Biology subjects

Pinto, D.

Publications and source records attributed to Pinto, D..

At least 19 recordsLinked to original sources

bioRxiv2026

DNA Methylation and Proteomic Profiling of Postmortem Brain Tissue Reveals Epigenetic Dysregulation and Neuroinflammatory in Fragile X-associated Tremor/Ataxia Syndrome (FXTAS)

BackgroundFragile X-associated Tremor/Ataxia Syndrome (FXTAS) is a late-onset neurodegenerative disorder caused by FMR1 premutation CGG repeat expansions (55-200 repeats). The epigenetic landscape of the FXTAS brain remains uncharacterized. We performed genome-wide DNA methylation profiling of postmortem prefrontal cortex tissue to identify differentially methylated positions (DMPs) and candidate genes, and sought protein-level support for a neuroinflammatory signal. MethodsDNA methylation was profiled in postmortem prefrontal cortex (Brodmann area 9) from 27 male FXTAS cases and 29 male controls using the Illumina MethylationEPIC array (EPICv1 and EPICv2 platforms), merging 721,802 common probes. Surrogate variable analysis (SVA) controlled for confounders. DMPs were defined by |{Delta}{beta}| > 0.10 and FDR < 0.05; exploratory Reactome 2024 pathway analysis was performed on the DMP-associated gene list. Targeted proteomic profiling was performed in the same brain region using the Olink (proximity extension assay) Inflammation panel in 9 FXTAS cases and 12 controls, with SVA-adjusted differential abundance analysis, and concordance assessment against a prior mass spectrometry dataset. ResultsWe identified 108 significant cg-type DMPs mapping to 80 genes (50 hypermethylated, 58 hypomethylated in FXTAS). The strongest signal was CYP2E1 (7 concordant hypomethylated DMPs, mean {Delta}{beta} = -0.143), an oxidative stress gene also implicated in Parkinsons disease. FTCD, a one-carbon cycle enzyme, carried 5 hypermethylated DMPs (mean {Delta}{beta} = +0.210). A cluster of DMP-associated genes with established roles in innate immune and NF-{kappa}B signaling, TRAF3 (the single most significant DMP among the inflammation genes, hypermethylated), BATF, RCOR1, and MSI2; they pointed toward neuroinflammatory dysregulation. Additional genes included LINGO1 (myelination inhibitor), SYT3 (synaptic vesicle), and SLC39A4 (zinc transporter). Exploratory Reactome enrichment using the DMP-associated gene set nominated themes including neuroinflammation resolution, axonal growth inhibition, zinc homeostasis, and CYP2E1 metabolism at nominal significance (p<0.05); however, the gene-to-pathway mapping rate was low and no pathway survived correction for multiple testing. Olink proteomic analysis independently identified 60 significantly altered inflammation proteins (59 downregulated), including CXCL8, CXCL10, IL6, IL15, IL18, TLR3, IRAK1/4, and complement C1QA, which were directionally concordant with prior mass spectrometry data. ConclusionsThis integrated study reveals a genome-wide epigenetic signature in the FXTAS prefrontal cortex implicating oxidative stress, myelination failure, zinc dysregulation, one-carbon cycle disruption, and most notably a coordinated set of epigenetically altered genes governing innate immune and NF-{kappa}B signaling. Convergence of TRAF3 hypermethylation with independent downregulation of TLR3 and NF-{kappa}B-pathway proteins at the protein level supports a coherent, cross-platform model of dysregulated neuroinflammatory signaling in FXTAS, identified here through individual gene- and protein-level convergence rather than formal pathway enrichment. FTCD hypermethylation proposes a self-reinforcing epigenetic loop via SAM depletion. These multi-omic findings establish FXTAS as a disorder of pervasive epigenetic reprogramming and nominate candidate genes for future mechanistic and therapeutic investigation.

genomics↗

bioRxiv2026

Galectin-8 regulates primary cilium in hypothalamic neurons through anL-type calcium channel/Aurora kinaseA/HDAC6 pathway impacting body energy balance

