Biology subjects

Palus, M.

Publications and source records attributed to Palus, M..

11 recordsLinked to original sources

bioRxiv2026

Structural basis of diverse antibody recognition of conserved coronavirus spike S2 epitopes that contribute to protective immunity

Conserved epitopes within the coronavirus spike S2 domain elicit broadly reactive antibodies, yet many characterized responses show limited neutralizing and variable protective activity, leaving their contribution to antiviral immunity unclear. Building on our previous mapping of evolutionarily conserved spike coldspots, we isolated human monoclonal antibodies targeting four conserved epitopes in the spike S2 domain: the internal fusion peptide (iFP), the central helix (CH), the connector domain (CD), and a membrane-proximal epitope in the heptad repeat 2 that we term the lower stalk (LS). A crystal structure of an LS-directed antibody defined a previously unresolved mode of antibody recognition of this membrane-proximal epitope, while cryogenic electron microscopy (cryo-EM) structures revealed that genetically diverse CH-specific antibodies use distinct binding modes to converge on conserved features of the prefusion S2 apex. Despite minimal neutralizing activity, CH- and LS-directed antibodies exhibited distinct antiviral functions. LS-directed antibodies mediated Fc{gamma} receptor-dependent effector activity in vitro, whereas the broadly reactive CH-directed antibody ch.007 lacked detectable antibody-dependent cellular cytotoxicity (ADCC) or cellular phagocytosis (ADCP) activity yet protected mice from lethal SARS-CoV-2 MA10 challenge, with protection abrogated by Fc{gamma} receptor-silencing mutations. Together, these findings expand the genetic, structural and functional landscape of human antibody responses to conserved coronavirus S2 epitopes and demonstrate that CH-directed antibodies can contribute to protective immunity through Fc-dependent mechanisms not predicted by in vitro neutralization or conventional in vitro Fc effector assays.

biophysics↗

bioRxiv2026

Host-derived lipids license proliferation of sterol-auxotrophic tick cells and promote flavivirus output

Sterol molecules play indispensable roles in the biology of cells and organisms. Yet, arthropods, including ticks, lack the capacity for de novo sterol biosynthesis and must rely on exogenous sources. How these organisms sense and utilise exogenous lipids at the cellular level remains poorly understood. Here, we show that host cholesterol and linoleic acid act as essential external signals that license proliferation of Ixodes ricinus tick cells. In lipid-depleted conditions, cells fail to proliferate despite retaining intracellular cholesterol, indicating that exogenous lipids function as regulatory cues rather than merely structural components. We further demonstrate that tick cells exhibit a non-canonical intracellular distribution of cholesterol, with predominant accumulation in lysosome-associated compartments, and that lipid availability induces a coordinated transcriptional program involving lipid uptake and trafficking machinery. Importantly, we find that limiting host lipid availability significantly reduces extracellular RNA output of tick-borne encephalitis virus (TBEV) from infected tick cells, indicating that viral production is affected by the metabolic state of the host cell. Together, our findings establish host-derived lipids as key regulators of cellular state in a sterol-auxotrophic organism and identify lipid availability as a determinant of flavivirus output. This work provides a conceptual framework linking nutrient sensing, cell proliferation, and vector-pathogen interactions.

microbiology↗

bioRxiv2026

Human antibodies against West Nile and related orthoflaviviruses

West Nile virus (WNV) is a mosquito-borne pathogen of global concern that can cause fatal neuroinvasive disease. No specific prophylaxis or treatment exists for WNV or related orthoflavivirus infections, and the determinants of human disease severity remain poorly understood. Here, we report that neutralizing autoantibodies against type I interferons do not impair antiviral antibody development. Among the fully human monoclonal antibodies with potent neutralizing activity against WNV that were discovered, W010 targets a unique epitope within the envelope protein domain III (EDIII) and confers both pre- and post-exposure protection in a murine WNV model, even when interferon signaling is impaired. A second protective antibody, W014, exhibits broad cross-neutralization of other pathogenic orthoflavivirus members, including Japanese encephalitis virus, Murray Valley encephalitis virus, Saint Louis encephalitis virus, and Usutu virus. These findings identify key neutralizing epitopes on WNV EDIII and provide candidates for the development of antibody-based interventions against encephalitic orthoflavivirus infections.

