Biology subjects

Zhang, L.

Publications and source records attributed to Zhang, L..

At least 271 records · Page 15Linked to original sources

bioRxiv2025

MicroRNA156 and its targeted SPL genes interact with the photoperiod, vernalization, and gibberellin pathways to regulate wheat heading time

Heading time has a large impact on adaptation to different environments and crop productivity. In this study, we characterized the effect of the endogenous age pathway on heading time and its interactions with the photoperiod and vernalization pathways in the leaves of tetraploid wheat (Triticum turgidum ssp. durum). Plants with reduced levels of microRNA156 or increased expression of its downstream targets, the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes SPL3, SPL4, and SPL13 exhibited accelerated heading time, with stronger effects under suboptimal inductive conditions. Earlier heading was associated with the upregulation of miR172 and flowering-promoting genes VRN1, FUL2, and FT1 and the downregulation of flowering-repressing genes AP2L1 and VRN2. Additionally, we uncovered complex interactions among SPL, SQUAMOSA (VRN1 and FUL2) and DELLA proteins that modulate wheat heading time. We showed that DELLA proteins, which are negative regulators in the gibberellic acid pathway, can interact with SPL proteins reducing their ability to induce flowering. We also discovered previously unknown interactions between SQUAMOSA and DELLA proteins in wheat that compete with the DELLA-SPL interactions, likely reducing DELLAs ability to repress SPL3 and SPL4 activity. Since SPL3 and SPL4 directly promote VRN1 and FUL2 transcription, these interactions generate a positive regulatory feedback loop that accelerates wheat heading time. Finally, we developed dominant miR156-resistant alleles rSPL3, rSPL4, and rSPL13 that accelerate wheat heading time under both optimal and suboptimal inductive conditions. These publicly available genetic resources can be used to fine tune heading time and improve wheat adaptation to changing environments. Significance statementWheat heading time is critical for adaptation to diverse environments. We generated dominant mutations for the SPL3, SPL4 and SPL13 genes that accelerate heading time. Different combinations of these mutations can be used to modulate heading time and improve wheat adaptation to changing environments.

plant biology↗

bioRxiv2025

Iron addicted colorectal cancers exploit Heme-Complex II axis to resist oxidative cell death

Colorectal cancer (CRC) cells are addicted to iron, which fuels nucleotide synthesis, mitochondrial respiration, and rapid proliferation. Yet paradoxically, high intracellular iron is cytotoxic to most other cells, raising the question of how CRC cells tolerate and exploit iron-rich environments. One pathway thought to mediate iron toxicity is ferroptosis, an iron-dependent form of cell death. However, most ferroptosis regulators were identified through synthetic chemical screens or small molecule activators, and it remains unclear whether these canonical pathways explain how iron itself triggers cell death, particularly in vivo. Here, using multi-omics profiling, CRISPR screening, and in vivo models, we uncover a heme-succinate dehydrogenase (SDH)-Coenzyme Q (CoQ) axis that enables CRC cells to buffer iron-induced oxidative stress. Heme-dependent SDH reduces CoQ, which redistributes to mitochondrial and plasma membranes to detoxify lipid ROS as a radical trapping antioxidant. This pathway functions alongside, and in some contexts independently of, canonical ferroptosis regulators. These findings reveal that CRCs co-opt metabolic cofactors not only for growth but also for survival under physiologically toxic iron levels, uncovering new vulnerabilities for therapy.

cancer biology↗

bioRxiv2025

Fusobacterium nucleatum outer membrane vesicles activate the TNFR1/NF-κB signaling pathway to promote OSCC proliferation