OBJETIVEFood intake, energy expenditure, and metabolic homeostasis depend on hypothalamic neurons responses to peripheral signals, such as leptin, involving the primary cilium (PC). The PC is crucial for signal transduction and is dynamically regulated by assembly/disassembly or reabsorption of its microtubules-based axoneme. Absence or reduction in the length of PC is associated with obesity and type-2 diabetes (T2D). In other cellular systems, PC reabsorption is primarily regulated by calcium-mediated activation of the Aurora kinase A (AurkA)/histone deacetylase C6 (HDAC6) axis, which promotes axonemal disassembly. Here, we explore the role of Galectin-8 (Gal-8), a glycan-binding protein, in regulating PC structure and signaling related to metabolic parameters in hypothalamic neurons. METHODSGal-8 effects were assessed in hypothalamic Clu-177 cells by analyzing the PC presence and length by immunofluorescence, PC dynamics, and intracellular calcium changes by in vivo cell imaging, activation of FAK, Src, AurkA, HDAC6 and STAT3 by immunoblot, and Gal-8 interactions with {beta}1-integrins by pull-down assays. Gal-8-KO mice were used to evaluate PC length in hypothalamic neurons, metabolic phenotype, and responses to Gal-8 intranasal administration. RESULTSIn Clu-177 cells, Gal-8 induced PC reabsorption and reduced responsiveness to leptin signaling towards STAT3 activation. PC reabsorption involves glycan-mediated Gal-8 interactions with a5b1 and a3b1 integrins, activation of FAK and Src leading to calcium influx through L-type calcium channels (LTCC), and subsequent AurkA/HDAC6 axis activation. Gal-8-KO mice showed longer PC in hypothalamic neurons, higher STAT3 activation, decreased body weight and food intake, improved glucose tolerance, higher locomotor activity, and a glycolytic respiratory exchange rate (RER). Daily intranasal Gal-8 administration for 4 days restored hypothalamic PC length and STAT3 signaling, as well as RER in Gal-8-KO mice to the level of WT mice. CONCLUSIONSEndogenous Gal-8 is required to maintain PC structure and leptin signaling in hypothalamic neurons, impacting body weight, energy balance, and glucose homeostasis. The mechanism involves calcium influx via LTCC downstream of b1-integrin/FAK/Src signaling and subsequent AurkA/HDAC6 axis activation. Both Gal-8 and the AurkA/HDAC6 axis may offer new therapeutic opportunities for treating metabolic diseases characterized by ciliogenesis impairment, including obesity and type-2 diabetes.

cell biology↗

bioRxiv2026

Three immunoregulatory signatures define non-productive HIV infection in CD4+ T memory stem cells

The persistent HIV reservoir constitutes the main obstacle to curing HIV/AIDS disease. Our understanding of how non-productive HIV infections are established in primary human CD4+ T cells during the first round of infection remains, however, incomplete. In this study, we leveraged the HIV reporter virus pMorpheus-V5 to delineate cellular expression patterns that are upregulated in non-productively infected primary CD4+ T memory stem cells (TSCM). We found that CD4+ TSCM harboring non-productive proviruses displayed a distinct transcriptomic signature comprising 118 upregulated genes. This non-productive expression profile was distinct from that of productively infected cells as well as from negative-exposed and mock-infected cells. Among the cellular genes most upregulated in CD4+ T cells harboring non-productive proviruses were CCR4-binding migratory chemokines (CCL22, CCL17), tryptophan catabolic enzymes (IDO1, KYNU), and genes encoding cytoskeletal rearrangement proteins (BASP1, TNFAIP2). Intracellular flow cytometry-based analyses confirmed that non-productively infected CD4+ TSCM cells were enriched for CCL22 and IDO1 co-expression compared to the other CD4+ memory subsets, underscoring a clear CD4+ T cell subset specificity for the upregulation of these two immune gene sets associated with non-productive infections. These findings suggest that primary human CD4+ TSCM harboring non-productive proviruses display a distinct immunoregulatory phenotype which may facilitate immune evasion and contribute to the persistence of the HIV reservoir.

microbiology↗

bioRxiv2024

Inclusion of Salicornia ramosissima biomass in diets for juvenile whiteleg shrimp (Penaeus vannamei) induces favourable but transient effects in the immune and oxidative status

