Biology subjects

Garcia, P.

Publications and source records attributed to Garcia, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Multi-lineage emergence of USA300 MRSA in in Chile and a potential role for environmental copper resistance

Methicillin-resistant S. aureus (MRSA) is prevalent worldwide, but individual strains of MRSA tend to spread and expand in relatively confined geographic areas. The USA300 lineage of MRSA is most well-known for its rapid epidemic spread in North America during the first decade of the 2000's leading to an overall increase in serious skin infections and the emergence of methicillin resistance in the majority of community acquired S. aureus infections. A distinct but closely related South American epidemic clade of MRSA USA300 (USA300-SAE), first reported in 2006, proliferated rapidly in Northern South America but was rarely found in other Latin American countries. In a new survey of 274 invasive MRSA isolates from 2022 collected in Chile, we saw a marked increase in USA300-SAE in Southern South America. We found that Chilean USA300-SAE is phylogenetically diverse and was likely introduced multiple times from multiple different South American countries over the course of more than a decade, but only recently became a highly prevalent clone. Using novel molecular diagnostic methods for isolates collected in 2023, we estimate that USA300-SAE made up more than 22% of invasive MRSA strains in Chile in that year and is likely still increasing. We show that copper-associated genes in the signature copper and mercury resistance mobile element (COMER) of USA300-SAE are strongly conserved, and that isogenic mutants of the copper resistance genes in COMER are highly susceptible to copper killing at concentrations seen in tap water. These findings suggest that environmental exposure to copper may provide a fitness advantage that enhances spread of this lineage.

microbiology↗

bioRxiv2026

Voluntary Exercise Differentially Affects High-Fat Induced Metabolic Phenotypes Across BXD Mouse Strains

Obesity and metabolic diseases such as diabetes reflect long-term interactions between diet, lifestyle, and genetics, variables that are hard to control in humans but can be systematically varied in mice, though behavioral variables like long-term exercise remain harder to model. Having previously phenotyped ~50 BXD strains, we identified BXD40, BXD43, and BXD100 as predisposed to voluntary wheel-running (~6 km/day at 24 weeks) with variable susceptibility to diet-induced obesity and diabetes. We followed these strains from 8-32 weeks on a 60% kcal/fat high-fat (HF) diet, with or without access to running wheels. Wheel usage declined from ~9 km/day in the first two weeks to a steady ~5 km/day thereafter yet still improved oral glucose tolerance by 35% over sedentary controls by 24 weeks. Despite equivalent body weight, runners ate 20% more relative to body weight, indicating the glucose benefit was independent of caloric intake. We next asked whether the gut microbiome contributes to this benefit. Long-term exercise produced only modest, cohort-dependent shifts in cecal microbial composition, though functional profiling revealed exercise-associated differences in carbohydrate- and glucose-metabolism pathways. Reciprocal bedding exchange between sedentary and running BXD43 cages reduced microbial differentiation in a taxon-specific manner and coincided with marked attenuation of the glucose phenotype, despite unchanged running behavior. Together, these findings validate BXD40, BXD43, and BXD100, alongside the canonical C57BL/6, as a model for studying diet, exercise, and genetics in metabolic disease, and implicate gut microbial taxa in shaping exercise's metabolic effects during HF feeding.

genetics↗

bioRxiv2026

PBF/PTTG1IP coordinates focal adhesion formation, polarity and cell motility

Directional cell migration requires cells to sense extracellular cues and coordinate adhesion, cytoskeletal remodelling and polarity, yet the molecular regulators that integrate these events remain incompletely defined. PTTG1-binding factor (PBF/PTTG1IP) is a transmembrane glycoprotein extensively characterised in pathological overexpression and cancer models, where elevated expression promotes tumourigenic cellular phenotypes. However, its endogenous physiological function remains poorly understood. Here, separate enrichment analyses of transcriptomic and phosphoproteomic profiles from PBF-overexpressing cells collectively highlighted cell adhesion, extracellular matrix organisation, cytoskeletal regulation and cell motility as major PBF-associated programmes. Using a novel Pbf knockout mouse model, we show that primary Pbf-KO mouse embryonic fibroblasts exhibit impaired migration and invasion. PBF loss reduced fibronectin adhesion, disrupted focal adhesion number, size and distribution, attenuated FAK Tyr397 phosphorylation and delayed early adhesion formation. Live-cell imaging and Golgi orientation assays further revealed altered actin organisation and impaired front-rear polarity in Pbf-KO cells. Key phenotypes were conserved in CRISPR-Cas9 PBF-KO human thyroid cancer cells, while targeted PBF re-expression restored migration in Pbf-KO MEFs. We thus identify PBF as an endogenous regulator of cell adhesion, polarity and directional motility, providing a framework for understanding how pathological PBF overexpression may promote invasive behaviour in cancer.