immunology↗

bioRxiv2026

EEG connectivity changes in early response to antidepressant treatment

ObjectiveFinding indicators of early response to antidepressant treatment in EEG signals recorded from patients suffering from major depressive disorder. MethodsFunctional brain connectivity networks based on weighted imaginary coherence and weighted imaginary mean phase coherence were computed for 176 patients for 6 different EEG frequency bands. Cross-hemispheric connectivity (CH) and lateral asymmetry (LA) were estimated from these networks based on EEG signals recorded before the beginning of treatment (V is1) and one week after the start of the treatment (V is2). Repeated measures ANOVA was used to check for statistically significant changes in connectivity based on these measures at V is2 w.r.t. V is1. Post-hoc analysis was performed with multiple pairwise comparison tests to determine which group means were significantly different. ResultsIt was found that CHV is2 was significantly reduced w.r.t. CHV is1 in the {beta}1 [12.5 - 17.5 Hz] frequency band for the responders to treatment. Also, LAV is2 was significantly increased w.r.t. LAV is1 in the {beta}1 frequency band for the responders. No such significant changes were observed for the non-responders. Brain networks constructed using both weighted imaginary coherence and weighted imaginary mean phase coherence were found to exhibit these results. For the CH connectivity changes, binarized networks and for the LA connectivity changes, weighted networks were found to be more reliable. ConclusionsResponders were found to show a reduction in cross-hemispheric connectivity and an increase in lateral asymmetry, both in the {beta}1 band while no such change was observed for the non-responders. SignificanceDecrease in cross-hemispheric connectivity and increase in lateral asymmetry in the {beta}1 band may represent candidate neurophysiological indicators of early treatment response, but they require independent replication before any clinical application can be considered.

neuroscience↗

bioRxiv2026

Graph-Based EEG Symmetry Features from the Temporal Lobe as Markers of Antidepressant Treatment Response

Major Depressive Disorder (MDD) is a mental disorder that affects millions globally and has highly individualized responses to antidepressant treatment. Identifying objective early markers that can distinguish responders from non-responders remains a critical challenge in personalized psychiatry. In this study, we investigate the role of brain symmetry in EEG-derived functional connectivity as a potential early marker of treatment response. Using resting-state EEG recordings from 176 patients diagnosed with MDD at baseline (Visit 1) and after one week of treatment (Visit 2), we construct graph-based representations of functional connectivity and define region-wise and electrode-wise temporal-lobe symmetry features. We focus on symmetry change scores (Visit 2 - Visit 1) across typical EEG frequency bands in both weighted and binary forms. Statistical analyses reveal a consistent group-level pattern in the and {beta} bands: responders show negative symmetry change scores, whereas non-responders show relative stability or weakly positive change scores. The contrast is strongest in the {beta}1 band and is more pronounced for binary symmetry metrics, while the band shows the same direction with slightly weaker significance. Physiologically, these opposite trajectories are consistent with a treatment-related shift toward more lateralized temporal-lobe network organization in responders and a more bilateral coupling pattern in nonresponders; however, these neurophysiological interpretations remain hypothesis-generating given the resting-state design and the absence of direct behavioral or task-based validation. To quantify whether temporal symmetry change scores contain reproducible discriminative signal under strict validation, we benchmark the proposed features in a supervised classification pipeline using repeated nested cross-validation. The best-performing configuration achieved a median out-of-sample AUC of 0.690 with a 95% bootstrap confidence interval of [0.611, 0.711], indicating modest but reproducible separability. Overall, temporal-lobe symmetry change features provide interpretable candidate markers of early antidepressant-related neurophysiological change that may complement existing EEG predictors in future multi-marker models, but they are not yet sufficient for standalone clinical decision support and require external validation in independent cohorts.

neuroscience↗

bioRxiv2025

Tattoo ink induces inflammation in the draining lymph node and impairs the immune response against a COVID-19 vaccine

