Biology subjects

Bao, X.

Publications and source records attributed to Bao, X..

70 records · Page 4Linked to original sources

bioRxiv2020

TRPM2 promotes pancreatic cancer by PKC/MAPK pathway

BackgroundThe mechanism of pancreatic cancer(PA) is not fully understanded. In our last report, TRPM2 plays a promising role in pancreatic cancer. However, the mechanism of TRPM2 is still unknown in this dismal disease. This study was designed to investigate the role and mechanism of TRPM2 in pancreatic cancer. MethodsTRPM2 overexpressed and siRNA plasmid were created and transfected with pancreatic cancer cell line(BxPC-3) to construct the cell model. We employed CCK-8, Transwell, scratch wound, and nude mice tumor bearing model to investigate the role of TRPM2 in pancreatic cancer. Besides, we collected the clinical data, tumor tissue sample(TT) and para-tumor sample(TP) from the pancreatic cancer patients treated in our hospital. We analyzed the mechanism of TRPM2 in pancreatic cancer by transcriptome analysis, Westernblot, and PCR. ResultsOverexpressed TRPM2 could promote pancreatic cancer in proliferation, migration, and invasion ability in no matter the cell model or nude mice tumor bearing model. TRPM2 level is highly negative correlated to the overall survival and progression-free survival time in PA patients, however, it is significantly increased in PA tissue as the tumor stage increases. The transcriptome analysis, GSEA analysis, Westernblot, and PCR results indicates TRPM2 is highly correlated with PKC/MAPK pathways. ConclusionTRPM2 could directly activate PKC by calcium or indirectly activate PKC{varepsilon} and PKC{delta} by increased DAG in PC, which promote PC by downstream MAPK/MEK pathway activation.

cancer biology↗

bioRxiv2020

Global Profiling of the Lysine Crotonylome in Different Pluripotent States

Pluripotent stem cells (PSCs) can be expanded in vitro in different culture conditions, resulting in a spectrum of cell states with distinct properties. Understanding how PSCs transition from one state to another, ultimately leading to lineage-specific differentiation, is important for developmental biology and regenerative medicine. Although there is significant information regarding gene expression changes controlling these transitions, less is known about post-translational modifications of proteins. Protein crotonylation is a newly discovered post-translational modification where lysine residues are modified with a crotonyl group. Here, we employed affinity purification of crotonylated peptides and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to systematically profile protein crotonylation in mouse PSCs in different states including ground, metastable and primed state, as well as metastable PSCs undergoing early pluripotency exit. We successfully identified 3628 high-confidence sites in 1426 proteins. These crotonylated proteins are enriched for factors involved in functions related to pluripotency such as RNA biogenesis, central carbon metabolism and proteasome function. Moreover, we found that increasing the cellular levels of crotonyl-CoA through crotonic acid treatment promotes proteasome activity in metastable PSCs and delays their differentiation, consistent with previous observations showing that enhanced proteasomal activity helps to sustain pluripotency. Our atlas of protein crotonylation will be valuable for further studies of pluripotency regulation and may also provide insights into the role of metabolism in other cell fate transitions.

cell biology↗

bioRxiv2020

Engineered Trimeric ACE2 Binds and Locks "Three-up" Spike Protein to Potently Inhibit SARS-CoVs and Mutants

SARS-CoV-2 enters cells via ACE-2, which binds the spike protein with moderate affinity. Despite a constant background mutational rate, the virus must retain binding with ACE2 for infectivity, providing a conserved constraint for SARS-CoV-2 inhibitors. To prevent mutational escape of SARS-CoV-2 and to prepare for future related coronavirus outbreaks, we engineered a de novo trimeric ACE2 (T-ACE2) protein scaffold that binds the trimeric spike protein with extremely high affinity (KD < 1 pM), while retaining ACE2 native sequence. T-ACE2 potently inhibits all tested pseudotyped viruses including SARS-CoV-2, SARS-CoV, eight naturally occurring SARS-CoV-2 mutants, two SARSr-CoVs as well as authentic SARS-CoV-2. The cryo-EM structure reveals that T-ACE2 can induce the transit of spike protein to "three-up" RBD conformation upon binding. T-ACE2 thus represents a promising class of broadly neutralizing proteins against SARS-CoVs and mutants.

bioengineering↗

bioRxiv2020

Molecular species selectivity of lipid transport creates a mitochondrial sink for di-unsaturated phospholipids

