Biology subjects

Guenther, S.

Publications and source records attributed to Guenther, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Cell-specific FUS loss enhances ageing-associated transcriptional elongation in lung fibrosis

Idiopathic pulmonary fibrosis (IPF) is an age-related, lethal lung disease affecting over 3 million people worldwide. During aging, impairment of diverse molecular processes compromises cellular homeostasis. Eukaryotic cells adapt to this ageing-associated stress by large-scale transcriptome changes affecting the expression of genes involved in signaling, protein homeostasis, cell plasticity and immune response. The molecular mechanisms regulating extensive transcriptome rearrangements leading to senescence in specific cell types of IPF lungs remain sparsely investigated. Here we uncover fundamental molecular mechanisms underlying cellular senescence by integrative analysis of multi-omics studies and functional experiments monitoring fibrotic and senescence hallmarks in primary lung fibroblasts from control and IPF patients. Loss-of-function of the DNA/RNA binding protein fused in sarcoma (FUS) in control fibroblasts enhanced fibrotic and senescence hallmarks resembling IPF fibroblasts. Dissecting the molecular mechanisms, reduced FUS levels in IPF fibroblasts abolished R-loop formation at transcription start sites (TSS), leading to increased RNA polymerase II (Pol II) recruitment and its phosphorylation at serine 2, resulting in enhanced translocation speed of elongating Pol II and increased expression of fibrosis- and senescence-related genes. Summarizing, FUS maintains low Pol II processivity in control fibroblasts by stabilizing R-loops at TSS, acting as a gatekeeper of fibrotic and age-associated transcriptional programs.

molecular biology↗

bioRxiv2026

Junb acts downstream of the Il-11/Stat3 signaling axis to limit tissue damage induced fibro-inflammation during regeneration

Inflammation is essential for regeneration yet can also drive fibroinflammatory remodeling; what determines these opposing outcomes remains unclear. Comparative transcriptomic analyses revealed that injured mouse hearts activated a broad inflammatory program, whereas zebrafish hearts mounted a restricted response characterized by selective il11 induction. This divergence extended across tissues and species: the non-regenerative mammalian injuries examined shared an inflammatory signature distinct from regenerative vertebrate contexts. We identified the AP-1 transcription factor Junb as an Il-11-Stat3-dependent regulator that restrains inflammation during fin fold regeneration. Combined loss of junba and junbb amplified a mammalian-like inflammatory program, increased neutrophil recruitment and fibroinflammatory gene expression, and reduced proliferation and regenerative outgrowth. Strikingly, dexamethasone or ibuprofen substantially restored regeneration in Junb deficient zebrafish larvae, demonstrating that hyperinflammation is a major determinant of regenerative failure. Thus, the Il-11-Stat3-Junb axis maintains a regeneration permissive inflammatory state preventing a regenerative response from shifting toward mammalian-like fibroinflammation.

immunology↗

bioRxiv2026

Co-option of CENP-A for activity-induced neuronal plasticity

Neuronal activation drives activity-dependent gene expression that underlies experience-associated synaptic modifications, learning and memory. Here we show that the histone variant CENP-A, best known for specifying centromere identity, is dynamically regulated by synaptic activity at both the RNA and protein levels in postmitotic neurons. Neuronal activation increases a non-centromeric nuclear pool of CENP-A while leaving centromeric CENP-A levels unchanged. Downregulation of CENP-A selectively reduces the activity-associated non-centromeric pool, impairs activity-dependent induction of immediate-early genes such as FOS and ARC, and disrupts hippocampus-dependent learning and memory. Furthermore, we find that activity-dependent neuronal responses in human embryonic stem cell-derived forebrain organoids similarly require CENP-A. Our results reveal a mitosis-independent, conserved role of CENP-A for driving plasticity in mammalian neurons.

