Biology subjects

Wang, K.

Publications and source records attributed to Wang, K..

At least 163 records · Page 9Linked to original sources

bioRxiv2025

Inhibition of Posterior Thalamic Nuclei Attenuates CGRP-induced Migraine-like Behavior in Mice

ObjectiveTo determine whether induction of migraine-like symptoms in mice by calcitonin gene-related peptide (CGRP) requires activation of the posterior thalamic nuclei (PoT) in the brain.BackgroundPrevious research found that both optical activation of the PoT and injection of CGRP into the PoT are sufficient to induce light aversive behavior in mice. The PoT is well known as a sensory integration center of light and pain signals in the brain. However, whether this region is required for touch hypersensitivity and light aversion following peripheral administration of CGRP was not known.MethodsThe PoT was injected in two strains of mice, inbred C57BL/6J and outbred CD-1, with viral vectors expressing inhibitory chemogenetic Designer Receptors Exclusively Activated by Designer Drugs (DREADDs). The inhibitory DREADDs were activated by systemic intraperitoneal (ip) injection of two designer drugs, clozapine N-oxide (CNO) and DREADD agonist compound 21 (C21). We used ip injection of CGRP to induce migraine-like phenotypes and tested whether we could rescue these phenotypes by bilateral chemogenetic inhibition of the PoT. The light/dark assay was used to measure light aversive behavior (a surrogate for photophobia) and the plantar von Frey assay to measure hindpaw touch sensitivity (a surrogate for extracephalic allodynia).ResultsWe successfully induced light aversive and hindpaw touch hypersensitivity phenotypes in mice using ip injections of CGRP. Activation of the inhibitory DREADDs in the PoT using ip CNO (5 mg/kg) was sufficient to partially rescue the touch hypersensitivity phenotype, but with off target effects in the control mice. Lowering the CNO dose to 1 mg/kg alleviated off target effects but was insufficient to rescue the touch hypersensitivity phenotype. On the other hand, C21 (1 mg/kg) fully rescued the touch hypersensitivity phenotype without any off target effects. Treatment with C21 also partially rescued the light aversion phenotype. These results were consistent across both C57BL/6J and CD-1 mouse strains.ConclusionInhibition of the PoT fully rescues CGRP-induced touch hypersensitivity and partially rescues light aversion in mice, indicating that the PoT is necessary for touch hypersensitivity and partially necessary for light aversive behaviors. These data suggest the PoT is part of a central network that receives peripheral CGRP-induced signals and thus could be harnessed for future targeted therapeutics for migraine.Plain language summaryThe posterior thalamus is a central brain region that contributes to migraine pathophysiology when stimulated. In this study, we asked if inhibition of this brain region could alleviate migraine-like phenotypes in mice. We found that inhibition of the posterior thalamus fully rescues touch hypersensitivity and partially rescues light aversive behavior, suggesting that the posterior thalamus is necessary for migraine pathophysiology and could offer a potential therapeutic target for migraine.

neuroscience↗

bioRxiv2025

PELSA-Decipher: a software tool for the processing and interpretation of ligand protein interaction dataset acquired by PELSA

Knowledge of protein-ligand interactions is essential for comprehending various aspects of life science, including drug mechanisms of action, regulatory processes in cellular metabolism and signaling, etc. Recently, a robust ligand modification-free method, termed as peptide-centric local stability assay (PELSA), is developed to identify the protein targets and binding regions of diverse ligands at proteomics scale. This method has unprecedented sensitivity and can be broadly applied to ligands including drugs, metabolites, metal ions, antibodies tec. However, the extraction of key information on ligand-protein interaction, including the binding protein, binding site, and binding affinity, is not a trivial task, which hampers the wide utilization of PELSA strategy by the research community. To address this, we developed a software tool, PELSA-Decipher, to facilitate the efficient processing of dataset obtained in PELSA experiment, including raw data processing, result visualization, and the generation of reports and high-quality images, thereby will greatly promote the broader applications of PELSA strategy. The PELSA-Decipher software can be downloaded free of charge from the website https://github.com/DICP-1809.

