Biology subjects

Ye, L.

Publications and source records attributed to Ye, L..

At least 109 records · Page 6Linked to original sources

bioRxiv2020

Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways

The intestinal epithelium senses nutritional and microbial stimuli using epithelial sensory enteroendocrine cells (EECs). EECs can communicate nutritional information to the nervous system, but similar mechanisms for microbial information are unknown. Using in vivo real-time measurements of EEC and nervous system activity in zebrafish, we discovered that the bacteria Edwardsiella tarda specifically activates EECs through the receptor transient receptor potential ankyrin A1 (Trpa1) and increases intestinal motility in an EEC-dependent manner. Microbial, pharmacological, or optogenetic activation of Trpa1+EECs directly stimulates vagal sensory ganglia and activates cholinergic enteric neurons through 5-HT. We identified a subset of indole derivatives of tryptophan catabolism produced by E. tarda and other gut microbes that potently activates zebrafish EEC Trpa1 signaling and also directly stimulates human and mouse Trpa1 and intestinal 5-HT secretion. These results establish a molecular pathway by which EECs regulate enteric and vagal neuronal pathways in response to specific microbial signals.

physiology↗

bioRxiv2020

HAP40 is a conserved central regulator of Huntingtin and a specific modulator of mutant Huntingtin toxicity

Perturbation of Huntingtin (HTT)s physiological function is one postulated pathogenic factor in Huntingtons disease (HD). However, little is known how HTT is regulated in vivo. In a proteomic study, we isolated a novel [~]40kDa protein as a strong binding partner of Drosophila HTT and demonstrated it was the functional ortholog of HAP40, an HTT associated protein shown recently to modulate HTTs conformation but with unclear physiological and pathologic roles. We showed that in both flies and human cells, HAP40 maintained conserved physical and functional interactions with HTT, loss of HAP40 resulted in similar phenotypes as HTT knockout, including animal viability and autophagy, and more strikingly, HAP40 depletion significantly reduced the levels of endogenous HTT, while HAP40 was mostly degraded via the proteasome in the absence of HTT. Interestingly, polyglutamine expansion in HTT did not affect its affinity for HAP40. However, HAP40 modulated HD pathogenesis in Drosophila model by regulating the overall protein levels and the toxicity of full-length mutant HTT. Together, our study uncovers a conserved mechanism governing the stability and in vivo functions of HTT, and demonstrates that HAP40 is a central and positive regulator of HTT, a potential modulator of HD pathogenesis and a promising candidate for "HTT-lowering" strategy against HD.

neuroscience↗

bioRxiv2020

C-Jun N-terminal kinase (JNK) pathway activation is essential for dental papilla cells polarization

During tooth development, dental papilla cells could develop into odontoblasts with polarized morphology and cell function, c-Jun N-terminal kinase (JNK) signaling could participate in this process. Histological staining, qPCR and Western Blot shown that activation of JNK signaling in polarized mouse dental papilla tissue. In vitro cell culture and organ culture method found JNK inhibitor SP600125 postponed tooth germ development and reduced the polarization, migration and differentiation of mouse dental papilla cells (mDPCs) in vitro. The expression of polarity-related genes including Prickle3, Golga2, Golga5 and RhoA was consistent with JNK signaling activation, by screening of up-regulated polarity-related genes during the process of dental papilla development and mDPCs or A11 differentiation. Further, constitutively active RhoA mutant (RhoA Q63L) partly rescue the inhibition of SP600125 on cell differentiation and polarity formation of mDPCs. This study suggests that JNK signaling has a positive role in dental papilla cells polarization formation.

cell biology↗

bioRxiv2020

Conserved anti-inflammatory effects and sensing of butyrate in zebrafish

Short chain fatty acids (SCFAs) are produced by microbial fermentation of dietary fiber in the gut. Butyrate is a particularly important SCFA with anti-inflammatory properties and is generally present at lower levels in inflammatory diseases associated with gut microbiota dysbiosis in mammals. We aimed to determine if SCFAs are produced by the zebrafish microbiome and if SCFAs exert conserved effects on zebrafish immunity as an example of the non-mammalian vertebrate immune system. We demonstrate that bacterial communities from adult zebrafish intestines synthesize all three main SCFA in vitro, although SCFA were below our detectable limits in zebrafish intestines in vivo. Immersion in butyrate, but not acetate or propionate, reduced the recruitment of neutrophils and M1-type pro-inflammatory macrophages to wounds. We found conservation of butyrate sensing by neutrophils via orthologs of the hydroxycarboxylic acid receptor 1 (hcar1) gene. Neutrophils from Hcar1-depeleted embryos were no longer responsive to the anti-inflammatory effects of butyrate, while macrophage sensitivity to butyrate was independent of Hcar1. Our data demonstrate conservation of anti-inflammatory butyrate effects and identify the presence of a conserved molecular receptor in fish.

