bioRxiv : the preprint server for biology最新文献

{"title":"CFTR mutation leads to intrinsic dysfunction in neutrophils from people with Cystic Fibrosis.","authors":"Frank H Robledo-Avila, Raul Rascon, Alejandra Montanez-Barragan, Veronica Loyo-Celis, Harpreet Singh, Karen S McCoy, Benjamin T Kopp, Santiago Partida-Sanchez","doi":"10.1101/2025.06.08.656500","DOIUrl":"https://doi.org/10.1101/2025.06.08.656500","url":null,"abstract":"<p><p>Cystic fibrosis (CF), a common genetic disease, is caused by a defective CF-transmembrane conductance regulator (CFTR). People with CF (pwCF) are prone to develop infections by opportunistic pathogens, including Burkholderia cenocepacia, leading to chronic inflammation and lung function loss. Neutrophils, the most abundant cells in the chronically inflamed lungs of pwCF, release granular proteins and oxida-tive products that contribute to tissue damage. The CFTR modulators are a new treat-ment for pwCF aiming to correct the subcellular location and function of the CFTR ion channel. The triple modulator combination of Elexacaftor, Tezacaftor, and Ivacaftor (ETI) or Trikafta® has significantly improved clinical symptoms and overall provided a better quality of life for pwCF. The mechanism by which the CFTR modulators help to restore the antimicrobial functions of neutrophils is unknown. The present study demonstrates that neutrophils functionally express CFTR and reveals how ETI modi-fies subcellular CFTR trafficking in CF neutrophils. In addition, ETI treatment reduces intracellular chloride levels in human neutrophils, indicating activation of CFTR-dependent chloride efflux (outflow). Finally, ETI treatment also re-established the intra-cellular antimicrobial killing of CF neutrophils by potentiating NADPH oxidase activity and producing Neutrophil Extracellular Traps (NETs). Together, our findings suggest that CFTR has an essential role in controlling neutrophil functions and that the CFTR modulators improve the health of pwCF by restoring the antimicrobial functions of CF neutrophils.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12157431/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144277351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sex-specific Effects of Outdoor Air Pollution on Subcortical Microstructure and Weight Gain: Findings from the ABCD Study®.","authors":"Miguel Ángel Rivas-Fernández, Jonatan Ottino-González, Sevan Esaian, Victoria E Goldman, Megan M Herting, Tanya L Alderete, Shana Adise","doi":"10.1101/2025.06.04.657916","DOIUrl":"https://doi.org/10.1101/2025.06.04.657916","url":null,"abstract":"<p><p>Obesity is associated with structural alterations of brain regions that support eating behavior. Exposure to air pollutants might exacerbate this association through neurotoxic effects on the brain. This study evaluated whether air pollution exposure 9-10 years old children, coupled with brain microstructure development in appetite-regulating regions, is associated with body mass index (BMI) changes over two years, and whether these associations differ by sex. Data were gathered from the Adolescent Brain Cognitive Development Study® (n _baseline =4,802, ages=9-10, males=49.9%, n _follow-up =2,439, ages=11-12, males=51.1%). Annual average estimates of ambient fine particulate matter (PM2.5), nitrogen dioxide (NO2), ground-level ozone (O3), and redox-weighted oxidative capacity (Oxwt, a joint measure of NO2 and O3) were gathered from youth's residential addresses. Brain microstructure in 16 subcortical regions was assessed using diffusion-weighted MRI, focusing on proxies of cellular and neurite density: restricted normalized isotropic (RNI) and directional (RND) diffusion, respectively. Linear mixed-effects models examined whether air pollution and brain microstructure are related to BMI changes over two years, and whether these associations differed by sex. Exposure to PM2.5 coupled with high RND estimates in right caudate nucleus, bilateral putamen, and pallidum were associated with higher BMI over time, with pronounced effects in males (all <i>p</i> <0.05). PM2.5 coupled with greater neurite density in regions involved in reward-processing and decision-making were associated with higher BMI over a 2-year follow-up, especially in males. This research highlights air pollution as a modifiable risk factor for how differences in basal ganglia neurite density map onto obesity risk, with important implications for public health policy.