bioinformatics↗

bioRxiv2025

Berberrubine Inhibits Helicobacter pylori by Inducing Oxidative Stress

Helicobacter pylori is a prevalent pathogen that colonizes the pylorus and contributes to the pathogenesis of gastric cancer. The increasing antibiotic resistance in H. pylori presents a substantial challenge for effective eradication, making the development of more effective therapeutic strategies imperative. In this study, we screened 37 pure compounds (purity >95%), 3 ethanol extracts, and 6 aqueous extracts from 6 different medicinal herbs for their potential inhibitory effects against H. pylori in vitro. Among the tested compounds, 15 exhibited inhibitory activity, with berberrubine demonstrating the strongest effect, characterized by a minimum inhibitory concentration (MIC) of 0.011 mg/ml. The comparative transcriptome analysis revealed a significant upregulation of the oxidative stress response related genes, such as fumC and sodB, in H. pylori treated with berberrubine. Further in vitro assays confirmed that berberrubine exerted antibacterial activity by stimulating oxidative stress, as evidenced by increased reactive oxygen species (ROS) production and impaired cell membrane integrity. Additionally, similar inhibitory tests were applied to Escherichia coli, a common gut opportunistic pathogen. The results showed that berberrubine inhibited E. coli through the same mechanism observed for H. pylori. In conclusion, berberrubine is a potent antibacterial agent against gastrointestinal pathogens, including H. pylori and E. coli, making it a promising candidate for further development as an antimicrobial therapeutic ImportanceThis study identified berberrubine as a potent antibacterial agent against gastrointestinal pathogens, including Helicobacter pylori and Escherichia coli by inducing cellular oxidative stress. Through increased reactive oxygen species (ROS) production and disruption of bacterial cell membrane integrity, berberrubine demonstrated strong efficacy in inhibiting drug-resistant pathogens. These findings highlight its potential as a promising therapeutic candidate for eradicating drug-resistant gastrointestinal pathogens.

microbiology↗

bioRxiv2025

Comparison of in silico predictions of action potential duration in response to inhibition of IKr and ICaL with new human ex vivo recordings

During drug development, candidate compounds are extensively tested for proar-rhythmic risk and in particular risk of Torsade de Pointes (TdP), as indicated by prolongation of the QT interval. Drugs that inhibit the rapid delayed rectifier K+ current (IKr) can prolong the action potential duration (APD) and thereby the QT interval, and so are routinely rejected. However, simultaneous inhibition of the L-type Ca2+ current (ICaL) can mitigate the effect of IKrinhibition, so that including both effects can improve test specificity. Mathematical models of the action potential (AP) can be used to predict the APD prolongation resulting from a given level of IKr and ICaL inhibition, but for use in safety-testing their predictive capabilities should first be carefully verified. We present the first systematic comparison between experimental drug-induced APD and predictions by AP models. New experimental data were obtained ex vivo for APD response to IKr and/or ICaL inhibition by applying 9 compounds at different concentrations to adult human ventricular trabeculae at physiological temperature. Compounds with similar effects on IKr and ICaL exhibited less APD prolongation compared to selective IKr inhibitors. We then integrated in vitro IC50 patch-clamp data for IKr and ICaL inhibition by the tested compounds into simulations with AP models. Models were assessed against the ex vivo data on their ability to recapitulate drug-induced APD changes observed experimentally. None of the tested AP models reproduced the APD changes observed experimentally across all combinations and degrees of IKr and/or ICaL inhibition: they matched the data either for selective IKr inhibitors or for compounds with comparable effects on IKr and ICaL. This work introduces a new benchmarking framework to assess the predictivity of current and future AP models for APD response to IKr and/or ICaL inhibition. This is an essential primary step towards an in silico framework that integrates in vitro data for translational clinical cardiac safety. Author summaryBefore an investigational drug reaches patients, it is tested in vitro to ensure it does not disrupt the hearts electric activity. This testing often focuses on the drugs ability to block a specific current called IKr, which, if inhibited, can prolong the heart cells action potential duration (APD), which is associated with an increased risk of irregular heartbeats (proarrhythmia). Our study examines how blocking another current, ICaL, along with IKr, affects APD. We found that adding ICaL inhibition may mitigate the proarrhythmic effects caused by IKr inhibition alone. Understanding this balance can improve how we assess the cardiac safety of new drugs, potentially saving promising compounds from being incorrectly discarded. Currently, mathematical models help predict such cardiac responses, but no existing model accurately predicted our findings. Our new data could aid in developing more predictive models in the future. This will contribute to safer drug development and more effective treatments.

