Biology subjects

Yang, D.

Publications and source records attributed to Yang, D..

At least 271 records · Page 15Linked to original sources

bioRxiv2019

Purification, identification, and characterization of two benzophenanthridine alkaloids from Corydalis longicalcarata rhizomes with anti-mitotic and polyploidy-inducing activities

Mitosis has long been a therapeutic target for the treatment of cancer. After conducting a phenotypic screen for anti-mitotic activity in a crude extract library of more than 2000 medicinal plants, we identified the rhizomes of Corydalis longicalcarata. Guided by the bioactivity-based assay, two benzophenanthridine alkaloids were purified and subsequently identified as corynoline and its close analog acetylcorynoline. This study uncovers a previously unknown antimitotic activity for these two phytochemicals, discovers their potential to be developed as anticancer drugs, and highlights their pleiotropic effects on cell division, including prevention of chromosome congression, compromise of spindle checkpoint response, and blockage of cytokinesis.

cancer biology↗

bioRxiv2019

Identification of a Central Neural Circuit that Regulates Anxiety-induced Bone Loss

The homeostasis of bone metabolism is finely regulated by the central nervous system and recent studies have suggested that mood disorders, such as anxiety, are closely related to bone metabolic abnormalities; however, our understanding of central neural circuits regulating bone metabolism is still largely limited. In this study, we first demonstrate that confined isolation of human participants under normal gravity resulted in decreased bone density and elevated anxiety levels. We then used an established mouse model to dissect the neural circuitry regulating anxiety-induced bone loss. Combining electrophysiological, optogenetic and chemogenetic approaches, we demonstrate that GABAergic neural circuitry in ventromedial hypothalamus (VMH) modulates anxiety-induced bone loss; importantly, the GABAergic input in VMHdm arose from a specific group of somatostatin neurons in the bed nucleus of the stria terminalis (BNST), which is both indispensable for anxiety-induced bone loss and able to trigger bone loss in the absence of stressors. VGLUT2 neurons in Nucleus tractus solitaries (NTS) and peripheral sympathetic system were employed by this BNST-VMH neural circuit to regulate anxiety-induced bone loss. Overall, we uncovered new GABAergic neural circuitry from the forebrain to hypothalamus, used in the regulation of anxiety-induced bone loss, and revealed a population of somatostatin neurons in BNST not previously implicated in bone mass regulation. These findings thus identify the underlying central neural mechanism of psychiatric disorders, such as anxiety, that influences bone metabolism at the circuit level.\n\nOne Sentence SummaryIdentification of a new GABAergic neural circuit from forebrain to hypothalamus used for regulation of anxiety-induced bone loss.

neuroscience↗

bioRxiv2019

The effects of polydisperse crowders on the compaction of the Escherichia coli nucleoid

DNA binding proteins, supercoiling, macromolecular crowders, and transient DNA attachments to the cell membrane have all been implicated in the organization of the bacterial chromosome. However, it is unclear what role these factors play in compacting the bacterial DNA into a distinct organelle-like entity, the nucleoid. By analyzing the effects of osmotic shock and mechanical squeezing on Escherichia coli, we show that macromolecular crowders play a dominant role in the compaction of the DNA into the nucleoid. We find that a 30% increase in the crowder concentration from physiological levels leads to a 3-fold decrease in the nucleoids volume. The compaction is anisotropic, being higher along the long axes of the cell at low crowding levels. At higher crowding levels the compression becomes isotropic, implying that E. coli nucleoids lack a well-defined backbone. We furthermore show that the compressibility of the nucleoid is not significantly affected by cell growth rates and by prior treatment with rifampicin. The latter results point out that in addition to poly-ribosomes, soluble cytoplasmic proteins have a significant contribution in determining the size of the nucleoid.

biophysics↗

bioRxiv2019

Stretching DNA to twice the normal length with single-molecule hydrodynamic trapping

