Biology subjects

Chang, X.

Publications and source records attributed to Chang, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

m6A-mediated epi-transcriptomic dysregulation underlies synaptic dysfunction in fragile X syndrome

Fragile X syndrome (FXS), the leading genetic cause of intellectual disability, arises from FMR1 gene silencing and loss of the FMRP protein. N6-methyladenosine (m6A) is a prevalent mRNA modification essential for post-transcriptional regulation. FMRP is known to bind to and regulate the stability of m6A-containing transcripts. However, how loss of FMRP impacts on transcriptome-wide m6A modifications in FXS patients remains unknown. To answer this question, we generated cortical neurons differentiated from induced pluripotent stem cells (iPSC) derived from healthy subjects and FXS patients. In electrophysiology recordings, we validated that synaptic and neuronal network defects in iPSC-derived FXS neurons corresponded to the clinical EEG data of the patients from which the corresponding iPSC line was derived. In analysis of transcriptome-wide methylation, we show that FMRP deficiency led to increased translation of m6A writers, resulting in hypermethylation that primarily affecting synapse-associated transcripts and increased mRNA decay. Conversely, in the presence of an m6A writer inhibitor, synaptic defects in FXS neurons were rescued. Taken together, our findings uncover that an FMRP-dependent epi-transcriptomic mechanism contributes to FXS pathogenesis by disrupting m6A modifications in FXS, suggesting a promising avenue for m6A- targeted therapies.

neuroscience↗

bioRxiv2024

ZMYND11 Functions in Bimodal Regulation of Latent Genes and Brain-like Splicing to Safeguard Corticogenesis

Despite the litany of pathogenic variants linked to neurodevelopmental disorders (NDD) including autism (ASD) and intellectual disability1,2, our understanding of the underlying mechanisms caused by risk genes remain unclear. Here, we leveraged a human pluripotent stem cell model to uncover the neurodevelopmental consequences of mutations in ZMYND11, a newly implicated risk gene3,4. ZMYND11, known for its tumor suppressor function, encodes a histone-reader that recognizes sites of transcriptional elongation and acts as a co-repressor5,6. Our findings reveal that ZMYND11-deficient cortical neural stem cells showed upregulation of latent developmental pathways, impairing progenitor and neuron production. In addition to its role on histones, ZMYND11 controls a brain-specific isoform switch involving the splicing regulator RBFOX2. Extending our findings to other chromatin-related ASD risk factors revealed similar developmental pathway activation and splicing dysregulation, partially rescuable through ZMYND11s regulatory functions.

neuroscience↗

bioRxiv2024

Contrasting patterns of specificity and transfer in human odor discrimination learning

Practice enhances olfactory performance. However, laboratory studies to date suggest that olfactory learning is largely restricted to the trained odors, posing a significant challenge for training-based rehabilitation therapies for olfactory loss. In this study, we introduce various types of odors to olfactory discrimination training, conducted unilaterally. We demonstrate contrasting patterns of specificity and transfer of learning, independent of adaptation and task difficulty. Individuals trained with odor mixtures of different ratios show long-term perceptual gains that completely transfer to the untrained nostril and effectively generalize to untrained mixtures dissimilar in structure and odor quality from the trained ones. Conversely, those trained with odor enantiomers show no transfer of learning across nostrils or to unrelated enantiomers, replicating our earlier findings (Feng & Zhou, 2019). Our observations indicate that concentration ratio and chirality represent distinct olfactory attributes. Furthermore, discrimination learning occurs at different stages of olfactory processing, depending on which attribute is task-relevant. These findings open up new avenues to enhance the effectiveness of olfactory training.

neuroscience↗

bioRxiv2024

METTL3 inhibition-activated cGAS/STING axis enhances immunotherapy and PARP inhibitor sensitivity of lung carcinoma