pharmacology and toxicology↗

bioRxiv2025

Rapaprotin is Activated by an Endopeptidase to Disassemble 26S Proteasome

The 19S regulatory particle (RP) associates with the 20S core particle (CP) to form the 26S proteasome, an evolutionarily conserved holoenzyme that plays key roles in both physiological and pathological processes. Proteasome inhibitors that target the catalytic subunits within the 20S have proven to be valuable research tools and therapeutics for various cancers. Herein we report the discovery of rapaprotin, a 26S proteasome assembly inhibitor from our natural product-inspired hybrid macrocycle rapafucin library. Rapaprotin induces apoptosis in both myeloma and leukemia cell lines. Genome-wide CRISPR-Cas9 screen identified a cytosolic enzyme, prolyl endopeptidase (PREP) that is required for the pro-apoptotic activity of rapaprotin. Further mechanistic studies revealed that rapaprotin acts as a molecular transformer, changing from an inactive cyclic form into an active linear form, rapaprotin-L, upon PREP cleavage, to block 26S proteasome activity. Time-resolved cryogenic electron microscopy (cryo-EM) revealed that rapaprotin-L induces dissociation of the 19S RP from the 26S holoenzyme, which was verified in cells. Furthermore, rapaprotin exhibits a marked synergistic effect with FDA-approved proteasome inhibitors and resensitizes drug-resistant multiple myeloma cells from patients to bortezomib. Taken together, these results suggest that rapaprotin is a new chemical tool to probe the dynamics of the 26S proteasome assembly and a promising anticancer drug lead.

pharmacology and toxicology↗

bioRxiv2025

Unveiling Candidate Drivers in Cancer Progression Using Somatic-IV Analysis

MotivationIdentifying causal drivers of cancer progression is crucial for developing effective anti-cancer therapies. However, disentangling causality from correlation remains challenging due to confounding factors within the complex genetic and transcriptomic landscapes of cancer. ResultsTo address this challenge, we introduce the Somatic Instrumental Variable analysis (Somatic-IV), which integrates genetic, transcriptomic, and clinical outcome data to identify candidate driver genes likely playing a causal role in disease progression. Somatic-IV estimates genetic-exposure and genetic-outcome associations, utilizing MR-Egger regression to estimate bias-reduced causal effects. We assessed the statistical properties and performance of Somatic-IV through a simulation study and demonstrated its utility in pancreatic adenocarcinoma (PDAC) and colorectal cancer (CRC). Our analysis identified ZBED2 and CSNK2A2 as likely drivers of PDAC and CRC cancer progression, respectively. Somatic-IV is a novel approach for generating target hypotheses and guiding the development of effective therapies for cancer patients. Availability and implementationThe Somatic-IV package is available at: https://github.com/wzhang1984/Somatic_IV_package

bioinformatics↗

bioRxiv2025

A genetic signature predicts aggressive paraganglioma sensitivity to dual PI3K-CDK4/6 inhibition therapy

Effective medical therapies for metastatic paraganglioma (mPPGL) are currently lacking, leading to dismal prognosis. Building on our knowledge of molecular mechanisms driving PPGL progression, we assessed the therapeutic potential of targeting two critical processes: PI3K signaling and cell cycle regulation. The efficacy of buparlisib (PI3Ki) and ribociclib (CDK4/6i), individually and combined, was assessed in vitro using PPGL cell lines, rat- and patient-derived primary cells, and in vivo using PPGL cells-derived mouse xenografts. The combination therapy demonstrated superior antitumor activity compared to single agents, particularly in vivo. Mechanistically, the efficacy of the combination therapy was associated to the downregulation of FOXM1-controlled genes implicated in mitotic spindle assembly and chromosomal segregation, leading to mitotic catastrophe. Data mining and qRT-PCR showed this genetic signature to be upregulated in human mPPGLs. This suggests that aggressive PPGLs exhibit heightened vulnerability to dual PI3K and CDK4/6 inhibition, offering a promising therapeutic avenue for these challenging cancers.

