Biology subjects

Fang, M.

Publications and source records attributed to Fang, M..

At least 55 records · Page 3Linked to original sources

bioRxiv2022

RNA velocity unraveled

We perform a thorough analysis of RNA velocity methods, with a view towards understanding the suitability of the various assumptions underlying popular implementations. In addition to providing a self-contained exposition of the underlying mathematics, we undertake simulations and perform controlled experiments on biological datasets to assess workflow sensitivity to parameter choices and underlying biology. Finally, we argue for a more rigorous approach to RNA velocity, and present a framework for Markovian analysis that points to directions for improvement and mitigation of current problems.

biophysics↗

bioRxiv2021

Spatiotemporal dynamics of molecular expression pattern and intercellular interactions in glial scar responding to spinal cord injury

Adult regeneration in spinal cord is poor in mammalian but remarkable in the neonatal mammals and some vertebrates, including fish and salamanders. Increasing evidences basis of this interspecies and ontogeny highlighted the pivotal roles of neuron extrinsic factors-the glial scar, which exert confusing inhibiting or promoting regeneration function, but the spatiotemporal ordering of cellular and molecular events that drive repair processes in scar formation remains poorly understood. Here, we firstly constructed tissue-wide gene expression measurements of mouse spinal cords over the course of scar formation using the spatial transcriptomics (ST) technology in Spinal cord injury (SCI) repair. We analyzed the transcriptomes of nearly 15449 spots from 32 samples and distinguished normal and damage response regions. Compared to histological changes, spatial mapping of differentiation transitions in spinal cord injury site delineated the possible trajectory between subpopulations of fibroblast, glia and immune cell more comprehensively and defined the extent of scar boundary and core more accurately. Locally, we identified gene expression gradients from leading edge to the core of scar areas that allow for re-understanding of the scar microenvironment and found some regulators in special cell types, such as Thbs1 and Col1a2 in macrophage, CD36 and Postn in fibroblast, Plxnb2 and Nxpe3 in microglia, Clu in astrocyte and CD74 in oligodendrocyte. Last, we profiled the bidirectional ligand-receptor interactions at the neighbor cluster boundary, contributing to maintain scar architecture during gliosis and fibrosis, and found GPR37L1_PSAP and GPR37_PSAP were top 2 enriched gene-pairs between microglia and fibroblast or microglia and astrocyte. Together, the establishment of these profiles firstly uncovered scar spatial heterogeneity and lineage trajectory, provide an unbiased view of scar and served as a valuable resource for CNS injury treatment. HighlightsO_LISpatial illustration of gene expression pattern after T10 right lateral hemisection. C_LIO_LISpatial atlas of scar formation by 21 cell types around damaged area. C_LIO_LIThe origin, trajectory reconstruction and functional diversity of cell types in different stages of scar formation. C_LIO_LINovel insights for glial scar boundary and potential benefits for recovery intervention after SCI. C_LI

neuroscience↗

bioRxiv2021

Whole-genome sequencing of Chinese native goat offers biological insights into cashmere fiber formation

Cashmere evolved naturally in the goat, and almost all breeds of goat can produce more or less cashmere fibers. However, the genetic alterations underlying cashmere trait selection are still unclear.We sequenced 120 Chinese native goat including two cashmere goat breeds (Ujumain, Chaidamu) and six ordinary goat breeds (Jining Gray, Matou, Guizhou Black, Jintang Black, Yunnan Black Bone, Chengdu Brown). The genome-wide selective sweep of cashmere goat and ordinary goat revealed a novel set of candidate genes as well as pathways, such as Nuclear factor kappa-B and Wnt Signaling pathways. Of them, the LHX2 gene regulating hair follicle development, was evident from the strongest selection signal when comparing the Uhumqin cashmere goat and ordinary goat. Interestingly, we identified a 582bp deletion at 367 kb upstream of LHX2 with higher frequency in cashmere goats and their ancient relatives. This mutation probably rises along the breeding procedures, and is putatively responsible for cashmere production and diameter, as revealed by association studies. Luciferase assay shows that the deletion, which acts as an insulator, restrains the expression of LHX2 by interfering its upstream enhancers.Our study discovers a novel insulator of the LHX2 involved in regulating cashmere production and diameter, which would be beneficial to understanding hair follicle development and regeneration. Our findings also provide new insights into the genetic formation of cashmere, and facilitate subsequent molecular breeding for cashmere goat improvement.