Single-molecule force spectroscopy has brought many new insights into nanoscale biology, from the functioning of molecular motors, to the mechanical response of soft materials within the cell. To expand the single-molecule toolbox, we have developed a surface-free force spectroscopy assay based on a high-speed hydrodynamic trap capable of applying extremely high tensions for long periods of time. High-speed single-molecule trapping is enabled by a rigid and gas-impermeable microfluidic chip, rapidly and inexpensively fabricated out of glass, double-sided tape and UV-curable adhesive. Our approach does not require difficult covalent attachment chemistries, and enables simultaneous force application and single-molecule fluorescence. Using this approach, we have induced a highly extended state with twice the contour length of B-DNA in regions of partially intercalated double-stranded (dsDNA) by applying forces up to 250 pN. This highly extended state resembles the hyperstretched state of dsDNA, which was initially discovered as a structure fully intercalated by dyes under high tension. It has been hypothesized that hyperstretched DNA could also be induced without the aid of intercalators if high-enough forces were applied, which matches our observation. Combining force application with single-molecule fluorescence imaging is critical for distinguishing hyperstretched DNA from single-stranded DNA that can result from peeling. High-speed hydrodynamic trapping is a powerful yet accessible force spectroscopy method that enables the mechanics of biomolecules to be probed in previously difficult to access regimes.

biophysics↗

bioRxiv2019

A high-content screen identifies the vulnerability of MYC-overexpressing cells to dimethylfasudil

A synthetic lethal effect arises when a cancer-associated change introduces a unique vulnerability to cancer cells that makes them unusually susceptible to a drugs inhibitory activity. The synthetic lethal approach is attractive because it enables targeting of cancers harboring specific genomic alterations, the products of which may have proven refractory to direct targeting. An example is cancer driven by overexpression of MYC. Here, we conducted a high-content screen for compounds that are synthetic lethal to elevated MYC using a small-molecule library to identify compounds that are closely related to, or are themselves, regulatory-approved drugs. The screen identified dimethylfasudil, a potent and reversible inhibitor of Rho-associated kinases ROCK1 and ROCK2. Close analogs of dimethylfasudil are used clinically to treat neurologic and cardiovascular disorders. The synthetic lethal interaction was conserved in rodent and human cell lines and could be observed with activation of either MYC or its paralog MYCN. The synthetic lethality seems specific to MYC overexpressing cells as it could not be substituted by a variety of oncogenic manipulations and synthetic lethality was diminished by RNAi-mediated depletion of MYC in human cancer cell lines. Collectively, these data support investigation of the use of dimethylfasudil as a drug that is synthetic lethal for malignancies that specifically overexpress MYC.\n\nSignificance StatementSynthetic lethal targeting of tumors overexpressing MYC holds promise for attacking aggressive malignancies. Here we describe a synthetic lethal interaction between dimethylfasudil and overexpression of MYC. Uniquely, this novel synthetic lethal interaction points toward an opportunity for synthetic lethality with a molecule likely to harbor favorable drug-like properties that enable systemic use.

cancer biology↗

bioRxiv2019

Ligand Entry into Fatty Acid Binding Protein via Local Unfolding instead of Gap Widening

Fatty acid binding proteins (FABPs) play an important role in transportation of fatty acids. Despite intensive studies, how fatty acids enter the protein cavity for binding is still controversial. Here, a gap-closed variant of human intestinal FABP was generated by mutagenesis, in which the gap is locked by a disulfide bridge. According to its structure determined here by NMR, this variant has no obvious openings as the ligand entrance and the gap cannot be widened by internal dynamics. Nevertheless, it still uptakes fatty acids and other ligands. NMR relaxation dispersion, chemical exchange saturation transfer and hydrogen-deuterium exchange experiments show that the variant exists in a major native state, two minor native-like state, and two locally unfolded states in aqueous solution. Local unfolding of either {beta}B-{beta}D or helix 2 can generate an opening large enough for ligands to enter the protein cavity, but only the fast local unfolding of helix 2 is relevant to the ligand entry process.\n\nStatement of SignificanceFatty acid binding proteins transport fatty acids to specific organelles in the cell. To enable the transport, fatty acids must enter and leave the protein cavity. In spite of many studies, how fatty acids enter the protein cavity remains controversial. Using mutagenesis and biophysical techniques, we have resolved the disagreement and further showed that local unfolding of the second helix can generate a transient opening to allow ligands to enter the protein cavity. Since lipid binding proteins are highly conserved in 3D structures and ligand binding, all of them may use the same local unfolding mechanism for ligand uptake and release.

