bioRxiv : the preprint server for biology最新文献

{"title":"MitoEdit: a pipeline for optimizing mtDNA base editing and predicting bystander effects.","authors":"Devansh Shah, Kelly McCastlain, Ti-Cheng Chang, Gang Wu, Mondira Kundu","doi":"10.1101/2025.01.22.634390","DOIUrl":"https://doi.org/10.1101/2025.01.22.634390","url":null,"abstract":"<p><strong>Motivation: </strong>Human mitochondrial DNA (mtDNA) mutations are causally implicated in maternally inherited mitochondrial respiratory disorders; however, the role of somatic mtDNA mutations in both late-onset chronic diseases and cancer remains less clear. Although recent advances in mtDNA base editing technology have the potential to model and characterize many of these mutations, current editing approaches are complicated by the potential for multiple unintentional edits (bystanders) that are only identifiable through empirical 'trial and error', thereby sacrificing valuable time and effort towards suboptimal construct development.</p><p><strong>Results: </strong>We developed MitoEdit, a novel tool that incorporates empirical base editor patterns to facilitate identification of optimal target windows and potential bystander edits. MitoEdit allows users to input DNA sequences in a text-based format, specifying the target base position and its desired modification. The program generates a list of candidate target windows with a predicted number of bystander edits and their functional impact, along with flanking nucleotide sequences designed to bind TALE (transcription activator-like effectors) array proteins. <i>In silico</i> evaluations indicate that MitoEdit can predict the majority of bystander edits, thereby reducing the number of constructs that need to be tested empirically. To the best of our knowledge, MitoEdit is the first tool to automate prediction of base edits.</p><p><strong>Availability and implementation: </strong>MitoEdit is freely available at Kundu Lab GitHub ( https://github.com/Kundu-Lab/mitoedit ).</p><p><strong>Contact: </strong>Corresponding email: Gang.Wu@stjude.org ; Mondira.Kundu@stjude.org.</p><p><strong>Supplementary information: </strong>Supplementary data are available at <i>Bioinformatics</i> online.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11785211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143082880","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":"ANDROGENS PROTECT ILC2S FROM FUNCTIONAL SUPPRESSION DURING INFLUENZA VIRUS INFECTION.","authors":"Sapana Kadel, Reegan A J Miller, Anna Karlik, Sean Turner, Abigael P Williams, Erola Ainsua-Enrich, Ibrahim Hatipoglu, Harini Bagavant, José Alberola-Ila, Joshua W Garton, Richard Pelikan, Susan Kovats","doi":"10.1101/2025.01.23.634583","DOIUrl":"https://doi.org/10.1101/2025.01.23.634583","url":null,"abstract":"<p><p>Biological sex differences in morbidity upon influenza A virus (IAV) infection are linked to stronger IFN-centered immune responses in females, yet the regulatory role of sex hormone receptors in immune cell subsets is incompletely understood. Lung-resident group 2 innate lymphoid cells (ILC2s) express notably high levels of androgen receptors (AR). In IAV infection, ILC2s produce type 2 cytokines and facilitate tissue repair, but they also may be functionally suppressed by type 1 cytokines. Here we report sex differences in the magnitude of lung ILC2 functional suppression at the peak of sublethal IAV infection. Relative to males, ILC2s in females show attenuated proliferation, decreased propensity for IL-5 and amphiregulin production and reduced expression of GATA3 and IL-33R, features supported by divergent transcriptomes. Equivalent inflammatory cytokine levels and viral load suggested sex differences in ILC2-intrinsic factors. Indeed, naïve female ILC2s showed elevated IFNGR expression and higher phospho-STAT1 levels following IFNγ stimulation, and lymphocyte-restricted STAT1 deficiency reversed IAV-induced suppression of female ILC2s. Lymphocyte-restricted AR deficiency or loss of androgens via orchiectomy led to increased IFNGR expression and suppression of male ILC2s. These data support the hypothesis that intrinsic AR activity regulates IFNGR-STAT1 signaling pathways to preserve canonical ILC2 function in males during IAV infection.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11785168/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143082891","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>VPS13D</i> mutations affect mitochondrial homeostasis and locomotion in <i>Caenorhabditis elegans</i>.","authors":"Xiaomeng Yin, Ruoxi Wang, Andrea Thackeray, Eric H Baehrecke, Mark J Alkema","doi":"10.1101/2025.01.22.634397","DOIUrl":"10.1101/2025.01.22.634397","url":null,"abstract":"<p><p>Mitochondria control cellular metabolism, serve as hubs for signaling and organelle communication, and are important for the health and survival of cells. <i>VPS13D</i> encodes a cytoplasmic lipid transfer protein that regulates mitochondrial morphology, mitochondria and endoplasmic reticulum (ER) contact, quality control of mitochondria. <i>VPS13D</i> mutations have been reported in patients displaying ataxic and spastic gait disorders with variable age of onset. Here we used CRISPR/Cas9 gene editing to create <i>VPS13D</i> related-spinocerebellar ataxia-4 (SCAR4) missense mutations and C-terminal deletion in <i>VPS13D</i> 's orthologue <i>vps-13D</i> in <i>C. elegans</i> . Consistent with SCAR4 patient movement disorders and mitochondrial dysfunction, <i>vps-13D</i> mutant worms exhibit locomotion defects and abnormal mitochondrial morphology. Importantly, animals with a <i>vps-13D</i> deletion or a N3017I missense mutation exhibited an increase in mitochondrial unfolded protein response (UPR ^mt ). The cellular and behavioral changes caused by <i>VPS13D</i> mutations in <i>C. elegans</i> advance the development of animal models that are needed to study SCAR4 pathogenesis.