Biology subjects

Perez, R.

Publications and source records attributed to Perez, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Systematic identification of DNA methylation biomarkers for tumor-type-specific detection

DNA methylation biomarkers for cancer diagnostics often underperform when tumor and background tissues share epigenetic programs, or when complex specimens with mixed cellular composition dilute tumor-derived signals and increase variability. To address these limitations, we developed a gene-centric, browser-based discovery platform that integrates genome-wide methylomes with matched transcriptomes and reference layers spanning pan-cancer tissues and leukocytes, enabling background-aware filtering beyond binary tumor-normal contrasts. Candidate loci are prioritized using combined thresholds on methylation effect size and intra-group variability to penalize stochastic and heterogeneous variation. In colorectal cancer, methylation-sensitive restriction enzyme quantitative PCR (MSRE-qPCR) validation in independent tissue cohorts confirmed multiple candidate loci with AUCs of 0.81-1.00. Using the same framework, MSRE-qPCR validation distinguished hepatocellular carcinoma from cirrhotic liver, and analysis of public tumor methylomes identified subtype-specific markers in lung adenocarcinoma and squamous-cell carcinoma. This resource bridges genome-scale epigenomic discovery with clinically accessible PCR-based methylation assays.

bioinformatics↗

bioRxiv2025

Caspase-11 Mediated Hyperinflammation Impairs CD8⁺ T Cell Immunity and Viral Clearance in Severe SARS-CoV-2 Infection

Severe SARS-CoV-2 infection is characterized by lung hyperinflammation, impaired interferon responses, and defective T-cell activation, yet the molecular drivers of these immune dysregulations remain incompletely understood. Caspase-11 (CASP11), a key mediator of the non-canonical inflammasome, has been shown to mediate an innate hyperinflammatory response and cytokine release in a non-severe, non-lethal SARS-CoV-2 infection model. However, the role played by CASP11 in severe SARS-CoV-2 disease and how it impacts adaptive immunity is not identified. Here, we newly discover that CASP11 exacerbates severe SARS-CoV-2 pathogenesis by amplifying early innate immune responses while concurrently impairing antiviral CD8 T-cell immunity. Using global knockouts, reciprocal bone marrow chimeras, and phagocyte-monocyte system (PMS) cell-specific CASP11 deletion models, we show that CASP11 deletion in monocyte-derived cells reduces lung inflammation, enhances type I and II interferon signaling, and promotes robust virus-specific effector CD8 T-cell response. This was associated with enhanced viral clearance and improved survival, even under lethal infection conditions. Importantly, CASP11 KO mice also exhibited faster resolution of post-viral inflammation, suggesting a role in long-term immune remodeling. These findings position CASP11 as a promising immunomodulatory target for acute and delayed manifestations of severe SARS-CoV-2.

microbiology↗

bioRxiv2025

Glycans modulate the adsorption of RBD Glycoproteins on polarizable surfaces

The complex interplay between glycans and protein conformational dynamics during adsorption onto polarizable surfaces opens several routes to exploring the glycans potential as molecular interactions modulators. Molecular simulations are able to dissect the interactions of Receptor Binding Domain (RBD) glycoproteins for different SARS-CoV-2 variants of concern (VoC), in both open and closed conformations, with polarizable planar interfaces. Advanced analysis projected on 2D revealed distinct adsorption mechanisms depending on the initial loci of the glycan within the protein wall. Hydrophobic surfaces facilitated stable adsorption for both RBD conformations. Conversely, hydrophilic surfaces exhibited reduced adsorption, particularly for the closed-RBD, where glycans predominantly formed hydrogen bonds. Glycans significantly modulated closed-RBD adsorption, either enhancing it by permanent tethering or impeding it depending on the two initial conformations and protein mutations (omicron). Results for the individual RBDs are shown to be consistent with simulations for the complete S1 spike glycoprotein. Our findings unveil novel glycan-mediated adsorption phenomena and provide fundamental insights into glycoprotein-surface interactions, paving the way for understanding glycan roles in protein aggregation and recognition at polarizable biological interfaces.

biophysics↗

bioRxiv2025

Multivalent Lipid MVL5 Micellar Nanoparticles Exhibit Dramatically Increased Loading of Paclitaxel with PEGylation Enhancing Human Cancer Cell Penetration Depth and Cytotoxicity