The cGAS/STING-mediated type I interferon response can augment antitumor activity, while the regulatory factors within this innate immune response remain elusive. Herein we found that the RNA m6A methyltransferase METTL3 was upregulated in lung carcinoma tissues. Elevated METTL3 level was correlated with diminished CD8+ T cell infiltration and cancer progression in lung carcinoma patients. METTL3 deficiency exacerbated nuclear DNA leakage into the cytoplasm, activating the cGAS pathway and thereby enhancing anti-tumor immunity. Mechanistically, METTL3 deficiency reduced the homologous recombination repair efficacy via downregulation of MSH5, a mutS family protein involved in DNA mismatch repair, leading to increased cytosolic DNA levels. m6A methylation of A2521 of MSH5 stabilized its mRNA via binding with IGF2BP2. On the other hand, m6A methylation of A1545 at the CDS of cGAS decreased mRNA stability and regulates its protein expression. Functionally, knockdown of METTL3 sensitized lung carcinoma cells to the PARP inhibitors. In vivo and clinical data confirmed the positive roles of METTL3 inhibition-activated cGAS/STING axis in tumor growth and lung adenocarcinoma progression. Collectively, METTL3 inhibition activates the cGAS/STING-mediated anti-tumor immunity via induction of cytosolic DNA and cGAS expression, which in turn regulate PARP inhibitor response and cancer progression in lung carcinoma.

cancer biology↗

bioRxiv2024

Enabling Transparent Toxicokinetic Modeling for Public Health Risk Assessment

Toxicokinetics describes the absorption, distribution, metabolism, and elimination of chemicals by the body. Predictions from toxicokinetic models provide key information for chemical risk assessment. Traditionally, these predictions extrapolate from experimental animal species data (for example, in rats) to humans. More recently, toxicokinetics has been used for extrapolation from in vitro "new approach methods (NAMs)" for toxicology to in vivo. Chemical-specific in vivo toxicokinetic data are often unavailable for the thousands of chemicals in commerce. Therefore, large amounts of in vitro data measuring chemical-specific toxicokinetics have been collected. These data enable "high-throughput toxicokinetic" or HTTK modeling. The httk R package provides a library of chemical-specific data from peer-reviewed HTTK studies. httk further provides a suite of tools for parameterizing and evaluating toxicokinetic models. httk uses the open-source language MCSim to describe models for compartmental and physiologically based toxicokinetics (PBTK), MCSim can convert the model descriptions into a high-speed C code script. New models are integrated into httk using the open-source package development functionality in R, a model documentation file (R script), and the HTTK model description code file (C script). In addition to HTTK models, httk provides a series of functionalities such as unit conversion, model parameterization, Monte Carlo simulations for uncertainty propagation and biological variability, in vivo-derived data for evaluating model predictions, and other model utility functions. Here, we describe in detail how to add new HTTK models to httk and take advantage of the pre-existing data and functionality in the package. As a demonstration, we describe the integration of the gas inhalation PBTK model into httk. Modern modeling approaches, as exemplified by httk, allow for clear communication, reproducibility, and public scrutiny. The intention of httk is to provide a transparent, open-source tool for toxicokinetics, bioinformatics, and public health risk assessment. Author SummaryWe describe the integration and evaluation of new physiologically based toxicokinetic (PBTK) models into an open-source R package. Adding a new model to the R package allows a modeler to use the existing tools and data for in vitro to in vivo extrapolation (IVIVE). Integration with the R statistical analysis environment further allows model assessment. This workflow is designed to create a more transparent and reproducible approach to toxicokinetic models developed for various exposure scenarios. Here, we demonstrate the model integration and evaluation workflow with an inhalation model. Additionally, we provide an evaluation of the overall package performance as new models, data, and functionality are added over time. Our results show that transparent development of models, and use of existing data within the open-source R package format, allows for improvement of in vitro to in vivo extrapolation estimations. IVIVE is vital for advancement of 21st century human health risk assessment.