neuroscience↗

bioRxiv2026

Reg3β removes aged neutrophils after myocardial infarction

AO_SCPLOWBSTRACTC_SCPLOWRecruitment and resolution of immune cell accumulation after myocardial infarction (MI) is critical for effective wound healing and prevention of maladaptive remodeling. Numerous signals are known to recruit neutrophils, critical drivers of inflammation, but knowledge about signals containing and resolving their accumulation is limited. We discovered that Regenerating-islet derived protein 3 beta (REG3{beta}) limits the persistence of neutrophils after MI, thereby promoting resolution of inflammation. REG3{beta} selectively binds to aged and hyperactive neutrophils and induces rapid cell death, enabling clearance via macrophage-mediated efferocytosis. Selective binding of REG3{beta} is achieved by interaction with paucimannosylated proteins that translocate from azurophile granules to the plasma membrane in an activation- and age-dependent manner. Endocytotic uptake and accumulation of REG3{beta} in lysosomes initiates programmed cell death of neutrophils via lyosomal membrane permeabilization and release of cathepsins. Our work establishes REG3{beta} as a local immune checkpoint essential for neutrophil resolution and cardiac repair.

immunology↗

bioRxiv2026

Stabilizing Plasmodium falciparum Proteins for Small Molecule Drug Discovery

Early-stage drug discovery relies on the availability of stable protein for reliable biophysical characterization of ligand binding. However, many Plasmodium falciparum proteins are challenging to produce in heterologous systems, which limits their experimental utility. To address this, we tested whether ProteinMPNN-guided sequence design could generate stabilized surrogate constructs that retain wild-type-like structure and binding thermodynamics. Designs were generated with constraints to maintain conserved and binding-site residues for three therapeutically relevant targets: PfBDP1-BRD, PfBDP4-BRD, and PfK13-KREP. The resulting constructs showed markedly increased thermal stability. Using PfBDP1-BRD as a benchmark, isothermal titration calorimetry confirmed that the stabilized variants retained wild-type-like binding thermodynamics with a known ligand. Extending this approach to other targets, a PfK13-KREP construct led to an apo structure with a binding pocket closely matching the wild type, and a stabilized PfBDP4-BRD surrogate - a previously unstable target - enabled the identification of PfBDP4-BRD binders and a 1.25 [A] co-crystal structure with a newly found inhibitor. Our findings demonstrate that computationally stabilized surrogates are practical and effective tools for robust biophysics and structure-enabled drug discovery against otherwise challenging malaria proteins.

biochemistry↗

bioRxiv2025

Ischemic stroke induces persistent alteration to brain stromal progenitor cells linked to chronic vascular dysfunction

Fibrotic scar formation after stroke serves a dual role: while essential for providing structural support during post-ischemic recovery, excessive fibrosis in the chronic phase of stroke impairs regenerative processes including axonal regrowth and neovascularization. The temporal dynamics of fibrosis are critical determinants of functional outcomes, as the balance between protective scarring and regenerative capacity differs across distinct stroke phases. Consequently, strategic modulation of fibrotic processes to preserve regenerative potential represents a promising therapeutic approach in stroke recovery. To understand the cellular mechanisms underlying this fibrotic response, we investigated stromal progenitor cell composition in the post-stroke brain. The vast majority of stromal progenitor cells (SPCs) are pericytes, with minorities comprising perivascular fibroblasts (PVFs) and vascular smooth muscle cells. We demonstrate that ischemic stroke drives a long-term shift in this composition, characterized by sustained expansion of the PVF population and excessive laminin deposition in the peri-infarct region, effects that persist for at least six months post-stroke. Single-cell RNA sequencing revealed sustained transcriptional and compositional alterations in the SPC population throughout chronic post-stroke phase, driven by AP-1-mediated signaling via TNF in both PVFs and pericytes. These changes correlate with long-term vasomotor dysfunction and capillary constriction in the peri-infarct region at six weeks post-stroke. Ischemic stroke drives aberrant, persistent PVF accumulation at the capillary bed with implications for post-stroke cerebrovascular dysfunction and recurrent stroke. Taken together, these findings reveal that ischemic stroke drives an aberrant long-term mis-localization of PVFs to the capillary bed that may have clinically-relevant implications for post-stroke cerebrovascular function as well as potential ramifications for recurrent stroke.

