Biology subjects

Gonzalez, C.

Publications and source records attributed to Gonzalez, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Pattern-triggered immunity induced by dsRNA against plant viruses involves two distinct branches, one of which depends on Coronatine insensitive1 (COI1)

Double-stranded RNA (dsRNA) is a conserved molecular signature of RNA virus generated during infection that can activate antiviral pattern-triggered immunity (PTI) in plants. However, the effectiveness of dsRNA-induced PTI against viruses from diverse taxa, its impact on different stages of the infection, as well as effectors used by viruses other than tobamoviruses to counteract this defense response remain poorly explored. Here, we established an Agrobacterium-mediated transient expression assay for inducing PTI through intracellular production of nonspecific dsRNA in Nicotiana benthamiana. Expression of nonspecific dsRNA restricted cell-to-cell movement and accumulation of three RNA viruses representing different taxonomic groups: Tobacco mosaic virus, Turnip mosaic virus, and Tobacco rattle virus. Co-expression of dsRNA together with a P25 movement protein (MP) mutant of Potato virus X (PVX) defective in RNA silencing suppression, prevented dsRNA-induced callose accumulation at plasmodesmata (PD) and restored efficient viral cell-to-cell movement. Interestingly, dsRNA also reduced viral RNA accumulation at the cellular level, revealing an impact of dsRNA-based PTI on virus replication independently of cell-to-cell movement. We further showed that the dsRNA-induced antiviral response required jasmonic acid (JA) signaling. Silencing of the JA receptor Coronatine insensitive1 (COI1) abolished dsRNA-induced PD callose deposition and the associated restriction of virus movement and accumulation. Accordingly, dsRNA-induced expression of defense-related genes was compromised in COI1-silenced plants. Next, we conducted RNA-seq analysis to identify early biological processes involved in COI1-dependent, dsRNA-induced immunity. The differential expression of 198 genes, some potentially involved in the regulation of callose accumulation, in COI1-silenced plants suggested that JA signaling contributes to shaping the transcriptional response to nonspecific dsRNA. Together, our findings establish nonspecific dsRNA-induced PTI as a multilayered antiviral response that restricts pathogen replication and cell-to-cell movement, and identify a heterologous MP, PVX P25, as an effector that counteracts the PD component of this defense response in a COI1-dependent manner.

plant biology↗

bioRxiv2026

Community assembly dynamics in a regulated stream: Insights from environmental DNA

Degradation of freshwater habitats, including the alteration of natural flow regimes by impoundment, is a major threat to native fishes. When dam removal is not possible, management actions to recover natural flow regimes can benefit native species, but monitoring community responses is crucial to show efficacy. We used eDNA metabarcoding to quantify spatiotemporal trends in fish assemblages along the longitudinal profile of a regulated stream where a court-ratified environmental flows framework is used to benefit native fishes. At a subset of sites, we also compared eDNA results with concurrent surveys conducted using long-term standardized fisheries monitoring techniques to evaluate concordance. From 59 eDNA samples collected over approximately 2 years, we detected 26 fish taxa, including 8 native species, with 25 taxa resolving to species level using a custom reference sequence database; one taxon could not be resolved between closely related species. Fish assemblages varied predictably along the longitudinal profile of the stream and by season (fall and spring). Diversity indices were higher at downstream sites and in fall, reflecting greater richness of warm-water non-native species. Evenness was similar among sites but shifts in species ranks suggests reordering processes drive spatiotemporal variation in assembly. Gradient forest analysis identified thirteen species associated with spatiotemporal gradients, including both native cold-water species and non-native warm-water species. Overall, eDNA results were concordant with conventional fisheries monitoring but eDNA detected significantly greater species richness through increased detection of rare species. eDNA results align with long-term monitoring that demonstrated assemblage shifts in upper, but not lower stream reaches, and extends the insights into spatial responses, species reordering, and ecology of rare species. These findings demonstrate the value of eDNA as a complementary tool for understanding community assembly dynamics, including responses to stream rehabilitation and ecosystem management.

ecology↗

bioRxiv2026

Progressive behavioral and cognitive decline in Drosophila harboring AD-associated APOE4 variants

