Biology subjects

Wang, J.

Publications and source records attributed to Wang, J..

At least 1,225 records · Page 68Linked to original sources

bioRxiv2024

Proteomic profiling of intracranial atherosclerotic plaque in the human brain

BackgroundIntracranial atherosclerotic disease (ICAD) is one of the major causes of ischemic stroke and associated with high risk of stroke recurrence. There are no reliable and specific fluid biomarkers for ICAD, and little is known about the proteomic profiling of ICAD. In this study we aimed to explore the feasibility of applying proteomics technology to profile intracranial atherosclerotic plaques extracted from postmortem human brain arteries. MethodsEighteen segments (5-10mm in length) of major arteries from 10 postmortem brains were collected from the Mount Sinai Neuropathology Brain Bank. Among these segments, 5 had no evidence of atherosclerotic disease, and 13 had wall thickening or visible plaques with various degree of stenosis. Proteins were extracted from the vessel segments, quantified, and digested into peptides. Subsequently, the peptides underwent tandem mass tag (TMT) labeling, pooling, and analysis using two-dimensional liquid chromatography-tandem mass spectrometry (LC/LC-MS/MS). Protein identification and quantification were performed using the JUMP software. Differentially expressed proteins (DEPs) were defined as proteins with p.adj < 0.05 and absolute log2 (fold change) > log2 (1.2). ResultsA total of 7,492 unique proteins were detected, and 6,726 quantifiable proteins were retained for further analysis. Among these, 265 DEPs, spanning on 252 unique gene, were found to be associated with ICAD by comparing the arterial segments with vs those without atherosclerotic disease. The top 4 most significant DEPs include LONP1, RPS19, MRPL12 and SNU13. Among the top 50 DEPs, FADD, AIFM1 and PGK1 were associated with atherosclerotic disease or cardiovascular events in previous studies. Moreover, the previously reported proteins associated with atherosclerosis such as APCS, MMP12, CTSD were elevated in arterial segments with atherosclerotic changes. Furthermore, the up-regulation of APOE and LPL, the ICAD GWAS risk genes, was shown to be associated with the plaque severity. Finally, gene set enrichment analysis revealed the DEP signature is enriched for biological pathways such as chromatin structure, plasma lipoprotein, nucleosome, and protein-DNA complex, peroxide catabolic and metabolic processes, critical in ICAD pathology. ConclusionsDirect proteomic profiling of fresh-frozen intracranial artery samples by MS-based proteomic technology is a feasible approach to identify ICAD-associated proteins, which can be potential biomarker candidates for ICAD. Further plaque proteomic study in a larger sample size is warranted to uncover mechanistic insights into ICAD and discover novel biomarkers that may help to improve diagnosis and risk stratification in ICAD.

systems biology↗

bioRxiv2024

In a Canine Model of Septic Shock, Cardiomyopathy Occurs Independent of Catecholamine Surges and Cardiac Microvascular Ischemia

