Biology subjects

Xu, Z.

Publications and source records attributed to Xu, Z..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

A unified eIF1A+ luminal cells-centered hypoxic and "cold" tumor microenvironment promotes PCa progression among different subtypes

PCa is a malignancy with high heterogeneity arises from both tumor microenvironment (TME) and histological subtypes. To achieve superior clinical efficacy, it is imperative to identify unified progression drivers within such heterogeneity in PCa, thereby enabling the development of more consistent and effective therapeutic strategies. In this study, we applied imaging mass cytometry to stain 39 proteins on 71 tissues comprising para-cancer, low-grade acinar adenocarcinoma (LgPAC), high-grade PAC (HgPAC), intraductal carcinoma (IDC) and ductal adenocarcinoma (DAC) tissues, obtaining the spatial proteomic landscape of 345,233 single cells. We discovered a hypoxic eIF1A+ luminal epithelial (LE) cluster exhibiting both translational activation and immunosuppressive properties, which was enriched in high-risk PCa including HgPAC, IDC and DAC, and associated which tumor progression and unfavorable prognosis. Additionally, eIF1A+ LE orchestrates the formation of an immunologically "cold" TME, characterized by the low infiltration of anti-cancer immune cells including PD1- T cells CD163- macrophages. Through in vivo validation and investigator-initiated study, we further found that Homoharringtonine, an inhibitor targeting protein translation process, effectively inhibited PCa growth, alleviated hypoxic microenvironment, and enhanced immune cell infiltration. This study is the first to apply spatial proteomics to delineate consistent molecular features across histological subtypes, providing transformative insights for clinical management of PCa.

cancer biology↗

bioRxiv2025

Inferring non-coding RNA regulatory network from transcriptomic data and curated databases

Non-coding RNAs (ncRNAs) have played an indispensable role in regulating gene expression and cellular processes. However, the complex regulatory circuits between ncRNAs and coding genes remain understudied. Major challenges for inferring ncRNA regulatory network (NRN) on a transcriptome-wide scale include high dimensionality of both ncRNA and coding gene expression data, their context-dependent interaction, and lack of validation. We hereby propose a comprehensive analytical framework, namely Construction and Analysis of non-coding RNA regulatory NETwork (CAR-NET), specifically designed to infer NRN from transcriptomic data and curated databases on experimentally validated ncRNA-gene interactions and disease-related ncRNAs. At its core is a novel computationally efficient Bayesian network structure learning method that leverages the semi-bipartite graph structure of NRN for dimension reduction, edge orientation and global network search. We also developed and applied algorithms to perform differential network, subnetwork and pathway analysis of the inferred network. We showed the strength of CAR-NET in simulations and three case studies, encompassing lncRNA regulation in brain development, miRNA differential regulation in renal cell carcinoma and regulation by different classes of ncRNAs in different cell lines using bulk or single cell RNA-seq data. An R-shiny app (https://github.com/kehongjie/CAR-NET) was developed to implement the method(s) with interactive GUI.

bioinformatics↗

bioRxiv2025

ERK and PKA signaling drive the evolutionary expansion of the cortex

The human cerebral cortex, essential for intelligence, cognition, and language, evolved its uniqueness through mechanisms that drive neuronal expansion. Here, we demonstrate that ERK and PKA signaling cooperatively preserve the neurogenic capacity of cortical radial glia (RGs) by inhibiting gliogenic YAP/TAZ and SHH signaling. YAP/TAZ signaling drives cortical RGs toward ependymal fate, while SHH signaling facilitates the generation of cortical tripotential intermediate progenitor cells that produce cortical astrocytes, oligodendrocytes, and olfactory bulb interneurons. During evolution, cortical outer radial glia (oRGs) acquire dominant ERK/PKA signaling through a self-reinforcing feedback mechanism that suppresses both YAP and SHH pathways, thereby significantly enhancing oRG self-renewal capacity and extending the neurogenic period. These findings reveal that cortical neurogenesis, gliogenesis, and evolutionary expansion are coordinately regulated by an integrated ERK, PKA, YAP/TAZ, and SHH signaling, identifying a unifying principle of mammalian cortical development and evolution.

