Biology subjects

Ren, H.

Publications and source records attributed to Ren, H..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

PRL1 negatively regulates Rho GTPase-independent and -dependent signaling pathways maintaining actin microfilament dynamic for pavement cell morphogenesis

Actin dynamic is critical for cell morphogenesis in plants, but the signaling mechanisms underlying its regulation are not well understood. Here we found PRL1 (Pleiotropic Regulatory Locus1) modulates leaf pavement cell (PC) morphogenesis in Arabidopsis by maintaining the dynamic homeostasis of actin microfilaments (MF). Our previous studies indicated PC shape formation was mediated by the counteracting ROP2 and ROP6 signaling pathways that promote the organization of cortical MF and microtubules (MT), respectively. Our genetic screen for ROP6 enhancers identified prl1 alleles. Genetic analysis suggested that prl1 acted synergistically with ROP2 and ROP6 in regulation of PC morphogenesis. We further found that the activities of ROP2 and ROP6 were increased and decreased in prl1 mutants, respectively. Interestingly prl1 was found to prefer to depolymerize MF independent of ROP2 and ROP6. Stress (high salinity and low temperature) induced similar changes of ROP activities as do prl1 mutations. Together our findings provided evidence that PRL1 governed two signaling pathways that counteractively maintain actin dynamics and resultant cell morphogenesis.

plant biology↗

bioRxiv2023

The scale-invariant covariance spectrum of brain-wide activity

Understanding neural activity organization is vital for deciphering brain function. By recording whole-brain calcium activity in larval zebrafish during hunting and spontaneous behaviors, we find that the shape of the neural activity space, described by the neural covariance spectrum, is scale-invariant: a smaller, randomly sampled cell assembly resembles the entire brain. This phenomenon can be explained by Euclidean Random Matrix theory, where neurons are reorganized from anatomical to functional positions based on their correlations. Three factors contribute to the observed scale invariance: slow neural correlation decay, higher functional space dimension, and neural activity heterogeneity. In addition to matching data from zebrafish and mice, our theory and analysis demonstrate how the geometry of neural activity space evolves with population sizes and sampling methods, thus revealing an organizing principle of brain-wide activity.

neuroscience↗

bioRxiv2023

DNA G-quadruplex is a transcriptional control device that regulates memory

The conformational state of DNA fine-tunes the transcriptional rate and abundance of RNA. Here we report that DNA G-quadruplex (G4-DNA) accumulates in neurons in an experience-dependent manner, and that this is required for the transient silencing and activation of genes that are critically involved in learning and memory. In addition, site-specific resolution of G4-DNA by dCas9-mediated deposition of the helicase DHX36 impairs fear extinction memory. Dynamic DNA structure states therefore represent a key molecular mechanism underlying memory consolidation. One-Sentence SummaryG4-DNA is a molecular switch that enables the temporal regulation of the gene expression underlying the formation of fear extinction memory.

neuroscience↗

bioRxiv2023

IL-15 enhances functional properties and responses of CD28-negative CD4+ cytotoxic T cells expanded in Systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is an autoimmune disorder that results in an attack by bodys immune system of its own tissues, causing chronic inflammation and tissue damage. T cells play a key role in the pathogenesis of SLE, as they secrete pro-inflammatory cytokines as well as mediate direct effects on target tissues. Recently, CD4-positive T cells with cytotoxic potential were showed to be involved in autoimmune disease progression and tissue damage. However, whether this cell type expands and plays effector functions in SLE patients remain to be elucidated. Analyzing single-cell RNA sequencing (scRNA-Seq) data and flow cytometry data, we find that cytotoxic CD4+CD28- T cells are present in SLE patients. We also show that these cells expand most prominently in patients affected by lupus nephritis, and they exhibit cytotoxic activity against human renal glomerular endothelial cells in vitro. In addition, our study suggests that Interleukin-15 (IL-15) promotes the expansion, proliferation and cytotoxic function of CD4+CD28- T cells in SLE patients. Tofacitinib, a selective JAK3 inhibitor, inhibits the effect of IL-15 on CD4+CD28- T cells. Together, our study clearly demonstrated that CD4+ CD28- T cells characterized by proinflammatory properties and cytolytic function expand in SLE patients. The pathogenic potential of these CD4+ CD28- T cells is driven by IL-15/IL-15R/JAK3/STAT5 signaling pathway, which may open new avenues for therapeutic intervention to prevent progression of SLE patients.

