Biology subjects

Ruiz, S.

Publications and source records attributed to Ruiz, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Nitazoxanide activates BMP9-ALK1-SMAD signaling cascade and improves HHT vascular pathology

ObjectiveHereditary hemorrhagic telangiectasia (HHT) is a vascular genetic disorder caused by endothelial cell dysfunction and characterized by telangiectasias and arteriovenous malformations (AVMs). HHT results primarily from loss-of-function mutations affecting components of the BMP9-ALK1-ENG-SMAD signaling cascade, a pathway essential for endothelial quiescence and vascular homeostasis, and currently lacks a cure. Here, we investigated whether nitazoxanide, an orally bioavailable drug with extensive clinical use, can modulate endothelial signaling relevant to HHT. Approach and ResultsNitazoxanide treatment activated SMAD1/5/8 signaling and increased expression of the downstream target ID1 in endothelial cells, while concurrently inhibiting mTOR signaling, indicating a dual modulatory effect on pathways implicated in HHT pathogenesis. In vivo, nitazoxanide activated SMAD signaling in BMP9/10-immunoblocked mice and significantly reduced AVM formation and hypervascularization. Importantly, nitazoxanide restored SMAD1/5/8 activation and ID1 expression in patient-derived blood outgrowth endothelial cells harboring loss-of-function mutations in ALK1 or SMAD4, which exhibit impaired BMP signaling. ConclusionThese findings identify nitazoxanide as a pharmacological modulator capable of activating BMP-SMAD signaling while restraining mTOR activity, thereby overcoming key signaling defects in HHT endothelial cells. Collectively, our results highlight nitazoxanide as a promising therapeutic candidate to target endothelial dysfunction in HHT.

cell biology↗

bioRxiv2026

Senescence-directed nanotherapy ameliorates fibrosis and overcomes immune exclusion in cancer

Fibrotic remodeling of tissues and tumors establishes immunosuppressive microenvironments that drive organ dysfunction and, in cancer, limit response to immunotherapy. Senescent-like cells are conserved drivers of fibrosis and therapeutic targets, yet their functional heterogeneity complicates therapeutic intervention. Here, we show that P-selectin is expressed by a subset of senescent-like cells in fibrotic tissues and tumors. Leveraging fucoidan-based nanoparticles that bind P-selectin, we developed senescence-modulating nanoparticles (SMNPs) to selectively target these disease-associated states. SMNPs exerted potent antifibrotic and immunomodulatory effects while improving therapeutic index. Mechanistically, we identified a pathogenic, immunosuppressive macrophage population as a functional target in vivo. In fibrotic tumors, niche remodeling restored immune infiltration and sensitized tumors to immune-checkpoint-based therapies. These findings establish SMNPs as a generalizable strategy to target pathogenic senescent cell subsets across fibrosis and cancer.

cancer biology↗

bioRxiv2025

Galectin-3 is a Nanotherapeutic Target in Graft-versus-Host Disease Mediated Kidney Injury

Kidney injury is a frequent and serious complication of allogeneic hematopoietic cell transplantation (HCT), yet its pathophysiology remains poorly understood and effective treatments are lacking. Through analysis of kidney tissue from HCT recipients, we identified substantial acute tubular injury and T cell infiltration that correlated with extra-renal graft-versus-host disease (GVHD) severity, linking systemic alloreactivity and post-transplant renal pathology. In murine models, GVHD was similarly associated with acute kidney injury, renal Th1-type T cell infiltration, and hyperactivation of NF-{kappa}B and JAK-STAT signalling. Notably, galectin-3, a damage-associated lectin, was upregulated in both patient biopsies and experimental GVHD target organs. Leveraging this pathological feature, we engineered galectin-3-targeted lipid nanoparticles for tissue-specific delivery of ruxolitinib, an approved GVHD therapy. Galectin-3 upregulation was also identified in canonical acute GVHD target organs including the liver and intestinal tract, and nanoparticle-delivered ruxolitinib substantially enhanced renal function, reduced systemic GVHD, and minimized hematologic toxicity compared to conventional drug administration. Our findings demonstrate renal involvement in acute GVHD and establish a nanoparticle-based strategy for precision delivery of immunomodulatory therapies to affected tissues.

bioengineering↗

bioRxiv2025

An angiopoietin-2 vaccine improves arteriovenous malformation pathology in hereditary hemorrhagic telangiectasia mice