BackgroundHigh levels of catecholamines are cardiotoxic and associated with stress-induced cardiomyopathies. Septic patients are routinely exposed to endogenously released and exogenously administered catecholamines, which may alter cardiac function and perfusion causing ischemia. Early during human septic shock, left ventricular ejection fraction (LVEF) decreases but normalizes in survivors over 7-10 days. Employing a septic shock model that reproduces these human septic cardiac findings, we investigated the effects of catecholamines on microcirculatory perfusion and cardiac function. MethodsPurpose-bred beagles received intrabronchial Staphylococcus aureus (n=30) or saline (n=6) challenges and septic animals recieved either epinephrine (1mcg/kg/min, n=15) or saline (n=15) infusions from 4 to 44 hours. Serial cardiac magnetic resonance imaging (CMR), invasive hemodynamics and laboratory data including catecholamine levels and troponins were collected over 92 hours. Adenosine-stress perfusion CMR was performed on eight of the fifteen septic epinephrine, and eight of the fifteen septic saline animals. High-dose sedation was titrated for comfort and suppress endogenous catecholamine release. ResultsCatecholamine levels were largely within the normal range throughout the study in animals receiving an intrabronchial bacteria or saline challenge. However, septic versus non-septic animals developed significant worsening of LV; EF, strain, and -aortic coupling that was not explained by differences in afterload, preload, or heart rate. In septic animals that received epinephrine versus saline infusions, plasma epinephrine levels increased 800-fold, pulmonary and systemic pressures significantly increased, and cardiac edema decreased. Despite this, septic animals receiving epinephrine versus saline during and after infusions, had no significant further worsening of LV; EF, strain, or -aortic coupling. Animals receiving saline had a sepsis-induced increase in microcirculatory reserve without troponin elevations. In contrast, septic animals receiving epinephrine had blunted microcirculatory perfusion and elevated troponin levels that persisted for hours after the infusion stopped. During infusion, septic animals that received epinephrine versus saline had significantly greater lactate, creatinine, and alanine aminotransferase levels. ConclusionsCardiac dysfunction during sepsis is not primarily due to elevated endogenous or exogenous catecholamines nor is it principally due to decreased microvascular perfusion-induced ischemia. However, epinephrine itself has potentially harmful long lasting ischemic effects during sepsis including impaired microvascular perfusion that persists after stopping the infusion. Clinical PerspectiveO_ST_ABSWhat is new?C_ST_ABSO_LIMyocardial depression of sepsis occurs without high levels of circulating catecholamines. C_LIO_LIWhereas large vessel coronary perfusion is known to be well maintained during sepsis, we show that during the myocardial depression of sepsis, in a model without exogenous catecholamine infusion, no perfusion abnormalities in the coronary microcirculation nor troponin elevations develop, indicating that the cardiac dysfunction of sepsis is not an ischemic injury. C_LIO_LIEpinephrine use during sepsis produces a form of injury tangential to the myocardial depression of sepsis. C_LIO_LIEpinephrine infusions depressed microcirculatory perfusion reserve and increased troponin I levels indicating a secondary prolonged mild ischemic effect on the myocardium. C_LI What are the clinical implications?O_LIProlonged high doses of epinephrine can secondarily contribute to perfusion abnormalities. C_LIO_LIDecoupling the septic heart from microvascular perfusion abnormalities and ischemia may lead to better strategies for managing shock associated with severe infections. In clinical practice in septic patients particularly potentially with coronary artery disease, commonly used vasopressors that are less associated with increased lactate production than epinephrine, alongside adjunct cardiac microcirculatory vasodilators, could help better maintain or improve cardiac performance during septic shock. C_LI

physiology↗

bioRxiv2024

Cardiac Magnetic Resonance Studies in a Large Animal Model that Simulates the Cardiac Abnormalities of Human Septic Shock

