Biology subjects

Zhao, M.

Publications and source records attributed to Zhao, M..

At least 217 records · Page 12Linked to original sources

bioRxiv2021

Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples

Archived formalin-fixed paraffin-embedded (FFPE) samples are the global standard format for preservation of the majority of biopsies in both basic research and translational cancer studies, and profiling chromatin accessibility in the archived FFPE tissues is fundamental to understanding gene regulation. Accurate mapping of chromatin accessibility from FFPE specimens is challenging because of the high degree of DNA damage. Here, we first showed that standard ATAC-seq can be applied to purified FFPE nuclei but yields lower library complexity and a smaller proportion of long DNA fragments. We then present FFPE-ATAC, the first highly sensitive method for decoding chromatin accessibility in FFPE tissues that combines Tn5-mediated transposition and T7 in vitro transcription. The FFPE-ATAC generates high-quality chromatin accessibility profiles with 500 nuclei from a single FFPE tissue section, enables the dissection of chromatin profiles from the regions of interest with the aid of hematoxylin and eosin (H&E) staining, and reveals disease-associated chromatin regulation from the human colorectal cancer FFPE tissue archived for more than 10 years. In summary, the approach allows decoding of the chromatin states that regulate gene expression in archival FFPE tissues, thereby permitting investigators, to better understand epigenetic regulation in cancer and precision medicine.

genomics↗

bioRxiv2021

Extrachromosomal DNA is associated with chromothripsis events and diverse prognoses in gastric cardia adenocarcinoma

Extrachromosomal DNA plays an important role in oncogene amplification in tumour cells and poor outcomes across multiple cancers. However, the function of extrachromosomal DNA in gastric cardia adenocarcinoma (GCA) is very limited. Here, we investigated the availability and function of extrachromosomal DNA in GCA from a Chinese cohort of GCA using whole-genome sequencing (WGS), whole-exome sequencing (WES), and immunohistochemistry. For the first time, we identified the ecDNA amplicons present in most GCA patients, and found that some oncogenes are present as ecDNA amplicons in these patients. We found that oncogene ecDNA amplicons in the GCA cohort were associated with the chromothripsis process and may be induced by accumulated DNA damage due to local dietary habits in the geographic region. Strikingly, we observed diverse correlations between the presence of ecDNA oncogene amplicons and prognosis, where ERBB2 ecDNA amplicons correlated with good prognosis, EGFR ecDNA amplicons correlated with poor prognosis, and CCNE1 ecDNA amplicons did not correlate with prognosis. Large-scale ERBB2 immunohistochemistry results from 1668 GCA patients revealed that there was a positive correlation between the presence of ERBB2 and prognosis in 2-7-year survival; however, there was a negative correlation between the presence of ERBB2 and prognosis in 0-2-year survival. Our observations indicate that the presence of ERBB2 ecDNA in GCA patients may represent a good prognosis marker.

genomics↗

bioRxiv2021

Megakaryocyte derived immune-stimulating cells regulate host-defense immunity against bacterial pathogens

Megakaryocytes (MKs) continuously produce platelets to support hemostasis and form a niche for hematopoietic stem cell maintenance in the bone marrow. MKs are also involved in inflammation responses; however, the mechanism remains poorly understood. Here, using single-cell sequencing we identified an MK-derived immune-stimulating cell (MDIC) population exhibiting both MK-specific and immune characteristics, which highly expresses CXCR4 and immune response genes to participate in host-protective response against bacteria. MDICs interact with myeloid cells to promote their migration and stimulate the bacterial phagocytosis of macrophages and neutrophils by producing TNF and IL-6. CXCR4high MDICs egress circulation and infiltrate into the spleen, liver, and lung upon bacterial infection. Ablation of MKs suppresses the innate immune response and T cell activation to impair the anti-bacterial effects in mice under the Listeria monocytogenes challenge. Using hematopoietic stem/progenitor cell lineage-tracing mouse line, we show that MDICs are generated from infection-induced emergency megakaryopoiesis in response to bacterial infection. Overall, we identify MDICs as an MK subpopulation, which regulates host-defense immune response against bacterial infection.