immunology↗

bioRxiv2022

Latitude influences stability via stabilizing mechanisms in naturally-assembled forest ecosystems at different spatial grains

Ecosystem stability reveals how ecosystems respond to global change over time. Yet, the focus of past research on small spatial grains and extents overlooks scale dependence and how broad-scale environmental gradients shape stability. Here, we use forest inventory data covering a broad latitudinal gradient from the temperate to the tropical zone to examine cross-scale variation in stability of aboveground biomass and underlying stabilizing mechanisms. While stability did not shift systematically with latitude at either spatial grain, we found evidence that species asynchrony increased towards the tropics at the small spatial grain while species stability decreased at both spatial grains. Moreover, latitude stabilized forest communities via its effects on both stabilizing mechanisms, which compensated for the weak and destabilizing effects of species richness. Yet, the trade-off in the relative importance of species stability and species asynchrony for stability was not mediated by latitude, suggesting that context-dependent factors - to a greater extent than macroecological ones - underlie large-scale patterns of stability. Our results highlight the crucial role of species asynchrony and species stability in determining ecosystem stability across broad-scale environmental gradients, suggesting that conserving biodiversity alone may not be sufficient for stabilizing naturally-assembled forest ecosystems.

ecology↗

bioRxiv2022

Bright and sensitive red voltage indicators for imaging action potentials in brain slices and pancreatic islets

As fast developing tools for observing cellular membrane potential, red-emitting genetically encoded voltage indicators (GEVIs) reduce auto-fluorescence background, allow multiplexed recordings, and enable all-optical electrophysiology, but have been limited by either insensitivity or dimness. Here, we report a pair of red GEVIs, Cepheid1b/s, with improved sensitivity, brightness, and photostability. Cepheid1 indicators faithfully report cellular excitability in pancreatic islets and neural activity in acute brain slices.

neuroscience↗

bioRxiv2022

Integrated transcriptome and lineage analyses reveal novel catecholaminergic cardiomyocytes contributing to the cardiac conduction system in murine heart

Cardiac conduction system (CCS) morphogenesis is essential for correct heart function yet is incompletely understood. Here we established the transcriptional landscape of cell types populating the developing heart by integrating single-cell RNA sequencing and spatial enhanced resolution omics-sequencing (Stereo-seq). Stereo-seq provided a spatiotemporal transcriptomic cell fate map of the murine heart with a panoramic field of view and in situ cellular resolution of the CCS. This led to the identification of a previously unrecognized cardiomyocyte population expressing dopamine beta-hydroxylase (Dbh+-CMs), which is closely associated with the CCS in transcriptomic analyses. To confirm this finding, genetic fate mapping by using DbhCre/Rosa26-tdTomato reporter mouse line was performed with Stereo-seq, RNAscope, and immunohistology. We revealed that Dbh+-derived CMs first emerged in the sinus venosus at E12.5, then populated the atrial and ventricular CCS components at E14.5, with increasing abundance towards perinatal stages. Further tracing by using DbhCFP reporter and DbhCreERT/Rosa26-tdTomato inducible reporter, we confirmed that Dbh+-CMs are mostly abundant in the AVN and ventricular CCS and this persists in the adult heart. By using DbhCre/Rosa26-tdTomato/Cx40-eGFP compound reporter line, we validated a clear co-localization of tdTomato and eGFP signals in both left and right ventricular Purkinje fibre networks. Finally, electrophysiological optogenetic study using cell-type specific Channelrhodopsin2 (ChR2) expression further elucidated that Dbh+-derived CMs form a functional part of the ventricular CCS and display similar photostimulation-induced electrophysiological characteristics to Cx40CreERT/ChR2-tdTomato CCS components. Thus, by utilizing advanced transcriptomic, mouse genetic, and optogenetic functional analyses, our study provides new insights into mammalian CCS development and heterogeneity by revealing novel Dbh+-CMs. HighlightsO_LIStereo-seq provided a spatiotemporal transcriptomic cell fate map of the murine heart with a panoramic field of view and in situ cellular resolution of the CCS. C_LIO_LIEstablished the transcriptional landscape of cell types populating the developing murine heart. C_LIO_LIRevealed previously unreported catecholaminergic cardiomyocyte populations contributing to the developing and mature murine cardiac conduction system. C_LI