BackgroundSeptic shock, in humans and in our well-established animal model, is associated with increases in biventricular end diastolic volume (EDV) and decreases in ejection fraction (EF). These abnormalities occur over 2 days and reverse within 10 days. Septic non-survivors do not develop an increase in EDV. The mechanism for this cardiac dysfunction and EDV differences is unknown. MethodsPurpose-bred beagles randomized to receive intrabronchial Staphylococcus aureus (n=27) or saline (n=6) were provided standard ICU care including sedation, mechanical ventilation, and fluid resuscitation to a pulmonary arterial occlusion pressure of over 10mmHg. No catecholamines were administered. Over 96h, cardiac magnetic resonance imaging, echocardiograms, and invasive hemodynamics were serially performed, and laboratory data was collected. Tissue was obtained at 66h from six septic animals. ResultsFrom 0-96h after bacterial challenge, septic animals vs. controls had significantly increased left ventricular wall edema (6%) and wall thinning with loss of mass (15%) which was more pronounced at 48h in non-survivors than survivors. On histology, edema was located predominantly in myocytes, the interstitium, and endothelial cells. Edema was associated with significantly worse biventricular function (lower EFs), ventricular-arterial coupling, and circumferential strain. In septic animals, from 0-24h, the EDV decreased from baseline and, despite cardiac filling pressures being similar, decreased significantly more in non-survivors. From 24-48h, all septic animals had increases in biventricular chamber sizes. Survivors biventricular EDVs were significantly greater than baseline and in non-survivors, where biventricular EDVs were not different from baseline. Preload, afterload, or HR differences did not explain these differential serial changes in chamber size. ConclusionSystolic and diastolic cardiac dysfunction during sepsis is associated with ventricular wall edema. Rather than differences in preload, afterload, or heart rate, structural alterations to the ventricular wall best account for the volume changes associated with outcome during sepsis. In non-survivors, from 0-24h, sepsis induces a more severe diastolic dysfunction, further decreasing chamber size. The loss of left ventricular mass with wall thinning in septic survivors may, in part explain, the EDV increases from 24-48h. However, these changes continued and even accelerated into the recovery phase consistent with a reparative process rather than ongoing injury. Clinical PerspectiveO_ST_ABSWhat is new?C_ST_ABSO_LIUtilizing multimodal imaging and hemodynamics, we demonstrate the cardiac changes of sepsis have injury and reparative phases. C_LIO_LIThe injury phase (0-24h) has EDV decreases more profound in non-survivors and is associated with worse ventricular compliance, myocardial edema, and diastolic dysfunction. C_LIO_LIThe recovery phase has left ventricular mass loss with wall thinning in survivors that explains the EDV increases (24-96h). These progressed into the EF recovery phase consistent with a reparative process removing damaged tissue. C_LIO_LIThis is the first controlled CMR sepsis study supporting ventricular wall edema is a fundamental aspect of sepsis pathophysiology and dry mass loss a reparative mechanism. C_LI What are the clinical implications?O_LIDespite optimizing filling pressures, the cardiac changes in ventricular wall structure and function associated with survival and non-survival in sepsis still occurred, thereby discounting fluid resuscitation as the major factor of therapeutic importance for cardiac function and survival. C_LIO_LIThe changes reported here have potential implications for sepsis treatment especially in the field of fluid resuscitation. These findings yield new understanding into the pathophysiology of sepsis cardiac dysfunction and allow for novel phenotyping and prognosticating of the syndrome with ventricular compliance and EDVs. This also offers potentially high yielding targets for research for new therapeutic approaches for sepsis and heart failure. C_LI

physiology↗

bioRxiv2024

The nanoscale organization of the Nipah virus fusion protein informs new membrane fusion mechanisms.

Paramyxovirus membrane fusion requires an attachment protein for receptor binding and a fusion protein for membrane fusion triggering. Nipah virus (NiV) attachment protein (G) binds to ephrinB2 or -B3 receptors, and fusion protein (F) mediates membrane fusion. NiV-F is a class I fusion protein and is activated by endosomal cleavage. The crystal structure of a soluble GCN4-decorated NiV-F shows a hexamer-of-trimer assembly. Here, we used single-molecule localization microscopy to quantify the NiV-F distribution and organization on cell and virus-like-particle membranes at a nanometer precision. We found that NiV-F on biological membranes forms distinctive clusters that are independent of endosomal cleavage or expression levels. The sequestration of NiV-F into dense clusters favors membrane fusion triggering. The nano-distribution and organization of NiV-F are susceptible to mutations at the hexamer-of-trimer interface, and the putative oligomerization motif on the transmembrane domain. We also show that NiV-F nanoclusters are maintained by NiV-F-AP-2 interactions and the clathrin coat assembly. We propose that the organization of NiV-F into nanoclusters facilitates membrane fusion triggering by a mixed population of NiV-F molecules with varied degrees of cleavage and opportunities for interacting with the NiV-G/receptor complex. These observations provide insights into the in-situ organization and activation mechanisms of the NiV fusion machinery.