cell biology↗

bioRxiv2026

Kaposi Sarcoma Herpes Virus Reprograms Mesenchymal Cell Glycosylation to control platelet-derived growth factor receptor A signaling

Kaposi sarcoma-associated herpesvirus (KSHV) reprograms host cellular pathways to promote viral persistence and tumor development by supporting the survival and expansion of infected and bystander cells. Among the signaling axes implicated in this process, oncogenic activation of receptor tyrosine kinases, particularly platelet-derived growth factor receptor alpha (PDGFRA), is a well-established hallmark of Kaposi sarcoma pathogenesis. However, the impact of virus-driven cell surface glycosylation changes in PDGFRA-associated signaling remains uncertain. Here, we identified a critical role for KSHV in reshaping the glycosylation landscape of mesenchymal stromal cells (MSCs), thereby reprogramming PDGFRA signaling. We show that KSHV infection enhances a unique glycan profile in human and mouse MSCs, enriched in branched complex N-glycans with limited (2-6) sialylation, Transcriptomic analyses of KSHV-infected MSCs and Kaposis Sarcoma patient samples revealed a coordinated dysregulation of pathways involved in carbohydrate metabolism, nucleotide-sugar transport, and sialic acid turnover, with a particular focus on sialic acid turnover (NPL/NEU3), the UDP-N-acetylglucosamine transporters SLC35A3/B4, and complex N-glycan elongation (MGAT5/B3GNT2/B4GALT1) as critical nodes underlying reduced (2-6) sialylation and increased N-glycan branching. This remodeled glycan landscape contributes to create a permissive context for galectin-1 (Gal-1) binding, which in turn enhances PDGFRA activation and downstream signaling. These findings identify an integral component of KSHV-driven mesenchymal cell reprogramming, unveiling a lectin-dependent mechanism of RTK activation in Kaposi sarcoma pathogenesis.

Cancer Biology↗

bioRxiv2026

Rho1 and Rgf3 regulate the expansion of the nuclear envelope during fission yeast mitosis/cytokinesis

The nuclear envelope (NE) surrounds the genetic material and is continuous with the endoplasmic reticulum (ER). In yeast and other organisms undergoing closed mitosis, nuclear envelope expansion (NME) is strictly required to accommodate spindle elongation and ensure proper chromosome segregation within a single nuclear compartment. Failure to expand the NE during mitosis leads to chromosome missegregation. Here, we show that deletion of the unstructured N-terminal domain of Rgf3, a Rho1-specific guanine nucleotide exchange factor (GEF), causes early mitotic defects that produce the characteristic "cut" phenotype of untimely cell division. The rgf3{Delta}N2 mutant displays spindle buckling, a hallmark of anaphase nuclei unable to properly expand the NE. From yeast to mammals, phosphatidic acid (PA)--a key precursor in phospholipid biosynthesis--is metabolized via two competing pathways, the cytidine diphosphate-diacylglycerol (CDP-DAG) and the Kennedy pathways, both contributing to lipid membrane homeostasis. We provide evidence that impaired Rho1 activation in rgf3{Delta}N2 selectively disrupts phospholipid synthesis through the CDP-choline branch of the Kennedy pathway. Thus, Rho1 promotes mitotic progression by modulating phospholipid biosynthesis to enable efficient NME during anaphase. HighlightsThe N-terminus of Rgf3 is required for proper nuclear envelope expansion (NME) during anaphase. The structurally flexible N-terminal domain of Rgf3 is essential for localized Rho1 activation. Active Rho1 drives mitotic membrane growth by modulating phospholipid synthesis through the Kennedy pathway.