developmental biology↗

bioRxiv2025

HCV infection induces ubiquitin-dependent degradation of LATS1, inactivating the Hippo pathway and upregulating transcription of the CYR61 and CTGF genes

Hepatitis C virus (HCV) is often associated with chronic liver diseases and significant alterations in host cellular signaling. However, the molecular mechanisms underlying HCV- related liver pathogenesis remain to be elucidated. The Hippo signaling pathway, a key regulator of cell proliferation and survival, plays a critical role in maintaining liver homeostasis. Here we investigated the role of the Hippo pathway in HCV-related pathogenesis. We demonstrated that HCV infection induces degradation of LATS1, a key regulator of the Hippo pathway. Degradation of LATS1 protein was restored by a proteasomal inhibitor, but not a lysosome inhibitor, indicating that HCV promotes proteasomal degradation of LATS1 protein. HCV-induced degradation of LATS1 protein was suppressed in si-Itch-transfected Huh-7.5 cells. These results suggest that Itch ubiquitin ligase is involved in ubiquitin-dependent degradation of LATS1 protein. Cell fractionation assays and immunofluorescence staining revealed that HCV infection promoted nuclear translocation of YAP1 protein, suggesting that HCV infection suppresses the Hippo pathway. Furthermore, the transcription of YAP1 target genes, CYR61 and CTGF, that are involved in tissue remodeling and proliferation, was upregulated in HCV-infected Huh-7.5 cells and in HCV-infected patients. Taken together, we propose that HCV promotes the ubiquitin-dependent proteasomal degradation of LATS1 protein, leading to suppression of the Hippo pathway, thereby upregulating transcription of CYR61 and CTGF genes. DATA SUMMARYAll data are presented in the main figures. Raw sequencing data, microscopy images, materials, and sequence information are available upon request. Correspondence and requests for materials should be addressed to Professor Ikuo Shoji. The data that support the findings of this study is available at bioRxiv (https://www.biorxiv.org/). IMPACT STATEMENTWe demonstrate evidence suggesting that HCV infection promotes the Itch-mediated ubiquitin-dependent degradation of LATS1 protein, a key factor for the Hippo pathway. HCV-induced ubiquitin-dependent degradation of LATS1 protein promotes inactivation of the Hippo pathway and nuclear translocation of YAP1 protein, thereby upregulating transcription of CYR61 and CTGF genes. We propose a novel molecular mechanism in which HCV infection promotes degradation of LATS1 protein, leading to inactivation of the Hippo pathway. Understanding HCV-induced inactivation of the Hippo pathway may lead to developing new strategies for preventing or treating HCV-related pathogenesis.

microbiology↗

bioRxiv2025

Allo-PED: Leveraging protein language models and structure features for allosteric site prediction

Allosteric regulation plays a pivotal role in modulating protein function and allosteric sites represent a promising target for drug discovery. However, identifying allosteric sites remains challenging due to their structural and evolutionary diversity. Here, we present AlloPED, a novel framework that combines protein language models and machine learning to predict allosteric sites with high accuracy. AlloPED consists of two modules: AlloPED-pocket, an ensemble model leveraging physicochemical features to predict allosteric pockets; and AlloPED-site, a dilated convolutional neural network (DCNN) augmented with a comprehensive attention mechanism for residue-level prediction. AlloPED-pocket achieves state-of-the-art performance on benchmark datasets, yielding an MCC of 0.544 and an AUC of 0.920, outperforming existing methods such as AllositePro and PARS. AlloPED-site further refines predictions using high-dimensional sequence embeddings from the ProtT5 protein language model, achieving a precision of 0.601, a recall of 0.422, and a specificity of 0.661. These results highlight the effectiveness of integrating ensemble learning and deep learning for allosteric site prediction. AlloPED also identifies critical determinants of allosteric sites, including residue clustering coefficients, van der Waals volume, and hydrophobic microenvironments. In summary, this framework provides a robust tool for advancing our understanding of allosteric regulation and facilitating structure-based drug design.

