bioRxiv : the preprint server for biology最新文献

{"title":"Characterisation of <i>Ornithobacterium hominis</i> colonisation dynamics and interaction with the nasopharyngeal microbiome in a South African birth cohort.","authors":"Celine C De Allende, Susannah J Salter, Siobhan E Brigg, Shantelle Claassen-Weitz, Kilaza S Mwaikono, Lesley Workman, Heather J Zar, Mark P Nicol, Julian Parkhill, Felix S Dube","doi":"10.1101/2025.05.24.655922","DOIUrl":"https://doi.org/10.1101/2025.05.24.655922","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Ornithobacterium hominis&lt;/i&gt; is a recently described Gram-negative bacterium that colonises the human nasopharynx and may be associated with poor upper respiratory tract health. Here, we describe the isolation of &lt;i&gt;O. hominis&lt;/i&gt; from samples collected from a South African birth cohort, creating the first archive of cultured strains of the species from Africa. Sequenced genomes from this archive reveal that South African &lt;i&gt;O. hominis&lt;/i&gt; is more similar to Australian strains than those from Southeast Asia, and that it may share genes with other members of the microbiome that are relevant for virulence, colonisation, and antibiotic resistance. Leveraging existing microbiome data from the cohort, &lt;i&gt;O. hominis&lt;/i&gt; was found to be closely associated with bacterial co-colonisers that are rare in non-carrier individuals, including &lt;i&gt;Suttonella&lt;/i&gt; , &lt;i&gt;Helcococcus&lt;/i&gt; , &lt;i&gt;Moraxella&lt;/i&gt; spp., and Gracilibacteria. Their collective acquisition has a significant impact on the diversity of nasopharyngeal communities that contain &lt;i&gt;O. hominis&lt;/i&gt; . Individuals who have not yet acquired &lt;i&gt;O. hominis&lt;/i&gt; have a higher abundance of &lt;i&gt;Moraxella&lt;/i&gt; (particularly &lt;i&gt;M. lincolnii&lt;/i&gt; ) than individuals who never acquire &lt;i&gt;O. hominis&lt;/i&gt; , suggesting that this could be a precursor state for successful colonisation. Finally, a novel co-coloniser species, &lt;i&gt;Helcococcus ekapensis&lt;/i&gt; , was successfully isolated and sequenced.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Data summary: &lt;/strong&gt;&lt;i&gt;Ornithobacterium hominis&lt;/i&gt; data have been deposited under project accession ERP149886. This comprises genome sequences for isolates SA-OH-C1 (ERR13967269), SA-OH-C2 (ERR13967270), SA-OH-C3 (ERR13967271), SA-OH-C4 (ERR13967272, ERR13967275), SA-OH-C5 (ERR13967273), SA-OH-C6 (ERR13967274, ERR13967276). Previously published 16S rRNA gene data are deposited under project accessions PRJNA790843 and PRJNA548658. &lt;i&gt;Helcococcus ekapensis&lt;/i&gt; genome data are deposited under project accession PRJEB85661.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Software used: &lt;/strong&gt;AMRFinderPlus v3.12.8: https://github.com/ncbi/amr AssembleBAC-ONT v1.1.1: https://github.com/avantonder/assembleBAC-ONT BAKTA v1.8.1: https://bakta.computational.bio/ BLAST v2.16.0: https://blast.ncbi.nlm.nih.gov/Blast.cgi Comprehensive Antibiotic Resistance Database (CARD) Resistance Gene Identifier (RGI) tool v1.2.1: https://card.mcmaster.ca/analyze/rgi Decontam v1.12 (R package): https://github.com/benjjneb/decontam Eggnog-mapper v2.0.1: http://eggnog-mapper.embl.de/ FastANI v1.1.0: https://github.com/ParBLiSS/FastANI Flye v2.9.2: https://github.com/fenderglass/Flye Guppy v6.5.7: https://community.nanoporetech.com/downloads/guppy/release_notes ISEScan v1.7.2.3: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1 Medaka v1.9.1: https://github.com/nanoporetech/medaka MEGA11: https://www.megasoftware.net/ MMseqs2 v17: https://github.com/soedinglab/MMseqs2 Mothur v1.44.3: https://github.com/mothur/mothur NetCoMi","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139837/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236427","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":"<i>In vivo</i> anti-tumor activity of high-dose parenteral ascorbic acid is mediated primarily via cofactor activity, not via oxidative stress.","authors":"Talia Akram, Rebecca A Luchtel, Vinay Dubey, Soma Seal, Ritesh Aggarwal, Hiroaki Sai, Niraj K