Biology subjects

Cheng, F.

Publications and source records attributed to Cheng, F..

At least 19 recordsLinked to original sources

bioRxiv2026

Interferon-induced OASL restricts ADAR1 p150 RNA binding and A-to-I RNA editing

The interferon (IFN)-inducible RNA editor ADAR1 p150 catalyzes adenosine-to-inosine (A-to-I) editing of host and viral double-stranded RNAs, limiting aberrant innate immune sensing and regulating gene expression. How ADAR1 p150 activity is regulated during host-virus interactions remains poorly understood. Here, we identify the IFN-stimulated gene OASL as an inhibitor of ADAR1 p150. OASL engages p150 through two distinct interactions: its N-terminal OAS domain associates with the RNA-binding domains in an RNA-dependent manner, whereas its C-terminal ubiquitin-like domains bind the Z domain independently of RNA. Despite their distinct canonical functions, the OAS and ubiquitin-like domains converge to limit ADAR1 p150 RNA binding and suppress A-to-I editing across the transcriptome. OASL also reverses p150-mediated suppression of antiviral and innate immune gene expression and counteracts p150-mediated enhancement of measles virus and vesicular stomatitis virus replication. Thus, OASL restrains ADAR1 p150, linking interferon signaling to the control of RNA editing and antiviral immunity.

molecular biology↗

bioRxiv2026

Transient tubular membrane injury is converted into persistent fibrosis through a macrophage-fibroblast relay

A central unresolved problem in acute kidney injury (AKI) is how a transient epithelial insult is converted into persistent fibrotic repair that drives progression toward chronic kidney disease. Although tubular, immune and stromal responses are individually well recognized, the mechanistically continuous relay linking these three compartments has remained unresolved. Here we define a directional information-conversion pathway spanning injured tubular epithelial cells, macrophages and fibroblasts. Time-resolved single-cell profiling identified a TREM2/SPP1 macrophage state that emerged as post-ischemic repair became fibrotic. Tubular injury remodeled phosphatidylserine (PS) species, increased oxidized PS and PS externalization, and generated a membrane-lipid context for TREM2 sensing, supported by PS masking, defined liposomes and orthogonal binding assays. Structure-function analysis separated R47-dependent phospholipid recognition from K183-dependent DAP12 coupling, linking membrane damage to SYK activation and NF-kB/AP-1-driven Spp1 transcription. Macrophage-derived SPP1 then activated ITGAV/ITGB1-associated FAK-SMAD2/3 signaling, fibroblast contraction and matrix production. Crucially, repair-phase SPP1 neutralization and post-injury Cx3cr1-lineage Trem2 deletion attenuated fibrosis, with delayed Trem2 deletion protective in both ischemic and obstructive injury. Human single-cell, spatial, urinary and tissue analyses showed cross-species and cross-scale convergence. These findings resolve how transient tubular membrane damage is successively transformed across three cellular compartments into persistent, yet interruptible, fibrotic repair.

pathology↗

bioRxiv2026

AAV VP1 unique region (VP1u) determines GPR108 dependence for AAV transduction of human airway epithelium and its rescue by Doxorubicin