cell biology↗

bioRxiv2021

MiR-384 Regulates Reelin by Inhibiting ADAMTS4 in Neuronal Cell Lines

MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level. The present study aims to investigate the role of miR-384 in Reelin by regulating ADAMTS4 in neuronal cell lines. Brain tissues from A{beta}1-42 induced mouse model of Alzheimers disease and the control group were collected. RT-PCR, Western blotting and immunohistochemistry were performed to detect the levels of ADAMTS4 and miR-384 in tissues. Luciferase reporter assay, Western blotting and in vitro assay were used to validate that ADAMTS4 was the target gene of miR-384. Neuronal cell line, Neuro-2a, was selected for transfection assay. ADAMTS4 was significantly down-regulated in hippocampi of Alzheimers disease mouse model, and negatively correlated with miR-384. Then, ADAMTS4 was identified as a direct target of miR-384. Over-expressing of miR-384 in Neuro-2a showed that ADAMTS4 and the cleaved Reelin fragments were down regulated, and proliferation of neuronal cell lines (Neuro-2a and SH-SY5Y) were inhibited through DAB-1 pathway. In conclusion, these results revealed that miR-384 may play a regulatory role in Reelin via inhibiting ADAMTS4 in neuronal cell lines.

biochemistry↗

bioRxiv2021

Actin dynamics as a multiscale integrator of cellular guidance cues

Cells are able to integrate multiple, and potentially competing, cues to determine a migration direction. For instance, in wound healing, cells follow chemical signals or electric fields to reach the wound edge, regardless of any local guidance cues. To investigate this integration of guidance cues, we monitor the actin-polymerization dynamics of immune cells in response to cues on a subcellular scale (nanotopography) and on the cellular scale (electric fields, EFs). In the fast, amoeboid-type migration, commonly observed in immune cells, actin polymerization at the cells leading edge is the driver of motion. The excitable systems character of actin polymerization leads to self-propagating, two-dimensional wavefronts that enable persistent cell motion. We show that EFs guide these wavefronts, leading to turning of cells when the direction of the EF changes. When nanoridges promote one-dimensional (1D) waves of actin polymerization that move along the ridges (esotaxis), EF guidance along that direction is amplified. 1D actin waves cannot turn or change direction, so cells respond to a change in EF direction by generating new 1D actin waves. At the cellular scale, the emergent response is a turning of the cell. For nanoridges perpendicular to the direction of the EF, the 1D actin waves are guided by the nanotopography, but both the average location of new actin waves and the whole cell motion are guided by the EF. Thus, actin waves respond to each cue on its intrinsic length scale, allowing cells to exhibit versatile responses to the physical microenvironment. Significance StatementEffective cell migration requires the integration of multiple, and sometimes competing, guidance cues. For instance, in wound healing, immune cells are guided towards a wound edge by long-range electrical and chemical cues that may conflict with guidance cues from the local environment. How cells combine and respond to such cues is not well understood. We demonstrate that multiple guidance mechanisms can act simultaneously, but on different scales. Nanotopography, a local mechanical cue, guides individual waves of actin polymerization, thereby biasing the direction cell motion on the time scale of these waves. An external electric field applied at the same time biases the locations of new waves of actin polymerization, leading to overall directed migration over long distance scales.

biophysics↗

bioRxiv2021

Transcriptomic encoding of sensorimotor transformation in the midbrain

Sensorimotor transformation, a process that converts sensory stimuli into motor actions, is critical for the brain to initiate behaviors. Although the circuitry involved in sensorimotor transformation has been well delineated, the molecular logic behind this process remains poorly understood. Here, we performed high-throughput and circuit-specific single-cell transcriptomic analyses of neurons in the superior colliculus (SC), a midbrain structure implicated in early sensorimotor transformation. We found that SC neurons in distinct laminae express discrete marker genes. Of particular interest, Cbln2 and Pitx2 are key markers that define glutamatergic projection neurons in the optic nerve (Op) and intermediate gray (InG) layers, respectively. The Cbln2+ neurons responded to visual stimuli mimicking cruising predators, while the Pitx2+ neurons encoded prey-derived vibrissal tactile cues. By forming distinct input and output connections with other brain areas, these neuronal subtypes independently mediate behaviors of predator avoidance and prey capture. Our results reveal that, in the midbrain, sensorimotor transformation for different behaviors may be performed by separate circuit modules that are molecularly defined by distinct transcriptomic codes.