genomics↗

bioRxiv2021

PyMVPD: A toolbox for multivariate pattern dependence

AO_SCPLOWBSTRACTC_SCPLOWCognitive tasks engage multiple brain regions. Studying how these regions interact is key to understand the neural bases of cognition. Standard approaches to model the interactions between brain regions rely on univariate statistical dependence. However, newly developed methods can capture multivariate dependence. Multivariate Pattern Dependence (MVPD) is a powerful and flexible approach that trains and tests multivariate models of the interactions between brain regions using independent data. In this article, we introduce PyMVPD: an open source toolbox for Multivariate Pattern Dependence. The toolbox includes pre-implemented linear regression models and artificial neural network models of the interactions between regions. It is designed to be easily customizable. We demonstrate example applications of PyMVPD using well-studied seed regions such as the fusiform face area (FFA) and the parahippocampal place area (PPA). Next, we compare the performance of different model architectures. Overall, artificial neural networks outperform linear regression. Importantly, the best performing architecture is region-dependent: MVPD subdivides cortex in distinct, contiguous regions whose interaction with FFA and PPA is best captured by different models.

neuroscience↗

bioRxiv2021

Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments

The question of how cell-to-cell differences in transcription rate affect RNA count distributions is fundamental for understanding biological processes underlying transcription. We argue that answering this question requires quantitative models that are both interpretable (describing concrete biophysical phenomena) and tractable (amenable to mathematical analysis). This enables the identification of experiments which best discriminate between competing hypotheses. As a proof of principle, we introduce a simple but flexible class of models involving a stochastic transcription rate coupled to a discrete stochastic RNA transcription and splicing process, and compare and contrast two biologically plausible hypotheses about transcription rate variation. One assumes variation is due to DNA experiencing mechanical strain, while the other assumes it is due to regulator number fluctuations. Although biophysically distinct, these models are mathematically similar, and we show they are hard to distinguish without comparing whole predicted probability distributions. Our work illustrates the importance of theory-guided data collection, and introduces a general framework for constructing and solving mathematically nontrivial continuous-discrete stochastic models. Significance StatementThe interpretation of transcriptomic observations requires detailed models of biophysical noise that can be compared and fit to experimental data. Models of intrinsic noise, describing stochasticity in molecular reactions, and extrinsic noise, describing cell-to-cell variation, are particularly common. However, integrating and solving them is challenging, and previous results are largely limited to summary statistics. We examine two mechanistically grounded stochastic models of transcriptional variation and demonstrate that (1) well-known regimes naturally emerge in limiting cases, and (2) the choice of noise model significantly affects the RNA distributions, but not the lower moments, offering a route to model identification and inference. This approach provides a simple and biophysically interpretable means to construct and unify models of transcriptional variation.

biophysics↗

bioRxiv2021

Chemoproteomic profiling reveals cellular targets of nitro-fatty acids

Nitro-fatty acids are a class of endogenous electrophilic lipid mediators with anti-inflammatory and cytoprotective effects in a wide range of inflammatory and fibrotic disease models. While these beneficial biological effects of nitro-fatty acids are mainly attributed to their ability to form covalent adducts with proteins, only a small number of proteins are known to be nitro-alkylated and the scope of protein nitro-alkylation remains undetermined. Here we describe the synthesis and application of a clickable nitro-fatty acid probe for the detection and first global identification of mammalian proteins that are susceptible to nitro-alkylation. 184 high confidence nitro-alkylated proteins were identified in human macrophages, majority of which are novel targets of nitro-fatty acids, including Extended synaptotagmin 2 (ESYT2), Signal transducer and activator of transcription 3 (STAT3), Toll-like receptor 2 (TLR2), Retinoid X receptor alpha (RXR) and Glucocorticoid receptor (NR3C1). In particular, we showed that 9-nitro-oleate covalently modified and inhibited dexamethasone binding to NR3C1. Bioinformatic analyses revealed that nitro-alkylated proteins are highly enriched in endoplasmic reticulum and transmembrane proteins, and are overrepresented in lipid metabolism and transport pathways. This study significantly expands the scope of protein substrates targeted by nitro-fatty acids in living cells and provides a useful resource towards understanding the pleiotropic biological roles of nitro-fatty acids as signaling molecules or as multi-target therapeutic agents.

biochemistry↗

bioRxiv2021

Molecular architecture determines brain delivery of a transferrin-receptor targeted lysosomal enzyme

