Biology subjects

Song, A.

Publications and source records attributed to Song, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Conserved and derived expression patterns and positive selection on dental genes reveal complex evolutionary context of ever-growing rodent molars

Continuously growing teeth are an important innovation in mammalian evolution, yet genetic regulation of continuous growth by stem cells remains incompletely understood. Dental stem cells responsible for tooth crown growth are lost at the onset of tooth root formation. Genetic signaling that initiates this loss is difficult to study with the ever-growing incisor and rooted molars of mice, the most common mammalian dental model species, because signals for root formation overlap with signals that pattern tooth size and shape (i.e., cusp patterns). Different species of voles (Cricetidae, Rodentia, Glires) have evolved rooted and unrooted molars that have similar size and shape, providing alternative models for studying roots. We assembled a de novo genome of Myodes glareolus, a vole with high-crowned, rooted molars, and performed genomic and transcriptomic analyses in a broad phylogenetic context of Glires (rodents and lagomorphs) to assess differential selection and evolution in tooth forming genes. We identified 15 dental genes with changing synteny relationships and six dental genes undergoing positive selection across Glires, two of which were undergoing positive selection in species with unrooted molars, Dspp and Aqp1. Decreased expression of both genes in prairie voles with unrooted molars compared to bank voles supports the presence of positive selection and may underlie differences in root formation. Bulk transcriptomics analyses of embryonic molar development in bank voles also demonstrated conserved patterns of dental gene expression compared to mice, with species-specific variation likely related to developmental timing and morphological differences between mouse and vole molars. Our results support ongoing evolution of dental genes across Glires, revealing the complex evolutionary background of convergent evolution for ever-growing molars.

evolutionary biology↗

bioRxiv2023

Endocytosis Inhibitors Block SARS-CoV-2 Pseudoparticle Infection of Mink Lung Epithelium

Both spill over and spill back of SARS-CoV-2 virus have been reported on mink farms in Europe and the United States. Zoonosis is a public health concern as dangerous mutated forms of the virus could be introduced into the human population through spillback. The purpose of our study was to determine the SARS-CoV-2 entry mechanism using mink lung epithelial cell line (Mv1Lu) and to block entry with drug inhibitors. Mv1Lu cells were susceptible to SARS-CoV-2 viral pseudoparticle infection, validating them as a suitable disease model for COVID-19. Inhibitors of TMPRSS2 and of endocytosis, two pathways of viral entry, were tested to identify those that blocked infection. Dyngo4a, a small molecule endocytosis inhibitor, significantly reduced infection, while TMPRSS2 inhibitors had minimal impact, supporting the conclusion that the entry of the SARS-CoV-2 virus into Mv1Lu cells occurs primarily through endocytosis. The small molecule inhibitors that were effective in this study could potentially be used therapeutically to prevent SARS-CoV-2 infection in mink populations. This study will facilitate the development of therapeutics to prevent zoonotic transmission of SARS-CoV-2 variants to other animals, including humans.

cell biology↗

bioRxiv2023

Imetelstat-Mediated Alterations in Fatty Acid Metabolism To Induce Ferroptosis As Therapeutic Strategy for Acute Myeloid Leukemia

Telomerase enables replicative immortality in most cancers including acute myeloid leukemia (AML). Imetelstat is a first-in-class telomerase inhibitor with clinical efficacy in myelofibrosis and myelodysplastic syndromes. Here, we develop an AML patient-derived xenograft (PDX) resource, and perform integrated genomics, transcriptomics, and lipidomics analyses combined with functional genetics to identify key mediators of imetelstat efficacy. In a randomized Phase II-like preclinical trial in PDX, imetelstat effectively diminishes AML burden, and preferentially targets subgroups containing mutant NRAS and oxidative stress-associated gene expression signatures. Unbiased, genome-wide CRISPR/Cas9 editing identifies ferroptosis regulators as key mediators of imetelstat efficacy. Imetelstat promotes the formation of polyunsaturated fatty acid-containing phospholipids, causing excessive levels of lipid peroxidation and oxidative stress. Pharmacological inhibition of ferroptosis diminishes imetelstat efficacy. We leverage these mechanistic insights to develop an optimized therapeutic strategy using oxidative stress-inducing chemotherapy to sensitize patient samples to imetelstat causing significant disease control in AML.

cancer biology↗

bioRxiv2023

Oncogenic drivers dictate immune control of acute myeloid leukemia.