cell biology↗

bioRxiv2022

Elongation of Very Long Chain Fatty Acids Like- 3 (Elovl3) is activated by ZHX2 and is a regulator of cell cycle progression

Zinc fingers and homeoboxes 2 (ZHX2) functions as a tumor suppressor in several models of hepatocellular carcinoma (HCC), presumably through its control of target genes. Previous microarray data suggested that Elongation of Very Long Chain Fatty Acids 3 (Elovl3), a member of the Elovl family which synthesize very long chain fatty acids (VLCFAs), is a putative ZHX2 target gene. VLCFAs are core component of ceramides and other bioactive sphingolipids, which are often dysregulated in diseases, including HCC. Since several previously identified ZHX2 targets become dysregulated in HCC, we investigated the relationship between ZHX2 and Elovl3 in liver damage and HCC. Here, using mouse and cell models, we demonstrate that Zhx2 positively regulates Elovl3 expression in the liver and that male-biased hepatic Elovl3 expression is established between 4-8 weeks of age in mice. Elovl3 is dramatically repressed in mouse models of liver regeneration and HCC and the reduced Elovl3 levels in the regenerating liver are associated with changes in hepatic very long chain fatty acids. Human hepatoma cell lines with forced Elovl3 expression have lower rates of cell growth; analysis of synchronized cells indicate that this reduced proliferation correlates with cells stalling in S-phase. Taken together, these data indicate that Elovl3 expression helps regulate cellular proliferation, possibly through control of VLCFAs, and its repression may be a contributing factor to HCC and explain, in part, the function of ZHX2 as a suppressor of HCC progression.

molecular biology↗

bioRxiv2022

TWISTED DWARF1 mediates myosin XI-associated vesicle trafficking required for auxin transport

Defects in plant development caused by loss-of the FKBP42, TWISTED DWARF1 (TWD1), have so far been accounted to a dual function of TWD1 acting as an ABCB chaperone that positively regulates ABCB biogenesis and transport activity. On the other hand, TWD1 was characterized as a modulator of actin cytoskeleton bundling and dynamics by interaction with ACTIN7, however, currently it is unclear if both events are connected. Here, we show that TWD1 positively regulates pollen tube germination and growth by controlling actin organization. We identify and verify myosin XI-K as TWD1 interacting protein, which is most likely linking the action of TWD1 on the actin cytoskeleton. We provide evidence that myosin XI-K is required for proper auxin exporter trafficking and auxin export. Further, we show that ER-localized TWD1 reshapes the ER network to overlay actin cables similar to mutations of myosin-XI and thus controls cytoplasmic streaming. In summary, our data support a model in that TWD1 functions as an ER-actin adapter proteins involved in myosin-dependent ER motility and cargo trafficking. Our findings provide a molecular explanation for the defects in early ABCB biogenesis in twd1 that are caused by defects in the three-way interaction between the ER, cytosolic myosin-XI and F-actin.

cell biology↗

bioRxiv2022

Inhibiting circRNA Cdr1as expression in the ILPFC of adult male C57BL/6J mice impairs fear extinction memory