Fusobacterium nucleatum (F. nucleatum, Fn) has emerged as a significant bacterium linked to cancer. However, the precise mechanisms by which Fn drives the progression of oral squamous cell carcinoma (OSCC) remain obscure. Outer membrane vesicles (OMVs), small vesicular structures secreted by Gram-negative bacteria, are known to contribute to their pathogenicity. This study investigated the role of Fn OMVs in oral cancer progression and the underlying mechanisms. MethodsMetagenomic sequencing was conducted on both oral cancer and control tissues. OMVs were isolated through ultracentrifugation. Cell proliferation assays on two cancer cell lines assessed the impact of Fn and its OMVs. Fn OMVs were administered to mice to evaluate their influence on tumorigenesis. RNA-seq was performed on OMV-treated cells to identify enriched genes, which were validated via qPCR and Western blot. Knockdown experiments were executed in vitro and in vivo to confirm the involvement of Fn OMVs in TNFR1-mediated NF-{kappa}B signaling. ResultsFn prevalence was markedly higher in oral cancer tissues compared to non-cancerous samples. In vitro, Fn and its OMVs significantly enhanced the growth and proliferation of oral cancer cell lines. Mice treated with Fn OMVs developed larger tumors than those receiving Fn alone. Furthermore, Fn OMVs notably induced TNFR1 expression and activated the NF-{kappa}B signaling pathway, as confirmed by RNA-seq, qPCR, and Western blot. TNFR1 knockdown significantly diminished the effects of Fn OMVs on cancer cell proliferation in vitro and tumor formation in vivo. ConclusionThis study compellingly demonstrates that Fn OMVs are pivotal in OSCC progression by directly activating TNFR1-mediated NF-{kappa}B signaling. These findings pave the way for future research into the prevention and treatment of oral cancer.

microbiology↗

bioRxiv2025

Rapid generation of ventral A9-like dopaminergic neurons from patterned iPSCs

In vitro modelling of highly vulnerable nigral dopaminergic (DA) neuronal subtypes in Parkinsons disease (PD), is necessary for studying disease mechanisms. Here, we optimized a new approach by expressing the pioneer neurogenic transcription factor, Achaete-scute-like 1 (Ascl1), implicated in determining dopaminergic fate. Sequential small-molecule patterning of iPSCs into early floor plate mesencephalic progenitors, followed by inducible Ascl1 expression, rapidly differentiates midbrain DA neurons. Immunocytochemistry and transcriptomic analysis of these patterned Ascl1-driven DA neurons (PA-DANs) confirmed midbrain-lineage specificity. Importantly, we found an enrichment of DA subpopulations that corresponded to the adult human ventral SOX6-positive A9 DA subtypes vulnerable in PD. Furthermore, we combined these ventral A9-like PA-DANs with human iPSC-derived midbrain astrocytes and microglia in defined ratios to generate mature 3D A9-like assembled organoids that display characteristic spontaneous neuronal activity and electrical propagation along the axon. Our method efficiently generates a mature and functional A9-like DA neuronal platform to study PD. HighlightsO_LISequential midbrain patterning and Ascl1 expression accelerates DA differentiation C_LIO_LIPA-DANs resemble human adult ventral A9-like DA subtypes vulnerable in PD C_LIO_LI3D assembled organoids show mature identity of PA-DANs, iAstrocytes and iMicroglia C_LIO_LIPA-DANs matured in 3D organoids show neuronal network activity within weeks C_LI eTOC blurbIn this study, Ullian and colleagues have developed a rapid method to differentiate dopaminergic neurons, using small molecules to generate early floor plate mesencephalic progenitors from human iPSCs and sequentially expressing a pioneer transcription factor, Ascl1, that accelerates uniform dopaminergic neurogenesis. Patterned Ascl1-driven dopaminergic neurons (PA-DANs) in 2D and 3D assembled organoids serve as a platform to study Parkinsons disease O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/685897v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1d83eb3org.highwire.dtl.DTLVardef@1fc7fa5org.highwire.dtl.DTLVardef@2033e3org.highwire.dtl.DTLVardef@2e8fa3_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

The Mycobacterium tuberculosis ESX-5 secretion system enables carbon source utilization and growth in mice