Cationic liposomes (CLs) with chain-melted fluid membranes are promising nanocarriers of hydrophobic drugs in cancer chemotherapy, including the frequently employed drug paclitaxel (PTX). CL formulations containing univalent N-[2,3-dioleoyloxy-1-propyl]trimethylammonium chloride (DOTAP), like EndoTAG-1TM, have shown limited success in clinical trials and challenges like endosomal entrapment, limited PTX membrane solubility, and difficulty with in vivo tumor targeting remain. Incorporation of 10 mol% cone-shaped poly(ethylene glycol)-lipid (PEG-lipid) to DOTAP-containing CLs transitions a fraction of the particles to micellar nanodiscs. These PTX--loaded PEGylated CLs and nanodiscs show enhanced cellular uptake in vitro and improved tumor penetration and proapoptotic activity compared to bare CLs in an in vivo solid breast cancer tumor model. Formulations incorporating the multivalent cationic lipid MVL5 (+5e) at 50 mol% form nanoparticles (NPs) comprised almost entirely of nanodiscs, and transition at 75 mol% MVL5 to short micellar rods coexisting with spheres, with rods further transitioning to long flexible rods upon PEGylation. Here, we report on the finding that MVL5-based micellar NPs with disc, rod, and spherical morphologies dramatically improve the solubility of PTX in their fluid lipid membranes by nearly three-fold compared to reference CLs modeled on the EndoTAG-1TM formulation. Cell viability assays revealed that this improved PTX solubility for MVL5 micellar NPs leads to improved cytotoxic efficacy, which is further improved by PEGylation. Remarkably, using fluorescent microscopy and image particle analysis, we find that the cellular uptake and penetration depth of MVL5 nanoparticles is significantly improved by PEGylation. The findings are consistent with a model where the rate-limiting step of PTX delivery by cationic lipid NPs is diffusion of endocytic vesicles containing NPs through the actin mesh near the cell surface combined with the hoping rate of PTX from endosomal membrane to nearby microtubules. PEGylated cationic lipid nanoparticles containing MVL5 therefore represent a very promising hydrophobic cancer drug delivery vehicle for nanomedicine applications.

bioengineering↗

bioRxiv2025

AI-based decoding of long covid cognitive impairments in mice using automated behavioral system and comparative transcriptomic analysis

Long COVID (LC) following SARS-CoV-2 infection affects millions of individuals world-wide and manifests with a variety of symptoms including cognitive dysfunction also known as "brain fog". This is characterized by difficulties in executive functions, planning, decision-making, working memory, impairments in complex attention, loss of ability to learn new skills and perform sophisticated brain tasks. No effective treatment options currently exist for LC-related cognitive dysfunction. Here, we use the IntelliCage, which is an automated tracking system of cognitive functions, following SARS-CoV-2 infection in mice, measuring the ability of each mouse within a group to perform tasks that mimic complex human behaviors, such as planning, decision-making, cognitive flexibility, and working memory. Artificial intelligence and machine learning analyses of the tracking data classified LC mice into distinct behavioral categories from non-infected control mice, permitting precise identification and quantification of complex cognitive dysfunction in a controlled, replicable manner. Importantly, we find that brains from LC mice with cognitive dysfunction exhibit transcriptomic alterations similar to those observed in humans suffering from LC-related cognitive impairments, including altered expression of genes involved in learning, executive functions, synaptic functions, neurotransmitters and memory. Together, our findings establish a validated murine model and an automated unbiased approach to study LC-related cognitive dysfunction for the first time, and providing a valuable tool for screening potential treatments and therapeutic interventions.

neuroscience↗

bioRxiv2025

2Danalysis: A toolbox for analysis of lipid membranes and biopolymers in two-dimensional space