Hereditary hemorrhagic telangiectasia (HHT) is a genetic vascular disorder that causes systemic arteriovenous malformations (AVMs) associated with severe complications. Angiopoietin (ANG)-2 has been identified as a consistently upregulated secreted protein across various HHT models, and neutralizing ANG2 reduces AVMs in mice. ANG2 has thus emerged as a potential target for HHT treatment. Here, we report the development of a peptide vaccine (ANG2-P3:CRM197) that selectively targets ANG2 over ANG1 and tested its effectiveness in decreasing retinal AVMs in neonatal mice injected with BMP9/10 blocking antibodies, a model of HHT. Litter groups from female C57BL/6 mice immunized with ANG2-P3:CRM197 received injections of anti-BMP9/10 antibodies, and their retinas were examined for vascular pathology. The potential toxicity of the vaccine was evaluated in females 12 months post-immunization through echocardiography, basic metabolic panels, and lipid profiles. Circulating anti-ANG2 antibodies were detected in nursing neonates of vaccinated females, with antibody levels comparable between litters and their dams, indicating effective antibody transfer from the dams. A significant decrease in AVM number and size was observed in the retinas of pups exposed to ANG2-P3:CRM197 antibodies compared to unexposed pups. Arterial and venous diameters were normalized in the vaccinated pups retinas. The vaccinated females showed no abnormalities in cardiac, liver, or kidney functions. A vaccine strategy targeting ANG2 appears safe and improves AVM pathology in HHT mice. These findings further support the potential of inhibiting ANG2 as a viable approach for treating AVMs in HHT. KEY POINTSO_LIA peptide vaccine that targets ANG2 reduced AVM number and size, and normalized arterial and venous diameters in a mouse model of HHT. C_LIO_LIThe vaccine did not cause any abnormalities in cardiac, liver, or kidney functions, and thus appeared safe. C_LI

cell biology↗

bioRxiv2025

Highly pathogenic avian influenza (HPAI) in South America, 2022-2025: temporality, affected species, and the southwards expansion to the Antarctic region.

The H5N1 highly pathogenic avian influenza (HPAI) virus has caused severe global losses, reaching South America in 2022 and Antarctica in 2024. Here we synthesize outbreak reports submitted to the World Organization for Animal Health (WOAH) by South American countries and document the viruss unprecedented expansion into Antarctica, affecting wild birds, wild mammals, and domestic poultry. More than 6 million domestic birds died or were culled, mostly from commercial operations. Of the 11 South American countries that reported H5N1 to WOAH, 10 reported infections in wild birds, spanning 104 species, 59.62% of which are migratory and predominantly non-trans-equatorial. Marine mammal cases occurred after wild bird detections, with the South American sea lion (Otaria flavescens) most affected, and several Antarctic bird species with migratory behavior were also reported in South America. To complement outbreak data, we examined available genomic sequences through phylogenetic and time-calibrated Bayesian analyses, which revealed multiple introduction events, viral diversity across regions, and evidence of interspecies transmission dynamics. These findings highlight the extensive ecological reach of H5N1 in the Southern Hemisphere and underscore the urgent need for a One Health approach that strengthens wildlife and backyard-poultry surveillance while fostering coordinated regional action to control and prevent further spread of HPAI. IMPORTANCEThe arrival of H5N1 highly pathogenic avian influenza (HPAI) in South America has caused severe mortality in wild birds, marine mammals, and domestic poultry, and has recently expanded into Antarctica. Understanding how the virus entered and spread across the continent is essential for preparedness and response. Using phylogenetic and time-calibrated analyses, we identify three independent introductions into South America, estimate their temporal windows of entry, and document repeated spillover across species, including into marine mammals and humans. These findings provide novel resolution beyond previous reports and highlight the extensive inter-country connectivity of circulating viruses. The unprecedented detection of HPAI in Antarctica further illustrates the ecological risks posed by ongoing southward spread. Together, this analysis underscores the urgent need for integrated One Health surveillance that bridges wildlife, domestic animal, and human health systems to mitigate the future impacts of HPAI in the region.

microbiology↗

bioRxiv2025

PACS1 syndrome variant alters proteomic landscape of developing cortical organoids

