Proteins. 2025 Jun 16. doi: 10.1002/prot.26852. Online ahead of print.

ABSTRACT

EgLIP1 is an oil-body lipase (EC 3.1.1.3) overexpressed in the fruit mesocarp of Elaeis guineensis (oil palm). Despite its significant role in fruit ripening and the hydrolysis of of triacylglycerol into free fatty acids (FFA) in oil palm, the molecular structure and functional understanding of EgLIP1 are yet to be fully elucidated. Phylogenetic analysis reveals that EgLIP1 shares homology with several plant oil-body lipases. The 3D structure of EgLIP1 was modeled using AlphaFold 2 with high confidence (pLDDT score of 89.7). Structural comparison with Rhizomucor miehei triacylglycerol lipase (RML) reveals that the regions β1, η1, α1, η2, β2, α2, α3, α4, α15, α16, and β15 represent novel insertions unique to EgLIP1, while the overall fold in other regions of the protein remains highly conserved in comparison to RML. Notably, an insertion of residue "PF" was also found in EgLIP1 and its plant orthologs. This insertion is located immediately before the lid domain helix, forming a kink facing toward the active lipase site. Enzyme-membrane surface interaction prediction suggests that α1, α3, α4, α15, and α16 are likely involved in anchoring EgLIP1 at the interface of the phospholipid monolayer of oil bodies. Molecular docking and molecular dynamics (MD) simulation analyses of EgLIP1 with its potential substrate, 1-palmitoylglycerol, demonstrate that the catalytic serine residue S308 and the GX oxyanion hole motif residue T223 can form hydrogen bonds with the carbonyl group of the ligand to initiate a nucleophilic attack on the substrate. Our structure-guided functional studies provide molecular insights into how EgLIP1 associates with oil bodies and catalyzes its potential substrates.

PMID:40521868 | DOI:10.1002/prot.26852

Curr Res Microb Sci. 2025 May 23;9:100410. doi: 10.1016/j.crmicr.2025.100410. eCollection 2025.

ABSTRACT

Winemaking is influenced by many factors, from the vineyard to the fermentation process. While traditional approaches have focused on vineyard treatments and controlled fermentations to ensure a stable product, global warming has made it necessary to reassess the effects of these factors on winemaking. This study aimed to evaluate the impact of vintage, management, and environmental settings on the composition of yeast populations driving grape spontaneous fermentations and defining the characteristics of the final product. Our results emphasize how climate change and the vineyard's yeast populations influence fermentation, showing that while the vintage plays a key role in grape composition, it s not the sole determinant of fermentation. The geographical location of the vineyard, alongside the management practices and vintage, shapes the composition and dynamics of yeast populations. Specific vineyard conditions sometimes lead to stable and unique yeast populations. Furthermore, the grape origin affects both the yeast population and the wine's volatile compounds, with certain yeast species, like Saccharomyces cerevisiae, being linked to specific environmental features. While vintage and climate change impact a smaller portion of the yeast population, the environment remains a significant influence. As fermentation progresses, the yeast populations retain vineyard-specific characteristics, underlining the strong connection between yeast dynamics and environmental factors. Understanding these interactions is crucial for adapting to global warming and optimizing wine fermentation processes. It will help improve wine quality, innovation, and specific wine characteristics through better management of microbial communities in the grape-wine ecosystem.

PMID:40521374 | PMC:PMC12164235 | DOI:10.1016/j.crmicr.2025.100410

Noncoding RNA Res. 2025 May 24;14:25-37. doi: 10.1016/j.ncrna.2025.05.011. eCollection 2025 Oct.

