Biology subjects

Peng, W.

Publications and source records attributed to Peng, W..

88 records · Page 5Linked to original sources

bioRxiv2020

Evidence of Superior and Inferior Sinoatrial Nodes in the Mammalian Heart

The initiation of rhythmic heartbeat is the earliest manifestation of new life after conception. A normal heartbeat originates as an action potential in a group of pacemaker cells of the sinoatrial node (SAN)1. Pacemaker cells are evident since early embryogenesis when the entire sinus venosus exhibits electric automaticity and possesses specific gene expression profile distinct from that of working myocardium2,3. During the subsequent looping and ballooning stages of cardiac development, pacemaker cells eventually localize into SAN near the superior vena cava (SVC) when the two horns of the sinus venosus coil in formation of the atria2. The heart rate and anatomical site of origin of pacemaker activity dynamically change in response to various physiological input such as autonomic stimuli and pharmacological interventions4. However, the mechanisms of dominant pacemaker shift are not well understood. Here, we present functional and molecular evidence of two competing right atrial pacemakers localized near the SVC and the inferior vena cava (IVC), which we call the superior and inferior SANs: sSAN and iSAN. Using ex vivo optical mapping techniques and RNA sequencing of rat and human hearts, we demonstrate that sSAN and iSAN preferentially control the fast and slow heart rates during sympathetic or parasympathetic stimulation, respectively. RNAseq confirmed unique transcriptional profiles of sSAN and iSAN, which differs from both atria and ventricles. We speculate that the anatomical locations of sSAN and iSAN are a result of the way the two horns of the sinus venosus twist into a mature chambered heart. We anticipate these findings would clarify previously observed migration of dominant pacemaker and corresponding changes in P-wave morphology in many species. Furthermore, we expect these findings will shed light onto pathogenesis of aberrant pacemakers responsible for life-threatening arrhythmias near orifices of other major vessels: SVC and IVC, coronary sinus, pulmonary veins, aorta and the right ventricular outflow tract.Competing Interest StatementThe authors have declared no competing interest.View Full Text

physiology↗

bioRxiv2020

Whole Genome Sequencing of 5 Tibetan Sheep Breeds Identifies Selective Signatures to Adaptability at Different High-Altitude Areas in Qinghai-Tibetan Plateau

Tibetan sheep is one of primitive Chinese sheep breeds, which achieved the divergence about 2500 years ago in Qinghai plateau region. According to different geographic conditions, especially altitudes, Tibetan sheep evolved into different breeds. In this study, we performed pooled whole genome resequencing of 125 individuals from 5 representative Tibetan sheep breeds. Comparative genomic analysis showed that they can be divided into different clades with a close genetic relationship. However, some genes with common selective regions were enriched for hypoxic adaptability in different breeds living at higher altitude, including GHR, BMP15 and CPLANE1. Furthermore, breed-specific selective regions about physical characteristics, especially wool growth, were found in genes such as BSND, USP24, NCAPG and LCORL. This study could contribute to our understanding about trait formation and offer a reference for breeding of Tibetan sheep.

genomics↗

bioRxiv2020

A GRAB sensor reveals activity-dependent non-vesicular somatodendritic adenosine release

The purinergic signaling molecule adenosine (Ado) modulates many physiological and pathological brain functions,but its spatiotemporal release dynamics in the brain remains largely unknown. We developed a genetically encoded GPCR-Activation-Based Ado sensor (GRABAdo) in which Ado-induced changes in the human A2A receptor are reflected by fluorescence increases. This GRABAdo revealed that neuronal activity-induced extracellular Ado elevation was due to direct Ado release from somatodendritic regions of the neuron, requiring calcium influx through L-type calcium channels, rather than the degradation of extracellular ATP. The Ado release was slow ([~]30 s) and depended on equilibrative nucleoside transporters (ENTs) rather than conventional vesicular release mechanisms. Thus, GRABAdo reveals an activity-dependent slow Ado release from somatodendritic region of the neuron, potentially serving modulating functions as a retrograde signal.

