Katja Koeppen
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View article: GLI3 Is Required for M2 Macrophage Polarization and M2-Mediated Waldenström Macroglobulinemia Growth and Survival
GLI3 Is Required for M2 Macrophage Polarization and M2-Mediated Waldenström Macroglobulinemia Growth and Survival Open
Waldenstrom macroglobulinemia (WM) is a non-Hodgkin B-cell lymphoma, characterized by bone marrow infiltration with plasma cells and lymphocytes. The tumor microenvironment (TME) plays an important role in mediating WM cell biology, but th…
View article: Systemic Sclerosis Dermal Fibroblast Exosomes Trigger Type 1 Interferon Responses in Keratinocytes via a <scp>TBK</scp> / <scp>JAK</scp> / <scp>STAT</scp> Signaling Axis
Systemic Sclerosis Dermal Fibroblast Exosomes Trigger Type 1 Interferon Responses in Keratinocytes via a <span>TBK</span> / <span>JAK</span> / <span>STAT</span> Signaling Axis Open
Objective Activation of type I interferon (IFN) response has been shown to correlate with disease activity in systemic sclerosis (SSc). It is currently unknown whether the tissue‐specific type I IFN activation is a consequence of the respo…
View article: <i>P. aeruginosa</i> tRNA-fMet halves secreted in outer membrane vesicles suppress lung inflammation in cystic fibrosis
<i>P. aeruginosa</i> tRNA-fMet halves secreted in outer membrane vesicles suppress lung inflammation in cystic fibrosis Open
The experiments in this report identify a novel mechanism, whereby tobramycin reduces inflammation in two models of CF. Tobramycin increased the secretion of tRNA-fMet halves in OMVs secreted by P. aeruginosa, which reduced the OMV-LPS-ind…
View article: <i>P. aeruginosa</i>tRNA-fMet halves secreted in outer membrane vesicles suppress lung inflammation in Cystic Fibrosis
<i>P. aeruginosa</i>tRNA-fMet halves secreted in outer membrane vesicles suppress lung inflammation in Cystic Fibrosis Open
Although tobramycin increases lung function in people with cystic fibrosis (pwCF), the density of Pseudomonas aeruginosa (P. aeruginosa) in the lungs is only modestly reduced by tobramycin; hence, the mechanism whereby tobramycin improves …
View article: Systemic Sclerosis dermal fibroblast exosomes trigger a Type 1 interferon response in keratinocytes through the TBK/JAK/STAT signalling axis
Systemic Sclerosis dermal fibroblast exosomes trigger a Type 1 interferon response in keratinocytes through the TBK/JAK/STAT signalling axis Open
Background Activation of Type I IFN response has been shown to correlates with disease activity in systemic sclerosis. It is currently unknown whether the tissue-specific Type I IFN activation is a consequence of the response observed in b…
View article: Rocket-miR, a translational launchpad for miRNA-based antimicrobial drug development
Rocket-miR, a translational launchpad for miRNA-based antimicrobial drug development Open
Developing software tools that leverage biological data sets to accelerate drug discovery is an important aspect of bioinformatic research. Here, we present a novel example: a web application called Rocket-miR that applies an existing bioi…
View article: 79 Tobramycin-induced secretion of Pseudomonas aeruginosa 5′ tRNA-fMet halves in outer membrane vesicles suppresses lung inflammation via AGO2-mediated gene silencing
79 Tobramycin-induced secretion of Pseudomonas aeruginosa 5′ tRNA-fMet halves in outer membrane vesicles suppresses lung inflammation via AGO2-mediated gene silencing Open
View article: 77 Rocket-miR, a translational launchpad for miRNA-based antimicrobial drug development
77 Rocket-miR, a translational launchpad for miRNA-based antimicrobial drug development Open
View article: Rocket-miR, a Translational Launchpad for miRNA-based Antimicrobial Drug Development
Rocket-miR, a Translational Launchpad for miRNA-based Antimicrobial Drug Development Open
Developing software tools that leverage biological datasets to accelerate drug discovery is an important aspect of bioinformatics research. Here we present a novel example: a web application called Rocket-miR that applies an existing bioin…
View article: An rRNA fragment in extracellular vesicles secreted by human airway epithelial cells increases the fluoroquinolone sensitivity of <i>P. aeruginosa</i>
An rRNA fragment in extracellular vesicles secreted by human airway epithelial cells increases the fluoroquinolone sensitivity of <i>P. aeruginosa</i> Open
