Biology subjects

Brazdilova, K.

Publications and source records attributed to Brazdilova, K..

5 recordsLinked to original sources

bioRxiv2026

Tissue-resident memory T cells are diminished in the Kaposi sarcoma tumor microenvironment of people living with HIV

Kaposi sarcoma (KS) is a rare neoplasm and an AIDS-defining diagnosis in people living with HIV (PLWH). Although and chronic infection with Kaposi sarcoma-associated herpesvirus (KSHV) contributes to KS progression, the local immune mechanisms that are lost during tumor progression remain incompletely understood. Here, we systematically characterized global patterns in the KS tumor microenvironment (TME) in both PLWH and HIV-negative individuals. Spatial transcriptomics revealed distinct niches comprising of tumor cells, immune cells, and surrounding skin cells. Tumor regions expressed a characteristic endothelial-fibroblastic signature attributable to KS tumor cells (CD34, LYVE1, SCN9A), TME regions expressed marker genes for T cells, B cells and cancer-associated fibroblasts. Analysis of putative cell-cell interactions demonstrated that tumor cells preferentially interact with cells of the TME, including T cells, indicating an important role as hub of cellular communication in KS. Immunofluorescence imaging confirmed increased numbers of T cells, specifically tissue-resident memory T cells (TRM), in KS samples compared to healthy skin, accompanied by a pronounced upregulation of PD-1 expression that was predominantly localized to the TME. Notably, we identified HIV-associated alterations in the KS immune microenvironment: PLWH exhibited loss of CXCR3+ and IFN-gamma producing CD8+ TRM cells in the KS TME compared to HIV-negative patients, a finding consistent with impaired antitumor immunity. Together, our findings reveal HIV-associated disruption of functional anti-tumor immunity in the KS TME of PLWH. Increased PD-1 expression within T cells of the TME highlights potential therapeutic use of immune checkpoint inhibitors in KS.

immunology↗

bioRxiv2026

Alternatively polarized neutrophils metabolically restrain macrophage-driven inflammation

Macrophage-driven inflammation underlies many inflammatory diseases, yet the mechanisms that restrain macrophage activation within inflamed tissues remain poorly understood. Using mouse models of foreign body granuloma formation and macrophage activation syndrome, we show that neutrophils accumulate at sites of inflammation and metabolically restrain macrophage-driven pathology. Neutrophil depletion or genetic impairment exacerbated tissue pathology, whereas induced neutrophilia attenuated inflammatory damage. Tissue-infiltrating neutrophils acquired an alternatively polarized state characterized by high arginase 1 activity that was regulated by an IL4Ra-STAT3-NOX2 signaling axis. Functionally, polarized neutrophils depleted extracellular arginine in an arginase 1-dependent manner, thereby limiting macrophage effector programs. Human neutrophils exhibited conserved regulation of arginase activity, and alternatively polarized neutrophils were detected in patients with sarcoidosis and macrophage activation syndrome. Together, these findings identify an arginine-dependent metabolic mechanism through which alternatively polarized neutrophils restrain macrophage-driven inflammation and reveal a previously unrecognized immune-regulatory role for these cells in chronic inflammatory disease.

immunology↗

bioRxiv2025

Uncovering the transcriptional hallmarks of endothelial cell aging via integrated single-cell analysis

Endothelial cells (ECs) are critical regulators of vascular function and exhibit specialized, organ-specific roles across tissues. During aging, these cells become dysfunctional, resulting in increased susceptibility to cardiovascular disease and its associated mortality. While single-cell transcriptomics studies have revealed extensive endothelial heterogeneity across tissues and conditions, a comprehensive atlas of human EC transcriptomes over the course of the adult human lifespan is still lacking. Here, we present the Human Aging Endothelial Cell Atlas (HAECA), a harmonized single-cell transcriptomic compendium of over 375,000 ECs from 12 human tissues throughout adulthood. Using HAECA, we identified age-associated transcriptional shifts, including a decline in angiogenic gene expression in venous ECs and widespread alterations in extracellular matrix (ECM)- and mechanotransduction-associated pathways. We validated these findings in aging human skin and further uncovered a p21-linked transcriptional program in ECs, confirmed in both in vitro and in vivo models and linked to cellular senescence. Together, our study provides a high-resolution transcriptome reference across spatial as well as temporal axes of the human endothelium.

cell biology↗

bioRxiv2022

TraceTrack, an Open-Source Software for Batch Processing, Alignment and Visualization of Sanger Sequencing Chromatograms

BackgroundDespite the advent of Next Generation Sequencing technology and its widespread applications, Sanger sequencing remains instrumental for molecular biology subcloning work in biological and medical research and indispensable for drug discovery campaigns. Although Sanger sequencing technology has been long established, existing software for processing and visualization of trace file chromatograms are limited in terms of functionality, scalability, and availability for commercial use. ResultsTo fill this gap, we developed TraceTrack, an open-source web application tool for batch alignment, analysis and visualization of Sanger trace files. TraceTrack offers high throughput matching of trace files to reference sequences, rapid identification of mutations and an intuitive chromatogram analysis. Comparative analysis between TraceTrack and existing software tools highlights the advantages of TraceTrack with regards to batch processing, visualization and export functionalities. TraceTrack is available at https://github.com/Merck/TraceTrack and also at https://tracetrack.dichlab.org as a web application. ConclusionTraceTrack is a web application for batch processing and visualization of Sanger trace file chromatograms that meets the increasing demand of industrial sequence validation workflows in pharmaceutical settings.

bioinformatics↗

bioRxiv2022

mRNAid, an Open-Source Platform for Therapeutic mRNA Design and Optimization Strategies

Recent COVID-19 vaccines unleashed the potential of mRNA-based therapeutics. mRNA optimization is indispensable for reducing immunogenicity, ensuring stability, and maximizing protein output. We present mRNAid, an experimentally validated software for mRNA optimization and visualization that generates mRNA sequences with comparable if not superior characteristics to commercially optimized sequences. To encompass all aspects of mRNA design, we also interrogated the impact of uridine content, nucleoside analogs and UTRs on expression and immunogenicity.

bioinformatics↗