Biology subjects

Cao, H.

Publications and source records attributed to Cao, H..

At least 91 records · Page 5Linked to original sources

bioRxiv2022

Obesity Disrupts Pituitary UPR Leading to NAFLD

Obesity is the major risk factor for nonalcoholic fatty liver disease (NAFLD), for which effective cures are lacking. Despite the notion that obesity is associated with aberrant levels and action of pituitary hormones that are essential for maintaining hepatic metabolic and inflammatory states, the intrinsic pituitary endocrine abnormalities and their systemic consequences are incompletely defined. By characterizing the impact of diet-induced obesity (DIO) on the pituitary whole tissue and single cell transcriptome, we demonstrated that obesity disrupts pituitary endoplasmic reticulum (ER) homeostasis by suppressing the inositol-requiring enzyme- (IRE1)-mediated adaptive unfolded protein response (UPR). We further showed that defective pituitary UPR by IRE1-deletion in the anterior pituitary strikingly augmented obesity-associated systemic metabolic abnormalities, particularly the NAFLD-associated pathologies. Conversely, enhancing the adaptive UPR in the anterior pituitary, by genetic gain-of-function of spliced X-box binding protein 1 (sXBP1), ameliorated the systemic and hepatic metabolic defects observed in mice with pituitary IRE1 deletion. Intriguingly, disruption of the UPR in the pituitary resulted in impaired hepatic UPR, which was in part due to a defective thyroid hormone receptor (THR)-mediated activation of hepatic Xbp1. In contrast, activation of the hepatic THR signaling improved obesity-associated glucose intolerance and attenuated the impaired hepatic ER homeostasis in anterior pituitary-IRE1 deficient mice. Together, our study provides the first insight into disruption of endocrine signaling-mediated inter-organ UPR communication drives obesity-associated hepatic pathologies. Unraveling these connections might uncover new therapeutic targets for NAFLD and other obesity-associated diseases.

physiology↗

bioRxiv2022

Statistical analysis of spatially resolved transcriptomic data by incorporating multi-omics auxiliary information

Effective control of false discovery rate is key for multiplicity problems. Here, we consider incorporating informative covariates from external datasets in the multiple testing procedure to boost statistical power while maintaining false discovery rate control. In particular, we focus on the statistical analysis of innovative high-dimensional spatial transcriptomic data while incorporating external multi-omics data that provide distinct but complementary information to the detection of spatial expression patterns. We extend OrderShapeEM, an efficient covariate-assisted multiple testing procedure that incorporates one auxiliary study, to make it permissible to incorporate multiple external omics studies, to boost statistical power of spatial expression pattern detection. Specifically, we first use a recently proposed computationally efficient statistical analysis method, spatial pattern recognition via kernels, to produce the primary test statistics for spatial transcriptomic data. Afterwards, we construct the auxiliary covariate by combining information from multiple external omics studies, such as bulk or single-cell RNA-seq data and genome wise association study data, using the Cauchy combination rule. Finally, we extend and implement the integrative analysis method OrderShapeEM on the primary p-values along with auxiliary data incorporating multi-omics information for efficient covariate-assisted spatial expression analysis. We conduct a series of realistic simulations to evaluate the performance of our method with known ground truth. Four case studies in mouse olfactory bulb, mouse cerebellum, human breast cancer and human heart tissues further demonstrate the substantial power gain of our method in detecting genes with spatial expression patterns compared to existing classic approaches that do not utilize any external information.

bioinformatics↗

bioRxiv2022

A novel PLS1 c.981+1G>A variant causes autosomal-dominant hereditary hearing loss in a family via up-regulation of the PI3K-Akt signaling pathway