Circular RNAs (circRNAs) comprise a novel class of regulatory RNAs that are abundant in the brain, particularly within synapses. They are highly stable, dynamically regulated, and display a range of functional roles, including as decoys for miRNAs and proteins and, in some cases, translation. Early work in animal models revealed an association between circRNAs and neurodegenerative and neuropsychiatric disorders; however, relatively few studies have shown a causal link between circRNA function and memory. To address this knowledge gap, we sequenced circRNAs in the synaptosome compartment of the medial prefrontal cortex of fear extinction trained male C57BL/6J mice and found 12837 circRNAs enriched at the synapse, including Cdr1as. Targeted knockdown of Cdr1as in the neural processes of the infralimbic prefrontal cortex of male C57BL/6J mice led to impaired fear extinction memory. Altogether, our findings highlight the importance of localised circRNA activity at the synapse for memory formation and suggest that circRNAs may have a more widespread effect on brain function than previously thought.

neuroscience↗

bioRxiv2022

Discovery of synapse-specific RNA N6-methyladenosine readers associated with the consolidation of fear extinction memory

The RNA modification N6-methyladenosine (m6A) is critically involved in the regulation of gene activity underlying experience-dependent plasticity, and is necessary for the functional interplay between RNA and RNA binding proteins (RBPs) in the nucleus. However, the complete repertoire of m6A-modified RNA interacting RBPs in the synaptic compartment, and whether they are involved in fear extinction, have yet to be revealed. Using RNA immunoprecipitation followed by mass spectrometry, we discovered 12 novel, synapsespecific, learning-induced m6A readers in the medial prefrontal cortex of male C57/B6 mice. m6A RNA-sequencing also revealed a unique population of learning-related m6A-modified RNAs at the synapse, which includes a variant of the long non-coding RNA (lncRNA) metastasis associated lung adenocarcinoma transcript 1 (Malat1). m6A-modified Malat1 binds to a subset of novel m6A readers, including cytoplasmic FMR1 interacting protein 2 (CYFIP2) and dihydropyrimidase-related protein 2 (DPYSL2) and a cell-type-specific, state-dependent, and synapse-specific reduction in m6A-modified Malat1 disrupts the interaction between Malat1 and DPYSL2 and impairs fear extinction. The consolidation of fear-extinction memory therefore relies on an interaction between m6A-modified Malat1 and select RBPs in the synaptic compartment.

neuroscience↗

bioRxiv2022

Orphan C/D box snoRNAs modulate fear-related memory processes in mice

C/D box small nucleolar RNAs (snoRNAs) comprise a class of small noncoding RNAs with important regulatory effects on cellular RNA function. Although it is well established that snoRNAs coordinate the post-transcriptional modification of pre-ribosomal and small nuclear RNAs by 2-O-methylation, which leads to enhanced RNA stability, whether they are necessary for memory-related processes remains relatively unexplored. Using targeted sequencing, we have identified more than 150 C/D box snoRNAs in the prefrontal cortex of male C57BL/6J mice, 31 of which are differentially expressed in response to fear extinction learning. We have also discovered a subset of snoRNAs, including many orphans, that are enriched in the synaptic compartment, including the orphan snoRNA snord64. An extinction learning-induced increase in synapse-enriched snord64 led to increased 2-O-methylation within the 3-UTR of the mRNA encoding the ubiquitin ligase RNF146. This effect was blocked by snord64 knockdown and was accompanied by attenuated forgetting of conditioned fear and the enhanced retrieval of fear extinction memory. Localized activity of orphan snoRNAs therefore represents a novel mechanism associated with fear-related learning and memory. Significance statementWe have discovered a population of experience-dependent small nucleolar RNAs (snoRNAs), and found that several of these are recruited to the synaptic compartment in response to fear extinction learning. In particular, the orphan snoRNA, snord64, drives the methylation of the mRNA encoding the ubiquitin ligase, RNF146, with a reduction in snord64 attenuating forgetting of conditioned fear and enhancing the retrieval of fear extinction memory. This study reveals a new mechanism of gene regulation associated with fear-related memory that involves the activity of synapse-enriched snoRNAs.