Mitochondria depend on the import of phospholipid precursors for the biosynthesis of the non-bilayer lipids phosphatidylethanolamine (PE) and cardiolipin required for proper function, yet the mechanism of lipid import remains elusive. Pulse labeling yeast with stable isotope-labeled serine followed by mass spectrometry analysis revealed that mitochondria preferentially import di-unsaturated phosphatidylserine (PS) for conversion to PE by the mitochondrial PS decarboxylase Psd1p. Several protein complexes tethering mitochondria to the endomembrane system have been implicated in lipid transport in yeast, including the endoplasmic reticulum (ER)-mitochondrial encounter structure (ERMES), ER-mitochondria complex (EMC) and the vacuole and mitochondria patch (vCLAMP). By limiting the availability of unsaturated phospholipids through overexpression of the glycerol-3-phosphate acyltransferase Sct1p, conditions were created to investigate the mechanism of lipid transfer and the contribution of the tethering complexes in vivo. Under these conditions, inactivation of ERMES components or the vCLAMP component Vps39p exacerbated the lipid phenotype, indicating that ERMES and Vps39 contribute to the mitochondrial sink for unsaturated acyl chains by mediating transfer of di-unsaturated phospholipids. The results support the concept that intermembrane lipid flow is rate-limited by molecular species-dependent lipid efflux from the donor membrane and driven by the lipid species concentration gradient between donor and acceptor membrane.

biochemistry↗

bioRxiv2019

Low-disturbance farming regenerates healthy critical zone towards sustainable agriculture

Intensive conventional farming has degraded farmland topsoil and seriously threaten food and environment security globally. Although low-disturbance practices have been widely adapted to restore soil health, whether this measure in a long run can potentially recover the critical deep soil to meet sustainable intensification of crop production are still unclear. Here we compared soil microbiome, physicochemical parameters along 3-m deep soil profiles, and crop yield in Northeast China subjected to ten years of farming practices at 3 levels of disturbance, including conventional tillage (CT), no-tillage without stover mulching (NTNS), and no-tillage with stover mulching (NTSM). We found that low-disturbance practices (NTNS and NTSM) promoted the ability of the deep soil to retain water, nitrogen and salt-extractable organic, regenerated whole-soil microbial diversity and metabolic function, improved topsoil organic carbon stock and corn yield in the drought year, showed the potential to reduce energy consumption and greenhouse gas emissions, thus regenerating highly efficient, sustainable agriculture.

ecology↗

bioRxiv2019

Engineered illumination devices for optogenetic control of cellular signaling dynamics

Spatially and temporally varying patterns of morphogen signals during development drive cell fate specification at the proper location and time. However, current in vitro methods typically do not allow for precise, dynamic, spatiotemporal control of morphogen signaling and are thus insufficient to readily study how morphogen dynamics impact cell behavior. Here we show that optogenetic Wnt/{beta}-catenin pathway activation can be controlled at user-defined intensities, temporal sequences, and spatial patterns using novel engineered illumination devices for optogenetic photostimulation and light activation at variable amplitudes (LAVA). The optical design of LAVA devices was optimized for uniform illumination of multi-well cell culture plates to enable high-throughput, spatiotemporal optogenetic activation of signaling pathways and protein-protein interactions. Using the LAVA devices, variation in light intensity induced a dose-dependent response in optoWnt activation and downstream Brachyury expression in human embryonic stem cells (hESCs). Furthermore, time-varying and spatially localized patterns of light revealed tissue patterning that models embryonic presentation of Wnt signals in vitro. The engineered LAVA devices thus provide a low-cost, user-friendly method for high-throughput and spatiotemporal optogenetic control of cell signaling for applications in developmental and cell biology.

bioengineering↗

bioRxiv2019

The identification of mecciRNAs and their roles in mitochondrial entry of proteins

Mammalian mitochondria have small genomes encoding very limited numbers of proteins. Over one thousand proteins and noncoding RNAs encoded by nuclear genome have to be imported from the cytosol into the mitochondria. Here we report the identification of hundreds of circular RNAs (mecciRNAs) encoded by mitochondrial genome. We provide both in vitro and in vivo evidence to show that mecciRNAs facilitate mitochondrial entry of nuclear-encoded proteins by serving as molecular chaperones in the folding of imported proteins. Known components of mitochondrial protein and RNA importation such as TOM40 and PNPASE interact with mecciRNAs and regulate protein entry. Expression of mecciRNAs is regulated, and these transcripts are critical for mitochondria in adapting to physiological conditions and diseases such as stresses and cancers by modulating mitochondrial protein importation. mecciRNAs and their associated physiological roles add categories and functions to eukaryotic circular RNAs, and shed novel lights on communication between mitochondria and nucleus.