ABSTRACT

Lung cancer is among the most frequently observed and lethal malignancies globally, and metastasis represents a critical determinant of patient outcomes. PTEN, a well-established tumor suppressor, has emerged as an important regulator in lung cancer progression. However, the molecular mechanism of PTEN gene suppressing lung cancer metastasis lacks deeper exploration. In this research, we identify and characterize LncPTEN1, a novel long non-coding RNA generated from PTEN gene. We show that YTHDC1 promotes the alternative splicing of LncPTEN1, resulting in significantly elevated LncPTEN1 expression in normal lung cells. Clinical analyses across multiple patient cohorts demonstrate that low LncPTEN1 expression strongly correlates with poor patient survival and increased metastasis, indicating its potential as a prognostic biomarker. Mechanistically, LncPTEN1 facilitates the interaction between Trim16 and Vimentin, promoting the ubiquitination and proteasomal degradation of Vimentin, thereby suppressing EMT-driven metastasis. The collective evidence from our investigation demonstrates that LncPTEN1 represents a novel tumor-suppressive lncRNA which inhibits lung cancer metastasis through promoting the degradation of Vimentin and inhibiting the EMT progress.

PMID:40521243 | PMC:PMC12167124 | DOI:10.1016/j.ncrna.2025.05.011

Front Cardiovasc Med. 2025 May 30;12:1488684. doi: 10.3389/fcvm.2025.1488684. eCollection 2025.

ABSTRACT

BACKGROUND: Deng's Yangxin Decoction (DYX) is a Chinese herbal formula used in clinical practice to treat patients with myocardial infarction (MI). However, its underlying mechanism remains unclear.

OBJECTIVE: This study aims to explore potential biomarkers and associated mechanisms of DYX for MI.

METHODS: Therapeutic targets for DYX were obtained based on the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, Traditional Chinese Medicine Integrated Database, and UniProt databases. Key targets were screened using topological analysis. Differentially expressed genes (DEGs) between MI patients and controls were obtained using open-source datasets. Weighted gene co-expression network analysis (WGCNA) was utilized to screen MI-related genes in the expression array. Hub biomarkers were determined by intersecting DEGs, protein-protein interaction networks, and WGCNA results. Molecular docking validated interactions between DYX components and hub biomarkers. Immune infiltration was assessed via CIBERSORT. Single-cell RNA sequencing analyzed hub biomarker expression in coronary plaques.

RESULTS: FOS was a core biomarker for DYX for MI. Molecular docking confirmed strong binding affinities between quercetin/baicalein and FOS. In addition, high expression of FOS was associated with immune infiltration of neutrophils, activated mast cells, activated dendritic cells, monocytes, and NK cells. FOS was also found to be expressed at high levels in mast and dendritic cells, monocytes, and some T cells in coronary plaques.

CONCLUSION: FOS is a target of DYX for the treatment of MI, and the mechanism of action may be related to the modulation of immune infiltration.

PMID:40520937 | PMC:PMC12163015 | DOI:10.3389/fcvm.2025.1488684

Int J Med Sci. 2025 May 9;22(11):2560-2569. doi: 10.7150/ijms.108086. eCollection 2025.

ABSTRACT

Zoledronic acid (ZOL) is an inhibitor of osteoclast-mediated bone resorption. It is used to treat osteoporosis and skeletal complications in patients with tumor-induced osteolysis. ZOL is also demonstrated to possess anti-cancer activity in several tumors via apoptosis induction. Doxycycline is well-known antibiotic used in treatment of infections caused by bacteria and certain parasites. In this study, we evaluated the possibility if doxycycline could be used as an effective adjuvant to ZOL against osteosarcoma cells. The data showed that co-treatment with doxycycline at non-toxic dose could significantly increase the anti-viability effect of ZOL in osteosarcoma HOS and MG-63 cells in MTT assay and colony formation assay, and largely increased the levels of apoptotic markers, cleaved caspase 3 and PARP, in ZOL-treated cells. Furthermore, as co-treatment with doxycycline, the levels of ROS and autophagy were enhanced in ZOL-treated cells. Administration of N-acetyl-L-cysteine, a reactive oxygen species (ROS) inhibitor, or autophagy inhibitor chloroquine both reduced anti-growth effect of this combined treatment, indicating that the increased ROS and autophagy should be involved in anti-viability effect of combined treatment with ZOL and doxycycline. Taken together, our findings suggested that combined treatment with ZOL and doxycycline may serve as a potential strategy for treating osteosarcoma.