Alzheimer's disease (AD) is the most prevalent neurodegenerative disorder, and its incidence is rising rapidly with population aging. Pathologically, AD is characterized by the accumulation of amyloid-beta (Abeta) plaques and hyperphosphorylated Tau neurofibrillary tangles. Human genomic studies have identified numerous risk alleles, with the APOE4 variant representing the strongest and most common genetic risk factor, present in approximately 75 percent of AD patients. However, APOE4 is neither necessary nor sufficient to cause disease, suggesting that additional genetic and environmental factors contribute to AD pathogenesis. Emerging evidence highlights a central role for oxidized lipid metabolism in AD. Disruption of lipid metabolism leads to lipid accumulation, reactive oxygen species (ROS) toxicity, and neurodegeneration, suggesting that oxidative stress may be a critical factor in enhancing AD susceptibility. To systematically investigate APOE function in vivo, we tested humanized Drosophila expressing the human APOE3 or APOE4 variants in place of the Drosophila ortholog Glial Lazarillo (GLaz). The lifespan of APOE3 and APOE4 flies does not differ under standard housing conditions, but the lifespan of APOE4 flies is significantly reduced when exposed to the ROS-promoting drug rotenone, supporting a multi-hit model of disease pathogenesis. APOE4 flies exposed to rotenone exhibit several AD-associated phenotypes, including age-related memory loss and chemosensory deficits, supporting the use of this model to investigate AD pathogenesis. Furthermore, progressive AD-associated phenotypes are also observed in APOE4 flies maintained on an obesogenic diet, suggesting that enhanced disease susceptibility is not specific to rotenone-induced stress but reflects a broader vulnerability to metabolic challenges. Together, these findings establish a scalable model to dissect APOE-dependent mechanisms and identify therapeutic targets in AD.

genetics↗

bioRxiv2026

From Code to Cure: Computationally Designed BMP-2 Binders Using AI-Integrated Pipelines for Controlled Bone Regeneration

Nonunion fractures remain a costly and persistent challenge in regenerative medicine, with current treatments limited by donor-site morbidity, restricted graft availability, and severe adverse effects associated with supraphysiological bone morphogenetic protein 2 (BMP-2) delivery, including ectopic ossification and inflammation. Endogenous BMP-2 signaling is tightly regulated in adult tissues, constraining the precision and scalability of approaches based on transcriptional upregulation or bolus growth factor administration. To address these limitations, we developed a two-phase integrated computational-experimental pipeline for the de novo design of protein binders targeting the BMP-2 knuckle epitope, a receptor-binding surface corresponding to BMPR-II engagement, enabling affinity-tuned modulation of BMP-2 activity rather than uncontrolled pathway activation. Phase I employed PyRosetta-based {beta}-strand motif grafting and physics-based docking protocols to generate 264 candidate binders, followed by deep-learning-driven refinement in Phase II using partial RFDiffusion and ProteinMPNN with AlphaFold2 validation, yielding 22 candidates with stable {beta}-sheet architectures consistent with knuckle-epitope targeting. Experimental validation demonstrated dose-dependent BMP-2 binding, with the lead construct exhibiting an apparent KD of 2.07 nM toward BMP-2. Targeted alanine substitutions revealed differential residue contributions, with mutation of T42 significantly disrupting binding, while other substitutions had more modest effects, indicating a partially hotspot-driven interface supported by other interactions.

bioengineering↗

bioRxiv2026

Production of membrane-embedded Bcl-2 proteins - Use of cell-free synthesis in continuous exchange for co-translational insertion of Bcl-2 proteins in lipid bilayer nanodiscs

The BCL-2 family proteins are key regulators of apoptosis, functionally divided in pro- and anti-apoptotic proteins, with a third group acting as regulators. Their ability to partition between the cytosol and intra-cellular membranes (essentially the mitochondrial outer membrane) is a primary regulator of their functions. A second contributor is their ability to form homotypic complexes (pro-pro or anti-anti) or heterotypic complexes (pro-anti). If the structures of monomeric cytosolic members have largely been characterized, the functional and structural study of membrane-embedded proteins remains incomplete. Unlocking this knowledge is expected to enable evaluating new therapeutic strategies to either activate pro-apoptotic members, or inactivate anti-apoptotic ones. Lipid bilayer nanodiscs and improved cell-free protein synthesis have provided the technical breakthrough to achieve the description at the atomic level of conformations and higher order assemblies of these proteins in their membrane-associated states. Here we describe detailed and straightforward protocols for generating nanodisc-inserted members of the Bcl-2 family, through the example of anti-apoptotic Bcl-xL, and pro-apoptotic Bax and Bak. Full-length, untagged proteins are expressed from bacterial extracts in the presence of pre-assembled nanodiscs to allow co/post-translational insertion in lipid bilayer, followed by affinity chromatography purification. A more detailed characterization is presented for Bak, to exemplify structural and mechanistic studies enabled by these methods. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/745005v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@5da1d1org.highwire.dtl.DTLVardef@12aca96org.highwire.dtl.DTLVardef@5a3e73org.highwire.dtl.DTLVardef@ba009d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

