Biology subjects

Gu, Q.

Publications and source records attributed to Gu, Q..

At least 19 recordsLinked to original sources

bioRxiv2026

Plantaricin JK from Lactiplantibacillus plantarum ZJ316 inhibits enterohemorrhagic Escherichia coli O104:H4 and alters fecal microbial communities in vitro

Enterohemorrhagic Escherichia coli (EHEC) O104:H4 is a highly virulent foodborne pathogen for which antibiotic therapy is contraindicated, severely restricting conventional treatment options; therefore, the development of novel antimicrobial strategies is essential. This study investigated the antibacterial activity and gut microbiota-modulating effects of plantaricin JK (PlnJK), a two-peptide bacteriocin from Lactiplantibacillus plantarum. Chemically synthesized PlnJK exhibited a minimum inhibitory concentration (MIC) of 32 M against E. coli O104:H4, disrupting membrane integrity as evidenced by increased extracellular conductivity, ATP depletion, and ultrastructural damage. In an in vitro fecal fermentation model, PlnJK reduced Escherichia-Shigella abundance from 36.70% to 30.60% which contains E. coli O104:H4-related taxa, enriched Clostridium (5.70% vs 2.40% in infection group), Rikenellaceae, and Lactobacillaceae, and significantly elevated short-chain fatty acid (SCFA) levels including butyrate (p < 0.01) and isovalerate (p < 0.05). To translate this into a deliverable format, CRISPR-Cas9-engineered L. plantarum strains with plnJK knockout, complementation, and overexpression were constructed. Compared with the chemically synthesized peptide, LAB-derived PlnJK--especially from the overexpression strain--showed superior efficacy in restoring microbial diversity and enhancing SCFA production, significantly increased Shannon index and reduced dominance (p < 0.01), while promoting butyrate (p < 0.01) and isovalerate (p < 0.01) production compared to the knockout control. The engineered strains further revealed a clear dose-dependent effect, as overexpression potentiated while knockout abolished the beneficial modulation. These findings demonstrate that PlnJK acts through membrane disruption and beneficially modulates gut microecology, with LAB-mediated in situ delivery offering a promising strategy for anti-EHEC live biotherapeutic development.

microbiology↗

bioRxiv2026

Integrative multi-omic analysis identifies tumor-intrinsic p38 as a driver of immune exclusion in human epithelial cancers

Patients with tumors not responding to immune-checkpoint inhibition (ICI) often harbor a non-T cell-inflamed tumor microenvironment, characterized by the absence of IFN-{gamma}-associated CD8+ T cells and dendritic cell activation. While the role of p38 mitogen-activated protein kinases (MAPKs) in regulating dendritic and myeloid cells is established, the tumor-intrinsic immunomodulatory function of p38 remains underexplored. Here, we identify tumor cell-intrinsic p38 signaling as a target candidate associated with immune exclusion and reduced immunotherapy response. In human papillomavirus-negative head and neck squamous carcinoma (HNSCC), molecular analysis of 395 tumor tissues revealed a p38-centered network enriched in non-T cell-inflamed tumors. Multi-cancer single-cell RNA sequencing analysis of over 200,000 cells further identifies p38 activation as a potential immune-exclusion program across multiple epithelial tumor types, including HNSCC and lung squamous cell carcinoma (LUSC), supported by tissue validation in [~]250 human biospecimens using multispectral imaging and digital spatial profiling. Functional studies demonstrate that p38 knockdown or pharmacologic inhibition in HNSCC and LUSC cell lines increases T cell migration, with CXCL16 identified as a chemokine mediator in vitro; neutralization of CXCL16 attenuated this effect. Together, these findings identify tumor-intrinsic p38 activation as a driver of immune exclusion in epithelial cancers and support its potential as a therapeutic target to overcome immunotherapy resistance.