microbiology↗

bioRxiv2024

Intermittent energy restriction inhibits tumor growth and enhances paclitaxel response in a transgenic mouse model of endometrial cancer

ObjectiveOverweight/obesity is the strongest risk factor for endometrial cancer (EC), and weight management can reduce that risk and improve survival. We aimed to establish the differential abilities of intermittent energy restriction (IER) and low-fat diet (LFD), alone and in combination with paclitaxel, to reverse the procancer effects of high-fat diet (HFD)-induced obesity in a mouse model of EC. MethodsLkb1fl/flp53fl/fl mice were fed high-fat diet (HFD) or LFD to generate obese and lean phenotypes, respectively. Obese mice were maintained on HFD or switched to LFD (HFD-LFD) or IER (HFD-IER). Ten weeks after induction of endometrial tumor, mice in each group received paclitaxel or placebo for 4 weeks. Body and tumor weights; tumoral transcriptomic, metabolomic and oxylipin profiles; and serum metabolic hormones and chemocytokines were assessed. ResultsHFD-IER and HFD-LFD, relative to HFD, reduced body weight; reversed obesity-induced alterations in serum insulin, leptin and inflammatory factors; and decreased tumor incidence and mass, often to levels emulating those associated with continuous LFD. Concurrent paclitaxel, versus placebo, enhanced tumor suppression in each group, with greatest benefit in HFD-IER. The diets produced distinct tumoral gene expression and metabolic profiles, with HFD-IER associated with a more favorable (antitumor) metabolic and inflammatory environment. ConclusionIn Lkb1fl/flp53fl/fl mice, IER is generally more effective than LFD in promoting weight loss, inhibiting obesity-related endometrial tumor growth (particularly in combination with paclitaxel), and reversing detrimental obesity-related metabolic effects. These findings lay the foundation for further investigations of IER as a EC prevention strategy in women with overweight/obesity.

cancer biology↗

bioRxiv2024

Identification of differentially methylated single-nucleotide m6A sites by incorporating site-specific antibody specificity

Various genome-wide and transcriptome-wide technologies are based on antibodies, however, the specificity of antibodies on different targets has not been characterized or considered in the analyses. The antibody-based MeRIP-seq is the most widely used method to determine the locations of N6-methyladenosine (m6A) on RNAs, especially for differential m6A analyses. However, the antibody specificities in different RNA regions and their resulting technical biases in differential m6A analyses have not been evaluated. Here, we evaluated the m6A antibody specificities using 100 pairs of spike-in RNAs with known m6A levels at single sites. Based on two replicates with different m6A levels on spike-in RNAs, we realized the m6A antibody specificities of the m6A sites on spike-in RNAs were greatly varied and mainly determined by the surrounding sequences of the m6A sites. Moreover, the MeRIP-seq signal fold change is the function of the real difference in m6A levels as well as the m6A antibody specificity. We then trained a machine learning model to predict the m6A antibody specificities of given sequences and predicted the m6A specificities of all RNA sequences surrounding the known m6A motif DRACH throughout the human transcriptome. Finally, we developed a Hierarchical statistic model for Differential Analysis of m6A Sites (HDAMS) by taking advantage of the predicted m6A specificities. We found that HDAMS can accurately determine the differentially methylated single-nucleotide m6A sites and the output more functionally relevant results. Our study not only provides a powerful tool for differential m6A analyses but also provides a methodological framework for other antibody-based studies to incorporate antibody specificities.

bioinformatics↗

bioRxiv2024

TMEM63B functions as a mammalian thirst receptor

Thirst drives animals to reinstate water homeostasis by fluid intake. An increase of blood osmolality is thought to induce thirst by activating a thirst receptor expressed in the subfornical organ (SFO), but the molecular identity of this receptor remains elusive. Here, we provide behavioral and functional evidence to show that TMEM63B functions as a mammalian thirst receptor in the SFO and mediates osmotic and dehydrated thirst. First, we showed that TMEM63B is expressed in SFO excitatory neurons and required for the neuronal responses to hypertonic stimulation. Heterologously expressed TMEM63B is activated by hypertonic stimuli and point mutations can alter the reversal potential of the channel. More importantly, purified TMEM63B in liposomes establishes osmolarity-gated currents. Finally, Tmem63b knockout mice have profound deficits in thirst, and deleting TMEM63B within the SFO neurons recapitulated this phenotype. Taken together, these results provide a molecular basis for thirst 82and demonstrate TMEM63B is the long-sought mammalian thirst receptor.