The whiteleg shrimp, Penaeus vannamei, is a highly valued and globally produced crustacean species. However, the rising cost of shrimp feed, exacerbated by increasing cereal prices, prompts the exploration of cost-effective and sustainable formulations for shrimp farming. This study investigates the potential of Salicornia ramosissima, a non-edible biomass co-product, as a substitute for wheat meal in juvenile whiteleg shrimp diets, aiming to create economically and ecologically sound formulations. The present study aimed to assess the impact of incorporating S. ramosissima into whiteleg shrimp aquafeeds on various aspects of shrimp development, including growth performance, survival, immune status, and oxidative status. A commercial-like diet was formulated and served as control, whereas four other diets contained S. ramosissima stems or a combination of leaves and seeds, both at inclusion levels of 5% and 10%, in addition to the control diet. Whiteleg shrimps were fed the experimental diets for 31 and 55 days, followed by a bacterial bath challenge to gauge their immune response to pathogens. At the end of the feeding period, whiteleg shrimps growth performance and survival rates remained consistent across all diets. However, whiteleg shrimp fed diets with S. ramosissima inclusion consumed more feed to achieve similar weights to those fed on the control diet, particularly in diets containing leaves and seeds at a 10% inclusion level, likely due to lower digestibility of dry matter, lipids, and energy. While S. ramosissima biomass inclusion did not affect shrimp weight, relative growth rate, or survival, it did lead to higher feed conversion ratios and feed intake, suggesting differences in nutrient digestibility and metabolic utilization. Additionally, S. ramosissima inclusion affected whiteleg shrimps overall body composition, particularly moisture and ash content. Dietary S. ramosissima inclusion modulated antioxidant enzyme activity in the shrimps hepatopancreas, indicating potential health improvements. The study also observed gene expression changes related to antioxidant enzymes, indicating an overall down-regulation with the inclusion of S. ramosissima. Despite challenges in feeding efficiency, the inclusion of S. ramosissima, especially stems, shows promise in reducing feed costs by utilizing a by-product. Furthermore, S. ramosissima inclusion led to subtle changes in certain plasma humoral parameters and hepatopancreas gene expression. Although some immune parameters varied, these effects appeared to diminish over time. In conclusion, this study highlights the potential of S. ramosissima as a functional feed ingredient capable of enhancing shrimps antioxidant response, aligning with global resource optimization and sustainability initiatives.

immunology↗

bioRxiv2024

Transcriptomic landscape of human induced pluripotent stem cell-derived osteogenic differentiation identifies a regulatory role of KLF16

Osteogenic differentiation is essential for bone development, metabolism, and repair; however, the underlying regulatory relationships among genes remain poorly understood. To elucidate the transcriptomic changes and identify novel regulatory genes involved in osteogenic differentiation, we differentiated mesenchymal stem cells (MSCs) derived from 20 human iPSC lines into preosteoblasts (preOBs) and osteoblasts (OBs). We then performed transcriptome profiling of MSCs, preOBs and OBs. The iPSC-derived MSCs and OBs showed similar transcriptome profiles to those of primary human MSCs and OBs, respectively. Differential gene expression analysis revealed global changes in the transcriptomes from MSCs to preOBs, and then to OBs, including the differential expression of 840 genes encoding transcription factors (TFs). TF regulatory network analysis uncovered a network comprising 451 TFs, organized into five interactive modules. Multiscale embedded gene co-expression network analysis (MEGENA) identified gene co-expression modules and key network regulators (KNRs). From these analyses, KLF16 emerged as an important TF in osteogenic differentiation. We demonstrate that overexpression of Klf16 in vitro inhibited osteogenic differentiation and mineralization, while Klf16+/- mice exhibited increased bone mineral density, trabecular number, and cortical bone area. Our study underscores the complexity of osteogenic differentiation and identifies novel regulatory genes such as KLF16, which plays an inhibitory role in osteogenic differentiation both in vitro and in vivo.

molecular biology↗

bioRxiv2023

Comparative genomics reveals the diversity of CRISPR-Cas systems among neonatal sepsis causing group B Streptococcus agalactiae