rAAV2.5T was identified through directed evolution of an AAV capsid library in polarized human airway epithelium (HAE) cultured at an air-liquid interface (ALI). The capsid gene of rAAV2.5T is a chimera of the N-terminal unique region of AAV2 VP1 (VP1u) and the VP2 and VP3 regions of AAV5 with a single A581T substitution at the variable region (VR) VIII of the capsids. GPR108, a G protein-coupled receptor, is known as an essential host factor for the transduction of rAAV2 but not of rAAV5. Both AAV2 and AAV5 VP1u colocalized well with GPR108 and, to a lesser extent, with the trans-Golgi network (TGN). GPR108 knockout (KO) abolished rAAV2.5T transduction in both HeLa cells and HAE-ALI cultures. Remarkably, short-term treatment with doxorubicin (DOX) at 2 {micro}M completely restored transduction, indicating that DOX can compensate for the loss of GPR108 function. DOX enhanced rAAV2.5T transduction by 50-100-fold in wild-type HAE-ALI cultures and by over 300-fold in the GPR108-deficient cultures. Mechanistic studies demonstrated that this enhancement resulted from altered intracellular trafficking that promoted efficient vector nuclear import, rather than increased vector internalization, proteasome inhibition, or activation of the DNA damage response. Importantly, we identified that the N-terminal 15 amino acids of AAV2 VP1u as the primary determinant of rAAV2.5T dependence on GPR108 for transduction. Collectively, these findings demonstrate that productive transduction of rAAV2.5T in polarized HAE cultures depends on GPR108-mediated intracellular trafficking that limits efficient nuclear entry, and that DOX can relieve this constraint by promoting efficient vector import. SignificanceAAV2.5T is an airway-tropic vector with considerable promise for pulmonary gene therapy. We found that host factor GPR108 is required for rAAV2.5T trafficking from the TGN to the nucleus and that this step constitutes a major bottleneck to productive transduction in polarized HAE. In contrast, KIAA0319L (AAVR) plays a key role in AAV intracellular trafficking from the endosome to the TGN but not in internalization into polarized HAE during apical transduction. Transient treatment with low-dose doxorubicin (DOX, 2 {micro}M) enhanced rAAV2.5T transduction in HAE by 50-100-fold through a significant increase in vector nuclear import. Notably, DOX can overcome the transduction deficit caused by GPR108 deficiency, but not that caused by AAVR deficiency. Mechanistically, the N-terminal 15 amino acids of the VP1u confer GPR108 dependence during rAAV2.5T apical transduction of polarized HAE. DOX bypasses this requirement by promoting efficient nuclear import without affecting vector internalization, inhibiting proteasomes, or inducing DNA damage response.

microbiology↗

bioRxiv2026

TBC1D23-AAVR Interaction Drives Endosome-to-TGN Trafficking Required for rAAV Transduction

The adeno-associated virus receptor (AAVR; also known as KIAA0319L) is the proteinaceous receptor required for the transduction of multi-serotype adeno-associated viruses (AAVs). While the extracellular polycystic kidney disease (PKD) domains of AAVR directly bind AAV capsids, the function of its C-terminal cytosolic domain (AAVR-C) in governing AAV internalization and intracellular trafficking remains undefined. Using targeted pulldown of AAVR-interacting host proteins with a glutathione S-Transferase (GST)-fused AAVR-C recombinant protein (GST-AAVR-C) as a bait, we identified that TBC1 domain family member 23 (TBC1D23), a specialized intracellular trafficking adaptor and bridging factor, binds AAVR via the AAVR-C and mediates AAVs endosome-to-trans-Golgi network (TGN) transport. Biolayer interferometry (BLI) demonstrates nanomolar-affinity binding between AAVR-C and the C-terminal scaffold domain of TBC1D23 (TBC1D23-C). CRISPR-mediated knockout of TBC1D23 severely impairs rAAV transduction across multiple human cell types, including polarized human airway epithelium (HAE). Loss of TBC1D23 disrupts convergence of internalized AAV capsids at the TGN, leading to diminished nuclear import of AAV vectors. Mutational analyses of AAVR-C reveal that its acidic residue cluster is required for TBC1D23 binding and AAV retrograde transport from the endosome to the TGN. Together, these findings define TBC1D23 as a receptor-proximal trafficking module that couples AAV-AAVR engagement to vesicle transport, revealing a missing core regulatory step in AAV retrograde transport that is essential for productive rAAV transduction. SignificanceRecombinant adeno-associated viruses (rAAVs) are widely used gene delivery vectors, yet the intracellular trafficking steps that enable productive transduction remain incompletely defined. We identify TBC1D23 as a critical host adaptor that directly binds the cytosolic tail of the AAV receptor (AAVR) and mediates retrograde transport of AAV vectors from endosomes to the trans-Golgi network (TGN). Disruption of the AAVR acidic residue cluster abolishes TBC1D23 binding, blocks TGN trafficking, impairs nuclear import, and severely reduces transduction across multiple serotypes and in polarized human airway epithelium. These findings reveal a receptor-proximal trafficking checkpoint essential for rAAV gene delivery and define a host-vector interface with potential for rational vector engineering and therapeutic modulation.