pharmacology and toxicology↗

bioRxiv2024

Dysregulated Airway Host Defense in Hyper IgE Syndrome due to STAT3 Mutations

RationaleHyper IgE syndrome (STAT3-HIES), also known as Jobs syndrome, is a rare immunodeficiency disease typically caused by dominant-negative STAT3 mutations. STAT3-HIES syndrome is characterized by chronic pulmonary infection and inflammation, suggesting impairment of pulmonary innate host defense. ObjectivesTo identify airway epithelial host defense defects consequent to STAT3 mutations that, in addition to reported mutant STAT3 immunologic abnormalities, produce pulmonary infection. MethodsSTAT3-HIES sputum was evaluated for biochemical/biophysical properties. STAT3-HIES excised lungs were harvested for histology; bronchial brush samples were collected for RNA sequencing and in vitro culture. A STAT3-HIES-specific mutation (R382W), expressed by lentiviruses, and a STAT3 knockout, generated by CRISPR/Cas9, were maintained in normal human bronchial epithelia under basal or inflammatory (IL1{beta}) conditions. Effects of STAT3 deficiency on transcriptomics, and epithelial ion channel, secretory, antimicrobial, and ciliary functions were assessed. Measurements and Main ResultsMucus concentrations and viscoelasticity were increased in STAT3-HIES sputum. STAT3-HIES excised lungs exhibited mucus obstruction and elevated IL1{beta} expression. STAT3 deficiency impaired CFTR-dependent fluid and mucin secretion, inhibited expression of antimicrobial peptides, cytokines, and chemokines, and acidified airway surface liquid at baseline and post-IL1{beta} exposure in vitro. Notably, mutant STAT3 suppressed IL1R1 expression. STAT3 mutations also inhibited ciliogenesis in vivo and impaired mucociliary transport in vitro, a process mediated via HES6 suppression. Administration of a {gamma}-secretase inhibitor increased HES6 expression and improved ciliogenesis in STAT3 R382W mutant cells. ConclusionsSTAT3 dysfunction leads to multi-component defects in airway epithelial innate defense, which, in conjunction with STAT3-HIES immune deficiency, contributes to chronic pulmonary infection.

cell biology↗

bioRxiv2024

Wampee chromosome-level reference genome elucidates fruit sugar-acid metabolism

Wampee (Clausena lansium) is an economically significant subtropical fruit tree widely cultivated in Southern China. High-quality genomic resources are unavailable, but they are essential for functional genomics and germplasm enhancement of wampee. Here, we provide a chromosome-level genome sequence for the wampee cultivar JinFeng and a population genomic analysis of 266 accessions. The 297.1 Mb wampee genome, containing nine chromosomes with a scaffold N50 of 29.2 Mb and encoding 23,468 protein-coding genes, showed a significant improvement over the previous version. We dissected the wampee population structure and genetic differentiation in China using population genomic analysis, which detected 110 and 671 genes under a selective sweep associated with sour and sweet wampee evolution in domesticated clones, respectively. Homozygous non-synonymous single nucleotide polymorphisms are likely associated with fruit flavor differentiation. A genome-wide association study identified 220 remarkable marker-trait associations for total acid content, harboring 289 genes encoding transcription factors, transporters, and enzymes involved in sugar and acid metabolism, which are potentially useful for sour and sweet taste development in wampee fruit. Furthermore, the ethylene response factor family gene ClERF061 and the SWEET family gene ClSWEET7 were identified. Linkage assessment between the relative expression levels of ClERF061 or ClSWEET7 and the total acid/total sugar contents implied their potential involvement in sugar-acid metabolism in wampee fruits. High-quality genome resources are valuable for expediting wampee research and genome-assisted breeding.

genomics↗

bioRxiv2024

Oolonghomobisflavans from Camellia sinensis disaggregate tau fibrils across Alzheimer's disease models

Alzheimers disease (AD) is a common debilitating neurodegenerative disease with limited treatment options. Amyloid-{beta} (A{beta}) and tau fibrils are well-established hallmarks of AD, which can induce oxidative stress, neuronal cell death, and are linked to disease pathology. Here, we describe the effects of Oolonghomobisflavan A (OFA) and Oolonghomobisflavan B (OFB) on tau fibril disaggregation and prionogenic seeding. Transcriptomic analysis of OF-treated animals reveals the induction of a proteostasis-enhancing and health-promoting signature. OFA treatment reduced the burden of Tau protein aggregation in a C. elegans model expressing pathogenic human tau ("hTau-expressing") and promoted Tau disaggregation and inhibited seeding in assays using ex vivo brain-derived paired helical filament tau protein fibrils from Alzheimers disease brain donors. Correspondingly, treatment with OF improved multiple fitness and aging-related health parameters in the hTau-expressing C. elegans model, including reproductive output, muscle function, and importantly, reversed the shortened lifespan stemming from pathogenic Tau expression. Collectively, this study provides new evidence supporting the neuroprotective effects of OFs and reveal a new therapeutic strategy for targeting AD and other neurodegenerative diseases characterized by tauopathy.