Cell Biology↗

bioRxiv2026

Chronic morphine treatment induces a conserved Smchd1-dependent epigenetic memory that disrupts X-chromosome inactivation and genomic imprinting

Epigenetic memory ensures stable inheritance of gene expression patterns critical for embryonic development. Environmental exposures can disrupt this memory, yet the mechanisms remain unclear. Here we demonstrate that chronic morphine exposure induces a persistent transcriptomic and epigenetic memory by repressing Smchd1, a key chromatin regulator, in mouse embryonic stem cells, preimplantation embryos, and human induced pluripotent stem cells. This repression compromises maintenance of X-chromosome inactivation and genomic imprinting, leading to sustained dysregulation of developmentally important gene clusters. Morphine-induced epigenetic alterations also involve changes in DNA methylation and histone modifications along the X chromosome and notably increased H3K27me3 at the Smchd1 locus. These findings reveal a conserved mechanism by which opioid exposure disrupts higher-order chromatin architecture and epigenetic memory during early development, potentially contributing to long-term developmental and clinical outcomes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/713629v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@16986cborg.highwire.dtl.DTLVardef@1108eaaorg.highwire.dtl.DTLVardef@66373org.highwire.dtl.DTLVardef@16b37f6_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2025

Functional divergence of the Arg/N-degron pathway between the crop Brassica rapa and the model plant Arabidopsis thaliana

The ubiquitin-dependent Arg/N-degron pathway relates the stability of a substrate protein to the nature of its N-terminal amino acid residue or its biochemical modifications, with some N-terminal residues being recognized by specific E3 ubiquitin ligases, resulting in the ubiquitylation and degradation of the substrate protein. Work in the model plant Arabidopsis thaliana has shown that the Arg/N-degron pathway is a key regulator of plant responses to hypoxia, which can be either physiological or a stress in the context of waterlogging or submergence. The role of the Arg/N-degron pathway in hypoxia response is mediated via the oxygen-dependent degradation of group VII ETHYLENE RESPONSE FACTOR (ERFVII) transcription factors, which act as the master regulators of the hypoxia response program in plants. Analysis of Arabidopsis mutants for different enzymatic components of the Arg/N-degron pathway has also revealed its roles in the regulation of responses to other abiotic stresses (e.g. salt stress), as well as to pathogens. Although much has been learned from studies in Arabidopsis about the functions of the Arg/N-degron pathway, very little is known about this pathway in crops, including in Brassica crops such as oilseed rape, cabbage or turnip. To determine functional similarities and divergence of the Arg/N-degron pathway between Arabidopsis and Brassica crops, we isolated and characterized the first Arg/N-degron pathway mutants in Brassica rapa (turnip, pak choi), a diploid Brassica crop closely related to oilseed rape. We focused on two enzymatic components, namely the arginine-transferases (ATEs) and the E3 ubiquitin ligase PROTEOLYSIS6 (PRT6). Our results show both similarities and divergence of function for these Arg/N-degron pathway components in B. rapa compared to Arabidopsis. Specifically, ATE mutants in B. rapa arrest their development at the seedling stage, which contrasts with the mild phenotypic defects of the equivalent Arabidopsis mutants. Double mutant lines for two of the three PRT6 genes in B. rapa indicated a constitutive activation of hypoxia response genes at the transcriptional level, as shown in the single prt6 mutant in Arabidopsis. However, contrary to Arabidopsis, the B. rapa double mutants were more sensitive to waterlogging and hypoxia, and did not show differential response to salt stress or to biotic stress compared to the wild type. The functional divergence identified likely reflects variability in each species in the substrate repertoire and/or in the regulation of pathways or targets downstream of Arg/N-degron pathway substrates. Such differences could be driven by direct selective pressures at N-termini (e.g. gain or loss of a destabilizing N-terminal residue), or by species-specific proteases that may generate destabilizing neo-N-termini after cleavage. These similarities and differences highlight the difficulties in translating research findings from Arabidopsis to crops, even within the same plant family (Brassicaceae) and highlight the need to study pathways in crops.

