Biology subjects

Bai, F.

Publications and source records attributed to Bai, F..

At least 19 recordsLinked to original sources

bioRxiv2026

Glioblastoma Hijacks Astrocyte Ribosomes to Feul Malignancy through Translatome Reprogramming

Cancer cells demand elevated protein synthesis, yet whether they directly requisition ribosomes from microenvironmental host cells remains unknown. Here, utilizing in vivo and in vitro ribosome tracing, we show that glioblastoma (GBM) cells hijack ribosomes from surrounding astrocytes via tunneling nanotube-like structures. This transfer supports GBM malignancy in both murine and patient derived models. Single cell RNA sequencing along with whole cell and cell source traceable ribosome profiling reveal that transferred ribosomes are translationally active and selectively reprogram the tumor translatome, prioritizing cell-cycle genes and driving interferon-response-mediated immune evasion. Through a genome wide CRISPR screen, we identify INTS12 as a critical mediator of ribosome transfer. Genetic inactivation or AAV-mediated knockdown of INTS12 impairs ribosome uptake, curbs translation and proliferation, remodels the immunosuppressive landscape, and extends survival in orthotopic models. Our study uncovers a parasitic translation-support mechanism in GBM, establishing INTS12 as a therapeutic vulnerability to disrupt ribosome transfer.

cancer biology↗

bioRxiv2026

IL-17A Restrains Antiviral Immunity to Promote Chikungunya Virus Infection and Pathogenesis in the Heart

Chikungunya virus (CHIKV) infection is increasingly linked to cardiovascular complications, but the mechanisms underlying CHIKV-induced cardiovascular disease (CVD) remain unclear, and targeted therapies are lacking. Although elevated interleukin-17A (IL-17A) levels have been reported in CHIKV patients and associated with cardiovascular pathology, its role in CHIKV-induced cardiac disease is poorly defined. To address this question, we employed our newly developed heterozygous interferon /{beta}/{gamma} receptor-deficient (Ifnag+/-) mice and primary human cardiac fibroblasts to investigate the contribution of IL-17A signaling to CHIKV-associated cardiac pathology. We found that CHIKV infection induced IL-17A production in the heart, and that mice deficient in Il17a (Il17a-/-) and in its receptor gene, Il-17ra (Il17ra-/-), exhibited marked resistance to CHIKV infection in both cardiac tissue and primary cardiac fibroblasts. Genetic deletion of IL-17A signaling significantly enhanced type I interferon responses and decreased viral burden in mouse hearts. Interestingly, blockade of IL-17RA with an FDA-approved monoclonal antibody for plaque psoriasis, Brodalumab, drastically increased type I interferon production and reduced viral replication in both human cardiac fibroblasts and human embryonic kidney 293 (HEK 293) cells. In addition, inhibition of IL-17A signaling suppressed the expression of pro-inflammatory mediators, including Il-1{beta}, Tnf-, and Cxcl2, reduced immune cell infiltration into cardiac tissue, and mitigated cardiac injury. Importantly, therapeutic blockade of IL-17A signaling after CHIKV infection reduced viral replication in both the heart and circulation. Collectively, these findings identify IL-17A signaling as a critical regulator of CHIKV replication and cardiac inflammation and highlight the IL-17A/IL-17RA axis as a promising therapeutic target for CHIKV-associated cardiovascular disease. ImportanceChikungunya virus (CHIKV) infection has been frequently associated with cardiovascular complications, yet the host pathways that promote viral infection and cardiac injury remain poorly understood. Here, we identify IL-17A signaling as a previously unrecognized regulator of CHIKV pathogenesis in the heart. Using a novel heterozygous interferon receptor-deficient mouse model and primary human cardiac fibroblasts, we demonstrate that IL-17A signaling facilitates CHIKV replication via suppressing antiviral type I interferon responses. Genetic deletion or pharmacological blockade with an FDA-approved monoclonal antibody of IL-17A signaling reduced viral burden, attenuated inflammatory cytokine production, limited immune cell infiltration, and protected against cardiac injury. Importantly, therapeutic inhibition of IL-17A signaling after infection remained effective in reducing viral replication in both cardiac tissue and circulation and mitigating cardiac damage. These findings reveal a critical role for the IL-17A/IL-17RA axis in linking antiviral immunity to CHIKV-induced cardiovascular disease and identify a potential translatable therapeutic target for CHIKV-caused cardiac complications.