physiology↗

bioRxiv2024

The Mechanism Insight into Bacterial Degradation of Pentachlorobiphenyl

Bacterial degradation mechanism for high chlorinated pentachlorobiphenyl (PentaCB) with worse biodegradability has not been fully elucidated, which could limit the full remediation of PCBs-combined pollution. In this research, using enzymatic screening method, a new PentaCB-degrading bacterium M. paraoxydans that has not been reported was obtained. The characteristic of its intracellular enzymes, proteome and metabolome variation during PentaCB degradation were investigated systematically. The results showed that PentaCB (PCB101, 1 mg/L) degradation rate could arrive 23.9% within 4 h till complete degradation within 12 h. The intracellular enzyme compound was optimally active at pH 6.0. The 12 up-regulated characterized proteins involved ABC transporter substrate-binding protein, translocase protein TatA and signal peptidase I (SPase I) indicated that functional proteins for PentaCB degradation were present both in the cytoplasm and outer surface of cytoplasmic membrane. There were also 5 differential metabolites strongly associated with above proteins in which the up-regulated 1, 2, 4-benzenetriol was enriched into the degradation pathways of benzoate, chlorocyclohexane, chlorobenzene and aminobenzoate. Bacterial degradation of PentaCB necessitates transmembrane transport, energy consumption, protein export, biofilm formation and quorum sensing. These findings hold significant theory and application value for PCBs biodegradation.

microbiology↗

bioRxiv2023

Personalized Pangenome References

Pangenomes, by including genetic diversity, should reduce reference bias by better representing new samples compared to them. Yet when comparing a new sample to a pangenome, variants in the pangenome that are not part of the sample can be misleading, for example, causing false read mappings. These irrelevant variants are generally rarer in terms of allele frequency, and have previously been dealt with using allele frequency filters. However, this is a blunt heuristic that both fails to remove some irrelevant variants and removes many relevant variants. We propose a new approach, inspired by local ancestry inference methods, that imputes a personalized pangenome subgraph based on sampling local haplotypes according to k-mer counts in the reads. Our approach is tailored for the Giraffe short read aligner, as the indexes it needs for read mapping can be built quickly. We compare the accuracy of our approach to state-of-the-art methods using graphs from the Human Pangenome Reference Consortium. The resulting personalized pangenome pipelines provide faster pangenome read mapping than comparable pipelines that use a linear reference, reduce small variant genotyping errors by 4x relative to the Genome Analysis Toolkit (GATK) best-practice pipeline, and for the first time make short-read structural variant genotyping competitive with long-read discovery methods.

bioinformatics↗

bioRxiv2023

Dynamics of Brain Lateralization and Genetic Underpinnings during Chinese Natural Speech Processing: Preferential Occurrence of Logic-Related Patterns in Males and Emotion-Related Patterns in Females

Though language is considered unique to humans with left dominant lateralization in the brain, the dynamic nature of the interplay between hemispheres during language processing remains largely unknown. Here, we investigated whole-brain functional dynamic lateralization patterns during Chinese language processing and potential sex disparities using functional MRI data of 20 subjects listening to narrative stories in a 7T MRI scanner. Our findings revealed two distinct dynamic lateralization states, with regions of the language system consistently showing the left lateralization but reversed lateralization for other regions. These two states, characterized by higher-level functioning regions exhibiting left- or right-lateralization, corresponded to the processing of rational and emotional contents, respectively. We observed pronounced inclinations towards the former state in males and the latter state in females, especially during the processing of rational contents. Finally, genetic analyses revealed that the sex differences in lateralization states were potentially influenced by sex hormones.

neuroscience↗

bioRxiv2023

Protein language models-assisted engineering of Uracil-N glycosylase enables programmable T-to-G and T-to-C base editing