Molecular simulations expand our ability to learn about the interplay of biomolecules. Biological membranes, composed of diverse lipids with varying physicochemical properties, are highly dynamic environments involved in cellular functions. Proteins, nucleic acids, glycans and bio-compatible polymers are the machinery of cellular processes both in the cytosol and at the lipid membrane interface. Lipid species directly modulate membrane properties, and affect the interaction and function of other biomolecules. Natural molecular diffusion results in changes of local lipid distribution, affecting the membrane properties. Projecting biophysical and structural membrane and biopolymer properties to a two-dimensional plane can be beneficial to quantify molecular signatures in a reduced dimensional space to identify relevant interactions at the interface of interest, i.e. the membrane surface or biopolymer-surface interface. Here, we present a toolbox designed to project membrane and biopolymer properties to a two-dimensional plane to characterize patterns of interaction and spatial correlations between lipid-lipid and lipid-biopolymer interfaces. The toolbox contains two hubs implemented using MDAKits architecture, one for membranes and one for biopolymers, that can be used independently or together. Three case studies demonstrate the versatility of the toolbox with detailed tutorials in GitHub. The toolbox and tutorials will be periodically updated with other functionalities and resolutions to expand our understanding of the structure-function relationship of biomolecules in two-dimensions. SIGNIFICANCE2Danalysis is a significant contribution for the systematic analysis of membrane and biopolymers simulations at planar interfaces. Developed under the open-source MDAKit framework, it enables efficient analysis of trajectories and provides versatile tools for projecting biophysical properties onto a two-dimensional plane. These capabilities enhance the visualization of spatial and temporal changes in membrane characteristics, such as order parameters, and support the study of biopolymer-surface interactions by analyzing adsorption and confinement mechanisms at 2D interfaces. The users can customize the toolbox to study complex 2D phenomena from molecular simulation.

biophysics↗

bioRxiv2024

Acidic Conditions Promote Clustering of Cancer Cell Derived Extracellular Vesicles and Enhance their Fusion with Synthetic Liposomes

Extracellular vesicles (EVs) are endogenous vesicles secreted by cells. Exosomes, a subset of EVs ranging from 30 to 150 nanometers in diameter, contain cytosolic proteins, gene-silencing miRNA, and gene-encoding mRNA and have roles in intercellular communication. Exosomes show promise as cancer chemotherapeutic drug delivery vehicles given their low immunogenicity and cell-specific delivery of luminal contents to the cytosol of target cells. However, loading exosomes with cancer chemotherapeutic drugs is inefficient, which limits their therapeutic application. To overcome this barrier, methods have been developed which allow fusion of EVs with synthetic liposomes preloaded with therapeutic drug. While these methods show more efficient fusion than passive incubation of EVs with liposomes, they risk either damage to the membrane proteins of the EVs or contamination of the final EV-liposome hybrid with residual depletant molecules, which can cause side effects or hinder content delivery. Here, we present a new, weakly perturbative method which uses acidic conditions (pH 5) to significantly enhance the fusion of EVs and synthetic, neutral liposomes (NLs) compared to passive incubation in pH 7.4 at 37 {degrees}C. An adapted Forster resonance energy transfer (FRET) based lipid mixing assay confirms that fusion is enhanced with this method. This significant finding implies that lipid-only synthetic liposomes are able to fuse with EVs, creating EV-liposome hybrids under relevant temperature and pH conditions, with no other non-lipidic component, such as fusogenic amphipathic peptides, added to the synthetic liposomes. Remarkably, differential interference contrast (DIC) and fluorescence microscopy show that this enhancement of fusion corresponds with the onset of clustering of mixtures of EVs and NLs, or EVs alone, in acidic but not neutral pH conditions. The findings support a hypothesis that content release from EVs in early to late endocytic environment may be a combination of protein-protein clustering interactions and a lipidic component. Further, this study provides a novel method for enhanced fusion of EVs and liposomes which is expected to preserve EV membrane proteins and functionality towards the development of therapeutic hybrid drug delivery vehicles in nanomedicine applications.

biophysics↗

bioRxiv2024

Modulation of SpyCatcher Ligation Kinetics by SpyTag Thioamide Substitution

Thioamide substitutions have been shown to impart valuable properties on peptides for biophysical experiments as well as cell or in vivo studies, but a rational understanding of thioamide effects on protein structure and protein-protein interactions is lacking. To elucidate their effects in {beta}-sheet structures, we have used SpyCatcher003-SpyTag003 as a host-guest system to study individual thioamide incorporation at eight different positions in the SpyTag peptide. We have demonstrated that incorporating thioamides into SpyTag at specific positions can result in a [~]2-fold faster ligating complex, as well as >2000-fold slower ligating complex. Biophysical analysis and structural modeling provide a reasonable explanation for most of the thioamide effects, altering hydrogen bond networks as well as modulating an n[->]{pi}* interaction within the SpyTag peptide. Our findings have important implications for potential applications of thioamide SpyTag variants, where the thioamide could impart protease stability in cells while also controlling the rate of ligation to SpyCatcher. These SpyCatcher-SpyTag host-guest experiments will also help to build a database for predicting thioamide effects on protein structure and function.