neuroscience↗

bioRxiv2022

Cell detoxification of secondary metabolites by P4-ATPase mediated vesicle transport

Mechanisms for cellular detoxification of drug compounds are of significant interest in human health. Cyclosporine A (CsA) and tacrolimus (FK506) are widely known antifungal and immunosuppressive microbial natural products. However, both compounds can result in significant side effects when used as immunosuppressants. The insect pathogenic fungus Beauveria bassiana shows resistance to CsA and FK506. However, the mechanisms underlying the resistance have remained unknown. Here, we identify a P4-ATPase gene, BbCRPA, from the fungus, which confers resistance via a unique vesicle mediated transport pathway that targets the compounds into detoxifying vacuoles. Interestingly, the expression of BbCRPA in plants promotes resistance to the phytopathogenic fungus Verticillium dahliae via detoxification of the mycotoxin cinnamyl acetate using a similar pathway. Our data reveal a new function for a subclass of P4-ATPases in cell detoxification. The P4-ATPases conferred cross-species resistance can be exploited for plant disease control and human health protection.

microbiology↗

bioRxiv2022

Fear extinction is regulated by long noncoding RNA activity at the synapse

Long noncoding RNAs (lncRNAs) represent a multidimensional class of regulatory molecules involved in many aspects of brain function. Emerging evidence indicates that lncRNAs are expressed at the synapse; however, a direct role for their activity in this subcellular compartment in memory formation has yet to be demonstrated. Using lncRNA capture-seq on synaptosomes, we identified a significant number of lncRNAs that accumulate at synapses within the infralimbic prefrontal cortex of adult male C57/Bl6 mice. Among these is a splice variant related to the stress-associated lncRNA, Gas5. RNA immunoprecipitation followed by mass spectrometry and single molecule imaging revealed that this Gas5 isoform, in association with the RNA binding proteins G3bp2 and Caprin1, regulates the activity-dependent trafficking and clustering of RNA granules in dendrites. In addition, we found that cell-type-specific, state-dependent, and synapse-specific knockdown of the Gas5 variant led to impaired fear extinction memory. These findings identify a new mechanism of fear extinction that involves the dynamic interaction between local lncRNA activity and the coordination of RNA condensates in the synaptic compartment.

neuroscience↗

bioRxiv2022

A toolkit of highly selective and sensitive genetically encoded neuropeptide sensors

Neuropeptides are key signaling molecules in the endocrine and nervous systems that regulate many critical physiological processes, including energy balance, sleep and circadian rhythms, stress, and social behaviors. Understanding the functions of neuropeptides in vivo requires the ability to monitor their dynamics with high specificity, sensitivity, and spatiotemporal resolution; however, this has been hindered by the lack of direct, sensitive and non-invasive tools. Here, we developed a series of GRAB (G protein-coupled receptor activation-based) sensors for detecting somatostatin (SST), cholecystokinin (CCK), corticotropin-releasing factor (CRF), neuropeptide Y (NPY), neurotensin (NTS), and vasoactive intestinal peptide (VIP). These fluorescent sensors utilize the corresponding GPCRs as the neuropeptide-sensing module with the insertion of a circular-permutated GFP as the optical reporter. This design detects the binding of specific neuropeptides at nanomolar concentration with a robust increase in fluorescence. We used these GRAB neuropeptide sensors to measure the spatiotemporal dynamics of endogenous SST release in isolated pancreatic islets and to detect the release of both CCK and CRF in acute brain slices. Moreover, we detect endogenous CRF release induced by stressful experiences in vivo using fiber photometry and 2-photon imaging in mice. Together, these new sensors establish a robust toolkit for studying the release, function, and regulation of neuropeptides under both physiological and pathophysiological conditions.