molecular biology↗

bioRxiv2019

Distinct gut metagenomics and metaproteomics signatures in prediabetics and treatment-naïve type 2 diabetics

BackgroundThe gut microbiota plays important roles in modulating host metabolism. Previous studies have demonstrated differences in the gut microbiome of T2D and prediabetic individuals compared to healthy individuals, with distinct disease-related microbial profiles being reported in groups of different age and ethnicity. However, confounding factors such as anti-diabetic medication hamper identification of the gut microbial changes in disease development.\n\nMethodWe used a combination of in-depth metagenomics and metaproteomics analyses of faecal samples from treatment-naive type 2 diabetic (TN-T2D, n=77), pre-diabetic (Pre-DM, n=80), and normal glucose tolerant (NGT, n=97) individuals to investigate compositional and functional changes of the gut microbiota and the faecal content of microbial and host proteins in Pre-DM and treatment-naive T2D individuals to elucidate possible host-microbial interplays characterising different disease stages.\n\nFindingsWe observed distinct differences characterizing the gut microbiota of these three groups and validated several key features in an independent TN-T2D cohort. We also demonstrated that the content of several human antimicrobial peptides and pancreatic enzymes differed in faecal samples between three groups, such as reduced faecal level of antimicrobial peptides and pancreatic enzymes in TN-T2D.\n\nInterpretationOur findings suggest a complex, disease stage-dependent interplay between the gut microbiota and the host and emphasize the value of metaproteomics to gain further insight into interplays between the gut microbiota and the host.\n\nFundingNational Key Research and Development Program of China, No. 2017YFC0909703, Shenzhen Municipal Government of China, No. JCYJ20170817145809215, and National Natural Science Foundation of China, No. 31601073.

microbiology↗

bioRxiv2019

Optogenetic control of Wnt signaling for modeling early embryogenic patterning with human pluripotent stem cells

The processes of cell proliferation, differentiation, migration, and self-organization during early embryonic development are governed by dynamic, spatially and temporally varying morphogen signals. Analogous tissue patterns emerge spontaneously in embryonic stem cell (ESC) models for gastrulation, but mechanistic insight into this self-organization is limited by a lack of molecular methods to precisely control morphogen signal dynamics. Here we combine optogenetic stimulation and single-cell imaging approaches to study self-organization of human pluripotent stem cells. Precise control of morphogen signal dynamics, achieved through activation of canonical Wnt/{beta}-catenin signaling over a broad high dynamic range (>500-fold) using an optoWnt optogenetic system, drove broad transcriptional changes and mesendoderm differentiation of human ESCs at high efficiency (>95% cells). Furthermore, activating Wnt signaling in subpopulations of ESCs in 2D and 3D cultures induced cell self-organization and morphogenesis reminiscent of human gastrulation, including changes in cell migration and epithelial to mesenchymal transition. Our findings thus reveal an instructive role for Wnt in directing cell patterning in this ESC model for gastrulation.

bioengineering↗

bioRxiv2019

Immune Landscape of Invasive Ductal Carcinoma Tumour Microenvironment Identifies a Prognostic and Immunotherapeutically Relevant Gene Signature