Despite safety concerns regarding the toxicity of tattoo ink, no studies have reported the consequences of tattooing on the immune response. In this work, we have characterized the transport and accumulation of different tattoo inks in the lymphatic system using a murine model. Upon quick lymphatic drainage, we observed that macrophages mainly capture the ink in the lymph node (LN). An initial inflammatory reaction at local and systemic levels follows ink capture. Notably, the inflammatory process is maintained over time as we observed clear signs of inflammation in the draining LN two months following tattooing. In addition, the capture of ink by macrophages was associated with the induction of apoptosis in both human and murine models. Furthermore, the ink accumulated in the LN altered the immune response against a COVID-19 vaccine. We observed a reduced antibody response following vaccination with a mRNA-based SARS-CoV-2 vaccine, which was associated with a decreased expression of the Spike protein in macrophages in the draining LN. Considering the unstoppable trend of tattooing in the population, our results are crucial in informing the toxicology programs, policymakers, and the general public regarding the potential risk of the tattooing practice associated with an altered immune response.

immunology↗

bioRxiv2024

Enhanced RNAi does not provide efficient innate antiviral immunity in mice in vivo.

In RNA interference (RNAi), long double-stranded RNA (dsRNA) is cleaved by Dicer endonuclease into small RNA interfering RNAs (siRNAs), which guide degradation of complementary RNAs. While RNAi mediates antiviral innate immunity in plants and many invertebrates, vertebrates adopted sequence-independent response and their Dicer produces siRNAs inefficiently because it is adapted to process small hairpin microRNA precursors in the gene-regulating microRNA pathway. Mammalian RNAi is thus a rudimentary pathway of unclear significance. To investigate its antiviral potential, we modified mouse Dicer locus to express a truncated variant (Dicer{Delta}HEL1) known to stimulate RNAi. Next, we analyzed how Dicer{Delta}HEL1/wt mice respond to four RNA viruses: Coxsackievirus B3 (CVB3) and encephalomyocarditis virus (ECMV) from Picornaviridae; tick-borne encephalitis virus (TBEV) from Flaviviridae; and lymphocytic choriomeningitis virus (LCMV) from Arenaviridae. Increased Dicer activity in Dicer{Delta}HEL1/wt mice did not elicit any antiviral effect. supporting insignificant antiviral function of endogenous mammalian RNAi in vivo. However, we also report that sufficiently high expression of Dicer{Delta}HEL1 suppressed LCMV in embryonic stem cells and in a transgenic mouse model. Altogether, mice with increased Dicer activity offer a new benchmark for identifying and studying viruses susceptible to mammalian RNAi in vivo.

molecular biology↗

bioRxiv2022

Human neutralizing antibodies to cold linear epitopes and to subdomain 1 of SARS-CoV-2

Emergence of SARS-CoV-2 variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes. Antibody fp.006 binds the fusion peptide and cross-reacts against coronaviruses of the four genera, including the nine human coronaviruses, through recognition of a conserved motif that includes the S2 site of proteolytic cleavage. Antibody hr2.016 targets the stem helix and neutralizes SARS-CoV-2 variants. Antibody sd1.040 binds to subdomain 1, synergizes with antibody rbd.042 for neutralization and, like fp.006 and hr2.016, protects mice when present as bispecific antibody. Thus, coldspot-guided antibody discovery reveals donor-derived neutralizing antibodies that are cross-reactive with Orthocoronavirinae, including SARS-CoV-2 variants. One sentence summaryBroadly cross-reactive antibodies that protect from SARS-CoV-2 variants are revealed by virus coldspot-driven discovery.

immunology↗

bioRxiv2022

Integrative assessment of the transcriptome and virome of the poultry red mite Dermanyssus gallinae.