PMID:40520888 | PMC:PMC12163417 | DOI:10.7150/ijms.108086

Food Chem X. 2025 May 30;28:102605. doi: 10.1016/j.fochx.2025.102605. eCollection 2025 May.

ABSTRACT

Acrylamide is formed during high-temperature treatment in foods and presents a significant health and regulatory challenge. This study evaluates the effects of calcium salts and phenolic acids alone or in combination with asparaginase and rosemary extract in wheat cookies and rye crispbread. Acrylamide content, product color, texture, and sensory properties were assessed. When calcium salts and phenolic acids were used alone, acrylamide was reduced by 46 % and 50 % compared to the control. A combination of these with asparaginase resulted in a reduction of acrylamide by up to 89 % using ellagic acid. Specific treatments reduced cookie hardness, but asparaginase addition reversed this effect. Color mainly remained unaffected. Sensory analysis of selected treatments confirmed no significant changes in cookie aroma, taste, color, texture, and acceptability. This work provides a new approach by combining selected treatments to mitigate acrylamide while preserving product quality.

PMID:40520700 | PMC:PMC12167442 | DOI:10.1016/j.fochx.2025.102605

Comput Struct Biotechnol J. 2025 May 23;27:2336-2346. doi: 10.1016/j.csbj.2025.05.034. eCollection 2025.

ABSTRACT

Cryptococcus neoformans is notorious for causing severe pulmonary and central nervous system infections, particularly in immunocompromised patients. High mortality rates, associated with its tropism and adaptation to the brain microenvironment and its drug resistance profile, make this pathogen a public health threat and a World Health Organization (WHO) priority. This study presents the first reconstructed genome-scale metabolic model (GSMM), iRV890, for C. neoformans var. grubii, which comprises 890 genes, 2598 reactions, and 2047 metabolites across four compartments. The GSMM iRV890 model was reconstructed using the open-source software tool merlin 4.0.2, is openly available in the well-established systems biology markup language (SBML) format and underwent validation using experimental data for specific growth and glucose consumption rates, and 222 nitrogen and carbon assimilation sources, with a 85 % prediction rate. Based on the comparison with GSMMs available for other pathogenic yeasts, unique metabolic features were predicted for C. neoformans, including key pathways shaping dynamics between C. neoformans and human host, as well as its underlying adaptions to the brain environment. Finally, the 96 predicted essential genes from the validated model are investigated as potential novel antifungal drug targets-including Erg4, Chs1, Fol1, and Fas1-which represent promising candidates for targeted drug development due to their absence in human cells.

PMID:40520592 | PMC:PMC12167027 | DOI:10.1016/j.csbj.2025.05.034

Mol Ther Nucleic Acids. 2025 May 19;36(2):102568. doi: 10.1016/j.omtn.2025.102568. eCollection 2025 Jun 10.

ABSTRACT

CRISPR-Cas12a gene editing offers an alternative to Cas9-based methods, providing better targeting of AT-rich regions, simplified guide RNA manufacturing, and high specificity. However, the efficacy of donor-based editing is subject to various factors, with template format playing a crucial role. Currently, the predominant non-viral template format for homology-directed repair (HDR) after nuclease-induced DNA breaks is double-stranded DNA, which is toxic when transfected at high doses. Others have demonstrated that using single-stranded DNA (ssDNA) with flanking double-stranded Cas-target-sequences (CTS) as a template for Cas9-mediated gene editing can mitigate this toxicity and increase knock-in efficiency. Here, we investigate CTS design for AsCas12a Ultra by exploring PAM orientation and binding requirements. Additionally, we rule out ssDNase activity of AsCas12a under cell-physiological Mg2+ conditions. Finally, we showcase the advantage of ssDNA donors with CTS (ssCTS) at high doses for delivering clinically relevant transgenes of varying sizes into three TCR-CD3 complex genes (TRAC, CD3ζ, CD3ε), achieving up to 90% knock-in rates for a 0.8kb-insert at the CD3ε locus. Long-read sequencing confirmed higher HDR rates and revealed that CTS reduced partial integration events compared to unmodified ssDNA. Overall, AsCas12a and ssCTS represent a platform for highly efficient knock-in in primary human T cells with minimal toxicity.