BackgroundThe fimbrin protein family contains a variety of proteins, of which Plastin1 (PLS1) is an important member. The latest researches show that variations in the coding region of PLS1 gene is related to the development of deafness. However, it remains unknown about the molecular mechanism of deafness caused by PLS1 gene variants. Methodswhole exome sequencing was performed on the affected family members and healthy ones to identify the pathogenic variants, followed by sanger sequencing. Minigene assay was conducted to investigate the impact of the variant on PLS1 mRNA splicing. The pathogenicity of the variant was further investigated in zebrafish. RNA-sequencing (RNA-seq) was done for analyzing the dysregulated downstream signaling pathways caused by knockdown of PLS1 expression. ResultsWe identified a novel variant PLS1 c.981+1G>A in a large Chinese family with hearing loss and demonstrated that the variant is responsible for the occurrence of hearing loss by inducing Exon8 skipping or deletion of Exon8 (47bp). The variant caused abnormal inner ear phenotypes, characterized by decreased mean otolith distance, anterior otolith diameter, posterior otolith diameter, and cochlear diameter, swimming speed and distance in zebrafish. Furthermore, silencing PLS1 expression significantly upregulated genes in the PI3K-Akt signaling pathway, including Col6a3, Spp1, Itgb3 and Hgf. ConclusionsPLS1 c.981+1G>A is a novel pathogenic variant for hearing loss by inducing Exon8 skipping or deletion of Exon8 (47bp). Up-regulation of the PI3K-Akt signaling pathway plays an important role in the pathogenesis of PLS-1 gene.

genetics↗

bioRxiv2022

A phenotype-based forward genetic screen identifies Dnajb6 as a sick sinus syndrome gene

Sick sinus syndrome (SSS) is a group of heart rhythm disorders caused by malfunction of the sinus node, the hearts primary pacemaker. Partially owing to its aging-associated phenotypic manifestation and low expressivity, molecular mechanisms of SSS remain difficult to decipher. Here, we aim to develop a phenotype-based forward genetic approach in the zebrafish (Danio rerio) animal model for discovering essential genes which dysfunction could result in SSS-like phenotypes. Previously we showed the generation of protein trap library by using a revertible gene-breaking transposon (GBT)-based insertional mutagenesis system. Here, we reported the generation of a collection of 35 zebrafish insertional cardiac lines derived from this protein trap library, which was screened using electrocardiographic measurements. As a result, three mutants with SSS-like phenotypes were identified. We then focused on one of these 3 GBT mutants called GBT411 in which dnajb6b gene was disrupted, and conducted expressional, genetic, transcriptome, and electrophysiological studies using both zebrafish and mouse models. These studies confirmed the identity of Dnajb6 as a novel SSS causative gene with a unique expression pattern within the specialized population of sinus node pacemaker cardiomyocytes that lack the expression of HCN4 channels. Together, this study demonstrates the feasibility of a genetic screening approach in an adult vertebrate animal model for discovering new genetic factors for a heart rhythm disorder such as SSS.

genetics↗

bioRxiv2022

Lineage-mosaic and mutation-patched spike proteins for broad-spectrum COVID-19 vaccine

The widespread SARS-CoV-2 in humans results in the continuous emergence of new variants. Recently emerged Omicron variant with multiple spike mutations sharply increases the risk of breakthrough infection or reinfection, highlighting the urgent need for new vaccines with broad-spectrum antigenic coverage. Using inter-lineage chimera and mutation patch strategies, we engineered a recombinant monomeric spike variant (STFK1628x), which showed high immunogenicity and mutually complementary antigenicity to its prototypic form (STFK). In hamsters, a bivalent vaccine comprised of STFK and STFK1628x elicited high titers of broad-spectrum antibodies to neutralize all 14 circulating SARS-CoV-2 variants, including Omicron; and fully protected vaccinees from intranasal SARS-CoV-2 challenges of either the ancestral strain or immune-evasive Beta variant. Strikingly, the vaccination of hamsters with the bivalent vaccine completely blocked the within-cage virus transmission to unvaccinated sentinels, for either the ancestral SARS-CoV-2 or Beta variant. Thus, our study provides new insights and antigen candidates for developing next-generation COVID-19 vaccines.