The Drosophila FET orthologue Cabeza is an essential cofactor for ETV4-mediated activation of GGAA microsatellite neoenhancers

The conversion of transcriptionally silent GGAA microsatellites (GGAA{micro}Sats) into functional enhancers by FET::ETS oncogenic fusions is a hallmark of Ewing sarcoma. However, emerging evidence implicates non-fused, full-length oncogenic ETS transcription factors in activating these repeats in other malignancies. Evaluating the in vivo transcriptional requirements of various human ETS factors in Drosophila, we found that human ETV4 uniquely binds and robustly activates GGAA{micro}Sats in a tissue-specific manner. This activation is strongly inhibited by the human ETS repressor ETV6. Taking advantage of low genetic redundancy in Drosophila, we identified Cabeza (Caz), the single fly FET orthologue, as a necessary cofactor for ETV4-mediated transcription at GGAA{micro}Sats. Conversely, EWS::FLI1-mediated transcriptional activation of GGAA{micro}Sats is entirely independent of endogenous Caz, highlighting the distinct mechanics of covalent tethering versus non-covalent physical complexes. Collectively, our findings provide definitive in vivo evidence that non-fused ETS factors cooperate with endogenous FET proteins to drive transcription from silent GGAA repeats, mechanistically validating this regulatory transformation known to operate as an oncogenic mechanism beyond Ewing sarcoma.

genetics↗

bioRxiv2026

Identification of two genomic cryptotypes of Plasmodium malariae in Africa

Plasmodium malariae is a neglected human malaria parasite that causes persistent, often asymptomatic infections and remains difficult to diagnose. Despite being generally associated with lower prevalence and severity than other malaria parasites, P. malariae represents a significant public health concern, particularly in Africa, but also as a zoonosis in South America with monkey-adapted Plasmodium brasilianum. Plasmodium malariae and P. brasilianum population genetic structure, evolutionary history, and adaptive potential remain poorly understood, largely due to the historical scarcity of whole-genome data. By screening 226 monkey samples from two Latin American countries, we identified 20 Plasmodium-positives across multiple primate species, highlighting the persistence of this parasite in sylvatic transmission cycles. We also investigated the evolutionary history and genetic diversity of P. malariae using whole-genome sequencing data. By combining 79 newly sequenced genomes with 248 publicly available genomes, we analyzed a filtered dataset comprising 179 P. malariae, two P. brasilianum, and two P. malariae-like genomes. Population structure analyses revealed the presence of two genetically distinct but recombining clusters across African P. malariae populations. These clusters occur across multiple African countries at varying frequencies, without clear geographic segregation. Genome-wide scans of genetic differentiation and selection further identified numerous cluster-specific signatures of adaptation, including loci putatively involved in interactions with human hosts and mosquito vectors. Our results provide the first evidence for fine-scale population substructure within African P. malariae and reveal ongoing adaptive processes that may contribute to its persistence and transmission. By uncovering previously unrecognized genetic diversity and selection patterns, this study highlights the importance of population genomic approaches for understanding the evolutionary dynamics of this neglected malaria parasite. Author summaryHuman malaria is most often associated with few well-studied parasites (Plasmodium falciparum and Plasmodium vivax), while other species have received far less attention. One such species is Plasmodium malariae, which often causes long-lasting infections with few or no symptoms. Because infections are difficult to detect, the true impact of this parasite is likely underestimated, particularly in Africa, where it is widespread. A closely related form, known as Plasmodium brasilianum, infects monkeys in South America with transmission between humans and wild animals. In our study, we analyzed the parasite genomes from infected people and monkeys to better understand the genetic diversity of these parasites, their population structure, and the molecular evidence of adaptation. We found evidence that P. brasilianum continues to circulate in several wild monkey species in South America. By analyzing nearly 300 genomes, we discovered that African P. malariae consists of two genetically distinct but recombining groups that coexist across the continent. These groups differ in specific regions of their genomes, including genes likely involved in interactions with human hosts and mosquito vectors. Our results reveal cryptic genetic diversity and structure with evidence of ongoing adaptation. These findings highlight the importance of including neglected parasites in malaria surveillance and control efforts.