Shenoy","doi":"10.1101/2025.05.21.655101","DOIUrl":"https://doi.org/10.1101/2025.05.21.655101","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The anti-tumor effect of high-dose ascorbic acid (AA) has been demonstrated in multiple &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; cancer models with the postulation of two primary categories of mechanisms: antioxidant/cofactor activity and H &lt;sub&gt;2&lt;/sub&gt; O &lt;sub&gt;2&lt;/sub&gt; -mediated oxidative damage. Both mechanisms have been conclusively demonstrated &lt;i&gt;in vitro&lt;/i&gt; . However, while parenteral high-dose AA-induced cofactor activity (TET-mediated DNA demethylation and prolyl/asparaginyl hydroxylase-mediated HIF activity inhibition via reduction of enzymatic Fe &lt;sup&gt;3+&lt;/sup&gt; to Fe &lt;sup&gt;2+&lt;/sup&gt; ) has been demonstrated intratumorally &lt;i&gt;in vivo&lt;/i&gt; in multiple models, the cumulative data on parenteral high-dose AA-induced intratumoral oxidative damage &lt;i&gt;in vivo&lt;/i&gt; has been inconclusive. Furthermore, the relative contribution of the seemingly opposing mechanisms towards &lt;i&gt;in vivo&lt;/i&gt; anti-cancer activity has not been studied concurrently. We therefore sought to definitively delineate the roles of both antioxidant/cofactor activity and prooxidant functions of high-dose AA in the &lt;i&gt;in vivo&lt;/i&gt; anti-tumor response. Using two syngeneic mouse tumor models, the AA-sensitive A20 model and the AA-resistant Renca model, we assessed markers of DNA and lipid oxidative damage as well as the specific roles of TET2 and AA transporter SLC23A2 in the anti-tumor response to parenteral high-dose AA. In the sensitive A20 model, loss of either &lt;i&gt;Tet2&lt;/i&gt; or &lt;i&gt;Slc23a2&lt;/i&gt; fully reversed anti-tumor activity. Similarly, overexpression of &lt;i&gt;Tet2&lt;/i&gt; in the resistant Renca model (which expresses high baseline levels of AA transporters SLC23A1 and SLC23A2, but does not express TET2), resulted in increased CD8 &lt;sup&gt;+&lt;/sup&gt; T cell infiltration and dramatic reduction in tumor growth overall. In both A20 and Renca models, high-dose parenteral AA &lt;i&gt;increased&lt;/i&gt; total intratumoral antioxidant capacity, and this was attenuated by &lt;i&gt;Slc23a2&lt;/i&gt; knockdown in A20. High-dose AA treatment also resulted in a &lt;i&gt;Tet2&lt;/i&gt; - and &lt;i&gt;Slc23a2&lt;/i&gt; -dependent increase in intratumoral 5-hydroxymethylcytosine. Intracellular oxidative damage markers, 8-OHdG and 4-HNE, were not induced in tumors by high-dose AA in either model. In contrast, these markers were robustly induced &lt;i&gt;in vitro&lt;/i&gt; by high-dose AA in A20 and Renca cells. Using dynamic real-time extracellular H &lt;sub&gt;2&lt;/sub&gt; O &lt;sub&gt;2&lt;/sub&gt; measurements with high-dose AA, difference in molecular oxygen concentration between standard &lt;i&gt;in vitro&lt;/i&gt; and hypoxic &lt;i&gt;in vivo&lt;/i&gt; conditions was identified as an important factor underlying the marked discrepancy between the abundant &lt;i&gt;in vitro&lt;/i&gt; and absent &lt;i&gt;in vivo&lt;/i&gt; intratumoral oxidative stress with high-dose AA. Furthermore, using additional syngeneic models resistant (MB49) and sensitive (MC38) to AA-induced potentiation of anti-PD1 checkpoint inhibition, we demonstrate that very low catalase expression does not confer sensitivity to high-dose AA &lt;i&gt;in vivo&lt;/i&gt; (further arguing agai","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139978/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236444","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":"Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens.","authors":"Samuel G Regalado, Chengxiang Qiu, Jean-Benoît Lalanne, Beth K Martin, Madeleine Duran, Cole Trapnell, Aidan Keith, Silvia Domcke, Jay Shendure","doi":"10.1101/2025.05.23.655669","DOIUrl":"https://doi.org/10.1101/2025.05.23.655669","url":null,"abstract":"<p><p>Genetic screens in organoids hold tremendous promise for accelerating discoveries at the intersection of genomics and developmental biology. Embryoid bodies (EBs) are self-organizing multicellular structures that recapitulate