plant biology↗

bioRxiv2025

Transcriptional Dysregulation in the Hippocampus of a murine model for Parkinson's Disease Cognition Impairment is Driven by Sex, Age, and Alpha-synuclein overexpression

Cognitive impairment is the most common and detrimental, but understudied non-motor symptom of Parkinsons disease (PD). Neuropathologically, it is associated with alpha-synuclein (Syn) misfolding and synapse loss in hippocampus and prefrontal cortex, leading to cognition loss and ultimately dementia. The molecular underpinnings of PD-associated cognitive dysfunction are unknown. In the present study, longitudinal gene expression profiling was performed to characterise molecular hippocampal alterations in a transgenic mouse overexpressing E46K mutated Syn, a model of early PD with loss of synaptophysin, a proxy marker of cognition, in hippocampus and cortex. Comparing 4 different ages of mice from both sexes showed that hippocampal gene expression changes were sexually dimorphic and strongly modulated by age and Syn overexpression. Pathways that emerged across different comparisons were connected to a variety of neuronal functions, collagen synthesis/remodelling, cellular stress, and inflammatory responses. The findings indicate that sex and age are essential covariates to consider when studying PD-associated cognitive decline. The uncovering of early events leading to disease in an animal model is an essential step toward prognostic biomarker identification and early interventions, which may have implications for monitoring, and for timing of therapeutic approaches.

neuroscience↗

bioRxiv2025

MYBL2 maintains stemness and promotes theta-mediated end joining in triple negative breast cancer

Triple negative breast cancer (TNBC) has a poor prognosis due to limited treatment options and high metastasis risk. Breast cancer (BC) stem/progenitor cells, also known as tumour initiating cells, are a small, difficult to target population within the tumour responsible for metastasis and therapy resistance. MYBL2 overexpression is commonly linked to poor prognosis and metastasis but its role in BC stem/progenitor cells remains elusive. To determine the role of MYBL2 in BC stem/progenitor cells we generated TNBC cell lines with inducible MYBL2 downregulation. Our findings reveal that elevated MYBL2 is essential for self-renewal, DNA repair, and replication stress response in these cells and lowering MYBL2 impairs stemness and self-renewal both in vitro and in vivo. Accordingly, our functional and mechanistic analyses indicate that high-MYBL2 stem/progenitor cells exhibit increased sensitivity to Pol{theta} inhibitors which is lost upon MYBL2 downregulation due to transcriptional suppression. Combining Pol{theta} inhibitors with ATR inhibitors further enhances this sensitivity, in vitro and ex vivo. This study thus identifies Pol{theta}/ATR inhibition as a synthetic lethality strategy to eradicate BC stem/progenitor cells and underscores MYBL2 expression as a biomarker for patient stratification in this treatment.

cancer biology↗

bioRxiv2024

Integrating in silico predictions with an engineered tissue assay identifies Perlecan as an age-perturbed re-quiescence cue for muscle stem cells

Skeletal muscle regeneration is mediated by resident muscle stem cells that produce progeny to repair or recreate muscle. Critical to this function is the ability to transition between states of proliferation and quiescence. This balancing act is disrupted with age, leading to eroded regenerative capacity. Notwistanding, mechanisms by which the regenerating niche directs MuSCs return to the dormant state are largely unknown. Since single-cell RNAseq methods exclude the analysis of multinucleated cells, we generated single-nuclei RNAseq datasets of regenerating muscle to capture the full breadth of myogenic progression. With this, we uncovered new transition states between differentiating myocytes and syncytial multinucleated cells. Using cell communication inference tools, we highlighted receptor-ligand interactions between MuSCs and fusing nuclei. We leveraged a bespoke biomimetic 3D niche that induces MuSC quiescence, to filter the predicted interactions using a Cas9-based functional genomics approach. We found the proteoglycan Perlecan (Hspg2) promotes MuSC re-quiescence. Hspg2 silencing in vivo, during muscle regeneration, induced an aging-like phenotype and perturbed MuSC re-quiescence. Notably, the temporal profile and overall levels of Perlecan were altered with age. Exogenous supplementation with Endorepellin (truncated Perlecan) rescued MuSC decline following aged muscle regeneration, offering a new therapeutic target. Thus, coupling in silico predictions with a 3D in vitro assay followed by in vivo investigations revealed a previously inaccessible window of biology; that spatiotemporal coordination of MuSC re-quiescence is directed by fusing myonuclei.