The pathogen Streptococcus agalactiae, or Group B Streptococcus (GBS) infection is the leading cause of neonatal sepsis and meningitis in neonates. In this study, we aimed to investigate the occurrence and diversity of the CRISPR-Cas system in S. agalactiae genomes using computational biology approaches. A total of 51 out of 52 complete genomes (98.07%) of S. agalactiae possess CRISPR arrays (75 CRISPR arrays) with 17 strains possessing multiple CRISPR arrays. There were only two CRISPR-Cas systems - type II-A system and type I-C system in S. agalactiae strains. RNA secondary structure analysis through direct repeat analysis showed that the analyzed strains could form stable secondary structures. The 16S rRNA phylogeny exhibited clustering of the strains into three major clades grouped on the type of CRISPR-Cas system. The anti-CRISPRs that contribute to CRISPR-Cas system diversity and prevent genome editing were also detected. These results provide valuable insights into elucidating the evolution, diversity, and function of CRISPR/Cas elements in this pathogen.

bioinformatics↗

bioRxiv2023

Rescue of Mycobacterium bovis DNA obtained from cultured strains during official surveillance of animal TB: key steps for robust whole genome sequence data generation

Epidemiological surveillance of animal tuberculosis (TB) based on whole genome sequencing (WGS) of Mycobacterium bovis has recently gained track due to its high resolution to identify infection sources, characterize the pathogen population structure, and for contact tracing. However, the workflow from bacterial isolation to sequence data analyses has several technical challenges that may severely impact the power to understand the epidemiological scenario and inform outbreak response. While trying to use archived DNA from cultured strains obtained during routine official surveillance of animal TB in Portugal, we struggled against three major challenges: the low amount of M. bovis DNA obtained from routinely processed animal samples; the lack of purity of M. bovis DNA, i.e. high levels of contamination with DNA from other organisms; and the co-occurrence of more than one M. bovis strain per sample (within-host mixed infection). The loss of an isolates genome is a missed link in transmission chain reconstruction, hampering the biological and epidemiological interpretation of data as a whole. Upon identification of these challenges, we implemented an integrated solution framework, based on whole genome amplification and a dedicated computational pipeline, to minimize their effects and recover as many genomes as possible. With the approaches described herein, we were able to recover 62 out of 100 samples that would have otherwise been lost. Based on these results, we discuss adjustments that should be made in official and research laboratories to facilitate sequential implementation of bacteriological culture, PCR, downstream genomics and computational-based methods. All of this in a time frame supporting data-driven intervention.

genomics↗

bioRxiv2023

The impact of common variants on gene expression in the human brain: from RNA to protein to schizophrenia risk

BackgroundThe impact of genetic variants on gene expression has been intensely studied at the transcription level, yielding invaluable insights into the association between genes and the risk of complex disorders, such as schizophrenia (SCZ). However, the downstream impact of these variants and the molecular mechanisms connecting transcription variation to disease risk are not well understood. ResultsWe quantitated ribosome occupancy in prefrontal cortex samples of the BrainGVEX cohort. Together with transcriptomics and proteomics data from the same cohort, we performed cis-Quantitative Trait Locus (QTL) mapping and identified, at 10% false discovery rate, 3,253 expression QTLs (eQTLs), 1,344 ribosome occupancy QTLs (rQTLs), and 657 protein QTLs (pQTLs) out of 7,458 genes from 185 samples. Of the eQTLs identified, only 34% have their effects propagated to the protein level. Further analysis on the effect size of prefrontal cortex eQTLs identified from an independent dataset clearly replicated the post-transcriptional attenuation of eQTL effects. We identified omics-specific QTLs and investigated their potential in driving disease risks. Using both a variant-based approach and a gene-based approach, we identified genes containing expression-specific QTLs (esQTLs), ribosome-occupancy-specific QTLs (rsQTLs), and protein-specific QTLs (psQTLs). Among the variant-based omics-specific QTL, 38 showed strong colocalization with brain associated disorder GWAS signals, 29 of them are esQTLs. From the gene-based approach, we found 11 brain associated disorder risk genes that are driven predominantly by omics-specific QTL, all of them are driven by variants impacting transcriptional regulation. To take a complementary approach to further investigate the functional relevance of genes driven predominantly by attenuated eQTL signals, we identified SCZ risk genes using each omics independently and then investigated the omics-specificity of the driver regulatory process for each risk gene. Using S-PrediXcan we identified 74 SCZ risk genes across the three omics, 30% of which were novel, and 67% of these risk genes were confirmed to be causal in a MR-Egger test. Notably, 52 out of the 74 risk genes were identified using eQTL data and 68% of these SCZ-risk-gene-driving eQTLs show little to no evidence of driving corresponding variations at the protein level. ConclusionThe effect of eQTLs on gene expression in the prefrontal cortex is commonly attenuated post-transcriptionally. Many of the attenuated eQTLs still correlate with GWAS signals of brain associated complex disorders, indicating the possibility that these eQTL variants drive disease risk through mechanisms other than regulating protein expression level. Further investigation is needed to elucidate the mechanistic link between attenuated eQTLs and brain associated complex disorders.

