Biology subjects

Perez, P.

Publications and source records attributed to Perez, P..

15 recordsLinked to original sources

bioRxiv2026

ZBTB7B is a Master Regulator of Salivary Acinar Cell Function

Salivary glands exhibit transcriptional programs that distinguish them from other tissues, yet the upstream regulatory logic underlying these programs is not well defined. To identify transcription factors (TFs) that structure salivary identity, we generated RNA-seq and ATAC-seq from human major and minor salivary glands and inferred TF[->]TF regulatory edges from high-confidence chromatin footprints. ZBTB7B emerged as the most connected regulator across salivary samples. To locate regulatory regions associated with salivary-specific transcription, we trained hidden Markov models (HMMs) on chromatin accessibility across 4 Mbp windows surrounding salivary-specific and non-salivary-specific transcription start sites. The resulting chromatin states distinguished promoter-proximal openness from distal enhancer activity and identified salivary-specific enhancers enriched for ZBTB7B motifs. These enhancer states correlated strongly with expression of salivary genes, including AQP5, indicating that distal regulation contributes substantially to salivary transcriptional specificity. To assess the consequences of losing Zbtb7b, we performed single-cell RNA-seq and spatial transcriptomics on submandibular and parotid glands from Zbtb7b knockout mice. Knockout mice exhibited reduced salivary flow, shifts in acinar cell proportions, and the emergence of a neonate-like acinar population characterized by loss of canonical secreted proteins and increased expression of MHC class I genes. These transcriptional and cellular changes occurred despite preserved gland architecture, suggesting that Zbtb7b stabilizes adult acinar identity rather than supporting structural maintenance. Together, these data identify ZBTB7B as a master regulator of salivary transcriptional networks, acting through both promoter-proximal and enhancer-level mechanisms, and demonstrate that loss of Zbtb7b disrupts acinar identity and impairs salivary function.

genomics↗

bioRxiv2026

Pharmacogenetic manipulation of Locus coeruleus activity in monkeys demonstrates its role in cognitive effort

The noradrenergic nucleus locus coeruleus (LC) is involved in numerous cognitive functions. Its activation often enhances sensory and motor performance and its activity correlates with arousal, which altogether suggest a general role in the mobilization of resources for cognition and action. We recently showed its strong and specific implication in physical effort and indirect evidence suggest that it might also be involved in cognitive effort. To address this question directly, we used a pharmacogenetic approach in rhesus macaques to selectively and reversibly inhibit LC neurons in a cognitively challenging task. Two monkeys were injected with viral vectors expressing inhibitory DREADDs (hM4Di) specifically in noradrenergic LC neurons, allowing reversible suppression of LC activity via systemic administration of deschloroclozapine (DCZ, 0.1 mg/kg). A third monkey served as a control and only received DCZ injections. Monkeys performed a simple hole-board task in which they searched for food rewards (raisins) hidden in a 5x5 grid of wells. In the transparent condition, rewards were visible, requiring minimal cognitive effort. In the opaque condition, rewards were hidden, such that monkey had to rely upon working memory to avoid revisiting empty wells. Thus, performance in opaque condition required more cognitive effort. Behavioral analysis showed that LC inhibition had no effect on performance in the transparent condition. However, in the opaque condition, it significantly impaired performance by increasing errors (revisits), without affecting the total number of rewards obtained, response times, or overall motivation. Monkeys compensated the decrease in success rate by performing more trials, indicating reduced efficiency rather than disengagement. These findings demonstrate that the LC plays a critical causal role in mobilizing cognitive resources for a demanding task. This is in line with the idea that the noradrenergic system contributes broadly to cognitive control and effort, extending previous findings on its involvement in physical effort. Overall, the study provides strong evidence linking LC activity to cognitive effort regulation, thereby complementing non-invasive studies in humans.