immunology↗

bioRxiv2026

Damaging RBM20 E-rich domain variants are not rescued by gene replacement

The promise of precision therapeutics in genetic cardiomyopathies relies on linking specific therapies to variant mechanisms. Missense variants in the cardiac splice regulator RBM20 cause a highly penetrant and arrhythmogenic dilated cardiomyopathy. Disease-causing variants in RBM20s arginine-serine rich (RS) domain act via formation of toxic gain of function cytoplasmic granules, but this is not true for a small number of clinically adjudicated pathogenic variants in its glutamate(E)-rich domain. To better define the effects of E-rich domain variants, we developed a scalable screen based on induced pluripotent stem cell (iPSC) cardiomyocyte differentiation that identified several additional damaging variants. Several of these reduced RBM20 protein abundance and stability. We therefore hypothesized that, unlike RS domain variants, these E-rich variants might be rescued by RBM20 overexpression. To test this hypothesis, we generated induced pluripotent stem cells (iPSCs) from a patient with a pathogenic E-rich domain variant (p.E913K), and confirmed reduced RBM20 protein expression in these RBM20+/p.E913K cells after differentiation to iPSC-derived cardiomyocytes (iPSC-CM, vs. engineered isogenic RBM20+/+). These iPSC-CMs also displayed aberrant transcriptional splicing, reduced contractility, increased calcium-induced calcium release, and nuclear localization of RBM20 protein, often with more than the two expected RBM20-centric splice factories. AAV-based overexpression of RBM20 reversed some, but not all of the mis-splicing events identified in RBM20+/p.E913K iPSC-CMs, and did not improve their abnormal contractility, calcium handling or supernumerary RBM20 nuclear granules. In summary, our data indicate that pathogenic E-rich domain variants reduce RBM20 protein abundance, but that their mechanism is unlikely to be explained by haploinsufficiency alone.

genetics↗

bioRxiv2026

A GPX4 phosphorylation switch by FGFR1 guards against ferroptosis

Ferroptosis is driven by lipid peroxidation, yet the mechanisms by which cells rapidly adjust their sensitivity to ferroptosis in response to extracellular cues remain elusive. We identify a direct phosphorylation switch controlling the activity of glutathione peroxidase 4 (GPX4), the core ferroptosis regulator. The receptor tyrosine kinase FGFR1 directly binds and phosphorylates GPX4 at Tyr180/Tyr196 in a kinase-dependent manner, requiring its Tyr730 as a docking site. This phosphorylation enhances GPX4s catalytic activity and suppresses ferroptosis. In cardiac ischemia/reperfusion injury, the FGFR1-GPX4 axis is suppressed, and a selective FGFR1 agonist (FGF-1{Delta}NT) reactivates it to protect against ferroptosis-mediated damage. Critically, a phosphorylation-deficient GPX4 knock-in mouse exhibits hypersensitivity to injury and non-responsive to this agonist, proving that GPX4 phosphorylation is essential. Our findings reveal a rapid mechanism for regulating ferroptosis via GPX4 tyrosine phosphorylation, directly linking receptor tyrosine kinase signaling to ferroptosis, and offering new strategies for treating ischemic-and other ferroptosis-associated diseases.

Cell Biology↗

bioRxiv2026

Rapid and robust sex determination from ancient enamel proteomes using protSexInferer

Accurate biological sex determination of ancient remains is critical for archaeological, anthropological, and forensic studies, but remains challenging for morphologically ambiguous and highly degraded endogenous DNA samples. Paleo-proteomics sex identification approaches, targeting sexually dimorphic amelogenin isoforms (AMELX and AMELY), present a promising solution. However, current workflows rely on manual verification of a few specific peptide markers, a process that lacks standardization and is susceptible to false-positive AMELY signals. To overcome these limitations, we developed protSexInferer, a lightweight, open-source bioinformatic pipeline for automated sex estimation from paleo-proteomic data. Our method uses the ratio of AMELY-specific peptides to all detected AMELY- and AMELX-specific peptides (i.e., the RAMELY value) rather than the mere presence or absence of AMELY signals for sex classification. We demonstrated that the RAMELY value clearly distinguishes male and female individuals in both reference and independent validation datasets, enabling reliable sex assignments even in cases where conventional intensity-based comparisons (e.g., AMELY-59M vs. AMELX-60) are ambiguous. This ratio-based approach effectively mitigates the impact of false-positive AMELY signals, therefore eliminating the need for time-consuming manual verification, and remains reliable even for samples with low peptide yields. Equipped with pre-constructed protein reference databases, protSexInferer provides a robust, standardized, and end-to-end solution for paleo-proteomic sex determination.