Acute myeloid leukemia (AML) is a genetically heterogeneous, aggressive hematological malignancy induced by distinct oncogenic driver mutations. The effect of specific AML oncogenes on immune activation or suppression has not been investigated. Here, we examine immune responses in genetically distinct models of AML and demonstrate that specific AML oncogenes dictate immunogenicity, the quality of immune response and immune escape through immunoediting. Specifically, expression of NrasG12D alone is sufficient to drive a potent anti-leukemia response through increased MHC Class II expression that can be overcome with increased expression of Myc. These data have important implications for the design and implementation of personalized immunotherapies for patients with AML. Statement of SignificanceThe endogenous immune response against acute myeloid leukemia (AML) is determined by leukemia-specific oncogenic driver mutations. Mutant Nras drives immunological selection of AML.

cancer biology↗

bioRxiv2022

Does Vaping Increase the Likelihood of SARS-CoV-2 Infection? Paradoxically Yes and No

Data on the relationship between electronic cigarettes (ECs) and SARS-CoV-2 infection are limited and contradictory. Evidence indicates that EC aerosols or nicotine increase ACE2, SARS-CoV-2 virus receptors, which increase virus binding and susceptibility. Our objectives were to determine if EC aerosols increased SARS-CoV-2 infection of human bronchial epithelial cells and to identify the causative chemical(s). A 3D organotypic model (EpiAirway) in conjunction with air liquid interface (ALI) exposure was used to test the effects of aerosols produced from JUUL "Virginia Tobacco" and BLU ECs, or individual chemicals (nicotine, propylene glycol, vegetable glycerin (PG/VG), and benzoic acid) on infection using SARS-CoV-2 pseudoparticles. Exposure of EpiAirway to JUUL aerosols increased ACE2, while BLU and lab-made EC aerosols containing nicotine increased ACE2 levels and TMPRSS2 activity, a spike protease that enables viral-cell fusion. Pseudoparticle infection of EpiAirway increased with aerosols produced from PG/VG, PG/VG plus nicotine, or BLU ECs. JUUL EC aerosols did not increase infection above controls. The baseline level of infection in JUUL treated aerosol groups was attributed to benzoic acid, which mitigated the enhanced infection caused by PG/VG or nicotine. The benzoic acid protection from enhanced infection continued at least 48 hours after exposure. TMPRSS2 activity was significantly correlated with e-liquid pH, which in turn was significantly correlated with infection, with lower pH blocking PG/VG and nicotine-induced-enhanced infection. While ACE2 levels increased in EpiAirway tissues exposed to EC aerosols, infection depended on the ingredients of the e-liquids. PG/VG and nicotine enhanced infection, an effect that was mitigated by benzoic acid.

cell biology↗

bioRxiv2022

Developmental role of macrophages modelled in human pluripotent stem cell derived intestinal tissue

Macrophages populate the embryo early in gestation but their role in the developmental process remains largely unknown. In particular, specification and function of macrophages in intestinal development remain unexplored. To study this event in human developmental context, we derived and combined human intestinal organoid and macrophages from pluripotent stem cells. Macrophages migrated into the organoid, proliferated, and occupied the emerging micro-anatomical niches of epithelial crypts and ganglia. They also acquired a similar transcriptomic profile to fetal intestinal macrophages and displayed tissue macrophage behaviors, such as recruitment to tissue injury. Using this model, we show that macrophages reduce glycolysis in mesenchymal cells and limit tissue growth without affecting tissue architecture, in contrast to the pro-growth effect of enteric neurons. In short, we engineered an intestinal tissue model populated with macrophages, and we suggest that resident macrophages contribute to regulation of metabolism and growth of the developing intestine.

developmental biology↗

bioRxiv2022

New Insights into How JUUL Electronic Cigarette Aerosols and Aerosol Constituents Affect SARS-CoV-2 Infection of Human Bronchial Epithelial Cells

