Authors: Carla Ruiz-Casas , Ferran Tarrés-Freixas, Núria Roca , Mònica Pérez , Guillermo Cantero , Laura Martín , Alex Olvera , Marta Ruiz-Riol , Christian Brander, Carla Usai, Júlia Vergara-Alert, and Joaquim Segalés
Publications and Resources
Publications
Long-term neurocognitive outcomes of SARS-CoV-2 infection in a hamster model
Abstract
Objectives. Post-COVID-19 condition (PCC) is a long-lasting, multisystemic syndrome affecting approximately 30% of individuals after acute COVID-19, with neurological symptoms among the most prevalent and debilitating. Despite its substantial global health impact, the biological mechanisms underlying PCC remain poorly understood, underscoring the need for validated animal models.
Methods. To address this, we conducted a longitudinal study using the golden Syrian hamster model, integrating virological, immunological, histopathological, and behavioral analyses from the acute phase to 60 days post-inoculation.
Results. Our results showed persistent viral RNA, prolonged immune dysregulation, and behavioral changes that mirrored key features of human PCC.
Discussion. Although fully reproducing PCC in animal models is inherently challenging due to its complex and heterogeneous presentation in humans, the use of complementary models with distinct phenotypes is essential for elucidating its pathophysiology. These results aim to contribute valuable insights into the biological basis of PCC and support the development of targeted preventative and therapeutic strategies.
Journal: Frontiers in Microbiology
Date: 2025 August 14
Vagus nerve dysfunction in the post–COVID-19 condition: a pilot cross-sectional study
Authors: Gemma Lladós, Marta Massanella, Roser Coll-Fernández, Raúl Rodríguez, Electra Hernández, Giuseppe Lucente, Cristina López, Cora Loste, José Ramón Santos, Sergio España-Cueto, Maria Nevot, Francisco Muñoz-López, Sandra Silva-Arrieta, Christian Brander, Maria José Durà, Patricia Cuadras, Jordi Bechini, Montserrat Tenesa, Alicia Martinez-Piñeiro, Cristina Herrero, Anna Chamorro, Anna Garcia, Eulalia Grau, Bonaventura Clotet, Roger Paredes, Lourdes Mateu, on behalf of theGermans Trias Long-COVID Unit group
Abstract
Objectives. The post–COVID-19 condition (PCC) is a disabling syndrome affecting at least 5%–10% of subjects who survive COVID-19. SARS-CoV-2 mediated vagus nerve dysfunction could explain some PCC symptoms, such as dysphonia, dysphagia, dyspnea, dizziness, tachycardia, orthostatic hypotension, gastrointestinal disturbances, or neurocognitive complaints.
Methods. We performed a cross-sectional pilot study in subjects with PCC with symptoms suggesting vagus nerve dysfunction (n = 30) and compared them with subjects fully recovered from acute COVID-19 (n = 14) and with individuals never infected (n = 16). We evaluated the structure and function of the vagus nerve and respiratory muscles.
Results. Participants were mostly women (24 of 30, 80%), and the median age was 44 years (interquartile range [IQR] 35–51 years). Their most prevalent symptoms were cognitive dysfunction 25 of 30 (83%), dyspnea 24 of 30 (80%), and tachycardia 24 of 30 (80%). Compared with COVID-19-recovered and uninfected controls, respectively, subjects with PCC were more likely to show thickening and hyperechogenic vagus nerve in neck ultrasounds (cross-sectional area [CSA] [mean ± standard deviation]: 2.4 ± 0.97mm2 vs. 2 ± 0.52mm2 vs. 1.9 ± 0.73 mm2; p 0.08), reduced esophageal-gastric-intestinal peristalsis (34% vs. 0% vs. 21%; p 0.02), gastroesophageal reflux (34% vs. 19% vs. 7%; p 0.13), and hiatal hernia (25% vs. 0% vs. 7%; p 0.05). Subjects with PCC showed flattening hemidiaphragms (47% vs. 6% vs. 14%; p 0.007), and reductions in maximum inspiratory pressure (62% vs. 6% vs. 17%; p ≤ 0.001), indicating respiratory muscle weakness. The latter findings suggest additional involvement of the phrenic nerve.
Discussion. Vagus and phrenic nerve dysfunction contribute to the complex and multifactorial pathophysiology of PCC.
Journal: Clinical Microbiology and Infection
Date: 2023 November 19
Animal models to study the neurological manifestations of the post-COVID-19 condition
Authors: Carla Usai, Lourdes Mateu, Christian Brander, Júlia Vergara-Alert and Joaquim Segalés.