</p><p><strong>Highlights: </strong>High PM2.5 exposure and subcortical neurite density is associated with weight gainPM2.5 and subcortical development associations with BMI are pronounced in malesSignificant associations with BMI were found in regions involved in food intake.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12157448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144277840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Neurotrophic Factor-α1/carboxypeptidase E regulates critical protein networks to rescue neurodegeneration, defective synaptogenesis and impaired autophagy in Alzheimer's Disease mice.","authors":"Lan Xiao, Pranav Sharma, Xuyu Yang, Daniel Abebe, Y Peng Loh","doi":"10.1101/2025.06.04.657876","DOIUrl":"https://doi.org/10.1101/2025.06.04.657876","url":null,"abstract":"<p><strong>Background: </strong>The global aging population is increasingly inflicted with Alzheimer's disease (AD), but a cure is still unavailable. Neurotrophic Factor-α1/carboxypeptidase E (NF-α1/CPE) gene therapy has been shown to prevent and reverse memory loss and pathology AD mouse models However, the mechanisms of action of NF-α1/CPE are not fully understood. We investigated if a non-enzymatic form of NF-α1/CPE-E342Q is efficient in reversing AD pathology and carried out a proteomic study to uncover the mechanisms of action of NF-α1/CPE in AD mice.</p><p><strong>Methods: </strong>AAV-human NF-α1/CPE and a non-enzymatic form, NF-α1/CPE -E342Q were delivered into hippocampus of 3xTg-AD mice and effects on cognitive function, neurodegeneration, synaptogenesis and autophagy were investigated. A quantitative proteomic analysis of hippocampus of 3xTg-AD mice with and without AAV-NF-α1/CPE treatment was carried out.</p><p><strong>Results: </strong>Hippocampal delivery of AAV-NF-α1/CPE-E342Q prevented memory loss, neurodegeneration and increase in activated microglia in 3xTg-AD mice, indicating its action is independent of its enzymatic activity. Quantitative proteomic analysis of hippocampus of 3xTg-AD mice that underwent NF-α1/CPE gene therapy revealed differential expression of >2000 proteins involving many metabolic pathways. Of these, two new proteins down-regulated by NF-α1/CPE: Nexin4 (SNX4) and Trim28 which increase Aβ production and tau levels, respectively were identified. Western blot analysis verified that they were reduced in AAV-NF-α1/CPE treated 3xTg-AD mice compared to untreated mice. Our proteomic analysis indicated synaptic organization as top signaling pathway altered as a response to CPE expression. Synaptic markers PSD95 and Synapsin1 were decreased in 3xTg-AD mice and were restored with AAV-NF-α1/CPE treatment. Proteomic analysis hypothesized involvement of autophagic signaling pathway. Indeed, multiple proteins known to be markers of autophagy were down-regulated in 3xTg-AD mice, accounting for impaired autophagy. Expression of these proteins were upregulated in 3xTg-AD mice with NF-α1/CPE gene therapy, thereby reversing autophagic impairment.</p><p><strong>Conclusions: </strong>This study uncovered vast actions of NF-α1/CPE in restoring expression of networks of critical proteins including those necessary for maintaining neuronal survival, synaptogenesis and autophagy, while down-regulating many proteins that promote tau and Aβ accumulation to reverse memory loss and AD pathology in 3xTg-AD mice. AAV-NF-α1/CPE gene therapy uniquely targets many metabolic levels, offering a promising holistic approach for AD treatment.</p><p><strong>Graphic abstract: </strong></p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12190346/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144500089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Na⁺-pumping mechanism driven by redox reactions in the NADH-quinone oxidoreductase from <i>Vibrio cholerae</i> relies on dynamic conformational changes.","authors":"Moe Ishikawa-Fukuda, Takehito Seki, Jun-Ichi Kishikawa, Takahiro Masuya, Kei-Ichi Okazaki, Takayuki Kato, Blanca Barquera, Hideto Miyoshi, Masatoshi Murai","doi":"10.1101/2025.06.01.656757","DOIUrl":"10.1101/2025.06.01.656757","url":null,"abstract":"<p><p>The Na⁺-pumping NADH-quinone oxidoreductase (Na⁺-NQR) is a key respiratory enzyme in many marine and pathogenic bacteria that couples electron transfer to Na⁺-pumping across the membrane. Earlier X-ray and cryo-EM structures of Na⁺-NQR from <i>Vibrio cholerae</i> suggested that the subunits harboring redox cofactors undergo conformational changes during catalytic turnover. However, these proposed rearrangements have not yet been confirmed. Here, we have identified at least five distinct conformational states of Na⁺-NQR using: mutants that lack specific cofactors, specific inhibitors or low-sodium conditions. Molecular dynamics simulations based on these structural insights indicate that 2Fe-2S reduction in NqrD/E plays a crucial role in triggering Na⁺ translocation by driving structural rearrangements in the NqrD/E subunits, which subsequently influence NqrC and NqrF positioning. This study provides the first structural insights into the mechanism of Na⁺ translocation coupled to electron transfer in Na⁺-NQR.