neuroscience↗

bioRxiv2022

Serum profiles of metabolomic and GDF-15 differentiate idiopathic pulmonary fibrosis from other interstital lung diseases: a preliminary study

Objective1.Explore the differential metabolites and metabolic pathways between different interstitial lung disease (ILD) and healthy controls, so as to find out new biomarkers and metabolic pathways of ILD and provide new biological targets for IPF diagnosis and treatment.2.Detect the levels of serum related fibrosis and metabolic indexes of ILD, explore the relationship between these indexes and the types and general parameters of ILD diseases, and focus on GDF-15 on the basis of metabonomics, explore new metabolic pathways related to ILD, and further expound the pathogenesis of idiopathic pulmonary fibrosis. Method1.According to the inclusion criteria and exclusion criteria, the ILD patients admitted to our hospital from January 1, 2021 to January 1, 2022 were signed with informed consent, and all of them had clear multidisciplinary diagnosis. At the same time, the physical examination in the health management center of our hospital was selected as the healthy control group. General clinical data of ILD patients and healthy controls were collected, including gender, age, onset, clinical manifestations, clinical biochemistry, lung function and other related data. Collect patients peripheral venous blood, keep serum samples, and analyze the serum of ILD patients and healthy controls by liquid chromatography-mass spectrometry (LC-MS) to obtain differential metabolites, metabolic maps and related data. According to the diagnosis, the patients were divided into Idiopathic pulmonary fibrosis (IPF), connective tissue disease-associated interstitial lung disease (CTD-ILD), other interstitial lung disease (ILD) patients and healthy control group. R statistical software was used to observe whether there are differential metabolites in IPF group and healthy control group, CTD-ILD group and healthy control group, other ILD groups and healthy control group, IPF group and CTD-ILD group, IPF group and other ILD groups, CTD-ILD group and other ILD groups by using positive and negative ion flow charts and score charts of orthogonal partial least squares-discriminant analysis. And the potential biomarkers were found through the S-plot diagram of OPLS-DA and the variable weight value VIP>1. ROC curve analysis of differential metabolites was carried out by SPSS21.0 software to analyze the value of differential diagnosis and find out new biomarkers with differential diagnosis significance. Based on KEGG database, the metabolic pathway enrichment analysis of differential metabolites was carried out to find out the main metabolic pathways. 2.Serum levels of type I collagen, KL-6, IL-1{beta}, TNF-, IGF-1 and GDF-15 were detected by Enzyme linked immunosorbent assay (ELISA) in all patients and healthy controls. Using SPSS21.0 statistical software and R statistical software, using T-test, variance analysis or nonparametric test method, according to different diagnoses (IPF/CTD-ILD/ other ILD/ healthy control group, ILD/ healthy control group, IPF/ other), the data were analyzed and compared in subgroups. Pearson correlation analysis was used to analyze the correlation between serum biomarkers and other factors such as lung function, metabolomics and so on. ROC curve was used to analyze the diagnostic efficiency of each index, and the best critical value, sensitivity and specificity were found out. Results1.Analysis of general clinical data and clinical indicators: 26 cases of IPF, 21cases of CTD-ILD, 23 cases of others ILD and 20 cases of healthy control group were included, respectively. There were significant differences in age, sex and smoking history among the four groups (P < 0.05), and the differences were statistically significant. There were statistically significant differences among IPF group, CTD-ILD group and other ILD groups in cough and expectoration symptoms, eosinophil count percentage, creatine kinase, creatine kinase isoenzyme, C-reactive protein and carbon monoxide diffusion capacity (DLco) (P < 0.05). 