paleontology↗

bioRxiv2026

Dual Inhibition of MYRF Cleavage by Its JM Region and PAN-1 CCT Gates Developmental Timing in C. elegans

Post-embryonic development proceeds through discrete stages, yet the mechanisms that coordinate transitions between stages remain incompletely defined. The transmembrane transcription factor MYRF undergoes intramolecular cleavage to release a nuclear-localized fragment essential for developmental progression in C. elegans. Previously, we showed that PAN-1 as a key partner required for MYRF activity during development. PAN-1 promotes MYRF trafficking to the cell membrane--an essential step for MYRF cleavage--through interactions between their extracellular domains (Xia et al., 2021). Here, we show that MYRF-1 cleavage and nuclear translocation oscillate with larval stage transitions in C. elegans, peaking mid-to-late stage and being suppressed during molts. Using endogenous gene editing and mutant reporters, we identify an uncharacterized juxtamembrane (JM) region in MYRF-1 that self-inhibits cleavage. JM deletion triggers premature MYRF-1 nuclear entry, early lin-4 activation, growth defects, and adult lethality. We further demonstrate that the cytoplasmic tail (CCT) of the transmembrane protein PAN-1 acts as a predominant trans-inhibitor of MYRF-1 cleavage, coupling extracellular association with cytoplasmic inhibition. PAN-1 CCT deletion causes near-constitutive MYRF-1 nuclear accumulation, leading to premature lin-4 activation, accelerated M-cell division, and larval lethality. Removing these inhibitory mechanisms on MYRF-1 cleavage overrides nutrient-responsive developmental checkpoints. These findings uncover dual inhibitory mechanisms governing MYRF-1 cleavage and establish MYRF-1 cleavage as a key gatekeeper of developmental timing.

developmental biology↗

bioRxiv2025

Genomic rearrangements at the MAT locus suggest reproductive shifts in Rhodotorula yeasts

Transitions from canonical outcrossing to rare, cryptic, or noncanonical reproduction are widespread in fungi, but how mating-type (MAT) systems are reorganized at the genomic and population levels during these shifts remains unclear. The coexistence of sexually reproducing species and putatively asexual lineages makes Rhodotorula a natural comparative system for addressing this question. We analyzed 249 globally sampled strains using a combination of long-read and short-read sequencing. Phylogenomics resolved three major clades and several closely related species complexes. Chromosome-scale assemblies confirmed physical separation of the pheromone/receptor (P/R) and homeodomain (HD) loci, whereas non-random P/R-HD associations revealed constrained tetrapolar inheritance. The P/R locus showed conserved synteny within mating types but extensive structural divergence between A1 and A2 alleles, whereas the HD locus remained compact and conserved. Mating-type distributions varied across clades, with both A1 and A2 present in Clade C, lineage-structured partitioning in Clade B, and pronounced A2 dominance in Clade A. Genome-wide linkage disequilibrium (LD) decay in putatively asexual R. mucilaginosa, although slower than in sexual R. diobovata, was consistent with historical recombination in a species without an observed sexual cycle. Clade A further exhibited deep trans-specific polymorphism of STE3.A2 and relaxed purifying selection, mosaic A2 P/R configurations retaining RHA.A1, A1/A2 and A2/A2 hybrid genomes, and A2-associated gene content beyond MAT loci. In conclusion, our findings underscore the dynamic nature of MAT-locus remodeling in Rhodotorula and establish this genus as a valuable model for investigating transitions from heterothallism toward reproductive strategies less dependent on opposite-type partners.

evolutionary biology↗

bioRxiv2025

Genomic Regions and Variant Analysis Reveal Candidate Genes Associated with Age at First Service in Chinese Holstein Heifers