neuroscience↗

bioRxiv2025

Ischemic injury triggers a protective microglial phenotype in models of Aβ pathology

Microglia are highly plastic cells that are capable of integrating subsequent insults. As the majority of Alzheimers Disease (AD) patients also show cerebrovascular pathology, we here aimed to dissect the interactions between AD and ischemic brain injury on the microglial response to amyloid beta (A{beta}) pathology. Surprisingly, we find that ischemic stroke in the presence of cerebral {beta}-amyloidosis results in the generation of a novel neuroprotective microglial phenotype. These microglia drive a rapid accumulation of highly dense A{beta} plaques that exhibit a relatively benign nature and are strikingly similar to A{beta} plaques observed in patients that are resilient to AD pathology. Thus, our data do not only highlight the impact of a co-morbid state of brain ischemia and A{beta} pathology on the microglial phenotype but also identify novel molecular pathways that may serve to promote beneficial microglial functions in AD.

neuroscience↗

bioRxiv2025

Soluble epoxide hydrolase upregulation in Alzheimer's disease promotes blood-brain barrier dysfunction

Recent advances in anti-amyloid therapies for Alzheimers disease have been promising, but they have also highlighted critical challenges, including increased vascular complications, such as amyloid-related imaging abnormalities. Emerging evidence suggests that the soluble epoxide hydrolase may be a promising therapeutic target due to the involvement of sEH-derived diols in inflammation, oxidative stress, and vascular destabilization. APPPS1 mice were crossed with an inducible soluble epoxide hydrolase knock-out mouse line. The knock-out was induced before onset of amyloid deposition, and then the mice were analyzed using histological, molecular, and RNA sequencing techniques. Here, we identify astrocytic soluble epoxide hydrolase as a key mediator of vascular instability in Alzheimers disease. Targeted astrocyte-specific deletion of soluble epoxide hydrolase in APPPS1 mice dramatically mitigated vascular changes, reducing the vascular amyloid burden by 67.95% and preserving VE-cadherin architecture. Importantly, vasomotion was markedly impaired in the Alzheimers disease model and was preserved in soluble epoxide hydrolase-deficient animals. Transcriptomic profiling of vasculature in APPPS1xsEH{Delta}AC mice revealed upregulated expression of genes critical for neurovascular protection. These findings identify soluble epoxide hydrolase as a central regulator of neurovascular dysfunction and underscore its therapeutic potential in increasing vascular stability in Alzheimers disease.

neuroscience↗

bioRxiv2025

A microprotein encoded by FERMT3 modulates endothelial cell protein catabolism and induces p53-mediated cell cycle arrest and senescence

BackgroundHuman endothelial cells express numerous microproteins (miPs) encoded by small open reading frames (smORFs) distributed throughout the genome, yet the biological functions of most remain unknown. This study set out to characterize a novel 69 amino acid miP encoded by a smORF located within the coding sequence of the FERM domain containing kindlin-3 transcript (miP-FERMT3). MethodsConfocal microscopy was used to determine the subcellular localization of miP-FERMT3 in endothelial cells and its interaction partners were determined by mass spectrometry and immunoblotting. RNA sequencing identified transcriptional alterations induced by miP-FERMT3 overexpression. Cell proliferation and cell cycle stages were assessed by live cell imaging, EdU incorporation and flow cytometry, while senescence was examined by senescence-associated {beta}-galactosidase staining, live cell imaging and RT-qPCR-based measurement of telomere length. ResultsIn endothelial cells miP-FERMT3 localized mainly to centriole subdistal appendages, where it interacted with proteins involved in ubiquitin- and proteasome-dependent protein catabolism, including PSMD9, CUL2 and TRIM8. Consistent with these interactions, cells expressing miP-FERMT3 exhibited increased global protein ubiquitination, enhanced centrosomal neddylation and elevated proteasomal activity. MiP-FERMT3 also promoted the nuclear accumulation of p53, which subsequently repressed FOXM1 expression, leading to the downregulation of genes required for cell-cycle progression and upregulation of genes involved in cell cycle inhibition, resulting in cell-cycle arrest. Cells expressing the miP also demonstrated multiple hallmarks of cellular senescence, including enlarged size, DNA damage, increased senescence-associated {beta}-galactosidase activity, telomere shortening and paracrine pro-inflammatory activation of naive endothelial cells. Analyses of independent murine and human transcriptomic and proteomic aging datasets further revealed that FERMT3 expression and protein abundance increase with age. ConclusionsThese findings identify miP-FERMT3 as a novel regulator of protein catabolism and p53-dependent cell cycle arrest and cellular senescence in endothelial cells. Given the aging-associated upregulation of FERMT3 in mouse and human endothelial cells, increased miP-FERMT3 expression may contribute to the onset of vascular senescence as a hallmark of aging.