biochemistry↗

bioRxiv2024

Adsorption-driven deformation and landing-footprints of the RBD proteins in SARS-CoV-2 variants onto biological and inanimate surfaces

Respiratory viruses, carried through airborne microdroplets, frequently adhere to surfaces, including plastics and metals. However, our understanding of the interactions between viruses and materials remains limited, particularly in scenarios involving polarizable surfaces. Here, we investigate the role of receptor-binding domain (RBD) mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native-biological interfaces, specifically the ACE2 receptor. Notably, we identify a twofold increase in structural deformations for the proteins receptor binding motif onto the inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore, the distribution of amino acids (landing-footprints) on the inanimate surface reveals a distinct regional asymmetry relative to the biological interface. In spite of the H-bonds formed at the hydrophilic substrate, the simulations consistently show a higher number of contacts and interfacial area with the hydrophobic surface, with the WT RBD adsorbed more strongly than the delta or omicron RBDs. In contrast, the adsorption of delta and omicron to hydrophilic surfaces was characterized by a distinctive hopping-pattern. The novel shock-absorbing mechanisms identified in the virus adsorption on inanimate surfaces could lead current experimental efforts in the design of virucidal surfaces.

biophysics↗

bioRxiv2023

Highly pathogenic avian influenza H5N1 virus infections in pinnipeds and seabirds in Uruguay: a paradigm shift to virus transmission in South America

The highly pathogenic avian influenza viruses of the clade 2.3.4.4b have caused unprecedented deaths in South American wild birds, poultry, and marine mammals. In September 2023, pinnipeds and seabirds appeared dead on the Uruguayan Atlantic coast. Sixteen influenza virus strains were characterized by real-time reverse transcription PCR and genome sequencing in samples from sea lions (Otaria flavescens), fur seals (Arctocephalus australis), and terns (Sterna hirundinacea). Phylogenetic and ancestral reconstruction analysis showed that these strains have pinnipeds as the most likely ancestral host, representing a recent introduction of the clade 2.3.4.4b in Uruguay. The Uruguayan and closely related strains from Peru (sea lions) and Chile (sea lions and a human case) carry mammalian adaptative residues 591K and 701N in the viral polymerase basic protein 2 (PB2). Our findings suggest that the clade 2.3.4.4b strains in South America may have spread from mammals to mammals and seabirds, revealing a new transmission route.

microbiology↗

bioRxiv2023

A novel thin plate spline methodology to model tissue surfaces and quantify tumor cell invasion in organ-on-chip-models

Organ-on-chip (OOC) models can be useful tools for cancer drug discovery. Advances in OOC technology have led to the development of more complex assays, yet analysis of these systems does not always account for these advancements, resulting in technical challenges. A challenging task in the analysis of these two-channel microfluidic models is to define the boundary between the channels so objects moving within and between channels can be quantified. We propose a novel imaging-based application of a thin plate spline method - a generalized cubic spline that can be used to model coordinate transformations - to model a tissue boundary and define compartments for quantification of invaded objects, representing the early steps in cancer metastasis. To evaluate its performance, we applied our analytical approach to an adapted OOC developed by Emulate, Inc., utilizing a two-channel system with endothelial cells in the bottom channel and colorectal cancer (CRC) patient-derived organoids (PDOs) in the top channel. Initial application and visualization of this method revealed boundary variations due to microscope stage tilt and ridge and valley-like contours in the endothelial tissue surface. The method was functionalized into a reproducible analytical process and web tool - the Chip Invasion and Contour Analysis (ChICA) - to model the endothelial surface and quantify invading tumor cells across multiple chips. To illustrate applicability of the analytical method, we applied the tool to CRC organoid-chips seeded with two different endothelial cell types and measured distinct variations in endothelial surfaces and tumor cell invasion dynamics. Since ChICA utilizes only positional data output from imaging software, the method is applicable to and agnostic of the imaging tool and image analysis system used. The novel thin plate spline method developed in ChICA can account for variation introduced in OOC manufacturing or during the experimental workflow, can quickly and accurately measure tumor cell invasion, and can be used to explore biological mechanisms in drug discovery.