neuroscience↗

bioRxiv2025

NK2R signaling governs intestinal lipid mobilization and mucosal inflammation

Neuropeptidergic control of lipid metabolism is conserved and increasingly implicated in metabolic diseases, but receptor-level mechanisms remain unclear. Here we identify the neurokinin-2 receptor (NK2R) as a central node linking tachykinin signals to intestinal lipid mobilization, epithelial composition, and mucosal inflammation. Across complementary genetic and pharmacological perturbations, modulation of NK2R drives bidirectional effects. Loss or blockade of NK2R increases postprandial triglyceridemia and expands intestinal lipid stores, whereas agonism suppresses chylomicron output, reduces adiposity, and improves glycemia in diet-induced obesity. Transcriptomic and cellular analyses indicate coordinated upregulation of lipid-metabolic programs with a concomitant dampening of immune pathways in the absence of NK2R, accompanied by sex-specific remodeling of secretory lineages and male-biased protection from colitis. NK2R signaling also shaped the fecal microbiota in a genotype- and diet-dependent manner, highlighting crosstalk among neuropeptide signaling, epithelial physiology, and host-microbe interactions. These findings position NK2R as a molecular switch for intestinal lipid handling and mucosal inflammation and suggest that NK2R-targeted agonists or antagonists could be deployed as context- and sex-dependent therapeutic strategies for metabolic disease and inflammatory bowel disease.

physiology↗

bioRxiv2024

The multimerization pathway of the glucocorticoid receptor

The glucocorticoid receptor (GR) is a leading drug target due to its anti-inflammatory and immunosuppressive roles. The functional oligomeric conformation of full-length GR (FL-GR), which is key for its biological activity, remains disputed. Here we present a new crystal structure of agonist-bound GR ligand-binding domain (GR-LBD) comprising eight copies of a non-canonical dimer. The biological relevance of this dimer for receptor multimerization in living cells has been verified by studying single-and double-point mutants of FL-GR in fluorescence microscopy (Number & Brightness) and transcriptomic analysis. Self-association of this GR-LBD basic dimer in two mutually exclusive assemblies reveals clues for FL-GR multimerization and activity in cells. We propose a model for the structure of multidomain GR based on our new data and suggest a detailed oligomerization pathway. This model reconciles all currently available structural and functional information and provides a more comprehensive understanding of the rare glucocorticoid resistance disorder (Chrousos syndrome).

biochemistry↗

bioRxiv2024

The Immunoregulatory Architecture of the Adult Oral Cavity

The immunoregulatory architecture of human oral tissues remains poorly defined despite their central role as barrier interfaces. We present the first integrated single-cell and dual-platform spatial-proteotranscriptomic atlas of oral tissues, profiling >250,000 single-cell transcriptomes and >4 million spatially-resolved cells across 13 niches. Using our AI-enabled AstroSuite (TACIT, Constellation, STARComm, hist2omics), we defined tissue cellular neighborhoods (TCNs) and multicellular interaction modules (MCIMs) in health, revealing peri-epithelial fibroblast-centered hubs enriched for effector cytokines. We harmonized eight fibroblast subtypes (universal, immune, peri-epithelial, peri-vascular, peri-neural, APC-like, stress-responsive, and myofibroblasts) with stress-responsive subtypes partitioning between mucosae (Type I) and glands (Type II). Spatial multiomics mapped receptor-ligand circuits and showed mucosal stress-responsive fibroblasts as immunoregulatory hubs. In chronic periodontitis, niche-aware integration of healthy and diseased datasets revealed rewiring of fibroblast phenotypes and ligand::receptor networks into interdigitated inflammatory and reparative niches. Disease neighborhoods exhibited fragmentation, expansion of MHC-I, MHC-II, and PD-L1 fibroblasts, and predicted spatial engagement with T cells at ectopic lymphoid structures. Drug2Cell analysis highlighted druggable stromal::immune networks. Together, this proteotranscriptomic atlas positions fibroblasts as central architects of structural immunity in human oral tissues and establishes a scalable framework for precision targeting of stromal::immune ecosystems across other barrier organs in health and chronic disease.