PACS1 syndrome is a neurodevelopmental disorder (NDD) resulting from a unique de novo p.R203W variant in Phosphofurin Acidic Cluster Sorting protein 1 (PACS1). PACS1 encodes a multifunctional sorting protein required for localizing furin to the trans-Golgi network. Although few studies have started to investigate the impact of the PACS1 p.R203W variant, the mechanisms by which the variant affects neurodevelopment are still poorly understood. In recent years, autism spectrum disorder (ASD) patient-derived brain organoids have been increasingly used to identify pathogenic mechanisms and possible therapeutic targets. While most of these studies evaluate the mechanisms by which ASD-risk genes affect the transcriptome, studies considering the proteome are limited. Here, we examine the effect of PACS1 p.R203W on the proteomic landscape of brain organoids using tandem mass tag (TMT) mass-spectrometry. Time series analysis between PACS1(+/+) and PACS1(+/R203W) organoids uncovered several proteins with dysregulated abundance or phosphorylation status, including known PACS1 interactors. Although we observed low overlap between proteins with altered expression and phosphorylation, the resulting dysregulated processes converged. The presence of the PACS1 p.R203W variant accelerated the emergence of proteins related to synaptogenesis and impaired vesicle loading and recycling. The earlier presence of these proteins and their related processes could lead to defective and/or incomplete synaptic function. Key dysregulated proteins observed in PACS1(+/R203W) organoids have been associated with several neurological diseases, and many are classified as NDD-causative and ASD-risk genes. Our results highlight that proteomic analyses not only enhance our understanding of general NDD mechanisms by complementing transcriptomic studies, but could also uncover additional targets, and therefore facilitate therapy development.

neuroscience↗

bioRxiv2024

Clock genes period and timeless control synaptogenesis in Drosophila motor terminals

Some neurons undergo rhythmic morphological changes that persist in constant darkness and require the expression of clock genes. Flight motoneuron MN5, one of the best studied neurons of Drosophila melanogaster exhibits several examples of this type of circadian structural plasticity. During the morning, when the fly is active, synaptic boutons are larger than during the night when the fly is resting though more synaptic boutons and synapses are observed. Here, by comparing bouton numbers at different timepoints in normal flies and in flies carrying loss-of-function mutations in clock genes timeless (tim) or period (per), we investigate whether the rhythmic changes in numbers of boutons and synapses require the expression of these genes. Absence of tim expression abolished the rhythm in bouton number whereas absence of per expression appeared to increase the rhythms amplitude. This indicates that in normal flies TIM protein is necessary to drive the normal rhythm of bouton number and PER probably has a damping effect on it. In addition, it appears that tim and per expression normally act as inhibitor of synaptogenesis because their loss-of-function mutations caused over-proliferation of synapses. Unexpectedly, TIM and PER were expressed in different cells. TIM was found in the glial sheath wrapping the motoneurons axon and PER was predominantly found along the axon, suggesting that the control of the rhythmic change in bouton and synapse numbers requires interactions between different cell types.

neuroscience↗

bioRxiv2024

Illuminating root-soil mechanics

Soil compaction and escalating global drought increase soil strength and stiffness. It remains unclear which plant root biomechanical mechanisms/traits enable growth in these harsh conditions. Here, we combine synchrotron X-ray computed tomography with spatially resolved X-ray diffraction to characterize the biomechanics of a replica root-soil system. We map the strain field around the root tip, finding strong agreement with finite element simulations, thereby demonstrating a promising new in-vivo measurement protocol.

biophysics↗

bioRxiv2024

STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging

We introduce Single-Cell Transcriptomics Analysis and Multimodal Profiling (STAMP), a scalable profiling approach of individual cells. Leveraging transcriptomics and proteomics imaging platforms, STAMP eliminates sequencing costs, to enable single-cell genomics from hundreds to millions of cells at an unprecedented low cost. Stamping cells in suspension onto imaging slides, STAMP supports single-modal (RNA or protein) and multimodal (RNA and protein) profiling and flexible, ultra-high-throughput formats. STAMP allows the analysis of a single or multiple samples within the same experiment, enhancing experimental flexibility, throughput and scale. We tested STAMP with diverse sample types, including peripheral blood mononuclear cells (PBMCs), dissociated cancer cells and differentiated embryonic stem cell cultures, as well as whole cells and nuclei. Combining RNA and protein profiling, we applied immuno-phenotyping of millions of blood cells simultaneously. We also used STAMP to identify ultra-rare cell populations, simulating clinical applications to identify circulating tumor cells (CTCs). Performing in vitro differentiation studies, we further showed its potential for large-scale perturbation studies. Together, STAMP establishes a new standard for cost-effective, scalable single-cell analysis. Without the need for sequencing, STAMP makes high-resolution profiling more affordable and accessible. Designed to meet the needs of research labs, diagnostic cores and pharmaceutical companies, STAMP holds the promise to transform our capacity to map human biology, diagnose diseases and drug discovery.