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11785166/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143082896","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":"Physiological analysis of the mechanism of Ci transcription factor activation through multiple Fused phosphorylation sites in Hedgehog signal transduction.","authors":"Hoyon Kim, Jamie Little, Jason Li, Bryna Patel, Daniel Kalderon","doi":"10.1101/2025.01.24.634727","DOIUrl":"https://doi.org/10.1101/2025.01.24.634727","url":null,"abstract":"<p><p>Hedgehog (Hh) proteins elicit dose-dependent transcriptional responses by binding Patched receptors to activate transmembrane Smoothened (Smo) proteins. Activated Smo inhibits Ci/Gli transcription factor phosphorylation by Protein Kinase A (PKA) and consequent proteolytic processing to repressor forms; it also promotes nuclear transport and activity of full-length Ci/Gli proteins to induce Hh target genes. Smo-activated Fused (Fu) kinase drives Ci activation in Drosophila, while Suppressor of Fused (Su(fu)) counters full-length Ci/Gli activity and stabilizes full-length Ci/Gli by direct binding to at least three surfaces. Here, we used CRISPR-generated designer <i>ci</i> alleles to investigate alterations to Fu phosphorylation sites and to regions around Ci-Su(fu) interfaces under physiological conditions in Drosophila imaginal wing discs. Surprisingly, we identified alterations that activate Ci without significant loss of stabilization by Su(fu) and contributions of multiple Fu target sites to Ci activation in the absence of Su(fu), suggesting that the affected sites mediate Ci activation by regulating Ci-Ci, rather than Ci-Su(fu) interactions. We propose that those interactions maintain full-length Ci in a closed conformation that also facilitates, and is stabilized by, cooperative Ci-Su(fu) binding. Access to binding partners necessary for Ci activation is promoted through phosphorylation of at least four Fu sites on Ci, likely by directly disrupting Ci-Ci contacts and one Ci-Su(fu) interface without substantial Ci-Su(fu) dissociation, contrary to previous proposals. We also found that the Ci binding partner, Costal 2 (Cos2), which silences Ci in the absence of Hh, can facilitate Ci activation by Fu kinase.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11785250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083026","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":"Dynamic Reprogramming of Stromal Pdgfra-expressing cells during WNT-Mediated Transformation of the Intestinal Epithelium.","authors":"O Pellon-Cardenas, P Rout, S Hassan, E Fokas, He Ping, I Patel, J Patel, O Plotsker, A Wu, R Kumar, M Akther, A Logerfo, S Wu, D E Wagner, D Boffelli, K D Walton, E Manieri, K Tong, J R Spence, N J Bessman, R A Shivdasani, M P Verzi","doi":"10.1101/2025.01.22.634326","DOIUrl":"https://doi.org/10.1101/2025.01.22.634326","url":null,"abstract":"<p><p>Stromal fibroblasts regulate critical signaling gradients along the intestinal crypt-villus axis ¹ and provide a niche that supports adjacent epithelial stem cells. Here we report that <i>Pdgfra</i> -expressing fibroblasts secrete ligands that promote a regenerative-like state in the intestinal mucosa during early WNT-mediated tumorigenesis. Using a mouse model of WNT-driven oncogenesis and single-cell RNA sequencing (RNA-seq) of mesenchyme cell populations, we revealed a dynamic reprogramming of Pdgfra ⁺ fibroblasts that facilitates WNT-mediated tissue transformation. Functional assays of potential mediators of cell-to-cell communication between these fibroblasts and the oncogenic epithelium revealed that TGFB signaling is notably induced in Pdgfra ⁺ fibroblasts in the presence of oncogenic epithelium, and TGFB was essential to sustain regenerative-like growth of organoids <i>ex vivo</i> . Genetic reduction of <i>Cdx2</i> in the β-catenin mutant epithelium elevated the fetal-like/regenerative transcriptome and accelerated WNT-dependent onset of oncogenic transformation of the tissue <i>in vivo</i> . These results demonstrate that Pdgfra ⁺ fibroblasts are activated during WNT-driven oncogenesis to promote a regenerative state in the epithelium that precedes and facilitates formation of tumors.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11785226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143082861","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":"Innate Immune Memory is Stimulus Specific.","authors":"Aoife O'Farrell, Zijian Niu, Jingxin Li, Laura C Van Eyndhoven, Kavitha Sarma, Arjun Raj","doi":"10.1101/2025.01.22.634275","DOIUrl":"https://doi.org/10.1101/2025.01.22.634275","url":null,"abstract":"<p><p>Innate immune memory (also termed trained immunity) is defined in part by its ability to cross-protect against heterologous pathogens, and can be generated by many different stimuli, suggesting a \"universal\" trained state. However, different stimuli could form distinct memories, leading to stimulus-specific trained responses. Here, we use primary human monocyte-derived macrophages to demonstrate phenotypic and epigenetic stimulus specificity of innate immune memory six days after initial exposure. Quantification of cytokine production with single-molecule RNA imaging demonstrates stimulus-specific patterns of response to restimulation at the single cell level. Differential licensing of inflammatory transcription factors is associated with encoding of specificities in chromatin. Trained cells show stronger responses to secondary stimuli that are more similar to the initial stimulus they experienced, suggesting a functional role for these stimulus-specific memories. Rather than activating a universal training state, our findings demonstrate that different stimuli impart specific memories that generate distinct training phenotypes in macrophages.