Biology subjects

Navarrete, M.

Publications and source records attributed to Navarrete, M..

14 recordsLinked to original sources

bioRxiv2026

APOE 4/4 promotes dysfunctional and inflammatory phenotypes concomitant with impaired maturation of hiPSC-derived astrocytes

Alzheimer's disease (AD) is the leading cause of dementia in the aging population, with the {varepsilon}4 allele of apolipoprotein E (APOE) being the strongest genetic risk factor. Although astrocytes are a major source of APOE, how APOE alleles affect astrocyte maturation and function remains unclear. We generated human induced pluripotent stem cell (hiPSC)-derived astrocytes from AD patients carrying {varepsilon}3/{varepsilon}3 and {varepsilon}4/{varepsilon}4 alleles and from healthy controls (HC). We also used isogenic gene-edited hiPSC lines homozygous for each APOE allele and an APOE knock-out line to identify allele-specific phenotypes and distinguish gain- from loss-of-function mechanisms. APOE 4/4 astrocyte cultures showed significant reductions in GFAP- and S100{beta}-positive cell percentages compared to APOE 2/2 and APOE 3/3, with no changes in GLT-1- and AQP4-positive cells. Astrocytes of all genotypes responded to IL-1{beta} + TNF by increasing proinflammatory cytokine expression and release, and to both IL-1{beta} + TNF and A{beta}1-42 by changing morphology, with APOE 4/4 astrocytes showing increased IL6 mRNA and morphological branching upon IL-1{beta} + TNF stimulation. Notably, under basal conditions, APOE 4/4 astrocytes showed significant reductions in glutamate uptake capacity and cell size alongside increased IL-6 release and CXCL3 mRNA expression. In A{beta}1-42 uptake experiments, the proportion of A{beta}+ astrocytes was higher in APOE 4/4 than in APOE KO cultures. Most phenotypes were absent in APOE KO astrocytes, suggesting that the effects of APOE 4/4 were predominantly mediated through gain-of-function mechanisms. Our results indicate that APOE 4/4 alters astrocyte morphological and molecular maturation while promoting inflammation, disturbing glutamate and A{beta} handling under basal conditions. It suggests that APOE {varepsilon}4/{varepsilon}4 genotype disrupts astrocyte development and key processes of cellular homeostasis early in Alzheimer's disease etiopathology.

neuroscience↗

bioRxiv2026

Data-Centric Evaluation of Protein Function Prediction Pipelines

Performance estimates in protein function prediction depend not only on model choice but also on upstream decisions that define the learning problem. Using antioxidant protein classification as a controlled case study, we evaluated how dataset harmonisation, protein representation, redundancy control, and partitioning strategy affect protein machine learning pipelines. We integrated 18,804 records from 12 publicly available dataset entries into a curated consensus dataset of 4,193 protein sequences. One-hot encoding and six pretrained protein language model representations were evaluated as model inputs and as similarity spaces for redundancy reduction and distance-aware splitting. Representation choice substantially altered dataset geometry, retained dataset size, class balance, and downstream evaluation. At representation-specific p90 thresholds, one-hot encoding retained the complete dataset, whereas pretrained embeddings retained between 5% and 25% of sequences. Distance-aware partitioning reduced apparent performance relative to random splitting by up to 0.15 MCC before redundancy control, while this difference narrowed after similarity filtering. Selected configurations nevertheless maintained high performance under stricter evaluation, reaching an MCC of 0.84. These findings show that performance estimates should be interpreted as outcomes of complete data-centric workflows rather than isolated properties of predictive models.