biophysics↗

bioRxiv2019

The Dynamic Strength of the Hair-Cell Tip Link Reveals Mechanisms of Hearing and Deafness

Our senses of hearing and balance rely on the extraordinarily sensitive molecular machinery of the inner ear to convert deflections as small as the width of a single carbon atom1,2 into electrical signals that the brain can process3. In humans and other vertebrates, transduction is mediated by hair cells4, where tension on tip links conveys force to mechanosensitive ion channels5. Each tip link comprises two helical filaments of atypical cadherins bound at their N-termini through two unique adhesion bonds6-8. Tip links must be strong enough to maintain a connection to the mechanotransduction channel under the dynamic forces exerted by sound or head movement--yet might also act as mechanical circuit breakers, releasing under extreme conditions to preserve the delicate structures within the hair cell. Previous studies have argued that this connection is exceptionally static, disrupted only by harsh chemical conditions or loud sound9-12. However, no direct mechanical measurements of the full tip-link connection have been performed. Here we describe the dynamics of the tip-link connection at single-molecule resolution and show how avidity conferred by its double stranded architecture enhances mechanical strength and lifetime, yet still enables it to act as a dynamic mechanical circuit breaker. We also show how the dynamic strength of the connection is facilitated by strong cis-dimerization and tuned by extracellular Ca2+, and we describe the unexpected etiology of a hereditary human deafness mutation. Remarkably, the connection is several thousand times more dynamic than previously thought, challenging current assumptions about tip-link stability and turnover rate, and providing insight into how the mechanotransduction apparatus conveys mechanical information. Our results reveal fundamental mechanisms that underlie mechanoelectric transduction in the inner ear, and provide a foundation for studying multi-component linkages in other biological systems.

biophysics↗

bioRxiv2019

Corona exchange dynamics on carbon nanotubes by multiplexed fluorescence monitoring

Noncovalent adsorption of DNA on nanoparticles has led to their widespread implementation as gene delivery tools and optical probes. Yet, the behavior and stability of DNA-nanoparticle complexes once applied in biomolecule-rich, in vivo environments remains unpredictable, whereby biocompatibility testing usually occurs in serum. Here, we demonstrate time-resolved measurements of exchange dynamics between solution-phase and adsorbed corona-phase DNA and protein biomolecules on single-walled carbon nanotubes (SWCNTs). We capture real-time binding of fluorophore-labeled biomolecules, utilizing the SWCNT surface as a fluorescence quencher, and apply this corona exchange assay to study protein corona dynamics on ssDNA-SWCNT-based dopamine sensors. We study exchange of two blood proteins, albumin and fibrinogen, adsorbing to and competitively displacing (GT)6 vs. (GT)15 ssDNA from ssDNA-SWCNTs. We find that (GT)15 binds to SWCNTs with a higher affinity than (GT)6 and that fibrinogen interacts with ssDNA-SWCNTs more strongly than albumin. Albumin and fibrinogen cause a 52.2% and 78.2% attenuation of the dopamine nanosensor response, coinciding with 0.5% and 3.7% desorption of (GT)6, respectively. Concurrently, the total surface-adsorbed fibrinogen mass is 168% greater than that of albumin. Binding profiles are fit to a competitive surface exchange model which recapitulates the experimental observation that fibrinogen has a higher affinity for SWCNTs than albumin, with a fibrinogen on-rate constant 1.61-fold greater and an off-rate constant 0.563-fold smaller than that of albumin. Our methodology presents a generic route to assess real-time corona exchange on nanoparticles in solution phase, and more broadly motivates testing of nanoparticle-based technologies in blood plasma rather than the more ubiquitously-tested serum conditions.