Current base editors use DNA deamination enzymes, such as cytidine deaminase (CBE) or adenine deaminase (ABE), to facilitate transition nucleotide substitutions. Combining CBE or ABE with glycosylase enzymes, including CGBE and AYBE, can induce limited transversion mutations. Nonetheless, a critical demand remains for base editors capable of generating alternative mutation types, such as T>G corrections, which could address over 17% of monogenic SNVs responsible for human genetic diseases. In this study, we leveraged protein language models to engineer a uracil-N-glycosylase (UNG) variant with altered substrate specificities to thymines (eTDG). Notably, after only two rounds of testing fewer than 50 predicted variants, more than 50% exhibited a 1.5-11-fold enhancement in enzymatic activities, a success rate much greater than random mutagenesis. When eTDG was fused with Cas9 nickase without deaminases, it effectively induced programmable T to G or T to C substitutions and precisely corrected db/db diabetic mutation in mice (up to 55%). Our findings not only establish orthogonal strategies for developing novel base editors, but also demonstrate the capacities of protein language models for optimizing enzymes without extensive task-specific training data or laborious experimental procedures.

bioengineering↗

bioRxiv2023

Disruption of Aldehyde Dehydrogenase 2 protects against 1 bacterial infection

The ALDH2*2 (rs671) variant present in >500 million individuals reduces ALDH2 function, impairing aldehyde detoxification. While aldehyde accumulation in these individuals is associated with numerous negative health consequences, a previous study showed a cohort of ALDH2*2 carriers are less likely to develop active pulmonary tuberculosis. Here, we present additional human data that support this finding and show ALDH2-deficiency in mice provides a fitness advantage during bacterial infections. We found aldehydes normally detoxified by ALDH2 killed the bacterial pathogens Mycobacterium tuberculosis and Francisella tularensis. Infected macrophages from Aldh2-/-mice had higher levels of formaldehyde and 4-hydroxynonenal, which enhanced their microbicidal capacity. Aldh2-/- mice were more resistant to infection with Mycobacterium tuberculosis and Francisella tularensis than parental mice and displayed elevated inflammatory cytokine and chemokine levels, accompanied by an increased accumulation of inflammatory monocytes and macrophages. These findings support a model in which host-derived aldehydes are robust innate immune effectors, limiting bacterial infection through both direct microbicidal activity and immune modulation. Collectively, this work may explain why the ALDH2*2 allele was selected for in humans.

microbiology↗

bioRxiv2023

Improving the solubility of pseudo-hydrophobic Alzheimer's Disease medicinal chemicals through co-crystal formulation

Natural products are ligands and potential inhibitors of Alzheimers disease (AD) tau. Dihydromyricetin (DHM) is a CNS active natural product. Despite having signature polyphenolic character, DHM is ostensibly hydrophobic owing to intermolecular hydrogen bonds that shield hydrophilic phenols. Our research shows DHM becomes ionized at near-neutral pH allowing formulation of salts with transformed solubility. The MicroED co-crystal structure with trolamine reveals DHM salts as metastable solids with unlocked hydrogen bonding and a thermodynamic bent to solubilize in water. All salt formulations show better inhibitory activity against AD tau than the non-salt form, with efficacies correlating to enhanced solubilities. These results underscore the role of structural chemistry in guiding selection of solubilizing agents for chemical formulation. We propose DHM salts are appropriate formulations for research as dietary supplements to promote healthy aging by combating protein misfolding. Additionally, DHM is a suitable lead for medicinal chemistry and possible development of CNS pharmaceuticals.

pharmacology and toxicology↗

bioRxiv2022

Causal network inference based on cross-validation predictability

Identifying causal relations or causal networks among molecules/genes, rather than just their correlations, is of great importance but challenging in biology and medical field, which is essential for unravelling molecular mechanisms of disease progression and developing effective therapies for disease treatment. However, there is still a lack of high-quality causal inference algorithms for any observed data in contrast to time series data. In this study, we developed a new causal concept for any observed data and its causal inference algorithm built on cross-validated predictability (CVP) can quantify the causal effects among molecules/genes in the whole system. The causality was extensively validated by combining a large variety of statistical simulation experiments and available benchmark data (simulated data and various real data). Combining the predicted causal network and the real benchmark network, the CVP algorithm demonstrates high accuracy and strong robustness in comparison with the mainstream algorithms. In particular, the CVP algorithm is robust in identifying reliable driver genes and network biomarkers from the perspective of network biology, with the prediction results outperforming the mainstream conventional methods for predicting driver genes. CRISPR-Cas9 knockdown experiments in the liver cancer have validated that the functional driver genes identified by the CVP algorithm effectively inhibit the growth and colony formation of liver cancer cells. By knockdown experiments, we demonstrated the accuracy and significance of the causality predicted by CVP and identified the novel regulatory targets of functional driver genes SNRNP200 and RALGAPB in the liver cancer. These inferred causal networks explain regulatory patterns in different biological contexts in a clear sense and provide biological insights into molecular mechanisms of disease progression from a causality perspective.