2. Metabonomics analysis: LC-MC total ion flow chart of serum samples and orthogonal partial least squares discriminant analysis (OPLS-DA) of serum samples showed the difference of ion peak intensity, and there were different metabolites among each group. The OPLS-DA model has good quality evaluation and reliable data analysis. There are 193, 115, 101, 188, 148 and 169 differential metabolites in IPF group and healthy control group, IPF group and CTD-ILD group, CTD-ILD group and other ILD groups, others ILD groups and healthy control group respectively. There is a correlation between the differential metabolites of each ILD subgroup and the healthy control group. The most relevant metabolic pathways in IPF mainly include choline metabolic pathway, metabolic pathway and linoleic acid metabolic pathway in cancer. The metabolic pathways most related to CTD-ILD and other ILD include choline metabolic pathway and retrograde neural signal metabolic pathway in cancer. Metabolic pathway and linoleic acid metabolic pathway may distinguish IPF from other ILD. Metabolites involved in metabolic pathway are L-Glutamate, PE(18:3(6Z,9Z,12Z)/P-18:0) and PC (18: 2 (9z, 12z)/20: 2 (11z, 14z)), respectively. There are three differential metabolites of linoleic acid pathway, namely 12,13-EpOME, 13S-HODE and PC(18:2(9Z,12Z)/20:2(11Z,14Z)). There are 35 kinds of differential metabolites in IPF group and healthy control group, and the top three places of AUC are 3- sulfodeoxycholic acid, 20,22-dihydrodigitalis glycoside, ({+/-}14) (15)-EET-SI, with AUC values of 0.985, sensitivity of 100% and specificity of 92.3%. L- acetylcarnitine, 5-hydroxydodecanoate and L-Glutamate are involved in significant enrichment pathways, among which the ROC curve area of L-Glutamate is the largest, with AUC value of 0.921, cutoff value of 40145.490, sensitivity of 80%, specificity of 96%, and participation in metabolic pathways. 3. Serum metabolism-related detection indexes: The six serum detection indexes of IPF group and CTD-ILD group are higher than those of healthy control group, and the difference is statistically significant (P < 0.05), but the difference between IPF group and CTD-ILD group is not statistically significant (P>0.05). The expression of GDF-15 in IPF group and non-IPF ILD group was higher than that in healthy control group, with significant difference, but there was no significant difference between IPF group and non-IPF ILD group. Type I collagen and IL-1{beta} were negatively correlated with DLco. KL-6 is negatively correlated with the measured values of VC and DLco; IGF-1 was negatively correlated with FVC, VC and DLco (all P<0.05). GDF-15 was positively correlated with type I collagen, KL-6, IL-1{beta}, TNF- and IGF-1, and the difference was statistically significant (P < 0.05). ROC curve shows that the area under ROC curve (AUC) of six serum indexes in IPF group is greater than 0.9; In CTD-ILD group, the AUC of IGF-1 was greater than 0.9, the cutoff value was 35.081ng/ml, the sensitivity was 90%, the specificity was 76%, and the area under ROC curve was greater than 0.8, and the difference was statistically significant. In other ILD groups, the ROC curve area of these six indicators ranged from 0.6 to 0.8, among which IGF-1, GDF-15 and TNF- had diagnostic value. In IPF, L-Glutamate was positively correlated with type I collagen, KL-6, IGF-1, IL-1{beta}, TNF- and GDF-15, and the difference was statistically significant (P < 0.05), with the highest correlation with IGF-1. ConclusionIn this study, the serum samples of IPF patients, CTD-ILD patients, other interstitial lung diseases and healthy controls were analyzed by LM-MS and ELISA, and the following conclusions were drawn. 1.There are differences in serum metabolites in different groups. IPF has three main metabolic pathways, namely choline metabolic pathway, metabolic pathway and linoleic acid metabolic pathway in cancer, among which metabolic pathway and linoleic acid metabolic pathway are different from other groups. There are 35 differential metabolites in IPF and healthy control group with the area under ROC curve larger than 0.80, among which the metabolites with the highest diagnostic value are 3- sulfodeoxycholic acid, 20,22-dihydrodigitalis glycoside and ({+/-}) 14 (15)-EET-SI. The AUC value of L- glutamic acid is the highest among the metabolites that participate in the enrichment pathway significantly. 2. The expressions of type I collagen, KL-6, IL-1{beta}, TNF-, IGF-1 and GDF-15 are different in different ILDs, which have potential diagnostic and differential diagnostic value, and are correlated with lung function indexes. In IPF, GDF-15 is positively correlated with L-Glutamate, which may be involved in metabolic pathway to further promote pulmonary fibrosis.