BackgroundThe relationship between the use of tobacco products and SARS-CoV-2 infection is poorly understood and controversial. Most studies have been done with tobacco cigarettes, while few have examined the effect of electronic cigarettes (ECs) on SARS-CoV-2 infection. We tested the hypothesis that EC fluids and aerosols with high concentrations of nicotine promote SARS-COV-2 infection by increasing viral entry into human respiratory epithelial cells. MethodsResponses of BEAS-2B cells to authentic JUUL aerosols or their individual constituents (propylene glycol (PG)/vegetable glycerin (VG) and nicotine) were compared using three exposure platforms: submerged culture, air-liquid-interface (ALI) exposure in a cloud chamber, and ALI exposure in a Cultex(R) system, which produces authentic heated EC aerosols. SARS-CoV-2 infection machinery was assessed using immunohistochemistry and Western blotting. Specifically, the levels of the SARS-CoV-2 receptor ACE2 (angiotensin converting enzyme 2) and a spike modifying enzyme, TMPRSS2 (transmembrane serine protease 2), were evaluated. Following each exposure, lentivirus pseudoparticles with spike protein and a green-fluorescent reporter were used to test viral penetration and the susceptibility of BEAS-2B cells to infection. ResultsNicotine, EC fluids, and authentic JUUL aerosols increased both ACE2 levels and TMPRSS2 activity, which in turn increased viral particle entry into cells. While most data were in good agreement across the three exposure platforms, cells were more responsive to treatments when exposed at the ALI in the Cultex system, even though the exposures were brief and intermittent. In the Cultex system, PG/VG, PG/VG/nicotine, and JUUL aerosols significantly increased infection above clean air controls. However, both the PG/VG and JUUL treatments were significantly lower than nicotine/PG/VG. PG/VG increased infection only in the Cultex(R) system, which produces heated aerosol. ConclusionOur data are consistent with the conclusion that authentic JUUL aerosols or their individual constituents (nicotine or PG/VG) increase SARS-CoV-2 infection. The strong effect produced by nicotine was modulated in authentic JUUL aerosols, demonstrating the importance of studying mixtures and aerosols from actual EC products. These data support the idea that vaping increases the likelihood of contracting COVID-19.

cell biology↗

bioRxiv2022

The Network Zoo: a multilingual package for the inference and analysis of biological networks

Inference and analysis of cellular biological networks requires software tools that integrate multi-omic data from various sources. The Network Zoo (netZoo; netzoo.github.io) is an open-source software suite to model biological networks, including context-specific gene regulatory networks and multi-omics partial correlation networks, to conduct differential analyses, estimate community structure, and model the transitions between biological states. The netZoo builds on our ongoing development of network methods, harmonizing the implementations in various computing languages (R, Python, MATLAB, and C) and between methods to allow a better integration of these tools into analytical pipelines. To demonstrate the value of this integrated toolkit, we analyzed the multi-omic data from the Cancer Cell Line Encyclopedia (CCLE) by inferring gene regulatory networks for each cancer cell line and associating network features with other phenotypic attributes such as drug sensitivity. This allowed us to identify transcription factors that play a critical role in both drug resistance and cancer development in melanoma. We also used netZoo to build a pan-cancer, multi-tiered CCLE map and used it to identify known metabolic hallmarks of cancer and to estimate novel context-specific elements that mediate post-transcriptional regulation. Because the netZoo tools are open-source and there is a growing community of both users and developers, we built an ecosystem to support community contributions, share use cases, and visualize networks online. As additional data types become available and our suite of methods grows, we will expand "the zoo" to incorporate an increasingly sophisticated collection of tools for network inference and analysis.

genomics↗

bioRxiv2022

Repulsive Sema3E-Plexin-D1 signaling coordinates both axonal extension and steering via activating an autoregulatory factor, Mtss1