bioinformatics↗

bioRxiv2025

Patient-derived liver biopsy organoids enable precision alcohol-associated liver disease modeling

Background & AimsAlcohol-associated liver disease (ALD) is a major cause of liver disease worldwide with scarce therapeutic options. Animal models poorly recapitulate advanced ALD precluding the development of new treatments. Organoids have emerged as a powerful human-based preclinical tool. However, current patient-derived liver organoids fail to recapitulate the epithelial heterogeneity and its generation requires liver surgical resections, thus limiting personalized disease modeling. Here, we report the development of organoids from liver needle biopsies (b-Orgs) from patients with ALD. Methodsb-Orgs were generated from tru-cut biopsies from patients at early (n=28) and advanced (n=34) stages of ALD. b-Orgs were characterized by immunofluorescence, bulk and single cell RNA-sequencing and compared to parental tissues. b-Orgs were used to model ALD progression, identify pathogenic drivers, induce alcohol-associated hepatitis (AH) and evaluate response to prednisolone. ResultsPhenotypic and functional analysis of b-Orgs showed hepatocyte- enriched features. Single-cell RNA-sequencing revealed a heterogeneous cell composition comprising hepatocyte, biliary and progenitor populations, mirroring the epithelial landscape found in patients with advanced ALD. Moreover, b-Orgs preserved disease-stage features and allowed to identify the association of ELF3 with cell plasticity and disease progression. Finally, stimulation of b-Orgs with drivers of ALD induced pathophysiological features of alcohol-associated hepatitis, including ROS production, lipid accumulation, inflammation and decreased cell proliferation, which were mitigated in response to prednisolone. Conclusions Overall, we provide a human-based model that recapitulates epithelial complexity and patient specific features, allowing to identify drivers of cell plasticity and expanding organoid-based liver disease modeling for personalized medicine. Impact and implications Here, we describe the generation of biopsy-derived organoids (b-Orgs) from patients with liver disease. b-Orgs reproduce the liver epithelial cell composition found in patients liver tissue and are efficiently generated from different stages of the disease, providing a platform for patient- tailored disease modeling and drug testing.

cell biology↗

bioRxiv2025

Calcium signals shape metabolic control of H3K27ac and H3K18la to regulate EGA

The use of assisted reproductive technologies (ART) has enabled the birth of over 9 million babies; but it is associated with increased risks of negative metabolic outcomes in offspring. Yet, the underlying mechanism remains unknown. Calcium (Ca2+) signals, which initiate embryo development at fertilization, are frequently disrupted in human ART. In mice, abnormal Ca2+ signals at fertilization impair embryo development and adult offspring metabolism. Changes in intracellular Ca2+ drive mitochondrial activity and production of metabolites used by the epigenetic machinery. For example, acetyl-CoA (derived mainly from pyruvate) and lactyl-CoA (derived from lactate) are used for writing H3K27ac and H3K18la marks that orchestrate initiation of development. Using both a genetic mouse model and treatment with ionomycin to raise intracellular Ca2+ of wild-type fertilized eggs, we found that excess Ca2+ at fertilization changes metabolic substrate availability, causing epigenetic changes that impact embryo development and offspring health. Specifically, increased Ca2+ exposure at fertilization led to increased H3K27ac levels and decreased H3K18la levels at the 1-cell (1C) stage, that persisted until the 2-cell (2C) stage. Ultralow input CUT&Tag revealed significant differences in H3K27ac and H3K18la genomic profiles between control and ionomycin groups. In addition, increased Ca2+ exposure resulted in a marked reduction in global transcription at the 1C stage that persisted through the 2C stage due to diminished activity of RNA polymerase I. Excess Ca2+ following fertilization increased pyruvate dehydrogenase activity (enzyme that converts pyruvate to acetyl-CoA) and decreased total lactate levels. Provision of exogenous lactyl-CoA before ionomycin treatment restored H3K18la levels at the 1C and 2C stages and rescued global transcription to control levels. Our findings demonstrate conclusively that Ca2+ dynamics drive metabolic regulation of epigenetic reprogramming at fertilization and alter EGA.