Mycobacterium tuberculosis uses several ESX type VII protein secretion systems for pathogenesis. M. tuberculosis ESX-5 is poorly characterized because it is essential for growth in standard lab culture conditions. To circumvent ESX-5 essentiality, we made an M. tuberculosis strain in which the central ESX-5 membrane component EccD5 can be conditionally depleted. Here, we use this strain to demonstrate that M. tuberculosis requires the ESX-5 secretion system to grow using specific carbon sources in vitro, to grow in cultured macrophages, and to replicate and disseminate in aerosol-infected mice. M. tuberculosis requires ESX-5 to use glycerol or glucose as the sole carbon source. Use of glycerol and glucose also depends on the outer membrane protein PPE51. We show that M. tuberculosis requires ESX-5 activity for outer membrane export and surface exposure of PPE51. Expression of the outer membrane porin MspA enabled growth of ESX-5 deficient M. tuberculosis on glycerol, suggesting that the main function of ESX-5 in vitro is to export nutrient transporters to the outer membrane. Importantly, depletion of EccD5 in acutely infected mice resulted in clearance of M. tuberculosis from lung tissues, demonstrating the critical importance of ESX-5 activity during infection. Our findings suggest that ESX-5 promotes M. tuberculosis pathogenesis by mediating export of outer membrane proteins that enable nutrient acquisition. ImportanceMycobacterium tuberculosis ESX type VII secretion systems play important roles in pathogenesis, but the functions of ESX-5 are not well characterized because it is essential for growth in standard lab culture conditions. We used a strain that conditionally expresses a central membrane component of the ESX-5 secretion apparatus to determine how ESX-5 impacts growth in lab cultures and in a mouse infection model. We found that M. tuberculosis requires ESX-5 to grow using several carbon sources and to grow in the lungs of infected mice. Inhibiting production of the ESX-5 secretion system in mice also led to clearance of M. tuberculosis from lung tissues. Our results demonstrate that the M. tuberculosis ESX-5 system is a critical virulence factor and suggest that ESX-5 is a strong candidate for anti-tubercular drug development.

microbiology↗

bioRxiv2025

Integrating Genomics into Multimodal EHR Foundation Models

AO_SCPLOWBSTRACTC_SCPLOWThis paper introduces an innovative Electronic Health Record (EHR) foundation model that integrates Polygenic Risk Scores (PRS) as a foundational data modality, moving beyond traditional EHR-only approaches to build more holistic health profiles. Leveraging the extensive and diverse data from the All of Us (AoU) Research Program, this multimodal framework aims to learn complex relationships between clinical data and genetic predispositions. The methodology extends advancements in generative AI to the EHR foundation model space, enhancing predictive capabilities and interpretability. Evaluation on AoU data demonstrates the models predictive value for the onset of various conditions, particularly Type 2 Diabetes (T2D), and illustrates the interplay between PRS and EHR data. The work also explores transfer learning for custom classification tasks, showcasing the architectures versatility and efficiency. This approach is pivotal for unlocking new insights into disease prediction, proactive health management, risk stratification, and personalized treatment strategies, laying the groundwork for more personalized, equitable, and actionable real-world evidence generation in healthcare.

bioinformatics↗

bioRxiv2025

Hemin Inhibits the Activation of STING in Macrophages by Inducing HO-1, Promoting Endometriosis Development

