Biology subjects

Jankowski, J.

Publications and source records attributed to Jankowski, J..

8 recordsLinked to original sources

bioRxiv2025

The role of Platelet-derived growth factor (PDGF) in uremic vascular calcification.

Vascular calcification is common in chronic kidney disease (CKD), contributing to increased cardiovascular morbidity and mortality. One of the proposed mechanisms of driving vascular calcification is a phenotypic switch of vascular smooth muscle cells (VSMCs). The platelet-derived growth factors (PDGFs) and their receptors (PDGFRs), particularly PDGFR-{beta}, were shown to modulate the VSMC phenotype. However, their role in uremic vascular calcification remained unclear. We adapted an ex vivo calcification model using murine aortas to simulate uremic conditions. Compared to control conditions, incubation with hemodialysate from CKD patients or using aortas from CKD animals both resulted in significantly increased PDGFR-{beta} phosphorylation and vascular calcification. Inhibition of PDGF signaling using soluble PDGFR-{beta} or the small molecule tyrosine kinase inhibitor imatinib significantly reduced uremic calcification and enhanced vascular elasticity. Next, we generated transgenic mice with a VSMC-specific, inducible expression of constitutively active PDGFR-{beta}. The aortas of these mice exhibited significantly increased vascular calcification ex vivo, which was further aggravated by uremic conditions. We established an in vivo model of accelerated vascular calcification and CKD in the transgenic mice, showing significantly aggravated vascular calcification and phenotypic switching of VSMCs compared to non-transgenic littermates. Finally, increased expression of phosphorylated PDGFR-{beta} and a VSMC phenotypic switching were detected in human arteries from patients with CKD compared to those without CKD. In conclusion, PDGFR-{beta} contributes to CKD-associated vascular calcification, representing a potential novel therapeutic target.

systems biology↗

bioRxiv2025

Y665F variant of mouse Stat5b protects against acute kidney injury through transcriptomic shifts in renal gene expression

The impact of single nucleotide polymorphisms (SNP) on physiology is often underestimated. One amino acid change can result in a variety of phenotypes apparent only in response to disease or injury. Even known pathogenic SNPs have widespread effects that are currently unaccounted for. In this study, we investigated the impact of the known activating and pathogenic STAT5BY665F mutation in a renal injury context in mice carrying this variant. Using ischemia-reperfusion model of acute kidney injury, immunohistochemistry, RNA-seq and ChIP-seq, we establish the protective role of STAT5B activation in renal epithelium and showcase the shifts in transcriptomic landscape in a tissue not associated with the usual human phenotype of the Stat5bY665F mutation. Our data indicate new links between the JAK/STAT pathway and known kidney injury markers, contribute to the understanding of the sexual dimorphism of renal disease, and provide new potential targets for JAK inhibitor- and amino acid transport modulation-based therapies.

genetics↗

bioRxiv2024

Sexually dimorphic renal expression of Klotho is directed by a kidney-specific distal enhancer responsive to HNF1b

Transcription enhancers are genomic sequences regulating common and tissue-specific genes and their disruption can contribute to human disease development and progression. Klotho, a sexually dimorphic gene specifically expressed in kidney, is well-linked to kidney dysfunction and its deletion from the mouse genome leads to premature aging and death. However, the sexually dimorphic regulation of Klotho is not understood. Here, we characterize two candidate Klotho enhancers using H3K27ac epigenetic marks and transcription factor binding and investigate their functions, individually and combined, through CRISPR-Cas9 genome engineering. We discovered that only the distal (E1), but not the proximal (E2) candidate region constitutes a functional enhancer, with the double deletion not causing Klotho expression to further decrease. E1 activity is dependent on HNF1b transcription factor binding site within the enhancer. Further, E1 controls the sexual dimorphism of Klotho as evidenced by qPCR and RNA- seq. Despite the sharp reduction of Klotho mRNA, unlike germline Klotho knockouts, mutant mice presented normal phenotype, including weight, lifespan, and serum biochemistry. Lastly, only males lacking E1 display more prominent acute, but not chronic kidney injury responses, indicating a remarkable range of potential adaptation to isolated Klotho loss, especially in female E1 knockouts, retaining renoprotection despite over 80% Klotho reduction.

genetics↗

bioRxiv2024

MicroRNA-26b protects against MASH development and can be efficiently targeted with lipid nanoparticles.