developmental biology↗

bioRxiv2025

Adolescent onset of volitional ethanol intake normalizes sex differences observed with adult-onset ethanol intake and negative affective behaviors during protracted forced abstinence

RationaleNegative affect during ethanol abstinence can lead to relapse and dependence. Voluntary ethanol drinking models are crucial for examining negative affect following chronic ethanol access, but female rodents often drink more ethanol than males, complicating comparisons between sexes. Since chronic adolescent ethanol use poses a substantial risk for later alcohol use disorder, we hypothesize that adolescence is a critical window for consolidating drinking behavior before major hormonal changes affect ethanol consumption. ObjectivesThis study compared sex differences in voluntary ethanol consumption and negative affective behavior in mice that initiated ethanol consumption during early adolescence ([~]PND30) or early adulthood (>PND49). MethodsMale and female C57BL/6J mice underwent the Chronic Drinking Forced Abstinence (CDFA) paradigm, with the "Ethanol" group given two-bottle choice access to ethanol and water, and the "Water" group given two water bottles. Ethanol intake and preference were measured over six weeks. Two weeks following ethanol removal, mice underwent behavioral testing for negative affective-like behavior. ResultsAdult-onset female mice consumed significantly more ethanol and displayed higher ethanol preference compared to adult-onset male mice. In contrast, adolescent-onset male and female mice consumed similar ethanol levels and displayed similar preference. We observed increased immobility during the forced swim test in adult-onset ethanol females, but not males, during protracted abstinence. However, both sexes of adolescent-onset ethanol mice displayed increased immobility during forced abstinence. ConclusionsThese findings highlight adolescence as a critical period during which both sexes voluntarily consume ethanol and are equally vulnerable to the behavioral disturbances associated with ethanol abstinence.

neuroscience↗

bioRxiv2025

The hollow truth: ethylene-triggered ROS, PCD, senescence, and autophagy drive hollow stem formation

Hollow stems have independently evolved multiple times across the plant kingdom, and play crucial roles in plant development and various environmental adaptations. However, the mechanisms underlying stem hollowness remain poorly understood. Water spinach (Ipomoea aquatica) is one of the few hollow-stemmed plants in the Convolvulaceae family, and its hollow stems are essential for thriving in aquatic environments. Using histochemical staining and transcriptome analysis, we identified programmed cell death (PCD) is involved in cavity formation of water spinach shoot tips. Single-cell transcriptome analysis further revealed that ethylene and reactive oxygen species (ROS) drive and regulate this process by activating transcription factors IaNAC074, IaNAC087, IaNAC029, IaNTL9, and IaTGA9, which initiate PCD, senescence, and autophagy, collectively controlling cell death. These findings were validated through treatments with ethylene and ROS reagents in water spinach and transient expression in tobacco. Additionally, transcriptomic data suggest that these mechanisms may also play a role in hollow stem formation in bamboo, highlighting the conservation of PCD regulatory mechanisms in plant development. This work not only fills a major knowledge gap in the adaptive mechanisms of hollow stem formation but also opens new avenues for agricultural and ecological applications, offering strategies to enhance crop tolerance to flooding and accelerate crop growth.

plant biology↗

bioRxiv2025

Targeting CD38 effectively prevents myelofibrosis in myeloproliferative neoplasms