neuroscience↗

bioRxiv2024

Multiple Loci for Foveolar Vision in Macaque Monkey

A common tenet of neural sensory representation is that species-specific behaviors are reflected in specialized brain organizations1. In humans and nonhuman primates, the central one degree of vision is processed by the foveola2, a retinal structure which comprises a high density of photoreceptors and is crucial for primate-specific high acuity vision, color vision, and gaze-directed visual attention3,4,5. In this study, we have developed high spatial resolution ultrahigh field 7T fMRI methods for functional mapping of foveolar visual cortex in awake monkeys. We provide evidence that, in the ventral pathway (V1-V4 and TEO), viewing of a central small spot elicits a ring of multiple (at least 8) foveolar representations per hemisphere. This ring surrounds a large area called the foveolar core. This is an area populated by millimeter-scale functional domains sensitive to fine stimuli and high spatial frequencies, consistent with foveolar visual acuity, as well as color and achromatic information, and motion. The unique position of the foveolar core suggests it may be a hub subserving higher order needs of foveolar function, such as integrating different spatial scales of representation, integrating local and global features in object perception, and bringing together the four quadrants of visual space. Thus, this elaborate re-representation of central vision signifies a cortical specialization for various foveation behaviors.

neuroscience↗

bioRxiv2024

Somite-independent regeneration of the axolotl primary body axis

Primary body-axis development is a highly conserved process that proceeds through somitogenesis and subsequent subdivision into dermatome, myotome, and sclerotome. Defects in somitic-clock genes such as Hes7 lead to vertebral-segmentation defects in mice and fish. Here we show that in the axolotl, although Hes7 is necessary for proper embryonic vertebral segmentation, it is-- surprisingly--dispensable during tail regeneration. We investigated the mechanism of vertebral segmentation during regeneration which initially occurs through extension of a cartilage rod ventral to the spinal cord. We find that the regenerating cartilage rod undergoes a periodic wrinkling that provides a template for vertebral segmentation. Via direct mechanical measurements and biophysical perturbations, we show that a model of compression-induced buckling instability can predict vertebral segmentation. The cartilage rod and other somitic derivatives (muscle, cartilage, tendon, fibroblasts) arise from tendon-like, Lfng+ multi-potent mesenchymal progenitors, which display a gene regulatory state distinct from somitic progenitors. In summary, we uncover a mechanism of vertebral segmentation during axolotl tail regeneration that is distinct from the somite-based developmental mechanism.

developmental biology↗

bioRxiv2024

SlWRKY80 recruits SlHDA1 to regulates the tomato fruit ripening and color transformation

Fruit ripening involves key transcription factors (TF). Despite the established importance of WRKY TFs in plant development, the involvement of WRKY and its underlying mechanism in the regulation of fruit ripening and color transformation remain unclear. Here, we discovered a phenomenon where SlWRKY80 is involved in the ripening and color transformation of tomato. Overexpression of SlWRKY80 shortened the color transition cycle of tomato fruit, whereas loss-of-function mutation in SlWRKY80 delays this process. On the 7th day after the color breakdown (Break+7), the fruit color was bright red in SlWRKY80-overexpression lines. SlWRKY80 could bind to downstream promoters of SlSGR1 and SlPSY1, thereby exerting a positive regulatory effect on the expression levels of SlSGR1 and SlPSY1. This regulatory activity led to the facilitation of chlorophyll a decomposition and carotenoid synthesis during the transition of fruit color, ultimately accelerating fruit ripening and color change. The SlWRKY80 knockout lines (slwrky80cr-3 and slwrky80cr-4) showed light red. Thr (The 69th amino acid) mutated to Ser of SlWRKY80 (slwrky80cr-46), SlHDA1 was recruited as a regulatory factor to enhance the regulation of downstream SlPSY1 by SlWRKY80, and inhibited the SlSGR1 expression by SlWRKY80 which maybe the reason why the slwrky80cr-46 knockout lines exhibited brown color. In conclusion, SlWRKY80 regulates the expression of SlSGR1 and SlPSY1 by recruiting SlHDA1, thereby regulating chlorophyll decomposition and carotenoid synthesis, and further participating in fruit maturation and related fruit color formation. This research has important guiding significance for breeding tomato germplasm with excellent commercial traits.