Understanding the genetic basis and identifying quantitative trait loci (QTL) for age at first service (AFS) is essential for improving reproductive efficiency and reducing economic costs in heifers rearing. We conducted a genome-wide association study (GWAS) for AFS using the genomic estimated breeding values (GEBVs) of 3,686 Chinese Holstein heifers, genotyped with 7,964,217 single nucleotide polymorphisms (SNPs) after quality control. Significant SNPs and candidate genes were identified and investigated through colocalization analysis of GWAS, expression QTL (eQTL), and splicing QTL (sQTL), and expression analysis in blood RNA sequencing (RNA-seq). The heritability estimate for AFS was moderate at 0.276 {+/-}0.025. Three QTL regions associated with AFS were identified: Region 1 on BTA6 (43688837-45007127 bp, 1.3 Mb with three 200kb windows), explaining 0.47% of genetic variance; Region 2 on BTA6 (62770788-62967316 bp) explaining 0.27% of the genetic variance; and Region 3 on BTA18 (6299721-6498934 bp) explaining 0.17% of the genetic variance. Combining GWAS and colocalization analysis, we identified ANAPC4, RBPJ, SEPSECS, SLC34A2, ZCCHC4, CCDC149, GNPDA2, GUF1, DHX15, SOD3, GUF1 and GNPDA2 as candidate genes. These genes are enriched in signaling pathways such as progesterone-mediated oocyte maturation, parathyroid hormone synthesis, secretion and action, and selenocompound metabolism. ANAPC4, DHX15, GUF1, SEPSECS, and SOD3 were also differently expressed genes (DEGs) in blood RNA-seq. Integrating the GWAS, colocalization, differential expression analysis, and existing literature, ANAPC4 and rs136363104 were highlighted as the putative causal gene and variant for puberty, respectively. In conclusion, our study identified three candidate regions and 12 candidate genes, confirming ANAPC4 as a putative causal gene influencing AFS. This research enhances the understanding of the genetic basis of AFS in Chinese Holstein heifers. The identified key genomic regions, candidate genes, and variants have the potential to improve reproductive efficiency and reduce economic costs in heifer rearing. Interpretative summaryThe economic burden of heifer-raising and reproductive inefficiency in dairy cattle is evident. The most important strategy for optimizing heifer-raising is selecting heifers with earlier puberty (sexual maturity) to shorten age at first service (AFS). In this study, we have identified key genomic regions and candidate genes on AFS in Chinese Holstein heifers by genome-wide association study, and validated them by colocalization and RNA-seq analysis. The findings have the potential to enhance the understanding of the genetic basis of reproductive traits, leading to more targeted breeding strategies for improved reproductive efficiency.

genetics↗

bioRxiv2025

Disulfide cross-linked redox-sensitive peptide condensates are efficient cell delivery vehicles of molecular cargo.

Biomolecular condensates (BCs) are phase-separated viscoelastic hubs within demixed solutions enriched in proteins and nucleic acids. Such condensates, also called membraneless organelles, are increasingly observed in cells and serve as transient hubs for spatial organization and compartmentalization of biomolecules. Along with the transiency of formation and dissolution, their ability to sequester molecules has inspired us to develop BCs as potential vehicles to transport and deliver molecular cargo. We recently reported the design of disulfide bond cross-linked phase-separating peptide (PSP) condensates that spontaneously dissolve in reducing conditions (JACS, 2024, 146, 255299). Based on the premise that the highly reducing cytoplasm could dissolve PSP condensates and release partitioned cargo, here, we demonstrate the ability of PSP condensates to deliver molecular cargo to the cytoplasm of HeLa cells efficiently. We show that PSP condensates deliver a variety of cargos that differ in their sizes and chemistries, including small molecules, peptides, GFP protein (31 kDa), DNA (1.7 kbp), and mRNA. The transfection efficiencies of PSP condensates for delivering DNA and mRNA were also significantly greater than those of a commercial transfection agent. With room to tailor the condensate properties based on cargo and cell types, these results showcase the potential of disulfide-cross-linked PSPs as effective and customizable cellular delivery vehicles, filling a critical demand gap for such delivery systems.

biophysics↗

bioRxiv2025

Testicular mRNA-LNP Delivery: A Novel Therapy for Genetic Spermatogenic Disorders

