Biology subjects

Zhu, J.

Publications and source records attributed to Zhu, J..

At least 181 records · Page 10Linked to original sources

bioRxiv2025

DynaRNA: Dynamic RNA Conformation Ensemble Generation with Diffusion Model

RNA plays a wide variety of roles in biological processes. In addition to serving as the coding messenger RNA (mRNA), the vast majority of RNAs function as non-coding RNAs (ncRNAs), where their dynamic structural ensemble is critical for mediating diverse biological functions. However, traditional experimental techniques and molecular dynamics (MD) simulations face significant challenges in characterizing the conformational dynamics of RNA, due to inherent methodological limitations and high computing power cost. We herein presented DynaRNA, a diffusion-based generative model for RNA conformation ensemble. DynaRNA employs denoising diffusion probabilistic model (DDPM) with equivariant graph neural network (EGNN) to directly model RNA 3D coordinates, enabling rapid exploration of RNA conformational space. DynaRNA enables end-to-end generation of RNA conformation ensemble reproducing experimental geometries without the need for Multiple Sequence Alignments (MSA) information. Our results demonstrate that DynaRNA effectively and accurately generate tetranucleotides ensemble with lower intercalation rate than molecular dynamics simulations. Besides, DynaRNA has the ability to capture rare excited states of HIV TAR(trans-activation response) element, and recapitulate de novo folding of tetraloops. DynaRNA serve as a versatile and efficient platform for modeling RNA structural dynamics, with broad implications potential in RNA structural biology, synthetic biology, and therapeutic development.

bioinformatics↗

bioRxiv2025

PFKFB2 is Pivotal for Metabolic Flexibility and Differential Glucose Utilization

BackgroundThe hearts constant energy demands make metabolic flexibility critical to its function as nutrient availability varies. The enzyme phosphofructokinase-2/fructose 2,6-bisphosphatase (PFKFB2) contributes to this flexibility by acting as a positive or negative regulator of cardiac glycolysis. We have previously shown that PFKFB2 is degraded in the diabetic heart and that a cardiac-specific PFKFB2 knockout (cKO) impacts ancillary glucose pathways and mitochondrial substrate preference. Therefore, defining PFKFB2s role in mitochondrial metabolic flexibility is paramount to understanding both metabolic homeostasis and metabolic syndromes. Further, it is unknown how PFKFB2 loss impacts the hearts response to acute stress. Here we examined how cardiac mitochondrial flexibility and the post-translational modification O-GlcNAcylation are affected in cKO mice in response to fasting or pharmacologic stimulation. MethodscKO and litter-matched controls (CON) were sacrificed in the fed or fasted (12 hours) states, with or without a 20 minute stimulant stress of caffeine and epinephrine. Mitochondrial respiration, metabolomics, and changes to systemic glucose homeostasis were evaluated. ResultscKO mice had moderate impairment in mitochondrial metabolic flexibility, affecting downstream glucose oxidation, respiration, and CPT1 activity. O-GlcNAcylation, a product of ancillary glucose metabolism, was upregulated in cKO hearts in the fed state, but this was ameliorated in the fasted state. Furthermore, metabolic remodeling in response to PFKFB2 loss was sufficient to impact circulating glucose in fasted and stressed states. ConclusionsPFKFB2 is essential for fed-to-fasted changes in cardiac metabolism and plays an important regulatory role in protein O-GlcNAcylation. Its loss also affects systemic glucose homeostasis under stressed conditions. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/656235v1_ufig1.gif" ALT="Figure 1000"> View larger version (50K): org.highwire.dtl.DTLVardef@158c873org.highwire.dtl.DTLVardef@1d0312eorg.highwire.dtl.DTLVardef@14ce8deorg.highwire.dtl.DTLVardef@4c4883_HPS_FORMAT_FIGEXP M_FIG C_FIG Research PerspectiveThis study raises and answers three key questions: how PFKFB2 contributes to cardiac mitochondrial metabolic flexibility, how post-prandial status regulates O-GlcNAcylation in a PFKFB2-dependent manner, and how altered cardiac glucose use impacts systemic glucose homeostasis under stress. These findings highlight a novel role for nutrient state in regulating cardiac metabolism, and especially O-GlcNAcylation, with PFKFB2 loss. Future studies should investigate whether reducing O-GlcNAcylation through fasting is sufficient to ameliorate pathological changes observed in the absence of PFKFB2.