Proinflammatory signaling is a hallmark of myeloproliferative neoplasms (MPNs). Several studies have shown that monocytes are a major source of proinflammatory cytokines and monocyte-derived fibrocytes play a pivotal role in the pathogenesis of myelofibrosis (MF). To further explore the role of monocytes in MF, we generated inducible NrasG12D/+Jak2V617F/+(NJ) mice. Recipients transplanted with NJ bone marrow cells developed MF with an early onset of anemia and monocytosis. In vitro, NJ recipients bone marrow nucleated cells exhibited increased quantity of CD45+CollagenI+ fibrocytes, which were mainly derived from the Ly6chigh monocytes. RNA sequencing identified a significant elevated expression of CD38 (a nicotinamide adenine dinucleotide (NAD)+ hydrolase) in Ly6chigh monocytes from NJ mice, which results in pronounced lower level of NAD+. In humans, CD14+ monocytes from MF patients showed significantly higher expression of CD38 than controls and monocytes from polycythemia vera (PV) patients with grade 1 fibrosis had higher CD38 expression than those without fibrosis. Finally, we tested that boosting NAD+ via pharmacological CD38 targeting or NAD+ precursor supplementation inhibited the differentiation of fibrocytes in vitro and observed that targeting CD38 can effectively prevent the onset of fibrosis in vivo. Collectively, our findings shed light on the role of CD38 in monocytes and suggest potential clinical applications such as use of CD38 as a biomarker of fibrotic progression and potential clinical utility of CD38 inhibition in patients with MF. Key PointsO_LICD38-overexpressing monocytes are increased in MF murine models and MPN patients progressing to fibrotic-phase disease. C_LIO_LIRestoring intracellular NAD+ levels using the CD38 inhibitor 78c prevented the development of fibrotic-phase disease in MPN murine models. C_LI

cancer biology↗

bioRxiv2025

Estimating the cis-heritability of gene expression using single cell expression profiles controls false positive rate of eGene detection

For gene expression traits, cis-genetic heritability can quantify the strength of genetic regulation in particular cell types, elucidating the cell-type-specificity of disease variants and genes. To estimate gene expression heritability, standard models require a single gene expression value per individual, forcing data from single cell RNA-sequencing (scRNA-seq) experiments to be "pseudobulked". Here, we show that applying standard heritability models to pseudobulk data overestimates gene expression heritability and produces inflated false positive rates for detecting cis-heritable genes. Therefore, we introduce a new method called scGeneHE (single cell Gene expression Heritability Estimation), a Poisson mixed-effects model that quantifies the cis-genetic component of gene expression using individual cellular profiles. In simulations, scGeneHE has a consistently well-calibrated false positive rate for eGene detection and unbiasedly estimates cis-heritability at many parameter settings. We applied scGeneHE to scRNA-seq data from 969 individuals, 11 immune cell types, and 822,552 cells from the OneK1K cohort to infer cell-type-specificity of genetic regulation at risk genes for immune-mediated diseases and trace the fluctuation of cis-heritability across cellular populations of varying resolution. In summary, we developed a new statistical method that resolves the analytical challenge of estimating gene expression cis-heritability from native scRNA-seq data.

genetics↗

bioRxiv2025

The first chromosomal-level genome assembly of an allotetraploid oyster

Tetraploid oysters are used to cross with diploids to produce triploid oysters that have become an important part of the oyster aquaculture industry worldwide. Although most tetraploid oysters are artificially induced autotetraploids, allotetraploids can be produced between closely related species, providing new opportunities for polyploid breeding and studying genome interactions. Using PacBio sequencing, Illumina sequencing, and high-throughput chromosome conformation capture scaffolding, we assembled the first high-quality genome assembly of an artificially induced allotetraploid between the Pacific oyster Crassostrea gigas and Portuguese oyster Crassostrea angulata. The assembled genome is 1.23 Gb, with a contig N50 of 2.56 Mb and a scaffold N50 of 57.22 Mb, and anchored to 20 chromosomes. The assembly contains 58,330 protein-coding genes, 98.34% of which are functionally annotated. The heterozygosity and the ratio of repetitive sequences is 5.50% and 46.43%, respectively. This chromosomal-level genome assembly of an allotetraploid oyster provides a valuable genetic resource for studying genome biology of molluscs and for advanced breeding of polyploids that are critical for the oyster aquaculture industry.