Axon guidance molecules are critical for neuronal pathfinding because they regulate directionality and growth pace during nervous system development. However, the molecular mechanisms coordinating proper axonal extension and turning are poorly understood. Here, Metastasis Suppressor 1 (Mtss1), a membrane protrusion protein, ensured axonal extension while sensitizing axons to the Semaphorin 3E (Sema3E)-Plexin-D1 repulsive cue. Sema3E-Plexin-D1 signaling enhanced Mtss1 expression in projecting striatonigral neurons. Mtss1 localized to the neurite axonal side and regulated neurite outgrowth in cultured neurons. Mtss1 also aided Plexin-D1 trafficking to the growth cone, where it signaled a repulsive cue to Sema3E. Mtss1 ablation reduced neurite extension and growth cone collapse in cultured neurons. Mtss1-knockout mice exhibited fewer striatonigral projections and irregular axonal routes and these defects were recapitulated in Plxnd1- or Sema3e-knockout mice. These findings demonstrate that repulsive axon guidance activates an exquisite autoregulatory program coordinating both axonal extension and steering during neuronal pathfinding.

developmental biology↗

bioRxiv2021

Branched ubiquitin chain binding and deubiquitination by UCH37 facilitate proteasome clearance of stress-induced inclusions

UCH37, also known as UCHL5, is a highly conserved deubiquitinating enzyme (DUB) that associates with the 26S proteasome. Recently it was reported that UCH37 activity is stimulated by branched ubiquitin chain architectures. To understand how UCH37 achieves its unique debranching specificity, we performed biochemical and NMR structural analyses and found that UCH37 is activated by contacts with the hydrophobic patches of both distal ubiquitins that emanate from a branched ubiquitin. In addition, RPN13, which recruits UCH37 to the proteasome, further enhances branched-chain specificity by restricting linear ubiquitin chains from having access to the UCH37 active site. In cultured human cells under conditions of proteolytic stress, we show that substrate clearance by the proteasome is promoted by both binding and deubiquitination of branched polyubiquitin by UCH37. Proteasomes containing UCH37(C88A), which is catalytically inactive, aberrantly retain polyubiquitinated species as well as the RAD23B substrate shuttle factor, suggesting a defect in recycling of the proteasome. These findings provide a foundation to understand how proteasome degradation of substrates modified by a unique ubiquitin chain architecture is aided by a DUB.

biochemistry↗

bioRxiv2021

RPAP2 regulates a transcription initiation checkpoint by prohibiting assembly of preinitiation complex

RNA polymerase II (Pol II)-mediated transcription in metazoan requires precise regulation. RNA polymerase II-associated protein 2 (RPAP2) was previously identified to transport Pol II from cytoplasm to nucleus and dephosphorylates Pol II C-terminal domain (CTD). We found that RPAP2 binds hypo/hyper-phosphorylated Pol II with undetectable phosphatase activity. Structure of RPAP2-Pol II shows mutually exclusive assembly of RPAP2-Pol II and pre-initiation complex (PIC) due to three steric clashes. RPAP2 prevents/disrupts Pol II-TFIIF interaction and impairs in vitro transcription initiation, suggesting a function in prohibiting PIC assembly. Loss of RPAP2 in cells leads to global accumulation of TFIIF and Pol II at promoters, indicating critical role of RPAP2 in inhibiting PIC assembly independent of its putative phosphatase activity. Our study indicates that RPAP2 functions as a gatekeeper to prohibit PIC assembly and transcription initiation and suggests a novel transcription checkpoint.

molecular biology↗

bioRxiv2020

A Chameleonic Macrocyclic Peptide with Drug Delivery Applications

Head-to-tail cyclized peptides are intriguing natural products with unique properties. The PawS-Derived Peptides (PDPs) are produced from precursors of seed storage albumins in species of the daisy family. Here we report an unusually large PDP with two disulfide bonds, identified from seeds of Zinnia elegans. In water, synthetic PDP-23 forms a unique dimeric structure in which two monomers containing two {beta}-hairpins cross-clasp and enclose a hydrophobic core, creating a square prism. This stable dimer can be split and each monomer unfolds to a V-shape in micelles or organic solvents. This chameleonic character is unusual for disulfide-rich peptides and engenders PDP-23 with potential for cell delivery and accessing novel targets. We demonstrated this by conjugating a rhodamine dye to the PDP-23 scaffold, creating a stable, cell-penetrating inhibitor of the P-glycoprotein drug efflux pump.