genomics↗

bioRxiv2024

Cycling DOF Factor mediated seasonal regulation of sexual reproduction and cold response is not conserved in Physcomitrium patens

Many land plants have evolved such that the transition from vegetative to reproductive development is synchronized with environmental cues. Examples of reproduction in response to seasonal cues can be found in both vascular and nonvascular species; however, most of our understanding of the molecular events controlling this timing has been worked out in angiosperm model systems. While the organism-level mechanisms of sexual reproduction vary dramatically between vascular and nonvascular plants, phylogenetic and transcriptomic evidence suggest paralogs in nonvascular plants may have conserved function with their vascular counterparts (Holm et al. 2010; Zhao et al. 2019; Genau et al. 2021). Given that Physcomitrium patens undergoes sexual reproductive development in response to photoperiodic and cold temperature cues (Hohe et al. 2002), it is well-suited for studying evolutionarily conserved mechanisms of seasonal control of reproduction. Thus, we used publicly available microarray data to identify genes differentially expressed in response to temperature cues (Fernandez-Pozo et al. 2020). We identified two CDF-like (CDL) genes in the P. patens genome that are the most like the angiosperm Arabidopsis thaliana CDFs based on conservation of protein motifs and diurnal expression patterns. In angiosperms, DNA-One Finger Transcription Factors (DOFs) play an important role in regulating photoperiodic flowering, regulating physiological changes in response to seasonal temperature changes, and mediating the cold stress response (Imaizumi et al. 2005; Kloosterman et al. 2013; Fornara et al. 2015; Ridge et al. 2016; Ding et al. 2018; Blair et al. 2022). We created knockout mutations and tested their impact on sexual reproduction and response to cold stress. Unexpectedly, the timing of sexual reproduction in the ppcdl double mutants did not differ significantly from wild type, suggesting that the PpCDLs are not necessary for seasonal regulation of this developmental transition. We also found that there was no change in expression of downstream cold-regulated genes in response to cold stress and no change in freezing tolerance in the knockout mutant plants. Finally, we observed no interaction between PpCDLs and the partial homologs of FKF1, an Arabidopsis thaliana repressor of CDFs. This is different from what is observed in angiosperms (Fornara et al. 2009; Corrales et al. 2014; Song et al. 2016, Li et al. 2013; Han et al. 2015, Wang et al. 2023, Li et al. 2009), which suggests that the functions of CDF proteins in angiosperms are not conserved in P. patens.

plant biology↗

bioRxiv2024

Lineage-specific CDK activity dynamics characterize early mammalian development

Cyclin-dependent kinases (CDK) are key regulatory enzymes that regulate proliferation dynamics and cell fate in response to extracellular inputs. It remains largely unknown how CDK activity fluctuates and influences cell commitment in vivo during early mammalian development. Here, we generated a transgenic mouse model expressing a CDK kinase translocation reporter (KTR) that enabled quantification of CDK activity in live single cells. By examining pre- and post- implantation mouse embryos at different stages, we observed a progressive decrease in CDK activity in cells from the trophectoderm (TE) prior to implantation. This drop correlated with the establishment of an FGF4-dependent signaling gradient through the embryonic-abembryonic axis. Furthermore, we showed that CDK activity levels do not determine cell fate decisions during pre-implantation development. Finally, we uncovered the existence of conserved regulatory mechanisms in mammals by revealing lineage-specific regulation of CDK activity in TE-like human cells.

developmental biology↗

bioRxiv2023

Interpretable Inflammation Landscape of Circulating Immune cells

Inflammation is a biological phenomenon involved in a wide variety of physiological and pathological processes. Although a controlled inflammatory response is beneficial for restoring homeostasis, it can become unfavorable if dysregulated. In recent years, major progress has been made in characterizing acute and chronic inflammation in specific diseases. However, a global, holistic understanding of inflammation is still elusive. This is particularly intriguing, considering the crucial function of inflammation for human health and its potential for modern medicine if fully deciphered. Here, we leverage advances in the field of single-cell genomics to delineate the full spectrum of circulating immune cell activation underlying inflammatory processes during infection, immune-mediated inflammatory diseases and cancer. Our single-cell atlas of >6.5 million peripheral blood mononuclear cells from 1047 patients and 19 diseases allowed us to learn a comprehensive model of inflammation in circulating immune cells. The atlas expanded our current knowledge of the biology of inflammation of immune-mediated diseases, acute and chronic inflammatory diseases, infection and solid tumors, and laid the foundation to develop a precision medicine framework using unsupervised as well as explainable machine learning. Beyond a disease-centered analysis, we charted altered activity of inflammatory molecules in peripheral blood cells, depicting discriminative inflammation-related genes to further understand mechanisms of inflammation. Finally, we have laid the groundwork for developing precision medicine diagnostic tools for patients experiencing pathologic inflammation by learning a classifier for inflammatory diseases, presenting cells in circulation as a powerful resource for patient diagnosis.