immunology↗

bioRxiv2020

Combined abdominal heterotopic heart and aorta transplant model in mice

AbstractBackground Allograft vasculopathy (AV) remains a major obstacle to long-term allograft survival. While the mouse aortic transplantation model has been proven as a useful tool for study of the pathogenesis of AV, simultaneous transplantation of the aorta alongside the transplantation of another organ may reveal more clinically relevant mechanisms that contribute to the pathogenesis of chronic allograft rejection. Therefore, we developed a combined abdominal heart and aorta transplantation model in mice which benefits from reducing animal and drug utilization, while providing an improved model to study the progressive nature of AV.Methods The middle of the infrarenal aorta of the recipient mouse was ligatured between the renal artery and its bifurcation. Proximal and distal aortotomies were performed at this site above and below the ligature, respectively, for the subsequent anastomoses of the donor aorta and heart grafts to the recipient infrarenal aorta in an end-to-side fashion. The distal anastomotic site of the recipient infrarenal aorta was connected with the outlet of the donor aorta. Uniquely, the proximal anastomotic site on the recipient infrarenal aorta was shared to connect with both the inlet of the donor aorta and the inflow tract to the donor heart. The outflow tract from the donor heart was connected to the recipient inferior vena cava (IVC).Results The median times for harvesting the heart graft, aorta graft, recipient preparation and anastomosis were 11.5, 8.0, 9.0 and 40.5 min, respectively, resulting in a total median ischemic time of 70 min. The surgery survival rate was more than 96% (29/30). Both the syngeneic C57Bl/6 aorta and heart grafts survived more than 90 days in 29 C57Bl/6 recipients. Further, Balb/c to C57Bl/6 allografts treated with anti-CD40L and CTLA4.Ig survived more than 90 days with a 100% (3/3) survival rate. (3/3).Conclusions This model is presented as a new tool for researchers to investigate transplant immunology and assess immunosuppressive strategies. It is possible to share a common anastomotic stoma on the recipient abdominal aorta to reconstruct both the aorta graft entrance and heart graft inflow tract. This allows for the study of allogeneic effects on both the aorta and heart from the same animal in a single survival surgery.Competing Interest StatementThe authors have declared no competing interest.AbbreviationsAVallograft vasculopathyCAVcardiac allograft vasculopathyIVCinferior vena cavaMHCmajor histocompatibility complexSVCsuperior vena cavaView Full Text

pathology↗

bioRxiv2020

Bcl6 Preserves the Suppressive Function of Regulatory T Cells during Tumorigenesis

During tumorigenesis, tumor infiltrating regulatory T (Treg) cells restrict the function of effector T cells in tumor microenvironment and thereby promoting tumor growth. The anti-tumor activity of effector T cells can be therapeutically unleashed, and is now being exploited for the treatment of various types of human cancers. However, the immune suppressive function of Treg cells remains a major hurdle to broader effectiveness of tumor immunotherapy. In this article, we reported that the deletion of Bcl6 specifically in Treg cells led to stunted tumor growth, which was caused by impaired Treg cell responses. Notably, Bcl6 is essential in maintaining the lineage stability of Treg cells in tumor microenvironment. Meanwhile, we found that the absence of follicular regulatory T (Tfr) cells, which is a result of Bcl6 deletion in Foxp3+ cells, was dispensable for tumor control. Importantly, the increased Bcl6 expression in Treg cells is associated with poor prognosis of human colorectal cancer and lymph node metastasis of skin melanoma. Furthermore, Bcl6 deletion in Treg cells exhibits synergistic effects with immune checkpoint blockade therapy. Collectively, these results indicate that Bcl6 actively participates in regulating Treg cell immune responses during tumorigenesis and can be exploited as a therapeutic target of anti-tumor immunity.

immunology↗

bioRxiv2019

An electrostatic-interaction-based mechanism triggering misfolding of prion proteins from cellular isoform to scrapie isoform