Cancer Biology↗

bioRxiv2026

A Web-based software toolkit for accessible and best-practice machine learning analyses in biomedical research

Machine learning is increasingly central to biomedical research, but using machine learning well often requires substantial computational expertise and methodological care to produce high-quality results. To make machine learning tools more accessible to biomedical researchers while supporting best-practice approaches, we developed the Galaxy Learning and Modeling (GLEAM) software toolkit. GLEAM enables researchers to perform supervised machine learning analyses through a set of web-based, code-free software tools for tabular, image, and multimodal biomedical datasets. GLEAM standardizes data partitioning, model selection, training, evaluation, and reporting, helping researchers apply machine learning with greater rigor and consistency. GLEAM runs on the Galaxy computational workbench and uses Galaxys core features to make all analyses accessible, reproducible, and scalable. We validated GLEAM on three biomedical tasks: predicting patient response to immunotherapy, skin lesion classification, and cancer recurrence prediction. Across these tasks, GLEAM produced highly accurate predictive models and improved transparency, reproducibility, and rigor.

bioinformatics↗

bioRxiv2026

Improve the Efficacy of B7-H3-Targeting Antibody-Drug Conjugate DS-7300a in TP53-deficient Tumors by Inducing Ferroptosis

Immune checkpoint B7-H3 is an emerging target for immunotherapy. DS-7300a is an advanced B7-H3-targeting antibody-drug conjugate (ADC) warheaded with the topoisomerase I inhibitor DXd. DS-7300a has demonstrated clinical activity, but molecular biomarkers to predict its therapeutic response remain elusive. TP53 is one of the most mutated tumor suppressor genes across cancers, and effective therapies are urgently needed for TP53-deficient cancers. Using prostate cancer (PCa) as a model system, we reported that DS-7300as anti-tumor efficacy is highly dependent on functional p53 in cancer cells, and TP53 defects confer resistance to DS-7300a. Mechanistically, we found that DS-7300a and its payload, DXd, induce DNA damage and activate the ATM/ATR/CHK signaling cascade, thereby stabilizing p53 and inducing a pro-apoptotic and senescence-associated transcriptome. In contrast, TP53-deficient cells fail to detect DXd-induced DNA damage, maintain a high proliferation rate, and exhibit low levels of apoptosis and senescence, thereby conferring resistance to DS-7300a. Ferroptosis is an iron-dependent form of regulated cell death triggered by lipid peroxidation, which is mechanistically and morphologically distinct from apoptosis. Interestingly, DS-7300a treatment elevates lipid peroxidation in TP53-deficient cancer cells and upregulates glutathione peroxidase 4 (GPX4), an antioxidant enzyme that mitigates lipid peroxidation. Using isogeneic xenograft models and a newly developed humanized B7-H3 PCa model, we demonstrated that inducing ferroptosis by pharmacological inhibition of GPX4 enhances DS-7300as efficacy in TP53-deficient tumors. Our studies demonstrate that TP53 status dictates anti-tumor responses to DS-7300a, and ferroptosis induction represents a promising therapeutic approach to overcome resistance to DS-7300a in malignancies harboring TP53 defects.

cancer biology↗

bioRxiv2026

CosMxScope: Scalable Reconstruction and Digital Pathology Integration of Imaging-Based Spatial Transcriptomics Data

Spatial transcriptomics technologies have transformed the capacity to quantify gene expression from human tissues, simultaneously capturing both the cell functional state and spatial organization at cellular and subcellular resolution. The CosMx Spatial Molecular Imager (SMI) is one of the leading platforms at single-cell spatial multi-modal omics profiling, capable of measuring thousands of RNA or protein targets per cell across whole slide sections. Data exported includes field-of-view (FOV) image tiles, subcellular transcript coordinates, and cell segmentation polygons, outputs that are rich in spatial information but not directly compatible with widely used digital pathology tools. Here we present CosMxScope, a lightweight open-source Python framework that bridges CosMx spatial outputs with histopathology visualization environments. CosMxScope provides functions for stitching FOV image tiles into reconstructed whole-slide images, converting cell segmentation polygons and transcript coordinates into GeoJSON objects which enabled further assessments within QuPath, and generating spatial visualization plots of cell types, transcript locations, and gene expression patterns. The framework is designed for practical use in translational research settings, enabling interactive exploration of spatial transcriptomic data alongside cell morphology. CosMxScope has been applied in multiple ongoing research projects involving CosMx profiling of human and mouse tissues, supporting pathology-based spatial analysis workflows. This open-source software is available at https://github.com/AivaraX-AI/CosMxScope.