PMID:40520364 | PMC:PMC12166421 | DOI:10.1016/j.omtn.2025.102568

Protein Sci. 2025 Jul;34(7):e70087. doi: 10.1002/pro.70087.

ABSTRACT

Many antimicrobial peptides (AMPs) function by disrupting the cell membranes of microbes. While this ability is crucial for their efficacy, it also raises questions about their safety. Specifically, the membrane-disrupting ability could lead to hemolysis. Traditionally, the hemolytic activity of AMPs is evaluated through experiments. To reduce the cost of assessing the safety of an AMP as a drug, we introduce ConsAMPHemo, a two-stage framework based on deep learning. ConsAMPHemo performs conventional binary classification of the hemolytic activities of AMPs and predicts their hemolysis concentrations through regression. Our model demonstrates excellent classification performance, achieving an accuracy of 99.54%, 82.57%, and 88.04% on three distinct datasets, respectively. Regarding regression prediction, the model achieves a Pearson correlation coefficient of 0.809. Additionally, we identify the correlation between features and hemolytic activity. The insights gained from this work shed light on the underlying physics of the hemolytic nature of an AMP. Therefore, our study contributes to the development of safer AMPs through cost-effective hemolytic activity prediction and by revealing the design principles for AMPs with low hemolytic toxicity. The codes and datasets of ConsAMPHemo are available at https://github.com/Cpillar/ConsAMPHemo.

PMID:40519190 | DOI:10.1002/pro.70087

Infect Control Hosp Epidemiol. 2025 Jun 16:1-3. doi: 10.1017/ice.2025.10207. Online ahead of print.

NO ABSTRACT

PMID:40518722 | DOI:10.1017/ice.2025.10207

Lancet Digit Health. 2025 Jun 14:100864. doi: 10.1016/j.landig.2025.02.004. Online ahead of print.

ABSTRACT

The notion of medical digital twins is gaining popularity both within the scientific community and among the general public; however, much of the recent enthusiasm has occurred in the absence of a consensus on their fundamental make-up. Digital twins originate in the field of engineering, in which a constantly updating virtual copy enables analysis, simulation, and prediction of a real-world object or process. In this Health Policy paper, we evaluate this concept in the context of medicine and outline five key components of the medical digital twin: the patient, data connection, patient-in-silico, interface, and twin synchronisation. We consider how various enabling technologies in multimodal data, artificial intelligence, and mechanistic modelling will pave the way for clinical adoption and provide examples pertaining to oncology and diabetes. We highlight the role of data fusion and the potential of merging artificial intelligence and mechanistic modelling to address the limitations of either the AI or the mechanistic modelling approach used independently. In particular, we highlight how the digital twin concept can support the performance of large language models applied in medicine and its potential to address health-care challenges. We believe that this Health Policy paper will help to guide scientists, clinicians, and policy makers in creating medical digital twins in the future and translating this promising new paradigm from theory into clinical practice.

PMID:40518342 | DOI:10.1016/j.landig.2025.02.004

Cancer Lett. 2025 Jun 13:217877. doi: 10.1016/j.canlet.2025.217877. Online ahead of print.

ABSTRACT

R-loop accumulation has emerged as a critical factor that induces DNA damage and compromises genomic integrity. However, the regulatory mechanisms governing the R-loop-induced DNA damage remain unclear. Here, FTSJ3 was determined to be a pivotal regulator of R-loop homeostasis and genomic stability. We demonstrated that FTSJ3 was specifically recruited to R-loop structures, where it prevented DNA damage by suppressing excessive R-loop formation. FTSJ3 expression was significantly upregulated in multiple cancer types, and its elevated expression levels correlated with unfavorable survival in patients with lung adenocarcinoma (LUAD). FTSJ3 depletion increased R-loop-dependent DNA damage. Inhibiting FTSJ3 expression sensitized lung cancer cells to cisplatin both in vitro and in vivo. FTSJ3 could be a genome guardian that limits R-loop-associated damage, suggesting its potential role as a cancer intervention therapeutic target and a predictive biomarker for chemotherapy responsiveness.