IntroductionEndometriosis (EMS) is an estrogen-dependent inflammatory disorder characterized by immune dysregulation. This condition profoundly affects the quality of life and reproductive health of nearly 200 million women of reproductive age worldwide and poses significant clinical challenges due to lack of diagnosis tools and effective treatment. Peritoneal macrophages play a central role in promoting the initiation and progression of EMS. Bioinformatics studies have indicated that the STimulator of INterferon Gene (STING) was downregulated in the macrophages in EMS, and this influenced their polarization and functional. However, the specific contribution of STING pathway alterations to EMS pathogenesis remains unclear. MethodsWe integrated scRNA-seq data from EMS patients and healthy controls-including lesions, eutopic endometrium, non-lesional tissue, and peritoneal fluid from EMS patients and healthy controls(n = 19,291 total samples)-to analyze macrophage STING expression and function. Mouse EMS model was generated by injecting uterus fragments into WT or STING-/- mice. Peritoneal fluid was collected and macrophage proportions and subtypes were assessed via flow cytometry. Macrophages were depleted in STING-/- mice prior to EMS induction to evaluate their role in disease progression. In vitro, hemin was used to treat macrophages to investigate how heme oxygenase-1 (HO-1) modulates the STING pathway, assessed through immunoblotting, co-immunoprecipitation, ELISA, and multiplex immunofluorescence. ResultsBioinformatic analysis revealed that macrophages within the EMS lesions are primarily derived from peritoneal macrophages and exhibit decreased STING expression, which correlated negatively with HO-1. STING-/- mice developed more numerous and larger EMS lesions, accompanied by a decreased proportion of large peritoneal macrophages and an increase in small peritoneal macrophages. A marked elevation in M2-type macrophages within the lesions was detected in STING-/- mice. In vitro, hemin-induced HO-1 suppressed STING pathway activation in macrophages. Mechanistically, HO-1 inhibited the translocation of STING from the endoplasmic reticulum to the Golgi, thereby suppressing STING signaling and facilitating EMS. ConclusionMacrophages are essential for lesion formation in STING-/- mice. In vitro, hemin promotes EMS progression via HO-1 - mediated suppression of the STING pathway. Our findings identify the heme-HO-1-STING axis as a key immunomodulatory pathway in EMS and suggest its potential as a therapeutic target. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/683839v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@6901beorg.highwire.dtl.DTLVardef@1f18d44org.highwire.dtl.DTLVardef@1716f6forg.highwire.dtl.DTLVardef@4ae22d_HPS_FORMAT_FIGEXP M_FIG Graphical abstract (Created in BioRender.com) Retrograde menstruation leads to the accumulation of heme in the peritoneal cavity, which upregulates HO-1 expression in peritoneal macrophages. HO-1 inhibits the translocation of STING from the endoplasmic reticulum to the Golgi apparatus in macrophages, thereby suppressing the STING pathway and promoting the development and progression of EMS. The progression of EMS, in turn, reinforces this mechanism, creating a self-sustaining vicious cycle. C_FIG

immunology↗

bioRxiv2025

Pan-cancer analysis reveals that tumor microbiomes generate specific epitopes through transcriptional reprogramming

The therapeutic promise of tumor microbial peptides faces a critical safety paradox: tumors and peritumor tissues harbor compositionally similar microbiomes, yet safe immunotherapy demands tumor-specific targeting. We performed comprehensive transcriptomic analysis of microbial communities from 1,868 tumor and peritumor samples across 11 cancer types. Although 88.5% of microbial species are present in both tissue types, tumor and peritumor tissues exhibit profound transcriptional divergence: only 34.1% of microbial genes are expressed in both tissue types, and merely 18.2% of predicted HLA-binding peptides overlap. This transcriptional divergence represents microbial transcriptional reprogramming (MTR) in tumor tissues, through which microbes activate distinct genomic regions while adapting to tumor microenvironmental pressures, thereby generating tumor-specific peptide repertoires. Using Microbial Transcriptional Reprogramming Index (MiTRI) to quantify MTR, we found that higher MiTRI values correlate with expanded immunogenic peptide repertoires. Mass spectrometry-based immunopeptidomics confirmed that 25% of naturally presented microbial peptides originate from MTR regions. Crucially, in microsatellite-stable colorectal cancer, neo-adjuvant therapy responders exhibited significantly higher MiTRI values. T cell receptors (TCRs) recognized MTR-derived epitopes at 2.10-fold higher rates than genome-wide epitopes, accounting for 79.1% of clonally expanded TCRs. These findings establish MTR as the principle that ensures the tumor-specificity and safety of micorbiome-directed immunotherapy.

cancer biology↗

bioRxiv2025

Discovery of a CHI3L1-Targeted Small Molecule Modulating Neuroinflammation in Alzheimers Disease via DNA-Encoded Library (DEL) Screening