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11785108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083019","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":"Cell-APP: A generalizable method for microscopic cell annotation, segmentation, and classification.","authors":"Anish Virdi, Ajit P Joglekar","doi":"10.1101/2025.01.23.634498","DOIUrl":"https://doi.org/10.1101/2025.01.23.634498","url":null,"abstract":"<p><p>High throughput fluorescence microscopy is an essential tool in systems biological studies of eukaryotic cells. Its power can be fully realized when all cells in a field of view and the entire time series can be accurately localized and quantified. These tasks can be mapped to the common paradigm in computer vision: instance segmentation. Recently, supervised deep learning-based methods have become state-of-the-art for cellular instance segmentation. However, these methods require large amounts of high-quality training data. This requirement challenges our ability to train increasingly performant object detectors due to the limited availability of annotated training data, which is typically assembled via laborious hand annotation. Here, we present a generalizable method for generating large instance segmentation training datasets for tissue-culture cells in transmitted light microscopy images. We use datasets created by this method to train vision transformer (ViT) based Mask-RCNNs (Region-based Convolutional Neural Networks) that produce instance segmentations wherein cells are classified as \"m-phase\" (dividing) or \"interphase\" (non-dividing). While training these models, we also address the dataset class imbalance between m-phase and interphase cell annotations, which arises for biological reasons, using probabilistically weighted loss functions and partisan training data collection methods. We demonstrate the validity of these approaches by producing highly accurate object detectors that can serve as general tools for the segmentation and classification of morphologically diverse cells. Since the methodology depends only on generic cellular features, we hypothesize that it can be further generalized to most adherent tissue culture cell lines.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11785174/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143082395","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":"Unified meta regression models for rare variant association studies.","authors":"Larissa Lauer, Manuel A Rivas","doi":"10.1101/2025.01.23.634522","DOIUrl":"https://doi.org/10.1101/2025.01.23.634522","url":null,"abstract":"<p><p>Rare variant association studies (RVAS) of complex traits have emerged as a powerful approach to advance drug discovery and diagnostics. Missense pathogenicity predictions from AlphaMissense based on structural context and protein language models improve the differentiation between benign and deleterious variants. Constraint metrics, on the other hand, allow researchers to pinpoint genomic regions under selective pressure that may not directly impact protein structure, but are more likely to contain functionally important mutations. Loss-of-function (LoF) variants, which result in the complete or partial loss of protein function, are particularly informative, as it is more straightforward to assess their downstream functional consequences. In this study, we present a unified meta regression model approach that incorporates the probability of pathogenicity, probability of constraint, and indicator whether a variant is a predicted loss-of-function or missense variant as features to model the observed effect size and uncertainty of effect size obtained from single-variant genetic analysis. We applied the unified meta regression model to 1,144 continuous phenotypes from UK Biobank using single variant summary statistics obtained from Genebass. We replicated our findings using the AllofUS cohort. For each gene discovery, we make available a characterization of whether constrained sites are associated with the phenotype, whether pathogenic sites determined by structural based predictions are associated with phenotype, and whether broader loss-of-function or missense variant annotation better explains the summary statistics observed. Our results are publicly available at Global Biobank Engine ( https://biobankengine.shinyapps.io/phenome-wide-unified-model/ ).