bioinformatics↗

bioRxiv2026

MAOMAO: An Ontology-Guided FAIR Resource for Harmonized Peptide Toxicity Data

Peptide toxicity is a critical safety and developability parameter in peptide discovery and therapeutic development, yet relevant information remains fragmented across databases, literature resources, and curated datasets. Here, we present MAOMAO, an ontology-guided FAIR-oriented resource that integrates and harmonizes peptide toxicity data from 54 sources. MAOMAO contains 71,701 unique peptide sequences across seven toxicity-related endpoints, represented as 501,907 sequence endpoint combinations with endpoint-specific evidence states and explicit encoding of unavailable information. The resource combines standardized terminology, a hierarchical toxicity vocabulary, evidence-aware state resolution, provenance-aware metadata, 41 physicochemical descriptors, 10 protein language model representations, and a one-hot baseline. It provides endpoint-specific benchmark partitions across splitting strategies and random seeds, reusable with numerical representations. MAOMAO establishes a reusable framework for peptide toxicity research and data-driven toxicology.

pharmacology and toxicology↗

bioRxiv2025

A post-transcriptional regulatory checkpoint controls the response of tumor-infiltrating cytotoxic CD4+ T cells to immunotherapy

Acquisition of cytotoxic activity in CD4+ T cells (TCTX) can promote potent anti-tumor activity thus holding promise as a therapeutic approach. However, how this activity is regulated remains poorly understood. Here, we demonstrate that tumor-infiltrating CD4+ TCTX activity is restrained by a post-transcriptional regulatory checkpoint. In untreated tumors, CD4+ TCTX exist in a poised state, characterized by abundant Gzmb mRNA but limited Granzyme B (GzmB) protein. Differentiation into poised TCTX is regulated by the Blimp-1-Bcl6 axis and requires type-I interferon signaling. Treatment with anti-CTLA-4 or anti-LAG-3 plus anti-PD-1 removed the block to GzmB protein production by repressing expression of the post-transcriptional regulator Zfp36l1. Constitutive Zfp36l1 expression abrogated the effects of anti-CTLA-4 while deletion of Zfp36l1 and its paralog Zfp36 triggered GzmB protein production and promoted tumor control. These data identify ZFP36/ZFP36L1 as a key post-transcriptional regulatory checkpoint of CD4+ TCTX activity and a potential immunotherapy target in cancer.

immunology↗

bioRxiv2025

Synthesis errors in oligonucleotides are propagated into the genome by homology-directed repair

Single-stranded oligonucleotides (ssODNs) are used as donor templates for therapeutic gene editing by CRISPR-Cas9 cleavage and homology-directed repair (HDR). Although ssODN sequence fidelity is critical to the safety and efficacy of editing, standard quality control methods cannot resolve individual nucleotide errors. By deep sequencing ssODNs from three manufacturers, and amplicons from edited hematopoietic stem/progenitor cells, we find that synthesis errors are present in all ssODNs tested at rates that vary more than two-fold among manufacturers, at positions that are dependent on sequence context. These synthesis errors are propagated into the genome by HDR at frequencies proportional to their abundance in the ssODN. In our sickle cell mutation correction protocol, the most prevalent SNEs are predicted to produce benign {beta}-globin variants, while the less frequent frameshift deletions will generate {beta}-thalassemia alleles. Current quality control standards are insufficient to detect these errors, and deep sequencing of ssODNs should be incorporated into regulatory submissions for clinical gene editing programs.

genomics↗

bioRxiv2024

Peptipedia v2.0: A peptide sequence database and user-friendly web platform. A major update

In recent years, peptides have gained significant relevance due to their therapeutic properties. The surge in peptide production and synthesis has generated vast amounts of data, enabling the creation of comprehensive databases and information repositories. Advances in sequencing techniques and artificial intelligence have further accelerated the design of tailor-made peptides. However, leveraging these techniques requires versatile and continuously updated storage systems, along with tools that facilitate peptide research and the implementation of machine learning for predictive systems. This work introduces Peptipedia v2.0, one of the most comprehensive public repositories of peptides, supporting biotechnological research by simplifying peptide study and annotation. Peptipedia v2.0 has expanded its collection by over 45% with peptide sequences that have reported biological activities. The functional biological activity tree has been revised and enhanced, incorporating new categories such as cosmetic and dermatological activities, molecular binding, and anti-ageing properties. Utilizing protein language models and machine learning, more than 90 binary classification models have been trained, validated, and incorporated into Peptipedia v2.0. These models exhibit average sensitivities and specificities of 0.877 {+/-} 0.0530 and 0.873 {+/-}0.054, respectively, facilitating the annotation of more than 3.6 million peptide sequences with unknown biological activities, also registered in Peptipedia v2.0. Additionally, Peptipedia v2.0 introduces description tools based on structural and ontological properties and user-friendly machinelearning tools to facilitate the application of machine-learning strategies to study peptide sequences. Peptipedia v2.0 is accessible under the Creative Commons CC BY-NC-ND 4.0 license at https://peptipedia.cl/.