Understanding how prion proteins refold from a cellular isoform (PrPC) to a disease-causing isoform (PrPSc) has been among the "ultimate challenges" in molecular biology, biophysics, pathology, and immunology. Conformational changes of prion proteins from PrPC to PrPSc involve the unfolding of a short -helix that overshadows the challenge. Considering the mechanisms of electrostatic attraction, thermal disturbance, hydrogen ion concentration, hydrophobic interaction, and the shielding effect of water molecules, this study reveals an electrostatic-interaction-based mechanism by means of which prion proteins refold in an aqueous environment. The electrostatic-interaction-induced protein unfolding mechanism causes a hydrophobic polypeptide segment to dangle out over the conglobate main body of the prion protein, thereby allowing the first triangular hydrophobic rung formation via hydrophobic interaction. A molecular model of PrPSc is proposed that allows the {beta}-solenoid with a triangular hydrophobic core. Statement of SignificanceWe present three main results that would revolutionize the understanding of pathology of prion diseases. First, the prion protein refolding (from cellular isoform to scrapie isoform) derives from the unfolding of the shortest -helix of PrPC, which provides a long polypeptide segment full of hydrophobic residues dangling out over the conglobate main body of the prion protein, thereby allowing formation of the first triangular hydrophobic rung via hydrophobic interaction. Second, polyanions-induced increasing in local concentration of hydrogen ion (i.e., the PH increase) undermines the shielding effect of water molecules, thereby allowing escape of the arginine side chains from the hydration shell, destabilizing the shortest -helix and initiating the refolding of PrPC. Third, a {beta}-solenoid structural model for PrPSc with a triangular hydrophobic core is proposed.

biophysics↗

bioRxiv2019

An inducible genome editing system for plants

Conditional manipulation of gene expression is a key approach to investigating the primary function of a gene in a biological process. While conditional and cell-type specific overexpression systems exist for plants, there are currently no systems available to disable a gene completely and conditionally. Here, we present a novel tool with which target genes can be efficiently conditionally knocked out at any developmental stage. The target gene is manipulated using the CRISPR-Cas9 genome editing technology, and conditionality is achieved with the well-established estrogen-inducible XVE system. Target genes can also be knocked-out in a cell-type specific manner. Our tool is easy to construct and will be particularly useful for studying genes which have null-alleles that are non-viable or show strong developmental defects.

plant biology↗

bioRxiv2019

Generation and quality control of maternal plasma lipidomics data associated with preterm birth

Preterm birth is not only one of the most common causes of infant deaths but also a great risk for them to have severe subsequent health problems. The causes of preterm birth may be due to a combination of genetic and environmental factors, however, it remains largely unknown. Here we report an untargeted lipidomics dataset of plasma specimens from 258 pregnant women at the stage of twelve to twenty-five gestational weeks. Among them, 44 had extremely to very preterm births, 54 had moderate preterm births, 71 had late preterm births and 89 had full-term deliveries. The metabolomic profiling was generated with an UPLC-MS in both the positive and negative mode, and putative identification of all the metabolites was provided by searching against online databases. The quality assessment performed on quality control samples showed that the data is reproducible, robust and reliable. Both the raw data files, the raw and processed data matrix were available on MetaboLights, which may be used as a valuable validation dataset for new findings and a test dataset for novel algorithms.

systems biology↗

bioRxiv2019

Machine learning aided analyses of thousands of draft genomes reveal plant- and environment-specific features of activated sludge process

Microorganisms in activated sludge (AS) play key roles in the wastewater treatment process. However, the ecological behavior of microorganisms in AS and their differences with microorganisms in other environments have mainly been studied using 16S rRNA gene that may not truly represent their in-situ functions. Here, we present 2045 bacterial and archaeal metagenome-assembled genomes (MAGs) recovered from 1.35 Tb of metagenomic sequencing data generated from 114 AS samples of 23 full-scale wastewater treatment plants (WWTPs). The average completeness and contamination of the MAGs are 82.0% and 2.0%, respectively. We find that the AS MAGs have obviously plant-specific features and few proteins are shared by different WWTPs, especially for WWTPs located in geographically distant areas. Despite the differences, specific functional traits (e.g. functions related to aerobic metabolism, nutrient sensing/acquisition, biofilm formation, etc.) of AS MAGs could be identified by a machine learning approach, and based on these traits, AS MAGs could be differentiated from MAGs of other environments with an accuracy of 96.6%. Our work provides valuable genome resources for future investigation of the AS microbiome and also introduces a novel approach to understand the microbial ecology in different ecosystems.