immunology↗

bioRxiv2023

3D-intrusions transport active surface microbial assemblages to the dark ocean

Subtropical oceans contribute significantly to global primary production, but the fate of the picophytoplankton that dominate in these low nutrient regions is poorly understood. Working in the subtropical Mediterranean, we demonstrate that subduction of water at ocean fronts generates 3D intrusions with uncharacteristically high carbon, chlorophyll, and oxygen that extend below the sunlit photic-zone into the dark ocean. These contain "fresh" picophytoplankton assemblages that resemble the photic-zone regions where the water originated. Intrusions propagate depth-dependent seasonal variations in microbial assemblages into the ocean interior. Strikingly, the intrusions included dominant biomass contributions from non-photosynthetic bacteria and enrichment of enigmatic heterotrophic bacterial lineages. Thus, the intrusions not only deliver material that differs in composition and nutritional character from sinking detrital particles, but also drive shifts in bacterial community composition, organic matter processing, and interactions between surface and deep communities. Modeling efforts paired with global observations demonstrate that subduction can flux similar magnitudes of particulate organic carbon as sinking export, but is not accounted for in current export estimates and carbon cycle models. Intrusions formed by subduction are a particularly important mechanism for enhancing connectivity between surface and upper mesopelagic ecosystems in stratified subtropical ocean environments that are expanding due to the warming climate.

ecology↗

bioRxiv2023

CDK6-mediated endothelial cell cycle acceleration drives arteriovenous malformations in hereditary hemorrhagic telangiectasia

Increased endothelial cell (EC) proliferation is a hallmark of arteriovenous malformations (AVMs) in hereditary hemorrhagic telangiectasia (HHT). The underlying mechanism and disease relevance of this abnormal cell proliferative state of the ECs remain unknown. Here, we report the identification of a CDK6-driven mechanism of cell cycle progression deregulation directly involved in EC proliferation and HHT vascular pathology. Specifically, HHT mouse liver ECs exhibited defects in their cell cycle control characterized by a G1/S checkpoint bypass and acceleration of cell cycle speed. Phosphorylated retinoblastoma (p-RB1)--a marker of G1/S transition through the restriction point--significantly accumulated in ECs of HHT mouse retinal AVMs and HHT patient skin telangiectasias. Mechanistically, ALK1 loss of function increased the expression of key restriction point mediators, and treatment with palbociclib or ribociclib, two CDK4/6 inhibitors, blocked p-RB1 increase and retinal AVMs in HHT mice. Palbociclib also improved vascular pathology in the brain and slowed down endothelial cell cycle speed and EC proliferation. Specific deletion of Cdk6 in ECs was sufficient to protect HHT mice from AVM pathology. Thus, CDK6-mediated endothelial cell cycle acceleration controls EC proliferation in AVMs and is a central determinant of HHT pathogenesis. We propose that clinically approved CDK4/6 inhibitors have repurposing potential in HHT.

cell biology↗

bioRxiv2023

Detection and Phylogenetic Analysis of Highly Pathogenic A/H5N1 Avian Influenza Clade 2.3.4.4b Virus in Chile, 2022

Since the emergence of the Highly Pathogenic Avian Influenza H5N1 goose/Guangdong (Gs/GD) lineage in China in 1996, these viruses have spread globally. This includes the recent introduction of the Gs/GD lineage 2.3.4.4b in the Americas in 2021, which has affected both wild and domestic bird populations causing high mortality. Since November 2022, reports of mortality in wild birds in numerous South American countries along the Pacific Migratory Flyway have been attributed to this lineage. Through an ongoing longitudinal avian influenza virus (AIV) surveillance, we determined that AIV prevalence remained below 1% in the Lluta river wetland from August through October 2022. However, there was a significant increase in prevalence to 2.6% and 11.7% in November and December respectively, coinciding with the arrival of migratory birds from the Northern Hemisphere. Of the AIV RT-qPCR positive environmental feces samples 7 were identified as A/H5. Sequencing of the COI gene demonstrated that the H5 positive samples were obtained from Peruvian pelican (n=1), Franklins gull (n=1), Gray gull (n=1), Elegant tern (n=2) and Black skimmer (n=2). Full genomes were obtained from 3 samples and the putative cleavage site composition of the HA was polybasic REKRRKR/GLF for all. Phylogenetic analysis of the samples revealed them to belong to the H5 2.3.4.4b clade, closely related to isolates obtained in Peru in late November. The emergence of H5 clade 2.3.4.4b in South America has an immediate impact on public health, animal production and wildlife, hence increased active surveillance is warranted.