Chitinase-3-like protein 1 (CHI3L1, also known as YKL-40) has emerged as a central effector of astrocyte-mediated neuroinflammation and a promising biomarker for Alzheimers disease (AD). However, small molecule CHI3L1 inhibitors that modulate neuroinflammation are limited. Here, we report the discovery of a CHI3L1-targeted small molecule, DEL-C1, identified through DNA-encoded library (DEL) screening and validated using orthogonal biophysical, computational, and cellular approaches. DEL-C1 demonstrated direct CHI3L1 binding in microscale thermophoresis (MST) and surface plasmon resonance (SPR) assays, with reversible and concentration-dependent association. Molecular docking and 100-ns molecular dynamics simulations revealed a stable binding mode within the CHI3L1 substrate groove, anchored by Tyr206 and flanked by Trp99 and Trp352, supporting a thermodynamically favorable interaction. In vitro ADME profiling indicated a balanced physicochemical profile, permeability, and metabolic stability, consistent with CNS drug-like properties. Functionally, DEL-C1 reversed CHI3L1-induced astrocyte dysfunction by restoring A{beta} uptake, lysosomal acidification, and proteolytic activity, while reducing CHI3L1 and IL-6 secretion. DEL-C1 also suppressed CHI3L1-driven NF-{kappa}B transcriptional activation, highlighting its anti-inflammatory potential. Collectively, this study establishes DEL-C1 as a promising small molecule modulator of CHI3L1 and a chemical tool to interrogate astrocyte-driven neuroinflammation in AD.

biophysics↗

bioRxiv2025

HLA-DQ2/8 genotype imprints strain-level gut microbiome and constrains pantothenate availability in healthy adults

HLA-DQ2/8 haplotypes are established genetic risk factors for autoimmune diseases and are known to influence gut microbiota assembly in early life. However, their impact on the adult microbiome and functional consequences for host physiology remain unclear. Here, we performed a genotype-stratified multi-omics analysis of 60 healthy adults, including 28 HLA-DQ2/8 carriers and 32 non-carriers. We found that host HLA-DQ2/8 genotype was significantly associated with gut microbiome composition, with an effect size exceeding that of sex and BMI. HLA-DQ2/8 carriers exhibited higher gut microbial alpha-diversity, lower virulence factor abundance, and a distinct species profile enriched in butyrate-producing taxa. We identified pervasive intra-species phylogenetic and functional divergence linked to the DQ2/8 genotype. This diversification reflects predicted HLA-restricted microbial peptide-binding specificities, suggesting a possible role for antigen presentation-mediated immune selection, a mechanism further supported by AlphaFold3 structural modeling. We found an enrichment of microbial pathways for pantothenate and coenzyme A (CoA) biosynthesis in carriers, primarily driven by functionally divergent Blautia obeum strains. This functional shift paralleled lower levels of serum pantothenate and HDL-cholesterol in the host. Our findings suggest a potential genotype-microbiome-host axis where antigen presentation-mediated immune selection may modulate microbial adaptation, with possible implications for the host availability of essential cofactor precursors and lipid metabolism.

microbiology↗

bioRxiv2025

CancerSubminer: an integrated framework for cancer subtyping using supervised and unsupervised learning on DNA methylation profiles

Human cancer is highly heterogeneous, resulting in variable drug resistance and clinical outcomes. This complexity hinders accurate prognosis prediction and the development of targeted therapies. Molecular subtyping addresses these challenges by grouping cancers into more homogeneous subsets based on molecular characteristics, enabling subtype-specific treatment strategies. Subtyping is crucial for early diagnosis, personalized therapy, and improved survival by capturing differential therapeutic responses. Existing approaches to cancer subtyping fall into supervised and unsupervised categories. Supervised methods, often trained on The Cancer Genome Atlas (TCGA), rely on predefined subtype annotations but face limitations in generalizability and novel subtype discovery. Unsupervised methods, while capable of identifying new subtypes, may overlook widely recognized ones, hindering consistency with established classifications. Multi-omics approaches improve accuracy but are constrained by costs and data collection. We propose CancerSubminer, a hybrid subtyping framework that integrates supervised and unsupervised learning. A subtype classifier is first trained on labeled data, after which clustering is applied to extracted features, with low-confidence samples reassigned to refine subtype boundaries. Model is retrained with the refined subtypes, and adversarial training corrects batch effects and learns domain-invariant features across labeled TCGA and unlabeled external datasets. A subsequent semi-supervised fine-tuning phase aligns subtypes between datasets and designates low-confidence samples as potential novel candidates. CancerSubminer was evaluated on five cancer types, including breast, bladder, brain, kidney, and thyroid cancers, using TCGA methylation data with annotated subtypes and unlabeled datasets from the Gene Expression Omnibus. The framework outperformed state-of-the-art subtyping models (iClusterPlus, iClusterBayes, NEMO) and clustering methods (Spectral, K-means). Kaplan-Meier survival analysis demonstrated significant prognostic separation (p < 0.05) for all cancers, including thyroid cancer where predefined subtypes showed no significance but CancerSubminer-derived subtypes did. These findings highlight CancerSubminers ability to identify distinct prognostic subtypes, mitigate batch effects, and improve prognostic stratification across heterogeneous datasets. CancerSubminer is publicly available at https://github.com/joungmin-choi/CancerSubminer.