Abstract
More than 40% of individuals infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have experienced persistent or relapsing multi-systemic symptoms months after the onset of coronavirus disease 2019 (COVID-19). This post-COVID-19 condition (PCC) has debilitating effects on the daily life of patients and encompasses a broad spectrum of neurological and neuropsychiatric symptoms including olfactory and gustative impairment, difficulty with concentration and short-term memory, sleep disorders and depression. Animal models have been instrumental to understand acute COVID-19 and validate prophylactic and therapeutic interventions. Similarly, studies post-viral clearance in hamsters, mice and nonhuman primates inoculated with SARS-CoV-2 have been useful to unveil some of the aspects of PCC. Transcriptomic alterations in the central nervous system, persistent activation of immune cells and impaired hippocampal neurogenesis seem to have a critical role in the neurological manifestations observed in animal models infected with SARS-CoV-2. Interestingly, the proinflammatory transcriptomic profile observed in the central nervous system of SARS-CoV-2-inoculated mice partially overlaps with the pathological changes that affect microglia in humans during Alzheimer’s disease and aging, suggesting shared mechanisms between these conditions. None of the currently available animal models fully replicates PCC in humans; therefore, multiple models, together with the fine-tuning of experimental conditions, will probably be needed to understand the mechanisms of PCC neurological symptoms. Moreover, given that the intrinsic characteristics of the new variants of concern and the immunological status of individuals might influence PCC manifestations, more studies are needed to explore the role of these factors and their combinations in PCC, adding further complexity to the design of experimental models.
Plasma proteomic profiling identifies CD33 as a marker of HIV control in natural infection and after therapeutic vaccination
Authors: Clara Duran-Castells, Anna Prats, Bruna Oriol-Tordera, Anuska Llano, Cristina Galvez, Javier Martinez-Picado, Ester Ballana, Edurne Garcia-Vidal, Bonaventura Clotet, Jose A Muñoz-Moreno, Thomas Hanke, José Moltó, Beatriz Mothe, Christian Brander, Marta Ruiz-Riol.
Abstract
Background: Biomarkers predicting the outcome of HIV-1 virus control in natural infection and after therapeutic interventions in HIV-1 cure trials remain poorly defined. The BCN02 trial (NCT02616874), combined a T-cell vaccine with romidepsin (RMD), a cancer-drug that was used to promote HIV-1 latency reversal and which has also been shown to have beneficial effects on neurofunction. We conducted longitudinal plasma proteomics analyses in trial participants to define biomarkers associated with virus control during monitored antiretroviral pause (MAP) and to identify novel therapeutic targets that can improve future cure strategies.
Methods: BCN02 was a phase I, open-label, single-arm clinical trial in early-treated, HIV infected individuals. Longitudinal plasma proteomes were analyzed in 11 BCN02 participants, including 8 participants that showed a rapid HIV-1 plasma rebound during a monitored antiretroviral pause (MAP-NC, ‘non-controllers’) and 3 that remained off ART with sustained plasma viremia <2000 copies/ml (MAP-C, ‘controllers’). Inflammatory and neurological proteomes in plasma were evaluated and integration data analysis (viral and neurocognitive parameters) was performed. Validation studies were conducted in a cohort of untreated HIV-1+ individuals (n = 96) and in vitro viral replication assays using an anti-CD33 antibody were used for functional validation.
Findings: Inflammatory plasma proteomes in BCN02 participants showed marked longitudinal alterations. Strong proteome differences were also observed between MAP-C and MAP-NC, including in baseline timepoints. CD33/Siglec-3 was the unique plasma marker with the ability to discriminate between MAPC-C and MAP-NC at all study timepoints and showed positive correlations with viral parameters. Analyses in an untreated cohort of PLWH confirmed the positive correlation between viral parameters and CD33 plasma levels, as well as PBMC gene expression. Finally, adding an anti-CD33 antibody to in vitro virus cultures significantly reduced HIV-1 replication and proviral levels in T cells and macrophages.
Sirtuin-2, NAD-Dependent Deacetylase, Is a New Potential Therapeutic Target for HIV-1 Infection and HIV-Related Neurological Dysfunction
Authors: Clara Duran-Castells, Anuska Llano, Ai Kawana-Tachikawa, Anna Prats, Ignacio Martinez-Zalacain, Mie Kobayashi-Ishihara, Bruna Oriol-Tordera, Ruth Peña, Cristina Gálvez, Sandra Silva-Arrieta, Bonaventura Clotet, Eva Riveira-Muñoz, Esther Ballana, Julia G. Prado, Javier Martinez-Picado, Jorge Sanchez, Beatriz Mothe, Dennis Hartigan-O’Connor, Tony Wyss-Coray, Andreas Meyerhans, Magnus Gisslén, Richard W. Price, Carles Soriano-Mas, José Antonio Muñoz-Moreno, Christian Brander, and Marta Ruiz-Riol.