neuroscience↗

bioRxiv2020

Single-cell transcriptome profiling an adult human cell atlas of 15 major organs

BackgroundAs core units of organ tissues, cells of various types play their harmonious rhythms to maintain the homeostasis of the human body. It is essential to identify the characteristics of cells in human organs and their regulatory networks for understanding the biological mechanisms related to health and disease. However, a systematic and comprehensive single-cell transcriptional profile across multiple organs of a normal human adult is missing. ResultsWe perform single-cell transcriptomes of 84,363 cells derived from 15 tissue organs of one adult donor and generate an adult human cell atlas. The adult human cell atlas depicts 252 subtypes of cells, including major cell types such as T, B, myeloid, epithelial, and stromal cells, as well as novel COCH+ fibroblasts and FibSmo cells, each of which is distinguished by multiple marker genes and transcriptional profiles. These collectively contribute to the heterogeneity of major human organs. Moreover, T cell and B cell receptor repertoire comparisons and trajectory analyses reveal direct clonal sharing of T and B cells with various developmental states among different tissues. Furthermore, novel cell markers, transcription factors and ligand-receptor pairs are identified with potential functional regulations in maintaining the homeostasis of human cells among tissues. ConclusionsThe adult human cell atlas reveals the inter- and intra-organ heterogeneity of cell characteristics and provides a useful resource in uncovering key events during the development of human diseases in the context of the heterogeneity of cells and organs.

cell biology↗

bioRxiv2020

A genetically encoded GRAB sensor for measuring serotonin dynamics in vivo

Serotonin (5-HT) is a phylogenetically conserved monoamine neurotransmitter modulating a variety of processes in the brain. To directly visualize the dynamics of 5-HT, we developed a genetically encoded GPCR-Activation-Based 5-HT (GRAB5-HT) sensor with high sensitivity, selectivity, and spatiotemporal resolution. GRAB5-HT, detected 5-HT release in multiple physiological and pathological conditions in both flies and mice, and thus provides new insights into the dynamics and mechanisms of 5-HT signaling.

neuroscience↗

bioRxiv2020

Modulation of metabolic functions through Cas13d-mediated gene knockdown in liver

RNA knockdown in vivo carries significant potential for disease modelings and therapies. Despite the emerging approaches of CRISPR/Cas9-mediated permanent knock out of targeted genes, strategies targeting RNA for disruption are advantageous in the treatment of acquired metabolic disorders when permanent modification of the genome DNA is not appropriate, and RNA virus infection diseases when pathogenic DNA is not available (such as SARS-Cov-2 and MERS infections). Recently, Cas13d, a family of RNA-targeting CRISPR effectors, has been shown to accomplish robust down-regulation of cellular RNAs in mammalian cells in vitro. Among the various Cas13d subtypes, CasRx (RfxCas13d) showed the most potent RNA knockdown efficiency in HEK293T cells. However, the RNA-targeting activity of Cas13d still needs to be verified in vivo. In this study, the CasRx system was demonstrated to efficiently and functionally knock down genes related to metabolism functions, including Pten, Pcsk9 and lncLstr, in mouse hepatocytes. CasRx-mediated simultaneous knockdown of multiple genes was also achieved by sgRNA arrays, providing a useful strategy to modulate complex metabolism networks. Moreover, the AAV (adeno-associated virus)-mediated delivery of CasRx and Pcsk9 sgRNAs into mouse liver successfully decreased serum PCSK9, resulting in significant reduction of serum cholesterol levels. Importantly, CasRx-mediated knockdown of Pcsk9 is reversible and Pcsk9 could be repeatedly down-regulated, providing an effective strategy to reversibly modulate metabolic genes. The present work supplies a successful proof-of-concept trial that suggests efficient and regulatory knockdown of target metabolic genes for a designed metabolism modulation in the liver.