genomics↗

bioRxiv2026

MauE from Calditrichota and Thermodesulfobacteriota reveal a new pathway for disulfide bond formation in bacteria

Disulfide bond formation is crucial to the structure and function of many proteins. It is known that there is diversity in the pathways for disulfide bond formation in bacteria and that there are gaps in our knowledge of these pathways. Using a combination of experimental and bioinformatic approaches we show that some of these gaps can be filled by a newly discovered oxidative folding pathway centered on methylamine utilization protein E (MauE). MauE has previously been associated with the methylamine utilization (MAU) gene cluster, which is involved in methylamine metabolism, in particular it is associated with the maturation of the small subunit of methylamine dehydrogenase. Here we show MauE from Caldithrix abyssi and Desulfatibacillum alphaticivorans functionally replace disulfide bond formation protein B (DsbB) in E. coli using two independent disulfide bond dependent assays. Furthermore, MauE is found in 14 species from 2 bacterial phyla that lack known pathways for structural disulfide bond formation, but which have proteins with structural disulfide bonds in the protein data bank. The active site for MauE was determined to be a conserved CXC motif. Using molecular docking predictions, we demonstrate that MauE is likely to interact with ubiquinone, similarly to the well characterized bacterial DsbB. We also constructed a dataset across thirty-five different phyla to demonstrate that MauE is potentially the second most common disulfide bond formation protein in bacterial disulfide bond formation pathways after DsbB. In addition, the distribution of MauE largely differs from the distribution of other MAU gene cluster markers affirming its role as a newly discovered generalist disulfide bond formation protein rather than being a specialized maturation factor for methylamine dehydrogenase. We also reveal further gaps in disulfide bond pathways, as well as species which may contain redundancies in their disulfide bond pathways.

biochemistry↗

bioRxiv2025

gffutilsAI: An AI-Agent for Interactive Genomic Feature Exploration in GFF files

AO_SCPLOWBSTRACTC_SCPLOWThe General Feature Format (GFF) is widely used to represent genomic annotations, but its hierarchical, multi-attribute structure makes manual querying and analysis challenging. Existing libraries such as gffutils provide programmatic interfaces, yet they require coding proficiency. gffutilsAI is a novel AI-powered command-line agent that enables researchers to perform interactive, natural-language-driven exploration of GFF files. Built on top of the gffutils library and the Strands AI agent framework, gffutilsAI integrates local and cloud-based large language models (LLMs) such as Llama 3.1, GPT-5, and Claude 3.5 to translate human queries into executable actions. The tool supports coordinate-based queries, attribute and GO searches, hierarchical traversal, statistical summaries, and CSV export, offering a new paradigm for accessible conversational genomics.

bioinformatics↗

bioRxiv2025

NOVEL SMALL-MOLECULE INHIBITORS OF THE PROTEIN KINASE DYRK: POTENTIAL THERAPEUTIC CANDIDATES IN CANCER

Dual-specificity tyrosine-regulated kinase 1A (DYRK1A) is crucial for normal brain development and its disruption has been linked to various cancers. DYRK1A drives glioblastoma (GBM) progression via stabilization of epidermal growth factor receptor (EGFR). Here we describe two, selective, benzothiazole-derived DYRK inhibitors, FC-2 and FC-3, obtained by structure-activity optimization of a natural product lead. Both compounds inhibit DYRK1A with nanomolar potency and display high selectivity across a kinase panel. The co-crystal structure of FC-3 with DYRK1A revealed ATP-competitive binding, with interactions at the hinge region and the DYRK-specific phenylalanine gatekeeper residue explaining target selectivity. Generation of inhibitor-resistant mutants confirmed DYRK1A as the primary cellular target. In GBM cell-models, FC-2 and FC-3 impaired neurosphere self-renewal, cell invasion, and EGFR stability, phenocopying DYRK1A loss. Both compounds crossed the blood-brain barrier and suppressed tumor growth, to prolong survival in intracranial xenografts. These findings identify FC-2 and FC-3 as selective small-molecule inhibitors of DYRK1A with potential therapeutic utility in GBM.

cancer biology↗

bioRxiv2025

Human Oncogene EWS::FLI1 Functions as a Pioneer Factor in Saccharomyces cerevisiae.