bioengineering↗

bioRxiv2019

Convergent genomic signatures of high altitude adaptation among domestic mammals

Abundant and diverse domestic mammals living on the Tibetan Plateau provide useful materials for investigating adaptive evolution and genetic convergence. Here, we utilized 327 genomes from horses, sheep, goats, cattle, pigs and dogs living at both high and low altitudes, including 73 genomes generated for this study, to disentangle the genetic mechanisms underlying local adaptation of domestic mammals. Although molecular convergence is comparatively rare at the DNA sequence level, we found convergent signature of positive selection at the gene level, particularly EPAS1 gene in these Tibetan domestic mammals. We also reported a potential function in response to hypoxia for the gene C10orf67, which underwent positive selection in three of the domestic mammals. Our data provides insight into adaptive evolution of high-altitude domestic mammals, and should facilitate the search for additional novel genes involved in the hypoxia response pathway.

evolutionary biology↗

bioRxiv2019

Axon-like protrusions promote small cell lung cancer migration and metastasis

Metastasis is the main cause of death in cancer patients but remains a poorly understood process. Small cell lung cancer (SCLC) is one of the most lethal and most metastatic types of human cancer. SCLC cells normally express neuroendocrine and neuronal gene programs but accumulating evidence indicates that these cancer cells become relatively more neuronal and less neuroendocrine as they gain the ability to metastasize. Here we show that mouse and human SCLC cells in culture and in vivo can grow cellular protrusions that resemble axons. The formation of these protrusions is controlled by multiple neuronal factors implicated in axonogenesis, axon guidance, and neuroblast migration. Disruption of these axon-like protrusions impairs cell migration in culture and inhibits metastatic ability in vivo. The co-option of developmental neuronal programs is a novel molecular and cellular mechanism that contributes to the high metastatic ability of SCLC.

cancer biology↗

bioRxiv2019

Universal activation mechanism of class A GPCRs

Class A G protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology. GPCR activation is an allosteric process that links agonist binding to G protein recruitment, with the hallmark outward movement of transmembrane helix 6 (TM6). However, what leads to TM6 movement and the key residue-level changes of this trigger remain less well understood. Here, by analyzing over 230 high-resolution structures of class A GPCRs, we discovered a modular, universal GPCR activation pathway that unites previous findings into a common activation mechanism, directly linking the bottom of ligand-binding pocket with G protein-coupling region. We suggest that the modular nature of the universal GPCR activation pathway allowed for the decoupling of the evolution of the ligand binding site, G protein binding region and the residues important for receptor activation. Such an architecture might have facilitated GPCRs to emerge as a highly successful family of proteins for signal transduction in nature.

bioinformatics↗

bioRxiv2019

Cell Type-Specific Modulation of Layer 6A Excitatory Microcircuits by Acetylcholine in Rat Barrel Cortex

Acetylcholine (ACh) is known to regulate cortical activity during different behavioral states, e.g. wakefulness and attention. Here we show a differential expression of muscarinic ACh receptors (mAChRs) and nicotinic AChRs (nAChRs) in different layer 6A (L6A) pyramidal cell (PC) types of somatosensory cortex. At low concentrations, ACh induced a persistent hyperpolarization in corticocortical (CC) but a depolarization in corticothalamic (CT) L6A PCs via M4 and M1 mAChRs, respectively. At [~]1 mM ACh depolarized exclusively CT PCs via 4{beta}2 subunit-containing nAChRs without affecting CC PCs. Miniature EPSC frequency in CC PCs was decreased by ACh but increased in CT PCs. In synaptic connections with a presynaptic CC PC, glutamate release was suppressed via M4 mAChR activation but enhanced by nAChRs via 4{beta}2 nAChRs when the presynaptic neuron was a CT PC. Thus, in layer 6A the interaction of mAChRs and nAChRs results in an altered excitability and synaptic release, effectively strengthening corticothalamic output while weakening corticocortical synaptic signaling.