genomics↗

bioRxiv2019

An optimized acetylcholine sensor for monitoring in vivo cholinergic activity

The ability to directly measure acetylcholine (ACh) release is an essential first step towards understanding its physiological function. Here we optimized the GRABACh (GPCR-Activation-Based-ACh) sensor with significantly improved sensitivity and minimal downstream coupling. Using this sensor, we measured in-vivo cholinergic activity in both Drosophila and mice, revealing compartmental ACh signals in fly olfactory center and single-trial ACh dynamics in multiple regions of the mice brain under a variety of different behaviors

neuroscience↗

bioRxiv2019

α-ketoglutaric acid stimulates muscle hypertrophy and fat loss through OXGR1-dependent adrenal activation

Beneficial effects of resistance exercise on metabolic health and particularly muscle hypertrophy and fat loss are well established, but the underlying chemical and physiological mechanisms are not fully understood. Here we identified a myometabolite-mediated metabolic pathway that is essential for the beneficial metabolic effects of resistance exercise in vivo. We showed that substantial accumulation of the tricarboxylic acid cycle intermediate -ketoglutaric acid (AKG) is a metabolic signature of resistance exercise performance. Interestingly, human plasma AKG level is also negatively correlated with BMI. Pharmacological elevation of circulating AKG induces muscle hypertrophy, brown adipose tissue (BAT) thermogenesis, and white adipose tissue (WAT) lipolysis in vivo. We further found that AKG stimulates the adrenal release of adrenaline through 2-oxoglutarate receptor 1 (OXGR1) expressed in adrenal glands. Finally, by using both loss-of-function and gain-of-function mouse models, we showed that OXGR1 is essential for AKG-mediated exercise-induced beneficial metabolic effects. These findings reveal an unappreciated mechanism for the salutary effects of resistance exercise, using AKG as a systemically-derived molecule for adrenal stimulation of muscle hypertrophy and fat loss.

molecular biology↗

bioRxiv2019

N-linked surface glycan biosynthesis, composition, inhibition, and function in cnidarian-dinoflagellate symbiosis

The success of symbioses between cnidarian hosts (e.g. corals and sea anemones) and micro-algal symbionts hinges on the molecular interactions that govern the establishment and maintenance of intracellular mutualisms. As a fundamental component of innate immunity, glycan-lectin interactions impact the onset of marine endosymbioses, but our understanding of the effects of cell surface glycome composition on symbiosis establishment remains limited. In this study, we examined the canonical N-glycan biosynthesis pathway in the genome of the dinoflagellate symbiont Breviolum minutum (family Symbiodiniaceae) and found it to be conserved with the exception of the transferase GlcNAc-TII (MGAT2). Using coupled liquid chromatography-mass spectrometry (LC-MS/MS), we characterized the cell surface N-glycan content of B. minutum, providing the first insight into the molecular composition of surface glycans in dinoflagellates. We then used the biosynthesis inhibitors kifunensine and swainsonine to alter the glycan composition of B. minutum. Successful high-mannose enrichment via kifunensine treatment resulted in a significant decrease in colonization of the model sea anemone Aiptasia (Exaiptasia pallida) by B. minutum. Hybrid glycan enrichment via swainsonine treatment, however, could not be confirmed and did not impact colonization. We conclude that functional Golgi processing of N-glycans is critical for maintaining appropriate cell surface glycan composition and for ensuring colonization success by B. minutum.

molecular biology↗

bioRxiv2019

The common neoantigens in colorectal cancer are predicted and validated to be presented or immunogenic

Colorectal cancer (CRC) is a malignant cancer with high incidence and mortality in the world, as the result of the traditional treatments. Immunotherapy targeting neoantigens can induce durable tumor regression in cancer patients, but is almost limited to individual treatment, resulting from the unique neoantigens. Many shared oncogenic mutations are detected, but whether the common neoantigens can be identified in CRC is unknown. Using the somatic mutations data from 321 CRC patients combined with a filter standard and 7 predicted algorithms, we screened and obtained 25 HLA-A*11:01 restricted common neoantigens with high binding affinity (IC50<50 nM) and presentation score (>0.9). Except the positive epitope KRAS_G12V8-16, 11 out of 25 common neoantigens were proved to be naturally processed and presented on constructed K562 cell surface by mass spectroscopy (MS), and 11 out of 25 common neoantigens specifically induced in vitro pre-stimulated cytotoxic lymphocyte (CTL) to secrete IFN-{gamma}. However, only 2 out of 25 common neoantigens were simultaneously presented and immunogenic. Moreover, using cell-sorting technology combined with single-cell RNA sequencing, the immune repertoire profiles of C1orf170_S418G413-421 and KRAS_G12V8-16-specific CTL were clarified. Therefore, common neoantigens with presentation and immunogenicity could be found in CRC, which would be developed as the universal targets for CRC immunotherapy.