biochemistry↗

bioRxiv2020

Stoichiometric Analysis of Protein Complexes by Cell Fusion and Single Molecule Imaging

The composition, stoichiometry and interactions of supramolecular protein complexes are a critical determinant of biological function. Several techniques have been developed to study molecular interactions and quantify subunit stoichiometry at the single molecule level; however, these typically require artificially low expression levels to achieve the low fluorophore concentration required for single molecule imaging, or use of detergent isolation of complexes that may perturb native subunit interactions. Here we present an alternative approach where protein complexes are assembled at physiological concentrations and subsequently diluted in situ for single-molecule level observations while preserving them in a near-native cellular environment. We show that coupling this in situ dilution strategy with single molecule techniques such as in vivo Fluorescence Correlation Spectroscopy (FCS), bleach step counting for quantifying protein complex stoichiometry, and two-color single molecule colocalization, improves the quality of data obtained using these single molecule fluorescence methods. Single Protein Recovery After Dilution (SPReAD) is a simple and versatile means of extending the concentration range of single molecule measurements into the cellular regime while minimizing potential artifacts and perturbations of protein complex stoichiometry. SIGNIFICANCE STATEMENTQuantifying the composition and stoichiometry of protein complexes in live cells is critical to understanding mechanisms involved in their function. Here we detail a method in which protein complexes are assembled intracellularly at physiological concentrations, but then diluted to levels suitable for single-molecule fluorescence observations while still within a cellular environment. The technique permits the use of common single molecule analysis techniques such as stepwise photobleaching quantification and fluorescence correlation spectroscopy to determine stoichiometry and functional interactions while avoiding artifacts that may occur from the use of detergent isolation methods or from the artificially low expression levels sometimes used to attain single molecule observation levels.

biophysics↗

bioRxiv2019

The Tung Tree (Vernicia Fordii) Genome Provides A Resource for Understanding Genome Evolution and Oil Improvement

Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil containing a high proportion of eleostearic acid ([~]80%). Here we report a high-quality, chromosome-scale tung tree genome sequence of 1.12 Gb with 28,422 predicted genes and over 73% repeat sequences. Tung tree genome was assembled by combining Illumina short reads, PacBio single-molecule real-time long reads and Hi-C sequencing data. Insertion time analysis revealed that the repeat-driven tung tree genome expansion might be due to long standing long terminal repeat (LTR) retrotransposon bursts and lack of efficient DNA deletion mechanisms. An electronic fluorescent pictographic (eFP) browser was generated based on genomic and RNA-seq data from 17 various tissues and developmental stages. We identified 88 nucleotide-binding site (NBS)-encoding resistance genes, of which 17 genes may help the tung tree resist the Fusarium wilt shortly after infection. A total of 651 oil-related genes were identified and 88 of them were predicted to be directly involved in tung oil biosynthesis. The fewer phosphoenolpyruvate carboxykinase (PEPC) genes, and synergistic effects between transcription factors and oil biosynthesis-related genes may contribute to high oil content in tung seeds. The tung tree genome should provide valuable resources for molecular breeding and genetic improvement.

bioinformatics↗

bioRxiv2019

EXoO-Tn: Tag-n-Map the Tn Antigen in the Human Proteome

Tn antigen (Tn), a single N-acetylgalactosamine (GalNAc) monosaccharide attached to protein Ser/Thr residues, is found on most solid tumors yet rarely detected in adult tissues, featuring it one of the most distinctive signatures of cancers. Although it is prevalent in cancers, Tn-glycosylation sites are not entirely clear owing to the lack of suitable technology. Knowing the Tn-glycosylation sites will spur the development of new vaccines, diagnostics, and therapeutics of cancers. Here, we report a novel technology named EXoO-Tn for large-scale mapping of Tn-glycosylation sites. EXoO-Tn utilizes glycosyltransferase C1GalT1 and isotopically-labeled UDP-Gal(13C6) to tag and convert Tn to Gal(13C6)-Tn, which has a unique mass being distinguishable to other glycans. This exquisite Gal(13C6)-Tn structure is recognized by OpeRATOR that specifically cleaves N-termini of the Gal(13C6)-Tn-occupied Ser/Thr residues to yield site-containing glycopeptides. The use of EXoO-Tn mapped 947 Tn-glycosylation sites from 480 glycoproteins in Jurkat cells. Given the importance of Tn in diseases, EXoO-Tn is anticipated to have broad utility in clinical studies.