</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11785203/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083079","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":"Engineering microalgal cell wall-anchored proteins using GP1 PPSPX motifs and releasing with intein-mediated fusion.","authors":"Kalisa Kang, Évellin do Espirito Santo, Crisandra Jade Diaz, Stephen Mayfield, João Vitor Dutra Molino","doi":"10.1101/2025.01.23.634604","DOIUrl":"https://doi.org/10.1101/2025.01.23.634604","url":null,"abstract":"<p><p>Harnessing and controlling the localization of recombinant proteins is critical for advancing applications in synthetic biology, industrial biotechnology, and drug delivery. This study explores protein anchoring and controlled release in <i>Chlamydomonas reinhardtii</i> , providing innovative tools for these fields. Using truncated variants of the GP1 glycoprotein fused to the plastic-degrading enzyme PHL7, we identified the PPSPX motif as essential for anchoring proteins to the cell wall. Constructs with increased PPSPX content exhibited reduced secretion but improved anchoring, pinpointing the potential anchor-signal sites of GP1 and highlighting the distinct roles of these motifs in protein localization. Building on the anchoring capabilities established with these glycomodules, we also demonstrated a controlled release system using a pH-sensitive intein derived from RecA from <i>Mycobacterium tuberculosis</i> . This intein efficiently cleaved and released PHL7 and mCherry that was fused to GP1 under acidic conditions, enabling precise temporal and environmental control. At pH 5.5, fluorescence kinetics demonstrated significant mCherry release from the pJPW4mCherry construct within 4 hours. In contrast, release was minimal under pH 8.0 conditions and negligible for the pJPW2mCherry (W2) control, irrespective of the pH. Additionally, bands on the Western blot at the expected size of mCherry also showed its efficient release from the mCherry::intein::GP1 fusion protein at pH 5.5. Conversely, at pH 8.0, no bands were detected. This anchor-release approach offers significant potential for drug delivery, biocatalysis, and environmental monitoring applications. By integrating glycomodules and pH-sensitive inteins, this study establishes a versatile framework for optimizing protein localization and release in <i>C. reinhardtii</i> , with broad implications for proteomics, biofilm engineering, and scalable therapeutic delivery systems.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11785195/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143082904","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":"History shapes regulatory and evolutionary responses to tigecycline in strains of <i>Acinetobacter baumannii</i> from the pre- and post-antibiotic eras.","authors":"Alecia B Rokes, Alfonso Santos-Lopez, Vaughn S Cooper","doi":"10.1101/2025.01.22.634413","DOIUrl":"https://doi.org/10.1101/2025.01.22.634413","url":null,"abstract":"<p><p>Evolutionary history encompasses genetic and phenotypic bacterial differences, but the extent to which history influences drug response and antimicrobial resistance (AMR) adaptation is unclear. Historical contingencies arise when elements from an organism's past leave lasting effects on the genome, altering the paths available for adaptation. We utilize strains isolated before and after widespread antibiotic use to study the impact of deep historical differences shaped by decades of evolution in varying antibiotic and host pressures. We evaluated these effects by comparing immediate and adaptive responses of two strains of <i>Acinetobacter baumannii</i> to the last-resort antibiotic, tigecycline (TGC). When grown in subinhibitory TGC, the two strains demonstrated divergent transcriptional responses suggesting that baseline transcript levels may dictate global responses to drug and their subsequent evolutionary trajectories. Experimental evolution in TGC revealed clear differences in population-genetic dynamics - with hard sweeps in populations founded by one strain and no mutations reaching fixation in the other strain. Transcriptomes of evolved populations no longer showed signatures of drug response, as was seen in the ancestors, suggesting that genetic adaptation may outweigh preexisting differences in transcriptional networks. Genetically, AMR was acquired through predictable mechanisms of increased efflux and drug target modification; however, the two strains adapted by mutations in different efflux regulators. Fitness tradeoffs of AMR were only observed in lineages evolved from the pre-antibiotic era strain, suggesting that decades of adaptation to antibiotics resulted in preexisting compensatory mechanisms in the more contemporary isolate, an important example of a beneficial effect of historical contingencies.</p><p><strong>Significance statement: </strong><i>Acinetobacter baumannii</i> is a high priority pathogen often causing multidrug resistant nosocomial infections. Many healthcare systems experience clonal outbreaks of <i>A. baumannii</i> infections, yet treatment strategies are often strain-agnostic, ignoring the importance of strain differences. We show that historical differences between two strains, one isolated prior to widespread antibiotic use and the other following decades of selection to clinical conditions, dictate transcriptional patterns and response to a last-resort antibiotic and influence the genetic and phenotypic routes of resistance adaptation. While our study focuses on two reference strains of <i>A. baumannii,</i> these findings can be more broadly applicable to other pathogenic organisms in which a better understanding of the forces influencing resistance adaptation is essential for combating the antimicrobial resistance crisis.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11785199/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143082908","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}