cell biology↗

bioRxiv2024

Spatial Deconvolution of Cell Types and Cell States at Scale Utilizing TACIT

Identifying cell types and states remains a time-consuming and error-prone challenge for spatial biology. While deep learning is increasingly used, it is difficult to generalize due to variability at the level of cells, neighborhoods, and niches in health and disease. To address this, we developed TACIT, an unsupervised algorithm for cell annotation using predefined signatures that operates without training data, using unbiased thresholding to distinguish positive cells from background, focusing on relevant markers to identify ambiguous cells in multiomic assays. Using five datasets (5,000,000-cells; 51-cell types) from three niches (brain, intestine, gland), TACIT outperformed existing unsupervised methods in accuracy and scalability. Integration of TACIT-identified cell with a novel Shiny app revealed new phenotypes in two inflammatory gland diseases. Finally, using combined spatial transcriptomics and proteomics, we discover under- and overrepresented immune cell types and states in regions of interest, suggesting multimodality is essential for translating spatial biology to clinical applications.

bioinformatics↗

bioRxiv2024

SARS-CoV-2 Infection of Salivary Glands Predisposes to Oral Candidiasis

Saliva contains antimicrobial peptides considered integral components of host innate immunity, and crucial for protection against colonizing microbial species. Most notable is histatin-5 which is exclusively produced in salivary glands with uniquely potent antifungal activity against the opportunistic pathogen Candida albicans. Recently, SARS-CoV-2 was shown to replicate in salivary gland acinar cells eliciting local immune cell activation. In this study, we performed mechanistic and clinical studies to investigate the implications of SARS-CoV-2 infection on salivary histatin-5 production and Candida colonization. Bulk RNA-sequencing of parotid salivary glands from COVID-19 autopsies demonstrated statistically significant decreased expression of histatin genes. In situ hybridization, coupled with immunofluorescence for co-localization of SARS-CoV-2 spike and histatin in salivary gland cells, showed that histatin was absent or minimally present in acinar cells with replicating viruses. To investigate the clinical implications of these findings, salivary histatin-5 levels and oral Candida burden in saliva samples from three independent cohorts of mild and severe COVID-19 patients and matched healthy controls were evaluated. Results revealed significantly reduced histatin-5 in SARS-CoV-2 infected subjects, concomitant with enhanced prevalence of C. albicans. Analysis of prospectively recovered samples indicated that the decrease in histatin-5 is likely reversible in mild-moderate disease as concentrations tended to increase during the post-acute phase. Importantly, salivary cytokine profiling demonstrated correlations between activation of the Th17 inflammatory pathway, changes in histatin-5 concentrations, and subsequent clearance of C. albicans in a heavily colonized subject. The importance of salivary histatin-5 in controlling the proliferation of C. albicans was demonstrated using an ex vivo assay where C. albicans was able to proliferate in COVID-19 saliva with low histatin-5, but not with high histatin-5. Taken together, the findings from this study provide direct evidence implicating SARS-CoV-2 infection of salivary glands with compromised oral innate immunity, and potential predisposition to oral candidiasis. AUTHOR SUMMARYSaliva contains antimicrobial peptides part of host innate immunity crucial for protection against colonizing microbial species. Most notable is the antifungal peptide histatin-5 produced in salivary glands cells. SARS-CoV-2 was shown to replicate in salivary gland cells causing tissue inflammation. In this study, we showed decreased expression of histatin genes in salivary glands from COVID-19 autopsies, and co-localization studies of SARS-CoV-2 spike and histatin revealed absence or minimal presence of histatin in acinar cells with replicating virus. To investigate the clinical implications of these findings, we conducted studies using saliva samples from subjects with mild to severe COVID-19, matched with healthy controls. Results revealed significantly reduced histatin-5 in SARS-CoV-2 infected subjects with enhanced prevalence of C. albicans. Prospective analysis indicated the decrease in histatin-5 is reversible in mild-moderate disease, and salivary cytokine profiling demonstrated activation of the Th17 inflammatory pathway. The importance of salivary histatin-5 in controlling the proliferation of C. albicans was demonstrated using an ex vivo assay where C. albicans was able to proliferate in saliva with low histatin-5, but not with high histatin-5. Collectively, the findings provide direct evidence implicating SARS-CoV-2 infection of salivary glands with compromised oral innate immunity and predisposition to oral candidiasis.

