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Qin, L.

Publications and source records attributed to Qin, L..

72 records · Page 4Linked to original sources

Gut regulates brain synaptic assembly through neuroendocrine signaling pathway

The gut-brain axis plays an essential role in regulating neural development in response to environmental stimuli, such as microbes or nutrients. Defects in gut-brain communication can lead to various neurological disorders. However, it remains unknown whether gut plays any intrinsic role in regulating neuronal development. Through a genetic screen in C. elegans, we uncovered that an intrinsic Wnt-endocrine pathway in gut regulates synaptic development and neuronal activity in brain. Specifically, the Wnt signaling upregulates the expression of the neuropeptide NLP-40 in the gut, which then facilitates presynaptic assembly through the neuronal expressed GPCR AEX-2 receptor during development. The NLP-40 acts most likely through modulating neuronal activity and promoting synaptic protein trafficking. Therefore, this study reveals a novel role of gut in synaptic development in the brain.

neuroscience↗

Phospholipase A2 inhibitor-loaded micellar nanoparticles attenuate inflammation and mitigate osteoarthritis progression

Treating osteoarthritis (OA) remains a major clinical challenge. Despite recent advances in drug discovery and development, no disease-modifying drug for knee OA has emerged with any significant clinical success, in part due to the lack of valid and responsive therapeutic targets and poor drug delivery within knee joints. In this work, we show that the amount of secretory phospholipase A2 (sPLA2) enzyme increases in articular cartilage in human and mouse OA cartilage tissues. We hypothesize that inhibition of sPLA2 activity may be an effective treatment strategy for OA. To develop a sPLA2-responsive and nanoparticle (NP)-based interventional platform for OA management, we incorporated a sPLA2 inhibitor (sPLA2i) into the phospholipid membrane of micelles. The engineered sPLA2i-loaded micellar nanoparticles (sPLA2i-NPs) were able to penetrate deep into the cartilage matrix, prolong retention in the joint space, and mitigate OA progression. These findings suggest that sPLA2i-NPs can be promising therapeutic agents for OA treatment.

bioengineering↗

Identification of Gli1 as a progenitor cell marker for meniscus development and injury repair

Meniscal tears are associated with a high risk of osteoarthritis but currently have no disease-modifying therapies. Using Gli1-CreER tdTomato mice, we found that Gli1+ cells contribute to the development of meniscus horns from 2 weeks of age. In adult mice, Gli1+ cells resided at the superficial layer of meniscus and expressed known mesenchymal progenitor markers. In culture, meniscal Gli1+ cells possessed high progenitor activities under the control of Hh signal. Meniscus injury at the anterior horn induced a quick expansion of Gli1+ cells. Normally, the tissue healed slowly, leading to cartilage degeneration. Ablation of Gli1+ cells further hindered this repair process. Strikingly, intra-articular injection of Gli1+ meniscal cells or an Hh activator right after injury accelerated the bridging of the interrupted ends and attenuated signs of osteoarthritis. Taken together, our work identified a novel progenitor population in meniscus and proposes a new treatment for repairing injured meniscus and preventing osteoarthritis.

developmental biology↗

LncRNA H19X is required for placenta development and angiogenesis through regulating a noncoding RNA regulatory network

H19X is a lncRNA specifically expressed in the placenta, whose expression is induced by hypoxia. H19X overexpression promoted trophoblast proliferation and invasion, while its knockdown or knockout inhibited trophoblast proliferation and invasion. Mechanistically, we demonstrated that reciprocal regulation exists with miR-424/miR-503 in the control of genes related to placental development and angiogenesis, including VEGF and VEGFR2. H19X inhibited ubiquitination of PIWIL1, thereby maintaining its stability and homeostatic expression of piRNAs. PIWIL1 overexpression rescued the defects of cell behavior caused by H19X KO. H19X deletion led to compromised HIF-1A/HIF-2A expression, which was correlated with the dysregulation of downstream genes under hypoxic conditions. CRISPR/Cas-9 knockout of H19X in animals led to defective placenta differentiation and compromised embryo development under hypoxic conditions. Western blotting showed reduced expression levels of PIWIL1 as well as angiogenesis marker genes, including VEGF and VEGFR2, in H19X KO mice. Thus, this study provides evidence of an unexpected link among lncRNA, miRNA, PIWIL1-related piRNA, and angiogenesis in placentation, the dysregulation of which leads to poor placental development and embryo loss under hypoxic conditions.

developmental biology↗

Type II collagen-positive progenitors are major stem cells to control skeleton development and vascular formation