cell biology↗

bioRxiv2024

The new SH3_T domain increases the structural and functional variability among SH3b-like CBDs from staphylococcal phage endolysins

Endolysins, proteins encoded by phages to lyse their hosts and release their progeny, have evolved to adapt to the structural features of each host. The endolysins from Staphylococcus-infecting phages typically feature complex architectures with two enzymatically active domains (EADs) and one cell wall-binding domain (CBD) belonging to the bacterial SH3 (SH3b) superfamily. This study focuses on three SH3b-like CBDs from exemplary staphylococcal phage endolysins (LysRODI, LysC1C, and LysIPLA5) that were structurally and functionally characterized. While RODI_CBD and C1C_CBD were assigned to the well-known SH3_5 family, a new family, SH3b_T, was identified using the CBD from LysIPLA5 as a model. GFP-fused CBDs were created to assess their differential binding to a collection of staphylococcal strains. IPLA5_CBD showed enhanced binding to Staphylococcus epidermidis, while RODI_CBD and C1C_CBD exhibited distinct binding profiles, with RODI_CBD targeting Staphylococcus aureus specifically and C1C_CBD displaying broad binding. Sequence comparisons suggested that a few differences in key amino acids could be responsible for the latter binding difference. The CBDs modulated the activity spectrum of synthetic EAD-CBD combinations in accordance with the previous binding profiles, but in a manner that was also dependent on the EAD present in the fusion protein. These results serve as a context for the diversity and versatility of SH3b domains in staphylococcal endolysins, providing insights on how (i) the CBDs from this superfamily have diverged to adapt to diverse bacterial ligands in spite of sharing a common fold; and (ii) the evolution of specificity relies on the EAD-CBD combination rather than solely the CBD. IMPORTANCEClinical management of bacterial infections is nowadays compromised by the rise in antimicrobial resistance. The development of new antimicrobial therapies with diverse modes of action is therefore of pivotal importance to complement the current standard of care. Phage endolysins are a new class of antibacterial agents based on rapid peptidoglycan degradation. The natural reservoir of phage endolysins offers a practically infinite diversity. This works reveals a broadly spread but still unknown phage endolysin domain targeting staphylococci while providing structural-functional insights that are paramount to understand the evolution of endolysins and how they can be applied as an antimicrobial.

molecular biology↗

bioRxiv2024

Park7 deletion leads to age- and sex-specific transcriptome changes involving NRF2-CYP1B1 axis in mouse midbrain astrocytes

AbstractdispeLoss-of-function mutations in PARK7, encoding for DJ-1, can lead to early onset Parkinsons disease (PD). In mice, Park7 deletion leads to dopaminergic deficits during aging, and increased sensitivity to oxidative stress. However, the severity of the reported phenotypes varies. To understand the early molecular changes upon loss of DJ-1, we performed transcriptomic profiling of midbrain sections from young mice. Interestingly, while at 3 months the transcriptomes of both male and female mice were unchanged compared to their wildtype littermates, an extensive deregulation was observed specifically in 8-month-old males. The affected genes are involved in processes such as focal adhesion, extracellular matrix interaction, and epithelial-to-mesenchymal transition (EMT), and enriched for primary target genes of Nuclear factor erythroid 2-related factor 2 (NRF2). Consistently, the antioxidant response was altered specifically in the midbrain of male DJ-1 deficient mice. Many of the misregulated genes are known target genes of estrogen and retinoic acid signaling and show sex-specific expression in wildtype mice. Depletion of DJ-1 or NRF2 in male, but not female primary astrocytes recapitulated many of the in vivo changes, including downregulation of cytochrome P450 family 1 subfamily B member 1 (CYP1B1), an enzyme involved in estrogen and retinoic acid metabolism. Interestingly, knock-down of CYP1B1 led to gene expression changes in focal adhesion and EMT in primary male astrocytes. Finally, male iPSC-derived astrocytes with loss of function mutation in the PARK7 gene also showed changes in the EMT pathway and NRF2 target genes. Taken together, our data indicate that loss of Park7 leads to sex-specific gene expression changes specifically in males through astrocytic alterations in the NRF2-CYP1B1 axis. These findings suggest higher sensitivity of males to loss of DJ-1 and might help to better understand variation in the reported Park7-/-phenotypes.