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12157696/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144277917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evidence for Transcriptomic Conservation Between the Main Cells of the <i>Drosophila</i> Prostate-Like Accessory Gland and Basal Cells of the Mammalian Prostate.","authors":"S Jaimian Church, April R Kriebel, Joshua D Welch, Laura A Buttitta","doi":"10.1101/2025.06.05.658085","DOIUrl":"10.1101/2025.06.05.658085","url":null,"abstract":"<p><p>The <i>Drosophila</i> accessory gland performs functions analogous to the mammalian prostate in production of seminal fluid components that are essential for male fertility. The mammalian prostate and <i>Drosophila</i> accessory glands share a similar tissue organization and structure. Both organs contain secretory epithelial cells forming a gland lumen, surrounded by a stroma with extracellular matrix enveloped by innervated muscle for organ contraction and fluid release. However, the <i>Drosophila</i> accessory gland secretory epithelium is postmitotic, polyploid and binucleate, and lacks a known stem cell population. By contrast, the mammalian prostate epithelium is made up of diploid luminal secretory cells and diploid basal cells that are maintained by at least two stem cell populations. Despite the differences in the tissues, it has been argued these tissues may share a 'deep homology' based on the expression of conserved genes during development. Here we performed a cross-species comparative analysis using single-cell RNA sequencing data from adult tissues using data from the <i>Drosophila</i> Fly Cell Atlas and mammalian adult prostate single-cell datasets. Our analysis provides additional evidence of transcriptomic similarity between the main epithelial cells of the <i>Drosophila</i> prostate-like accessory gland and the basal epithelial cells of the mammalian prostate. While we do not know whether these similarities reflect shared evolutionary homology, or independently derived features due to shared tissue functions, our results strengthen the arguments that the <i>Drosophila</i> accessory gland can be used to effectively model aspects of human prostate biology and disease.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12157375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144277480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interlinked roles for HEB and Id3 in fetal gamma-delta T cell commitment and functional programming.","authors":"Johanna S Selvaratnam, Juliana Dutra Barbosa da Rocha, Vinothkumar Rajan, Helen Wang, Emily C Reddy, Miki S Gams, Cornelis Murre, Cynthia J Guidos, Juan Carlos Zúñiga-Pflücker, Michele K Anderson","doi":"10.1101/2025.06.08.658490","DOIUrl":"10.1101/2025.06.08.658490","url":null,"abstract":"<p><p>γδ T cells that produce IL-17 (γδT17) play essential roles in barrier immunity, but the gene networks that install their functions are not well understood. We previously linked T cell receptor (TCR) signal strength to the proportional upregulation of <i>Id3</i> during T cell development, which antagonizes the activity of HEB (encoded by <i>Tcf12</i>), and showed that HEB is required for γδT17 development. To understand how HEB and Id3 regulate γδT17 cell development, we conducted single cell RNA-sequencing on fetal thymic γδ T cells from <i>Tcf12</i>-deficient mice. γδ T cells lacking HEB exhibited profound alterations in the expression of the genes encoding the TCRγ and TCRδ chains, accompanied by a decrease in expression of genes in the early γδ T cell specification network. Surprisingly, <i>Id3</i> was among the most severely decreased genes in HEB-deficient γδ T cell precursors, suggesting a requirement for HEB in <i>Id3</i> expression. Analysis of fetal thymic γδ T cells in <i>Id3</i>-deficient mice revealed that the TCRγ and TCRδ repertoires were unaffected, and expression of early γδ T cell genes was unperturbed. However, later stage regulators of γδT17 cell differentiation were decreased, and <i>Id3</i>-deficient γδ T cells were defective in IL-17 production. Therefore, our findings reveal an interlinked network in which HEB is initially required to upregulate <i>Id3</i> expression, which in turn enables the later stages of γδT17 cell development and functional programming.