immunology↗

bioRxiv2019

Fluorescent biosensor for real-time interaction dynamics of host proteins with HIV-1 capsid tubes

The human immunodeficiency virus 1 (HIV-1) capsid serves as a binding platform for proteins and small molecules from the host cell that regulate various steps in the virus life cycle. However, there are currently no quantitative methods that use assembled capsid lattices for measuring host-pathogen interaction dynamics. Here we developed a single molecule fluorescence biosensor using self-assembled capsid tubes as biorecognition elements and imaged capsid binders using total internal reflection fluorescence microscopy in a microfluidic setup. The method is highly sensitive in its ability to observe and quantify binding, obtain dissociation constants, extract kinetics with an extended application of using more complex analytes that can accelerate characterisation of novel capsid binders.

biophysics↗

bioRxiv2019

Characterization and repurposing of the endogenous Type I-F CRISPR-Cas system of Zymomonas mobilis for genome engineering

Establishment of production platform organisms through prokaryotic engineering represents an efficient means to generate alternatives for yielding renewable biochemicals and biofuels from sustainable resources. Zymomonas mobilis, a natural facultative anaerobic ethanologen, possesses many attractive physiological attributes, making it an important industrial microorganism. To facilitate the broad applications of this strain for biorefinery, an efficient genome engineering toolkit for Z. mobilis was established in this study by repurposing the endogenous Type I-F CRISPR-Cas system upon its functional characterization, and further updated. This toolkit includes a series of genome engineering plasmids, each carrying an artificial self-targeting CRISPR and a donor DNA for the recovery of recombinants. Using the updated toolkit, genome engineering purposes were achieved with efficiencies of up to 100%, including knockout of cas3 gene, replacement of cas3 with the mCherry-encoding rfp gene, nucleotide substitutions in cas3, and deletion of two large genomic fragments up to 10 kb. This study established thus far the most efficient, straightforward and convenient genome engineering toolkit for Z. mobilis, and laid a foundation for further native CRISPRi studies in Z. mobilis, which extended the application scope of CRISPR-based technologies, and could also be applied to other industrial microorganisms with unexploited endogenous CRISPR-Cas systems.

bioengineering↗

bioRxiv2019

High-resolution cryo-EM structures of the E. coli hemolysin ClyA oligomers

Pore-forming proteins (PFPs) represent a functionally important protein family, that are found in organisms from viruses to humans. As a major branch of PFPs, bacteria pore-forming toxins (PFTs) permeabilize membranes and usually cause the death of target cells. E. coli hemolysin ClyA is the first member with the pore complex structure solved among -PFTs, employing -helices as transmembrane elements. ClyA is proposed to form pores composed of various numbers of protomers. With high-resolution cryo-EM structures, we observe that ClyA pore complexes can exist as newly confirmed oligomers of a tridecamer and a tetradecamer, at estimated resolutions of 3.2 [A] and 4.3 [A], respectively. The 2.8 [A] cryo-EM structure of a dodecamer dramatically improves the existing structural model. Structural analysis indicates that protomers from distinct oligomers resemble each other and neighboring protomers adopt a conserved interaction mode. We also show a stabilized intermediate state of ClyA during the transition process from soluble monomers to pore complexes. Unexpectedly, even without the formation of mature pore complexes, ClyA can permeabilize membranes and allow leakage of particles less than [~]400 Daltons. In addition, we are the first to show that ClyA forms pore complexes in the presence of cholesterol within artificial liposomes. These findings provide new mechanistic insights into the dynamic process of pore assembly for the prototypical -PFT ClyA.