Previous studies have revealed that type II collagen positive (Col2+) cells represent a kind of skeleton stem cells (SSC) and their descendants contribute to chondrocytes, osteoblasts, Cxcl12 (chemokine (C-X-C motif) ligand 12)-abundant stromal cells and bone marrow stromal/mesenchymal progenitor cells in postnatal life. To further elucidate the function of Col2+ progenitors, we generated mice with ablation of either embryonic or postnatal Col2+ cells. Embryonic ablation of Col2+ progenitors caused the mouse die at newborn with the absence of all skeleton except partial craniofacial bone, as well as multiple organ development defects and blood vessel loss. Postnatal ablation of Col2+ cells causes mouse growth retardation and collagenopathy phenotype. By examining Col2+ cells ablated mice, we found that, besides contributing to long bone and vertebral bone development, Col2+ cells are also involved in calvaria bone development. Meanwhile, Col2+ cells are the major cells to contribute all skeletal development including spine, rib and long bones. Moreover, our functional study provide evidence that intramembranous ossification is involved in craniofacial bone formation and long bone development, but not participates in spine development. By performing lineage tracing experiments in embryonic or postnatal mice, we discovered that the presence of Col2+ progenitors not only within the bone marrow and growth plate (GP) but also within articular cartilage. Moreover, the number and differentiation ability of Col2+ progenitors were decreased with age in long bone and knee. Furthermore, fate-mapping studies revealed that Col2+ progenitors also contributed to CD31+ blood vessel endothelial development in calvariae bone, long bone and many organs. Interestingly, we found only 25.4% CD31+ blood vessel endothelial in long bone but almost all the CD31+ blood vessel endothelial in calvariae bone are differentiated from Col2+ cells. Consistently, postnatal Col2+ cells differentiated to both chondrocytes and CD31+ blood vessel endothelial cells during bone fracture healing. Therefore, this study reveals that Col2+ progenitors are the major source of endochondral ossification, and they also contribute to vascular development in multiple organs and fracture repair.

developmental biology↗

Bone marrow adipogenic lineage precursors (MALPs) promote osteoclastogenesis in bone remodeling and pathologic bone loss

Bone is maintained by coupled activities of bone-forming osteoblasts/osteocytes and bone-resorbing osteoclasts and an alternation of this relationship can lead to pathologic bone loss such as in osteoporosis. It is well known that osteogenic cells support osteoclastogenesis via synthesizing RANKL. Interestingly, our recently identified bone marrow mesenchymal cell population--marrow adipogenic lineage precursors (MALPs) that form a multi-dimensional cell network in bone--was computationally demonstrated to be the most interactive with monocyte-macrophage lineage cells through highly and specifically expressing several osteoclast regulatory factors, including RANKL. Using an adipocyte-specific Adipoq-Cre to label MALPs, we demonstrated that mice with RANKL deficiency in MALPs have a drastic increase of trabecular bone mass in long bones and vertebrae starting from 1 month of age but that their cortical bone is normal. This phenotype was accompanied by diminished osteoclast number and attenuated bone formation at the trabecular bone surface. Reduced RANKL signaling in calvarial MALPs also abolished osteolytic lesions after lipopolysaccharide (LPS) injections. Furthermore, in ovariectomized mice, elevated bone resorption was partially attenuated by RANKL deficiency in MALPs. In summary, our studies identified MALPs as a critical player in controlling bone remodeling during normal bone metabolism and pathological bone loss in a RANKL-dependent fashion.

cell biology↗

YAP and TAZ promote periosteal osteoblast precursor expansion and differentiation for fracture repair