genetics↗

bioRxiv2023

Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data

Sample-wise deconvolution methods have been developed to estimate cell-type proportions and gene expressions in bulk-tissue samples. However, the performance of these methods and their biological applications has not been evaluated, particularly on human brain transcriptomic data. Here, nine deconvolution methods were evaluated with sample-matched data from bulk-tissue RNAseq, single-cell/nuclei (sc/sn) RNAseq, and immunohistochemistry. A total of 1,130,767 nuclei/cells from 149 adult postmortem brains and 72 organoid samples were used. The results showed the best performance of dtangle for estimating cell proportions and bMIND for estimating sample-wise cell-type gene expression. For eight brain cell types, 25,273 cell-type eQTLs were identified with deconvoluted expressions (decon-eQTLs). The results showed that decon-eQTLs explained more schizophrenia GWAS heritability than bulk-tissue or single-cell eQTLs alone. Differential gene expression associated with multiple phenotypes were also examined using the deconvoluted data. Our findings, which were replicated in bulk-tissue RNAseq and sc/snRNAseq data, provided new insights into the biological applications of deconvoluted data.

genomics↗

bioRxiv2023

Therapeutic and vaccine-induced cross-reactive antibodies with effector function against emerging Omicron variants

Currently circulating SARS-CoV-2 variants acquired convergent mutations at receptor-binding domain (RBD) hot spots1. Their impact on viral infection, transmission, and efficacy of vaccines and therapeutics remains poorly understood. Here, we demonstrate that recently emerged BQ.1.1. and XBB.1 variants bind ACE2 with high affinity and promote membrane fusion more efficiently than earlier Omicron variants. Structures of the BQ.1.1 and XBB.1 RBDs bound to human ACE2 and S309 Fab (sotrovimab parent) explain the altered ACE2 recognition and preserved antibody binding through conformational selection. We show that sotrovimab binds avidly to all Omicron variants, promotes Fc-dependent effector functions and protects mice challenged with BQ.1.1, the variant displaying the greatest loss of neutralization. Moreover, in several donors vaccine-elicited plasma antibodies cross-react with and trigger effector functions against Omicron variants despite reduced neutralizing activity. Cross-reactive RBD-directed human memory B cells remained dominant even after two exposures to Omicron spikes, underscoring persistent immune imprinting. Our findings suggest that this previously overlooked class of cross-reactive antibodies, exemplified by S309, may contribute to protection against disease caused by emerging variants through elicitation of effector functions.

immunology↗

bioRxiv2022

Covert detection of own-name and semantic violations in task-irrelevant speech, in a realistic Virtual Cafe

Detecting that someone has said your name is one of the most famous examples for incidental processing of supposedly-unattended speech. However, empirical investigation of this so-called "cocktail party effect" has yielded conflicting results. We present a novel empirical approach for revisiting this effect under highly ecological conditions, by immersing participants in a multisensory virtual cafe environment and using realistic stimuli and tasks. Participants listened to conversational speech from a character sitting across from them, while a barista in the back of the cafe called out food orders. Unbeknownst to them, the barista sometimes called orders containing their own name or semantic violations. We used combined measurements of brain activity (EEG), eye-gaze and galvanic skin response to assess the response-profile to these two probes in the task-irrelevant barista-stream. Both probes elicited unique neural and physiological responses relative to control stimuli, indicating that the system indeed processed these words and detected their unique status, despite being task-irrelevant. Interestingly, these responses were covert in nature and were not accompanied by gaze-shifts towards the barista character. This pattern demonstrates that under these highly ecological conditions, listeners incidentally pick up information from task-irrelevant speech, emphasizing the dynamic and non-binary nature of attention in real-life environments.

neuroscience↗

bioRxiv2022

An ecological investigation of the capacity to follow simultaneous speech and preferential detection of ones' own name

