Biology subjects

Cornberg, M.

Publications and source records attributed to Cornberg, M..

4 recordsLinked to original sources

bioRxiv2025

Non-selective beta blockers reduce bystander CD8+ T cell activation in decompensated liver cirrhosis

Cirrhosis is characterized by immune dysfunction in which activated CD8 T cells fuel systemic inflammation and disease progression. Non-selective beta-blockers (NSBB), widely prescribed for portal hypertension, have incompletely understood immunomodulatory effects. Here we show that CD8 T cells express {beta}2-adrenergic receptors, enriched in bystander relative to antigen-specific subsets. In vitro, the NSBB propranolol selectively suppressed cytokine-driven bystander activation, reducing CD69CXCR6 and NKG2D populations and pro-inflammatory cytokines, while preserving antigen-specific responses. Transcriptomic profiling after NSBB treatment revealed downregulation of interferon signaling pathway via STAT1. In paired blood and ascites samples from patients with decompensated cirrhosis (n = 31), NSBB therapy was associated with reduced bystander-activated CD8 T cells. In a retrospective cohort (n = 624), NSBB therapy correlated with lower systemic and intrahepatic inflammation. These findings identify {beta}-adrenergic blockade as a mechanism that restrains bystander CD8 T cell responses without impairing antigen-specific immunity, supporting NSBB therapy as a strategy to mitigate inflammation and improve outcomes in cirrhosis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/688703v1_ufig1.gif" ALT="Figure 1000"> View larger version (29K): org.highwire.dtl.DTLVardef@191c6dcorg.highwire.dtl.DTLVardef@196aef0org.highwire.dtl.DTLVardef@1b73c83org.highwire.dtl.DTLVardef@e5d6fb_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Unifying DNA methylation-based in silico cell-type deconvolution with methyldeconv

SummaryCell-type deconvolution is widely applied to gene expression and DNA methylation data, but access to methods for the latter remains limited. We introduce deconvMe, a new R package that simplifies access to DNA methylation-based deconvolution methods predominantly for blood data, and we additionally compare their estimates to those from gene expression and experimental ground truth data using a unique matched blood dataset.

bioinformatics↗

bioRxiv2025

Detection of Paracoccus yeei in Spontaneous Bacterial Peritonitis using Rapid, Long Read Sequencing

Ascites is a common complication in patients with decompensated liver cirrhosis. Spontaneous bacterial peritonitis (SBP) is the most frequent infection, affecting up to 30% of hospitalized patients with ascites. Multidrug-resistant bacteria in patients with liver cirrhosis are becoming more common, particularly in nosocomial infections. With early detection and adequate antibiotic therapy, the mortality rate of SBP can be reduced from over 90% to 15-20%. However, the etiologic agent remains undetected by conventional pathogen diagnostics from ascites in more than half of the patients. Here, we describe a robust workflow combining long read metagenome sequencing with best practices for low microbial biomass sample processing and bioinformatic analytics, to detect and characterize pathogens from the cirrhotic ascites of SBP patients, as a complement to routine microbiological diagnostics. This approach identified Paracoccus yeei as a likely etiologic agent for a patient who developed a fever after successful treatment of an Escherichia coli infection. Analysis of the genome of P. yeei recovered directly from ascites delineated pathogenicity-related features and an antimicrobial resistance profile consistent with the patients treatment. Pangenome phylogenetics placed the P. yeei strain closest to isolates associated with abdominal infections. Our study underscores the utility of metagenomics for a rapid and comprehensive assessment of infectious agents, suggesting a novel and rarely reported pathogen contributing to SBP with potential implications for diagnostics and therapeutic strategies. ImportanceOur study demonstrates the clinical utility of real-time, long-read metagenomics in identifying elusive pathogens in Spontaneous Bacterial Peritonitis (SBP), a condition with high mortality and frequently inconclusive conventional diagnostics. By uncovering Paracoccus yeei as a likely secondary etiologic agent and characterizing its pathogenicity and AMR profile, our findings expand the known etiology of SBP and emphasize the potential of metagenomics to improve diagnostic accuracy, guide targeted treatment, and ultimately reduce mortality rates in infectious diseases. This approach could shape future clinical practice for managing complex infections.

microbiology↗

bioRxiv2024

Enhancing HBV-specific T cell responses through a combination of epigenetic modulation and immune checkpoint inhibition

ObjectiveChronic hepatitis B virus (HBV) infection results in the exhaustion of HBV-specific T cells and the development of epigenetic imprints that impair immune responses and limit the effectiveness of immune checkpoint inhibitor (ICI) monotherapy, such as PD-L1. This study aimed to determine whether the DNA methyltransferase inhibitor decitabine (DAC) can reverse these epigenetic imprints and enhance the efficacy of ICI in restoring HBV-specific T cell responses. MethodsWe investigated HBV-specific CD4+ and CD8+ T cell responses by 10-day in vitro stimulation of peripheral blood mononuclear cells (PBMCs) from patients with chronic HBV infection. PBMCs were stimulated with HBV core-specific overlapping peptide pools and HLA-A*02-restricted peptides, including core18 and pol455. The immunomodulatory effect of the combination of DAC/PD-L1 was assessed via flow cytometry. Responder stratification was investigated by comparison of clinical characteristics, ex vivo DNA methylation analysis of PBMCs, and determination of IFN{gamma} plasma levels. ResultsTreatment with DAC and PD-L1 enhanced HBV-specific CD4+ T cell responses in a significant proportion of 53 patients, albeit with variability. The effect was independent of the HBcrAg level. Ex vivo DNA methylation revealed hypermethylation of key genes like IFNG among DAC-responders versus non-responders, supported by altered ex vivo IFN{gamma} plasma levels. Further analysis of HBV-specific CD8+ T cell responses in 22 HLA-A*02-positive patients indicated distinct response patterns between HBV-core18- and HBV-pol455-specific T cells, with pol455-specific CD8+ T cells showing increased susceptibility to DAC/PD-L1, surpassing PD-L1 monotherapy response. ConclusionsThe combination of DAC and PD-L1 shows promising effects in improving HBV-specific T cell responses in vitro. Our study highlights the potential of remodeling exhaustion-associated epigenetic signatures to enhance HBV-specific T cell restoration, suggesting a novel immunotherapeutic avenue for chronic HBV infections. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/611632v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@156d0fborg.highwire.dtl.DTLVardef@b22d2corg.highwire.dtl.DTLVardef@1b3c4e2org.highwire.dtl.DTLVardef@1430bbf_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIRemodeling epigenetic signatures with a DNA methyltransferase inhibitor enhances the effectiveness of immune checkpoint inhibition in restoring HBV-specific T cell responses. C_LIO_LIResponsiveness is associated with specific IFN{gamma} DNA methylation patterns and plasma levels. C_LIO_LIEpigenetic remodeling had distinct effects on two CD8 T cell epitopes, with more pronounced effects on HBV-pol455-specific CD8+ T cell responses. C_LI

immunology↗