cell biology↗

bioRxiv2025

Haematopoietic loss of KDM6A impairs cardiac recovery in heartfailure via epigenetic reprogramming of myeloid cells

Clonal haematopoiesis (CH) is recognized as a potent independent risk factor for cardiovascular disease (CVD). While mutations in common CH-associated genes, such as DNMT3A and TET2, have been extensively studied, the pathological roles of other CH mutations remain poorly understood. Among these is KDM6A (UTX), an X-linked histone demethylase recently found to be commonly mutated in patients with heart failure. The mechanistic implications of KDM6A mutations in cardiac dysfunction remain largely unknown. Here, using multi-omics profiling and functional characterisation of murine models and patient-derived data, we demonstrate that haematopoietic loss of KDM6A substantially impairs cardiac recovery following myocardial infarction (MI). KDM6A deficiency enhances systemic and cardiac inflammation, characterized by augmented myeloid cell infiltration into the infarcted murine heart. Single-cell chromatin accessibility and single-cell RNA sequencing analyses revealed profound epigenetic and transcriptional reprogramming in KDM6A-deficient myeloid cells, notably CCR2 recruited macrophages and neutrophils. These cells exhibited heightened inflammatory (Il1b, Nlpr3, Saa3) and chemotactic signatures (Ccr2, Mif, Cxcl12), increased activation of inflammatory transcription factor networks (AP-1, C/EBP), disrupted chromatin architecture, and enhanced glycolytic activity. Clinically, patients with heart failure harbouring KDM6A-driven CH exhibited increased pro-inflammatory monocyte signatures (CCR2, NLPR3, NFKB1, FOS, JUN, IL6R, IL32), underscoring the translational relevance. Integrative analyses further predicted pathogenic crosstalk between KDM6A-mutated monocytes and cardiac resident cells and was experimentally validated by demonstrating that KDM6A-silenced macrophages drive cardiomyocyte hypertrophy and cardiac fibroblast activation. Our findings establish a critical mechanistic link between KDM6A-driven CH, immune dysregulation, and worsened cardiac outcomes post-MI, highlighting novel avenues for personalized therapeutic strategies in heart failure.

cell biology↗

bioRxiv2025

Ferroptosis governs lymphatic vessel growth and regression

Whether, when, and how lymphatic vessels undergo cell death remains poorly understood. Here we identify ferroptosis as a physiological, cell-intrinsic regulator of the lymphatic endothelial cell survival during development and following injury, in stark contrast to the resilient organotypic blood endothelial cells. The lymphatic susceptibility to ferroptosis stems from tampered cystine/ hydropersulfide metabolism, alongside reduced glutathione availability triggered by an SH3RF3 E3 ligase mediated GPX4 degradation, and enhanced integration of polyunsaturated fatty acid enriched membrane phospholipids. Inducing ferroptosis genetically or pharmacologically elevated lymphatic lipid peroxidation, halted embryonic lymphangiogenesis and prevented post-injury lymphatic overgrowth while simultaneously shaped immune responses. Conversely, ferroptosis inhibition through saturated fatty acid supplementation led to pathological lymphatic hyperplasia. Targeting lymphatic ferroptotic mechanisms holds promise against pathological lymphatic growth in response to injury.