PMID:40517939 | DOI:10.1016/j.canlet.2025.217877

Microb Pathog. 2025 Jun 13:107804. doi: 10.1016/j.micpath.2025.107804. Online ahead of print.

ABSTRACT

miRNAs are one of the important epigenetic mechanisms involved in toxicity by post-transcriptionally regulating gene expression. They are thus important markers for the occurrence and development of diseases. The cellular action of many Clostridium perfringens toxins involves initial binding to a receptor located on the plasma membrane of target cells, followed by activation of intracellular pathways and various cytopathic effects that ultimately lead to cell death. Here, we provide a bioinformatic study on the regulatory role of miRNAs in C. perfringens infection and predict miRNAs that affect the action mechanism of four toxins to reduce their adverse effects at the molecular level. In this study, consideration is given to the toxicological mechanisms associated with four major C. perfringens toxins (α , β2, ε, ι). The roles that miRNAs play in these mechanisms and the interactions between them and their target genes are explained. As a result, the ways that miRNAs are regulated in the pathogenicity signaling pathways are revealed which highlights the roles played by miRNAs in preventing and controlling the harmful effects of the C. perfringens toxins. It is hoped that this study will provide a theoretical basis for the prevention and control of the damage caused by these toxins.

PMID:40517914 | DOI:10.1016/j.micpath.2025.107804

J Mol Diagn. 2025 Jun 13:S1525-1578(25)00135-7. doi: 10.1016/j.jmoldx.2025.04.012. Online ahead of print.

ABSTRACT

Evaluating robustness of somatic mutation detections is essential when utilizing whole exome sequencing (WES) for treatment decision-making. A comprehensive evaluation was conducted using tumor WES from the FDA-led Sequencing Quality Control Phase 2 (SEQC2) project, in which multiple library kits sequenced identical DNA materials across three labs to benchmark analytical validity. These workflows included various read aligner (BWA, Bowtie2, DRAGEN-Aligner, DRAGMAP, and HISAT2) and mutation caller (Mutect2, TNscope, DRAGEN-Caller, and DeepVariant) combinations. The results revealed that DRAGEN exhibited superior performance, achieving mean F1-scores of 0.966 and 0.791 for SNV and INDEL detection, respectively. Among open-source software, BWA Mutect2 and HISAT2 Mutect2 combinations showed the highest mean F1-scores for SNV (0.949) and INDEL (0.722), respectively. The analyses indicated that high-quality data can be analyzed as having worse results, and vice versa. Evaluations of COSMIC reported mutations unveiled discrepancies across enrichment kits. IDT enrichment kits showed a higher false negative rate, while Agilent WES kits tended to miss mutations in CBL and IDH1, and Roche library kits tended to miss the mutations in PIK3CB. For drug-related biomarkers, Sentieon TNscope tended to underestimate tumor mutation burden and overlook crucial drug-resistance mutations such as FLT3 (c.G1879A: p.A627T) for cytarabine resistance in leukemia and MAP2K1 (c.G199A:p.D67N) for BRAF inhibitors in melanoma. The findings highlight the importance of robust bioinformatic analysis in identifying tumor mutations and guiding clinical decision-making.

PMID:40517896 | DOI:10.1016/j.jmoldx.2025.04.012

Commun Chem. 2025 Jun 14;8(1):186. doi: 10.1038/s42004-025-01558-3.