Delivery of biotherapeutics across the blood-brain barrier (BBB) is a challenge. Many approaches fuse biotherapeutics to platforms that bind the transferrin receptor (TfR), a brain endothelial cell target, to facilitate receptor-mediated transcytosis across the BBB. Here, we characterized the pharmacological behavior of two distinct TfR-targeted platforms fused to iduronate 2-sulfatase (IDS), a lysosomal enzyme deficient in mucopolysaccharidosis type II (MPS II), and compared the relative brain exposures and functional activities of both approaches in mouse models. IDS fused to a moderate-affinity, monovalent TfR binding enzyme transport vehicle (ETV:IDS) resulted in widespread brain exposure, internalization by parenchymal cells, and significant substrate reduction in the CNS of an MPS II mouse model. In contrast, IDS fused to a standard high-affinity bivalent antibody (IgG:IDS) resulted in lower brain uptake, limited biodistribution beyond brain endothelial cells, and reduced brain substrate reduction. These results highlight important features likely to impact the clinical development of TfR-targeting platforms in MPS II and potentially other CNS diseases. SummaryBrain delivery, biodistribution and pharmacodynamics of a lysosomal enzyme fused to a moderate-affinity transferrin receptor-directed blood-brain barrier enzyme transport vehicle are superior to a traditional high-affinity anti-TfR monoclonal antibody fusion.

neuroscience↗

bioRxiv2020

Regulating enzymatic reactions in Escherichia coli utilizing light-responsive cellular compartments based on liquid-liquid phase separation

Enzymatic reactions in cells are well organized into different compartments, among which protein-based membraneless compartments formed through liquid-liquid phase separation (LLPS) are believed to play important roles1,2. Hijacking them for our own purpose has promising applications in metabolic engineering3. Yet, it is still hard to precisely and dynamically control target enzymatic reactions in those compartments4. To address those problems, we developed Photo-Activated Switch in E. coli (PhASE), based on phase separating scaffold proteins and optogenetic tools. In this system, a protein of interest (POI) can be enriched up to 15-fold by LLPS-based compartments from cytosol within only a few seconds once activated by light, and become fully dispersed again within 15 minutes. Furthermore, we explored the potentiality of the LLPS-based compartment in enriching small organic molecules directly via chemical-scaffold interaction. With enzymes and substrates co-localized under light induction, the overall reaction efficiency could be enhanced. Using luciferin and catechol oxidation as model enzymatic reactions, we found that they could accelerate 2.3-fold and 1.6-fold, respectively, when regulated by PhASE. We anticipate our system to be an extension of the synthetic biology toolkit, facilitating rapid recruitment and release of POIs, and reversible regulation of enzymatic reactions.

synthetic biology↗

bioRxiv2020

Transferrin receptor is another receptor for SARS-CoV-2 entry

Angiotensin-converting enzyme 2 (ACE2) has been suggested as a receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry to cause coronavirus disease 2019 (COVID-19). However, no ACE2 inhibitors have shown definite beneficiaries for COVID-19 patients, applying the presence of another receptor for SARS-CoV-2 entry. Here we show that ACE2 knockout dose not completely block virus entry, while TfR directly interacts with virus Spike protein to mediate virus entry and SARS-CoV-2 can infect mice with over-expressed humanized transferrin receptor (TfR) and without humanized ACE2. TfR-virus co-localization is found both on the membranes and in the cytoplasma, suggesting SARS-CoV-2 transporting by TfR, the iron-transporting receptor shuttling between cell membranes and cytoplasma. Interfering TfR-Spike interaction blocks virus entry to exert significant anti-viral effects. Anti-TfR antibody (EC50 ~16.6 nM) shows promising anti-viral effects in mouse model. Collectively, this report indicates that TfR is another receptor for SARS-CoV-2 entry and a promising anti-COVID-19 target.

microbiology↗

bioRxiv2020

Reconstitution of an intact clock that generates circadian DNA binding in vitro

Circadian clocks control gene expression in the complex milieu of cells. Here, we reconstituted under defined conditions in vitro the cyanobacterial circadian clock system which includes an oscillator, signal-transduction pathways, transcription factor, and promoter DNA. The system oscillates autonomously with a near 24 h period, remains phase coherent for many days, and allows real-time observation of each component simultaneously without user intervention. This reassembled clock system provides new insights into how a circadian clock exerts control over gene expression and can serve in the area of synthetic biology as a new platform upon which to build even more complexity. One Sentence SummaryAn autonomously oscillating circadian clock-controlled gene regulatory circuit is studied in vitro using a real-time high-throughput assay.