microbiology↗

bioRxiv2026

An autonomous LLM agent platform for computational binder design and conjugation-aware prioritization of antibody drug conjugates

Large language model (LLM) agents have automated tool use in chemistry, but orchestrating multi-step computational biology workflows--spanning structure prediction, protein design, and covalent conjugation--remains manually intensive. Here we present Open Intelligence Hub (OIH), an autonomous LLM-agent platform that dynamically plans and executes 32 containerised tools for protein binder design and antibody-drug conjugate (ADC) prioritization. OIH introduces tier-based decision routing, ipSAE-guided interface filtering, and failure-to-knowledge distillation from 265 curated cases. Across five oncology targets, the agent correctly classified all five evaluated targets and required human correction for hotspot selection in only one case, producing binders ranked by ipSAE (Nectin-4 ipTM = 0.87, HER2 ipTM = 0.85). A controlled ablation suggests that the agents PPI-informed routing yields improved downstream ipTM and ipSAE scores than epitope-guided alternatives. The LLM-agnostic architecture enables deployment with local or commercial models without pipeline changes. All results are computational predictions awaiting experimental validation.

bioinformatics↗

bioRxiv2026

Nucleoid-associated proteins sense phage-induced genome damage to elicit abortive infection

Bacteria have evolved diverse immune strategies to detect and neutralize bacteriophage infection. Here, we describe an unprecedented paradigm in which a chromosome-architecting nucleoid-associated protein (NAP) is repurposed as a viral infection sensor. When phage attack leads to genome degradation, the NAP sensor is released from the nucleoid to the cytoplasm, where it binds and activates diverse immune effectors. One such effector is a nucleotide-modifying toxin normally existing as an inactive homotetramer. NAP binding converts it into a catalytically active heterotrimer that halts both transcription and translation. Phylogenetic analyses unveiled the high modularity, polyphyletic origin, and wide distribution of NAP-mediated defenses. Collectively, we define a distinct class of defense systems in which bacteria sense phage-induced genome damage through NAP relocation, highlighting an unexpected but essential role for these proteins as sentinels of genome integrity.

microbiology↗

bioRxiv2026

Identification of Human Transferrin Receptor as an Entry Co-receptor for Parvovirus B19 Infection of Human Erythroid Progenitor Cells