bioinformatics↗

bioRxiv2023

Systematic comparison of Amber force fields for the mechanical properties of double-stranded DNA

AbstractThe response of double-stranded DNA to external mechanical stress plays a central role in its interactions with the protein machinery in the cell. Modern atomistic force fields have been shown to provide highly-accurate predictions for the fine structural features of the duplex. In contrast, and despite their pivotal function, less attention has been devoted to the accuracy in the prediction of the elastic parameters. Several reports have addressed the flexibility of double-stranded DNA via all-atom molecular dynamics, yet the collected information is insufficient to have a clear understanding of the relative performance of the various force fields. In this work, we fill this gap by performing a systematic study in which several systems, characterized by different sequence contexts, are simulated with the most up-to-date force fields, bcs1 and OL15, in the presence of external forces with increasing magnitude. Analysis of our results, together with their comparison with previous work focused on bsc0, allows us to unveil the differences in the predicted rigidity between the newest force fields, and suggests a road map to test their performance against experiments.

biophysics↗

bioRxiv2023

Integration of Patient-Derived Organoids and Organ-on-Chip Systems: Investigating Colorectal Cancer Invasion within the Mechanical and GABAergic Tumor Microenvironment

Three-dimensional (3D) in vitro models are essential in cancer research, but they often neglect physical forces. In our study, we combined patient-derived tumor organoids with a microfluidic organ-on-chip system to investigate colorectal cancer (CRC) invasion in the tumor microenvironment (TME). This allowed us to create patient-specific tumor models and assess the impact of physical forces on cancer biology. Our findings showed that the organoid-on-chip models more closely resembled patient tumors at the transcriptional level, surpassing organoids alone. Using omics methods and live-cell imaging, we observed heightened responsiveness of KRAS mutant tumors to TME mechanical forces. These tumors also utilized the {gamma}-aminobutyric acid (GABA) neurotransmitter as an energy source, increasing their invasiveness. This bioengineered model holds promise for advancing our understanding of cancer progression and improving CRC treatments. HighlightsO_LIMicrofluidic organ-on-chip system integrated with patient-derived CRC organoids C_LIO_LIPhysical forces influence invasion, particularly in KRAS mutant tumor cells C_LIO_LIGABAergic signaling contributes to increased invasion within a dynamic TME C_LIO_LIThis model explores patient heterogeneity, TME interactions, and cancer progression C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/557797v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1b181bborg.highwire.dtl.DTLVardef@bc5b6eorg.highwire.dtl.DTLVardef@16b4fcorg.highwire.dtl.DTLVardef@c43b9f_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

Semi-synthetic CoA-alpha-Synuclein Constructs Trap N-terminal Acetyltransferase NatB for Binding Mechanism Studies

N-terminal acetylation is a chemical modification carried out by N-terminal acetyltransferases (NATs). A major member of this enzyme family, NatB, acts on much of the human proteome, including -synuclein (S), a synaptic protein that mediates vesicle trafficking. NatB acetylation of S modulates its lipid vesicle binding properties and amyloid fibril formation, which underlies its role in the pathogenesis of Parkinsons disease. Although the molecular details of the interaction between human NatB (hNatB) and the N-terminus of S have been resolved, whether the remainder of the protein plays a role in interacting with the enzyme is unknown. Here we execute the first synthesis, by native chemical ligation, of a bisubstrate inhibitor of NatB consisting of coenzyme A and full-length human S, additionally incorporating two fluorescent probes for studies of conformational dynamics. We use cryo-electron microscopy (cryo-EM) to characterize the structural features of the hNatB/inhibitor complex and show that, beyond the first few residues, S remains disordered when in complex with hNatB. We further probe changes in the S conformation by single molecule Forster resonance energy transfer (smFRET) to reveal that the C-terminus expands when bound to hNatB. Computational models based on the cryo-EM and smFRET data help to explain the conformational changes and their implications for hNatB substrate recognition and specific inhibition of the interaction with S. Beyond the study of S and NatB, these experiments illustrate valuable strategies for the study of challenging structural biology targets through a combination of protein semi-synthesis, cryo-EM, smFRET, and computational modeling.

biochemistry↗

bioRxiv2022

Uncovering context-specific genetic-regulation of gene expression from single-cell RNA-sequencing using latent-factor models

Genetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and environmental conditions. We developed SURGE, a method for unsupervised discovery of context-specific expression quantitative trait loci (eQTLs) from single-cell transcriptomic data. This allows discovery of the contexts or cell types modulating genetic regulation without prior knowledge. Applied to peripheral blood single-cell eQTL data, SURGE contexts capture continuous representations of distinct cell types and groupings of biologically related cell types. We demonstrate the disease-relevance of SURGE context-specific eQTLs using colocalization analysis and stratified LD-score regression.

bioinformatics↗

bioRxiv2022

Facing lethal temperatures: heat shock response in desert and temperate ants

Several genera of desert ants have adapted to endure prolonged exposure to high temperatures. The study of these ants is essential to unravel how species respond and adapt to thermal stress. We investigated the thermal tolerance and the transcriptomic heat stress response of three desert ant genera (Cataglyphis, Melophorus and Ocymyrmex) and two temperate genera (Formica and Myrmica) to explore convergent and specific adaptations. We found a variable transcriptomic response among desert species exposed to similar levels of physiological heat-stress: Cataglyphis holgerseni and Melophorus bagoti differentially regulated very few transcripts, 0.12% (54/44,525) and 0.14% (53/38,726) respectively, while Cataglyphis bombycina and Ocymyrmex robustior showed greater expression alterations affecting 0.6% (253/41,912) and 1.53% (698/45,701) of their transcriptomes, respectively. These two responsive mechanisms - reactive and constitutive - were related to desert species thermal tolerance survival pattern and convergently evolved in distinct desert ant genera. By comparison, the two temperate species differentially expressed thousands of transcripts more than desert ants in response to heat stress (affecting 8% and 12,71% of F. fusca and Myr. sabuleti transcriptomes), suggesting that keeping restrained gene expression is an important adaptation in heat adapted species. Finally, we found a significant overlap of the molecular pathways activated in response to heat-stress in temperate and desert species, and our data revealed that larger gene expression responses also affected a greater number of taxonomically restricted genes. These results suggest that the molecular processes involved in heat-stress response are mostly evolutionary conserved in ants, but new genes may also play a role.

molecular biology↗

bioRxiv2021

Accurate sequence-dependent coarse-grained model for conformational and elastic properties of double-stranded DNA

We introduce MADna, a sequence-dependent coarse-grained model of double-stranded DNA (dsDNA), where each nucleotide is described by three beads localized at the sugar and base moieties, and at the phosphate group. The sequence dependence is included by considering a step-dependent parameterization of the bonded interactions, which are tuned in order to reproduce the values of key observables obtained from exhaustive atomistic simulations from literature. The predictions of the model are benchmarked against an independent set of all-atom simulations, showing that it captures with high fidelity the sequence dependence of conformational and elastic features beyond the single step considered in its formulation. A remarkably good agreement with experiments is found for both sequence-averaged and sequence-dependent conformational and elastic features, including the stretching and torsion moduli, the twist-stretch and twist-bend couplings, the persistence length and the helical pitch. Overall, for the inspected quantities, the model has a precision comparable to atomistic simulations, hence providing a reliable coarse-grained description for the rationalization of singlemolecule experiments and the study of cellular processes involving dsDNA. Owing to the simplicity of its formulation, MADna can be straightforwardly included in common simulation engines.

biophysics↗

bioRxiv2021

Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19

Type I interferon (IFN-I) neutralizing autoantibodies have been found in some critical COVID-19 patients; however, their prevalence and longitudinal dynamics across the disease severity scale, and functional effects on circulating leukocytes remain unknown. Here, in 284 COVID-19 patients, we found IFN-I autoantibodies in 19% of critical, 6% of severe and none of the moderate cases. Longitudinal profiling of over 600,000 peripheral blood mononuclear cells using multiplexed single-cell epitope and transcriptome sequencing from 54 COVID-19 patients, 15 non-COVID-19 patients and 11 non-hospitalized healthy controls, revealed a lack of IFN-I stimulated gene (ISG-I) response in myeloid cells from critical cases, including those producing anti-IFN-I autoantibodies. Moreover, surface protein analysis showed an inverse correlation of the inhibitory receptor LAIR-1 with ISG-I expression response early in the disease course. This aberrant ISG-I response in critical patients with and without IFN-I autoantibodies, supports a unifying model for disease pathogenesis involving ISG-I suppression via convergent mechanisms.

immunology↗