biochemistry↗

bioRxiv2020

AI-aided design of novel targeted covalent inhibitors against SARS-CoV-2

The focused drug repurposing of known approved drugs (such as lopinavir/ritonavir) has been reported failed for curing SARS-CoV-2 infected patients. It is urgent to generate new chemical entities against this virus. As a key enzyme in the life-cycle of coronavirus, the 3C-like main protease (3CLpro or Mpro) is the most attractive for antiviral drug design. Based on a recently solved structure (PDB ID: 6LU7), we developed a novel advanced deep Q-learning network with the fragment-based drug design (ADQN-FBDD) for generating potential lead compounds targeting SARS-CoV-2 3CLpro. We obtained a series of derivatives from those lead compounds by our structure-based optimization policy (SBOP). All the 47 lead compounds directly from our AI-model and related derivatives based on SBOP are accessible in our molecular library at https://github.com/tbwxmu/2019-nCov. These compounds can be used as potential candidates for researchers in their development of drugs against SARS-CoV-2.

pharmacology and toxicology↗

bioRxiv2020

Transferrin-dependent crosstalk between the intestinal tract and commensal microbes contributes for immune tolerance

Crosstalks between gastrointestinal tract and commensal microbes regulate immune tolerance and maintain host intestinal homeostasis. However, molecular events that regulate the crosstalks remain poorly understood. Here, we show that microbial products (lipopolysaccharide, lipoteichoic acid and DNA) up-regulate host transferrin, an iron supplier of commensal bacteria, to induce hosts immune tolerance by negatively regulating toll-like receptor (TLR) signaling. Transferrin level in germ-free and broad-spectrum antibiotics-treated mice is much less than that in normal mice. Transferrin is found to silence TLR signaling complex by directly interacting with CD14, a co-receptor of many TLRs. Transferrin knock-down impaired host tolerogenic responses as well as broad-spectrum antibiotics treatment. Our findings reveal that commensal bacteria up-regulate and beneficially use host transferrin as a negative regulator of TLR signaling to shape host immunity and contribute for intestinal tolerance.

immunology↗

bioRxiv2019

Transferrin plays a central role to maintain coagulation balance by interacting with clotting factors

Coagulation balance is maintained through fine-tuning interactions among clotting factors. Physiological concentrations of clotting factors are huge difference. Especially, coagulation proteases concentration (pM to nM) is much lower than their natural inactivator antithrombin III (AT-III, [~]3 M). Here we show that transferrin (normal plasma concentration [~]40 M) interacts with fibrinogen, thrombin, FXIIa and AT-III with different affinity to maintain coagulation balance. Normally, transferrin is sequestered by binding with fibrinogen (normal plasma concentration [~]10 M) with a molar ratio of 4:1. In atherosclerosis, abnormally up-regulated transferrin interacts with and potentiates thrombin/FXIIa and blocks AT-IIIs inactivation on coagulation proteases by binding to AT-III, and thus induces hypercoagulability. In mouse models, transferrin-overexpression aggravated atherosclerosis while transferrin-knockdown, anti-transferrin antibody or designed peptides interfering transferrin-thrombin/FXIIa interactions alleviated it. Collectively, these findings identify transferrin as a clotting factor and an adjuster for maintaining coagulation balance and modify the coagulation cascade.

molecular biology↗

bioRxiv2019

Iron-deficiency and estrogen are associated with ischemic stroke by up-regulating transferrin to induce hypercoagulability

In the accompanying manuscript, transferrin has been demonstrated to maintain coagulation balance by interacting with clotting factors, suggesting that elevated transferrin causes thromboembolic diseases and factors up-regulating transferrin is associated with thrombosis. Here we show that transferrin and transferrin-thrombin/FXIIa complexes are elevated in plasma and cerebrospinal fluid of ischemic stroke (IS) patients with iron-deficiency anemia (IDA) history, IDA patients and venous thromboembolism patients using combined oral contraceptives (CC) as well as ID mice, suggesting an association of transferrin up-regulation with ID and CC. ID and estrogen up-regulated transferrin through hypoxia and estrogen response elements located at transferrin gene enhancer and promoter region, respectively. ID, exogenous transferrin/estrogen administration or transferrin over-expression promoted hypercoagulability and aggravated IS, while anti-transferrin antibody, transferrin knockdown or designed peptide inhibitors interfering transferrin-thrombin/FXIIa interaction exerted anti-IS effects in vivo. Collectively, the results reveal that factors (i.e., ID and CC) up-regulating transferrin are risk factors of thromboembolic diseases.