Uniform testicular maturation arrest is a severe form of male infertility characterized by the presence of germ cells that do not complete spermatogenic development. It is usually caused by meiotic arrest with genetic variants and difficult to treat via drugs or surgery. mRNA-lipid nanoparticle (LNP) delivery is a promising therapeutic option for maturation arrest with monogenic variants via protein replacement therapy. Herein, a spermatocytes-tropic LNP (Pool1-LNP3) was identified via a library of 30 ionizable lipids screening. And in vivo delivery of this novel LNP composition using rete testis microinjection was showed to be high spermatocytes targeting with high transfection efficiency. Thereafter, it was revealed that in vivo delivery of Pool1-LNP3 encapsulating Msh5 mRNA could promote crossover formation and restore spermatogenesis in Msh5D486Y/D486Y mouse models with DSB recombination defects. Notably, the offspring without genomic integration was born using intracytoplasmic sperm injection (ICSI) derived from rescue of Msh5D486Y/D486Ymouse and embryo transfer. Furthermore, no obvious inflammation and histologic damage in any tissue were detected after in vivo delivery of mRNA-LNP. In addition, it was demonstrated that Maps mRNA-LNP3 recovered spermatogenesis in Maps KO mouse with meiotic arrest. Altogether, these findings suggested that this spermatocytes-tropic mRNA-LNP delivery could become a viable and broad applicable strategy for treatment of spermatogenic disorders with genetic defects, providing a foundation for future clinical application.

molecular biology↗

bioRxiv2025

PhysDock: A Physics-Guided All-Atom Diffusion Model for Protein-Ligand Complex Prediction

Accurate prediction of protein-ligand complexes remains a central challenge in structural biology. Traditional methods are computationally inefficient and prone to local minima, whereas deep learning approaches struggle to capture structural flexibility and physical plausibility. We introduce PhysDock, a physics-guided diffusion model that uniquely integrates (i) all-atom diffusion to model ligand flexibility and protein precision-flexibility (i.e., subtle conformational adjustments); (ii) physical priors as diffusion conditioning, alongside two-phase physics guidance during the denoising diffusion to ensure physical plausibility. PhysDock demonstrates state-of-the-art performance in redocking benchmarks and excels in the more challenging cross-docking assessments. For practical utility, PhysDock (i) resolves cannabinoid receptor selectivity across diverse molecules, achieving accuracy comparable to experiments; (ii) distinguishes most drug candidates from weak binders in virtual screening of NTRK3 kinase, while uncovering novel candidates with structural insights. PhysDock serves as a versatile tool for protein-ligand complex prediction, with substantial potential to accelerate structure-based drug discovery.

bioinformatics↗

bioRxiv2025

Senescence-induced reparative fibroblasts enable scarless wound healing in aged murine skin.

It has been reported that elderly individuals exhibit reduced scarring during the wound healing process compared to younger adults. However, the underlying mechanisms responsible for this phenomenon remain poorly understood. Here, we revealed that aged mice exhibited more pronounced regenerative outcomes compared to young mice, characterized by increased hair follicle numbers and collagen fiber features closer to normal skin. Single-cell sequencing identified a reparative fibroblast subpopulation (Prss35+Fib) enriched in the aged group, which promotes regeneration through communication with epithelial cells, macrophages, and T cell subpopulations via PTN and EREG signaling. Spatial transcriptomics validated this communication pattern by elucidating cell proximity and locating the regenerative niche in the upper dermis. Finally, EREG treatment significantly enhanced regenerative outcomes in young mice, while the small wound model of aged mice, lacking the reparative fibroblast and EREG signaling, failed to achieve regeneration. Collectively, our findings advance the understanding of regenerative plasticity in aging and provide new insights for designing scarless therapeutic strategies.

cell biology↗

bioRxiv2025

Tumor hypoxia adaptation depends on FLAD1 mediated mitochondrial metabolic reprogramming

Hypoxia, a hallmark of solid tumors, promotes the malignant progression and is challenging to target. Metabolic reprogramming and the resulting metabolic vulnerabilities provide a promising strategy to target tumor hypoxia. Here we systematically compared the metabolic network differences between hypoxic and non-hypoxic cells, and developed a deep learning model, "DepFormer", to predict the dependent metabolic genes in hypoxic tumor cells. The performance of DepFormer was validated using CRISPR screening dataset. Oxidative phosphorylation was identified as the most significantly hypoxia-dependent metabolic pathway, and FLAD1 was predicted to be one of the key hypoxia-dependent metabolic genes. FLAD1 locus is amplified, and FLAD1 expression is upregulated in various tumor types, especially in hypoxic tumors. FLAD1 depletion compromises tumors adaptation to hypoxia by disrupting mitochondrial complex II activity, leading to an imbalance between succinate and fumarate, and consequent failure to adapt to hypoxia. Subsequently, we identified a drug-like inhibitor of FLAD1, which selectively inhibits the growth of tumor cells under hypoxia. Our findings reveal FLAD1 as an innovative therapeutic target for hypoxic tumors.