Many situations require focusing attention on one speaker, while monitoring the environment for potentially important information. Some have proposed that dividing attention among two speakers involves behavioral tradeoffs, due to limited cognitive resources. However the severity of these tradeoffs, particularly under ecologically-valid circumstances, is not well understood. We investigated the capacity to process simultaneous speech using a dual-task paradigm simulating task demands and stimuli encountered in real-life. Participants listened to conversational narratives (Narrative Stream) and monitored a stream of announcements (Barista Stream), to detect when their order was called. We measured participants performance, neural activity and skin conductance as they engaged in this dual-task. Participants achieved extremely high dual-task accuracy, with no apparent behavioral tradeoffs. Moreover, robust neural and physiological responses were observed for target-stimuli in the Barista Stream, alongside significant neural speech-tracking of the Narrative Stream. These results suggest that humans have substantial capacity to process simultaneous speech and do not suffer from insufficient processing resources, at least for this highly ecological task-combination and level of perceptual load. Results also confirmed the ecological validity of the advantage for detecting ones own name at the behavioral, neural and physiological level, highlighting the contribution of personal relevance when processing simultaneous speech.

neuroscience↗

bioRxiv2022

Imprinted antibody responses against SARS-CoV-2 Omicron sublineages

SARS-CoV-2 Omicron sublineages carry distinct spike mutations and represent an antigenic shift resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters result in potent plasma neutralizing activity against Omicron BA.1 and BA.2 and that breakthrough infections, but not vaccination-only, induce neutralizing activity in the nasal mucosa. Consistent with immunological imprinting, most antibodies derived from memory B cells or plasma cells of Omicron breakthrough cases cross-react with the Wuhan-Hu-1, BA.1 and BA.2 receptor-binding domains whereas Omicron primary infections elicit B cells of narrow specificity. While most clinical antibodies have reduced neutralization of Omicron, we identified an ultrapotent pan-variant antibody, that is unaffected by any Omicron lineage spike mutations and is a strong candidate for clinical development.

immunology↗

bioRxiv2022

ACE2 engagement exposes the fusion peptide to pan-coronavirus neutralizing antibodies

Coronaviruses use diverse Spike (S) glycoproteins to attach to host receptors and fuse with target cells. Using a broad screening approach, we isolated from SARS-CoV-2 immune donors seven monoclonal antibodies (mAbs) that bind to all human alpha and beta coronavirus S proteins. These mAbs recognize the fusion peptide and acquire high affinity and breadth through somatic mutations. Despite targeting a conserved motif, only some mAbs show broad neutralizing activity in vitro against alpha and beta coronaviruses, including Omicron BA.1 variant and bat WIV-1, and reduce viral titers and pathology in vivo. Structural and functional analyses show that the fusion peptide-specific mAbs bind with different modalities to a cryptic epitope which is concealed by prefusion-stabilizing 2P mutations and becomes exposed upon binding of ACE2 or ACE2-mimicking mAbs. This study identifies a new class of pan-coronavirus neutralizing mAbs and reveals a receptor-induced conformational change in the S protein that exposes the fusion peptide region.

immunology↗

bioRxiv2021

Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift

The recently emerged SARS-CoV-2 Omicron variant harbors 37 amino acid substitutions in the spike (S) protein, 15 of which are in the receptor-binding domain (RBD), thereby raising concerns about the effectiveness of available vaccines and antibody therapeutics. Here, we show that the Omicron RBD binds to human ACE2 with enhanced affinity relative to the Wuhan-Hu-1 RBD and acquires binding to mouse ACE2. Severe reductions of plasma neutralizing activity were observed against Omicron compared to the ancestral pseudovirus for vaccinated and convalescent individuals. Most (26 out of 29) receptor-binding motif (RBM)-directed monoclonal antibodies (mAbs) lost in vitro neutralizing activity against Omicron, with only three mAbs, including the ACE2-mimicking S2K146 mAb1, retaining unaltered potency. Furthermore, a fraction of broadly neutralizing sarbecovirus mAbs recognizing antigenic sites outside the RBM, including sotrovimab2, S2X2593 and S2H974, neutralized Omicron. The magnitude of Omicron-mediated immune evasion and the acquisition of binding to mouse ACE2 mark a major SARS-CoV-2 mutational shift. Broadly neutralizing sarbecovirus mAbs recognizing epitopes conserved among SARS-CoV-2 variants and other sarbecoviruses may prove key to controlling the ongoing pandemic and future zoonotic spillovers.