biophysics↗

bioRxiv2018

The allotetraploid origin and asymmetrical genome evolution of common carp Cyprinus carpio

Common carp (Cyprinus carpio) is an allotetraploid Cyprinid species derived from recent whole genome duplication and provides an excellent model system for studying polyploid genome evolution in vertebrates. To explore the origins and consequences of tetraploidy in C. carpio, we generated three chromosome-level new reference genomes of C. carpio and compared them to the related diploid Cyprinid genome sequences. We identified a progenitor-like diploid Barbinae lineage by analysing the phylogenetic relationship of the homoeologous genes of C. carpio and their orthologues in closely related diploid Cyprinids. We then characterized the allotetraploid origin of C. carpio and divided its genome into two homoeologous subgenomes that are marked by a distinct genome similarity to their diploid progenitor. On the basis of the divergence rates of homoeologous genes and transposable elements in two subgenomes, we estimated that the two diploid progenitor species diverged approximately 23 million years ago (Mya) and merged to form the allotetraploid C. carpio approximately 12.4 Mya, which likely correlated with environmental upheavals caused by the extensive uplift of the Qinghai-Tibetan Plateau. No large-scale gene losses or rediploidization were observed in the two subgenomes. Instead, we found extensive homoeologous gene expression bias across twelve surveyed tissues, which indicates that subgenome B is dominant in homoeologous expression. DNA methylation analysis suggested that CG methylation in promoter regions plays an important role in altering the expression of these homoeologous genes in allotetraploid C. carpio. This study provides an essential genome resource and insights for extending further investigation on the evolutionary consequences of vertebrate polyploidy.

genomics↗

bioRxiv2018

A genetically-encoded fluorescent sensor enables rapid and specific detection of dopamine in flies, fish, and mice

Dopamine (DA) is a central monoamine neurotransmitter involved in many physiological and pathological processes. A longstanding yet largely unmet goal is to measure DA changes reliably and specifically with high spatiotemporal precision, particularly in animals executing complex behaviors. Here we report the development of novel genetically-encoded GPCR-Activation-Based-DA (GRABDA) sensors that enable these measurements. In response to extracellular DA rises, GRABDA sensors exhibit large fluorescence increases ({Delta}F/F0[~]90%) with sub-second kinetics, nanomolar to sub-micromolar affinities, and excellent molecular specificity. Importantly, GRABDA sensors can resolve a single-electrical-stimulus evoked DA release in mouse brain slices, and detect endogenous DA release in the intact brains of flies, fish, and mice. In freely-behaving mice, GRABDA sensors readily report optogenetically-elicited nigrostriatal DA release and depict dynamic mesoaccumbens DA changes during Pavlovian conditioning or during sexual behaviors. Thus, GRABDA sensors enable spatiotemporal precise measurements of DA dynamics in a variety of model organisms while exhibiting complex behaviors.

neuroscience↗

bioRxiv2017

Predicting CTCF-mediated chromatin interactions by integrating genomic and epigenomic features

The CCCTC-binding zinc finger protein (CTCF)-mediated network of long-range chromatin interactions is important for genome organization and function. Although this network has been considered largely invariant, we found that it exhibits extensive cell-type-specific interactions that contribute to cell identity. Here we present Lollipop--a machine-learning framework--which predicts CTCF-mediated long-range interactions using genomic and epigenomic features. Using ChIA-PET data as benchmark, we demonstrated that Lollipop accurately predicts CTCF-mediated chromatin interactions both within and across cell-types, and outperforms other methods based only on CTCF motif orientation. Predictions were confirmed computationally and experimentally by Chromatin Conformation Capture (3C). Moreover, our approach reveals novel determinants of CTCF-mediated chromatin wiring, such as gene expression within the loops. Our study contributes to a better understanding about the underlying principles of CTCF-mediated chromatin interactions and their impact on gene expression.

systems biology↗