cancer biology↗

bioRxiv2025

Processing of Genomic RNAs by Dicer in Bat Cells Limits SARS-CoV-2 Replication

Bats are reservoirs for numerous viruses that cause serious diseases in other animals and humans. Several mechanisms are proposed to contribute to the tolerance of bats to these pathogens. This study investigates the response of bat cells to double-stranded RNA generated by SARS-CoV-2 replication. Here, we found the involvement of Dicer in the processing of viral genomic RNAs during SARS-CoV-2 infection. Examining RNA sequencing of infected cells, small-interfering RNA (siRNA)-like fragments were found derived from viral RNAs. Depletion of Dicer showed a reduction in these RNAs and an increase in viral loads suggesting unlike other mammals, bats may use Dicer to limit viral replication. This prompted the exploration of key dsRNA sensors in bat cells. Our analysis showed significant upregulation of OAS1 and MX1 in response to dsRNA, while PKR levels remained low, suggesting alternative dsRNA-response mechanisms are present that eschew the common PKR-based system. These results further show how bats employ distinct strategies for antiviral defense that may contribute to tolerating viral infections. They suggest the involvement of Dicer in antiviral mechanisms in bats, a function not observed in other mammals. This highlights a mechanism for bat originating viruses to evolve features that in other animals could cause extreme antiviral responses such as is seen with SARS-CoV-2. GRAPHICAL SUMMARY O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/632425v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1755d68org.highwire.dtl.DTLVardef@475cb8org.highwire.dtl.DTLVardef@1185813org.highwire.dtl.DTLVardef@13e847a_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

LCORL and STC2 variants increase body size and growth rate in cattle and other animals

Using ancestral recombination graphs, we investigated recent selection signatures in European beef cattle breeds, pinpointing sweep-driving variants in the LCORL and STC2 loci with notable effects on body size and growth rate. The ACT-to-A frameshift mutation in LCORL occurs mainly in central-European cattle, and stimulates growth. Remarkably, convergent truncating mutations were also found in commercial breeds of sheep, goats, pigs, horses, dogs, rabbits, and chickens. In the STC2 gene, we identified a missense mutation (A60P) located within the conserved region across vertebrates. We validated the two natural mutations in gene-edited mouse models, where both variants in homozygous carriers increase the average weight by 11%. Our findings provide insights into a seemingly recurring gene target of body size enhancing truncating mutations across domesticated species, and offer valuable targets for gene editing-based breeding in animals.

genetics↗

bioRxiv2024

PhenoScreen: A Dual-Space Contrastive Learning Framework-based Phenotypic Screening Method by Linking Chemical Perturbations to Cellular Morphology

Phenotypic drug discovery (PDD) screens compounds in cellular models that represent disease-relevant phenotypes, offering a compelling alternative to traditional target-based approaches. Unlike conventional methods, where compounds act on a single predefined target, PDD identifies compounds capable of exerting therapeutic effects through multiple targets and mechanisms. This makes PDD particularly valuable for discovering first-in-class drugs, especially for diseases with poorly understood molecular mechanisms or those lacking validated therapeutic targets. By enabling broader exploration of biological systems and uncovering multi-target drugs (polypharmacology), PDD provides a powerful strategy for tackling complex diseases. In this study, we introduce PhenoScreen, a deep learning framework designed to advance PDD by utilizing large-scale compound-phenotype association data. Through contrastive learning, PhenoScreen connects chemical space with cellular morphological profiles, allowing for accurate prediction of compound-induced phenotypic changes. PhenoScreen can also accurately identfiy lead compounds which could induce user defined phenotypic shift but more novel scaffolds using different levels of phenotypic information reflected by diverse compounds. The model was validated across multiple screening tasks and successfully predicted active compounds inducing user-specified phenotypes with varying inhibitory effects in the osteosarcoma phenotypic model. Further, other than showing effectiveness to osteosarcoma, our experiments also showed that PhenoScreen demonstrated strong generalization to rhabdomyosarcoma, and the active compound we screened had an IC50 of up to 1.842 M, suggesting its ability to capture key phenotypic features shared across cancer cells. These results underscore PhenoScreens potential to accelerate drug discovery by identifying novel therapeutic pathways and increasing the diversity of viable drug candidates. PhenoScreen is accessible online via our groups web server for compound virtual screening at https://bailab.siais.shanghaitech.edu.cn/services/PhenoScreen/, and the source codes are available at https://github.com/Shihang-Wang-58/PhenoScreen.