biochemistry↗

bioRxiv2025

IL-17A-driven Macrophage Disorder Promotes Plaque Instability in Psoriatic Atherosclerosis

Psoriasis is a common chronic inflammatory skin disease that predisposes individuals to cardiovascular diseases such as atherosclerosis. However, the underlying mechanisms linking these conditions have not yet been fully elucidated. Recent studies have indicated that the inflammatory cytokine IL-17A plays a significant role in both diseases. The aim of this study was to investigate how psoriasis affects the stability of atherosclerotic plaques via the IL-17A/IL-17RA pathway. We performed single-cell sequencing on patients with both psoriasis and atherosclerosis to analyze changes in the immune microenvironment within their carotid plaques and psoriatic lesions. We found that IL-17A significantly upregulated the expression of pro-inflammatory factors (e.g., CXCL8) in macrophages of psoriatic atherosclerosis patients, leading to weakening of the fibrous cap structure of plaques. Additionally, IL-17A further exacerbated plaque instability by interfering with macrophage lipid metabolism, particularly sphingolipid metabolism. Finally, using in vitro experiments and animal models, we demonstrated that IL-17A enhances pro-inflammatory and metabolic abnormalities in macrophages by downregulating PPAR{gamma}. Therapeutic strategies targeting IL-17A may contribute to the simultaneous mitigation of psoriasis and atherosclerosis-associated cardiovascular risk, providing new directions for clinical intervention.

cell biology↗

bioRxiv2025

Ketogenic diet prevents obesity-associated pancreatic cancer independent of weight loss and induces pancreatic metabolic reprogramming

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with poor outcomes. Obesity is a risk factor for several cancers including PDAC due to metabolic dysregulation and inflammation. The ketogenic diet (KD) can alter metabolism and has been evaluated for its effects on tumor progression in non-obese but not obese PDAC using genetically engineered mouse models (GEMMs). We hypothesized that ketone bodies and a KD alter cell and tumor metabolism. We show that ketone treatments altered pyrimidine metabolism in PDAC cells. Moreover, in an obese PDAC GEMM, KD prevented tumor progression independent of weight loss but promoted PDAC in a non-obese PDAC GEMM. The KD-specific delay of obesity-associated PDAC was associated with pancreatic metabolic shifts in pyrimidine, cysteine and methionine, and arginine and proline pathways. These findings suggest potential benefits of a KD in preventing obesity-associated PDAC, but highlights some risks in non-obese settings.

cancer biology↗

bioRxiv2025

Identification and Characterization of PLUTO-201, a Novel Long Non-Coding RNA Associated with Poor Outcomes in Prostate Cancer

Background: Despite extensive investigation, the factors promoting aggressive prostate cancer are poorly understood. In particular, despite a few prominent examples, the role of long non-coding RNAs (lncRNAs) is largely unknown. Methods: We performed a comprehensive analysis of whole-genome transcriptome data to identify differential expression across 1,567 patients with prostate cancer, then correlated differential expression with risk of metastatic recurrence. We characterized the lncRNA most associated with metastasis in vitro and in vivo to investigate the mechanism by which it promotes aggressive prostate cancer. Results: We have identified a novel lncRNA, Prostate Cancer Associated hnRNPK Interacting Transcript (PCAHIT), which is strongly associated with metastasis and poor overall survival in men with prostate cancer. We find that overexpression/knockdown of PCAHIT in pre-clinical models of prostate cancer modulates proliferation rates and markers of an aggressive phenotype through regulation of steroid biosynthesis and expression of the MHC class I complex, driving increased growth in androgen-depleted conditions and decreased susceptibility to T cell-mediated cytotoxicity. We further find that the heterogeneous nuclear ribonucleoprotein hnRNPK directly binds PCAHIT and is indispensable for its activity. Conclusions: Overall, our findings indicate that PCAHIT is a driver of aggressive prostate cancer phenotypes and poor clinical outcomes through suppression of the immune response and increased androgen-independent cancer growth. PCAHIT is a potential biomarker of aggressive disease.