microbiology↗

bioRxiv2022

A Low-Cost, 3D-Printed Biosensor for Rapid Detection of Escherichia coli

Detection of bacterial pathogens is significant in the fields of food safety, medicine, public health, etc. If bacterial pathogens are not treated promptly, antimicrobial resistance is possible and can lead to morbidity and mortality. Current bacterial detection methodologies rely on laboratory-based techniques that pose limitations such as long turnaround detection times, expensive costs, inadequate accuracy, and required trained specialists. Here, we describe a cost-effective and portable 3D-printed electrochemical biosensor that facilitates rapid detection of certain Escherichia coli (E. coli) strains (DH5, BL21, TOP10, and JM109) within 15 minutes using 500 L of sample and costs $2.50 per test. The sensor displayed an excellent limit of detection (LOD) of 53 cfu, limit of quantification (LOQ) of 270 cfu, and showed cross-reactivity with strains BL21 and JM109 due to shared epitopes. This advantageous diagnostic device is a potential candidate for high-frequency testing at point of care as well as applicable to various fields where pathogen detection is of interest.

bioengineering↗

bioRxiv2022

Identification of bacteria strains using the Recombinase Polymerase Amplification assay on a miniaturized solid-state pH sensor

Rapid identification of bacteria based on nucleic acid amplification allows dealing with the detection of pathogens in clinical, food, and environmental samples. Amplification product must be detected and analyzed by external devices or integrated complicated optical systems. Here, we developed a solid-state pH electrode based on iridium oxide (IrO2) films to measure released hydrogen ions (H+) from isothermal nucleic acid (NA) amplification of bacterial samples. By recombinase polymerase amplification (RPA), we achieved rapid (< 15 min) and sensitive (<30 copies) detection with an accuracy of about 0.03 pH. The RPA-based hydrogen ion sensing assay shows higher specificity, sensitivity, and efficiency as the same polymerase chain reaction (PCR) methods. We initially used the RPA-based sensor to detect E. coli species in laboratory samples. Among, 27 random laboratory samples of E. coli samples, 6 were found to be DH5alpha, 9 BL21, 3 HB101, 6 TOP10, and 3 JM109. The electrical detection of amplification provides generally applicable techniques for the detection of nucleic acid amplification, enabling molecular diagnostic tests in the field and integrating data transmission to the mobile device. These results can be future developed into an efficient tool for rapid on-site detection of bacterial pathogens in clinical samples.

bioengineering↗

bioRxiv2021

CyanoHABs: inevitable evolutionary ecological consequence for low nutrient-requiring cyanobacteria in water eutrophication

Cyanobacterial harmful algal blooms (CyanoHABs) arise as cyanobacteria dominate phytoplankton communities when nutrient levels increase from oligotrophic state. From a wholistic perspective, this longstanding altered phytoplankton structure results from two conditions: one sufficient condition that cyanobacteria can grow maximally with elevated nutrients; one necessary condition that co-living algae cannot grow fast or dominate at the same levels. The sufficient condition, the special mechanism of CyanoHABs at the population level, has been established as the synergistic interaction between superior cyanobacterial ecophysiology and elevated nutrients. But it is unknown how these functions arise or whether they are under directed evolution to water eutrophication. The necessary condition, the general mechanism of CyanoHABs at the community level, is little understood: why co-living algae cannot form blooms as cyanobacteria? Literature and bioinformatics analyses show that the superior ecophysiology undergoes no directed positive evolution to worldwide eutrophication in general or any local eutrophic waters in particular; instead, these functions are under strong purifying selection and likely acquired through early adaptive radiation in nutrient-deficient conditions, as functions enabling extant cyanobacteria to occupy other niches. The general mechanism turns out to be quite straightforward: cyanobacteria are simple life forms and thus have lower per capita nutrient demand for growth, compared to co-existing eukaryotic algae in cell size and structure, genome size, size of genome-scale metabolic networks, cell content, nutrient requirement. Lower nutrient demand is proved by existing field nutrient supplementation. Both the special and general mechanisms of CyanoHABs are tentative frameworks awaiting further theoretic improvement and empirical assessment.

evolutionary biology↗

bioRxiv2021

Attractor Landscapes as a Model Selection Criterion in Data Poor Environments

Modeling of systems for which data is limited often leads to underdetermined model identification problems, where multiple candidate models are equally adherent to data. In such situations additional optimality criteria are useful in model selection apart from the conventional minimization of error and model complexity. This work presents the attractor landscape as a domain for novel model selection criteria, where the number and location of attractors impact desirability. A set of candidate models describing immune response dynamics to SARS-CoV infection is used as an example for model selection based on features of the attractor landscape. Using this selection criteria, the initial set of 18 models is ranked and reduced to 7 models that have a composite objective value with a p-value < 0.05. Additionally, the impact of pharmacologically induced remolding of the attractor landscape is presented.