Parvovirus B19 (B19V), a member of the genus Erythroparvovirus within the Parvoviridae family, infects human erythroid progenitor cells (EPCs) of bone marrow and fetal liver, and causes various hematological disorders. The minor capsid protein VP1 of B19V contains a unique N-terminal region (VP1u) that facilitates virus binding and internalization into EPCs via its receptor-binding domain (RBD). We previously identified tyrosine protein kinase receptor UFO (AXL) as a proteinaceous receptor for B19V infection of EPCs. In this study, we employed an ascorbate peroxidase 2 (APEX2)-based proximity labeling method to identify host proteins that are associated with B19V VP1u during entry. This analysis revealed human transferrin receptor 1 (hTfR) as a key host protein associated with VP1u. hTfR knockdown in UT7/Epo-S1 cells, a B19V-permissive human megakaryoblastoid leukemia cell line, showed significantly reduced B19V internalization and replication. Biolayer interferometry (BLI) assays confirmed a direct interaction between B19V VP1u and hTfR extracellular domain (ECD). Inhibition of VP1u interaction with hTfR ECD, either by a monoclonal antibody targeting the apical domain of the ECD or human ferritin, a natural ligand of hTfR that binds the apical domain, significantly reduced VP1u binding to hTfR, as well as B19V internalization and B19V replication in ex vivo-expanded EPCs. Furthermore, mutant RBD proteins that bear amino acid substitutions in the three helical domains nearly abolished RBD binding to hTfR and significantly reduced the ability to inhibit B19V infection of EPCs. Collectively, our findings establish hTfR as a B19V entry co-receptor that mediates B19V internalization into its natural host EPCs. SignificanceB19V causes severe hematological disorders, including transient aplastic crisis, chronic pure red cell aplasia, and hydrops fetalis, by selectively infecting erythroid progenitor cells (EPCs). Despite its clinical impact, no approved antivirals or vaccines exist, largely due to limited understanding of viral entry mechanisms. A unique feature of B19V is the externalization of the VP1 unique region (VP1u) from the viral capsid, which mediates receptor engagement. Our prior studies identified AXL as an attachment receptor for B19V. Here, we identify that human transferrin receptor 1 (hTfR) acts as a critical co-receptor that directly binds VP1u and promotes viral internalization. Inhibition of the VP1u-hTfR interaction by competitive binding of hTfR with either an anti-hTfR monoclonal antibody or human ferritin significantly reduces B19V internalization and replication in ex vivo-expanded EPCs, highlighting a link between VP1u binding to the apical domain of hTfR and viral internalization. RBD mutants that disrupt its interaction with hTfR barely inhibited B19V infection in EPCs. These findings support a receptor-switch model in which AXL mediates attachment and hTfR drives internalization. Defining these mechanisms provides a foundation for developing antiviral strategies targeting B19V entry into EPCs.

microbiology↗

bioRxiv2026

Single-Platform Nanopore Sequencing Enables Diploid Telomere-to-Telomere Genome Assembly and Haplotype-Resolved 3D Chromatin Maps

Telomere-to-telomere (T2T) genome assembly has transformed human genomics by resolving centromeres, segmental duplications, and other previously inaccessible regions. However, most diploid T2T assemblies rely on the combination of multi-platform sequencing strategies including short read genome sequencing, PacBio HiFi, Oxford Nanopore ultra-long reads, and chromatin conformation capture data (Hi-C), limiting both scalability and accessibility. Here, we present a streamlined Nanopore-only workflow for diploid human T2T assembly using three ultra-long and one Pore-C PromethION flow cell per individual. Across 23 genetically diverse individuals, we generated 360 gapless chromosomes and 446 near-complete T2T scaffolds, achieving median consensus accuracy of QV50 without Duplex sequencing or hybrid polishing. Assembly continuity, gene completeness, and structural variant detection were comparable to multi-platform Human Pangenome Reference Consortium assemblies. Pore-C data enabled chromosome-scale haplotype phasing without parental information and supported generation of haplotype-resolved chromatin contact maps. Integrated methylation and 3D genome analyses revealed allele-specific chromatin organization at imprinted loci and clear signatures of X-chromosome inactivation. Our openly accessible dataset expands public T2T resources and demonstrates that reference-grade diploid assemblies, phased methylomes, and 3D genome maps can be derived from a single sequencing platform. This approach reduces technical barriers and supports scalable population and functional genomics in the T2T era.

genomics↗

bioRxiv2026

Interactome mapping in human excitatory neurons reveals novel risk genes and pathways in Alzheimer's disease