immunology↗

bioRxiv2021

Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry

Understanding broadly neutralizing sarbecovirus antibody responses is key to developing countermeasures effective against SARS-CoV-2 variants and future spillovers of other sarbecoviruses. Here we describe the isolation and characterization of a human monoclonal antibody, designated S2K146, broadly neutralizing viruses belonging to all three sarbecovirus clades known to utilize ACE2 as entry receptor and protecting therapeutically against SARS-CoV-2 beta challenge in hamsters. Structural and functional studies show that most of the S2K146 epitope residues are shared with the ACE2 binding site and that the antibody inhibits receptor attachment competitively. Viral passaging experiments underscore an unusually high barrier for emergence of escape mutants making it an ideal candidate for clinical development. These findings unveil a key site of vulnerability for the development of a next generation of vaccines eliciting broad sarbecovirus immunity.

immunology↗

bioRxiv2021

Assessing the sensitivity of EEG-based frequency-tagging as a metric for statistical learning

AO_SCPLOWBSTRACTC_SCPLOWStatistical Learning (SL) is hypothesized to play an important role in language development. However, the behavioral measures typically used to assess SL, particularly at the level of individual participants, are largely indirect and often have low sensitivity. Recently, a neural metric based on frequency-tagging has been proposed as an alternative and more direct measure for studying SL. Here we tested the sensitivity of frequency-tagging measures for studying SL in individual participants in an artificial language paradigm, using non-invasive EEG recordings of neural activity in humans. Importantly, we use carefully constructed controls, in order to address potential acoustic confounds of the frequency-tagging approach. We compared the sensitivity of EEG-based metrics to both explicit and implicit behavioral tests of SL, and the correspondence between these presumed converging operations. Group-level results confirm that frequency-tagging can provide a robust indication of SL for an artificial language, above and beyond potential acoustic confounds. However, this metric had very low sensitivity at the level of individual participants, with significant effects found only in 30% of participants. Conversely, the implicit behavior measures indicated that SL has occurred in 70% of participants, which is more consistent with the proposed ubiquitous nature of SL. Moreover, there was low correspondence between the different measures used to assess SL. Taken together, while some researchers may find the frequency-tagging approach suitable for their needs, our results highlight the methodological challenges of assessing SL at the individual level, and the potential confounds that should be taken into account when interpreting frequency-tagged EEG data.

neuroscience↗

bioRxiv2021

A human antibody that broadly neutralizes betacoronaviruses protects against SARS-CoV-2 by blocking the fusion machinery

The repeated spillovers of {beta}-coronaviruses in humans along with the rapid emergence of SARS-CoV-2 escape variants highlight the need to develop broad coronavirus therapeutics and vaccines. Five monoclonal antibodies (mAbs) were isolated from COVID-19 convalescent individuals and found to cross-react with multiple {beta}-coronavirus spike (S) glycoproteins by targeting the stem helix. One of these mAbs, S2P6, cross-reacts with more than twenty human and animal {beta}-coronavirus S glycoproteins and broadly neutralizes SARS-CoV-2 and pseudotyped viruses from the sarbecovirus, merbecovirus and embecovirus subgenera. Structural and functional studies delineate the molecular basis of S2P6 cross-reactivity and broad neutralization and indicate that this mAb blocks viral entry by inhibiting membrane fusion. S2P6 protects hamsters challenged with SARS-CoV-2 (including the B.1.351 variant of concern) through direct viral neutralization and Fc-mediated effector functions. Serological and B cell repertoire analyses indicate that antibodies targeting the stem helix are found in some convalescent donors and vaccinees but are predominantly of narrow specificity. Germline reversion of the identified cross-reactive mAbs revealed that their unmutated ancestors are specific for the endemic OC43 or HKU1 viruses and acquired enhanced affinity and breadth through somatic mutations. These data demonstrate that conserved epitopes in the coronavirus fusion machinery can be targeted by protective antibodies and provide a framework for structure-guided design of pan-{beta}-coronavirus vaccines eliciting broad protection.

immunology↗