bioinformatics↗

bioRxiv2026

A metabolically resistant spexin analogue, LIT-01-144, induces potent non-opioid peripheral antinociception in persistent pain via activation of GALR2

Chronic pain affects a significant portion of the global population and imposes substantial clinical and socioeconomic burdens. Current treatments mainly rely on opioid analgesics, which carry serious risks of dependence and misuse, underscoring the urgent need for alternative therapeutic strategies. Galanin receptors (GALR1-3) are known to be involved in modulating pain, yet their specific roles remain poorly understood due to the lack of receptor subtype-selective ligands. Recently, spexin has been identified as an endogenous peptide that selectively activates GALR2 and GALR3, offering a new scaffold for developing pharmacological tools targeting these receptor subtypes. In this study, we report the design and characterization of a modified spexin analog, LIT-01-144, engineered through N-terminal functionalization with a fluorocarbon chain to improve metabolic stability while preserving receptor selectivity. In vitro assays showed that LIT-01-144 has high potency at GALR2 and GALR3, with minimal activity at GALR1. Pharmacokinetic studies revealed a significantly longer plasma half-life compared to native spexin and no central nervous system penetration. In mice, intracerebroventricular administration of LIT-01-144 produced strong antinociceptive effects at doses ten times lower than spexin. While systemic administration showed no notable antinociception in naive animals, LIT-01-144 significantly reduced pain responses in a mouse model of persistent inflammatory pain induced by complete Freunds adjuvant (CFA). This antinociceptive activity was specifically mediated through GALR2 and was independent of opioid receptor pathways. In situ hybridization further showed an increase in Galr2-positive neurons in dorsal root ganglia of inflamed mice. Overall, these findings highlight GALR2 as a promising peripheral target for developing non-opioid analgesics and demonstrate the potential of LIT-01-144 as a valuable tool for understanding GALR2-mediated mechanisms of pain modulation.

pharmacology and toxicology↗

bioRxiv2025

A Generative Foundation Model for Cryo-EM Densities

Single-particle cryo-electron microscopy (cryo-EM) enables structure determination of macromolecular complexes, yet reconstructions are often degraded by noise, anisotropic sampling and reconstruction artifacts. Correcting these effects is an ill-posed inverse problem that requires strong prior knowledge in addition to experimental data. Here we introduce cryoFM, a generative foundation model for cryo-EM densities that unifies data-driven structural priors with dataset-specific constraints within a Bayesian inference framework. CryoFM is trained in an unsupervised manner on thousands of high-quality cryo-EM maps using flow matching, learning a generalizable prior over macromolecular density distributions. Combined with explicit likelihood models describing experimental degradations, cryoFM enables flow posterior sampling, an inference-only procedure that performs denoising and restoration and refinement while remaining explicitly constrained by dataset-derived statistics. We show that this framework improves density reconstruction and refinement across diverse experimental settings, including preferred-orientation datasets and cases with strong spatial heterogeneity in signal-to-noise ratio, without introducing hallucinated features. In addition, cryoFM can be fine-tuned into conditional generative models for density post-processing, yielding maps with improved interpretability and fewer artifacts compared to existing supervised approaches. Together, cryoFM establishes generative foundation models as a principled and controllable framework for cryo-EM density reconstruction and modification.

biophysics↗

bioRxiv2025

Lysine-R2HGylation identified as a post-translational modification in R2HG-elevated cancers