genetics↗

bioRxiv2022

Oxidative stress-induced MMP- and γ-secretase-dependent VE-cadherin processing is modulated by the proteasome and BMP9/10

Classical cadherins, including vascular endothelial (VE)-cadherin, are targeted by matrix metalloproteinases (MMPs) and {gamma}-secretase during adherens junction (AJ) disassembly, a mechanism that might have relevance for endothelial cell (EC) integrity and vascular homeostasis. Here, we show that oxidative stress triggered by H2O2 exposure induced efficient VE-cadherin proteolysis by MMPs and {gamma}-secretase in human umbilical endothelial cells (HUVECs). The cytoplasmic domain of VE-cadherin produced by {gamma}-secretase, VE-Cad/CTF2 - a fragment that has eluded identification so far - could readily be detected after H2O2 treatment. VE-Cad/CTF2, released into the cytosol, was tightly regulated by proteasomal degradation and was sequentially produced from an ADAM10/17-generated C-terminal fragment, VE-Cad/CTF1. Interestingly, BMP9 and BMP10, two circulating ligands critically involved in vascular maintenance, significantly reduced VE-Cad/CTF2 levels during H2O2 challenge, as well as mitigated H2O2-mediated actin cytoskeleton disassembly during VE-cadherin processing. Notably, BMP9/10 pretreatments efficiently reduced apoptosis induced by H2O2, favoring endothelial cell recovery. Thus, oxidative stress is a trigger of MMP- and {gamma}-secretase-mediated endoproteolysis of VE-cadherin and AJ disassembly from the cytoskeleton in ECs, a mechanism that is negatively controlled by the EC quiescence factors, BMP9 and BMP10.

cell biology↗

bioRxiv2022

The homeobox transcription factor DUXBL controls exit from totipotency

Upon exit from the totipotent 2-cell (2C) embryo stage, the 2C-associated transcriptional program needs to be efficiently silenced. However, the molecular mechanisms involved in this process remain mostly unknown. Here, we demonstrate that the 2C-specific transcription factor DUX directly induces the expression of DUXBL to promote this silencing. Indeed, DUX expression in Duxbl-knockout ESC causes increased induction of the 2C-transcriptional program, whereas DUXBL overexpression impairs 2C-associated transcription. CUT&RUN analyses show that DUXBL gains accessibility to DUX-bound regions in DUX-induced ESC while it is unable to bind those regions in uninduced cells. Mechanistically, we determined that DUXBL interacts with TRIM24 and TRIM33, two members of the tripartite motif superfamily involved in gene silencing and co-localizes with them in nuclear foci upon DUX expression. Furthermore, DUXBL downregulation in mouse zygotes leads to a penetrant 2C-stage arrest. Our data reveals an unexpected role for DUXBL in controlling the exit from totipotency.

developmental biology↗

bioRxiv2022

An Atlas of Cells in the Human Tonsil

Palatine tonsils are secondary lymphoid organs representing the first line of immunological defense against inhaled or ingested pathogens. Here, we present a comprehensive census of cell types forming the human tonsil by applying single-cell transcriptome, epigenome, proteome and adaptive immune repertoire sequencing as well as spatial transcriptomics, resulting in an atlas of >357,000 cells. We provide a glossary of 121 annotated cell types and states, and disentangle gene regulatory mechanisms that drive cells through specialized lineage trajectories. Exemplarily, we stratify multiple tonsil-resident myeloid slancyte subtypes, establish a distant BCL6 superenhancer as locally active in both follicle-associated T and B cells, and describe SIX5 as a potentially novel transcriptional regulator of plasma cell maturation. Further, our atlas is a reference map to understand alterations observed in disease. Here, we discover immune-phenotype plasticity in tumoral cells and microenvironment shifts of mantle cell lymphomas (MCL). To facilitate such reference-based analysis, we develop HCATonsilData and SLOcatoR, a computational framework that provides programmatic and modular access to our dataset; and allows the straightforward annotation of future single-cell profiles from secondary lymphoid organs.

immunology↗