bioinformatics↗

bioRxiv2024

CIB2 as a Ca2+ Sensor for Auditory Mechano-Electrical Transduction and Linked to Genetic-Heterogeneity of TMC1 in Hearing Loss

Non-syndromic sensorineural hearing loss is characterized by genetic heterogeneity, leading to potential clinical misdiagnosis. TMC1, a unique causative gene associated with deafness, exhibits variants with autosomal dominant and recessive inheritance patterns. TMC1 codes for the transmembrane channel-like 1 (TMC1), a key component of the mechano-electrical transduction (MET) machinery for hearing. However, the molecular mechanism of Ca2+ regulation in MET, which is essential for sound perception, remains unclear. CIB2, another MET component associated with deafness, can bind with calcium and may play a role in MET gating. Our study reveals that the TMC1-CIB2 complex undergoes a Ca2+-induced conformational change, highlighting the crucial role of Ca2+ in MET. We identified a vertebrate-specific binding site on TMC1, named CR3, that interacts with apo CIB2, with the binding interface linked to hearing loss. Using an in-vivo animal model, we demonstrated that disruption of the calcium-sensing site of CIB2 perturbs the MET channel conductivity, confirming its role as a Ca2+ sensor for MET. Additionally, after systematically analyzing the hearing-loss variants, we observed that dominant mutations of TMC1 are often located near the ion pore or at the binding interfaces with the Ca2+ sensor CIB2. This provides a detailed mechanism of the genetic heterogeneity of TMC1 in hearing loss at an atomic level.

molecular biology↗

bioRxiv2024

Sodium/Potassium ATPase Alpha 1 Subunit Fine-tunes Platelet GPCR Signaling Function and is Essential for Thrombosis

BackgroundThrombosis is a major cause of myocardial infarction and ischemic stroke. The sodium/potassium ATPase (NKA), comprising and {beta} subunits, is crucial in maintaining intracellular sodium and potassium gradients. However, the role of NKA in platelet function and thrombosis remains unclear. MethodsWe utilized wild-type (WT, 1+/+) and NKA 1 heterozygous (1+/-) mice, aged 8 to 16 weeks, of both sexes. An intravital microscopy-based, FeCl3-induced carotid artery injury thrombosis model was employed for in vivo thrombosis assessment. Platelet transfusion assays were used to evaluate platelet NKA 1 function on thrombosis. Human platelets isolated from healthy donors and heart failure patients treated with/without digoxin were used for platelet function and signaling assay. Complementary molecular approaches were used for mechanistic studies. ResultsNKA 1 haplodeficiency significantly reduced its expression on platelets without affecting sodium homeostasis. It significantly inhibited 7.5% FeCl3-induced thrombosis in male but not female mice without disturbing hemostasis. Transfusion of 1+/-, but not 1+/+, platelets to thrombocytopenic WT mice substantially prolonged thrombosis. Treating WT mice with low-dose ouabain or marinobufagenin, both binding NKA 1 and inhibiting its ion-transporting function, markedly inhibited thrombosis in vivo. NKA 1 formed complexes with leucine-glycine-leucine (LGL)-containing platelet receptors, including P2Y12, PAR4, and thromboxane A2 receptor. This binding was significantly attenuated by LGL>SFT mutation or LGL peptide. Haplodeficiency of NKA 1 in mice or ouabain treatment of human platelets notably inhibited ADP-induced platelet aggregation. While not affecting 10% FeCl3-induced thrombosis, NKA 1 haplodeficiency significantly prolonged thrombosis time in mice treated with an ineffective dose of clopidogrel. ConclusionNKA 1 plays an essential role in enhancing platelet activation through binding to LGL-containing platelet GPCRs. NKA 1 haplodeficiency or inhibition with low-dose ouabain and marinobufagenin significantly inhibited thrombosis and sensitized clopidogrels anti-thrombotic effect. Targeting NKA 1 emerges as a promising antiplatelet and antithrombotic therapeutic strategy.

cell biology↗