R-2-Hydroxyglutarate (R2HG), an oncometabolite predominantly produced by mutated isocitrate dehydrogenase 1/2 (IDH1/2) in various cancers, is known to drive cancer progression through noncovalent inhibition of -ketoglutarate (KG)-dependent enzymes. In this work, we propose an alternative mechanism wherein R2HG contributes to cancer development via covalent modification of biologically critical lysines, a process termed lysine-R2HGylation (KR2HG). We designed and synthesized R2HG-mimicking probes, demonstrating their effectiveness in facilitating KR2HG target profiling and site mapping. We identified KR2HG as a previously unrecognized post-translational modification, confirmed its C5-linkage on GSTP1(K209), and demonstrated that SIRT5 functions as a deacylase for GSTP1-KR2HG in vitro. Furthermore, we found that R2HG slightly but significantly inhibits the enzymatic activity of GSTP1 through KR2HG and dramatically suppresses monocyte differentiation via this catalytically important lysine modification. Our findings provide an alternative perspective on the role of R2HG in leukemia progression and offer a practical tool for the clinical investigation of R2HG-elevated cancers.

molecular biology↗

bioRxiv2025

Human Rhinovirus 16 impacts cilia structure in 3D cultured primary bronchial epithelial tissue through alternative splicing of host cilia RNAs.

Human rhinoviruses (HRV) are a leading cause of the common cold but can often lead to respiratory complications such as wheeze in young children. In a transcriptomic study of respiratory nasal swab specimens from children hospitalised with acute wheeze, a significant alteration was found in the expression of the serine/arginine rich splicing factor (SRSF) kinase, SRPK1, between HRV positive children with acute exacerbations and HRV negative controls. As this kinase can regulate host RNA splicing, we hypothesised that HRV infection could dysregulate the expression of host mRNAs to affect antiviral functions or to alter the morphological features of the infected respiratory epithelium. Here, we show that pharmacological inhibition of SRPK1 in primary bronchial epithelial cells resulted in increased HRV16 replication while overexpression of SRPK1 reduced viral replication. In a primary bronchial epithelial 3D model infected with HRV16 decreased phosphorylation of SRSF1, 3 and 6 was observed. Furthermore, transcriptomic and alternative splicing (AS) bioinformatic analysis revealed the significantly altered AS of 1228 host genes during infection. Subsequent pathway analysis revealed the enrichment of most of these genes in networks related to cilia development and function. HRV16 infection led to significantly decreased cilia length and total cilia numbers in the primary bronchial epithelial 3D model together with changes to selected cilia proteins. Overall, this investigation has unravelled novel cellular networks implemented during HRV infection that may lead to acute exacerbations of respiratory infections. Author summaryHuman rhinoviruses cause the common cold. In immunocompetent individuals this is usually a self-limiting infection. However, in young children and the elderly, infection can lead to complications such as bronchiolitis, croup, and wheezing. Rhinovirus infection can exacerbate chronic conditions such as cystic fibrosis, chronic obstructive pulmonary disease and asthma. Understanding the molecular pathology of this exacerbation could lead to new avenues for therapy. In this study, we discovered that a multifunctional cellular enzyme called serine arginine protein kinase 1 (SRPK1) is a restriction factor for human rhinovirus 16 (HRV16) infection. One key cellular function of SRPK1 is to regulate RNA splicing through modifying the SR proteins that normally enhance splicing. In three dimensional tissues grown from human bronchial epithelial cells, we found that HRV16 infection led to decreased levels of modified SR proteins. This change resulted in significant alterations in RNA expression in the infected cell. Most of these alterations affected production of the correct versions of cilia proteins resulting in reduced cilia numbers and cilia blunting. This type of damage due to HRV infection would result in inefficient clearance of subsequent viral infections prolonging the viral infection leading to lower respiratory tract infection and to exacerbations of existing chronic disease.