In response to bone fracture, periosteal progenitor cells proliferate, expand, and differentiate to form cartilage and bone in the fracture callus. These cellular functions require the coordinated activation of multiple transcriptional programs, and the transcriptional regulators Yes-associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ) regulate osteochondroprogenitor activation during endochondral bone development. However, recent observations raise important distinctions between the signaling mechanisms used to control bone morphogenesis and repair. Here, we tested the hypothesis that YAP and TAZ regulate osteochondroprogenitor activation during endochondral bone fracture healing. Constitutive YAP and/or TAZ deletion from Osterix-expressing cells impaired both cartilage callus formation and subsequent mineralization. However, this could be explained either by direct defects in osteochondroprogenitor differentiation after fracture, or by developmental deficiencies in the progenitor cell pool prior to fracture. Consistent with the second possibility, we found that developmental YAP/TAZ deletion produced long bones with impaired periosteal thickness and cellularity. Therefore, to remove the contributions of developmental history, we next generated adult onset-inducible knockout mice (using Osx1-CretetOff) in which YAP and TAZ were deleted prior to fracture, but after normal development. Adult onset-induced YAP/TAZ deletion had no effect on cartilaginous callus formation, but impaired bone formation at 14 days post-fracture (dpf). Earlier, at 4 dpf, adult onset-induced YAP/TAZ deletion impaired the proliferation and expansion of osteoblast precursor cells located in the shoulder of the callus. Further, activated periosteal cells isolated from this region at 4 dpf exhibited impaired osteogenic differentiation in vitro upon YAP/TAZ deletion. Finally, confirming the effects on osteoblast function in vivo, adult onset-induced YAP/TAZ deletion impaired bone formation in the callus shoulder at 7 dpf, prior to the initiation of endochondral ossification. Together, these data show that YAP and TAZ promote the expansion and differentiation of periosteal osteoblast precursors to accelerate bone fracture healing.

developmental biology↗

PD-L1 upregulation by IFN-α/γ-mediated Stat1 suppresses anti-HBV T cell response

Programmed death ligand 1 (PD-L1) has been recently shown to be a major obstacle to antiviral immunity by binding to its receptor programmed death 1 (PD-1) on specific IFN-{gamma} producing T cells in chronic hepatitis B. Currently, IFN- is widely used to treat hepatitis B virus(HBV) infection, but its antiviral effect vary greatly and the mechanism is not totally clear. We found that IFN-/{gamma} induced a marked increase of PD-L1 expression in hepatocytes. Signal and activators of transcription (Stat1) was then identified as a major transcription factor involved in IFN-/{gamma}-mediated PD-L1 elevation both in vitro and in mice. Blockage of the PD-L1/PD-1 interaction by a specific mAb greatly enhanced HBV-specific T cell activity by the gp96 adjuvanted therapeutic vaccine, and promoted HBV clearance in HBV transgenic mice. Our results demonstrate the IFN-/{gamma}-Stat1-PD-L1 axis plays an important role in mediating T cell hyporesponsiveness and inactivating liver-infiltrating T cells in the hepatic microenvironment. These data raise further potential interest in enhancing the anti-HBV efficacy of IFN- and therapeutic vaccines.

molecular biology↗

CRISPR screening of porcine sgRNA library identified host factors essential for Japanese encephalitis virus replication

Japanese encephalitis virus (JEV) is a mosquito-borne zoonotic flavivirus that causes encephalitis and reproductive disorders in mammalian species. However, key host genes involved in the JEV life cycle and cell death are poorly understood. Here, we designed 85,674 single guide RNAs (sgRNAs) targeting 17,743 protein-coding genes, 11,053 long ncRNAs (lncRNAs), and 551 microRNAs (miRNAs) in the porcine genome, and subsequently developed a porcine sgRNA library and genome-scale CRISPR/Cas9 knockout (PigGeCKO) system. These sgRNAs were delivered into porcine kidney-15 (PK-15) cells that constitutively express Cas9, positive selection screening of the resulting PigGeCKO cell collection for resistance to JEV-induced cell death led to the identification of several previously unreported genes required for JEV infection. We conducted follow-up studies to verify the dependency of JEV on these genes, and identified functional contributions for six of the many candidate JEV-related host genes, including an endoplasmic reticulum membrane protein complex subunit 3 (EMC3) and calreticulin (CALR). Additionally, we identified that four genes associated with heparan sulfate proteoglycans (HSPGs) metabolism, specifically those responsible for HSPG sulfurylation, facilitated JEV entry into PK-15 cells. Thus, beyond our development of the largest CRISPR-based functional genomic screening platform for pig research to date, this work deepens our basic understanding of flavivirus infection and identifies multiple potentially vulnerable targets for the development of medical and breeding technologies to prevent and treat diseases caused by Japanese encephalitis virus.

genetics↗

Large-scale Analysis of 2,152 dataset reveals key features of B cell biology and the antibody repertoire