ABSTRACT

Alpha-synuclein (aSyn) plays a crucial role in Parkinson's disease, with various aggregates proposed as pathogenic triggers and therapeutic targets. However, anti-aSyn aggregation compounds often fail due to limited knowledge of the underlying molecular basis. In particular, interactions with lipid membranes are central to both physiological and pathological roles of aSyn, yet their underlying mechanisms remain unclear. Disrupting this balance may drive Parkinson's onset and progression, underscoring the need for a mechanistic understanding of pure and lipid-mediated aggregation. Building on well-established in vitro aggregation studies, we propose a mathematical model of aSyn accumulation incorporating both aggregation routes via a nucleation-conversion-polymerization process with self-amplifying loops and toxic oligomers. Model calibration uses data from in vitro assays mimicking physiologically relevant conditions, providing insights into transient and stable aSyn intermediates. Incorporating aSyn-lipid interactions enables in silico exploration of how lipid-to-aSyn ratio influences aggregation, with possible implications for neurodegeneration. Sensitivity analysis highlights secondary nucleation inhibition as a potential anti-aggregation strategy. Overall, our work contributes to a unified framework for investigating in vitro aSyn aggregation and evaluating Parkinson's therapies by building on existing models. It can serve as a stand-alone tool and a modular component in multiscale models, with potential applications in quantitative systems pharmacology.

PMID:40517155 | DOI:10.1038/s42004-025-01558-3

Biochem Pharmacol. 2025 Jun 12:117049. doi: 10.1016/j.bcp.2025.117049. Online ahead of print.

ABSTRACT

Recently, we postulated the existence of 'multitarget binding sites', reoccurring structural motifs that interconnect otherwise structurally, functionally, and/or phylogenetically distant proteins. In this study, we functionally assessed a selection of 23 multitarget ATP-binding cassette (pan-ABC) transporter modulators against zebrafish (Danio rerio) organic anion transporting polypeptide (drOatp1d1), a transport protein of the solute carrier (SLC) superfamily. Zebrafishes are important in vivo models in drug development to evaluate drug pharmacokinetics and pharmacodynamics. In total, 87.0% of the compounds were identified as drOatp1d1 transport inhibitors despite the relative phylogenetic distance of drOatp1d1 to other Oatps/OATPs. The observed effects resembled the ones observed for human OATP1A2, OATP1B1, OATP1B3, and OATP2B1, and potent hit molecules appeared to bind to a potential drOatp1d1 binding site derived from a OATP1B1 cryo-EM structure - strengthening the notion of common structural motifs between membrane transporters. The bioactivity of Pranlukast (PRA) on human OATPs could be accurately predicted based on its activity on drOatp1d1. The collection of pan-ABC transporter modulators also showed activity against other zebrafish (i.e., drAbcb4) and non-zebrafish (i.e., mumAbca1) membrane transporters, ultimately rendering it a suitable tool to translate between species to tackle the undruggability of membrane transporters and potentially other proteins by addressing conserved structural motifs.

PMID:40516762 | DOI:10.1016/j.bcp.2025.117049

Environ Pollut. 2025 Jun 12:126653. doi: 10.1016/j.envpol.2025.126653. Online ahead of print.

ABSTRACT

An unprecedented oil spill occurred along the Northeast Coast of Brazil in late 2019, affecting the Environmental Protection Area Costa dos Corais (APACC), the largest Brazilian marine conservation unit, posing a risk to this complex ecosystem. By applying passive ecotoxicological biomonitoring, this study aimed to evaluate whether the remaining contamination from such an oil spill affected the population of the marine clam Tivela mactroides by assessing multiple biomarkers, regarding antioxidant enzyme activities (SOD, CAT), biotransformation (GST, GSH), oxidative damage (MDA), and neurotoxicity (AChE) in gills and digestive glands, and PAH bioaccumulation. The clam tissues and sediment were sampled in three locations (Paripueira, Japaratinga and Maragogi beaches), which were differently affected by the accident, and during three sampling periods, starting one year after the accident began. We detected Σ16PAHs in the clam soft tissues and in the sediment samples, all with lower concentrations. Differential biomarker responses were observed in both clam tissues, as denoted by the Integrated Biomarker Response Index (IBR). However, there was no correlation between PAH bioaccumulation and biomarker responses in T. mactroides, suggesting the occurrence of multiple stress factors in such a marine protected area. This study demonstrated that multiple biomarkers assessment in the marine clam T. mactroides is a suitable approach for biomonitoring of marine areas in Brazil affected by the 2019 oil spill. However, we emphasize that further long-term studies must be conducted to better understand the environmental impacts caused by an oil spill of such magnitude.