systems biology↗

bioRxiv2022

Increased receptor affinity and reduced recognition by specific antibodies contribute to immune escape of SARS-CoV-2 variant Omicron

In this report, we mechanistically reveal how the Variant of Concern (VOC) SARS-CoV-2 Omicron (B.1.1.529) escapes neutralizing antibody responses, by characterization of this variant, and wildtype Wuhan and Delta variant (B.1.617.2). Convalescent sera as well as sera obtained from participants who received two or three doses of mRNA vaccines (Moderna-mRNA-1273(R) or Pfizer-BNT162b2(R)) were used for comparison in this study. Our data demonstrate that both the Delta as well as Omicron variants exhibit higher affinity for the receptor ACE2, facilitating infection and causing antibody escape by receptor affinity (affinity escape), due to reduced ability of antibodies to compete with RBD-receptor interaction and virus neutralization. In contrast, only Omicron but not Delta variant escaped antibody recognition, most likely because only Omicron exhibit the mutation at position E484 associated with reduced recognition, resulting in further reduced neutralization (specificity escape). Nevertheless, the immunizations with RNA based vaccines resulted in marked viral neutralization in vitro for all strains, compatible with the fact that Omicron is still largely susceptible to vaccination-induced antibodies, despite affinity- and specificity escape.

immunology↗

bioRxiv2022

High-Throughput Screening for Myelination Promoting Compounds Using Human Stem Cell-derived Oligodendrocyte Progenitor Cells Identifies Novel Targets

Promoting myelination capacity of endogenous oligodendrocyte precursor cells (OPCs) is a promising therapeutic approach for central nervous system demyelinating disorders such as Multiple Sclerosis (MS). To aid in the discovery of myelination promoting compounds, we generated an advanced, genome engineered, human pluripotent stem cell (hPSC) line that consist of three reporters (identification-and-purification tag, GFP, and secreted NanoLuc) driven by the endogenous PDGFR, PLP1 and MBP genes, respectively. Based upon this line, we established a high-throughput drug screening platform and performed a small molecule screen with 2500 bioactive molecules. In addition to a number of previously known pathways, our screening effort identified new pathways whose inhibition enhance oligodendrocyte maturation and myelination. Although further genetic and molecular validation is required, the identified inhibitors could potentially be repurposed to develop remyelination therapy for MS and other demyelinating disorders.

neuroscience↗

bioRxiv2021

Virus-like particles (VLPs) are efficient tools for boosting mRNA-induced antibodies

mRNA based vaccines against COVID-19 have proven most successful at keeping the SARS-CoV-2 pandemic at bay in many countries. Recently, there is an increased interest in heterologous prime-boost vaccination strategies for COVID-19 to maintain antibody response for the control of continuously emerging SARS-CoV-2 variants of concern (VoCs) and to overcome other obstacles such as supply shortage, costs and reduced safety issues or inadequate induced immune-response. In this study, we investigate the antibody responses induced by heterologous prime-boost with vaccines based on mRNA and virus-like particles (VLPs). The VLP-based mCuMVTT-RBM vaccine candidate and the approved mRNA-1273 vaccine were used for this purpose. We find that homologous prime boost regimens with either mRNA or VLP induced high levels of high avidity antibodies. Optimal antibody responses were, however, induced by heterologous regimens both for priming with mRNA and boosting with VLP and vice versa, priming with VLP and boosting with mRNA. Thus, heterologous prime boost strategies may be able to optimize efficacy and economics of novel vaccine strategies.

immunology↗