systems biology↗

bioRxiv2021

Emergence of an adaptive epigenetic cell state in human bladder urothelial carcinoma evolution

Intratumor heterogeneity (ITH) of bladder cancer (BLCA) facilitates therapy resistance and immune evasion to affect clinical prognosis directly. However, the molecular and cellular mechanism generating ITH in BLCA remains elusive. Here we show that a TM4SF1-positive cancer subpopulation (TPCS) drives ITH diversification in BLCA. By extensive profiling of the epigenome and transcriptome of BLCA from 79 donors across all stages, we elucidated the evolution trajectories of luminal and basal BLCA. TPCS emerges from the basal trajectory and shows extensive transcriptional plasticity with a distinct epigenomic landscape. Clinically, TPCS were enriched in advanced stage patients and associated with poor prognosis. Our results showed how cancer adapts to its environment by adopting a stem cell-like epigenomic landscape.

cancer biology↗

bioRxiv2021

Aldehyde dehydrogenase 3A1 deficiency leads to mitochondrial dysfunction and impacts salivary gland stem cell self-renewal, differentiation and survival

Adult salivary stem/progenitor cells (SSPC) have an intrinsic property to self-renew in order to maintain tissue architecture and homeostasis. Adult salivary glands have been documented to harbor SSPC, which have been shown to play a vital role in the regeneration of the glandular structures post radiation damage. We have previously demonstrated that activation of aldehyde dehydrogenase 3A1 (ALDH3A1) after radiation reduced aldehyde accumulation in SSPC, leading to less apoptosis and improved salivary function. We subsequently found that sustained pharmacological ALDH3A1 activation is critical to enhance regeneration of murine submandibular gland after radiation damage. Further investigation shows that ALDH3A1 function is crucial for SSPC self-renewal and differentiation even in the absence of radiation stress. Salivary glands from Aldh3a1-null mice have fewer acinar structures than wildtype mice. ALDH3A1 deletion or pharmacological inhibition in SSPC leads to a decrease in mitochondrial DNA copy number, lower expression of mitochondrial specific genes and proteins, structural abnormalities, lower membrane potential, and reduced cellular respiration. Loss or inhibition of ALDH3A1 also elevates ROS levels and accumulation of ALDH3A1 substrate 4-hydroxynonenal (4-HNE, a lipid peroxidation product), leading to decreased survival of murine SSPC that can be rescued by treatment with 4-HNE specific carbonyl scavengers. Our data indicate that ALDH3A1 activity protects mitochondrial function and is important for the development and regeneration activity of SSPC. This knowledge will help to guide our translational strategy of applying ALDH3A1 activators in the clinic to prevent radiation-related hyposalivation in head and neck cancer patients.

cell biology↗

bioRxiv2021

Evaluating test-retest reliability and sex/age-related effects on temporal clustering coefficient of dynamic functional brain networks

The multilayer dynamic network model has been proposed as an effective method to understand how the brain functions dynamically. Specially, derived from the definition of clustering coefficient in static networks, the temporal clustering coefficient provides a direct measure of topological stability of dynamic brain networks and shows potential in predicting altered brain functions in both normal and pathological conditions. However, test-retest reliability and demographic-related effects on this measure remain to be evaluated. Using a publicly available dataset from the Human Connectome Project consisting of 337 young healthy adults (157 males/180 females; 22 to 37 years old), the present study investigated: (1) the test-retest reliability of temporal clustering coefficient across four repeated resting-state functional magnetic resonance imaging scans as measured by intraclass correlation coefficient (ICC); and (2) sex- and age-related effects on temporal clustering coefficient. The results showed that (1) the temporal clustering coefficient had overall moderate test-retest reliability (ICC > 0.40 over a wide range of densities) at both global and subnetwork levels; (2) female subjects showed significantly higher temporal clustering coefficient than males at both global and subnetwork levels, in particular within the default-mode and subcortical regions; (3) temporal clustering coefficient of the subcortical subnetwork was negatively correlated with age in young adults. Our findings suggest that temporal clustering coefficient is a reliable and reproducible approach for the identification of individual differences in brain function, and provide evidence for sex and age effects on human brain dynamic connectome.