Ewing sarcoma (EwS) is an aggressive, human-exclusive tumor typically driven by the EWS::FLI1 fusion protein. To assess whether the neomorphic functions of EWS::FLI1 are fundamentally dependent on evolutionarily recent cofactors such as ETS transcription factors (ETS-TFs), Plycomb group (PcG) proteins, CBP/p300, or specific subunits of the BAF complex, we expressed EWS::FLI1 in the model organism Saccharomyces cerevisiae. This minimal system was chosen because several key EWS::FLI1s cofactors possess greatly reduced sequence homology (e.g., BAF) or are lacking altogether (e.g., ETS-TFs, PcG, or CBP/p300). We used co-IP/MS to map the yeast interactome, Chip-Seq to identify gDNA binding sequences, RNA-Seq for global gene expression, and engineered reporters to test conversion of (GGAA) tandem repeats (GGAASat) into neoenhancers. We found that the yeast EWS::FLI1 interactome was more limited and qualitatively distinct from its human counterpart, sharing core machinery (e.g. RNA Polymerase II, FACT) but lacking the BAF/SWI-SNF and spliceosome complexes, and showing strong enrichment for the SAGA chromatin remodeling complex. We also found that EWS::FLI1 binds to hundreds of sites in the yeast genome with a clear preference for putative ETS-TF consensus sequences and (CA) dinucleotide repeats. Yet, EWS::FLI1 expressing cells presented only minimal transcriptional dysregulation, a stark contrast to the extensive changes observed in humans and Drosophila cells. Finally, we found that EWS::FLI1 successfully converted silent GGAASat sequences into active enhancers in yeast. This remarkable result occurs despite the absence of homologs for key human activators, such as CBP/p300, strongly suggesting that EWS::FLI1 can mobilize functionally related, non-homologous pathways to establish neoenhancers at GGAASat sites. Altogether, our results indicate that EWS::FLI1s core ability to drive GGAASat-dependent gene expression is a conserved, ancient property, while GGAASat-independent extensive transcriptome reprogramming is dependent on co-factors and pathways specific to animal cells.

cancer biology↗

bioRxiv2025

Maternal Light and Temperature Modulate Seed Longevity in Arabidopsis

Seed longevity is defined as the length of time a seed can preserve its germination capacity, and it is a relevant trait for disciplines from agriculture to ecology. Seed longevity is a polygenic trait influenced by genetic and environmental factors. Despite the recognized impact of climate change on many reproductive aspects of plant biology, studies focused on how these new conditions affect this trait are scarce. In this work, we describe how environmental conditions to which the plants are exposed during seed development, termed the maternal environment effect, modulate longevity of the new developed seeds. Eight Arabidopsis thaliana natural accessions were grown on a combination of four different environmental scenarios: 22{degrees}C or 27{degrees}C at both low-light or high-light intensity. The combined effect of both 27{degrees}C and high light conditions generated seeds with higher longevity, although the effect is accession dependent. Similarly, an anticorrelation was found between seed dormancy and seed longevity when seeds were developed at 22{degrees}C under HL conditions, highlighting the importance of the environment in determining final seed properties. Transcriptome analysis of the Bor-4 accession, whose seeds presented the highest difference in longevity between conditions, revealed a very dynamic composition of stored mRNAs modulated by the four different environmental conditions during seed development. Nearly 80% of the differentially expressed genes exhibited a combined effect when both temperature and light-intensity were altered. Results suggest that seeds subjected to higher temperature and light intensity are primed with antioxidant defences and have a higher potential to deploy raffinose family oligosaccharides, which would be critical to safeguard cellular components during the ageing process.

plant biology↗

bioRxiv2025

Reduced efficacy of an anti-toxin vaccine from senescence-driven attenuation of toxin virulence