bioinformatics↗

bioRxiv2024

Candida glabrata maintains two Hap1 homologs, Zcf27 andZcf4, for distinct roles in ergosterol gene regulation to mediate sterol homeostasis under azole and hypoxic conditions

Candida glabrata exhibits innate resistance to azole antifungal drugs but also has the propensity to rapidly develop clinical drug resistance. Azole drugs, which target Erg11, is one of the three major classes of antifungals used to treat Candida infections. Despite their widespread use, the mechanism controlling azole-induced ERG gene expression and drug resistance in C. glabrata has primarily revolved around Upc2 and/or Pdr1. In this study, we determined the function of two zinc cluster transcription factors, Zcf27 and Zcf4, as direct but distinct regulators of ERG genes. Our phylogenetic analysis revealed C. glabrata Zcf27 and Zcf4 as the closest homologs to Saccharomyces cerevisiae Hap1. Hap1 is a known zinc cluster transcription factor in S. cerevisiae in controlling ERG gene expression under aerobic and hypoxic conditions. Interestingly, when we deleted HAP1 or ZCF27 in either S. cerevisiae or C. glabrata, respectively, both deletion strains showed altered susceptibility to azole drugs, whereas the strain deleted for ZCF4 did not exhibit azole susceptibility. We also determined that the increased azole susceptibility in a zcf27{Delta} strain is attributed to decreased azole-induced expression of ERG genes, resulting in decreased levels of total ergosterol. Surprisingly, Zcf4 protein expression is barely detected under aerobic conditions but is specifically induced under hypoxic conditions. However, under hypoxic conditions, Zcf4 but not Zcf27 was directly required for the repression of ERG genes. This study provides the first demonstration that Zcf27 and Zcf4 have evolved to serve distinct roles allowing C. glabrata to adapt to specific host and environmental conditions. IMPORTANCEInvasive and drug-resistant fungal infections pose a significant public health concern. Candida glabrata, a human fungal pathogen, is often difficult to treat due to its intrinsic resistance to azole antifungal drugs and its capacity to develop clinical drug resistance. Therefore, understanding the pathways that facilitate fungal growth and environmental adaptation may lead to novel drug targets and/or more efficacious antifungal therapies. While the mechanisms of azole resistance in Candida species have been extensively studied, the roles of zinc cluster transcription factors, such as Zcf27 and Zcf4, in C. glabrata have remained largely unexplored until now. Our research shows that these factors play distinct yet crucial roles in regulating ergosterol homeostasis under azole drug treatment and oxygen-limiting growth conditions. These findings offer new insights into how this pathogen adapts to different environmental conditions and enhances our understanding of factors that alter drug susceptibility and/or resistance.