microbiology↗

bioRxiv2019

High fat diet induces microbiota-dependent silencing of enteroendocrine cells

Enteroendocrine cells (EECs) are specialized sensory cells in the intestinal epithelium that sense and transduce nutrient information. Consumption of dietary fat contributes to metabolic disorders, but EEC adaptations to high fat feeding were unknown. Here, we established a new experimental system to directly investigate EEC activity in vivo using a zebrafish reporter of EEC calcium signaling. Our results reveal that high fat feeding alters EEC morphology and converts them into a nutrient insensitive state that is coupled to endoplasmic reticulum (ER) stress. We called this novel adaptation \"EEC silencing\". Gnotobiotic studies revealed that germ-free zebrafish are resistant to high fat diet induced EEC silencing. High fat feeding altered gut microbiota composition including enrichment of Acinetobacter species, and we identified an Acinetobacter strain sufficient to induce EEC silencing. These results establish a new mechanism by which dietary fat and gut microbiota modulate EEC nutrient sensing and signaling.

developmental biology↗

bioRxiv2018

The landscapes of DNA methylation associated with the transcriptomic network in laying hens and broilers get insight to embryonic muscle development in chicken

As DNA methylation is one of the key epigenetic mechanisms involved in embryonic development, elucidating its relationship with non-coding RNA and genes is essential for understanding early development. In this study, we performed single-base-resolution bisulfite sequencing together with RNA-seq to explore the genetic basis of embryonic muscle development in chicken. Comparison of methylome profiles between broilers and laying hens revealed that lower methylation in broilers might contribute to muscle development. Differential methylated region (DMR) analysis between two chicken lines showed that the majority of DMRs were hypo-DMRs for broilers. Differential methylated genes were significantly enriched in muscle development-related terms at E13 and E19. Furthermore, by constructing the network of the lncRNAs, we identified a lncRNA, which we named MYH1-AS, that potentially regulated muscle development. These findings reveal an integrative landscape of late period of embryonic myogenesis in chicken and give rise to a comprehensive understanding of epigenetic and transcriptional regulation, in skeletal muscle development. Our study provides a reliable data resource for further muscle studies.

bioinformatics↗

bioRxiv2018

The LIM-Only Protein FHL2 is Involved in Autophagy to Regulate the Development of Skeletal Muscle

Four and a half LIM domain protein 2 (FHL2) is a LIM domain protein expressed in muscle tissue whose deletion is causative of myopathies. Although FHL2 has a confirmed important role in muscle development, its autophagy-related function in muscle differentiation has not been fully determined. To explore the role of FHL2 in autophagy-related muscle regulation, FHL2-silenced and -overexpressing C2C12 mouse cells were examined. Immunofluorescence and co-immunoprecipitation assay findings showed that FHL2 silencing reduced LC3- protein expression and the amount of LC3 that co-immunoprecipitated with FHL2, indicating that FHL2 interacts with LC3- in the formation of autophagosomes. Moreover, the expression of muscle development marker genes such as MyoD1 and MyoG was lower in FHL2-silenced C2C12 cells but not in FHL2-overexpressing C2C12 cells. Electron microscopy analysis revealed large empty autophagosomes in FHL2-silenced myoblasts, while flow cytometry suggested that FHL2 silencing made cells more vulnerable to staurosporine-induced cell death. In conclusion, we propose that FHL2 interacts with LC3- in autophagosome formation to regulate the development of muscle cells.

molecular biology↗

bioRxiv2018

Niacin fine-tunes energy homeostasis through canonical GPR109A signaling

Niacin has long been considered as a high-potency drug for beneficially treating lipid abnormalities, however, its anti-atherosclerotic effects have been challenged by recent studies. Here, we demonstrated that oral supplementation of niacin resulted in a significant reduction in body weight and fat mass without affecting food intake in high-fat diet-fed wild-type mice, but not in GPR109A-defeicient mice. Further investigation showed that niacin challenge led to a remarkable inhibition of hepatic lipogenesis via a GPR109A-dependent ERK1/2/AMPK pathway. Additionally, we demonstrated that niacin treatment stimulated thermogenesis in brown adipose tissue by induction of thermogenic genes via GPR109A. Moreover, we observed that mice exposed to niacin exhibited a dramatic decrease in intestinal absorption of fatty acids. Together, our data demonstrate that acting on GPR109A, niacin shows the potential to maintain energy homeostasis by fine-tuning hepatic lipogenesis, BAT/beige thermogenesis and intestinal fat absorption, representing a potential approach to the treatment of lipid abnormalities.

cell biology↗

bioRxiv2018

A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping

The advent of long-read sequencing technologies has greatly facilitated assemblies of large eukaryotic genomes. In this paper, Oxford Nanopore sequences generated on a MinION sequencer were combined with BioNano Genomics Direct Label and Stain (DLS) optical maps to generate a chromosome-scale de novo assembly of the repeat-rich Sorghum bicolor Tx430 genome. The final hybrid assembly consists of 29 scaffolds, encompassing in most cases entire chromosome arms. It has a scaffold N50 value of 33.28Mbps and covers >90% of Sorghum bicolor expected genome length. A sequence accuracy of 99.67% was obtained in unique regions after aligning contigs against Illumina Tx430 data. Alignments showed that 99.4% of the 34,211 public gene models are present in the assembly, including 94.2% mapping end-to-end. Comparisons of the DLS optical maps against the public Sorghum Bicolor v3.0.1 BTx623 genome assembly suggest the presence of substantial genomic rearrangements whose origin remains to be determined.