neuroscience↗

bioRxiv2021

Encoding model for continuous motion-sensitive neurons in the intermediate and deep layers of pigeon Optic Tectum

There are typical neurons in the intermediate and deep layers of the optic tectum of avian, which are sensitive to small continuous moving targets. Based on this sensitivity of these neurons to continuous moving targets, the hypothesis of directed energy accumulation in dendrite field of these neurons is proposed. Based on the phenomenon that single dendrite activation can induce somatic spikes in vitro, the hypothesis of sequential probability activation mechanism of soma is proposed. Combined with the above hypotheses, the information encoding model of these typical neurons is constructed. Moreover, electrophysiological experiments and model simulations are carried out to obtain the response of neurons to visual stimuli of sequential motion, random motion and random sequential motion. Results show that the encoding model fits the response properties of continuous motion-sensitive neurons well. This study is of great significance for understanding the neurophysiological process of small-target perception for avian tectofugal pathway and the construction of the brain-inspired small-target detection algorithm.

neuroscience↗

bioRxiv2021

Coronary blood vessels from distinct origins converge to equivalent states during mouse and human development

Most cell fate trajectories during development follow a diverging, tree-like branching pattern, but the opposite can occur when distinct progenitors contribute to the same cell type. During this convergent differentiation, it is unknown if cells "remember" their origins transcriptionally or whether this influences cell behavior. Most coronary blood vessels of the heart develop from two different progenitor sources--the endocardium (Endo) and sinus venosus (SV)--but whether transcriptional or functional differences related to origin are retained is unknown. We addressed this by combining lineage tracing with single-cell RNA sequencing (scRNAseq) in embryonic and adult mouse hearts. Shortly after coronary development begins, capillary ECs transcriptionally segregated into two states that retained progenitor-specific gene expression. Later in development, when the coronary vasculature is well-established but still remodeling, capillary Ecs again segregated into two populations, but transcriptional differences were primarily related to tissue localization rather than lineage. Specifically, ECs in the heart septum expressed genes indicative of increased local hypoxia and decreased blood flow. Adult capillary ECs were more homogeneous with respect to both lineage and location. In agreement, SV- and Endo-derived ECs in adult hearts displayed similar responses to injury. Finally, scRNAseq of developing human coronary vessels indicated that the human heart followed similar principles. Thus, over the course of development, transcriptional heterogeneity in coronary ECs is first influenced by lineage, then by location, until heterogeneity declines in the homeostatic adult heart. These results highlight the plasticity of ECs during development, and the validity of the mouse as a model for human coronary development.

developmental biology↗

bioRxiv2021

Structural Insights Into the Initiation and Elongation of Ubiquitination by Ubr1

The N-end rule pathway was one of the first ubiquitin (Ub)-dependent degradation pathways to be identified. Ubr1, a single-chain E3 ligase, targets proteins bearing a destabilizing residue at the N-terminus (N-degron) for rapid K48-linked ubiquitination and proteasome-dependent degradation. How Ubr1 catalyses the initiation of ubiquitination on the substrate and elongation of the Ub chain in a linkage-specific manner through a single E2 ubiquitin-conjugating enzyme (Ubc2) remains unknown. Here, we report the cryo-electron microscopy structures of two complexes representing the initiation and elongation intermediates of Ubr1 captured using chemical approaches. In these two structures, Ubr1 adopts different conformations to facilitate the transfer of Ub from Ubc2 to either an N-degron peptide or a monoubiquitinated degron. These structures not only reveal the architecture of the Ubr1 complex but also provide mechanistic insights into the initiation and elongation steps of ubiquitination catalysed by Ubr1.