microbiology↗

bioRxiv2025

The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge

Despite the rise of single particle cryo-electron microscopy (cryo-EM) as a premier method for resolving macromolecular structures at atomic resolution, methods to address molecular heterogeneity in vitrified samples have yet to reach maturity. With an increasing number of new methods to analyze the multitude of heterogeneous states captured in single particle images, a systematic approach to validation in this field is needed. With this motivation, we issued a challenge to the community to analyze two cryo-EM particle image sets of thyroglobulin that exhibit continuous conformational heterogeneity. The first dataset was experimental and the second was generated with a simulator, allowing control over the distribution of molecular structures and enabled direct comparison between participants submissions and the ground truth molecular structures and distributions. Participants were asked to submit 80 volumes representing the heterogeneous ensemble and estimate their respective populations in the image sets provided. Participation of the research community in the challenge was strong, with submissions from nearly all developers of heterogeneity methods, resulting in 41 submissions across both datasets. Submissions qualitatively exceeded expectations, with the molecular motions identified by methods resembling both each other and the ground truth motion. However, quantitatively assessing these similarities was a challenge in and of itself. In the process of assessing the submissions, we developed several validation metrics, most of which require reference to the underlying ground truth volumes. However, we have also explored the use of metrics that do not necessarily reference ground truth. This is particularly apt for experimental datasets where ground truth is inaccessible. These approaches allowed us to assess the similarity and accuracy in volume quality, molecular motions, and conformational distribution of di!erent submissions. These metrics and the e!orts of all participants help chart a path forward for the improvements of heterogeneity methods for cryo-EM and for future challenges to validate these new methods as they continue to be developed by the community.

biophysics↗

bioRxiv2025

DIFFERENTIAL ROLES OF RAD18 IN REPRESSING CARCINOGEN- AND ONCOGENE-DRIVEN MUTAGENESIS IN VIVO

The DNA repair protein RAD18 activates Y-family Trans-Lesion Synthesis (TLS) DNA polymerases that are DNA damage-tolerant and potentially error-prone. RAD18 is also frequently overexpressed and pathologically activated in cancer cells. However, the extent to which RAD18 shapes cancer genomes and impacts tumorigenesis is unclear. Therefore, we tested the effect of Rad18 status on chemically-induced and oncogene-driven tumorigenesis. In a chemically-induced oral carcinogenesis model, acute (2-16 days) 4NQO-treatment induces expression of Rad18 and TLS polymerase mRNAs in mouse oral epithelial cells prior to emergence of oral squamous cell carcinomas (OSCCs). Chronic (8 week) 4NQO-treatment leads to onset of oral tumors that is accelerated in Rad18-/- mice when compared with Rad18+/+ animals. Analysis of OSCC exomes reveals increased levels of G(C)>T(A) transversions in Rad18-/- tumors when compared with Rad18+/+. Therefore, Rad18 promotes error-free bypass of 4NQO-induced DNA lesions and suppresses 4NQO-induced oral carcinogenesis. In a KrasG12D-induced lung carcinogenesis model, Rad18-deficiency did not affect rates or incidence of oncogene-induced lung tumors or mutations. Taken together, we demonstrate that Rad18 has context-specific tumor-suppressive activity. Given the prevalence of 4NQO-like environmental exposures, RAD18 is highly likely to shape human cancer genomes and perhaps influence other aspects of the tumorigenic process.

cancer biology↗

bioRxiv2025

A Paradigm Shift in Walking, Sleep, and Exercise: Unique Effects on Blood Oxygen Saturation, Oxygen Diffusion, and Cellular Metabolism