Dermanyssus gallinae is a blood-feeding mite that parasitises on wild birds and farmed poultry. The D. gallinae mite has a short life cycle of fewer than two weeks from the egg to an egg-laying female. The remarkably swift processing of blood, together with the capacity to blood-feed in most developmental stages, makes this mite a highly debilitating pest. We have constructed developmental stage-specific transcriptomes, through Illumina RNA-seq, to mine the repertoire of protein-encoding mRNA transcripts, products of which participate in key processes that ensure the success of blood digestion, rapid ontogeny, and immunity. As a result of high reproductive capacity, the prevalence of D. gallinae in egg-producing poultry farms globally causes significant economic losses. Acaricides that are used to limit the reproduction of D. gallinae mites target cys-loop ion channels, which are widely shared across the phylogeny of invertebrates. To catalogue a comprehensive list of potential invertebrate-specific ion channels, we have constructed and analysed an additional RNA-seq library of D. gallinae micro-dissected midguts, a tissue with direct exposure to host blood and potential anti-parasitics. We phylogenetically defined groups of cys-loop proteins and probed their sensitivity to selected acaricides. Ultimately, we have catalogued all assembled transcripts and their expression values in a hyper-linked excel sheet with available sequences of individual contigs. The transcriptomic data were complemented by mass-spectrometry (MS)-based metabolite identification and by viability assays using selected inhibitors applied either by microinjection or through artificial membrane feeding. Additionally, we have described the RNA-virome of D. gallinae and identified a novel virus dubbed Red Mite Quaranjavirus 1.

microbiology↗

bioRxiv2021

Bispecific antibody prevents SARS-CoV-2 escape and protects mice from disease

Neutralizing antibodies targeting the receptor binding domain (RBD) of the SARS-CoV-2 Spike (S) are among the most promising approaches against coronavirus disease 2019 (COVID-19)1,2. We developed a bispecific, IgG1-like molecule (CoV-X2) based on two antibodies derived from COVID-19 convalescent donors, C121 and C1353. CoV-X2 simultaneously binds two independent sites on the RBD and, unlike its parental antibodies, prevents detectable S binding to Angiotensin-Converting Enzyme 2 (ACE2), the virus cellular receptor. Furthermore, CoV-X2 neutralizes SARS-CoV-2 and its variants of concern, as well as the escape mutants generated by the parental monoclonals. In a novel animal model of SARS-CoV-2 infection with lung inflammation, CoV-X2 protects mice from disease and suppresses viral escape. Thus, simultaneous targeting of non-overlapping RBD epitopes by IgG-like bispecific antibodies is feasible and effective, combining into a single molecule the advantages of antibody cocktails.

immunology↗

bioRxiv2021

Low-pathogenic virus induced immunity against TBEV protects mice from disease but not from virus entry into the CNS

Tick-borne encephalitis virus (TBEV) is a leading cause of vector-borne viral encephalitis with expanding endemic regions across Europe. Although currently used inactivated whole virus vaccines are effective, vaccination breakthroughs have been reported for which the reasons are unclear. In this study we tested in mice the efficacy of pre-infection with a closely related low-virulent flavivirus, Langat virus (LGTV strain TP21), or a naturally avirulent TBEV strain (TBEV-280) in providing protection against lethal infection with the highly virulent TBEV strain TBEV-Hypr (referred to as TBEV-Hypr). LGTV has been evaluated as an experimental live vaccine against TBE, but further development was abandoned due to too high residual pathogenicity of a LGTV-based vaccine. Here we show that prior infection with TP21 or TBEV-280 is efficient in protecting mice from lethal TBEV-Hypr challenge. Histopathological analysis of brains from non-immunized control mice revealed neuronal TBEV infection and necrosis. Neuroinflammation, gliosis and neuronal necrosis was however also observed in some of the TP21 and TBEV-280 pre-infected mice although at reduced frequency as compared to the non-immunized TBEV-Hypr infected control mice. Interestingly, qPCR detected the presence of viral RNA in the brains and spinal cord of both TP21 and TBEV-280 immunized mice after TBEV-Hypr challenge, but significantly reduced compared to mock-immunized mice. Our results indicate that although TBEV-Hypr infection is effectively controlled in the periphery upon immunization with low-virulent LGTV or naturally avirulent TBEV-280, it may still enter the CNS of these animals. These findings improve our understanding of potential causes for vaccine failure in individuals vaccinated with TBE vaccines.

immunology↗