molecular biology↗

bioRxiv2024

Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst

Studies in the mouse demonstrate the importance of fibroblast growth factor (FGF) and extra-cellular receptor tyrosine kinase (ERK) in specification of embryo-fated epiblast and yolk-sac-fated hypoblast cells from uncommitted inner cell mass (ICM) cells prior to implantation. Molecular mechanisms regulating specification of early lineages in human development are comparatively unclear. Here we show that exogenous FGF stimulation leads to expanded hypoblast molecular marker expression, at the expense of the epiblast. Conversely, we show that specifically inhibiting ERK activity leads to expansion of epiblast cells functionally capable of giving rise to naive human pluripotent stem cells. Single-cell transcriptomic analysis indicates that these epiblast cells downregulate FGF signalling and upregulate molecular markers associated with naive pluripotency. Our functional study demonstrates for the first time the molecular mechanisms governing ICM specification in human development, whereby segregation of the epiblast and hypoblast lineages occurs during maturation of the mammalian embryo in an ERK signal-dependent manner.

developmental biology↗

bioRxiv2024

Rgf1 GEF activity toward Rho1 defines a new actin-dependent signal to determine growth sites independently of microtubules and Tea1

Cellular asymmetry begins with the selection of a discrete point on the cell surface that triggers Rho-GTPases activation and localized assembly of the cytoskeleton to establish new growth zones. The cylindrical shape of fission yeast is organized by microtubules that deliver the landmark Tea1-Tea4 complex at the cell tips to define the growth poles. However, only a few tea1{Delta} cells mistaken the direction of growth, indicating that they manage to detect their growth sites. Here we show that Rgf1 (Rho1-GEF) and Tea4 are components of the same complex and that Rgf1 activity toward Rho1 is required for strengthen Tea4 at the cell tips. Moreover, in cells lacking Tea1, selection of the correct growth site depends on Rgf1 and on a correctly polarized actin cytoskeleton, both necessary for Rho1 activation at the pole. We propose an actin-dependent mechanism driven by Rgf1-Rho1 that marks the poles independently of microtubules and the Tea1-Tea4 complex.

cell biology↗

bioRxiv2023

Parkinson's disease-related Miro1 mutation induces mitochondrial dysfunction and loss of dopaminergic neurons in vitro and in vivo

The complex and heterogeneous nature of Parkinsons disease (PD) is still not fully understood, however, increasing evidence supports mitochondrial impairments as a major driver of neurodegeneration in PD. Recently, the regulator of mitochondrial homeostasis Miro1 has been linked genetically and pathophysiologically to PD. Using 2D and 3D patient-based induced pluripotent stem cells models, including an isogenic control, showed that the Miro1 p.R272Q mutation leads to mitochondrial impairments including increased oxidative stress, disrupted mitochondrial bioenergetics and altered metabolism. This was accompanied by increased -synuclein levels in 2D dopaminergic neurons and by a significant reduction of dopaminergic neurons within midbrain organoids. Knock-in mice expressing mutant p.R285Q Miro1 (orthologue of the human p.R272Q mutation) confirmed the PD-specific dopaminergic neuronal loss in the substantia nigra, accumulation of striatal phosphorylated -synuclein accompanied by behavioral alterations. These findings demonstrate that mutant Miro1 is sufficient to comprehensively model PD-relevant phenotypes in vitro and in vivo, reinforcing its pivotal role in PD pathogenesis.