Hypoxia underlies or complicates a wide range of chronic conditions, including cancer, arthritis, chronic pain, multiple sclerosis, stroke, chronic kidney disease, diabetes and more. Research is presented supporting indications that slower-paced exercises may develop states of relaxation, combined with enhanced respiration, which may trigger accelerated diffusion and facilitated oxygen use in the cells, stimulating cellular regeneration and healing. Metarobic theory is proposed as a physiological explanation for the benefits of slower-paced exercises, and as a good fit with aerobic and anaerobic categories of exercise. Metarobic theory posits that the momentary post activity drop in blood oxygen saturation (SpO2) following slow-paced exercises, and intermittently during sleep, may be the result of increased oxygen diffusion and metabolism. Metarobic effects may explain the non-aerobic health benefits of slower paces of walking, tai chi, qigong, and other slow-paced exercises, as well as the healing benefits of sleep. Research from the current study is presented, which supports that the momentary large drops in SpO2 ranging from 85% to 92% (m=89.2%{+/-}1.79) following slower-paced exercises, and periodically during sleep, may indicate a shift in the use and metabolism of oxygen. It is suggested that the momentary drop in SpO2 may follow an accelerated period of oxygen diffusion in response to hypoxic areas of the body, and a need for enhanced healing and cellular regeneration. In relation to sleep, this contrasts to current theory that lower levels of SpO2 during sleep result from more shallow respiration, due to the body needing less oxygen during sleep, resulting in hypoxemia. The end effect of slow-paced exercises and sleep may be to reverse or moderate hypoxia in the body through metarobic effects including enhanced oxygen diffusion, supporting healing and cellular regeneration.

physiology↗

bioRxiv2024

XRN1 supplies free nucleotides to feed alphavirus replication

Several RNA viruses induce widespread degradation of cellular mRNAs upon infection; however, the biological significance and mechanistic details of this phenomenon remain unknown. Here, we make use of a model alphavirus, Sindbis virus (SINV), to fill this knowledge gap. We found that SINV triggers cellular RNA decay through the exonuclease XRN1 and the 5-to-3 degradation machinery (5-3DM). These proteins accumulate at viral replication organelles (VROs) and interact with the non-structural protein 1 (nsP1), bringing mRNA degradation into proximity with vRNA synthesis. Our data suggest that monophosphate nucleotides released by cellular RNA decay are recycled through the salvage pathway to feed viral replications. Our work thus reveals a fundamental connection between cellular mRNA degradation and viral replication via nucleotides repurposing. Research highlightsO_LI5-3 RNA decay is essential for the replication of a wide range of viruses. C_LIO_LIXRN1 directly interacts with transcripts which are degraded during infection. C_LIO_LIRNA decay factors and salvage pathway members localise to viral factories. C_LIO_LISupplying nucleosides to several 5-3DM deficient cells facilitates SINV infection. C_LI

biochemistry↗

bioRxiv2024

SS-31 protects against bleomycin-induced lung injury and fibrosis

ObjectiveThe aim of this research was to investigate if the mitochondria-targeting peptide SS-31 could serve as a protective measure against bleomycin-induced pulmonary fibrosis in mice. MethodMice were split into four groups named CON group, SS-31 group, BLM group, and the BLM+ SS-31 group. SS-31 was administered daily from the day prior to the experiment for the control and model groups. Mice were euthanized after 28 days of the experiment, following which blood, bronchoalveolar lavage fluid, and lung tissue were collected for analysis. ResultsThe study demonstrated that SS-31 could potentially mitigate the reduction in mice. It was observed through HE and Masson staining, immunohistochemistry, hydroxyproline detection, and fibrosis index measurement via Western blot that SS-31 could alleviate pulmonary fibrosis caused by BLM. Electron microscopy and ATP detection further suggested that SS-31 might help protect mitochondrial structure and function. It was also found that SS-31 could reduce reactive oxygen species and myeloperoxidase, thereby alleviating the reduction of antioxidant factor MPO and SOD, as well as diminishing the inflammatory factors TNF-, IL-1 {beta}, and IL-6. ConclusionThe mitochondria-targeting drug SS-31 exhibited potential in mitigating bleomycin-induced pulmonary fibrosis, improving mitochondrial structural and functional damage, stabilizing the balance between oxidative and antioxidant systems, reducing inflammatory factor expression, and improving apoptosis in lung tissue.