cancer biology↗

bioRxiv2025

Native-like soluble E1E2 glycoprotein heterodimers on self-assembling protein nanoparticles for hepatitis C virus vaccine design

Hepatitis C virus (HCV) is a leading cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma worldwide. E1E2-based HCV vaccine development has been hindered by the challenge of producing a soluble E1E2 (sE1E2) antigen that faithfully recapitulates the native glycoprotein heterodimer found on virions. Based on available cryo-electron microscopy (cryo-EM) structures, we rationally engineered sE1E2 for genotype 1a H77 by truncating the E1 and E2 stems (Cut1), removing a putative fusion peptide (pFP)-containing region in E1 (Cut2), and stabilizing the E1-E2 interface with diverse heterodimeric scaffolds. All H77 sE1E2.Cut1+2 scaffolds showed native-like E1-E2 association and robust binding to the broadly neutralizing antibody (bNAb) AR4A. A genotype 1a HCV-1 sE1E2.Cut1+2 variant scaffolded by a modified SpyTag/SpyCatcher (SPY{Delta}N) was selected for in vitro, structural, and immunogenic characterization. The structure of this sE1E2 scaffold in complex with bNAbs was analyzed by cryo-EM and negative-stain EM (nsEM), with an nsEM-based approach developed for antibody epitope mapping. HCV-1 sE1E2.Cut1+2.SPY{Delta}N was displayed on self-assembling protein nanoparticles (SApNPs) to enhance immunogenicity. HCV-1 sE1E2.Cut1+2.SPY{Delta}N heterodimer and SApNPs with wildtype and modified glycans were tested in mice, revealing the beneficial effects of multivalent display and oligomannose enrichment. Our study provides a rigorous foundation for next-generation HCV vaccine development. ONE-SENTENCE SUMMARYRational design, characterization, and in vivo assessment of HCV soluble E1E2 heterodimer and nanoparticles will inform vaccine development.

microbiology↗

bioRxiv2025

Spatial geometry-aware deep learning for deciphering tissue structure from spatially resolved transcriptomics

Recent advances in spatially resolved transcriptomics have enabled high-throughput gene expression profiling while preserving spatial context, thereby facilitating the investigation of spatial heterogeneity within tissues. Here, we present SpatialGEO, a spatial geometry-aware deep learning framework designed to decipher tissue organizational structures through dual-encoder feature extraction and geometric graph learning. Experimental results demonstrate the superior accuracy of SpatialGEO in identifying spatial regions across datasets encompassing diverse biological contexts and spatial resolutions. Moreover, SpatialGEO uncovers key mechanisms of immune evasion and regulation within the tumor microenvironment and provides novel biological insights into mouse embryonic development.

bioinformatics↗

bioRxiv2025

A Multimodal Graph Learning Framework for Versatile Spatial Transcriptomics Analysis with SpatialModal

The development of spatial transcriptomics(ST) technologies enables the exploration of tissue structure and cellular function within a spatial context. However, mainstream analytical methods primarily focus on the gene expression modality itself and struggle to fully leverage auxiliary information from histological images, which limits precise dissection of complex biological structures. To address this, we propose SpatialModal, a multimodal graph learning framework that effectively integrates gene expression data and histological images from spatial transcriptomics to construct unified spatial representations. SpatialModal effectively captures synergistic interactions between modalities by jointly modeling intra- and inter-modal complementary features while incorporating spatial adjacency information. Furthermore, it employs a dual contrastive learning strategy to enhance the discriminative power of representations, thereby enabling efficient and robust analysis of tissue structures. We validate the effectiveness of this approach on multiple public datasets covering diverse tissue types, species, and resolutions. Experiments demonstrate that SpatialModal exhibits significant advantages in downstream tasks, including spatial domain identification, gene expression reconstruction, and pseudotime inference, and accurately elucidates the hierarchical structure of the mouse cortex as well as the metabolic-immune dynamic boundaries in the breast cancer microenvironment. Additionally, SpatialModal shows exceptional robustness in single-cell resolution and multi-slice integration tasks, providing an efficient and broadly applicable analytical tool for spatial transcriptomics research.