cancer biology↗

bioRxiv2025

Cholesterol efflux protein, ABCA1, supports anti-cancer functions of myeloid immune cells

Although immune therapy has seen significant advances, the majority of breast and other solid tumors do not respond or quickly develop de novo resistance. One factor driving resistance is highly immune suppressive myeloid cells (MCs) such as macrophages. Previous work has established clinical links between cholesterol and cancer outcome, and that MC function can be regulated through disruption in cholesterol metabolism. Thus, we screened for proteins that were expressed in MCs, involved in cholesterol homeostasis and whose expression was associated with survival; we identify the cholesterol efflux protein ABCA1. Preclinical studies revealed that ABCA1 activity resulted in increased anti-cancer functions of macrophages: enhanced tumor infiltration, decreased angiogenic potential, reduced efferocytosis, and improved support of CD8+ T cell activity. Mechanistically, different AKT isoforms are involved, through both PI3K dependent and independent mechanisms. Assessment of human blood and breast tumors revealed correlations between ABCA1 in macrophages and angiogenic potential, VEGFA, and CD8 T cell abundance and activity, highlighting the clinical relevance of our findings. The culmination of the effects of ABCA1 on MC function were demonstrated through increased tumor growth and metastasis in mice with MC specific knockout of ABCA1. Therefore, modulating ABCA1 activity within MCs may represent a novel approach to immune therapy.

cancer biology↗

bioRxiv2025

PROBind: A Web Server for Prediction, Analysis and Visualization of Protein-Protein and Protein-Nucleic Acid Binding Residues

Protein-protein and protein-nucleic acids interactions are fundamental to numerous cellular functions, yet only a small fraction have been experimentally characterized. Although modern computational methods have been developed for predicting interacting residues in proteins, they are challenging to use due to individual installation and execution requirements, lack of a standardized input or output format, and absence of support for result analysis. Moreover, methods trained using structures of complexes or intrinsically disordered regions, may not perform well on other types. To overcome these challenges, we develop PROBind, a web server for predicting, analyzing, and interactively visualizing protein, DNA and RNA binding residues from both protein sequences and structures. PROBind integrates 12 predictors trained on structural or disordered proteins, and supports the upload of results from external predictors. By normalizing and averaging predictions from multiple predictors targeting the same ligand type, PROBind generates meta-predictions that balance discrepancies among different methods. Furthermore, it provides interactive graphical tools for result analysis and contextualization. Overall, PROBind accommodates diverse ligand types and supports predictions and analysis based on both structure and sequence data, overcoming the limitations of existing tools. PROBind is freely accessible at https://www.csuligroup.com/PROBind.

bioinformatics↗

bioRxiv2025

A Comparative Evaluation of Computational Models for RNA modification detection using Nanopore sequencing with RNA004 Chemistry