cell biology↗

bioRxiv2025

Endothelial expression of ZBTB16 protects against cardiac aging

Background and aimAging significantly increases the risk of cardiovascular diseases, characterized by progressive cardiac dysfunction. The vascular niche is crucial for maintaining cardiac homeostasis, yet endothelial cell (EC) impairment during aging remains poorly understood. This study investigates epigenetically regulated mechanisms mediating EC-dependent cardiac aging and identifies a critical role of Zinc finger and BTB domain-containing protein 16 (ZBTB16). MethodsChromatin accessibility (snATAC-seq) and transcriptomic (snRNA-seq) analyses were performed on aged hearts to identify age-related regulatory changes. Functional studies using genetic models, assessed cardiac aging phenotypes. In vitro assays examined EC senescence and secretory profiles, while co-culture experiments analyzed the impact of ZBTB16-deficient EC supernatants on fibroblasts, cardiomyocytes, and neurons. Overexpression experiments in vitro and in vivo tested the potential for ZBTB16 to mitigate aging-associated dysfunction. ResultsAged hearts exhibited decreased chromatin accessibility and expression of the transcription factor ZBTB16 in both human and mice. Loss of ZBTB16 in young mice, including Zbtb16 haploinsufficient and endothelial-specific knockout mice, led to premature aging, diastolic dysfunction, and increased secretion of pro-fibrotic and inflammatory factors. Supernatants from ZBTB16-deficient ECs activated fibroblasts, induced cardiomyocyte hypertrophy, and impaired neuronal sprouting. Overexpression of ZBTB16 reversed these effects in senescent ECs and aged mice and reduced diastolic dysfunction. Mechanistic studies identified key downstream targets of ZBTB16, including nuclear receptor-interacting protein 1 (NRIP1). ZBTB16 suppressed NRIP1 expression, limiting fibroblast activation and pro-fibrotic signaling. ConclusionsZBTB16 is a key regulator of endothelial function, maintaining vascular niche homeostasis and mitigating aging-associated cardiac dysfunction. Its loss promotes EC senescence and pro-fibrotic signaling, contributing to diastolic dysfunction. Overexpression of ZBTB16 presents a potential therapeutic strategy for preserving cardiac function during aging. These findings establish a novel role for ZBTB16 in endothelial aging and cardiovascular disease prevention. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/681100v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1a56e2org.highwire.dtl.DTLVardef@13e23fforg.highwire.dtl.DTLVardef@ad681eorg.highwire.dtl.DTLVardef@8eca8b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Differentiation hierarchy in adult B cell acute lymphoblastic leukemia at clonal resolution

While a differentiation hierarchy with leukemia-initiating stem cells (LICs) at the apex is well documented for acute myeloid leukemia, the existence of LICs and their trajectories in B cell acute lymphoblastic leukemia (B-ALL) are debated. B-ALL is a malignant disease displaying considerable phenotypical and functional heterogeneity, yet the underlying cellular organization remains largely elusive. This study aims to investigate the hierarchical landscape of B-ALL by combining barcoding and multiome single cell data to unveil the differentiation architecture and temporal dynamics of leukemic differentiation at clonal and single cell resolution in vivo. Single-cell transcriptome and AbSeq analysis of lentiviral barcoded and transplanted patient-derived B-ALL cells revealed interconnected subpopulations, which could be prospectively isolated via surface markers and exhibited distinct leukemogenicity. Barcode tracking demonstrated the ability of cells to differentiate from a source cluster into differentiated progeny. Using machine learning we identified expression patterns predicting their differentiation potential of each barcoded cell within the immature cell compartment. To determine the dynamical properties of clones, we have designed a mathematical model that simulates the development of these subpopulations from a clonally diverse stem cell compartment. The model confirmed the most likely cluster of origin, supporting our functional data, and revealed the variability in dynamical properties between clones, while largely excluding plasticity. Hence, our work demonstrates a unidirectional differentiation in B-ALL with an immature population exhibiting a high leukemogenic potential. Key pointsO_LIA differentiation hierarchy with distinct leukemogenesis potential in B-ALL is demonstrated via clonal tracing and mathematical modeling. C_LIO_LIClonal differentiation behavior, while heterogeneous, is cell intrinsically controlled and predictable, yet independent from expansion. C_LI