genomics↗

bioRxiv2025

Genetically encoded protein oscillators for FM streaming of single-cell data

Wireless devices use frequency modulation (FM) to reliably transmit information. Here, we establish a biochemical analogue of this paradigm using genetically encoded protein oscillators (GEOs) as carrier signals for real-time streaming of single-cell data. The GEO platform leverages evolutionarily diverse MinDE-family ATPase and Activator modules to generate fast synthetic protein oscillations in cells, where the waveform is controlled by both circuit biochemistry and intrinsic cellular physiology. This allows for diverse data encoding strategies, including noise-resistant FM reporters that broadcast proteasomal degradation or transcriptional dynamics; and autoencoder circuits that directly couple shifts in cell physiology to GEO waveform. Deploying GEOs in human embryonic stem cells allowed us to track single-cell developmental states in living populations during differentiation, revealing distinct patterns of spatiotemporal heterogeneity along endoderm, mesoderm, and ectoderm trajectories. The GEO platform establishes a dynamically controllable biochemical carrier signal, unlocking new high-fidelity FM data-encoding paradigms for continuous single-cell analysis.

synthetic biology↗

bioRxiv2025

Excavating Podocyte-Protective Targets of phloroglucinol-terpene hybrids Utilizing AI Models and Omics Analysis

Lupus nephritis (LN) is a multifactorial autoimmune inflammatory disorder, with podocyte dysfunction or structural abnormalities playing a pivotal role in its pathogenesis. Eucalyptus leaves, traditionally employed in folk medicine, have demonstrated notable efficacy in managing non-infectious inflammations. Eucarbwenstols D (R14) is a novel phloroglucinol-terpene that has been isolated from Eucalyptus robusta. To further refine potential targets, we utilized an AI scoring system and successfully identified the epidermal growth factor receptor (EGFR) as the novel target of R14. This discovery was built upon the foundation of transcriptome and connectivity mapping (CMap) analysis. Molecular docking and molecular dynamics simulations were employed to analyze the interaction between R14 and EGFR, surface plasmon resonance (SPR) and homogeneous time-resolved fluorescence (HTRF) assays were utilized to accurately quantify the binding affinity between R14 and EGFR. Western blot (WB) and immunofluorescence assays were then conducted to explore the downstream signaling pathways initiated by EGFR, specifically the PI3K/AKT/mTOR pathway. These assays demonstrated that R14 modulates the expression of apoptotic proteins Bax and Bcl-2 through this pathway, thereby exerting a protective effect on podocytes from undergoing apoptosis. The modulation of key podocyte proteins, nephrin and podocin, further substantiates this protective effect. Overall, we have applied a novel AI algorithm model that transcends bioinformatics analysis to precise identification of the novel podocyte target of R14. In this study, R14 was identified for the first time as a novel scaffold compound for EGFR inhibition. Moreover, R14 has demonstrated its capacity to inhibit podocyte apoptosis, thereby protecting these critical cells. This discovery establishes a robust theoretical foundation for the use of phloroglucinol-terpene hybrids (PTHs) in the treatment of LN.

cell biology↗

bioRxiv2025

Spatial Total RNA Sequencing of Formalin-Fixed Paraffin Embedded Tissues by spRandom-seq

Current oligo(dT) primers-based spatial transcriptomic methods are limited to fresh or fresh-frozen samples due to the low efficiency of oligo(dT) primers in capturing RNAs in degraded or microbial samples. Here, we have developed a random primer-based spatial total RNA sequencing (spRandom-seq) technology for simultaneously capturing whole host and microbial RNAs in formalin-fixed paraffin-embedded (FFPE) tissues. spRandom-seq eliminated 3 or 5 gene-body biases and outperformed oligo(dT)-based 10X Visium with an 8-fold higher capturing rate for lncRNA and other non-polyadenylated RNA biotypes, including miRNA, snRNA and miscRNA. In the clinical FFPE sections of breast cancer, we revealed the inherent heterogeneity within the tumor region. We also simultaneously captured host and microbial RNAs in Klebsiella pneumoniae-infected sections. Totally, spRandom-seq provided a versatile tool for both clinical pathology and infection biology with established spatial platforms, ensuring ease of operation and large-scale applications.

