not transfer CE from HDL into the cell. These results suggest that HDL, PCPE2, SR-BI, and possibly LPL are associated in an interactome that is required for CE transport into the cell. In the absence of these interactions lipid transport is significantly disrupted.

biochemistry↗

bioRxiv2018

Cochaperones enable Hsp70 to fold proteins like a Maxwell’s demon

The heat shock protein 70 (Hsp70) chaperones, vital to the proper folding of proteins inside cells, consume ATP and require cochaperones in assisting protein folding. It is unclear whether Hsp70 can utilize the free energy from ATP hydrolysis to fold a protein into a native state that is thermodynamically unstable in the chaperone-free equilibrium. Here we present a model of Hsp70-mediated protein folding, which predicts that Hsp70, as a result of differential stimulation of ATP hydrolysis by its Hsp40 cochaperone, dissociates faster from a substrate in fold-competent conformations than from one in misfolding-prone conformations, thus elevating the native concentration above and suppressing the misfolded concentration below their respective equilibrium values. Previous models would not make or imply these predictions, which are experimentally testable. Our model quantitatively reproduces experimental refolding kinetics, predicts how modulations of the Hsp70/Hsp40 chaperone system affect protein folding, and suggests new approaches to regulating cellular protein quality.

biophysics↗

bioRxiv2018

Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-affected Corneas

PURPOSEKeratoconus (KC) is the most common corneal ectasia. We aimed to determine the differential expression of coding and long noncoding RNAs (lncRNAs) in human corneas affected with KC.\n\nMETHODS200ng total RNA from the corneas of 10 KC patients and 8 non-KC normal controls was used to prepare sequencing libraries with the SMARTer Stranded RNA-Seq kit after ribosomal RNA depletion. Paired-end 50bp sequences were generated using Illumina HiSeq 2500 Sequencer. Differential analysis was done using TopHat and Cufflinks with a gene file from Ensembl and a lncRNA file from NONCODE. Pathway analysis was performed using WebGestalt. Using the expression level of differentially expressed coding and noncoding RNAs in each sample, we correlated their expression levels in KC and controls separately and identified significantly different correlations in KC against controls followed by visualization using Cytoscape.\n\nRESULTSUsing |fold change| [≥] 2 and a false discovery rate [≤] 0.05, we identified 436 coding RNAs and 584 lncRNAs with differential expression in the KC-affected corneas. Pathway analysis indicated the enrichment of genes involved in extracellular matrix, protein binding, glycosaminoglycan binding, and cell migration. Our correlation analysis identified 296 pairs of significant KC-specific correlations containing 117 coding genes enriched in functions related with cell migration/motility, extracellular space, cytokine response, and cell adhesion, suggesting the potential functions of these correlated lncRNAs, especially those with multiple pairs of correlations.\n\nCONCLUSIONSOur RNA-Seq based differential expression and correlation analyses have identified many potential KC contributing coding and noncoding RNAs.

genomics↗

bioRxiv2018

MicroRNA-122 supports robust innate immunity in hepatocytes by suppressing STAT3 phosphorylation

The intrinsic innate immunity of hepatocytes is essential for the control of hepatitis viruses and influences the outcome of antiviral therapy. MicroRNA-122 (miR-122) is the most abundant microRNA in hepatocytes and is a central player in liver biology and disease. However, little is known about the role of miR-122 in hepatocyte innate immunity. Herein, we show that restoring miR-122 levels in hepatoma cells markedly increased the activation of both type III and type I interferons (IFNs) in response to hepatitis C virus (HCV) RNA or poly(I:C). We determined that miR-122 promotes IFN production through down-regulating the tyrosine (Tyr705) phosphorylation of STAT3. We show that STAT3 represses IFN activation by inhibiting interferon regulatory factor 1 (IRF1), which is rate-limiting for maximal IFN expression, especially type III IFNs. Through large-scale screening, we identified that miR-122 targets MERTK, FGFR1 and IGF1R, three oncogenic receptor tyrosine kinases that directly promote STAT3 phosphorylation. These findings reveal a previously unknown role for miR-122 in hepatic immunity and indicate a new potential strategy for treating hepatic infections through targeting STAT3.

molecular biology↗