cancer biology↗

bioRxiv2025

Erlotinib induces 3D genome rearrangements in lung cancer cells activating tumor suppressor genes through FOXA2-bound Epromoters

Non-small cell lung cancer (NSCLC) is the most frequent lung cancer (LC). While erlotinib is an epidermal growth factor (EGFR) tyrosine kinase inhibitor (TKI) used in the treatment of NSCLC, it remains unclear how this FDA-approved drug affects the genome. We performed integrative multi-omics studies in human pulmonary carcinoma cells to elucidate the epigenetic mechanisms induced by erlotinib. We identified 746 genes (including 34 tumor suppressor genes, TSG) that were upregulated after treatment with erlotinib or gefitinib (another EGFR-TKI). Interestingly, 45% of the upregulated genes (including 24 TSG) were in broad domains of the euchromatin histone mark H3K4me3, and 63% (including 26 TSG) exhibited reduced levels of the heterochromatin histone mark H3K27me3 after erlotinib treament. Further, H3K27ac-specific chromosome conformation capture-based methods revealed that erlotinib significantly increased number and length of chromatin loops between promoters of upregulated genes and active enhancers. We also detected augmented chromatin accessibility after erlotinib treatment at the promoters of upregulated genes, which correlated with binding of the transcription activator FOXA2. Remarkably, we identified gene clusters that seem to be upregulated by promoters with enhancer activity (Epromoters) enriched with FOXA2. The clinical relevance of our findings was confirmed by data from The Cancer Genome Atlas, showing significantly improved survival outcomes in LC patients with high levels of FOXA2 and/or the 34 TSG found upregulated by erlotinib. Our results establish 3D genome rearrangements as molecular mechanism mediating EGFR-TKI effects in NSCLC cells, supporting the design of more specific therapies for NSCLC targeting different chromatin features.

cancer biology↗

bioRxiv2025

Statistical crystallography reveals an allosteric network in SARS-CoV-2 Mpro

To interpret and transmit biological signals, proteins use correlated motions. Experimental determination of these dynamics with atomic resolution remains a key challenge. Here, using thousands of crystals of the main protease (Mpro) from SARS-CoV-2, we were able to infer a model of the proteins correlated motions. Mpro is regulated by concentration, becoming enzymatically active after forming a homodimer. To understand the correlated motions that enable dimerization to activate catalysis, we employed our model, predicting which regions of the dimerization domain are structurally linked to the active site. Mutations at these positions, expected to disrupt catalysis, resulted in a dramatic reduction in activity in one case, a mild effect in the second, and none in the third. Additional crystallography and biophysical experiments provide a mechanistic explanation for these results. Our work suggests that a statistical crystallography can determine protein correlated motions and rationalize their biological function. TeaserCrystallography at scale goes beyond a single structure, revealing native-state protein dynamics.

biochemistry↗

bioRxiv2025

A novel inhibitor against the bromodomain PfBDP1 of the malaria pathogen Plasmodium falciparum