bioinformatics↗

bioRxiv2025

Adventitial leptin receptor-expressing fibroblasts are preferential contributors to fibrotic remodeling of the heart post infarction

BackgroundCardiac fibrosis, a hallmark of heart failure and an unmet clinical need, arises from pathological activation of pre-existing cardiac fibroblasts (CFs), but the contribution of CF heterogeneity to this process remains unclear. MethodsMurine models were used to lineage trace or deplete a specific sub-population of CFs at baseline and after myocardial infarction (MI). Transcriptional and epigenetic differences between fibroblast subsets were assessed using next-generation sequencing. Conservation in humans was evaluated through single-cell RNA-seq datasets and histological examination. ResultsIn mice, fibroblasts were the sole cardiac cell type expressing the signaling-capable isoform of the leptin receptor (LepR). LepR+ CFs emerged neonatally, occupied a defined niche in the coronary adventitia, exhibited enhanced hedgehog signaling, and responded to leptin. After MI, LepR-Cre+ CFs proliferated more than interstitial CFs, became a predominant fibroblast lineage in the scar, and their genetic ablation reduced fibrosis while improving function. LepR+ CFs were also detected in the human heart, where they were embedded in an adipocyte-rich niche. ConclusionsThese findings identify adventitial fibroblasts as key drivers of pathological remodeling and demonstrate that fibroblasts, rather than cardiomyocytes, are the principal responders to leptin in the heart, redefining how this major endocrine pathway influences cardiac remodeling and disease.

cell biology↗

bioRxiv2025

KF/parabrachial complex PACAP - glutamate pathway to the extended amygdala couples rapid autonomic and delayed endocrine responses to acute hypotension

The calyx of Held is a giant axo-somatic synapse classically confined to the auditory brainstem. We recently identified morphologically similar calyx-like terminals in the extended amygdala (EA) that arise from the ventrolateral parabrachial complex and co-express PACAP, CGRP, VAChT, VGluT1, and VGluT2, targeting PKC{delta}+/GluD1+ EA neurons. Here we asked whether this parabrachial-EA pathway participates in compensation during acute hypotension. In rats given hydralazine (10 mg/kg, i.p.), we quantified Fos protein during an early phase (60 min) and a late phase (120 min). Early after hypotension, Fos surged in a discrete subpopulation of the parabrachial Kolliker-Fuse (KF) region and in the EA, whereas magnocellular neurons of the supraoptic and paraventricular nuclei (SON/PVN) remained largely silent. By 120 min, magnocellular SON/PVN neurons were robustly Fos-positive. Confocal immunohistochemistry showed that most Fos+ PKC{delta}/GluD1 EA neurons were encircled by PACAP+ perisomatic terminals (80.8%), of which the majority co-expressed VGluT1 (88.1%). RNAscope in situ hybridization further identified a selective KF population co-expressing Adcyap1 (PACAP) and Slc17a7 (VGluT1) that became Fos-positive during the early phase. Together these data suggest that a KFPACAP/VGluT1 projection forms calyceal terminals around PKC{delta}/GluD1 EA neurons, providing a high-fidelity route for rapid autonomic rebound to falling blood pressure, while slower endocrine support is subsequently recruited via neurohormone-magnocellular activation. This work links multimodal parabrachial output to temporally layered autonomic-neuroendocrine control. Short abstractAcute hypotension triggers rapid autonomic compensation followed by slower endocrine support. We identify a Kolliker-Fuse (KF) PACAP/VGluT1 pathway to the extended amygdala (EA) that initiates the fast limb. In hydralazine-treated rats, Fos rose at 60 min in KF and EA but not in magnocellular SON/PVN; by 120 min SON/PVN were strongly Fos-positive. Confocal microscopy showed that [~]81% of Fos+ PKC{delta}/GluD1 EA neurons were surrounded by PACAP+ calyceal terminals, [~]88% of which co-expressed VGluT1. RNAscope revealed a selective KF Adcyap1/Slc17a7 population that became Fos-positive early. We conclude that KF PACAP/VGluT1 calyces onto PKC{delta}/GluD1 EA neurons provide a high-fidelity autonomic pathway that precedes vasopressin-mediated endocrine compensation.