Alzheimers disease (AD) is an irreversible neurodegenerative disease defined by its molecular hallmarks - amyloid beta peptide plaques and neurofibrillary Tau tangles. Despite significant progress that has been made in uncovering a large number of genetic risk factors through extensive genomic sequencing and genetic studies, the molecular mechanisms driving AD-associated pathology and cognitive decline remain poorly understood. Therefore, alongside the identification of more risk genes, it is also paramount to study how these genes function and influence each other within the cellular pathways and overall molecular networks in AD-relevant brain cell types. However, current human protein-protein interactome datasets were all generated in either yeast or generic human cell lines. Consequently, many important neuronal interactions, especially neuron-specific ones, have yet been discovered. To address this critical gap, we developed a highly scalable, high-quality interactome mapping pipeline in human excitatory neurons derived from induced pluripotent stem cells (iPSC), and generated a comprehensive, neuron-specific interactome map, named ADNeuronNet, for key AD risk genes. ADNeuronNet consists of 1,767 high-confidence interactions among 1,189 proteins and is the only dataset enriched with neuron-specific genes when compared to known protein interactions, including previous large-scale interactome maps, for the same baits in the literature. Within ADNeuronNet, we identified 1,375 novel interactions, many of which are likely neuron specific. For example, we identified a neuron-specific interactor, RIN2, for major AD risk factor BIN1 and confirmed RIN2s function in recruiting BIN1 to RAB5 positive early endosomes, a process that has been well-associated with AD etiology. Additionally, we performed quantitative interaction perturbation analyses on AD risk genes with AD-associated mutations or isoforms and identified significant changes in 99 protein interactions among 11 different protein variants. Finally, we found that subunits from the anaphase-promoting complex/cyclosome (APC/C), another novel BIN1 interactors identified by ADNeuronNet, mediated modulation of Tau-aggregation in neurons via regulation of APOE expression, uncovering a previously unrecognized BIN1-APC/C-APOE regulatory axis in AD pathobiology. In summary, these findings illustrate how our neuron-specific ADNeuronNet can be leveraged to uncover new risk gene candidates and cellular pathways that help advance our understanding of molecular mechanisms underlying AD etiology.

systems biology↗

bioRxiv2026

Multi-Omic Analyses of Dietary Fatty Acid-Microbe-Host Interactions Reveal Metaorganismal Lipid Metabolic Crosstalk Impacting Cardiometabolic Disease

Following a meal, our gut microbiome and human cells collaborate via metaorganismal metabolic circuits to produce diverse nutrient metabolites that systemically circulate to influence health and disease. Although there are now several examples of bacterial fiber-, amino acid-, and micronutrient-derived metabolites impacting cardiometabolic disease, very little is known in regards to how diet-microbe-host interactions impact lipid homeostasis. Here we address this by defining dietary fatty acid substrate availability in germ-free versus conventionally-raised mice coupled to deep multi-omic metabolic phenotyping. Our data demonstrate that the effects of dietary saturated (SFA), monounsaturated (MUFA), and polyunsaturated fatty acids (PUFA) on the host lipidome, transcriptome, proteome and metabolome are uniquely impacted by resident microbiota. Also, the hepatic levels of both pro-inflammatory and pro-resolving lipid mediators are strongly influenced by dietary fatty acid-microbe interactions. This study presents a unique resource to the nutrition and metabolism research community to advance our understanding of metaorganismal lipid metabolism. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/705588v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@4fc7e3org.highwire.dtl.DTLVardef@1cc1dc8org.highwire.dtl.DTLVardef@1b7648dorg.highwire.dtl.DTLVardef@12a8088_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGRAPHICAL ABSTRACTC_FLOATNO C_FIG

biochemistry↗

bioRxiv2025

Dysregulation of innate immunity and cellular metabolism through virus-induced deISGylation

Interferon-stimulated gene 15 (ISG15) regulates diverse cellular responses including antiviral immunity through its conjugation to proteins, a process known as ISGylation. Several pathogens, including SARS-CoV-2, subvert ISGylation by encoding deISGylating enzymes. However, the direct targets and physiological consequences of coronaviral deISGylation remain poorly defined. Here, we ablated the deISGylating activity of the SARS-CoV-2 papain-like protease (PLpro) and found that loss of deISGylation boosted innate immune activation, attenuated virus replication, and promoted viral clearance in human cells and in mice. Through untargeted metabolomics and ISGylome proteomics analyses, combined with functional studies, we discovered in molecular detail how the activities of key metabolic enzymes in glycolysis, the pentose phosphate pathway, and oxidative stress are controlled by PLpro deISGylation. These findings provide fundamental new insight into how reversible ISGylation regulates immunity and metabolic processes at the molecular level and highlight viral deISGylation as a major viral tactic for rewiring immunometabolism.