genetics↗

bioRxiv2023

A spatial threshold for astrocyte calcium surge

Astrocytes are active cells involved in brain function through the bidirectional communication with neurons, in which the astrocyte calcium signal plays a crucial role. Synaptically-evoked calcium increases can be localized to independent subcellular domains or expand to the entire cell, i.e., calcium surge. In turn, astrocytes may regulate individual synapses by calcium-dependent release of gliotransmitters. Because a single astrocyte may contact [~]100,000 synapses, the control of the intracellular calcium signal propagation may have relevant consequences on brain function by regulating the spatial range of astrocyte neuromodulation of synapses. Yet, the properties governing the spatial dynamics of the astrocyte calcium signal remains poorly defined. Imaging subcellular responses of cortical astrocytes to sensory stimulation in mice, we show that sensory-evoked astrocyte calcium responses originated and remained localized in domains of the astrocytic arborization, but eventually propagated to the entire cell if a spatial threshold of >23% of the arborization being activated was surpassed. Using transgenic IP3R2-/- mice, we found that type-2 IP3 receptors were necessary for the generation of the astrocyte calcium surge. We finally show using in situ electrophysiological recordings that the spatial threshold of the astrocyte calcium signal consequently determined the gliotransmitter release. Present results reveal a fundamental property of astrocyte calcium physiology, i.e., a spatial threshold for the astrocyte intracellular calcium signal propagation, which depends on astrocyte intrinsic properties and governs the astrocyte integration of local synaptic activity and the subsequent neuromodulation. One-Sentence SummaryThere is a spatial threshold for the astrocyte intracellular calcium signal propagation that is determined by astrocyte intrinsic properties and controls gliotransmission.

neuroscience↗

bioRxiv2023

Astrocytic Foxo1 regulates hippocampal spinogenesis and synaptic plasticity to enhance fear memory

Astrocytes are active players in brain circuits, sensing and responding to neuronal activity, impacting behavior production. Activation of astrocytes triggers intracellular calcium elevations displaying complex spatiotemporal properties. Intracellular calcium activity is thought to underlie synaptic transmission, metabolism, and brain homeostasis modulation. However, the calcium-dependent signaling pathways involved in these processes are poorly understood, representing a critical knowledge gap in this field. To reveal calcium-dependent signaling pathways involved in circuit structure and function, we performed a multi-level analysis of the inositol 1,4,5-triphosphate receptor type 2 knockout (IP3R2 KO) mouse model which lacks somatic calcium elevations specifically in astrocytes. We focused on the hippocampus, a brain region responsible for cognitive function and emotional behaviors. The transcriptomic analysis of hippocampal tissue revealed that the lack of astrocytic somatic calcium causes the differential expression of hundreds of genes. Among these, 76 genes are regulated by the astrocyte-specific Foxo1 transcription factor. This transcription factor is over-expressed in the hippocampal astrocytes of this mouse model and regulates the expression of genes involved in spinogenesis and synaptic coverage. A detailed morphological analysis of hippocampal pyramidal neurons revealed dendrites with a shift to a more immature spine profile. This spine profile shift may underlie previously described a reduction of long-term depression and performance in fear memory tasks observed in this mouse model. Indeed, we confirmed that these mice lacking astrocytic somatic calcium display an enhancement of long-term fear memory. To verify a causal relationship between these structural, synaptic, and behavioral observations, we used a viral approach to induce the over-expression of Foxo1 in hippocampal astrocytes in naive C57BL/6J mice. This viral-driven over-expression of Foxo1 in astrocytes of the stratum radiatum replicated the shift to an immature spine profile in dendrites of pyramidal neurons crossing the territory of these astrocytes and led to a reduction of long-term depression in the same region. Finally, this manipulation was sufficient to enhance long-term fear memory. The detailed characterization of the mouse model lacking astrocytic somatic calcium revealed that astrocytes modulate hippocampal circuit structure and function through Foxo1 signaling to enhance fear memory.

neuroscience↗

bioRxiv2022

Response of sleep slow oscillations to acoustic stimulation is evidenced by distinctive synchronization processes