biophysics↗

bioRxiv2021

Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants

The emergence of SARS-CoV-2 variants that threaten the efficacy of existing vaccines and therapeutic antibodies underscores the urgent need for new antibody-based tools that potently neutralize variants by targeting multiple sites of the spike protein. We isolated 216 monoclonal antibodies targeting SARS-CoV-2 from plasmablasts and memory B cells of COVID-19 patients. The three most potent antibodies targeted distinct regions of the RBD, and all three neutralized the SARS-CoV-2 variants B.1.1.7 and B.1.351. The crystal structure of the most potent antibody, CV503, revealed that it binds to the ridge region of SARS-CoV-2 RBD, competes with the ACE2 receptor, and has limited contact with key variant residues K417, E484 and N501. We designed bispecific antibodies by combining non-overlapping specificities and identified five ultrapotent bispecific antibodies that inhibit authentic SARS-CoV-2 infection at concentrations of <1 ng/mL. Through a novel mode of action three bispecific antibodies cross-linked adjacent spike proteins using dual NTD/RBD specificities. One bispecific antibody was >100-fold more potent than a cocktail of its parent monoclonals in vitro and prevented clinical disease in a hamster model at a 2.5 mg/kg dose. Notably, six of nine bispecific antibodies neutralized B.1.1.7, B.1.351 and the wild-type virus with comparable potency, despite partial or complete loss of activity of at least one parent monoclonal antibody against B.1.351. Furthermore, a bispecific antibody that neutralized B.1.351 protected against SARS-CoV-2 expressing the crucial E484K mutation in the hamster model. Thus, bispecific antibodies represent a promising next-generation countermeasure against SARS-CoV-2 variants of concern.

immunology↗

bioRxiv2021

Two interacting transcriptional coactivators cooperatively control plant immune responses

The phytohormone salicylic acid (SA) plays a pivotal role in plant defense against biotrophic and hemibiotrophic pathogens. Genetic studies have identified NPR1 and EDS1 as two central hubs in plant local and systemic immunity. However, it is unclear how NPR1 orchestrates gene regulation and whether EDS1 directly participates in transcriptional reprogramming. Here we show that NPR1 and EDS1 synergistically activate Pathogenesis-Related (PR) genes and plant defenses by forming a protein complex and co-opting with Mediator. In particular, we discover that EDS1 functions as an autonomous transcriptional coactivator with intrinsic transactivation domains and physically interacts with the CDK8 subunit of Mediator. Upon SA induction, EDS1 is directly recruited by NPR1 onto the PR1 promoter via physical NPR1-EDS1 interactions, thereby potentiating PR1 activation. We further demonstrate that EDS1 stabilizes NPR1 protein and NPR1 transcriptionally upregulates EDS1 in plant-pathogen interactions. Our results reveal an elegant interplay of key coactivators with Mediator and elucidate novel molecular mechanisms for activating transcription during immune responses.

plant biology↗

bioRxiv2021

Withaferin A promotes white adipose browning and prevents obesity through sympathetic nerve-activated Prdm16-FATP1 axis

The increasing prevalence of obesity has resulted in demands for the development of new effective strategies for obesity treatment. The Withaferin A (WA) shows a great potential for prevention of obesity by sensitizing leptin signaling in the hypothalamus. However, the mechanism underlying the weight- and adiposity-reducing effects of WA remains to be elucidated. Here, we report that WA treatment induced white adipose tissue (WAT) browning, elevated energy expenditure (EE), decreased respiratory exchange ratio (RER), and prevented high-fat diet (HFD)-induced obesity. The sympathetic chemical denervation dampened the WAT browning and also impeded the reduction of adiposity in WA-treated mice. WA markedly up-regulated the levels of Prdm16 and FATP1 (Slc27a1) in the inguinal WAT (iWAT), and this was blocked by sympathetic denervation. Prdm16 or FATP1 knockdown in iWAT abrogated the WAT browning-inducing effects of WA, and restored the weight gain and the adiposity in WA-treated mice. Together, these findings suggest that WA induces WAT browning through the sympathetic nerve-adipose axis; and the adipocytic Prdm16-FATP1 pathway mediates the promotive effects of WA on white adipose browning.