microbiology↗

bioRxiv2025

Differential inclusion formation of an aggregation-prone protein reveals differences in the proteostasis capacity of neuronal cell lines

Maintaining proteome integrity is essential for cellular function and survival. Disruptions in proteostasis lead to the aggregation of proteins into inclusions, a process that underlies many neurodegenerative diseases. To quantitatively assess the proteostasis capacity of neuronal cells, we employed an aggregation-prone double mutant form of firefly luciferase (denoted FlucDM) as a reporter protein. We compared two commonly used neuronal cell lines, mouse neuroblastoma cells (Neuro-2a) and a motor neuron-like hybrid line (NSC-34), to evaluate their ability to prevent the aggregation of proteins into intracellular inclusions. We observed a significantly greater propensity of FlucDM to form inclusions in NSC-34 cells compared to Neuro-2a cells. This suggests a reduced capacity of NSC-34 cells for managing aggregation-prone proteins. Proteomic profiling of FlucDM inclusions purified from both cell types revealed cell-type-specific engagement of the proteostasis machinery with aggregation-prone proteins. Comparing the proteomic profiles of key arms of the proteostasis network between these two cell lines revealed that the endoplasmic reticulum (ER) unfolded protein response is differentially expressed. This study establishes a quantitative platform for assessing cellular proteostasis capacity and underscores the importance of cell-type context in proteome maintenance. These insights have implications for understanding the selective vulnerability of neurons in protein misfolding disorders.

cell biology↗

bioRxiv2025

Cell type-specific master metabolic regulators of Alzheimer's disease

Alzheimers disease (AD) exhibits metabolic heterogeneity; yet, the consequences on metabolic dynamics in a cell-type-specific manner and the underlying metabolite-sensor network basis remain unclear. Here, we show that neurons exhibit a striking decrease in energy and lipid-related metabolic activity, contrasted by an increase in microglial metabolism associated with neuroinflammation. To identify cell-type specific master metabolic regulators of AD underlying the metabolic alterations in AD, we introduce scFUMES (single cell FUnctional MEtabolite-Sensor), an algorithm integrating single-cell RNA sequencing, interactomics, genomics, transcriptomics, and metabolomics from human brain biobanks. Applied to two AD-vulnerable regions (middle temporal gyrus and dorsolateral prefrontal cortex), scFUMES uncovers hundreds of AD-associated regulators, with neurons and microglia showing the most interactions. Particularly, scFUMES pinpoints genetics-informed master metabolic regulators across AD severity, sex and APOE genotype (e.g., PPARD-glycerol in microglia). Experimental testing reveals that two interaction pairs predicted by scFUMES, neuronal palmitic acid bound fatty acid binding protein 3 and gut metabolite indole-3-propionic acid binding to kynurenine aminotransferase 1, both lower pathological tau species in AD. Collectively, scFUMES systematically maps AD master metabolic regulators, offering insights into cellular metabolic heterogeneity and therapeutic strategies for AD and other AD-related dementia if broadly applied.

systems biology↗

bioRxiv2025

DrugLM: A Unified Framework to Enhance Drug-Target Interaction Predictions by Incorporating Textual Embeddings via Language Models