It remains unclear why vaccines targeting prominent microbial virulence factors often fail in clinical trials. Because microbial virulence depends on interaction with the host immune system, we investigated how changes in host immune function alter vaccine efficacy. Using a vaccine against Staphylococcus aureus alpha toxin (Hla), which targets host metalloprotease ADAM10 on myeloid cells, we show that Hla virulence is reduced in aged mice due to diminished ADAM10 activity and impaired myeloid cell function. Depletion of myeloid cells with cyclophosphamide in young mice similarly reduced toxin virulence. Immunization against Hla conferred strong protection against Staphylococcus aureus infection in young but not aged mice. These findings indicate that pathogenic functions of microbial factors characterized in immunocompetent young animals may not predict virulence or vaccine efficacy in immunocompromised hosts. These findings underscore the need to account for host immune status in the development and evaluation of vaccines targeting microbial virulence factors.

microbiology↗

bioRxiv2025

Teleost-specific ictacalcins exhibit similar structural organization, cation-dependent activation and transcriptional regulation as human S100 proteins

S100 proteins are highly versatile calcium-binding proteins from vertebrates. Following extracellular release, they become instrumental in immune and antimicrobial defenses, initiating the inflammatory response through receptor signaling and providing direct control of bacterial invaders via nutritional immunity. While mammalian S100s have been extensively studied, very little is known about the more recently discovered S100 proteins from teleost fish, including those with no strict orthologs in mammals. Comparable functioning between both clades would allow to expand their study into the highly popular zebrafish model, particularly suited for live imaging and mechanistic exploration of immune and inflammatory processes. To fill the gap of knowledge on teleost S100s, we here provide a detailed structural and biochemical characterization of S100i1 and S100i2 from Danio rerio, two teleost-specific S100s absent in mammals. We demonstrate that they nevertheless share conserved tertiary and quaternary organization with mammalian S100s. In addition, they exhibit comparable calcium binding properties and undergo a similar calcium-dependent activation mechanism. Furthermore, they display analogous expression pattern, being enriched in tissues highly exposed to the environment like gills and skin, the latter constituting an important reservoir of S100 proteins in mammals. Finally, our results show, for the very first time, that s100i2/i2 gene expression is differentially modulated in sterile disease conditions associated with sustained inflammation or high hypoxic state. Altogether, these findings underline the strong parallelism existing between mammalian and teleost-specific S100 proteins despite their divergent evolution, opening up new avenues to explore their biology in the zebrafish model.

immunology↗

bioRxiv2025

Circular RNA Circ-Cdr1as modulates Macrophage phenotype and Cardiac Reparative Function by Circ-Cdr1as-miR-7-Klf4 pathway