Direct RNA sequencing from Oxford Nanopore Technologies (ONT) has become a valuable method for studying RNA modifications such as N6-methyladenosine (m6A), pseudouridine ({psi}), and 5-methylcytosine (m5C). Recent advancements in the RNA004 chemistry substantially reduce sequencing errors compared to previous chemistries (e.g., RNA002), thereby promising enhanced accuracy for epitranscriptomic analysis. In this study, we benchmark the performance of two state-of-the-art RNA modification detection models capable of handling RNA004 data - ONTs Dorado and m6Anet - using two wild-type (WT) cell lines, HEK293T and HeLa, with respective ground truths from GLORI and eTAM-seq, and their paired in vitro transcribed (IVT) RNA as negative controls. We found that under default settings and considering sites with [≥]10% modification ratio and [≥]10X coverage, Dorado has higher recall ([~]0.92) than m6Anet ([~]0.51) for m6A detection. Among the overlapping methylated sites between ground truth and computational predictions, there are high correlations of site-specific m6A modification stoichiometry, with correlation coefficient of [~]0.89 for Dorado-truth comparison and [~]0.72 for m6Anet-truth comparison. However, combined assessment of WT and IVT datasets show that while the per-site false positive rate (FPR) can be lower ([~]8% for Dorado and [~]33% for m6Anet), both computational tools can have high per-site false discovery rate (FDR) of m6A ([~]40% for Dorado and [~]80% for m6Anet) due to the low prevalence of m6A in transcriptome, with a similar trend observed for pseudouridine ([~]95% FDR for Dorado). Additional motif analysis reveals that both Dorado and m6Anet exhibit high heterogeneity of false positive calls across sequence contexts, suggesting that sequence contexts help determine accuracy of specific modification calls. There is also a substantial overlap of false positive calls between the two IVT samples, suggesting a post-filtering strategy to improve modification calling by compiling a set of low-confidence sites with a probabilistic model from several IVT samples across diverse cells/tissues. Our analysis highlights key strengths and limitations of the current generation of m6A detection algorithms and offers insights into optimizing thresholds and interpretability. The IVT datasets generated by the RNA004 chemistry provides a publicly available benchmark resource for further development and refinement of computational methods.

bioinformatics↗

bioRxiv2025

Two-step voltage-sensor activation of the human KV7.4 channel and effect of a deafness-associated mutation

Voltage-gated, potassium-selective KV7.4 channels are expressed in the inner ear and are crucial for hair-cell function and survival. Loss-of-function variants of KCNQ4, the gene encoding KV7.4-channel subunits, cause non-syndromic progressive hearing loss (DFNA2). KV7.4 opening requires a voltage-dependent conformational change (activation) of the charged voltage-sensor domains (VSDs), and its transduction to the pore. Previously, fast charge displacement was reported during VSD activation at negative potentials, but it is unclear how this is coupled to slow channel opening occurring at more depolarized potentials. Here, we optically tracked KV7.4 VSD activation with voltage-clamp fluorometry, leveraging two different fluorophores and pulsed excitation, to thoroughly characterize VSD movements. We found that VSD activation comprises several voltage-dependent transitions, some of which had kinetics and voltage-dependence matching those of channel opening and closing. The deafness-associated mutation R216H, which substitutes a charged amino-acid in the VSD, impaired both VSD movements and channel opening, shifting them towards more depolarized potentials. This suggested that R216H impaired KV7.4 function by destabilizing VSD activation. Using molecular dynamics, we found that H216 reduced intramolecular interactions, thus decreasing the stability of an active VSD conformation. We propose that the KV7.4 VSD activates in two steps: a fast movement at negative voltages that represents a first transition to an intermediate state of activation; and this is followed by slower, depolarized component that represents subsequent full VSD activation, which drives channel opening.

biophysics↗

bioRxiv2025

m3C is a mitochondrial mRNA modification which promotes tumor progression

Mitochondrial mRNA modifications are suggested to play a role in fine-tuning mitochondrial gene expression and function. However, the epitranscriptomic landscape of mitochondrial mRNA (mt-mRNA) remains poorly explored. Here, we uncover N3-methylcytosine (m3C) as a novel mt-mRNA that is catalyzed by METTL8, an enzyme previously known to modify mt-tRNA. Transcriptome-wide mapping reveals that METTL8-dependent m3C is enriched in mt-mRNAs encoding complex I subunits of the respiratory chain. Additionally, METTL8 is highly expressed in various cancers, notably in cervical cancer. METTL8 depletion impairs cell migration in vitro and reduces tumor growth in mouse xenografts. Finally, transcriptomic analyses further link METTL8 expression to oncogenic pathways, mitochondrial functions and complex I activity. Together, our results reveal a novel mitochondrial mRNA modification that promotes cancer progression.

cell biology↗

bioRxiv2025

Neuronal cell adhesion molecule (NRCAM) variant defined by microexon skipping is an essential, antigenically distinct, and targetable surface proteoform in high-grade glioma