MotivationAccurate prediction of drug-target interactions (DTIs) is central to computational drug discovery, offering the potential to reduce experimental costs and accelerate development timelines. While existing deep learning approaches such as Graph Neural Networks and Transformers have shown promise, they often overlook the rich semantic information embedded in textual descriptions of drugs and targets. These descriptions encode critical biomedical knowledge, including mechanisms of action, biological pathways involved, and therapeutic effects of drugs, which can enhance DTI prediction performance. ResultsWe introduce DrugLM, a unified framework that integrates embeddings derived from large language models (LLMs) into DTI-specific model architectures. DrugLM leverages textual descriptions of drugs and targets to generate semantic embeddings using a range of pretrained LLMs. These embeddings can be seamlessly incorporated into existing DTI models. We systematically evaluate multiple LLMs on benchmark DTI datasets and demonstrate strong performance even without fine-tuning. Moreover, supervised parameter-efficient fine-tuning of the LLMs further improves embedding quality, leading to enhanced prediction accuracy. Notably, a simple multilayer perceptron (MLP) using only LLM-derived embeddings surpasses several established DTI methods, underscoring the power of semantic features. Our findings highlight the practical value of integrating LLMs into DTI pipelines and offer a straightforward recipe for improved drug discovery: LLM embeddings of drugs and targets are both effective and easy to use. AvailabilityOur code and dataset are available at https://github.com/ShPhoebus/DrugLM

bioinformatics↗

bioRxiv2025

Metastatic niche mediated activation of metastasis initiating cells in ovarian cancer through miR-193b-3p downregulation via the ERK/EZH2/DNMT1 axis

Extensive metastasis at the time of diagnosis is a major contributor to the poor prognosis of ovarian cancer (OC) patients. There is a critical need to better understand the mechanism of regulation of metastasis to develop effective treatment strategies targeting the process. Metastasis initiating cells (MICs) have cancer stem cell-like properties along with the ability to invade. Their potential role in OC is unique as the dissemination from the primary tumors involves passive processes like exfoliation. However, the role of MICs during OC metastatic colonization is critical and poorly understood. Using an organotypic 3D culture model of the human omentum, we have studied the productive crosstalk between OC MICs and the metastatic microenvironment. We report the role of miR-193b-3p, a clinically relevant metastasis suppressor microRNA, which is downregulated in the OC by paracrine signals from the microenvironment, inducing the MIC phenotype. Using heterotypic coculture models, conditioned medium experiments, secretome analysis, inhibition, and rescue experiments, we show that bFGF and IGFBP6 secreted by mesothelial cells in the microenvironment induce miR-193b-3p downregulation in OC MICs via the ERK/EZH2/DNMT1 axis. The miR-193b-3p downregulation induced an increased expression of its target cyclin D1, which imparted a cancer stem cell phenotype. Urokinase, another target of miR-193b-3p, induced invasive growth. Together, these targets impart the MIC phenotype to the OC cells. miR-193b-3p replacement therapy could suppress metastasis in a patient derived xenograft model of OC metastasis, indicating the translational potential of this approach to target MICs in OC patients.

cancer biology↗

bioRxiv2025

Promoting social connectedness through multi-person neurofeedback

Humans are inherently driven to build meaningful relationships, but attempts to socially connect with others are not always successful. This study investigates whether social connectedness can be improved by intentionally regulating inter-brain coupling, a neural correlate of successful social interactions. Using a multi-person neurofeedback system (i.e., a multi-brain computer interface), we showed dyads real-time visualizations of the extent to which their brainwaves (EEG signals) were "in sync". Our results showed that, compared to a sham control group, dyads who received multi-brain neurofeedback exhibited an increase in inter-brain coupling, and, critically, that this increase was associated with a higher sense of social connectedness. A chain mediation analysis suggested that this experience of enhanced social connectedness may have been driven by a sense of joint control and shared intentionality. Together, our findings showcase the potential for regulating inter-brain coupling to optimize human social relationships and behaviors.

neuroscience↗

bioRxiv2025

Mitochondrial dysfunction in Machado Joseph disease: insights from a multi-model system