microbiology↗

bioRxiv2023

Polybacterial intracellular coinfection of epithelial stem cells in periodontitis

Periodontitis affects billions of people worldwide. To address interkingdom relationships of microbes and niche on periodontitis, we generated the first sin-gle-cell meta-atlas of human periodontium (34-sample, 105918-cell), harmo-nizing 32 annotations across 4 studies1-4. Highly multiplexed immunofluores-cence (32-antibody; 113910-cell) revealed spatial innate and adaptive immune foci segregation around tooth-adjacent epithelial cells. Sulcular and junctional keratinocytes (SK/JKs) within epithelia skewed toward proinflammatory phe-notypes; diseased JK stem/progenitors displayed altered differentiation states and chemotactic cytokines for innate immune cells. Single-cell metagenomics utilizing unmapped reads revealed 37 bacterial species. 16S and rRNA probes detected polybacterial intracellular pathogenesis ("co-infection") of 4 species within single cells for the first time in vivo. Challenging coinfected primary human SK/JKs with lipopolysaccharide revealed solitary and synergistic ef-fects. Coinfected single-cell analysis independently displayed proinflammatory phenotypes in situ. Here, we demonstrate the first evidence of polybacterial intracellular pathogenesis in human tissues and cells--potentially influencing chronic diseases at distant sites.

cell biology↗

bioRxiv2022

ABLs and TMKs are co-receptors for extracellular auxin

Extracellular perception of auxin, an essential phytohormone in plants, has been debated for decades. Auxin binding protein 1 (ABP1) physically interacts with quintessential transmembrane kinases (TMKs) and was proposed to act as an extracellular auxin receptor, but its role was disputed because abp1 knockout mutants lack obvious morphological phenotypes. Here we identified two new auxin-binding proteins, ABL1 and ABL2, that are localized to the apoplast and directly interact with the extracellular domain of TMKs in an auxin-dependent manner. Furthermore, functionally redundant ABL1 and ABL2 genetically interact with TMKs and exhibit functions that are overlapping with those of ABP1 as well as independent of ABP1. Importantly, the extracellular domain of TMK1 itself binds auxin and synergizes with either ABP1 or ABL1 in auxin binding. Thus, our findings discovered new auxin receptors ABL1 and ABL2 having functions overlapping with but distinct from ABP1 and acting together with TMKs as co-receptors for extracellular auxin.

plant biology↗

bioRxiv2022

Myosin II regulatory light chain phosphorylation and formin availability modulate cytokinesis upon changes in carbohydrate metabolism.

Cytokinesis, which achieves the separation of daughter cells after mitosis completion, relies in animal cells on a contractile actomyosin ring (CAR), made of actin and class II myosins, whose activity is heavily influenced by regulatory light chain (RLC) phosphorylation. However, in simple eukaryotes such as fission yeast Schizosaccharomyces pombe, regulation of CAR dynamics by RLC phosphorylation seems dispensable. We found that redundant phosphorylation at Ser35 of the S. pombe RLC homolog Rlc1 by the p21-activated kinases Pak1 and Pak2, modulates Myosin II Myo2 activity and becomes essential for cytokinesis and cell growth during respiration. Previously, we showed that the Stress Activated Protein Kinase Pathway (SAPK) MAPK Sty1 controls fission yeast CAR integrity by downregulating formin For3 levels (Gomez-Gil et al.,2020). Here we report that reduced availability of formin For3-nucleated actin filaments for the CAR is the main reason for the required control of myosin II contractile activity by RLC phosphorylation during respiration-induced oxidative stress. Hence, recovery of For3 levels with antioxidants bypasses the control of Myosin II function regulated by RLC phosphorylation to allow cytokinesis and cell proliferation during respiration. Therefore, a fine-tuned interplay between Myosin II function by Rlc1 phosphorylation and environmentally controlled actin filament availability is critical for a successful cytokinesis in response to a switch to a respiratory carbohydrate metabolism.