aspects of early mammalian embryogenesis. We set out to perform a CRISPR screen perturbing all transcription factors (TFs) in murine EBs. Specifically, a library of TF-targeting guide RNAs (gRNAs) was used to generate mouse embryonic stem cells (mESCs) bearing single TF knockouts. Aggregates of these mESCs were induced to form mouse EBs, such that each resulting EB was 'mosaic' with respect to the TF perturbations represented among its constituent cells. Upon performing single cell RNA-seq (scRNA-seq) on cells derived from mosaic EBs, we found many TF perturbations exhibiting large and seemingly significant effects on the likelihood that individual cells would adopt certain fates, suggesting roles for these TFs in lineage specification. However, to our surprise, these results were not reproducible across biological replicates. Upon further investigation, we discovered cellular bottlenecks during EB differentiation that dramatically reduce clonal complexity, curtailing statistical power and confounding interpretation of mosaic screens. Towards addressing this challenge, we developed a scalable protocol in which each individual EB is monoclonally derived from a single mESC and genetically barcoded. In a proof-of-concept experiment, we show how these monoclonal EBs enable us to better quantify the consequences of TF perturbations as well as 'inter-individual' heterogeneity across EBs harboring the same genetic perturbation. Looking forward, monoclonal EBs and EB-derived organoids may be powerful tools not only for genetic screens, but also for modeling Mendelian disorders, as their underlying genetic lesions are overwhelmingly constitutional ( <i>i.e.</i> present in all somatic cells), yet give rise to phenotypes with incomplete penetrance and variable expressivity.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139999/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236478","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":"Combined MEG and EEG suggest a limbic source network of the P3 including retrosplenial cortex and hippocampus.","authors":"Diptyajit Das, Matti S Hämäläinen, Andrew R Dykstra, Andre Rupp, Alexander Gutschalk","doi":"10.1101/2025.03.24.645008","DOIUrl":"10.1101/2025.03.24.645008","url":null,"abstract":"<p><p>The P3 is evoked by most target and salient distractor stimuli, but its neural generators have remained controversial. Here we reevaluate the role of retro-splenial cortex and hippocampus as potential generators of the P3. Combined magneto- and electroencephalography signals were recorded during a visual oddball paradigm. Observers were instructed to respond to rare targets of a deviant shape and ignore rare non-targets of a deviant color. Source analysis was based on noise-normalized minimum norm estimates in an individual, MRI-based cortical source space. Critically, the source space was extended with the hippocampus. Source analysis showed strong sources in retrosplenial cortex and hippocampus at the P3 peak. Subsequent activity was observed in insula and anterior mid-cingulate cortex. The source configuration was similar for rare target and non-target stimuli. Simulations and further analyses show that the source in retrosplenial cortex is strongly attenuated in magnetoencephalography, whereas the source in hippocampus contributes to both recording modalities. These data support that retrosplenial cortex is a main generator of the P3 in EEG and that the hippocampal P3 source can be recorded with extracranial EEG and MEG. The source configuration presented here suggests that the P3 is confined to limbic circuits.