Abstract
The implementation and access to combined antiretroviral treatment (cART) have dramatically improved the quality of life of people living with HIV (PLWH). However, some comorbidities, such as neurological disorders associated with HIV infection still represent a serious clinical challenge. Soluble factors in plasma that are associated with control of HIV replication and neurological dysfunction could serve as early biomarkers and as new therapeutic targets for this comorbidity. We used a customized antibody array for determination of blood plasma factors in 40 untreated PLWH with different levels of viremia and found sirtuin-2 (SIRT2), an NAD-dependent deacetylase, to be strongly associated with elevated viral loads and HIV provirus levels, as well as with markers of neurological damage (a-synuclein [SNCA], brain-derived neurotrophic factor [BDNF], microtubule-associated protein tau [MAPT], and neurofilament light protein [NFL]). Also, longitudinal analysis in HIV-infected individuals with immediate (n = 9) or delayed initiation (n = 10) of cART revealed that after 1 year on cART, SIRT2 plasma levels differed between both groups and correlated inversely with brain orbitofrontal cortex involution. Furthermore, targeting SIRT2 with specific small-molecule inhibitors in in vitro systems using J-LAT A2 and primary glial cells led to diminished HIV replication and virus reactivation from latency. Our data thus identify SIRT2 as a novel biomarker of uncontrolled HIV infection, with potential impact on neurological dysfunction and offers a new therapeutic target for HIV treatment and cure.
Skin treatment with non-thermal plasma modulates the immune system through miR-223-3p and its target genes
Authors: Annika Engel, Nicole Ludwig, Friederike Grandke, Viktoria Wagner, Fabian Kern, Tobias Fehlmann, Georges P Schmartz, Ernesto Aparicio-Puerta, Dominic Henn, Barbara Walch-Rückheim, Matthias Hannig, Stefan Rupf, Eckart Meese, Matthias W Laschke, Andreas Keller.
Abstract
Non-thermal plasma, a partially ionized gas, holds significant potential for clinical applications, including wound-healing support, oral therapies, and anti-tumour treatments. While its applications showed promising outcomes, the underlying molecular mechanisms remain incompletely understood. We thus apply non-thermal plasma to mouse auricular skin and conducted non-coding RNA sequencing, as well as single-cell blood sequencing. In a time-series analysis (five timepoints spanning 2 hours), we compare the expression of microRNAs in the plasma-treated left ears to the unexposed right ears of the same mice as well as to the ears of unexposed control mice. Our findings indicate specific effects in the treated ears for a set of five miRNAs: mmu-miR-144-5p, mmu-miR-144-3p, mmu-miR-142a-5p, mmu-miR-223-3p, and mmu-miR-451a. Interestingly, mmu-miR-223-3p also exhibits an increase over time in the right non-treated ear of the exposed mice, suggesting systemic effects. Notably, this miRNA, along with mmu-miR-142a-5p and mmu-miR-144-3p, regulates genes and pathways associated with wound healing and tissue regeneration (namely ErbB, FoxO, Hippo, and PI3K-Akt signalling). This co-regulation is particularly remarkable considering the significant seed dissimilarities among the miRNAs. Finally, single-cell sequencing of PBMCs reveals the downregulation of 12 from 15 target genes in B-cells, Cd4+ and Cd8+ T-cells. Collectively, our data provide evidence for a systemic effect of non-thermal plasma.
SingmiR: a single-cell miRNA alignment and analysis tool
Authors: Annika Engel; Shusruto Rishik; Pascal Hirsch; Verena Keller; Tobias Fehlmann; Fabian Kern; Andreas Keller
Abstract
Single-cell RNA sequencing (RNA-seq) has revolutionized our understanding of cell biology, developmental and pathophysiological molecular processes, paving the way toward novel diagnostic and therapeutic approaches. However, most of the gene regulatory processes on the single-cell level are still unknown, including post-transcriptional control conferred by microRNAs (miRNAs). Like the established single-cell gene expression analysis, advanced computational expertise is required to comprehensively process newly emerging single-cell miRNA-seq datasets. A web server providing a workflow tailored for single-cell miRNA-seq data with a self-explanatory interface is currently not available. Here, we present SingmiR, enabling the rapid (pre-)processing and quantification of human miRNAs from noncoding single-cell samples. It performs read trimming for different library preparation protocols, generates automated quality control reports and provides feature-normalized count files. Numerous standard and advanced analyses such as dimension reduction, clustered feature heatmaps, sample correlation heatmaps and differential expression statistics are implemented. We aim to speed up the prototyping pipeline for biologists developing single-cell miRNA-seq protocols on small to medium-sized datasets. SingmiR is freely available to all users without the need for a login at https://www.ccb.uni-saarland.de/singmir.