neuroscience↗

bioRxiv2021

Cardiotoxic effects of methamphetamine associated with electrophysiological and epigenetic aberrations in Zebrafish

Long-term methamphetamine (Meth) abuse damages functional and molecular changes in the brain that causes chronic and relapsing disease. In this study, we sought to investigate a relationship between cardiotoxicity and arrhythmia with associated Meth abuse in zebrafish to identify and to understand the adverse cardiac symptoms associated with Meth as well as to assess the applicability of zebrafish as an appropriate model for cardiac-related drug screening studies. Over a two-week duration, zebrafish were first treated with various concentrations of Meth, ranging from 0 to 50 M. Immediately after treatment, zebrafish underwent electrocardiogram (ECG) measurement for electrophysiological analysis. Results show that a higher incidence of increased heart rate over the duration of the experiment, corroborating with results from previous human case studies involving Meth users. However, abnormalities commonly cited in those same case studies, such as prolongation of QTc, were not significantly presented in obtained ECG recordings. We have also conducted genetic, epigenetic, and histochemical analysis in an attempt to understand the cardiotoxic effects of Meth on zebrafish cardiac function. These results suggested myocardial damage and decrease in gene expression associated with normal physiological function. Finally, this paper provides insights into potential reasons for the apparent discrepancies in our data with prior research as well as an outlook of zebrafish cardiotoxic drug screening studies.

physiology↗

bioRxiv2021

Simultaneous Cardiac and Neurological Monitoring to Assess Chemical Exposures and Drug Toxicity in Xenopus Laevis

Simultaneous monitoring of electrocardiogram (ECG) and electroencephalogram (EEG) under chemical exposure requires innovative engineering techniques that can capture minute physiological changes in studied animal models. However, this is often administered with a bulky system that may cause signal distortions and discomfort for animals. We develop an integrated bioelectronic sensing system to provide simultaneous ECG and EEG assessment in real-time under chemical exposure for Xenopus laevis. The microelectrode array (MEA) membrane with integrated ECG and EEG sensing offers an opportunity to achieve multichannel noninvasive electrophysiological monitoring with favorable dimensions and spatial resolution. To validate the performance of our system, we assessed the ECG and EEG of Xenopus under exposure of Pentylenetetrazol (PTZ), an epilepsy-inducing drug. Effects of PTZ were detected with clear ECG and EEG alterations, including frequent ictal and interictal EEG events, 30 dB average EEG amplitude elevations, abnormal ECG morphology, and heart rate changes. Overall, our Xenopus-based real-time electrophysiology monitoring system holds high potential for many applications in drug screening and remote environmental toxicity monitoring.

physiology↗

bioRxiv2021

dsMTL - a computational framework for privacy-preserving, distributed multi-task machine learning

Multitask learning allows the simultaneous learning of multiple communicating algorithms. It is increasingly adopted for biomedical applications, such as the modeling of disease progression. As data protection regulations limit data sharing for such analyses, an implementation of multitask learning on geographically distributed data sources would be highly desirable. Here, we describe the development of dsMTL, a computational framework for privacy-preserving, distributed multi-task machine learning that includes three supervised and one unsupervised algorithms. dsMTL is implemented as a library for the R programming language and builds on the DataSHIELD platform that supports the federated analysis of sensitive individual-level data. We provide a comparative evaluation of dsMTL for the identification of biological signatures in distributed datasets using two case studies, and evaluate the computational performance of the supervised and unsupervised algorithms. dsMTL provides an easy- to-use framework for privacy-preserving, federated analysis of geographically distributed datasets, and has several application areas, including comorbidity modeling and translational research focused on the simultaneous prediction of different outcomes across datasets. dsMTL is available at https://github.com/transbioZI/dsMTLBase (server-side package) and https://github.com/transbioZI/dsMTLClient (client-side package).