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805376","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":"Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies.","authors":"Anna E Elz, Derrik Gratz, Annalyssa Long, David Sowerby, Azi Hadadianpour, Evan W Newell","doi":"10.1101/2025.05.19.654974","DOIUrl":"https://doi.org/10.1101/2025.05.19.654974","url":null,"abstract":"<p><p>The rapid development of updated and new commercially available single-cell transcriptomics platforms provides users with a range of experimental options. Cost, sensitivity, throughput, flexibility, and ease of use, all influence the selection of an optimal workflow. We performed a comprehensive comparison of single-cell transcriptomic approaches using multiple standardized PBMCs from different donors. We report on standard single-cell metrics including cell recovery, sequencing efficiency, sensitivity, cell annotation, and differential gene expression for seven recently available kits that interrogate whole transcriptome mRNA, and two that include TCR profiling. We also discuss workflow throughput, sample requirements, timing, cost, and labor as critical factors to consider. In addition to variable experimental constraints imposed by each platform, our findings highlight differences in cell recovery and sensitivity, which we found to significantly influence the ability to resolve cell subtypes. This work provides a basis by which users can balance performance and practical considerations when selecting a single-cell RNA sequencing platform.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139828/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236550","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":"Inflammation-induced endothelial cell activation and angiogenic sprouting are downmodulated by ubiquitin-specific peptidase 20.","authors":"Bipradas Roy, Jiao-Hui Wu, Neil J Freedman, Sudha K Shenoy","doi":"10.1101/2025.05.20.655129","DOIUrl":"https://doi.org/10.1101/2025.05.20.655129","url":null,"abstract":"<p><p>Nuclear factor-κB (NFκB) mediates inflammation-driven angiogenesis, which promotes growth of atherosclerotic plaques and tumors. The deubiquitinase ubiquitin-specific peptidase 20 (USP20) suppresses NFκB activation in vascular smooth muscle cells (SMCs) and attenuates atherosclerosis, but the role of USP20 in endothelial cells (ECs) was undefined. We tested whether USP20 activity diminishes NFκB signaling in ECs and thereby diminishes angiogenesis. Cytokine-induced NFκB activity was elevated in primary ECs isolated from <i>Usp20 ^-/-</i> mice as compared with ECs from wild-type (WT) mice. Similarly, cytokine-induced NFκB activity was elevated in mouse coronary endothelial cells (MCECs) expressing catalytically inactive USP20 (USP20-DN) or phospho-mimetic USP20(S334D). In contrast, cytokine stimulation of MCECs expressing WT USP20 (USP20-WT) or phospho-resistant USP20(S334A) produced blunted NFκB activity. Assessed by scratch-wound healing and spheroid assays, migration and angiogenesis of MCECs, respectively, were (a) increased by USP20-DN or USP20(S334D), and (b) decreased by USP20-WT or USP20(S334A). Angiogenesis assessed by the aortic ring assay was significantly increased in <i>Usp20 ^-/-</i> mice and was suppressed by TPCA-1, an inhibitor of NFκB signaling. Angiogenesis was augmented in USP20(S334D) mouse aortic rings but reduced in USP20(S334A) mice. By screening known angiogenesis factors, we identified matrix metalloproteinase 3 (MMP3), a transcriptional target of NFκB, as a gene that is also regulated by USP20 expression and Ser334 phosphorylation. Inhibiting MMP3 reduced angiogenic sprouting in the <i>Usp20 ^-/-</i> mouse aortic rings. We conclude that USP20 expression inversely correlates with the extent of angiogenesis, and that inhibiting USP20 Ser334 phosphorylation could be a useful strategy to constrain inflammation-driven angiogenesis under pathological circumstances, like cancer and atherosclerosis.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236593","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":"Transient lung eosinophilia during breakthrough influenza infection in vaccinated mice is associated with protective and balanced Type 1/2 immune responses.","authors":"Lauren A Chang, Stephen T Yeung, Prajakta Warang, Moataz Noureddine, Gagandeep Singh, Brett T Webb, Michael Schotsaert","doi":"10.1101/2025.05.19.654943","DOIUrl":"https://doi.org/10.1101/2025.05.19.654943","url":null,"abstract":"<p><p>Eosinophils are agile cells that participate in a multitude of homeostatic and inflammatory responses in the lung, ranging from allergic asthma to antiviral defense against respiratory viral infection. In the context of vaccination followed by viral