pharmacology and toxicology↗

bioRxiv2024

In Situ Integration of Porous Polyethylene Nanomembrane with Wound Exudates for Scarless Healing

Achieving scarless wound repair through innovative material designs, such as hydrogels infused with growth factors and cells, has been extensively explored. In this study, we introduce a scarless healing material called pgPE, which is based on a porous and biologically inert ultra-high molecular weight polyethylene (UHMWPE) nanomembrane. This highly flexible nanomembrane conforms closely to the wound site and effectively absorbs wound-associated species into its nanopores, forming pgPE in situ. The resulting pgPE creates an ideal environment that fosters physiological metabolism while acting as a barrier against pathogens. Our findings demonstrate that pgPE facilitates complete skin reconstruction, including the regeneration of hair follicles. Additionally, we characterized the immune microenvironment and hypoxic conditions, revealing that pgPE alleviates hypoxia and modulates immune responses, thereby promoting healing towards a scar-free outcome. The integration of wound-associated species within pgPE has been evidenced through three-dimensional Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) analysis of postmortem samples. This study highlights the potential of personalized solutions that align with physiological systems for enhanced wound healing.

bioengineering↗

bioRxiv2024

The splicing factor kinase, SR protein kinase 1 (SRPK1) is essential for late events in the human papillomavirus life cycle.

Human papillomaviruses (HPV) infect epithelial causing benign lesions. However, the so-called "high risk" HPVs that infect the anogenital regions and the oropharynx can cause precancerous lesions that can progress to malignant tumours. Understanding the HPV life cycle is important to the discovery of novel antiviral therapies. HPV uses cellular splicing for the production of the full suite of viral mRNAs. Members of the serine/arginine rich (SR) protein family can positively regulate splicing. SR protein activity and cellular location is regulated by kinases through phosphorylation of their serine-arginine domains. SR protein kinase 1 (SRPK1) phosphorylates SR proteins to licence their nuclear entry and can promote nuclear splicing in conjunction with another SR protein kinase, Clk1. SRPIN340 is a specific SRPK1 inhibitor that has been reported to inhibit replication of HCV, Sindbis virus and HIV. Using organotypic raft cultures supporting the HPV16 life cycle, we show that SRPIN340 inhibits the expression of the viral replication and transcription factor, E2. Drug-mediated loss of E2 is specifically associated with inhibition of late gene expression since early gene expression is unaffected. RNA sequencing revealed that SRPIN340 treatment resulted in many gene expression changes opposite to those induced by HPV16 infection. In particular, the loss of epithelial barrier structure and immune function was restored. SRPIN340 treatment resulted in changes in alternative splicing of 935 RNAs and pathway analysis showed a predominance of changes to RNAs encoding proteins involved in chromatin conformation, DNA repair and RNA processing. SRPIN340 treatment was not associated with changes in proliferation or differentiation of keratinocytes. Collectively, these results provide evidence that SRPK1 is a host factor that is essential for HPV16 replication and therefore, targeting this factor, or the phosphorylation events it mediates, could be considered as a therapeutic strategy for HPV16 infection. AUTHOR SUMMARYHuman papillomavirus (HPV) can cause precancerous and cancerous tumours of the anogenital region, for example, the cervix. HPV infects epithelial cells and utilizes the host cell gene expression machinery to produce its own proteins. Splicing is a key mechanism used by HPV to synthesise messenger RNAs that encode the viral proteins. Splicing is positively controlled by SR proteins which require to be phosphorylated by SR protein kinase (SRPK) to enter the nucleus and regulate splicing. SRPIN340 is a specific inhibitor of SRPK. SRPIN340 treatment of HPV16-infected epithelial cells resulted in loss of expression of the viral replication and transcription factor, E2 and abrogation of late events in the viral life cycle. SRPIN340 treatment counteracted some gene expression changes to the epithelium known to be cause by HPV infection. These data suggest that SRPK1 is essential for the HPV life cycle and that it could be a potential anti-viral target.