cell biology↗

bioRxiv2021

The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities

The glucocorticoid receptor (GR) is a ubiquitously expressed transcription factor that controls metabolic and homeostatic processes essential for life. Although numerous crystal structures of the GR ligand-binding domain (GR-LBD) have been reported, the functional oligomeric state of the full-length receptor, which is essential for its transcriptional activity, remains disputed. Here we present five new crystal structures of agonist-bound GR-LBD, along with a thorough analysis of previous structural work. Biologically relevant homodimers were identified by studying a battery of GR point mutants including crosslinking assays in solution and quantitative fluorescence microscopy in living cells. Our results highlight the relevance of non-canonical dimerization modes for GR, especially of contacts made by loop L1-3 residues such as Tyr545. Our work unveils likely pathophysiologically relevant quaternary assemblies of the nuclear receptor with important implications for glucocorticoid action and drug design.

biochemistry↗

bioRxiv2021

Stress-dependent inhibition of cell polarity through unbalancing the GEF/GAP regulation of Cdc42

Cdc42 rules cell polarity and growth in fission yeast. It is negatively and positively regulated by GTPase-activating proteins (GAPs) and by Guanine nucleotide Exchange factors (GEFs), respectively. Active Cdc42-GTP localizes to the poles, where it associates with numerous proteins constituting the polarity module. However, little is known about its down-regulation. We describe here that oxidative stress causes Sty1 kinase-dependent Cdc42 inactivation at cell poles. Both the amount of active Cdc42 at poles and cell length inversely correlate with Sty1 activity, explaining the elongated morphology of{Delta} sty1 cells. We have created stress-blinded cell poles by either eliminating two Cdc42 GAPs or through the constitutive tethering of a GEF to the cell tips, and biochemically demonstrate that Rga3 is a direct substrate of Sty1. We propose that stress-activated Sty1 promotes GTP hydrolysis and prevents GEF activity at the cell tips, thus leading to the inhibition of Cdc42 and polarized growth cessation.

cell biology↗

bioRxiv2020

Conscious processing of narrative stimuli synchronizes heart rate between individuals

Heart rate has natural fluctuations that are typically ascribed to autonomic function. Recent evidence suggests that conscious processing can affect the timing of the heartbeat. We hypothesized that heart rate is modulated by conscious processing and therefore dependent on attentional focus. To test this, we leverage the observation that neural processes can be synchronized between subjects by presenting an identical narrative stimulus. As predicted, we find significant inter-subject correlation of the heartbeat (ISC-HR) when subjects are presented with an auditory or audiovisual narrative. Consistent with the conscious processing hypothesis, we find that ISC-HR is reduced when subjects are distracted from the narrative, and that higher heart rate synchronization predicts better recall of the narrative. Finally, patients with disorders of consciousness who are listening to a story have lower ISC-HR, as compared to healthy individuals, and that individual ISC-HR might predict a patients prognosis.. We conclude that heart rate fluctuations are partially driven by conscious processing, depend on attentional state, and may represent a simple metric to assess conscious state in unresponsive patients.

neuroscience↗

bioRxiv2019

Combined behavioral and electrophysiological evidence for a direct cortical effect of prefrontal tDCS on disorders of consciousness