neuroscience↗

bioRxiv2023

Repression of pattern-triggered immune responses by hypoxia

Biotic and abiotic stresses frequently co-occur in nature, yet, relatively little is known about how plants co-ordinate the response to combined stresses. Previous research has shown that protein degradation by the ubiquitin/proteasome system is central to the regulation of multiple independent stress response pathways in plants. The Arg/N-degron pathway is a subset of the ubiquitin/proteasome system that targets proteins based on their N-termini and has been specifically implicated in the responses to biotic and abiotic stresses, including hypoxia via accumulation of ERF-VII transcription factors, which orchestrate the onset of the hypoxia response program. Here, we investigated the role of the Arg/N-degron pathway in mediating the crosstalk between coinciding abiotic and biotic stresses using hypoxia treatments and the flg22 elicitor of pattern-triggered immunity (PTI), respectively. We uncovered a link between the transcriptional responses of plants to hypoxia and flg22. Combined hypoxia/flg22 treatments showed that hypoxia represses the flg22 transcriptional program, as well as the expression of pattern recognition receptors, MAPK signalling and callose deposition during PTI, through mechanisms that are mostly independent from the ERF-VIIs. These findings aid understanding of the trade-offs between plant responses to combined abiotic/biotic stresses in the context of our efforts to increase crop resilience to global climate change. Our results also show that the well-known repressive effect of hypoxia on innate immunity in animals also applies to plants. Significance statementUnderstanding how plants regulate the crosstalk between stress response pathways is key to our efforts to increase crop resilience and mitigate yield losses caused by global climate change. Despite the urgency to do so, relatively little is known about how plants respond to combined stresses, which frequently occur in nature. Here, we show that the hypoxia response program and the basal layer of plant immunity (pattern-triggered immunity or PTI) share components. Our data also show that hypoxia represses several key aspects of PTI, a situation akin to that discovered in animals decades ago. These findings have implications for our ability to develop resilient crops by limiting the negative trade-offs that exist between hypoxia response and immunity.

plant biology↗

bioRxiv2023

Widespread dissemination of ESBL-producing Salmonella enterica serovar Infantis exhibiting intermediate fluoroquinolone resistance and harboring blaCTX-M-65-positive pESI-like megaplasmids in Chile