plant biology↗

bioRxiv2024

scGND: Graph neural diffusion model enhances single-cell RNA-seq analysis

Single-cell sequencing technologies have played a pivotal role in advancing biomedical research over the last decade. With the evolution of deep learning, a variety of models based on deep neural networks have been developed to improve the precision of single-cell RNA sequencing (scRNA-seq) analysis from multiple angles. However, deep learning models currently used in scRNA-seq analysis frequently suffer from a lack of interpretability. In this study, we present a novel physics-informed graph generative model, termed Single Cell Graph Neural Diffusion (scGND). This model is founded on solid mathematical concepts and provides enhanced interpretability. Unlike methods that focus solely on gene expression in individual cells, scGND concentrates on the cell-cell interaction graph, incorporating two key physical concepts: local and global equilibrium. We show that achieving a balance between local and global equilibrium significantly improves the geometric properties of the graph, aiding in the extraction of inherent biological insights from the cell-cell interaction graph at multiple scales. The effectiveness of scGND has been proven through benchmark tests involving five independent scRNA-seq datasets from various tissues and species. scGND consistently achieves better or comparable results comparing with several established competitors in both clustering and trajectory analysis. scGND represents a comprehensive generative model based on cell graph diffusion, demonstrating considerable promise for both theoretical and practical applications in scRNA-seq data analysis.

bioinformatics↗

bioRxiv2024

In-silico Drug Repurposing pipeline for Epilepsy: Integrating Deep Learning and Structure-based Approaches

Due to considerable global prevalence and high recurrence rate, the pursuit of effective new medication for epilepsy treatment remains an urgent and significant challenge. Drug repurposing emerges as a cost-effective and efficient strategy to combat this disorder. This study leverages the transformer-based deep learning methods coupled with molecular binding affinity calculation to develop a novel in-silico drug repurposing pipeline for epilepsy. The number of candidate inhibitors against 24 target proteins encoded by gain-of-function (GOF) genes implicated in epileptogenesis ranged from zero to several hundreds. Our pipeline has repurposed the medications with most anti-epileptic drugs (AEDs) and nearly half psychiatric medications, highlighting the effectiveness of our pipeline. Furthermore, Lomitapide, a cholesterol-lowering drug, first emerged as particularly noteworthy, exhibiting high binding affinity for 10 targets and verified by molecular dynamics (MD) simulation and mechanism analysis. These findings provided a novel perspective on therapeutic strategies for other central nervous system (CNS) disease.

pharmacology and toxicology↗

bioRxiv2024

Endogenous labeling empowers accurate detection of m6A from single long reads of direct RNA sequencing