bioinformatics↗

bioRxiv2025

m5C RNA Methylation Is Dysregulated by Oncogenic Herpesviruses via c-Myc Signaling to Counteract Host Antiviral Factors

Herpesviruses are a group of double-stranded DNA viruses known to develop versatile viral strategies to escape host immune surveillance for promoting their replication and propagation. This is illustrated by Kaposis sarcoma-associated herpesvirus (KSHV), an oncogenic gamma-herpesvirus that overcomes host immune suppression by multiple mechanisms. In this study, we reported that KSHV dysregulates 5-methylcytosine (m5C) modification and mRNA stability of host antiviral factors to benefit its lytic replication. KSHV lytic reactivation or de novo challenge led to downregulation of m5C RNA methyltransferases, NSUN2 and NSUN1 (NSUN2/1), while NSUN2/1 depletion promoted KSHV lytic replication. Such KSHV-mediated downregulation of NSUN2/1 is via suppression of the transcriptional factor c-Myc. We further performed the RNA bisulfite sequencing (RNA-BS-seq) to identify KSHV-dependent m5C modification of host mRNAs. KSHV lytic reactivation led to the significant reduction of m5C methylation and mRNA stability of TRIM25, a key activator of the RIG-I pathway, while TRIM25 depletion indeed promoted KSHV lytic replication. These host-virus interaction events were also observed in the infection of another oncogenic gamma-herpesvirus Epstein-Barr virus (EBV). Overall, our results highlighted a new strategy for human gamma-herpesviruses to counteract host antiviral factors and promote their lytic replication by manipulating host m5C RNA methylation. Significance StatementOur study has identified a novel viral mechanism of human gamma-herpesviruses to manipulate host RNA methylation machineries to subvert immune defenses and enhance viral lytic replication. In particular, our new data showed that KSHV/EBV downregulate the key 5-methylcytosine (m5C) RNA writers NSUN2/1 via c-Myc, and thus decrease m5C modification and stability of TRIM25 mRNA. As TRIM25 is a key E3 ubiquitin ligase in RIG-I signal transduction, its inhibition disrupts RIG-I mediated antiviral sensing and thus favors viral lytic replication. As human gamma-herpesviruses are critical pathogens that highly associate with multiple human diseases especially certain tumors, such studies are significant to shed light in improving the fundamental understanding of virus-host interactions and identifying new host targets for future translational applications.

microbiology↗

bioRxiv2025

Follistatin-like protein 1 interacts with programmed cell death 4 to promote vascular mimicry in hepatocellular carcinoma by activating the PI3K/AKT/mTOR signaling pathway

Hepatocellular carcinoma (HCC), the most common type of liver cancer, is highly prone to recurrence and metastasis after curative treatment. However, the molecular mechanisms governing these post-management setbacks remain largely unknown. Previous studies found that the high expression of follistatin-like protein 1 (FSTL1) in tumors is implicated in recurrence, metastasis, and poor patient prognosis. In this study, we aimed to investigate the role of FSTL1 in HCC. We found that FSTL1 overexpression was positively correlated with vascular mimicry and poor prognosis. In vitro experiments confirmed that the interaction between FSTL1 and programmed cell death 4 (PDCD4) activates epithelial-to-mesenchymal transition and promotes the proliferation, invasion, and migration of liver cancer cells. The protein-protein interaction between FSTL1 and PDCD4 significantly promotes VM as well as the expression of the pro-angiogenic vascular endothelial growth factor by activating AKT/mTOR signaling. Our data suggest that FSTL1 may be a potential target for the treatment of HCC. Implications: Our findings indicate that the protein FSTL1 may be a novel therapeutic target for managing patients with HCC.

cancer biology↗

bioRxiv2025

Miniaturized and accessible functional ultrasound imaging system for freely moving mice