BackgroundMultidrug-resistant (MDR) Salmonella Infantis has disseminated worldwide, mainly linked to the consumption of poultry products. Evidence shows dissemination of this pathogen in Chile; however, studies are primarily limited to phenotypic data or involve few isolates. As human cases of Salmonella Infantis infections have substantially increased in recent years, a better understanding of its molecular epidemiology and antimicrobial-resistance profiles are required to inform effective surveillance and control measures. MethodsWe sequenced 396 Salmonella Infantis genomes and analyzed them with all publicly available genomes of this pathogen from Chile (440 genomes in total), representing isolates from environmental, food, animal, and human sources obtained from 2009 to 2022. Based on bioinformatic and phenotypic methods, we assessed the population structure, dissemination among different niches, and AMR profiles of Salmonella Infantis in the country. FindingsThe genomic and phylogenetic analyses showed that Salmonella Infantis from Chile comprised several clusters of highly related isolates dominated by sequence type 32. The HC20_343 cluster grouped an important proportion of all isolates. The latter was the only cluster associated with pESI-like megaplasmids, and up to 12 acquired AMR genes/mutations predicted to result in an MDR phenotype. Accordingly, antimicrobial-susceptibility testing revealed a strong concordance between the AMR genetic determinants and their matching phenotypic expression, indicating that a significant proportion of HC20_343 isolates produce extended- spectrum {beta}-lactamases and have intermediate fluoroquinolone resistance. HC20_343 Salmonella Infantis were spread among environmental, animal, food, and human niches, showing a close relationship between isolates from different years and sources, and a low intra-source genomic diversity. InterpretationOur findings show a widespread dissemination of MDR Salmonella Infantis from the HC20_343 cluster in Chile. The high proportion of isolates with resistance to first-line antibiotics and the evidence of active transmission between the environment, animals, food, and humans highlight the urgency of improved surveillance and control measures in the country. As HC20_343 isolates predominate in the Americas, our results suggest a high prevalence of ESBL- producing Salmonella Infantis with intermediate fluoroquinolone resistance in the continent. FundingAgencia de Investigacion y Desarrollo de Chile (ANID) through FONDECYT de Postdoctorado Folio 3230796 and Folio 3210317, FONDECYT Regular Folio 1231082, and ANID - Millennium Science Initiative Program - ICN2021_044. Research in contextO_ST_ABSEvidence before the studyC_ST_ABSIn the last decade, emergent multidrug-resistant Salmonella Infantis has spread worldwide, primarily linked to poultry product consumption. However, in most countries from the Americas Region, such as Chile, the extent of the dissemination of emergent Salmonella Infantis and its molecular epidemiology remains unknown. In May and September 2023, an online search was conducted using the Google engine and the PMC database with the terms "Salmonella," "Infantis," and "Chile," with no language restrictions. We assessed the results to select those presenting antimicrobial resistance, epidemiologic, or genomic data directly associated with isolates from Chile (13 studies). The selected studies showed that the prevalence of Salmonella Infantis in poultry-meat production systems, its resistance to different antibiotics, and the number of human cases of infection caused by this serovar have increased since 2014-2016. However, these reports were limited to phenotypic data or involved the genomic analysis of a few isolates (<50) obtained from the same source. No study has assessed the genomic epidemiology of the Salmonella Infantis population at the country level. Added value of this studyHere, we present the first large-scale genomic epidemiology analysis of Salmonella Infantis in Chile, including isolates from environmental, food, animal, and human sources obtained from 2009 to 2022. We found that Salmonella Infantis in Chile is divided into several clusters of highly related isolates and that only a single cluster, the HC20_343, was associated with multiple antimicrobial-resistance determinants and pESI-like megaplasmids. We also report that isolates from this cluster are widespread among most sources, including irrigation water, poultry, food, and human cases. Detection of AMR determinants coupled with antimicrobial- susceptibility testing indicated that most HC20_343 isolates are ESBL-producers and have intermediate resistance to ciprofloxacin. Population structure analysis of this foodborne pathogen evidenced an active transmission of MDR Salmonella Infantis between different niches. This study reveals the widespread dissemination of MDR Salmonella Infantis in Chile. Implications of all the available evidenceThe evidence indicates that emerging Salmonella Infantis from the HC20_343 cluster is spreading among various niches, including irrigation water, poultry, and food, causing human infections in Chile. Its resistance to first-line antibiotics used for treating salmonellosis in individuals with a higher risk of severe or invasive infections is concerning. Currently, most surveillance and control efforts to reduce salmonellosis in Chile are focused on the poultry industry, and the study of outbreaks does not include whole-genome sequence analyses. Our findings highlight the urgent necessity to improve the surveillance and control measures to include agricultural waters to prevent contamination of produce and the further dissemination of resistance genes in the environment. As the HC20_343 cluster is highly prevalent in the Americas, further research involving large-scale genomic population analyses would shed light on the extent of the dissemination and transmission routes of emergent Salmonella Infantis in the continent and may contribute to informing surveillance and control policies.

genomics↗

bioRxiv2023

A heterozygous CEBPA mutation disrupting the bZIP domain causes MDS disease progression

Myelodysplastic syndrome disease (MDS) has a variable risk for progression to AML. Mutations in CEBPA are associated with a high risk of disease progression, but whether this mutation is causative for AML development is unclear. To answer this question, we generated patient-derived, MDS-specific iPSCs recapitulating the patient disease phenotype upon differentiation to blood, with hematopoietic progenitor cells showing erythroid and myeloid-dysplasia. Introduction of a frameshift mutation affecting the C/EBP bZIP domain led to disease progression, with a reduction in clonogenic potential, block in granulocyte development and increased self-renewal capacity of erythroid progenitors. ATAC-seq revealed that the acquisition of this mutation reshaped the chromatin landscape at distal cis-regulatory regions, promoting changes in clonal composition as observed by single cell RNAseq. Our work identifies mutant CEBPA as causative for MDS disease progression, providing a new isogenic MDS experimental model for drug screening to improve diagnostic and therapeutic strategies. HighlightsO_LIDevelopment of isogenic iPSC model of clonal evolution of MDS C_LIO_LIMonoallelic disruption of CEBPA bZIP domain is causative for MDS disease progression C_LIO_LIMonoallelic disruption of CEBPA bZIP reshapes chromatin landscape C_LIO_LIPatient derived iPSCs recapitulate drug responsiveness C_LI

cancer biology↗