BackgroundMechanisms of macrophage switching from pro-inflammatory to anti-inflammatory phenotypes are not well understood. Circular RNAs (circRNAs), a new class of non-coding RNAs, are implicated in immune modulation. We recently identified circ-cdr1as as a regulator of macrophage phenotype in bone marrow derived macrophages (BMDM), however, their role in immunomodulation during cardiovascular injury remains unknown. MethodsCell-specific expression levels of circ-cdr1as was determined in a mouse hearts post-myocardial infarction (MI). Circ-cdr1as was overexpressed in fluorescently labeled BMDMs and injected into the ischemic myocardium immediately following MI. Effect of AAV9-mediated systemic delivery of circ-Cdr1as on post-MI cardiac function and structure was determined. Downstream mechanisms were studied using gain and loss of function strategies. ResultsCardiac cell specific expression analysis showed significant downregulation of circ-cdr1as only in macrophages and cardiomyocytes. Overexpression of circ-cdr1as in BMDMs, injected into the ischemic myocardium retained their anti-inflammatory phenotype and significantly improved left ventricular (LV) functions and reduced infarct size. Systemic delivery of AAV9-circ-cdr1as showed similar cardiac reparative activity. Mechanistically, circ-cdr1as directly binds and sponge microRNA-7 and increases the expression of target KLF4. Loss and gain of function studies show that modulation of miR-7 and KLF recapitulates macrophage phenotypic changes. ConclusionsCirc-cdr1as plays a crucial role in regulating the anti-inflammatory phenotype of macrophages through modulation of miR-7 and its target gene KLF4. Therefore, circ-cdr1as holds potential as an anti-inflammatory regulator in tissue inflammation post-cardiac injury. Novelty and SignificanceO_ST_ABSWhat is Known?C_ST_ABSO_LIDespite continued research in elucidating mechanisms involved in cardiovascular disease and benefits of approved guideline-based therapies, the leading cause of deaths worldwide continues to be cardiovascular diseases (CVDs) with an increasing incidence of heart failure. C_LIO_LIAdvances in high-throughput RNA sequencing (RNA-seq) allowed the identification of novel transcripts such as microRNAs (miRNA), long non-coding RNAs (lncRNAs), and circular RNAs (circRNA). circular RNAs have recently emerged as promising candidates for targeted therapy due to their circular structure that confers resistance to exonucleases, their capability to regulate gene expression by modulating miRNA activity, sequester proteins by acting as protein sponges, C_LIO_LISeveral studies identified circRNAs to be differentially expressed following myocardial infarction (MI) and to play a role in immunity by contributing to the process of macrophage polarization, appropriate activation of macrophages when exposed to LPS, and inhibition of macrophage biogenesis. However, there are currently no published studies into the role of circular RNAs in the regulation of macrophage plasticity during cardiac injury. C_LI What New information Does This Article Contribute?O_LIWe provide evidence that circ-cdr1as expression is downregulated in the heart 3 days post MI and specifically in cardiomyocytes and macrophages. C_LIO_LIOur study provides promising evidence that overexpression of circ-cdr1as may be cardioprotective by reducing cardiomyocyte apoptosis, enhancing angiogenesis, limiting infarct size, increasing percentage of anti-inflammatory macrophages, and overall preserving post-MI cardiac function. C_LIO_LIMechanistically, we identified a reciprocal relationship between circ-cdr1as and miR-7 at 3 days post-MI and in naive, pro-, and anti-inflammatory macrophages indicating circ-cdr1as role as a miRNA sponge. This suggests that circ-cdr1as/miR-7/Klf4 play a crucial role in cardiac injury and macrophage phenotype. C_LI

cell biology↗

bioRxiv2024

Local Synthesis of Reticulon-1C Lessens the Outgrowth of Injured Axons by Controlling Spastin Activity

The regenerative potential of developing cortical axons depends on intrinsic mechanisms, such as axon-autonomous protein synthesis, that are still not fully understood. An emerging factor in this regenerative response is the bi-directional interplay between microtubule dynamics and the axonal endoplasmic reticulum (ER). We hypothesize that locally synthesized ER proteins regulate microtubule dynamics and the regeneration of cortical axons. RNA data-mining identified the ER-shaping protein Reticulon-1 as a relevant candidate across eight axonal transcriptomes. Using microfluidic chambers, we demonstrate that local knockdown of Reticulon-1 synthesis increases the outgrowth of injured cortical axons while reducing their distal tubulin levels. Furthermore, we show by live-cell imaging that axonal Reticulon-1 knockdown restores the microtubule growth rate and track length modified by injury. Interestingly, local inhibition of the microtubule- severing protein Spastin prevents the axonal knockdown-mediated effects over outgrowth and tubulin levels. We demonstrate that the Reticulon-1C isoform is locally synthesized within axons and support its isoform-specific role in attenuating Spastin-mediated microtubule severing. These findings uncover a mechanism by which axonal protein synthesis finely controls microtubule dynamics and outgrowth upon injury.

neuroscience↗

bioRxiv2024

Weighted Ensemble Approach for Knowledge Graph completion improves performance

This study introduces a weighted ensemble method called "WeightedKgBlend" for link prediction in knowledge graphs which combines the predictive capabilities of two types of Knowledge Graph completion methods: knowledge graph embedding and path based reasoning. By dynamically assigning weights based on individual model performance, WeightedKgBlend surpasses standalone methods, demonstrating superior predictive accuracy when tested to discover drug-disease candidates over a large-scale biomedical knowledge graph called Mechanistic Repositioning Network. This research highlights the efficacy of an integrated approach combining multiple methods in drug discovery, showcasing improved performance and the potential for transformative insights in the realm of biomedical knowledge discovery.

bioinformatics↗

bioRxiv2024

Podoplanin Positive Cell-derived Extracellular Vesicles Contribute to Cardiac Amyloidosis After Myocardial Infarction