PMID:40516676 | DOI:10.1016/j.envpol.2025.126653

Cell. 2025 Jun 12:S0092-8674(25)00576-8. doi: 10.1016/j.cell.2025.05.026. Online ahead of print.

ABSTRACT

When a material enters the body, it is immediately attacked by hundreds of proteins, organized into complex networks of binding interactions and reactions. How do such complex systems interact with a material, "deciding" whether to attack? We focus on the complement system of ∼40 blood proteins that bind microbes, nanoparticles, and medical devices, initiating inflammation. We show a sharp threshold for complement activation upon varying a fundamental material parameter, the surface density of potential complement attachment points. This sharp threshold manifests at scales spanning single nanoparticles to macroscale pathologies, shown here for diverse engineered and living materials. Computational models show these behaviors arise from a minimal subnetwork of complement, manifesting percolation-type critical transitions in the complement response. This criticality switch explains the "decision" of a complex signaling network to interact with a material.

PMID:40516526 | DOI:10.1016/j.cell.2025.05.026

Methods Mol Biol. 2025;2940:93-107. doi: 10.1007/978-1-0716-4615-1_9.

ABSTRACT

Single-cell RNA sequencing (scRNA-seq) is a revolutionary technology capable of analyzing host and viral transcripts and host-virus interactions at the single-cell level. Viral infection is a complex process involving interactions between the virus and the host cell. While traditional research methods often have difficulty revealing cellular heterogeneity and dynamics during viral infections, scRNA-seq technology, which enables the sequencing of individual cells, provides a powerful tool for the in-depth study of viral-host interactions. scRNA-seq was able to reveal the mechanism of molecular changes in host cells during viral infection, providing new ideas and methods for the diagnosis and treatment of viral infections. This article describes the application, advantages, and experimental procedures of scRNA-seq in host virology.

PMID:40515904 | DOI:10.1007/978-1-0716-4615-1_9

Methods Mol Biol. 2025;2940:43-61. doi: 10.1007/978-1-0716-4615-1_6.

ABSTRACT

Upon invasion of host cells, viruses trigger a wide range of changes in the host genome, including alterations in chromatin conformation, gene expression regulation, DNA methylation, and histone modification. These genomic changes not only contribute to viral replication and latency but also may promote disease onset and progression by interfering with the host immune response. The profound impact of viral infection on the host genome has become an important area of current virology research. With the continuous advancements in genomics, 3D genome technology has become a powerful tool for revealing chromatin folding and interactions in three dimensions. In virology, 3D genomic technology can be used to determine how viruses regulate host gene expression by altering the conformation of the host chromatin, which in turn drives viral infections and related diseases. In recent years, Hi-C technology, a high-resolution 3D genome analysis method, has revealed how viruses integrate into host chromatin by capturing spatial contacts in three dimensions, providing insights into how these interactions affect the viral lifecycle, latent state, and host immune response. In a SARS-CoV-2 study, Hi-C technology revealed the interactions between the virus and specific regions of the host genome and elucidated how these interactions dynamically regulate the viral replication process and the modulation of the host immune response. By capturing spatial contacts at high resolution, Hi-C technology provides a unique molecular perspective for the study of viral infection mechanisms and promotes the further development of virology research. This chapter focuses on the basic principles of 3D genome technology and its application in virology, with a particular emphasis on the innovative use of Hi-C technology in the study of viruses such as SARS-CoV-2, especially its important contributions to understanding viral integration sites and chromatin recombination mechanisms. This chapter will also elaborate on the Hi-C experimental steps, required materials, and data analysis process, providing researchers with clear operational guidelines and assisting in the in-depth exploration of viral infection mechanisms.

PMID:40515901 | DOI:10.1007/978-1-0716-4615-1_6