BackgroundInvasive ductal carcinoma (IDC) is a clinically and molecularly distinct disease. Tumour microenvironment (TME) immune phenotypes play crucial roles in predicting clinical outcomes and therapeutic efficacy.\n\nMethodIn this study, we depict the immune landscape of IDC by using transcriptome profiling and clinical characteristics retrieved from The Cancer Genome Atlas (TCGA) data portal. Immune cell infiltration was evaluated via single-sample gene set enrichment (ssGSEA) analysis and systematically correlated with genomic characteristics and clinicopathological features of IDC patients. Furthermore, an immune signature was constructed using the least absolute shrinkage and selection operator (LASSO) Cox regression algorithm. A random forest algorithm was applied to identify the most important somatic gene mutations associated with the constructed immune signature. A nomogram that integrated clinicopathological features with the immune signature to predict survival probability was constructed by multivariate Cox regression.\n\nResultsThe IDC were clustered into low immune infiltration, intermediate immune infiltration, and high immune infiltration by the immune landscape. The high infiltration group had a favourable survival probability compared with that of the low infiltration group. The low-risk score subtype identified by the immune signature was characterized by T cell-mediated immune activation. Additionally, activation of the interferon- response, interferon-{gamma} response and TNF- signalling via the NF{kappa}B pathway was observed in the low-risk score subtype, which indicated T cell activation and may be responsible for significantly favourable outcomes in IDC patients. A random forest algorithm identified the most important somatic gene mutations associated with the constructed immune signature. Furthermore, a nomogram that integrated clinicopathological features with the immune signature to predict survival probability was constructed, revealing that the immune signature was an independent prognostic biomarker. Finally, the relationship of VEGFA, PD1, PDL-1 and CTLA-4 expression with the immune infiltration landscape and the immune signature was analysed to interpret the responses of IDC patients to immune checkpoint inhibitor therapy.\n\nConclusionTaken together, we performed a comprehensive evaluation of the immune landscape of IDC and constructed an immune signature related to the immune landscape. This analysis of TME immune infiltration patterns has shed light on how IDC respond to immune checkpoint therapy and may guide the development of novel drug combination strategies.

cancer biology↗

bioRxiv2018

PhenotypeXpression: sub-classification of disease states using public gene expression data and literature

The success of personalized medicine relies on proper disease classification and subtyping. Differential gene expression among disease subtypes can have a significant impact on treatment effect. This complicates the role of clinicians seeking more tailored diagnoses in cases where granular disease subtypes are not well defined. PhenotypeXpression (PhenoX) is a tool for rapid disease subtyping using publicly available gene expression data and literature. PhenoX aggregates and clusters gene expression data to determine potential disease subtypes, and develops a phenotypic profile for each subtype using term co-occurrences in published literature. Although the availability of public gene expression data is limited, we are able to observe clearly defined subtypes for several conditions.

bioinformatics↗

bioRxiv2018

GrgA as a potential target of selective antichlamydials

Chlamydia is a common pathogen that can causes serious complications in the reproductive system and eyes. Lack of vaccine and other effective prophylactic measures coupled with the largely asymptomatic nature and unrare clinical treatment failure calls for development of new antichlamydials, particularly selective antichlamydials without adverse effects on humans and the beneficial microbiota. We previously reported that benzal-N-acylhydrazones (BAH) can inhibit chlamydiae without detectable adverse effects on host cells and beneficial lactobacilli that dominate the human vaginal microbiota among reproductive-age women. However, the antichlamydial mechanism of BAH is not known. Whereas 4 single nucleotide polymorphisms (i.e., SNP1-4) were identified in a rare Chlamydia variant with a low level of BAH resistance, termed MCR, previous studies failed to establish a causal effect of any particular SNP(s). In the present work, we performed recombination to segregate the four SNPs. Susceptibility tests indicate that the R51G GrgA allele is both necessary and sufficient for the low level of BAH resistance. Thus, the Chlamydia-specific transcription factor GrgA either is a direct target of BAH or regulates BAH susceptibility. We further confirm an extremely low rate of BAH resistance in Chlamydia. Our findings warrant exploration of GrgA as a therapeutic and prophylactic target for chlamydial infections.

microbiology↗

bioRxiv2018

Expression profile analysis of circular RNAs in essential hypertension by microarray and bioinformatics.

Circular RNAs (circRNAs), widely found in human cells, are involved in disease and play an important role in progression. To determine whether circRNAs are related in essential hypertension (EH), we analyzed the expression profile of circRNAs and miRNAs in 5 EH and 5 healthy controls cases which were screened by microarray. Through microarray data and public data analysis, differently expressed transcripts were divided into modules, and circRNAs were functionally annotated by miRNAs. The expression of two circRNAs, has_circ_0037909 and has_circ_0105015, were validated in EH by qRT-PCR, which may be associated with EH. Further analysis showed that two circRNAs might through immune system by up-regulation circRNAs and down-regulation expression. These circRNAs biological functions need to be further validated.

genetics↗

bioRxiv2018

Influence of food and Nosema ceranae infection on the gut microbiota of Apis cerana workers