physiology↗

bioRxiv2021

Bacterium-Enabled Transient Gene Activation by Artificial Transcription Factor for Resolving Gene Regulation in Maize

Cellular functions are diversified through intricate transcription regulations, and an understanding gene regulation networks is essential to elucidating many developmental processes and environmental responses. Here, we employed the Transcriptional-Activator Like effectors (TALes), which represent a family of transcription factors that are synthesized by members of the {gamma}-proteobacterium genus Xanthomonas and secreted to host cells for activation of targeted host genes. Through delivery by the maize pathogen, Xanthomonas vasicola pv. vasculorum, designer TALes (dTALes), which are synthetic TALes, were used to induce the expression of the maize gene glossy3 (gl3), a MYB transcription factor gene involved in the cuticular wax biosynthesis. RNA-Seq analysis of leaf samples identified 146 gl3 downstream genes. Eight of the nine known genes known to be involved in the cuticular wax biosynthesis were up-regulated by at least one dTALe. A top-down Gaussian graphical model predicted that 68 gl3 downstream genes were directly regulated by GL3. A chemically induced mutant of the gene Zm00001d017418 from the gl3 downstream gene, encoding aldehyde dehydrogenase, exhibited a typical glossy leaf phenotype and reduced epicuticular waxes. The bacterial protein delivery of artificial transcription factors, dTALes, proved to be a straightforward and powerful approach for the revelation of gene regulation in plants.

plant biology↗

bioRxiv2021

Mechanistic insight into substrate processing and allosteric inhibition of human p97

p97 processes ubiquitinated substrates and plays a central role in cellular protein homeostasis. Previous studies have showed that it is a potential drug target for cancer, neurodegenerative disease, and viral infections. Here, we report a series of cryo-electron microscopy (cryo-EM) structures of substrate-engaged human p97 complex that captured "power stroke"-like motions of both the D1 and D2 ATPase rings of p97. A key feature of these structures is the critical conformational changes of the inter-subunit signaling (ISS) motifs, which tightens the binding of nucleotides and neighboring subunits, and contributes to the spiral staircase conformation of the D1 and D2 rings. We further determined the cryo-EM structure of human p97 in complex with NMS-873, the most potent p97 inhibitor. The structures showed that NMS-873 binds at a cryptic groove in the D2 domain and interacts with the ISS motif, preventing its conformational change, thus blocking substrate translocation allosterically.

biophysics↗

bioRxiv2021

Separated and overlapping neural coding of face and body identity

Recognising a persons identity often relies on face and body information, and is tolerant to changes in low-level visual input (e.g. viewpoint changes). Previous studies have suggested that face identity is disentangled from low-level visual input in the anterior face-responsive regions. It remains unclear which regions disentangle body identity from variations in viewpoint, and whether face and body identity are encoded separately or combined into a coherent person identity representation. We trained participants to recognize three identities, and then recorded their brain activity using fMRI while they viewed face and body images of the three identities from different viewpoints. Participants task was to respond to either the stimulus identity or viewpoint. We found consistent decoding of body identity across viewpoint in the fusiform body area, right anterior temporal cortex, middle frontal gyrus and right insula. This finding demonstrates a similar function of fusiform and anterior temporal cortex for bodies as has previously been shown for faces, suggesting these regions may play a general role in extracting high-level identity information. Moreover, we could decode identity across neural activity evoked by faces and bodies in the early visual cortex, right inferior occipital cortex, right parahippocampal cortex and right superior parietal cortex, revealing a distributed network that encodes person identity abstractly. Lastly, identity decoding was consistently better when participants attended to identity, indicating that attention to identity enhances its neural representation. These results offer new insights into how the brain develops an abstract neural coding of person identity, shared by faces and bodies.