To overcome the paucity of known tumor-specific surface antigens in pediatric high-grade glioma (pHGG), we contrasted splicing patterns in pHGGs and normal brain samples. Among alternative splicing events affecting extracellular protein domains, the most pervasive alteration was the skipping of [≤]30 nucleotide-long exons. Several of these skipped microexons mapped to L1-IgCAM family members, such as NRCAM. Bulk and single-nuclei short- and long-read RNA-seq revealed uniform skipping of NRCAM microexons 5 and 19 in virtually every pHGG sample. Importantly, the {Delta}ex5{Delta}ex19 (but not the full-length) NRCAM proteoform was essential for pHGG cell migration and invasion in vitro and tumor growth in vivo. We developed a monoclonal antibody selective for {Delta}ex5{Delta}ex19 NRCAM and demonstrated that "painting" of pHGG cells with this antibody enables killing by T cells armed with an FcRI-based universal immune receptor. Thus, pHGG-specific NRCAM and possibly other L1-IgCAM proteoforms are promising and highly selective targets for adoptive immunotherapies.

cancer biology↗

bioRxiv2025

Quantifying Metagenomic Strain Associations fromMicrobiomes with Anpan

Genetic and genomic variation among microbial strains can dramatically influence their phenotypes and environmental impact, including on human health. However, inferential methods for quantifying these differences have been lacking. Strain-level metagenomic profiling data has several features that make traditional statistical methods challenging to use, including high dimensionality, extreme variation among samples, and complex phylogenetic relatedness. We present Anpan, a set of quantitative methods addressing three key challenges in microbiome strain epidemiology. First, adaptive filtering designed to interrogate microbial strain gene carriage is combined with linear models to identify strain-specific genetic elements associated with host health outcomes and other phenotypes. Second, phylogenetic generalized linear mixed models are used to characterize the association of sub-species lineages with such phenotypes. Finally, random effects models are used to identify pathways more likely to be retained or lost by outcome-associated strains. We validated our methods by simulation, showing that we achieve more accurate effect size estimation and a lower false positive rate compared to alternative methodologies. We then applied our methods to a dataset of 1,262 colorectal cancer patients, identifying functionally adaptive genes and strong phylogenetic effects associated with CRC status, sometimes complementing and sometimes extending known species-level microbiome CRC biomarkers. Anpans methods have been implemented as a publicly available R library to support microbial community strain and genetic epidemiology in a variety of contexts, environments, and phenotypes.

bioinformatics↗

bioRxiv2025

Delineating JunB's Crucial Function in Mature Th17 Cells through Inducible Targeted Protein Degradation

The AP-1 transcription factor JunB is essential for the differentiation of pathogenic T helper 17 (Th17) cells, which are key mediators of autoimmune diseases such as multiple sclerosis and colitis. While the importance of JunB during Th17 polarization is known, its role in mature Th17 cells--critical therapeutic targets in these diseases--remains unclear. In this study, we employed the dTAG system, a targeted protein degradation approach, to deplete JunB in Th17 cells generated both in vitro and in vivo. During pathogenic Th17 cell differentiation, JunB degradation replicated known effects of JunB deficiency, including reduced expression of interleukin (IL)-17A and the genes encoding ROR{gamma}t (Rorc) and the IL-23 receptor (Il23r). In contrast, in mature pathogenic Th17 cells, JunB degradation downregulated Il23r without affecting IL-17A or Rorc expression. Furthermore, JunB degradation compromised the viability of mature pathogenic Th17 cells. Transcriptomic analyses revealed that JunB regulates distinct gene sets during Th17 polarization compared to mature Th17 cells. The gene Inhba, which encodes activin A, was identified as a JunB target in both stages. Supplementation with activin A restored IL-17A and Rorc expression during pathogenic Th17 cell differentiation. These findings demonstrate that JunB maintains mature pathogenic Th17 cell phenotypes, including IL-23 receptor expression, and supports pathogenic Th17 cell survival. As IL-23 signaling is crucial for sustaining pathogenic Th17 cells, targeting JunB may offer a therapeutic strategy to limit Th17-driven autoimmune inflammation.