neuroscience↗

bioRxiv2025

Effective repurposed antivirals against an emerging virus

The ongoing global monkeypox virus (MPXV) outbreak urgently needs effective medications, which be accelerated through drug repurposing. However, it is challenging to poinpoint protein targets. Here we introduce a novel method rooted in molecular evolutionary theory for quick drug target identification for MPXV. It identifies drug targets as positively selected genes of viral proteins which bind host proteins. From the identified targets, we select a top gene product OPG021 for virtural drug screening. One top-ranked drug nilotinib is experimentally shown to have a significant 69% of antiviral efficacy of the FDA-approved antiviral tecovirimat (TPOXX(R) or ST-246). Higher binding affinity but not antiviral efficacy of repursposed drugs than FDA-approved drugs suggests the complexity of drug repurposing and underscores the importance of experimental validation. This innovative drug target identification strategy will contribute to combating the ongoing MPXV outbreak and other viral acute and chronic viral diseases.

pathology↗

bioRxiv2025

A Machine Learning Approach Reveals CRISPR-Cas I-F as a Genomic Marker of Antibiotic Susceptibility in Uropathogenic E. coli

BackgroundAntimicrobial resistance (AMR) in Escherichia coli is a critical global health challenge, particularly in urinary tract infections, where first-line treatments are increasingly compromised. While horizontal gene transfer (HGT) via mobile genetic elements is a major driver of AMR, the genomic factors that may constrain resistance gene acquisition remain underexplored. CRISPR-Cas systems, which provide adaptive immunity against foreign DNA, could influence AMR dynamics, but their role in E. coli remains incompletely understood. MethodsWe conducted a comprehensive whole-genome analysis of uropathogenic E. coli isolates, including a newly sequenced collection from Australian clinical samples and an independent, globally sourced validation cohort. Antimicrobial susceptibility profiles were integrated with CRISPR-Cas subtype classification, resistance gene burden, and mobile element content. Elastic net regression, adaptive lasso, and tree-based machine learning models were used to identify genomic predictors of resistance, with performance validated across both datasets. ResultsCRISPR-Cas subtype I-F was consistently associated with susceptibility to antibiotics commonly acquired through HGT, including trimethoprim and ampicillin, and linked to lower ARG and MGE burden. In contrast, Type I-E arrays, especially when co-occurring with orphan I-F arrays, were associated with increased resistance. These associations remained robust after adjusting for phylogroup, plasmid content, and genomic background, and were validated across datasets. ConclusionsSubtype-specific CRISPR-Cas systems shape antibiotic resistance profiles in E. coli, with Type I-F functioning as a potential genomic barrier to ARG acquisition. These findings highlight CRISPR array typing as a novel biomarker for AMR risk prediction and surveillance, and suggest new opportunities for leveraging CRISPR-based mechanisms to limit resistance propagation in clinical contexts.

genomics↗

bioRxiv2025

PTH-Induced Behavioral and Metabolic Alterations in Mouse Models of Hyperparathyroidism