infection, such as breakthrough infection, eosinophils have been linked to aberrant Th2 responses like vaccine-enhanced respiratory disease (VAERD). Here, we demonstrate that the lung immune cell composition, cytokine and chemokine repertoire, histopathological profile, and systemic humoral response of breakthrough influenza infection in mice is distinct from that of primary influenza infection or allergic sensitization, canonical Type 1 and 2 immune responses, respectively. Longitudinal comparison of breakthrough infection with allergic sensitization and primary influenza infection demonstrated major differences in lung immunity between treatment groups in female, BALB/c mice. Breakthrough infection mice exhibit lung eosinophil infiltration that peaks at 7-10 days post-challenge, enriched for the Siglec-F ^hi subset, but in the absence of overt pro-inflammatory cytokine/chemokine signals, high viral titers, severe lung lesions, goblet cell hyperplasia, allergic levels of total IgE, or enhanced morbidity. Multiparameter fluorescence imaging corroborated findings from flow cytometry and also unveiled interactions between CD101 ⁺ Siglec-F ⁺ cells with CD3 ⁺ cells in the lung tissue space. Imaging also revealed a marked absence of eosinophil or neutrophil extracellular traps in the lungs of breakthrough infection mice, in contrast with allergic sensitization and primary influenza infection, respectively. Altogether, our findings provide a deeper understanding of the kinetics and cell-cell interplay during non-pathological, balanced Type 1/2 immune responses in vaccinated hosts during breakthrough infection.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236694","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":"Cheminformatic identification of small molecules targeting acute myeloid leukemia.","authors":"Megan R Daneman, Bernadetta Meika, Elissa Tjahjono, Alexey V Revtovich, Leonid A Stolbov, Scott R Gilbertson, Vladimir V Poroikov, Natalia V Kirienko","doi":"10.1101/2025.05.20.655224","DOIUrl":"https://doi.org/10.1101/2025.05.20.655224","url":null,"abstract":"<p><p>Acute myeloid leukemia (AML) is an aggressive hematological malignancy that has poor prognosis and high relapse rates with cytotoxic chemotherapeutics. Previously, we identified modulators of mitochondrial function, PS127-family compounds, that were cytotoxic to AML and were characterized by two predicted functions: apoptotic agonism and thioredoxin/glutathione reductase inhibition (T/GRi). Here, we uncovered a third critical predicted function: autophagic induction. A cheminformatics screening of ∼4.2 million compounds for molecules with high probability of these three functions yielded 93 hits, 81 of which were closely related to PS127-family molecules. <i>In silico</i> hits selected for validation selectively killed AML cells, activated apoptosis, required functional autophagy, and interfered with glutathione metabolism, confirming predicted functions. This increased pools of cytosolic and mitochondrial ROS and decreased oxygen consumption and ATP synthesis. Differential scanning fluorimetry implicated glutathione reductase as a direct target of these molecules. Structurally-unrelated compounds from different clusters caused the same phenotype, validating our structure-blind screening approach. Furthermore, strong synergy between these compounds and the AML treatment midostaurin underscores their therapeutic potential.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236429","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":"Identification and Characterization of PLUTO-201, a Novel Long Non-Coding RNA Associated with Poor Outcomes in Prostate Cancer.","authors":"Hui Li, Noah S Younger, Bhavna Malik, Hyun Jin Shin, Chao Zhang, Yashar Niknafs, Shuang George Zhao, Kari Wilder-Romans, Sethuramasundaraman Pitchiaya, Sumin Han, Travis Barnard, Paul Lloyd, Meng Zhang, Lisa N Chesner, Marsha Calvert, Emily A Egusa, Jun Zhu, Jonathan Chou, Rajdeep Das, Vishal Kothari, Tanu Shenoy, Morgan E Diolaiti, Rohit Malik, John R Prensner, Alma Burlingame, Alan Ashworth, Arul M Chinnaiyan, Felix Feng, Haolong