Antibody repertoire sequencing (Ig-seq) has been widely used in studying humoral responses, with promising results. However, the promise of Ig-seq has not yet been fully realized, and key features of the antibody repertoire remain elusive or controversial. To clarify these key features, we analyzed 2,152 high-quality heavy chain antibody repertoires, representing 582 donors and a total of 360 million clones. Our study revealed that individuals exhibit very similar gene usage patterns for germline V, D, and J genes and that 53 core V genes contribute to more than 99% of the heavy chain repertoire. We further found that genetic background is sufficient but not necessary to determine usage of V, D, and J genes. Although gene usage pattern is not affected by age, we observed a significant sex preference for 24 V genes, 9 D genes and 5 J genes, but found no positional bias for V-D and D-J recombination. In addition, we found that the number of observed clones that were shared between any two repertoires followed a linear model and noted that the mutability of hot/cold spots and single nucleotides within antibody genes suggested a strand-specific somatic hypermutation mechanism. This population-level analysis resolves some critical characteristics of the antibody repertoire and thus may serve as a reference for research aiming to unravel B cell-related biology or diseases. The metrics revealed here will be of significant value to the large cadre of scientists who study the antibody repertoire.

immunology↗

The B. subtilis Rok protein compacts and organizes DNA by bridging

Rok from Bacillus subtilis is an abundant DNA binding protein similar in function to H-NS-like proteins found in many proteobacteria. Rok binds across the genome with a preference for A/T rich DNA. Such DNA often contains genes of foreign origin that are silenced due to Rok binding. Rok also has been implied in global organization of the B. subtilis genome. However, how Rok binds to DNA and how it represses transcription is unclear. Also, it is unknown whether Rok-mediated gene repression can be induced or relieved following changes in physico-chemical conditions, as noted for H-NS-like proteins. Here we investigate the DNA binding properties of Rok and determine the effects of physico-chemical conditions on these properties. We demonstrate that Rok is a DNA bridging protein similar to H-NS like proteins from E. coli (H-NS), Pseudomonas sp. (MvaT) and Mycobacteria (Lsr2). Strikingly, unlike these proteins, the ability of Rok to bridge DNA is not affected by changes in physico-chemical conditions. Not being a direct sensor of such changes sets Rok apart from other H-NS like proteins. It implies the existence of other (protein-mediated) mechanisms to relieve Rok-mediated gene silencing in response to changes in environmental conditions.

molecular biology↗

Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins

H-NS proteins act as osmotic sensors translating changes in osmolarity into altered DNA binding properties, thus, regulating enterobacterial genome organization and genes transcription. The molecular mechanism underlying the switching process and its conservation among H-NS family members remains elusive.\n\nHere, we focus on the H-NS family protein MvaT from P. aeruginosa and demonstrate experimentally that its protomer exists in two different conformations, corresponding to two different functional states. In the half-opened state (dominant at low salt) the protein forms filaments along DNA, in the fully opened state (dominant at high salt) the protein bridges DNA. This switching is a direct effect of ionic strengths on electrostatic interactions between the appositively charged DNA binding and N-terminal domains of MvaT. The asymmetric charge distribution and intramolecular interactions are conserved among the H-NS family of proteins. Therefore, our study establishes a general paradigm for the molecular mechanistic basis of the osmosensitivity of H-NS proteins.

biochemistry↗

Single cell transcriptomics identifies a unique adipocyte population that regulates bone marrow environment

Bone marrow mesenchymal lineage cells are a heterogeneous cell population involved in bone homeostasis and diseases such as osteoporosis. While it is long postulated that they originate from mesenchymal stem cells (MSCs), the true identity of MSCs and their in vivo bifurcated differentiation routes into osteoblasts and adipocytes remain poorly understood. Here, by employing single cell transcriptome analysis, we identified MSCs and delineated their bi-lineage differentiation paths in young, adult and aging mice. Among several newly discovered mesenchymal subpopulations, one is a distinct population of adipose-lineage cells that we named marrow environment regulating adipose cells (MERAs). MERAs are non-proliferative, post-progenitor cells that express many mature adipocyte markers but are devoid of lipid droplets. They are abundant in the bone marrow of young mice, acting as pericytes and stromal cells that form numerous connections among themselves and with other cells inside bone, including endothelial cells. Genetic ablation of MERAs disrupts marrow vessel structure, promotes de novo bone formation. Taken together, MERAs represent a unique population of adipose lineage cells that exist only in the bone marrow with critical roles in regulating bone and vessel homeostasis.

cell biology↗

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↗

Metagenomic Next-generation Sequencing of Cerebrospinal Fluid for the Diagnosis of Central Nervous System Infections: A Multicentre Prospective Study