BackgroundAmyloidosis is a major long-term complication of chronic disease; however, whether it represents one of the complications of post-myocardial infarction (MI) is yet to be fully understood. MethodsUsing wild-type and knocked-out MI mouse models and characterizing in vitro the exosomal communication between bone marrow-derived macrophages and activated mesenchymal stromal cells (MSC) isolated after MI, we investigated the mechanism behind Serum Amyloid A 3 (SAA3) protein overproduction in injured hearts. ResultsHere, we show that amyloidosis occurs after MI and that amyloid fibers are composed of macrophage-derived SAA3 monomers. SAA3 overproduction in macrophages is triggered by exosomal communication from a subset of activated MSC, which, in response to MI, acquire the expression of a platelet aggregation-inducing type I transmembrane glycoprotein named Podoplanin (PDPN). Cardiac MSCPDPN+ communicate with and activate macrophages through their extracellular vesicles or exosomes. Specifically, MSCPDPN+ derived exosomes (MSCPDPN+ Exosomes) are enriched in SAA3 and exosomal SAA3 protein engages with Toll-like receptor 2 (TRL2) on macrophages, triggering an overproduction and impaired clearance of SAA3 proteins, resulting in aggregation of SAA3 monomers as rigid amyloid deposits in the extracellular space. The onset of amyloid fibers deposition alongside extra-cellular-matrix (ECM) proteins in the ischemic heart exacerbates the rigidity and stiffness of the scar, hindering the contractility of viable myocardium and overall impairing organ function. Using SAA3 and TLR2 deficient mouse models, we show that SAA3 delivered by MSCPDPN+ exosomes promotes post-MI amyloidosis. Inhibition of SAA3 aggregation via administration of a retro-inverso D-peptide, specifically designed to bind SAA3 monomers, prevents the deposition of SAA3 amyloid fibrils, positively modulates the scar formation, and improves heart function post-MI. ConclusionOverall, our findings provide mechanistic insights into post-MI amyloidosis and suggest that SAA3 may be an attractive target for effective scar reversal after ischemic injury and a potential target in multiple diseases characterized by a similar pattern of inflammation and amyloid deposition. NOVELTY AND SIGNIFICANCEWhat is known? O_LIAccumulation of rigid amyloid structures in the left ventricular wall impairs ventricle contractility. C_LIO_LIAfter myocardial infarction cardiac Mesenchymal Stromal Cells (MSC) acquire Podoplanin (PDPN) to better interact with immune cells. C_LIO_LIAmyloid structures can accumulate in the heart after chronic inflammatory conditions. C_LI What information does this article contribute? O_LIWhether accumulation of cumbersome amyloid structures in the ischemic scar impairs left ventricle contractility, and scar reversal after myocardial infarction (MI) has never been investigated. C_LIO_LIThe pathophysiological relevance of PDPN acquirement by MSC and the functional role of their secreted exosomes in the context of post-MI cardiac remodeling has not been investigated. C_LIO_LIAmyloid structures are present in the scar after ischemia and are composed of macrophage-derived Serum Amyloid A (SAA) 3 monomers, although mechanisms of SAA3 overproduction is not established. C_LI SUMMARY OF NOVELTY AND SIGNIFICANCEHere, we report that amyloidosis, a secondary phenomenon of an already preexisting and prolonged chronic inflammatory condition, occurs after MI and that amyloid structures are composed of macrophage-derived SAA3 monomers. Frequently studied cardiac amyloidosis are caused by aggregation of immunoglobulin light chains, transthyretin, fibrinogen, and apolipoprotein in a healthy heart as a consequence of systemic chronic inflammation leading to congestive heart failure with various types of arrhythmias and tissue stiffness. Although chronic MI is considered a systemic inflammatory condition, studies regarding the possible accumulation of amyloidogenic proteins after MI and the mechanisms involved in that process are yet to be reported. Here, we show that SAA3 overproduction in macrophages is triggered in a Toll-like Receptor 2 (TLR2)-p38MAP Kinase-dependent manner by exosomal communication from a subset of activated MSC, which, in response to MI, express a platelet aggregation-inducing type I transmembrane glycoprotein named Podoplanin. We provide the full mechanism of this phenomenon in murine models and confirm SAA3 amyloidosis in failing human heart samples. Moreover, we developed a retro-inverso D-peptide therapeutic approach, "DRI-R5S," specifically designed to bind SAA3 monomers and prevent post-MI aggregation and deposition of SAA3 amyloid fibrils without interfering with the innate immune response.

immunology↗