Background & AimsThe prevalence of metabolic dysfunction-associated steatohepatitis (MASH) is increasing, urging more research into the underlying mechanisms. MicroRNA-26b (miR-26b) might play a role in several MASH-related pathways. Therefore, we aimed to determine the role of miR-26b in MASH and its therapeutic potential using miR-26b mimic-loaded lipid nanoparticles (LNPs). MethodsApoe-/-Mir26b-/-, Apoe-/-LysMcreMir26bfl/fl mice, and respective controls were fed a western-type diet to induce MASH. Plasma and liver samples were characterized regarding lipid metabolism, hepatic inflammation, and fibrosis. Additionally, miR-26b mimic-loaded LNPs were injected in Apoe-/-Mir26b-/- mice to rescue the phenotype and key results were validated in human precision-cut liver slices. Finally, kinase profiling was used to elucidate underlying mechanisms. ResultsApoe-/-Mir26b-/- mice showed increased hepatic lipid levels, coinciding with increased expression of scavenger receptor a and platelet glycoprotein 4. Similar effects were found in mice lacking myeloid-specific miR-26b. Additionally, hepatic TNF and IL-6 levels and amount of infiltrated macrophages were increased in Apoe-/- Mir26b-/- mice. Moreover, Tgfb expression was increased by the miR-26b deficiency, leading to more hepatic fibrosis. A murine treatment model with miR-26b mimic-loaded LNPs reduced hepatic lipids, rescuing the observed phenotype. Kinase profiling identified increased inflammatory signaling upon miR-26b deficiency, which was rescued by LNP treatment. Finally, miR-26b mimic-loaded LNPs also reduced inflammation in human precision-cut liver slices. ConclusionsOverall, our study demonstrates that the detrimental effects of miR-26b deficiency in MASH can be rescued by LNP treatment. This novel discovery leads to more insight into MASH development, opening doors to potential new treatment options using LNP technology. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/580792v2_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@b8b5b8org.highwire.dtl.DTLVardef@a26333org.highwire.dtl.DTLVardef@11ed2a0org.highwire.dtl.DTLVardef@963208_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2023

circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging

MotivationCircular RNAs (circRNAs) are long non-coding RNAs (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis and treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline to systematically assess the sponging potential of circRNAs. ResultsWe developed circRNA-sponging, a nextflow pipeline that (1) identifies circRNAs via backsplicing junctions detected in RNA-seq data, (2) quantifies their expression values in relation to their linear counterparts spliced from the same gene, (3) performs differential expression analysis, (4) identifies and quantifies miRNA expression from miRNA-sequencing (miRNA-seq) data, (5) predicts miRNA binding sites on circRNAs, (6) systematically investigates potential circRNA-miRNA sponging events, (7) creates a network of competing endogenous RNAs, and (8) identifies potential circRNA biomarkers. We showed the functionality of the circRNA-sponging pipeline using RNA sequencing data from brain tissues, where we identified two distinct types of circRNAs characterized by a specific ratio of the number of the binding site to the length of the transcript. The circRNA-sponging pipeline is the first end-to-end pipeline to identify circRNAs and their sponging systematically with raw total RNA-seq and miRNA-seq files, allowing us to better indicate the functional impact of circRNAs as a routine aspect in transcriptomic research. Availabilityhttps://github.com/biomedbigdata/circRNA-sponging Contactmarkus.daniel.hoffmann@tum.de; markus.list@tum.de Supplementary MaterialSupplementary data are available at Bioinformatic Advances online.

bioinformatics↗

bioRxiv2022

TF-Prioritizer: a java pipeline to prioritize condition-specific transcription factors