neuroscience↗

bioRxiv2019

Mapping Vector Field of Single Cells

Single-cell RNA-seq, together with RNA velocity and metabolic labeling, reveals cellular states and transitions at unprecedented resolution. Fully exploiting these data, however, requires dynamical models capable of predicting cell fate and unveiling the governing regulatory mechanisms. Here, we introduce dynamo, an analytical framework that reconciles intrinsic splicing and labeling kinetics to estimate absolute RNA velocities, reconstructs velocity vector fields that predict future cell fates, and finally employs differential geometry analyses to elucidate the underlying regulatory networks. We applied dynamo to a wide range of disparate biological processes including prediction of future states of differentiating hematopoietic stem cell lineages, deconvolution of glucocorticoid responses from orthogonal cell-cycle progression, characterization of regulatory networks driving zebrafish pigmentation, and identification of possible routes of resistance to SARS-CoV-2 infection. Our work thus represents an important step in going from qualitative, metaphorical conceptualizations of differentiation, as exemplified by Waddingtons epigenetic landscape, to quantitative and predictive theories.

systems biology↗

bioRxiv2019

The anti-apoptotic proteins Bcl-2 and Bcl-xL suppress Beclin1/Atg6-mediated lethal autophagy in polyploid cells

Inhibition of Aurora-B kinase is a synthetic lethal therapy for tumors that overexpress the MYC oncoprotein. It is currently unclear whether co-occurring oncogenic alterations might influence this synthetic lethality by confering more or less potency in the killing of tumor cells. To identify such modifers, we utilized isogenic cell lines to test a variety of cancer genes that have been previously demonstrated to promote survival under conditions of cellular stress, contribute to chemoresistance and/or suppress MYC-primed apoposis. We found that Bcl-2 and Bcl-xL, two antiapoptotic members of the Bcl-2 family, can partially suppress the synthetic lethality, but not multinucleation, elicited by a panaurora kinase inhibitor, VX-680. We demonstrate that this suppression stems from the rescue of autophagic cell death, specifically of multinucleated cells, rather than a general inhibition of apoptosis. Bcl-2 inhibits VX-680-induced death of polyploid cells by interacting with the autophagy protein Beclin1/Atg6 and rescue requires localization of Bcl-2 to the endoplasmic reticulum. These findings expand on previous conclusions that autophagic death of polyploid cells is mediated by Atg6. Bcl-2 and Bcl-xL negatively modulate MYC-VX-680 synthetic lethality and it is the anti-autophagic activity of these two Bcl-2 family proteins, specifically in multinucleate cells, that contributes to resistance to Aurora kinase-targeting drugs.

cancer biology↗

bioRxiv2019

High Throughput Evolution of Near Infrared Serotonin Nanosensors

Release and reuptake of neuromodulator serotonin, 5-HT, is central to mood regulation and neuropsychiatric disorders, whereby imaging serotonin is of fundamental importance to study the brains serotonin signaling system. We introduce a reversible near-infrared nanosensor for serotonin (nIRHT), for which synthetic molecular recognition toward serotonin is systematically evolved from ssDNA-carbon nanotube constructs generated from large libraries of 6.9 x 1010 unique ssDNA sequences. nIRHT produces a [~]200% fluorescence enhancement upon exposure to serotonin with a Kd = 6.3 {micro}M affinity. nIRHT shows selective responsivity towards serotonin over serotonin analogs, metabolites, and receptor-targeting drugs, and a 5-fold increased affinity for serotonin over dopamine. Further, nIRHT can be introduced into the brain extracellular space in acute slice, and can be used to image exogenous serotonin reversibly. Our results suggest evolution of nanosensors could be generically implemented to rapidly develop other neuromodulator probes, and that these probes can image neuromodulator dynamics at spatiotemporal scales compatible with endogenous neuromodulation.

neuroscience↗

bioRxiv2019

Selective Activation of TASK-3-containing K+ Channels Reveals Their Therapeutic Potentials in Analgesia