microbiology↗

bioRxiv2024

Early-life antibiotic exposure leads to gut microbial dysbiosis associated with neurodevelopment and neuroregeneration

Early-life is a critical period for neurodevelopment and establishment of gut microbiota, which are highly susceptible to antibiotic exposure. Here, we aimed to investigate association between gut microbiota and metabolites with neurodevelopment and neuroregeneration in early-life after antibiotic exposure. To induce microbial dysbiosis in offspring, a broad-spectrum antibiotic cocktail was administered to mice dams. The prefrontal lobe, spinal cord tissues and gut sample of offspring were collected at different time with or without spinal cord crush injury. 16S rRNA sequencing and metabolomics were performed to analyze the gut microbiota and metabolites. NG2 glia were cultured and treated by mitochondrial fusion and fission compounds and metabolites. Maternal antibiotic exposure significantly affected neuronal maturation, NG2 glia proliferation, prefrontal cortex myelination and injured spinal cord neuroregeneration of offspring. Mice in antibiotic exposure group exhibited disruption of gut microbiota and metabolites, along with lower Ace, Chao and Shannon indexes, higher relative abundance of Enterobacter and Escherichia_Shigella, lower lactobacillus and Streptococcus genus, and downregulated Cyclo(Arg-Gly-Asp-D-Phe-Val), Ampicilloyl, DG(8:0/i-19:0/0:0), Petasinine and 6-Hydroxymelatonin glucuronide. These metabolites were enriched in alpha-Linolenic acid metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, linoleic acid metabolism. 6-Hydroxymelatonin glucuronide, PC(20:3/0:0), PC(20:2/0:0), Ameltolide, DG(8:0/i-19:0/0:0), Inproquone, and Chorismate were the cores of networks between gut microbiota and metabolites and negatively associated with neurodevelopment and neuroregeneration. Additionally, gut microbiota metabolites promoted NG2 glia differentiation, partly through reversing the effects of mitochondrial fusion/fission compounds. Totally, antibiotic exposure in early-life changed the composition, abundance, and metabolites of gut microbiota in offspring, which was associated with neurodevelopment and neuroregeneration.

microbiology↗

bioRxiv2024

Melanocortin-4 receptor antagonist TCMCB07 alleviates chemotherapy-induced anorexia and weight loss

Cancer patients undergoing chemotherapy often experience anorexia and weight loss that significantly deteriorates overall health, reduces treatment tolerance and quality of life, and worsens oncologic outcomes. There are currently few effective therapeutic options to mitigate these side effects. The central melanocortin system, which plays a pivotal role in regulating appetite and energy homeostasis, presents a logical target for treating anorexia and weight loss. In this preclinical study, we evaluated the efficacy of TCMCB07, a synthetic antagonist of the melanocortin-4 receptor, in mitigating anorexia and weight loss in several rat models of chemotherapy: cisplatin, 5-fluorouracil, cyclophosphamide, vincristine, doxorubicin, and a combination of irinotecan and 5-fluorouracil. Our results indicate that peripheral administration of TCMCB07 improved appetite, stabilized body weight, preserved fat and heart mass, and slightly protected lean mass after multiple cycles of chemotherapy. Furthermore, combining TCMCB07 with a growth differentiation factor 15 antibody enhanced treatment effectiveness. Similar effects from TCMCB07 treatment were observed in a rat tumor model following combination chemotherapy. No significant adverse effects nor increased chemotherapy-related toxicities were observed with TCMCB07 treatment. These findings suggest that peripheral administration of TCMCB07 holds promise as a therapeutic approach for alleviating chemotherapy-induced anorexia and weight loss, potentially benefiting numerous patients undergoing chemotherapy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/613069v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@cbe32borg.highwire.dtl.DTLVardef@1af55e7org.highwire.dtl.DTLVardef@30deb1org.highwire.dtl.DTLVardef@6c39a3_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