Mibianto: ultra-efficient online microbiome analysis through k-mer based metagenomics
Authors: Pascal Hirsch; Leidy-Alejandra G Molano; Annika Engel; Jens Zentgraf; Sven Rahmann; Matthias Hannig; Rolf Müller; Fabian Kern; Andreas Keller; Georges P Schmartz
Abstract
Quantifying microbiome species and composition from metagenomic assays is often challenging due to its time-consuming nature and computational complexity. In Bioinformatics, k-mer-based approaches were long established to expedite the analysis of large sequencing data and are now widely used to annotate metagenomic data. We make use of k-mer counting techniques for efficient and accurate compositional analysis of microbiota from whole metagenome sequencing. Mibianto solves this problem by operating directly on read files, without manual preprocessing or complete data exchange. It handles diverse sequencing platforms, including short single-end, paired-end, and long read technologies. Our sketch-based workflow significantly reduces the data volume transferred from the user to the server (up to 99.59% size reduction) to subsequently perform taxonomic profiling with enhanced efficiency and privacy. Mibianto offers functionality beyond k-mer quantification; it supports advanced community composition estimation, including diversity, ordination, and differential abundance analysis. Our tool aids in the standardization of computational workflows, thus supporting reproducibility of scientific sequencing studies. It is adaptable to small- and large-scale experimental designs and offers a user-friendly interface, thus making it an invaluable tool for both clinical and research-oriented metagenomic studies. Mibianto is freely available without the need for a login at: https://www.ccb.uni-saarland.de/mibianto
A single-cell atlas to map sex-specific gene-expression changes in blood upon neurodegeneration
Authors: Friederike Grandke; Tobias Fehlmann; Fabian Kern; David M. Gate; Tobias William Wolff; Olivia Leventhal; Divya Channappa; Pascal Hirsch; Edward N. Wilson; Eckart Meese; Chuanyu Liu; Quan Shi; Matthias Flotho; Yongping Li; Cynthia Chen; Yeya Yu; Jiangshan Xu; Michael Junkin; Zhifeng Wang; Tao Wu; Longqi Liu; Yong Hou; Katrin I. Andreasson; Jenny S. Gansen; Elvira Mass; Kathleen Poston; Tony Wyss-Coray; Andreas Keller
Abstract
The clinical course and treatment of neurodegenerative disease are complicated by immune-system interference and chronic inflammatory processes, which remain incompletely understood. Mapping immune signatures in larger human cohorts through single-cell gene expression profiling supports our understanding of observed peripheral changes in neurodegeneration. Here, we employ single-cell gene expression profiling of over 909k peripheral blood mononuclear cells (PBMCs) from 121 healthy individuals, 48 patients with mild cognitive impairment (MCI), 46 with Parkinson’s disease (PD), 27 with Alzheimer’s disease (AD), and 15 with both PD and MCI. The dataset is interactively accessible through a freely available website (https://www.ccb.uni-saarland.de/adrcsc). In this work, we identify disease-associated changes in blood cell type composition and the gene expression in a sex-specific manner, offering insights into peripheral and solid tissue signatures in AD and PD.
Time to HIV viral rebound and frequency of post-treatment control after analytical interruption of antiretroviral therapy: an individual data-based meta-analysis of 24 prospective studies
Authors:
Abstract
The only current strategy to test efficacy of novel interventions for sustained HIV control without antiretroviral therapy (ART) among people with HIV (PWH) is through an analytical treatment interruption (ATI). Inclusion of ‘placebo’ controls in ATIs poses ethical, logistical, and economic challenges. To understand viral dynamics and rates of post-treatment control (PTC) after ATI among PWH receiving either placebo or no intervention, we undertook an individual-participant data meta-analysis. In total, 24 eligible prospective studies with 382 individuals with ≥5 plasma HIV RNA viral loads (pVLs) within the first 84 days post-ATI were included. Early-ART was defined as ART initiation within 6 months of HIV acquisition; others were classified as late-ART or unknown. Median age was 42 years, 91% male, 75% white, 45% received early-ART. Median time to pVL >50, >400, and >10,000 copies/mL was 16 days (interquartile range [IQR]:13-25), 21 (IQR:15-28), and 32 (IQR:20-35), respectively. PTC defined as pVL <50 copies/mL at day 84 occurred in 4% (n = 14) of participants (6% early-ART and 1% late-ART). Sustained PTC of pVL <50 copies/ml after 84 days is rare in PWH, especially in those starting ART late. Our findings inform future interventional HIV cure/remission trials on study size and design.