BackgroundInfectious encephalitis and meningitis are often treated empirically without identification of the causative pathogen. Metagenomic next-generation sequencing (mNGS) is a high throughput technology that enables the detection of pathogens independent of prior clinical or laboratory information.\n\nMethodsThe present study was a multicentre prospective evaluation of mNGS of cerebrospinal fluid (CSF) for the diagnosis of suspected central nervous system infections.\n\nResultsA total of 276 patients were enrolled in this study between Jan 1, 2017 and Jan 1, 2018. Identification of an etiologic pathogen in CSF by mNGS was achieved in 101 patients (36.6%). mNGS detected 11 bacterial species, 7 viral species, 2 fungal species, and 2 parasitic species. The five leading positive detections were varicella-zoster virus (17), Mycobacterium tuberculosis (14), herpes simplex virus 1 (12), Epstein-Barr virus (12), and Cryptococcus neoformans (7). False positives occurred in 12 (4.3%) patients with bacterial infections known to be widespread in hospital environments. False negatives occurred in 16 (5.8%) patients and included bacterial, viral and fungal aetiologies.\n\nConclusionsmNGS of CSF is a powerful diagnostic method to identify the pathogen for many central nervous system infections.

genomics↗

Airway epithelial integrin β4 suppresses allergic inflammation by decreasing CCL17 production

Airway epithelial cells (AECs) play a key role in asthma susceptibility and severity. Integrin {beta}4 (ITGB4) is a structural adhesion molecule that is downregulated in the airway epithelium of asthma patients. Specific ITGB4 deficiency in AECs induces exaggerated Th2 responses, severe allergen-induced airway inflammation and airway hyperresponsiveness (AHR) in mouse model of allergic asthma. However, the underlying mechanisms remain unexplored. In this study, we determine the role of ITGB4 of AECs in the regulation of Th2 response and in the induction of asthma and identify the underpinning molecular mechanisms. We found that ITGB4 deficiency led to exaggerated Th2 cells infiltration, inflammation and AHR and higher production of CCL17 in HDM treated mice. ITGB4-regulated CCL17 production in AECs was regulated by EGFR, ERK and NF-{kappa}B pathways. EFGR-antagonist treatment or the neutralization of CCL17 by antibody inhibited exaggerated pathological marks in HDM-challenged ITGB4-deficient mice. Together, these results demonstrated that ITGB4 of AECs negatively regulates the development of Th2 responses of allergic asthma by down-regulation of EGFR and CCL17 pathway.

immunology↗

The bacterial chromatin protein HupA can remodel DNA and associates with the nucleoid in Clostridium difficile

The maintenance and organization of the chromosome plays an important role in the development and survival of bacteria. Bacterial chromatin proteins are architectural proteins that bind DNA, modulate its conformation and by doing so affect a variety of cellular processes. No bacterial chromatin proteins of C. difficile have been characterized to date.\n\nHere, we investigate aspects of the C. difficile HupA protein, a homologue of the histone-like HU proteins of Escherichia coli. HupA is a 10 kDa protein that is present as a homodimer in vitro and self-interacts in vivo. HupA co-localizes with the nucleoid of C. difficile. It binds to the DNA without a preference for the DNA G+C content. Upon DNA binding, HupA induces a conformational change in the substrate DNA in vitro and leads to compaction of the chromosome in vivo.\n\nThe present study is the first to characterize a bacterial chromatin protein in C. difficile and opens the way to study the role of chromosomal organization in DNA metabolism and on other cellular processes in this organism.

microbiology↗

Co-adaption of tRNA Gene Copy Number and Amino Acid Usage Influences Translation Rates in Three Life Domains

The cellular translation process should obey the principle of maximizing efficiency and minimizing resource and energy costs. Here, we validated this principle by focusing on the basic translation components of tRNAs and amino acids. To most efficiently utilize these components, we reasoned that the quantities of the 20 tRNAs and their corresponding amino acids would be consistent in an organism. The two values should match at both the organismal and protein scales. For the former, they co-vary to meet the need to translate more proteins in fast-growing or larger cells. For the latter, they are consistent to different extents for various proteins in an organism to comply with different needs of translation speed. In this work, 310 out of 410 genomes in three domains had significant co-adaptions between the tRNA gene copy number and amino acid composition, and thus validating the principle at the organism scale. Furthermore, fast-growing bacteria co-adapt better than slow-growing ones. Highly expressed proteins and those connected to acute responses have better co-adaption, illustrating the principle at the individual protein scale. Experimentally, manipulating the tRNA gene copy number to optimize co-adaption between enhanced green fluorescent protein (EGFP) and tRNA gene set of Escherichia coli indeed lifted the translation rate (speed). Our results also contribute to revealing a translation rate-associated factor with universal and global effects. From a practical perspective, our findings suggest a strategy to increase the expression of target proteins and have implications for designing chassis cells in the field of synthetic biology field.

genomics↗