genomics↗

bioRxiv2025

Predicting Neuroplasticity Effects of Continuous Theta Burst Stimulation with Biomarkers from the Motor Evoked Potential TMS Input-Output Curve

The field of neuromodulation lacks predictors of individual differences in plasticity that influence responses to repetitive transcranial magnetic stimulation (rTMS). Continuous theta burst stimulation (cTBS), a form of rTMS known for its inhibitory effects, shows variable responses between individuals, potentially due to differences in neuroplasticity. Predicting individual cTBS effects could vastly enhance its clinical and experimental utility. This study explores whether motor evoked potential (MEP) input-output (IO) parameters measured prior to neuromodulation can predict motor cortex responses to cTBS. IO curves were sampled from healthy adults by recording MEPs over a range of single pulse TMS intensities to obtain parameters including MEPmax and S50 (midpoint intensity). Subjects later received cTBS over the same location of motor cortex and their MEPs before and after stimulation were compared. Both MEPmax and S50 predicted responses, significantly correlating (p<0.05, R2>0.25) with individuals MEP changes at 10, 20, and 30 minutes after cTBS. Further, we introduced and validated an easily implementable biomarker that does not require the time-consuming sampling of full IO curve: MEP130RMT (median of 10 MEPs at 130% RMT). MEP130RMT was also a strong predictor of cTBS response (p<0.005, R2>0.3). Head-to-head comparison against a previously studied genetic biomarker of rTMS responses (BDNF polymorphism) showed that IO based predictors had a superior performance in explaining more response variability. Thus, IO curves derived prior to cTBS administration can reliably predict cTBS-induced changes in cortical excitability. This work points toward an accessible strategy for tailoring stimulation procedures in both diagnostic and therapeutic applications of rTMS, and potentially boosting response rate to other brain stimulation approaches. HIGHLIGHTSO_LIBaseline TMS-MEP Input-Output (IO) Curve parameters significantly predict MEP responses to M1 cTBS. C_LIO_LIHigher MEPmax at baseline predicts more robust inhibitory response to cTBS, while higher midpoint intensity (S50) is associated with less response. C_LIO_LID We developed and validated a new biomarker MEP130RMT, which predicts cTBS response using just 10 baseline MEPs from single TMS pulses of 130% RMT intensity. C_LIO_LIHead to head comparison against BDNF genotyping shows superior performance of IO biomarkers. C_LI

neuroscience↗

bioRxiv2025

Homeodomain protein Sxi1α regulates cell-cell fusion during distinct sexual reproduction modes in Cryptococcus deneoformans