Functional ultrasound (fUS) imaging provides brain-wide activity maps with high spatiotemporal resolution and deep penetration, positioning it as a key technology for future non-invasive brain-computer interfaces (BCIs). Realizing this potential, particularly for chronic BCI applications requiring long-term monitoring in naturalistic settings, critically depends on significant system miniaturization to overcome the cost and complexity limitations of current platforms. Addressing this challenge, we present mini-fUS, a miniaturized, cost-effective fUS platform engineered for accessibility without compromising core performance for demanding neuroscience research. The system features a compact transmit-receiver, low-noise power supply, and high-speed data transfer, achieving pulse repetition frequencies up to 5 kHz with negligible jitter. Real-time GPU-accelerated beamforming and singular value decomposition (SVD) enable whole-brain activity mapping, demonstrated here in freely moving mice at up to 3.57 Hz with [~]100 {micro}m spatial resolution and 15 mm penetration depth. Validated through recordings of brain activity during sensory stimulation, anesthesia, and behavior, this design defines a practical hardware-software framework for fUS. By significantly improving accessibility and enabling robust monitoring in mobile subjects, this work advances the development of fUS for both fundamental research and future BCI technologies, while clarifying essential fUS operational principles.

neuroscience↗

bioRxiv2025

The spliceosome component U1-70k loads nascent transcripts onto FVE/SGS3 via co-condensation to embark on RNA silencing

Despite biochemical framework of RNA silencing has been studied well, how nascent transcripts enter RNA silencing remains poorly understood. Here we recovered U1-70k, a canonical spliceosome factor, as a novel component in posttranscriptional gene silencing (PTGS). We show that U1-70k interacts with SGS3 and FVE, two key components that supply RNA substrate for RNA-dependent RNA polymerase 6 (RDR6) to generate dsRNA. U1-70k promotes the loading of nascent RNA into the SGS3/FVE complex in the nucleus, which is subsequently translocated onto RDR6 in the cytosol. Importantly, U1-70k contains C-terminal low complexity (LC) domain and displays liquid-liquid phase separation (LLPS) pattern. U1-70k forms co-condensate with SGS3, another intrinsically disordered protein (IDP). The co-condensation is critical for PTGS as U1-70k LC variants display reduced SGS3 co-condensation, loss of RNA loading onto SGS3, and impaired RNAi function. Taken together, U1-70k channels nascent RNA to SGS3/FVE via its LLPS action to enter PTGS pathway.

molecular biology↗

bioRxiv2025

BioMiner: A Multi-modal System for Automated Mining of Protein-Ligand Bioactivity Data from Literature

Protein-ligand bioactivity data published in the literature are essential for drug discovery, yet manual curation struggles to keep pace with rapidly growing literature. Automated bioactivity extraction remains challenging because it requires not only interpreting biochemical semantics distributed across text, tables, and figures, but also reconstructing chemically exact ligand structures (e.g., Markush structures). To address this bottleneck, we introduce BO_SCPLOWIOC_SCPLOWMO_SCPLOWINERC_SCPLOW, a multi-modal extraction framework that explicitly separates bioactivity semantic interpretation from ligand structure construction. Within BO_SCPLOWIOC_SCPLOWMO_SCPLOWINERC_SCPLOW, bioactivity semantics are inferred through direct reasoning, while chemical structures are resolved via a chemical-structure-grounded visual semantic reasoning paradigm, in which multi-modal large language models operate on chemically grounded visual representations to infer inter-structure relationships, and exact molecular construction is delegated to domain chemistry tools. For rigorous evaluation and method development, we further establish BO_SCPLOWIOC_SCPLOWVO_SCPLOWISTAC_SCPLOW, a comprehensive benchmark comprising 16,457 bioactivity entries curated from 500 publications. BO_SCPLOWIOC_SCPLOWMO_SCPLOWINERC_SCPLOW validates its extraction ability and provides a quantitative baseline, achieving an F1 score of 0.32 for bioactivity triplets. BO_SCPLOWIOC_SCPLOWMO_SCPLOWINERC_SCPLOWs practical utility is demonstrated via three applications: (1) extracting 82,262 data from 11,683 papers to build a pre-training database that improves downstream models performance by 3.9%; (2) enabling a human-in-the-loop workflow that doubles the number of high-quality NLRP3 bioactivity data, helping 38.6% improvement over 28 QSAR models and identification of 16 hit candidates with novel scaffolds; and (3) accelerating protein-ligand complex bioactivity annotation, achieving a 5.59-fold speed increase and 5.75% accuracy improvement over manual workflows in PoseBusters dataset. BO_SCPLOWIOC_SCPLOWMO_SCPLOWINERC_SCPLOW and BO_SCPLOWIOC_SCPLOWVO_SCPLOWISTAC_SCPLOW provide a scalable extraction methodology and a rigorous benchmark, paving the way to unlock bioactivity data that previously required extensive human effort. All data and code are available at GitHub.