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12157620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144277657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Study of combination CAR T-cell treatment for glioblastoma using mathematical modeling.","authors":"Runpeng Li, Michael Barish, Margarita Gutova, Christine E Brown, Russell C Rockne, Heyrim Cho","doi":"10.1101/2025.06.04.657886","DOIUrl":"10.1101/2025.06.04.657886","url":null,"abstract":"<p><p>Glioblastoma is a highly aggressive and difficult-to-treat brain cancer that resists conventional therapies. Recent advances in chimeric antigen receptor (CAR) T-cell therapy have shown promising potential for treating glioblastoma; however, achieving optimal efficacy remains challenging due to tumor antigen heterogeneity, the tumor microenvironment, and T-cell exhaustion. In this study, we developed a mathematical model of CAR T-cell therapy for glioblastoma to explore combinations of CAR T-cell treatments that take into account the spatial heterogeneity of antigen expression. Our hybrid model, created using the multicellular modeling platform PhysiCell, couples partial differential equations that describe the tumor microenvironment with agent-based models for glioblastoma and CAR T-cells. The model captures cell-to-cell interactions between the glioblastoma cells and CAR T-cells throughout treatment, focusing on three target antigens: IL-13R<i>α</i>2, HER2, and EGFR. We analyze tumor antigen expression heterogeneity informed by expression patterns identified from human tissues and investigate patient-specific combination CAR T-cell treatment strategies. Our model demonstrates that an early intervention is the most effective approach, especially in glioblastoma tumors characterized by mixed antigen expression. However, in tissues with clustered antigen patterns, we find that sequential administration with specific CAR T-cell types can achieve efficacy comparable to simultaneous administration. In addition, spatially targeted delivery of CAR T-cells to specific tumor regions with matching antigen is an effective strategy as well. Our model provides a valuable platform for developing patient-specific CAR T-cell treatment plans with the potential to optimize scheduling and locations of CAR T-cell injections based on individual antigen expression profiles.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12157650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144277892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Membranes arrest the coarsening of mitochondrial condensates.","authors":"Sanjaya V B D Aththawala Gedara, Surya Teja Penna, Marina Feric","doi":"10.1101/2025.06.06.658068","DOIUrl":"https://doi.org/10.1101/2025.06.06.658068","url":null,"abstract":"<p><p>Mitochondria contain double membranes that enclose their contents. Within their interior, the mitochondrial genome and its RNA products are condensed into ~100 nm sized (ribo)nucleoprotein complexes. How these endogenous condensates maintain their roughly uniform size and spatial distributions within membranous mitochondria remains unclear. Here, we engineered an optogenetic tool (mt-optoIDR) that allowed for controlled formation of synthetic condensates upon light activation in live mitochondria. Using live cell super-resolution microscopy, we visualized the nucleation of small, yet elongated condensates (mt-opto-condensates), which recapitulated the morphologies of endogenous mitochondrial condensates. We decoupled the contribution of the double membranes from the environment within the matrix by overexpressing the dominant negative mutant of a membrane fusion protein (Drp1K38A). The resulting bulbous mitochondria had significantly more dynamic condensates that coarsened into a single, prominent droplet. These observations inform how mitochondrial membranes can limit the growth and dynamics of the condensates they enclose, without the need of additional regulatory mechanisms.