BackgroundGut microbiota plays an essential role in bees health. To elucidate the effect of food and Nosema ceranae infection on the gut microbiota of honeybee Apis cerana, we used 16S rRNA sequencing to survey the gut microbiota of honeybee workers fed with sugar water or beebread and inoculated with or without N. ceranae.\n\nResultsThe gut microbiota of A. cerana is dominated by Serratia, Snodgrassella, and Lactobacillus genera. The overall gut microbiota diversity was significantly differential by food type. The N. ceranae infection significantly affects the gut microbiota only at bees fed with sugar water. Higher abundance of Lactobacillus, Gluconacetobacter and Snodgrassella and lower abundance of Serratia were found in bees fed with beebread than with sugar water. N. ceranae infection led to higher abundance of Snodgrassella and lower abundance of Serratia in sugar-fed bees. Imputed bacterial KEGG pathways showed the significant metagenomics functional differences by feeding and N. ceranae infections. Furthermore, A. cerana workers fed with sugar water showed lower N. ceranae spore loads but higher mortality than those fed with beebread. The cumulative mortality was strongly positive correlated (rho=0.61) with the changes of overall microbiota dissimilarities by N. ceranae infection.\n\nConclusionsBoth food and N. ceranae infection significantly affect the gut microbiota in A. cerana workers. Beebread feeding not only provide better nutrition but also help establish a more stabled gut microbiota therefore protect bee in response to N. ceranae infection.\n\nAbstract ImportanceGut microbiota plays an essential role in bees health. Scientific evidence suggests the diet and infection can affect the gut microbiota and modulate the gut health, however the interplay between those two factors and bee gut microbiota is not well known. In this study, we used high-throughput sequencing method to monitor the changes of gut microbiota by both food intake and the Nosema ceranae infection. Our result showed that the gut microbiota composition and diversity of Asia Honeybee was significantly associated with both food intake and the N. ceranae infection. More interestingly, bees fed with beebread showed higher microbiota stability and less mortality than those fed with sugar water when infected by N. ceranae. Those data suggest the potential role of beebread, not only providing better nutrition but also helping establish a more stabled gut microbiota to protect bee against N. ceranae infection.

microbiology↗

bioRxiv2018

A role for GrgA in regulation of σ28-dependent transcription in the obligate intracellular bacterial pathogen Chlamydia trachomatis

The sexually transmitted obligate intracellular bacterial pathogen Chlamydia trachomatis has a unique developmental cycle consisting of two contrasting cellular forms. Whereas the primary Chlamydia sigma factor, {sigma}66, is involved in the expression of the majority of chlamydial genes throughout the developmental cycle, expression of several late genes requires the alternative sigma factor {sigma}28. In prior work we identified GrgA as a Chlamydia-specific transcription factor that activates {sigma}66-dependent transcription by binding DNA and interacting with a non-conserved region (NCR) of {sigma}66. Here, we extend these findings by showing GrgA can also activate {sigma}28-dependent transcription through direct interaction with {sigma}28. We measure the binding affinity of GrgA for both {sigma}66and {sigma}28, and we identify regions of GrgA important for {sigma}28-dependent transcription. Similar to results obtained with {sigma}66, we find that GrgAs interaction with {sigma}28 involves a NCR located upstream of conserved region 2 of {sigma}28. Our findings suggest GrgA is an important regulator of both {sigma}66- and {sigma}28-dependent transcription in C. trachomatis and further highlight NCRs of bacterial RNA polymerase as targets for regulatory factors unique to particular organisms.

microbiology↗

bioRxiv2017

Exportin Crm1 is repurposed as a docking protein to generate microtubule organizing centers at the nuclear pore

Non-centrosomal microtubule organizing centers (MTOCs) are important for microtubule organization in many cell types. In fission yeast Schizosaccharomyces pombe, the protein Mto1, together with partner protein Mto2 (Mto1/2 complex), recruits the {gamma}-tubulin complex to multiple non-centrosomal MTOCs, including the nuclear envelope (NE). Here, we develop a comparative-interactome mass spectrometry approach to determine how Mto1 localizes to the NE. Surprisingly, we find that Mto1, a constitutively cytoplasmic protein, docks at nuclear pore complexes (NPCs), via interaction with exportin Crm1 and cytoplasmic FG-nucleoporin Nup146. Although Mto1 is not a nuclear export cargo, it binds Crm1 via a nuclear export signal-like sequence, and docking requires both Ran in the GTP-bound state and Nup146 FG repeats. In addition to determining the mechanism of MTOC formation at the NE, our results reveal a novel role for Crm1 and the nuclear export machinery in the stable docking of a cytoplasmic protein complex at NPCs.

cell biology↗