Li","doi":"10.1101/2025.05.21.655369","DOIUrl":"https://doi.org/10.1101/2025.05.21.655369","url":null,"abstract":"<p><p>Despite extensive investigation, the factors promoting aggressive prostate cancer are poorly understood. By performing a comprehensive analysis of whole-genome transcriptome data to identify differential expression across 1,567 patients with prostate cancer, we now report the identification of a novel lncRNA, Prostate Locus of Uncharacterized Transcript Outlier 201 (PLUTO-201), which is strongly associated with metastasis and poor overall survival in men with prostate cancer. We find that overexpression/knockdown of PLUTO-201 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 PLUTO-201 and is indispensable for its activity. Overall, our findings indicate that PLUTO-201 is a driver of aggressive prostate cancer phenotypes and poor clinical outcomes.</p><p><strong>Statement of significance: </strong>Identification and characterization of PLUTO-201, a novel lncRNA driving aggressive biology in prostate cancer, sheds new light on the mechanisms driving aggressive prostate cancer and will motivate therapeutic and biomarker development.</p><p><strong>Statement of translational relevance: </strong>The factors promoting prostate cancer progression and metastasis are poorly understood, resulting in a lack of therapeutic targets and prognostic biomarkers for this disease. Here, we have identified the novel long non-coding RNA (lncRNA) PLUTO-201 as strongly associated with prostate cancer progression and metastasis in patients with localized prostate cancer undergoing prostatectomy. We show that PLUTO-201 promotes proliferation, invasion, and metastasis in multiple prostate cancer models both <i>in vitro</i> and <i>in vivo</i> . Mechanistically, we find that PLUTO-201 downregulates MHC class 1 and upregulates steroid biosynthesis by interacting with the heterogeneous nuclear ribonucleoprotein K (hnRNPK), leading to decreased T cell-mediated cytotoxicity and increased resistance to androgen receptor inhibition. Altogether, this study provides strong evidence for a critical role of PLUTO-201 in prostate cancer progression and metastasis, and a rationale for further exploration of PLUTO-201 as a therapeutic target and prognostic biomarker for patients with prostate cancer.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139821/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236583","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":"Integrative Multi-Omics Analysis Identifies Nuclear Factor I as a Key Driver of Dysregulated Purine Metabolism in DIPG.","authors":"Ian Mersich, Sunny Congrove, Matthew Horchar, Roman Caceres, Ranjithmenon Muraleedharan, Janki Desai, Pankaj Desai, Larry Sallans, Julie A Reisz, Abby Grier, Matthew R Hass, Omer Donmez, Cailing Yin, Matthew T Weirauch, Leah Kottyan, Charles B Stevenson, Claire Sun, Peter de Blank, Natasha Pillay-Smiley, Trent R Hummel, Nagarajan Elumalai, Ali Tavassoli, Ron Firestein, Timothy N Phoenix, Angelo D'Alessandro, Biplab Dasgupta","doi":"10.1101/2025.05.21.655327","DOIUrl":"https://doi.org/10.1101/2025.05.21.655327","url":null,"abstract":"<p><p>Diffuse intrinsic pontine glioma (DIPG) is a devastating brainstem cancer in children, with a median survival of under one year and limited treatment options. Over 80% of DIPGs possess a H3K27M mutation. To identify metabolic vulnerabilities linked to this mutation, we utilized a multi-omics approach in H3K27M-expressing cells, patient-derived cell lines, and mouse models. We show that by reprogramming chromatin landscape the mutation aberrantly induces NFI transcriptional activity, leading to misregulated purine metabolism. The mutation amplifies purine biosynthesis and degradation via the enzymes ATIC and PNP, respectively. Unregulated purine degradation relieves the negative feedback of purines on their own synthesis allowing continuous synthesis, use and degradation making DIPGs reliant on purine biosynthesis. Targeting ATIC reduced tumor progression and improved survival in mice. We propose ATIC as a potential novel target in DIPG.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236595","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}