neuroscience↗

bioRxiv2021

Quantifying the impact of electric fields on single-cell motility

Cell motility in response to environmental cues forms the basis of many developmental processes in multicellular organisms. One such environmental cue is an electric field (EF), which induces a form of motility known as electrotaxis. Electrotaxis has evolved in a number of cell types to guide wound healing, and has been associated with different cellular processes, suggesting that observed electrotactic behaviour is likely a combination of multiple distinct effects arising from the presence of an EF. In order to determine the different mechanisms by which observed electrotactic behaviour emerges, and thus to design EFs that can be applied to direct and control electrotaxis, researchers require accurate quantitative predictions of cellular responses to externally-applied fields. Here, we use mathematical modelling to formulate and parametrise a variety of hypothetical descriptions of how cell motility may change in response to an EF. We calibrate our model to observed data using synthetic likelihoods and Bayesian sequential learning techniques, and demonstrate that EFs bias cellular motility through only one of a selection of hypothetical mechanisms. We also demonstrate how the model allows us to make predictions about cellular motility under different EFs. The resulting model and calibration methodology will thus form the basis for future data-driven and model-based feedback control strategies based on electric actuation. SIGNIFICANCEElectrotaxis is attracting much interest and development as a technique to control cell migration due to the precision of electric fields as actuation signals. However, precise control of electrotactic migration relies on an accurate model of how cell motility changes in response to applied electric fields. We present and calibrate a parametrised stochastic model that accurately replicates experimental single-cell data and enables the prediction of input-output behaviour while quantifying uncertainty and stochasticity. The model allows us to elucidate and quantify how electric fields perturb the motile behaviour of the cell. This model and the associated simulation-based calibration methodology will be central to future developments in the control of electrotaxis.

biophysics↗

bioRxiv2021

A triple-negative matrix-producing breast carcinoma is arrested by tumor-targeting Salmonella typhimurium A1-R in a PDOX model

Background/AimMatrix-producing breast carcinoma (MPBC), is a rare, recalcitrant and highly aggressive. The present study aimed to determine the efficacy of tumor-targeting Salmonella typhimurium (S. typhimurium) A1-R on a triple-negative MPBC in a patient-derived orthotopic xenograft (PDOX) model. MethodsThe PDOX model was established in the left second mammary gland of a nude mouse by surgical orthotopic implantation (SOI) of the patient triple-negative MPBC PDOX models were randomized into two groups: G1, control group (n=6); G2, tumor-targeting S. typhimurium A1-R group (n=7, intravenous (i.v.) injection via tail vein, weekly, for two weeks). All mice were sacrificed on day 15. Tumor volume and body weight were measured one time per week. ResultsS. typhimurium A1-R arrested tumor growth compared to the control group (P = 0.016). ConclusionThe results of the present study suggest that S. typhimurium A1-R has future clinical potential in triple-negative MPBC patients.

cancer biology↗

bioRxiv2021

Female gametophyte expressed Arabidopsis thaliana lipid transfer proteins AtLtpI.4 and AtLtpI.8 provide a link between callose homeostasis, pollen tube guidance, and fertilization success

Non-specific lipid transfer proteins (LTPs) represent a sub-class among the large family of Cysteine-rich proteins (CRPs) specific to land plants. LTPs possess a hydrophobic cavity, enabling them to bind and stabilize a variety of lipid molecules outside membranes. In line with the existence of an N-terminal signal peptide, secreted LTPs represent a well-suited mobile signal carrier in the plants extracellular matrix. Thus, LTPs are currently considered as key players to mediate the bulk flow of lipids between membranes/compartments as well as the buildup of lipid barrier polymers including cutin and suberin. Here, we show that floral expressed Arabidopsis thaliana AtLtpI.4 (AtLTP2) and AtLtpI.8 (AtLTP5), mutually control cell-cell communication between growing pollen tubes and ovules during fertilization. Arabidopsis mutants lacking functional AtLtpI.4 and AtLtpI.8 exhibit significantly reduced fertilization success. Cross-pollination and cell biological analyses revealed that AtLtpI.4/I.8 double mutants are impaired in pollen tube guidance towards ovules. Our finding that the AtLtpI.4/I.8 phenotype correlates with aberrant callose depositions in the micropylar region during ovule development suggests that both LTPs represent novel players of a joint signaling pathway that controls callose homeostasis in the female gametophyte.

plant biology↗