systems biology↗

bioRxiv2019

Real-time Continuous Hand Motion Myoelectric Decoding by Automated Data Labeling

In this paper an automated data labeling (ADL) neural network was proposed to streamline dataset collecting for real-time predicting the continuous motion of hand and wrist, these gestures are only decoded from a surface electromyography (sEMG) array of eight channels. Unlike collecting both the bio-signals and hand motion signals as samples and labels in supervised learning, this algorithm only collects the unlabeled sEMG into an unsupervised neural network, in which the hand motion labels are auto-generated. The coefficient of determination (r2) for three DOFs, i.e. wrist flex/extension, wrist pro/supination, hand open/close, was 0.86, and 0.87 respectively. The comparison between real motion labels and auto-generated labels shows that the latter has earlier response than former. The results of Fitts law test indicate that ADL has capability of controlling multi-DOFs simultaneously even though the training set only contains sEMG data from single DOF gesture. Moreover, no more hand motion measurement needed which greatly helps upper-limb amputee imagine the gesture of residual limb to control a dexterous prosthesis.

bioengineering↗

bioRxiv2019

PAG neurons encode a simplified action-selective signal during aggression

SummaryWhile the ventromedial hypothalamus, ventrolateral area (VMHvl) is now well established as a critical locus for the generation of conspecific aggression, its role is complex, with populations of neurons responding during the motivational, sensory, and action phases of aggression, and also during social interactions with the opposite sex. It has been previously unclear how the brain uses this complex multidimensional signal and generates a discrete action: the attack. Here we find that the largest posterior target of the VMHvl, the lateral periaqueductal gray (lPAG) encodes a simplified attack-selective signal during aggression. Single units in the lPAG exhibit greater selectivity for the attack action during aggression than VMHvl neurons and a subpopulation of neurons in the PAG exhibit short-latency, time-locked spiking relative to the activity of jaw muscles for biting during attack. In addition, channelrhodopsin assisted circuit mapping reveals a preferential projection from VMHvl glutamatergic cells to lPAG glutamatergic cells. Using projection-specific fiber photometry, we find that this excitatory projection conveys male-biased signals from the VMHvl to downstream glutamatergic PAG neurons that integrate ongoing male-related activity over several seconds, which suggests that action-selectivity is generated by a combination of both pre and postsynaptic filtering mechanisms.

neuroscience↗

bioRxiv2019

Neural Anatomy and Optical Microscopy (NAOMi) Simulation for evaluating calcium imaging methods

The past decade has seen a multitude of new in vivo functional imaging methodologies. However, the lack of ground-truth comparisons or evaluation metrics makes large-scale, systematic validation impossible. Here we provide a new framework for evaluating TPM methods via in silico Neural Anatomy and Optical Microscopy (NAOMi) simulation. Our computationally efficient model generates large anatomical volumes of mouse cortex, simulates neural activity, and incorporates optical propagation and scanning to create realistic calcium imaging datasets. We verify NAOMi simulations against in vivo two-photon recordings from mouse cortex. We leverage this access to in silico ground truth to perform direct comparisons between different segmentation algorithms and optical designs. We find modern segmentation algorithms extract strong neural time-courses comparable to estimation using oracle spatial information, but with an increase in the false positive rate. Comparison between optical setups demonstrate improved resilience to motion artifacts in sparsely labeled samples using Bessel beams, increased signal-to-noise ratio and cell-count using low numerical aperture Gaussian beams and nuclear GCaMP, and more uniform spatial sampling with temporal focusing versus multi-plane imaging. Overall, by leveraging the rich accumulated knowledge of neural anatomy and optical physics, we provide a powerful new tool to assess and develop important methods in neural imaging.

neuroscience↗