bioinformatics↗

bioRxiv2025

Cold-activated hepatocyte derived exosomes promote BAT thermogenesis through miR-293-5p

The liver-adipose axis serves as a fundamental regulatory network governing systemic lipid homeostasis, with hepatic-derived signals orchestrating adipose tissue plasticity through multimodal mechanisms. Comprehensive elucidation of these bidirectional crosstalk mechanisms may reveal novel therapeutic strategies for metabolic disorders. Our investigation demonstrates that cold exposure induces hepatic secretion of exosomes that potentiate adipose thermogenic activation in both in vitro and in vivo models. This thermogenic potentiation is mechanistically linked to cold-induced upregulation of hepatocyte-derived exosomal miR-293-5p. Notably, pharmacological administration of miR-293-5p agomir significantly attenuates diet- induced obesity and associated metabolic dysregulation in murine models. Through mechanistic interrogation, we identified Tet1 as a direct downstream target of miR- 293-5p, where ectopic Tet1 expression disrupts brown adipose tissue (BAT) thermogenic programming independently of miR-293-5p modulation. Our findings establish cold-activated hepatocyte exosomes as endocrine signaling mediators containing thermogenic microRNA cargos, with miR-293-5p emerging as a regulatory nexus coordinating mitochondrial bioenergetics and systemic energy equilibrium through liver-adipose cross-talk.

genetics↗

bioRxiv2025

The GSA Family in 2025: A Broadened Sharing Platform for Multi-Omics and Multimodal Data

The Genome Sequence Archive Family (GSA family) provides a suite of database resources for archiving, retrieving, and sharing multi-omics data for the global academic and industrial communities. It currently comprises four distinct database members: the Genome Sequence Archive (GSA, https://ngdc.cncb.ac.cn/gsa/), the Genome Sequence Archive for Human (GSA-Human, https://ngdc.cncb.ac.cn/gsa-human/), the open Archive for Miscellaneous Data (OMIX, https://ngdc.cncb.ac.cn/omix/), and the Open Biomedical Imaging Archive (OBIA, https://ngdc.cncb.ac.cn/obia). Compared to the 2021 version, the GSA family has significantly expanded by introducing a new database member, the OBIA, and through comprehensive upgrades to the existing ones. Notable enhancements to the existing members include broadening the range of accepted data types, enhancing the quality control systems, fine-tuning the data retrieval system, and refining the data-sharing management mechanisms.

genomics↗

bioRxiv2025

Transmembrane Serine Protease TMPRSS11B promotes an acidified tumor microenvironment and immune suppression in lung squamous cell carcinoma

Lung cancer is the leading cause of cancer-related deaths worldwide. Existing therapeutic options have limited efficacy, particularly for lung squamous cell carcinoma (LUSC), underscoring the critical need for the identification of new therapeutic targets. We previously demonstrated that the Transmembrane Serine Protease TMPRSS11B promotes transformation of human bronchial epithelial cells and enhances lactate export from LUSC cells. To determine the impact of TMPRSS11B activity on the host immune system and the tumor microenvironment (TME), we evaluated the effect of Tmprss11b depletion in a syngeneic mouse model. Tmprss11b depletion significantly reduced tumor burden in immunocompetent mice and triggered an infiltration of immune cells. RNA FISH analysis and spatial transcriptomics in the autochthonous Rosa26-Sox2-Ires-GfpLSL/LSL; Nkx2-1fl/fl; Lkb1fl/fl (SNL) model revealed an enrichment of Tmprss11b expression in LUSC tumors, specifically in Krt13+ hillock-like cells. Ultra-pH sensitive nanoparticle imaging and metabolite analysis identified regions of acidification, elevated lactate, and enrichment of M2-like macrophages in LUSC tumors. These results demonstrate that TMPRSS11B promotes an acidified and immunosuppressive TME and nominate this enzyme as a therapeutic target in LUSC.