Sex-specific homeodomain (HD) proteins are key regulators of cell identity and sexual development in fungi, typically functioning as heterodimers to govern transcription. In the human fungal pathogens Cryptococcus neoformans and Cryptococcus deneoformans, the HD proteins Sxi1 and Sxi2a (Sex-inducer 1 and 2a) have been characterized as interacting components that play critical roles in sexual development during x a sexual reproduction. cells are the predominant mating type in natural populations of Cryptococcus, and unisexual (same-sex) mating can also occur in certain genetic backgrounds. The roles of Sxi1 and Sxi2a in unisexual reproduction are not fully understood. To elucidate the functions of Sxi1 and Sxi2a, we first applied AlphaFold3 prediction, which identified potential heterodimeric and homodimeric complexes. Formation of a Sxi2a homodimer was then experimentally validated through yeast two-hybrid assays. We subsequently deleted SXI1 and SXI2a in the hyper-filamentous self-fertile C. deneoformans strains XL280 and XL280a. Disruption of these genes did not result in noticeable defects in vegetative growth, virulence-associated traits, colony morphology, sporulation, or competitive fitness during unisexual crosses. Interestingly, both bilateral (mutant x mutant) and unilateral (mutant x wildtype) crosses involving the sxi1{Delta} mutant significantly increased - cell fusion efficiency, suggesting a previously unrecognized inhibitory role for Sxi1 in regulating same-sex cell fusion. Consistently, genes encoding mating pheromones and the -pheromone receptor Ste3 were upregulated in the sxi1{Delta} fusion assays. Transcriptomic analysis of sxi1{Delta} and sxi2a{Delta} mutants led to the identification of unique subsets of genes negatively regulated by each transcription factor during unisexual reproduction. Additionally, x a crosses between null mutants of sxi1{Delta} and sxi2a{Delta} revealed differential regulation of mating-type (MAT) loci genes dependent only on Sxi1 or Sxi2a. Together, our findings reveal a novel role for Sxi1 in governing cell fusion and demonstrate that Sxi1 and Sxi2a have distinct transcriptional control during unisexual and x a sexual reproduction, potentially exerting opposing regulation of sex-specific MAT genes. Author SummaryAnalogous to processes observed in many eukaryotic organisms, fungal sexual reproduction reshuffles genetic material, producing novel genetic variants with increased fitness and/or adaptive potential. The human fungal pathogen Cryptococcus deneoformans is widespread in the environment and can cause severe infections in immunocompromised individuals. Sexual reproduction in this species occurs between cells of either opposite mating types ( x a mating) or the same mating type ( x and a x a unisexual reproduction). The mating type-specific homeodomain transcription factors Sxi1 and Sxi2a are known to form a complex that broadly controls sexual development following and a cell fusion. Here, we find that Sxi1 inhibits cell-cell fusion during unisexual reproduction, while its partner, Sxi2a, shows only limited inhibition in certain genetic contexts. Further, we show that Sxi1 and Sxi2a regulate transcription of distinct gene sets during both x a and unisexual reproduction, including many within the mating-type (MAT) loci, often in opposing manners. Together, these findings reveal that Sxi1 and Sxi2a function both cooperatively and independently, thereby allowing for a more flexible and finely-tuned mating control system than previously recognized, providing insight into how this organism generates genetic variation and adapts to changing environments.

microbiology↗

bioRxiv2025

Repurposing AZD-5991 for inhibiting growth and biofilm formation of Staphylococcus aureus by disrupting the cell membrane and targeting FabI.

Staphylococcus aureus infections have already become a major threat to public health worldwide. Drug resistance and biofilm formation are two critical factors that significantly affect the efficacy of the antimicrobial treatment of S. aureus infections using conventional antibiotics. Therefore, the discovery of novel antimicrobial agents with potent antibacterial and antibiofilm activity has become a hotspot in recent years. Here, we first demonstrated the remarkable inhibitory activity of AZD-5991, a selective Mcl-1 inhibitor, against S. aureus. The MIC50 and MIC90 of AZD-5991 against S. aureus were 12.5 M, and AZD-5991 significantly inhibited the growth of S. aureus at a subinhibitory concentration of 1/2 x MIC. Besides, AZD-5991 displayed bactericidal activity and a robust capacity for inhibiting biofilm formation against S. aureus with very low drug toxicity against host cell lines. Our data demonstrated the disruption of S.aureus cell integrity by AZD-5991 through membrane permeability assays and the ingredients of the bacterial phospholipids could neutralize the antibacterial activity of AZD-5991. Moreover, whole-genome sequencing and proteomic analysis were also applied to gain insights into the possible impact of AZD-5991 on the fatty metabolism of S. aureus. Furthermore, the antibacterial activity of AZD-5991 was significantly elevated by exogenous fatty acids linoleic acid (C18:2 {Delta} 9,12) and arachidonic acid (C20:4 {Delta} 5,8,11,14). Lastly, the biolayer interferometry assay supported the direct interaction of AZD-5991 with FabI, a necessary protein related closely to bacterial growth and fatty acid metabolism. Conclusively, this study suggests that AZD-5991 could inhibit the planktonic growth and biofilm formation of S. aureus by disrupting the cell membrane and targeting FabI. AZD-5991 might be a promising new antibiotic candidate for the antimicrobial treatment of S. aureus infections resistant to traditional clinical drugs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/638150v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@658444org.highwire.dtl.DTLVardef@cea949org.highwire.dtl.DTLVardef@1cc003dorg.highwire.dtl.DTLVardef@23de22_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