BackgroundEukaryotic gene expression is controlled by cis-regulatory elements (CREs), including promoters and enhancers, which are bound by transcription factors (TFs). Differential expression of TFs and their binding affinity at putative CREs determine tissue- and developmental-specific transcriptional activity. Consolidating genomic data sets can offer further insights into the accessibility of CREs, TF activity, and, thus, gene regulation. However, the integration and analysis of multi-modal data sets are hampered by considerable technical challenges. While methods for highlighting differential TF activity from combined chromatin state data (e.g., ChIP-seq, ATAC-seq, or DNase-seq) and RNA-seq data exist, they do not offer convenient usability, have limited support for large-scale data processing, and provide only minimal functionality for visually interpreting results. ResultsWe developed TF-Prioritizer, an automated pipeline that prioritizes condition-specific TFs from multi-modal data and generates an interactive web report. We demonstrated its potential by identifying known TFs along with their target genes, as well as previously unreported TFs active in lactating mouse mammary glands. Additionally, we studied a variety of ENCODE data sets for cell lines K562 and MCF-7, including twelve histone modification ChIP-seq as well as ATAC-seq and DNase-seq datasets, where we observe and discuss assay-specific differences. ConclusionTF-Prioritizer accepts ATAC-seq, DNase-seq, or ChIP-seq and RNA-seq data as input and identifies TFs with differential activity, thus offering an understanding of genome-wide gene regulation, potential pathogenesis, and therapeutic targets in biomedical research.

bioinformatics↗

bioRxiv2021

Predicting Bird Distributions Under Global Change

An introduction to predictive distribution modelling for conservation to encourage novel perspectives. The rapid pace and potentially irreversible consequences of global change create an urgent need to predict the spatial responses of biota for conservation to better inform the prioritization and management of terrestrial habitats and prevent future extinctions. Here, we provide an accessible entry point to the field to guide near-future work building predictive species distribution models (SDMs) by synthesizing a technical framework for the proactive conservation of avian biodiversity. Our framework offers a useful approach to navigate the challenges surrounding the large spatio-temporal resolution of datasets and datasets that favor hypothesis testing at broad spatio-temporal scales and coarse resolutions, which can affect our ability to assess the validity of current predicted distributions. We explain how to improve the accuracy of predictive models by determining the extent to which: 1) dispersal limitation impacts the rate of range shifts, 2) taxa are rare at their range limits, and 3) land use and climate change interact. Finally, we offer approaches to filling knowledge gaps by creatively leveraging existing methods and data sources. RESUMENUna introduccion a la modelizacion predictiva de la distribucion para la conservacion con el fin de fomentar nuevas perspectivas. El rapido ritmo y las consecuencias potencialmente irreversibles del cambio global crean una necesidad urgente de predecir las respuestas espaciales de la biota para la conservacion, con el fin de informar mejor la priorizacion y gestion de los habitats terrestres y prevenir futuras extinciones. Aqui proporcionamos un punto de entrada accesible al campo para guiar el trabajo del futuro proximo en la construccion de modelos predictivos de distribucion de especies (SDM), sintetizando un marco tecnico para la conservacion proactiva de la biodiversidad aviar. Nuestro marco ofrece un enfoque util para navegar por los retos que rodean a la gran resolucion espacio-temporal de los conjuntos de datos y a los conjuntos de datos que favorecen la comprobacion de hipotesis a escalas espacio-temporales amplias y resoluciones gruesas, lo que puede afectar a nuestra capacidad para evaluar la validez de las distribuciones predichas actuales. Explicamos como mejorar la precision de los modelos predictivos determinando hasta que punto 1) la limitacion de la dispersion influye en el ritmo de los cambios de area de distribucion, 2) los taxones son raros en los limites de su area de distribucion, y 3) el uso del suelo y el cambio climatico interactuan. Por ultimo, proponemos enfoques para colmar las lagunas de conocimiento aprovechando de forma creativa los metodos y fuentes de datos existentes.

ecology↗

bioRxiv2021

Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules

Recently, a short, interferon-inducible isoform of Angiotensin-Converting Enzyme 2 (ACE2), dACE2 was identified. ACE2 is a SARS-Cov-2 receptor and changes in its renal expression have been linked to several human nephropathies. These changes were never analyzed in context of dACE2, as its expression was not investigated in the kidney. We used Human Primary Proximal Tubule (HPPT) cells to show genome-wide gene expression patterns after cytokine stimulation, with emphasis on the ACE2/dACE2 locus. Putative regulatory elements controlling dACE2 expression were identified using ChIP-seq and RNA-seq. qRT-PCR differentiating between ACE2 and dACE2 revealed 300- and 600-fold upregulation of dACE2 by IFN and IFN{beta}, respectively, while full length ACE2 expression was almost unchanged. JAK inhibitor ruxolitinib ablated STAT1 and dACE2 expression after interferon treatment. Finally, with RNA-seq, we identified a set of genes, largely immune-related, induced by cytokine treatment. These gene expression profiles provide new insights into cytokine response of proximal tubule cells.

genomics↗