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12157474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144277718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"It's a wrap: deriving distinct discoveries with FDR control after a GWAS pipeline.","authors":"Benjamin B Chu, Zihuai He, Chiara Sabatti","doi":"10.1101/2025.06.05.658138","DOIUrl":"10.1101/2025.06.05.658138","url":null,"abstract":"<p><p>Recent work has shown how to test conditional independence hypotheses between an outcome of interest and a large number of explanatory variables with false discovery rate control (FDR), even without access to individual level data. In the case of genome-wide association studies (GWAS) specifically, summary statistics resulting from the standard analysis pipeline can be used as input of a procedure which identifies distinct signals across the genome with FDR control. This secondary analysis requires sampling of negative controls (knockoff) from a distribution determined by the linkage disequilibrium patterns in the genome of the population under study. In prior work, we have pre-computed this distribution for European genomes, starting from information derived from the UK Biobank. Thus, researchers working with European GWASes can carry out a knockoff analysis with minimal computational costs, using the distributed routine GhostKnockoffGWAS. Here we introduce and release a new software (solveblock) that extends this capability to a much richer collection of studies. Given a set of genotyped samples, or a reference dataset, our pipeline efficiently estimates the high-dimensional correlation matrices that describe correlation structures across the genome, making rather common sparsity assumptions. Taking this sample-specific estimate as input, the software identifies groups of genetic variants that are highly correlated, and uses them to define an appropriate resolution for conditional independence hypotheses. Finally, we compute the distribution for the exchangeable negative controls necessary to test these hypotheses. The output of solveblock can be passed directly to GhostKnockoffGWAS, allowing users to carry out the complete analysis in a two step procedure. We illustrate the performance of the routine analyzing data from five UK Biobank sub-populations. In simulations, our method controls FDR. Analyzing real data relative to 26 phenotypes of varying polygenicity in British individuals, we make an average of ≈ 19 additional discoveries, compared to standard marginal association testing. Our code, precompiled software, and processed files for these five subpopulations are openly shared.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12157521/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144277676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TITAN-RNA: A hybrid-capture sequencing panel detects known and unknown <i>Flaviviridae</i> for diagnostics and vector surveillance.","authors":"Chloe M Murrell, Aiman Sabaawy, Xiyu Wang, Nagi Hashimoto, Kristina Ceres, Yining Sun, Jordan D Zehr, Aine Lehane, Emily Mader, Natalie Bailey, Marie V Lilly, Laura Plimpton, Guillaume Reboul, Joel J Brown, Kelly Sams, Lauren Singh, Ethan Seiz, Ellie Bourgikos, Chantal B F Vogels, Alexander T Ciota, Victoria Schnurr, Jennifer Grenier, Xavier Berthet, Ana I Bento, Laura Harrington, Maria Diuk-Wasser, Ximena Olarte-Castillo, Laura B Goodman","doi":"10.1101/2025.06.08.658352","DOIUrl":"10.1101/2025.06.08.658352","url":null,"abstract":"<p><p>Clinical testing and public health surveillance can be significantly improved by incorporating sequencing-based molecular detection and subtyping for real-time monitoring of virus evolution. With phylogenetic analysis used for speciation and variant subtyping, target analyte specificity can be relaxed well beyond typical parameters acceptable in PCR-based diagnostics. Hybrid capture is a promising way to enrich large numbers of sequences with maximal flexibility, using standard molecular biology laboratory equipment and small benchtop sequencers. Here, we report the development and bench validation of a hybrid capture based next-generation sequencing diagnostic panel for all known viral tick-borne pathogens, TITAN-RNA. Based on systematic testing with simulated novel viruses and field samples, we determined a 10% tolerance for evenly distributed mutations or 27% tolerance for naturally occurring viral divergence. The TITAN-RNA extrapolated limit of detection in blood is 19.1 genome copies by complementary log-log analysis, and linearity performance (R² ≥ 0.99) is amenable for its use as a quantitative assay. As proof of principle for public health surveillance and evolutionary studies, we report two putatively novel segmented <i>Flavi-</i>like viruses in New York State, USA, identified from the invasive <i>Haemaphysalis longicornis</i> tick.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12157608/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144277925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}