bioinformatics↗

bioRxiv2021

Fetal Electrocardiogram Extraction from the Mother's Abdominal Signal Using the Ensemble Kalman Filter

Fetal electrocardiogram (fECG) assessment is essential throughout pregnancy to monitor the wellbeing and development of the fetus, and to possibly diagnose potential congenital heart defects. Due to the high noise incorporated in the abdominal ECG (aECG) signals, the extraction of fECG has been challenging. And it is even a lot more difficult for fECG extraction if only one channel of aECG is provided, i.e. in a compact patch device. In this paper, we propose a novel algorithm based on the Ensemble Kalman Filter (EnKF) for non-invasive fECG extraction from a single-channel aECG signal. To assess the performance of the proposed algorithm, we used our own clinical data, obtained from a pilot study with 10 subjects each of 20 min recording, and data from the PhysioNet 2013 Challenge bank with labeled QRS complex annotations. The proposed methodology shows the average positive predictive value (PPV) of 97.59%, sensitivity (SE) of 96.91%, and F1-score of 97.25% from the PhysioNet 2013 Challenge bank. Our results also indicate that the proposed algorithm is reliable and effective, and it outperforms the recently proposed Extended Kalman Filter (EKF) based algorithm.

bioengineering↗

bioRxiv2021

Kindlin-2 preserves integrity of the articular cartilage to protect against osteoarthritis

Osteoarthritis (OA) is an aging-related degenerative joint disease, which has no cure partly due to limited understanding of its pathological mechanism(s). Here we report that the focal adhesion protein Kindlin-2, but not Kindlin-1 or -3, is highly expressed in articular chondrocytes of the hyaline cartilage, which is dramatically decreased in the degenerated articular cartilage of aged mice and patients with OA. Inducible deletion of Kindlin-2 in chondrocytes at adult stage leads to spontaneous OA and much severe OA lesions in the mice receiving the surgery of destabilization of the medial meniscus. Mechanistically, Kindlin-2 deficiency promotes mitochondrial oxidative stress and activates Stat3 in articular chondrocytes, leading to Runx2-mediated chondrocyte hypertrophic differentiation and catabolism. In vivo, systemic pharmacological blockade of Stat3 activation or genetic ablation of Stat3 in chondrocytes reverses aberrant accumulation of Runx2 and ECM-degrading enzymes and limits OA deteriorations caused by Kindlin-2 deficiency. Furthermore, genetic inactivation of Runx2 in chondrocytes reverses structural changes and OA lesions caused by Kindlin-2 deletion without down-regulating p-Stat3 in articular chondrocytes. Of translational significance, intraarticular injection of Kindlin-2-expressing adeno-associated virus decelerates progression of aging- and instability-induced knee joint OA in mice. Collectively, we identify a novel pathway comprising of Kindlin-2, Stat3 and Runx2 in articular chondrocytes responsible for maintaining integrity of the articular cartilage and define a potential therapeutic target for OA.

pathology↗

bioRxiv2021

A Novel Art of Electrocardiogram Assessment in Zebrafish for Cardiovascular Disease Studies and Drug Screening

The zebrafish (Dario rerio) has proven to be an excellent animal model for biological research owing to its small size, low cost for maintenance, short generation time, amenable genetics, and optical transparency. Zebrafish have been extensively used in cardiovascular studies in which mutant lines with cardiovascular defects were introduced and analyzed. Despite the small size, technological advances have paved the way to effectively assess cardiac functions of zebrafish. Here, we present a novel art for long-term simultaneous monitoring and analysis of electrocardiogram (ECG) in multiple zebrafish with controlled environment. The system helps minimize the effect of anesthetic drug and temperature to cardiac rhythm side effects as well as save time and efforts by 40-50 fold compared with the conventional approach. We further employed the system to study the Na+ sensitivity in the development of sinus arrest in Tg(SCN5A-D1275N) fish, a study model of the sick sinus syndrome, as well as the relationship between this variant and drug administration. The novel ECG system developed in this study holds promise to greatly accelerate other cardiovascular studies and drug screening using zebrafish.

bioengineering↗