Severe brain injuries can lead to long-lasting disorders of consciousness (DoC) such as vegetative state/unresponsive wakefulness syndrome (VS/UWS) or minimally conscious state (MCS). While behavioral assessment remains the gold standard to determine conscious state, EEG has proven to be a promising complementary tool to monitor the effect of new therapeutics. Encouraging results have been obtained with invasive electrical stimulation of the brain, and recent studies identified transcranial direct current stimulation (tDCS) as an effective approach in randomized controlled trials. This non-invasive and inexpensive tool may turn out to be the preferred treatment option. However, its mechanisms of action and physiological effects on brain activity remain unclear and debated. Here, we stimulated 60 DoC patients with the anode placed over left-dorsolateral prefrontal cortex in a prospective open-label study. Clinical behavioral assessment improved in twelve patients (20%) and none deteriorated. This behavioral response after tDCS coincided with an enhancement of putative EEG markers of consciousness: in comparison with non-responders, responders showed increases of power and long-range cortico-cortical functional connectivity in the theta-alpha band, and a larger and more sustained P300 suggesting improved conscious access to auditory novelty. The EEG changes correlated with electric fields strengths in prefrontal cortices, and no correlation was found on the scalp. Taken together, this prospective intervention in a large cohort of DoC patients strengthens the validity of the proposed EEG signatures of consciousness, and is suggestive of a direct causal effect of tDCS on consciousness.

neuroscience↗

bioRxiv2018

Removal of the C6 vaccinia virus interferon-β inhibitor in the hepatitis C vaccine candidate MVA-HCV elicited in mice high immunogenicity in spite of reduced host gene expression

Hepatitis C virus (HCV) represents a major global health problem for which a vaccine is not available. MVA-HCV is a unique HCV vaccine candidate based in the modified vaccinia virus Ankara (MVA) vector expressing the nearly full-length genome of HCV genotype 1a that elicits broad and polyfunctional CD8+ T-cell responses in mice. With the aim to improve the immune response of MVA-HCV and due to the importance of interferon (IFN) in HCV infection, we deleted in MVA-HCV the vaccinia virus (VACV) C6L gene, encoding an inhibitor of IFN-{beta} that prevents activation of the transcription factors IRF3 and IRF7. The resulting vaccine candidate (MVA-HCV {Delta}C6L) expresses all HCV antigens and deletion of C6L had no effect on viral growth in permissive chicken cells. In human monocyte-derived dendritic cells, infection with MVA-HCV {Delta}C6L triggered severe down-regulation of IFN-{beta}, IFN-{beta}-induced genes and cytokines similarly to MVA-HCV, as defined by real-time PCR and microarray analysis. In infected mice both vectors had a similar profile of recruited immune cells and induced comparable levels of adaptive and memory HCV-specific CD8+ T-cells, mainly against p7+NS2 and NS3 HCV proteins, with a T cell effector memory (TEM) phenotype. Furthermore, antibodies against E2 were also induced. Overall, our findings showed that while these vectors had a profound inhibitory effect on gene expression of the host, they strongly elicited CD8+ T cell and humoral responses against HCV antigens. These observations add support to the consideration of these vectors as potential vaccine candidates against HCV.\n\nIMPORTANCEHepatitis C virus represents a global health problem with 71 million of people infected worldwide. While direct-acting antivirals agents can cure hepatitis C virus infection in most of patients, their high cost and the emergence of drug resistant variants make them not a feasible and affordable strategy to eradicate the virus. Therefore, a vaccine is an urgent goal that requires efforts in understanding the correlates of protection for hepatitis C virus clearance. Poxvirus vectors, in particular the attenuated modified vaccinia virus Ankara, are ideal as vaccine candidates due to their ability to induce both T and B cell immune responses against heterologous antigens and protection against a wide spectrum of pathogens. Here we describe the generation, genetics and immunogenicity elicited by MVA-HCV {Delta}C6L, a novel vaccine candidate for hepatitis C virus that expresses nearly all of hepatitis C proteins but lacks an IFN-{beta} inhibitor, the C6 vaccinia virus protein.

immunology↗