cancer biology↗

bioRxiv2025

The sialylation pattern of dietary glycopeptides is vital for inhibiting pathogens and modulating gut microbiota in elderly individuals

N-glycosylation is a post-translational modification of proteins that can influence the structure and function of glycoproteins. Edible birds nest (EBN) contains highly sialylated mucins with N-glycans and O-glycans, while casein glycomacropeptide (CGMP) is modified with only O-glycans. We prepare EBN sialoglycopeptides through sequential protease treatment and their inhibitory effects on pathogens, including Candida albicans, Helicobacter pylori, and avian influenza virus (AIV), as well as their modulation of gut microbiota in elderly individuals, were compared with CGMP. N-glycan analysis revealed the presence of multiantenna N-glycans, characterized by sialylation and bisecting GlcNAc in the EBN glycopeptides. EBN glycopeptides significantly inhibited C. albicans and H. pylori. However, the removal of terminal sialic acid from EBN glycopeptides resulted in a marked reduction of this inhibitory effect. Using Maackia Amurensis Lectin II as an AIV mimic, EBN glycopeptides effectively inhibited AIV adhesion to MDCK cells. In vitro fecal fermentation using fecal samples from elderly individuals revealed that the EBN glycopeptide group exhibited remarkable probiotic effects on the gut microbiota, increasing the relative abundance of beneficial bacteria such as Lactobacillus and Roseibacterium, while decreasing the relative abundance of harmful bacteria such as Escherichia-Shigella and Klebsiella. Overall, EBN glycopeptide, rich in sialylated N-glycans and O-glycans, strongly inhibited pathogenic microorganisms and showed superior probiotic properties compared to CGMP with sole O-glycosylation.

biochemistry↗

bioRxiv2025

Epigenetic Modulation, Intra-tumoral Microbiome and Immunity in Early Onset Colorectal Cancer

BackgroundThe incidence of colorectal cancer (CRC) in young adults (age of diagnosis < 50 years old) has been rapidly increasing. Although [~]20% of early-onset (EO) CRC cases are due to germline mutations, the etiology of the majority of EOCRC cases remains poorly understood. Non-genetic factors such as environmental exposure and lifestyle changes are likely to have a direct link to the increased incidence of sporadic EOCRC. We hypothesize that such factors may be observable as differences in the EOCRC epigenome, microbiome and immunome. We sought to address this by comparing differences in DNA methylation from the cohort of colorectal cancer patients in The Cancer Genome Atlas (TCGA). Further, we carefully identified intra-tumoral microbes from TCGA and two other datasets and then related the microbes to EOCRC status and deconvolved immune cell abundances. We found that DNA methylation (DNAm) age acceleration by12 years when compared with average-onset CRC (AOCRC) patients. Differentially methylated sites associated with genes are related to CREB signaling in neurons, G protein coupled receptor signaling, phagosome formation and S100 family signaling. These differences were validated in the gene expression from TCGA and a second, larger real-world dataset from the Oncology Research Information Exchange Network (ORIEN). However, no consistent differences were observed in the intra-tumor microbes between EOCRC and AOCRC. Interestingly, the most abundant microbes interacted with the immune systems differently between the EOCRC and AOCRC tumors, characterized by more, larger, positive correlations in EOCRC. These data suggest epigenetic modulation and accelerated aging may play a key role in the development of EOCRC. SIGNIFICANCEWe investigated whether environmentally driven factors contribute to early-onset colorectal cancer (EOCRC). We observed accelerated epigenetic aging in EOCRC and epigenetic changes associated with chronic inflammation. Tumor immune cell abundances correlated more strongly with microbes in EOCRC than average-onset CRC. These data suggest a dysregulation of immune response in EOCRC, driving chronic inflammation and tissue aging.

cancer biology↗