Although plenty of machine learning models have been developed to detect m6A RNA modification sites using the electric current signals of ONT direct RNA sequencing (DRS) reads, the landscape of m6A on different RNA isoforms is still a mystery due to their limited capacity to distinguish the m6A on individual long reads and RNA isoforms. The primary challenge in training the model with single-read accuracy is the difficulty of obtaining the training data from individual DRS reads that comprehensively represent the m6A on endogenous RNAs. Here, we endogenously label the methylated m6A sites on single ONT DRS reads by APOBEC1-YTH induced C-to-U mutations, strategically positioned 10-100 nt away from the known m6A sites on the same reads. Adopting a semi-supervised leaning strategy, we obtain 700,438 reliable 5-mer single-read level m6A signals, providing a comprehensive representation of m6A on endogenous RNAs. Leveraging this dataset, we develop m6Aiso, a deep residual neural network model that not only accurately identifies and quantifies known m6A sites but also reveals unknown, subtly methylated m6A sites responsive to METTL3 depletion. Analyzing m6Aiso-determined m6A on single reads and isoforms uncovers distance-dependent linkages of m6A sites along single molecules, as well as differential methylation of identical m6A sites on different isoforms. Moreover, we find wide-spread functionally important dynamic changes of m6A sites on specific isoforms during epithelial-mesenchymal transition (EMT). The pivotal utilization of the endogenous labeling strategy empowers m6Aiso to achieve remarkable precision in pinpointing m6A on individual molecules, underscores its effectiveness in elucidating the intricate dynamics and complexities of m6A across RNA isoforms.

bioinformatics↗

bioRxiv2024

Nephrectomy and high-salt diet inducing pulmonary hypertension and kidney damage by increasing Ang II concentration in rats

BackgroundPulmonary hypertension (PH) is a common complication in patients with chronic kidney disease (CKD), affecting prognosis. However, the pathogenesis is not clear, and the lack of a stable animal model is a significant factor. MethodsIn this study, a rat model of chronic kidney disease with pulmonary hypertension (CKD-PH) was developed through 5/6 nephrectomy combined with a high-salt diet. The models hemodynamics and pathological changes in multiple organs were dynamically assessed. Lung tissues and serum were collected from the model rats to measure the expression of ACE2, the expression levels of vascular active components related to the renin-angiotensin-aldosterone system (RAAS), and changes in the serum metabolic profile of the model. ResultsAfter 14 weeks post-surgery, the CKD-PH rat model exhibited significant changes in hemodynamic parameters indicative of pulmonary arterial hypertension, along with alterations such as right ventricular hypertrophy. However, no evidence of pulmonary vascular remodeling was observed. An imbalance in the renin-angiotensin-aldosterone system was identified in the CKD-PH rat models. Downregulation of ACE2 expression was observed in pulmonary tissues. The serum metabolic profile of the CKD-PH rat models showed distinct differences compared to the sham surgery group. ConclusionsThe development of pulmonary arterial hypertension in CKD-PH rats may be primarily attributed to the disruption of the renin-angiotensin-aldosterone system (RAAS), coupled with a decrease in ACE2 expression in pulmonary vascular endothelial tissues and metabolic disturbances.

pathology↗

bioRxiv2024

Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through multiple mechanisms

Selective pressures have given rise to a number of SARS-CoV-2 variants during the prolonged course of the COVID-19 pandemic. Recently evolved variants differ from ancestors in additional glycosylation within the spike protein receptor-binding domain (RBD). Details of how the acquisition of glycosylation impacts viral fitness and human adaptation are not clearly understood. Here, we dissected the role of N354-linked glycosylation, acquired by BA.2.86 sub-lineages, as a RBD conformational control element in attenuating viral infectivity. The reduced infectivity could be recovered in the presence of heparin sulfate, which targets the "N354 pocket" to ease restrictions of conformational transition resulting in a "RBD-up" state, thereby conferring an adjustable infectivity. Furthermore, N354 glycosylation improved spike cleavage and cell-cell fusion, and in particular escaped one subset of ADCC antibodies. Together with reduced immunogenicity in hybrid immunity background, these indicate a single spike amino acid glycosylation event provides selective advantage in humans through multiple mechanisms. HIGHLIGHTSN354 glycosylation acts as a conformational control element to modulate infectivity Reduced infectivity could be recovered by altered binding mode of heparin sulfate N354 glycosylation improved fusogenicity and conferred escape from ADCC antibodies N354 glycosylation reduced immunogenicity and conferred immune evasion

microbiology↗

bioRxiv2024

Ligand supplementation restores the cancer therapy efficacy of an antirheumatic drug auranofin from serum inactivation