biochemistry↗

bioRxiv2018

Coupled Reaction Networks for Noise Suppression

Noise is intrinsic to many important regulatory processes in living cells, and often forms obstacles to be overcome for reliable biological functions. However, due to stochastic birth and death events of all components in biomolecular systems, suppression of noise of one component by another is fundamentally hard and costly. Quantitatively, a widelycited severe lower bound on noise suppression in biomolecular systems was established by Lestas et. al. in 2010, assuming that the plant and the controller have separate birth and death reactions. This makes the precision observed in several biological phenomena, e.g., cell fate decision making and cell cycle time ordering, seem impossible. We demonstrate that coupling, a mechanism widely observed in biology, could suppress noise lower than the bound of Lestas et. al. with moderate energy cost. Furthermore, we systematically investigate the coupling mechanism in all two-node reaction networks, showing that negative feedback suppresses noise better than incoherent feedforward achitectures, coupled systems have less noise than their decoupled version for a large class of networks, and coupling has its own fundamental limitations in noise suppression. Results in this work have implications for noise suppression in biological control and provide insight for a new efficient mechanism of noise suppression in biology.

systems biology↗

bioRxiv2018

Hippocampal signature of associative memory measured by chronic ambulatory intracranial EEG

Some patients with medically refractory focal epilepsy are chronically implanted with a brain-responsive neurostimulation device (the RNS(R) System), permitting neurophysiological measurements at millisecond resolution. This clinical device can be adapted to measure hippocampal dynamics time-locked to cognitive tasks. We illustrate the technique with a proof of concept in three patients previously implanted with the RNS System as they engage in an associative memory task, measured months apart. Hippocampal activity measured in successful encoding in RNS System patients mirrors that in surgical patients during intracranial electroencephalography (iEEG), suggesting that chronic iEEG allows sensitive measurements of hippocampal physiology over prolonged timescales.

neuroscience↗

bioRxiv2017

Dietary xenoestrogens significantly alter cellular metabolism induced by palbociclib/letrozole combination cancer therapy

HighlightsO_LISynergism of combined palbociclib/letrozole chemotherapy was examined by global metabolomics\nC_LIO_LICombination therapy led to more pronounced effects on the MCF-7 metabolome than single agents\nC_LIO_LIDietary phyto- and mycoestrogens significantly affected the metabolic and anti-oncogenic response of the drugs\nC_LIO_LIImplications of these bio-active chemicals on therapeutic success in breast cancer patients appear plausible\nC_LI\n\nIn BriefWarth et al. used innovative global metabolomics and pathway prediction technology to describe the metabolic effects of the combined palbociclib/letrozole breast cancer therapy. Moreover, the role of dietary xenoestrogens on this treatment was examined by metabolite data, proliferation experiments, and functional assays.\n\nSummaryRecently, the palbociclib/letrozole combination therapy was granted accelerated FDA approval for the treatment of estrogen receptor (ER) positive breast cancer. Since the underlying metabolic effects of these drugs are yet unknown, we investigated their synergism at the metabolome level in MCF-7 cells. As xenoestrogens interact with the ER, we additionally aimed at deciphering the impact of the phytoestrogen genistein, and the estrogenic mycotoxin zearalenone on this treatment. A global metabolomics approach was applied to unravel metabolite and pathway modifications. The results clearly showed that the combined effects of palbociclib and letrozole on cellular metabolism were far more pronounced than that of each agent alone and potently influenced by xenoestrogens. This behavior was confirmed in proliferation experiments and functional assays. Specifically, amino acids and central carbon metabolites were attenuated while higher abundances were observed for fatty acids and most nucleic acid related metabolites. Interestingly, exposure to model xenoestrogens appeared to partially counteract these effects.

cancer biology↗

bioRxiv2017

Decoding the orientation of contrast edges from MEG evoked and induced responses

1Visual gamma oscillations have been proposed to subserve perceptual binding, but their strong modulation by diverse stimulus features confounds interpretations of their precise functional role. Overcoming this challenge necessitates a comprehensive account of the relationship between gamma responses and stimulus features. Here we used multivariate pattern analyses on human MEG data to characterize the relationships between gamma responses and one basic stimulus feature, the orientation of contrast edges. Our findings confirmed we could decode orientation information from induced responses in two dominant frequency bands at 24-32 Hz and 50-58 Hz. Decoding was higher for cardinal than oblique orientations, with similar results also obtained for evoked MEG responses. In contrast to multivariate analyses, orientation information was mostly absent in univariate signals: evoked and induced responses in early visual cortex were similar in all orientations, with only exception an inverse oblique effect observed in induced responses, such that cardinal orientations produced weaker oscillatory signals than oblique orientations. Taken together, our results showed multivariate methods are well suited for the analysis of gamma oscillations, with multivariate patterns robustly encoding orientation information and predominantly discriminating cardinal from oblique stimuli.

neuroscience↗