genomics↗

bioRxiv2017

Direct in vivo mapping of functional suppressors in glioblastoma genome

Glioblastoma (GBM) is one of the deadliest cancers, with limited effective treatments and single-digit five-year survival 1-7. A causative understanding of genetic factors that regulate GBM formation is of central importance 8-19. However, a global, quantitative and functional understanding of gliomagenesis in the native brain environment has been lacking due to multiple challenges. Here, we developed an adeno-associated virus (AAV) mediated autochthonous CRISPR screen and directly mapped functional suppressors in the GBM genome. Stereotaxic delivery of an AAV library targeting significantly mutated genes into fully immunocompetent conditional Cas9 mice robustly led to gliomagenesis, resulting in tumors that recapitulate features of human GBM. Targeted capture sequencing revealed deep mutational profiles with diverse patterns across mice, uncovering in vivo roles of previously uncharacterized factors in GBM such as immune regulator B2m, zinc finger protein Zc3h13, transcription repressor Cic, epigenetic regulators Mll2/3 and Arid1b, alongside canonical tumor suppressors Nf1 and Pten. Comparative cancer genomics showed that the mutation frequencies across all genes tested in mice significantly correlate with those in human from two independent patient cohorts. Co-mutation analysis identified frequently co-occurring driver combinations, which were validated using AAV minipools, such as Mll2, B2m-Nf1, Mll3-Nf1 and Zc3h13-Rb1. Distinct from Nf1-oncotype tumors, Rb1-oncotype tumors exhibit undifferentiated histopathology phenotype and aberrant activation of developmental reprogramming signatures such as Homeobox gene clusters. The secondary addition of Zc3h13 or Pten mutations drastically altered the gene expression profiles of Rb1 mutants and rendered them more resistant to the GBM chemotherapeutic temozolomide. Our study provides a systematic functional landscape of GBM suppressors directly in vivo, opening new paths for high-throughput molecular mapping and cancer phenotyping.

systems biology↗

bioRxiv2017

Pooled AAV-CRISPR Screen with Targeted Amplicon Sequencing

High-resolution, high-throughput direct in vivo screening of functional genetic factors in native tissues has long been challenging. Adeno-associated viruses (AAV) are powerful carriers of transgenes and have been shown to mediate efficient genome editing in various organs in mice. Here, we developed a new technological approach, Pooled AAV-CRISPR Screen with Targeted Amplicon Sequencing (PASTAS), and demonstrated its application for directly mapping functional cancer driver variants in the mouse liver in an autochthonous manner. Intravenous delivery of an AAV-CRISPR library targeting a set of the most frequently mutated tumor suppressor genes into fully immunocompetent conditional Cas9 knock-in mice consistently generated highly complex autochthonous liver tumors. The molecular landscapes of these genetically diverse tumors were mapped out by deep direct readout of Cas9-generated variants at predicted sgRNA cut sites using molecular inversion probe sequencing. Co-occurrence and correlation analyses as well as validation with lower complexity minipools further confirmed the potency of various co-mutated drivers. The PASTAS method can be applied to virtually any gene sets, any cancer types, or any type of in vivo genetic studies other than cancer.

systems biology↗

bioRxiv2017

Mapping in vivo genetic interactomics through Cpf1 crRNA array screening

Genetic interactions lay the foundation of biological networks in virtually all organisms. Due to the complexity of mammalian genomes and cellular architectures, unbiased mapping of genetic interactions in vivo is challenging. Cpf1 is a single effector RNA-guided nuclease that enables multiplexed genome editing using crRNA arrays. Here we designed a Cpf1 crRNA array library targeting all pairwise permutations of the most significantly mutated nononcogenes, and performed double knockout screens in mice using a model of malignant transformation as well as a model of metastasis. CrRNA array sequencing revealed a quantitative landscape of all single and double knockouts. Enrichment, synergy and clonal analyses identified many unpredicted drivers and co-drivers of transformation and metastasis, with epigenetic factors as hubs of these highly connected networks. Our study demonstrates a powerful yet simple approach for in vivo mapping of unbiased genetic interactomes in mammalian species at a phenotypic level.

genetics↗