Auranofin, an FDA-approved antirheumatic gold drug, has gained ongoing interest in clinical studies for treating advanced or recurrent tumors. However, gold ions dynamic thiol exchange nature strongly attenuates its bioactivity due to the fast formation of covalent albumin-gold adducts. Here we report that newly-added thiols can modulate the dynamic albumin-gold binding and recover the therapeutic efficacy. Initially, we found that auranofin supplemented with its own thiol ligand, TGTA (1-thio-{beta}-D-glucose tetraacetate), significantly restored the anticancer activities in cells and patient-derived xenograft models. Then, screening a collection of ligand fragments followed by machine learning evaluation unveiled diverse synergizing thiols, including pantethine that effectuates auranofin at a low dosage used for rheumatoid arthritis. Interestingly, the thiol exchange inside cells accounts for a cuproptosis-like phenotype induced by auranofin. Together, we believe the ligand-enabled dynamic modulation strategy is of value to researchers and clinicians contemplating metallodrugs and ligand-like molecules in cancer therapy.

cancer biology↗

bioRxiv2024

Increased regional P2X7R expression detected by GSK1482160 PET in a tauopathy mouse model

Neuroinflammation plays an important role in Alzheimers disease and primary tauopathies. The aim of the current study was to map [18F]GSK1482160 for imaging of purinergic P2X7R in Alzheimers disease and primary tauopathy mouse models. MicroPET was performed using [18F]GSK1482160 in widely used mouse models of Alzheimers disease (APP/PS1, 5xFAD and 3xTg), 4-repeat tauopathy (rTg4510) mice and age-matched wild-type mice. Increased uptake of [18F]GSK1482160 was observed in the cortex and basal forebrain of 7-month-old rTg4510 mice compared to age-matched wild-type mice and compared to 3-month-old rTg4510 mice. Nonparametric Spearmans rank analysis revealed a positive correlation between tau [18F]APN-1607 uptake and [18F]GSK1482160 in the hippocampus of rTg4510 mice. No significant differences in the uptake of [18F]GSK1482160 were observed between wild-type mice and APP/PS1 mice (5, 10 months), 5xFAD mice (3, 7 months) or 3xTg mice (10 months). Immunofluorescence staining further indicated the distribution of P2X7Rs in the brains of 7-month-old rTg4510 mice with accumulation of tau inclusion compared to wild-type mice. These findings provide in vivo imaging evidence for increased P2X7R in the brains of tauopathy model mice.

neuroscience↗

bioRxiv2024

Genomic features of NF1-associated peripheral nerve sheath tumors: a cohort analysis from the Johns Hopkins NF1 biospecimen repository

Neurofibromatosis type 1 (NF1) is an inherited neurocutaneous condition that predisposes to the development of peripheral nerve sheath tumors (PNST) including cutaneous neurofibromas (CNF), plexiform neurofibromas (PNF), atypical neurofibromatous neoplasms with unknown biological potential (ANNUBP), and malignant peripheral nerve sheath tumors (MPNST). The successful advancement of therapeutic development for NF1-associated PNST necessitates the systematic acquisition and analysis of human tumor specimens and their corresponding model systems. RNA sequencing (RNAseq) and whole exome sequencing (WES) data were generated from 73 and 114 primary human tumor samples, respectively. These pre-processed data, standardized for immediate computational analysis, are accessible through the NF Data Portal, allowing immediate interrogation. This analysis combines new and previously released samples, offering a comprehensive view of the entire cohort sequenced. As a dedicated effort to systematically bank tumor samples from people with NF1, in collaboration with molecular geneticists and computational biologists to advance understanding of NF1 biology, the Johns Hopkins NF1 biospecimen repository offers access to samples and genomic data to promote advancement of NF1-related therapies.

bioinformatics↗