Spinocerebellar ataxia type-3 (SCA3), also known as Machado Joseph disease, MJD) is a fatal, neurodegenerative disease belonging to the polyglutamine repeat disease family, caused by inheritance of an abnormal form of the ATXN3 gene, carrying a longer than usual trinucleotide repeat sequence. Within this study we explored mitochondrial function in a range of different experimental models of MJD, including transgenic zebrafish, mice and neuronal cells, to gain an understanding of mitochondrial function in the disease, and possible mechanisms of any dysfunction. Firstly, we examined the transgenic CMVMJD135 mouse model that develops impaired movement, neurodegeneration and decreased survival. We performed proteomic analysis on brain lysates extracted from a cohort of male and female WT and MJD mice, for analysis of differences in male and female mice separately. We identified that a major difference predicted by Ingenuity Pathway Analysis to be in both male and female MJD mice was related to impaired oxidative phosphorylation and mitochondrial dysfunction. We examined primary neuron cultures obtained from CMVMJD135 mice, validating the findings of the proteomic analysis, and finding changes to mitochondrial morphology, as well. We further examined a transgenic zebrafish model of MJD that expresses EGFP fused human ataxin-3 with short or long polyQ stretches (23 or 84Q, respectively) in neurons (expression driven under the elav/HuC promoter). The MJD zebrafish also exhibit altered mitochondrial electron transport chain complex protein levels, together with enhanced sensitivity to rotenone administration, which may be a valuable readout for treatment investigation studies in the future. Together, this study confirms, and extends on, the growing body of evidence suggesting that mitochondrial dysfunction plays a role in MJD, warranting investigation for therapeutic intervention.

neuroscience↗

bioRxiv2025

Gene regulatory logic of the interferon-β enhancer contains multiple selectively deployed modes of transcription factor synergy

Type I interferon IFN{beta} is a key regulator of the immune response, and its dysregulated expression causes disease. The regulation of IFN{beta} promoter activity has been a touchpoint of mammalian gene control research since the discovery of functional synergy between two stimulus-responsive transcription factors (TFs) nuclear factor kappa B (NF{kappa}B) and interferon regulatory factors (IRF). However, subsequent gene knockout studies revealed that this synergy is condition-dependent such that either NF{kappa}B or IRF activation can be dispensable, leaving the precise regulatory logic of IFN{beta} transcription an open question. Here, we developed a series of quantitative enhancer states models of IFN{beta} expression control and evaluated them with stimulus-response data from TF knockouts. Our analysis confirmed that TF synergy is a hallmark of the regulatory logic but that it need not involve NF{kappa}B, as synergy between two adjacent IRF dimers is sufficient. We found that a sigmoidal binding curve at the distal site renders the dual IRF synergy mode ultrasensitive, allowing it only in conditions of high IRF activity upon viral infection. In contrast, the proximal site has high affinity and enables expression in response to bacterial exposure through synergy with NF{kappa}B. However, its accessibility is controlled by the competitive repressor p50:p50, which prevents basal IRF levels from synergizing with NF{kappa}B, such that NF{kappa}B-only stimuli do not activate IFN{beta} expression. The enhancer states model identifies multiple synergy modes that are accessed differentially in response to different immune threats, enabling a highly stimulus-specific but also versatile regulatory logic for stimulus-specific IFN{beta} expression. SIGNIFICANCEPrecise regulation of the immune cytokine IFN{beta} is essential for human health. Classic studies established that the transcription factors NF{kappa}B and IRF function synergistically in activating IFN{beta} expression. However, more recent data revealed that either factor may be dispensable in certain conditions, leaving the regulatory logic of IFN{beta} transcription an open question. In this study, we evaluated several quantitative models to determine what regulatory logic can account for the available data. We found that the enhancer exhibits multiple synergy modes with specific transcription capabilities that are deployed in a condition-dependent manner. The resulting IFN{beta} regulatory logic model reveals how stimulus-specificity is achieved, and may be tuned, thereby overcoming a bottleneck in predictive modeling the control of innate immune responses.

systems biology↗