Closed loop acoustic stimulation (CLAS) during sleep has shown to boost slow wave (SW) amplitude and spindle power. Moreover, sleep SW are suggested to be classified based on different processes of neuronal synchronization. Following this, different types of SW events may have distinct functional roles and be differentially affected by external stimuli. However, the SW synchronization processes affected by CLAS are not well understood. Here, we studied the effect of CLAS on the dissociation of SW events based on two features of neuronal synchronization in the EEG (topological spread and wave slope). We evaluated and classified individual SW events of fourteen healthy subjects during a CLAS stimulated (STM) and a control night (CNT). Three main categories of SW events were found denoting (C1) steep-slope SW with global spread, (C2) flat-slope waves with localized spread and homeostatic regulation, and (C3) multipeaked flat-slope events with global spread. Comparing between conditions, we found a consistent increase of event proportion and trough amplitudes for C1 events during the time of stimulation. Furthermore, we found similar increases in post-stimulus spectral power in {theta}, {beta} and {sigma} frequencies for CNT vs STIM condition independently of sleep stage or SW categories. However, topological analysis showed differentiated spatial dynamics in N2 and N3 for SW categories and the co-occurrence with spindle events. Our findings reveal the nature of post-stimulus SW and suggest that CLAS boosts SW amplitudes by increasing neuronal synchronization of wave troughs, leading thus the post-stimulus SW-spindle co-occurrence.

neuroscience↗

bioRxiv2022

Cueing motor memory reactivation during NREM sleep engenders learning-related changes in precuneus and sensorimotor structures

Memory reactivation during Non-Rapid Eye Movement (NREM) sleep is important for memory consolidation but it remains unclear exactly how such activity promotes the development of a stable memory representation. We used Targeted Memory Reactivation (TMR) in combination with longitudinal structural and functional MRI to track the evolution of a motor memory trace over 20 days. We show that repeated reactivation of motor memory during sleep leads to increased precuneus activation 24 h post-TMR. Interestingly, a decrease in precuneus activity over the next 10 days predicts longer-term cueing benefit. We also find both functional and structural changes in sensorimotor cortex in association with effects of TMR 20 days post-encoding. These findings demonstrate that TMR can engage precuneus in the short-term while also impacting on task-related structure and function over longer timescales.

neuroscience↗

bioRxiv2021

Ongoing neural oscillations predict the post-stimulus outcome of closed loop auditory stimulation during slow-wave sleep.

The large slow oscillation (SO, 0.5-2Hz) that characterises slow-wave sleep is crucial to memory consolidation and other physiological functions. Manipulating slow oscillations can enhance sleep and memory, as well as benefitting the immune system. Closed-loop auditory stimulation (CLAS) has been demonstrated to increase the SO amplitude and to boost fast sleep spindle activity (11-16Hz). Nevertheless, not all such stimuli are effective in evoking SOs, even if they are precisely phase-locked. Here, we studied whether it is possible to use ongoing activity patterns to determine which oscillations to stimulate in order to effectively enhance SOs or SO-locked spindle activity. To this end, we trained classifiers using the morphological characteristics of the ongoing SO, as measured by electroencephalography (EEG), to predict whether stimulation would lead to a benefit in terms of the resulting SO and spindle amplitude. Separate classifiers were trained using trials from spontaneous control and stimulated datasets, and we evaluated their performance by applying them to held-out data both within and across conditions. We were able to predict both when large SOs will occur spontaneously, and whether a phase-locked auditory click will effectively enlarge them with an accuracy of ~70%. We were also able to predict when stimulation would elicit spindle activity with an accuracy of ~60%. Finally, we evaluate the importance of the various SO features used to make these predictions. Our results offer new insight into SO and spindle dynamics and provide a new method for online optimisation of stimulation. HIGHLIGHTS- Random forest classifiers can predict spontaneous and stimulated SOs and spindle amplitudes. - Morphological wave features predicted the response of SOs and spindles to CLAS. - SO amplitude during the click is the main predictor for post-stimulus SO amplitude. - Prediction of spindle activity did not differ in accuracy for stimulated vs spontaneous data.

neuroscience↗

bioRxiv2020

Microglia-to-astrocyte communication modulates synaptic and cerebrovascular functions following traumatic brain injury