Parathyroid hormone (PTH) is a critical endocrine regulator of calcium homeostasis and bone remodeling and is widely employed in clinical settings through synthetic analogs for the treatment of osteoporosis. Although traditionally considered a peripheral regulator, emerging evidence indicates that PTH also exerts effects through the central nervous system (CNS). This study investigated the neuropsychiatric impact of elevated PTH and explored potential CNS involvement using multiple murine models of hyperparathyroidism (HPT). Distinct behavioral phenotypes were observed across models, indicating that psychiatric symptoms vary depending on disease etiology and progression. The effects of hPTH(1-34), a clinically approved PTH analog, were further assessed in male and female mice. Under pharmacological concentrations, hPTH(1-34) enhanced locomotor activity in males but induced mild anxiety-like behavior in females. These behavioral changes in females were independent of the estrus cycle and were amplified by ovariectomy. Metabolic analysis indicates PTH affects the basic metabolism by inhibiting the respiratory exchange ratio, promotes the energy expenditure and locomotion without affecting the food consumption in a 48hr range. To further investigate the molecular effect of PTH in the brain, a PTH1R-Cre mouse line was generated to map PTH receptor-1 (PTH1R) expression. Widespread expression of PTH1R was detected across the brain, including in both neuronal and non-neuronal cell populations. These findings suggest that PTH may influence behavior through interactions with PTH1R-expressing cells in brain vasculature and circumventricular regions. However, further studies are warranted to define the specific brain nuclei and cell types involved in PTH-driven modulation of neurobehavioral function.

neuroscience↗

bioRxiv2025

De novo recovery of Ghana virus, an African bat Henipavirus, reveals differential tropism and attenuated pathogenicity compared to Nipah virus

Henipaviruses (HNVs) like Nipah (NiV) and Hendra (HeV) viruses represent severe zoonotic threats. Ghana virus (GhV), identified in 2012, is the only African bat henipavirus with a near-complete genome assembly. However, without isolates in culture, GhV biology, pathogenicity, and zoonotic potential remain poorly understood. Using reverse genetics, we recovered a full-length infectious clone of GhV at BSL-4 following rational reconstruction of its incomplete 3' leader and modification of a non-canonical transcriptional initiation site. GhV demonstrated restricted receptor tropism (ephrin-B2 but not ephrin-B3) and distinct innate immune antagonism. Replication was attenuated in primary human cells, but was enhanced in bat cells. In Syrian golden hamsters, GhV infection caused no disease or mortality. Furthermore, a chimeric NiV encoding the GhV receptor-binding protein was completely attenuated in vivo, implicating ephrin-B3 receptor usage as a critical determinant of HNV pathogenesis. These findings elucidate GhV zoonotic potential and inform strategies for virus surveillance and control. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/679836v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@1e5addcorg.highwire.dtl.DTLVardef@1f96850org.highwire.dtl.DTLVardef@12f842eorg.highwire.dtl.DTLVardef@8f013c_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Long-read sequencing-based atlas of tissue-specific expression of Drp1 transcript variants

Dynamin-related protein 1 (Drp1), encoded by DNM1L, is essential for mitochondrial fission, but its functional roles remain unclear due to isoform-specific effects from alternative splicing. Short-read RNA sequencing fails to resolve full-length isoforms involving distant exons, limiting our understanding. Here, we applied targeted long-read sequencing to profile full-length DNM1L transcripts in human left ventricle and iPSC-derived cardiomyocytes, recovering all annotated isoforms with conserved expression patterns and isoforms 1-4 being most abundant. Functional assays revealed that isoform abundance does not predict enzymatic activity. Extending this to six mouse tissues, we identified distinct, tissue-enriched expression profiles. Functional rescue in Drp1-knockout mouse embryonic fibroblasts showed isoform-dependent differences in mitochondrial fission. Isoforms lacking the A-insert (e.g., b and d) robustly rescued fission, while isoforms enriched in brain or muscle showed only partial rescue, suggesting exons 2 and 3 negatively regulate Drp1 activity. Our cross-species atlas integrates long-read transcriptomics with functional validation, revealing how isoform diversity underpins tissue-specific mitochondrial dynamics and physiological roles of Drp1. SummaryUsing long-read sequencing, we mapped full-length DNM1L/Dnm1l isoforms in human and mouse tissues, uncovering tissue-specific expression and isoform-dependent mitochondrial fission activity. This reveals how alternative splicing shapes Drp1 function, with implications for understanding its role in health and disease.

cell biology↗