The rise of drug resistances in malaria necessitates the exploration of novel therapeutic strategies. Targeting epigenetic pathways could open new, promising treatment avenues. In this study, we focus on PfBDP1, an essential bromodomain protein in P. falciparum. Utilizing the pan-selective bromodomain inhibitor MPM6, we identified a potent initial hit and subsequently developed it into a nanomolar binder. Through a combination of virtual docking, isothermal titration calorimetry, and X-ray crystallography, we elucidated the molecular interactions of the new inhibitors with PfBD1. Our findings include the first cocrystallized structures of PfBD1 and PvBD1 with these inhibitors, providing insights into their binding mechanisms. Further validation using conditional knockdown of PfBDP1 in P. falciparum demonstrated parasite sensitivity to the inhibitor, underscoring its potential as a targeted therapeutic approach against malaria.

biochemistry↗

bioRxiv2024

Concerted loss of micro-RNAs uncovers multi-level restructuring of gene regulation in rodents

BackgroundThe regulatory network that coordinates gene expression ultimately determines the phenotype of an organism. Micro-RNAs (miRNAs) are post-transcriptional regulators involved in key biological processes. Lineage-specific losses of multiple miRNA families are rare, and reported cases of multiple miRNA losses coincide with significant changes in gene regulation resulting in body plan modifications. Recently, 15 mammalian miRNA families were found to be missing in the Eumuroidea, the rodent lineage that includes the model organisms mouse and rat. However, the impact of their absence on the gene regulatory networks in this lineage remains unknown. ResultsThe in silico characterization of all 15 miRNAs revealed that their absence is best explained by multiple independent losses. Analyzing their target genes in humans reveals a significant enrichment of GO- terms linked to cellular and developmental processes. Overexpressing two of the co-absent miRNAs, Mir-197 and Mir-769, in human and mouse inducible pluripotent stem cells (iPSCs) resulted in significantly perturbed expression patterns in both species. In silico target site prediction revealed a significant enrichment of direct targets exclusively in the down-regulated genes. Four genes were down-regulated in both mouse and human and maximum parsimony suggests that the corresponding miRNA target sites were already present in the last common ancestor of mammals. The response of these genes to miRNA overexpression in mice, therefore, unveils remnants of the ancient gene regulatory network that have persisted until today. The evolutionary age of these regulatory connections provides initial evidence that the miRNA losses in Eumuroidea must have had consequences for the regulation of gene expression. Notably, we show that the miRNA loss in the Eumuroidea coincides with the largest lineage-specific loss of transcription factors within the mammals. ConclusionsThe impact of miRNA losses has thus far been investigated on a gene-by-gene basis. Our findings indicate that cooperative effects between miRNAs should be considered when assessing the impact of miRNA loss. We provide evidence that the Eumuroidea have modified their gene regulatory networks on two levels, transcriptionally and post-transcriptionally. It will now be interesting to precisely chart the differences in gene regulation and assess their combined impact on the suitability of mice and rats as model systems for human disease.

genetics↗

bioRxiv2024

The transaminase-omega-amidase pathway is a redox switch in glutamine metabolism that generates alpha-ketoglutarate

Oxidative stress is caused by short-lived molecules and metabolic changes belong to the fastest cellular responses. Here we studied how the endothelial cell metabolome reacts to acute oxidative challenges (menadione or H2O2) to identify redox-sensitive metabolic enzymes. H2O2 selectively increased -ketoglutaramate (KGM), a largely uncharacterized metabolite produced by glutamine transamination and a yet unrecognized intermediate of endothelial glutamine catabolism. The enzyme nitrilase-like 2 {omega}-amidase (NIT2) converts KGM to -ketoglutarate (KG). Reversible oxidation of specific cysteine in NIT2 by H2O2 inhibited its catalytic activity. Furthermore, a variant in the NIT2 gene that decreases its expression is associated with high plasma KGM level in humans. Endothelial-specific knockout mice of NIT2 exhibited increased levels of KGM and impaired angiogenesis. Knockout of NIT2 impaired endothelial cell proliferation and sprouting and induced senescence. In conclusion, we show that the glutamine transaminase-{omega}-amidase pathway is a metabolic switch in which NIT2 is the redox-sensitive enzyme. The pathway is modulated in humans and functionally important for endothelial glutamine metabolism.

physiology↗