Background and purposeActivation of astrocytes contributes to synaptic remodeling, tissue repair and neuronal survival following traumatic brain injury (TBI). However, the mechanisms by which these cells interact to infiltrated inflammatory cells to rewire neuronal networks and repair brain functions remain poorly understood. Here, we explored how TLR4-induced astrocyte activation modified synapses and cerebrovascular integrity following TBI. Experimental approachWe used pharmacological and genetic approaches to determine how functional astrocyte alterations induced by activation of TLR4-pathway in inflammatory cells regulate synapses and neurovascular unit after TBI. For that, we used calcium imaging, immunofluorescence, flow cytometry, blood-brain barrier (BBB) integrity assessment and molecular and behavioral tools. Key resultsShortly after a TBI there is a recruitment of excitable and reactive astrocytes mediated by TLR4-pathway activation with detrimental effects on PSD-95/VGlut1 synaptic puncta, BBB integrity and neurological outcome. Pharmacological blockage of the TLR4-pathway with TAK242 partially reverted many of the observed effects. Synapses and BBB recovery after TAK242 administration were not observed in IP3R2-/- mice, indicating that effects of TLR4-inhibition depend on the subsequent astrocyte activation. In addition, TBI increased the astrocytic-protein thrombospondin-1 necessary to induce a synaptic recovery in a sub-acute phase. Conclusions and implicationsOur data demonstrate that TLR4-mediated signaling, most probably though microglia and/or infiltrated monocyte-astrocyte communication, plays a crucial role in the TBI pathophysiology and that its inhibition prevents synaptic loss and BBB damage accelerating tissue recovery/repair, which might represent a therapeutic potential in CNS injuries and disorders. Declaration of transparency and scientific rigourThis Declaration acknowledges that this paper adheres to the principles for transparent reporting and scientific rigour of preclinical research as stated in the BJP guidelines for Design & Analysis, Immunoblotting and Immunochemistry, and Animal Experimentation, and as recommended by funding agencies, publishers and other organisations engaged with supporting research. Bullet point summaryWhat is already known: O_LIAstrocytes and microglia participate in the early cerebral and synaptic response after traumatic brain injury. C_LIO_LITLR4 antagonism exerts neuroprotection in acute brain injuries. C_LI What this study adds: O_LIAcute astrocyte activation contributes to synaptic loss and BBB breakdown in the acute phase of TBI, and synaptic remodeling in the sub-acute phase. C_LIO_LIAstrocyte activation is mediated by microglia/infiltrating-monocytes activation through TLR4 receptors. C_LI Clinical significance: O_LIInhibition of astrocyte activation through TLR4 antagonism could be a promising option for TBI treatment. C_LI

neuroscience↗

bioRxiv2018

Oscillatory infrasonic modulation of the cochlear amplifier by selective attention

Evidence shows that selective attention to visual stimuli modulates the gain of cochlear responses, probably through auditory-cortex descending pathways. At the cerebral cortex level, amplitude and phase changes of neural oscillations have been proposed as a correlate of selective attention. However, whether sensory receptors are also influenced by the oscillatory network during attention tasks remains unknown. Here, we searched for oscillatory attention-related activity at the cochlear receptor in humans. We used an alternating visual/auditory selective attention task and measured electroencephalographic activity simultaneously to distortion product otoacoustic emissions (a measure of cochlear receptor-cell activity). In order to search for cochlear oscillatory activity, the otoacoustic emission signal, was included as an additional channel in the electroencephalogram analyses. This method allowed us to study dynamic changes of cochlear oscillations in the same range of frequencies (1-35 Hz) in which cognitive effects are commonly observed in electroencephalogram works. We found the presence of low frequency (<10 Hz) brain and cochlear amplifier oscillations during periods of selective attention to visual and auditory stimuli. Notably, switching between auditory and visual attention modulates the amplitude and the temporal order of brain and inner ear oscillations. These results extend the role of the oscillatory activity network during cognition in neural systems to the receptor level.

neuroscience↗