molecular biology↗

bioRxiv2022

CMLD-2 Attenuates Myofibroblast Activation and Bleomycin-Induced Pulmonary Fibrosis in Mice through Antagonizing ELAVL1-Mediated Osteopontin mRNA Stabilization

BackgroundFibroblast-myofibroblasts transition (FMT) is one of the hallmark cellular processes in pulmonary fibrosis. This study is to investigate the effects of CMLD-2 in FMT and pulmonary fibrosis, which antagonizes HuR, a supposedly key regulatory RNA binding protein (RBP). MethodsHuR or other deferentially expressed RBPs during TGF-{beta}1-induced FMT were analyzed by transcriptomic methods, and further validated in vitro or in fibrotic lung specimens. The effects of HuR overexpression, down-regulation or inhibition by an antagonist CMLD-2 were analyzed in FMT or bleomycin-induced experimental lung fibrosis. HuR-targeting RNA and their interactions were analyzed by CLIP-seq. ResultsHuR, hnRNPA1, hnRNPE1, TIA1 and TFRC were significantly up-regulated, while ESRP1, ESRP2 and TTP were significantly down-regulated. Cytoplasmic expression of HuR was activated in IPF lung tissue and rat lungs of bleomycin-induced fibrosis. HuR overexpression induced -SMA and collagen I expression, increased the proliferation and migration capacities of fibroblasts with or without the stimulation of TGF-{beta}1. HuR knockdown by shRNA inhibited the proliferation, transition, collagen production and migration properties in fibroblasts or in TGF-{beta}1-stimulated myofibroblasts. Combinative analysis of RNA-seq and CLIP-seq data revealed major HuR binding motifs and several HuR-bound, differentially expressed mRNAs in FMT, specifically SPP1 mRNA encoding osteopontin. HuR-mediated SPP1 mRNA stabilization was further validated by RIP-PCR and half-life analysis using SPP1 mutant transcripts. Inhibiting HuR using CMLD-2 attenuated SPP1/osteopontin expression, TGF-{beta}1-induced FMT in vitro and bleomycin-induced pulmonary fibrosis in mice. Nuclear-cytoplasmic shuttle of HuR was activated in TGF-{beta}1-induced FMT, which was inhibited by p38MAPK (SB203580) or PKC (Go-6976) inhibition, but not associated with phosphorylation of HuR. ConclusionsFibroblast-myofibroblast transition is activated by HuR-SPP1 mRNA interactions, and CMLD-2 is potentiated to be a therapeutic agent targeting HuR for fibroblast-myofibroblast transition and pulmonary fibrosis.

molecular biology↗

bioRxiv2022

KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping

MotivationThe growing number of microbial reference genomes enables the improvement of metagenomic profiling accuracy but also imposes greater requirements on the indexing efficiency, database size, and runtime of taxonomic profilers. Additionally, most profilers focus mainly on bacterial, archaeal, and fungal populations, while less attention is paid to viral communities. ResultsWe present KMCP, a novel k-mer-based metagenomic profiling tool that utilizes genome coverage information by splitting the reference genomes into chunks and then stores k-mers in a modified and optimized COBS index for fast alignment-free sequence searching. KMCP combines k-mer similarity and genome coverage information to reduce the false positive rate of k-mer-based taxonomic classification and profiling methods. Benchmarking results based on simulated and real data demonstrate that KMCP, despite a longer running time than all other methods, not only allows the accurate taxonomic profiling of prokaryotic and viral populations but also provides confident pathogen detection in clinical samples of low depth. Availability and ImplementationThe software is open-source under the MIT license and available at https://github.com/shenwei356/kmcp.

bioinformatics↗