immunology↗

bioRxiv2025

1,3- and 1,4-linked Polysaccharides Uptake in Intestinal Cells Relies on Clathrin/Dynamin 1/Rab5-dependent Endocytosis

Natural polysaccharides are considered to be a promising feedstock for manufacturing sustainable materials. However, polysaccharides are believed by most biologists that they could not be absorbed by intestinal mucosa to enter circulation system owing to their high hydrophilicity and large molecule size. Herein, {beta}-1,3-linked glucan (GFPBW1) and -1,4-linked glucan (WGE) is used as the model polysaccharide and the transport experiments show that different linked and charged polysaccharides can permeate Caco-2 cell monolayers. The in vivo experiments demonstrate that GFPBW1 and WGE are detectable in rodent plasma and liver after oral administration the isotope (99mTc, 3H) and fluorescein labeled polysaccharides. Further study show that polysaccharide uptake requires clathrin heavy chain (CLTC) and its associated factors Rab5 and dynamin1 in intestinal cells using gene-knockdown strategies and inhibitors. Strikingly, polysaccharide absorption is attenuated in both CLTC intestine deficient mice and Rab5, dynamin1 conventional-knockout mice. Importantly, membrane receptors bone morphogenetic protein receptor type IA (BMPRIA), Dectin-1 and epidermal growth factor receptor (EGFR) are also critical for specific structural polysaccharide internalization. These findings provide novel insight to understand polysaccharide absorption mechanism and lay foundation for oral polysaccharide- based new drugs development.

pharmacology and toxicology↗

bioRxiv2024

Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina

Most genetic risk variants linked to ocular diseases are non-protein coding and presumably contribute to disease through dysregulation of gene expression, however, deeper understanding of their mechanisms of action has been impeded by an incomplete annotation of the transcriptional regulatory elements across different retinal cell types. To address this knowledge gap, we carried out single-cell multiomics assays to investigate gene expression, chromatin accessibility, DNA methylome and 3D chromatin architecture in human retina, macula, and retinal pigment epithelium (RPE)/choroid. We identified 420,824 unique candidate regulatory elements and characterized their chromatin states in 23 sub-classes of retinal cells. Comparative analysis of chromatin landscapes between human and mouse retina cells further revealed both evolutionarily conserved and divergent retinal gene-regulatory programs. Leveraging the rapid advancements in deep-learning techniques, we developed sequence-based predictors to interpret non-coding risk variants of retina diseases. Our study establishes retina-wide, single-cell transcriptome, epigenome, and 3D genome atlases, and provides a resource for studying the gene regulatory programs of the human retina and relevant diseases.

genomics↗

bioRxiv2024

CDH3-AS1 antisense RNA enhances P-cadherin translation and acts as a tumor suppressor in melanoma

Thousands of regulatory noncoding RNAs (ncRNAs) have been annotated; however, their functions in gene regulation and contributions to cancer formation remain poorly understood. To gain a better understanding of the influence of ncRNAs on gene regulation during melanoma progression, we mapped the landscape of ncRNAs in melanocytes and melanoma cells. Nearly half of deregulated genes in melanoma are ncRNAs, with antisense RNAs (asRNAs) comprising a large portion of deregulated ncRNAs. CDH3-AS1, the most significantly downregulated asRNA, overlaps the CDH3 gene, which encodes P-cadherin, a transmembrane glycoprotein involved in cell adhesion that was also reduced in melanoma. Overexpression of CDH3-AS1 increased cell aggregation and reduced xenograft tumor growth, mimicking the tumor-suppressive effects of CDH3. CDH3-AS1 interacted with CDH3 mRNA and enhanced P-cadherin protein levels. Interestingly, secondary structures at the CDH3 5 end regulated P-cadherin translation, and ribosome profiling revealed that CDH3-AS1 promotes ribosome occupancy at the CDH3 mRNA. Notably, ribosome occupancy was generally increased in mRNAs having cognate asRNA that are complementary to the 5UTR. Taken together, this study revealed the CDH3-AS1-mediated enhancement of P-cadherin translation, underscoring the broader potential of asRNAs as regulators of protein-coding genes and their role in diseases like melanoma.

molecular biology↗