The paucity of selective agonists for TASK-3, a member of two-pore domain K+ (K2P) channels, has contributed to our limited understanding of its biological functions. By targeting a novel druggable transmembrane cavity using a structure-based drug design approach, we discovered a biguanide compound, CHET3, as a highly selective allosteric activator for TASK-3-containing K2P channels, including TASK-3 homomer and TASK-3/TASK-1 heteromer. CHET3 displayed unexpectedly potent analgesic effects in vivo in a variety of acute and chronic pain models in rodents that could be abolished by pharmacology or genetic ablation of TASK-3. We further found that TASK-3-containing channels anatomically define a unique subset population of small-sized, TRPM8, TRPV1 or tyrosine hydroxylase-positive nociceptive sensory neurons and functionally regulate their membrane excitability, supporting CHET3 analgesia in thermal hyperalgesia and mechanical allodynia under chronic pain. Overall, our proof-of-concept study reveals TASK-3-containing K2P channels as a novel druggable target for treating pain.\n\nOne Sentence SummaryIdentification of a novel drug target and its new hit compounds for developing new-generation non-opioid analgesics.

pharmacology and toxicology↗

bioRxiv2019

Aberrant Clonal Hematopoiesis Following Lentiviral Transduction of HSPC in a Rhesus Macaque

Lentiviral vectors (LV) have been used for the delivery of genes into hematopoietic stem and progenitor cells (HSPC) in clinical trials worldwide. LV, in contrast to retroviral vectors, have not been associated with insertion site-associated malignant clonal expansions, and thus have been considered safer. Here, however, we present a case of markedly abnormal dysplastic clonal hematopoiesis impacting the erythroid, myeloid and megakaryocytic lineages in a rhesus macaque transplanted with HSPCs that were transduced with a LV containing a strong retroviral murine stem cell virus (MSCV) constitutive promoter-enhancer in the LTR. 9 insertions were mapped in the abnormal clone, resulting in overexpression and aberrant splicing of several genes of interest, including the cytokine stem cell factor and the transcription factor PLAG1. This case represents the first clear link between a lentiviral insertion-induced clonal expansion and a clinically abnormal transformed phenotype following transduction of normal primate or human HSPC, and are thus concerning, and suggest that strong constitutive promoters should not be included within LV vectors.

molecular biology↗

bioRxiv2018

A critical role of the T3SS effector EseJ in intracellular trafficking and replication of Edwardsiella piscicida in non-phagocytic cells

Edwardsiella piscicida (E. piscicida) is an intracellular pathogen within a broad spectrum of hosts. Essential to E. piscicida virulence is its ability to survive and replicate inside host cells, yet the underlying mechanisms and the nature of the replicative compartment remain unclear. Here, we characterized its intracellular lifestyle in non-phagocytic cells and showed that intracellular replication of E. piscicida in non-phagocytic cells is dependent on its type III secretion system. Following internalization, E. piscicida is contained in vacuoles that transiently mature into early endosomes, but subsequently bypasses the classical endosome pathway and fusion with lysosomes which depends on its T3SS. Following a rapid escape from the degradative pathway, E. piscicida was found to create a specialized replication-permissive niche characterized by endoplasmic reticulum (ER) markers. We also found that a T3SS effector EseJ is responsible for intracellular replication of E. piscicida by preventing endosome/lysosome fusion. Furthermore, in vivo experiments confirmed that EseJ is necessary for bacterial colonization of E. piscicida in both mice and zebrafish. Thus, this work elucidates the strategies used by E. piscicida to survive and proliferate within host non-phagocytic cells.\n\nAuthor summaryE. piscicida is a facultative intracellular bacterium associated with septicemia and fatal infections in many animals, including fish and humans. However, little is known about its intracellular life, which is important for successful invasion of the host. The present study is the first comprehensive characterization of E. piscicidas intracellular life-style in host cells. Upon internalization, E. piscicida is transiently contained in Rab5-positive vacuoles, but the pathogen prevents further endosome maturation and fusion with lysosomes by utilizing an T3SS effector EseJ. In addition, the bacterium creates an specialized replication niche for rapid growth via an interaction with the ER. Our study provides new insights into the strategies used by E. piscicida to successfully establishes an intracellular lifestyle that contributes to its survival and dissemination during infection.

pathology↗