Human RNA fragments transported in extracellular vesicles interfere with Pseudomonas aeruginosa drug efflux pumps. A combination of rRNA fragments and ciprofloxacin packaged in nanoparticles or EVs may benefit patients with antibiotic-resi…
View article: ESKAPE Act Plus: Pathway Activation Analysis for Bacterial Pathogens
ESKAPE Act Plus: Pathway Activation Analysis for Bacterial Pathogens Open
ESKAPE pathogens are bacteria of concern because they develop antibiotic resistance and can cause life-threatening infections, particularly in more susceptible immunocompromised people. ESKAPE Act PLUS is a user-friendly web application th…
View article: CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies
CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies Open
Researchers studying cystic fibrosis (CF) pathogens have produced numerous RNA-seq datasets which are available in the gene expression omnibus (GEO). Although these studies are publicly available, substantial computational expertise and ma…
View article: An rRNA fragment in extracellular vesicles secreted by human airway epithelial cells increases the fluoroquinolone sensitivity of <i>P. aeruginosa</i>
An rRNA fragment in extracellular vesicles secreted by human airway epithelial cells increases the fluoroquinolone sensitivity of <i>P. aeruginosa</i> Open
Lung infection by antibiotic resistant strains of Pseudomonas aeruginosa is a well-known concern for immunocompromised hosts including people with lung diseases such as cystic fibrosis. We have previously demonstrated that extracellular ve…
View article: CF-Seq, An Accessible Web Application for Rapid Re-Analysis of Cystic Fibrosis Pathogen RNA Sequencing Studies
CF-Seq, An Accessible Web Application for Rapid Re-Analysis of Cystic Fibrosis Pathogen RNA Sequencing Studies Open
Researchers studying cystic fibrosis (CF) pathogens have produced numerous RNA-seq datasets which are available in the gene expression omnibus (GEO). Although these studies are publicly available, substantial computational expertise and ma…
View article: The Candida albicans Cdk8-dependent phosphoproteome reveals repression of hyphal growth through a Flo8-dependent pathway
The Candida albicans Cdk8-dependent phosphoproteome reveals repression of hyphal growth through a Flo8-dependent pathway Open
Ssn3, also known as Cdk8, is a member of the four protein Cdk8 submodule within the multi-subunit Mediator complex involved in the co-regulation of transcription. In Candida albicans , the loss of Ssn3 kinase activity affects multiple phen…
View article: Origin of most abundant sRNAs from the sequence-based characterization of EV sRNA content
Origin of most abundant sRNAs from the sequence-based characterization of EV sRNA content Open
909 most abundant unique sequences with at least 100 counts per sample accounted for 60% of total reads for sequences detected in all 3 replicate samples. Listed are the nucleotide sequence (column 1), sequence length (column 2), number of…
View article: Proteomics data of EV-exposed P. aeruginosa and unexposed controls
Proteomics data of EV-exposed P. aeruginosa and unexposed controls Open
Normalized peak intensities for each sample as well as average log2 fold changes and p-values for 1619 proteins that were detected in duplicate runs of all six samples. EVs were derived from three individual human airway epithelial cell do…
View article: Proteomics data of P. aeruginosa expressing the rRNA fragment compared to empty vector controls
Proteomics data of P. aeruginosa expressing the rRNA fragment compared to empty vector controls Open
Normalized peak intensities for each sample as well as average log2 fold changes and p-values for 1911 proteins that were detected in at least two of three replicate samples.
View article: 471: Short RNAs in extracellular vesicles secreted by human airway epithelial cells increase antibiotic sensitivity of Pseudomonas aeruginosa
471: Short RNAs in extracellular vesicles secreted by human airway epithelial cells increase antibiotic sensitivity of Pseudomonas aeruginosa Open
View article: Let-7b-5p in vesicles secreted by human airway cells reduces biofilm formation and increases antibiotic sensitivity of <i>P. aeruginosa</i>
Let-7b-5p in vesicles secreted by human airway cells reduces biofilm formation and increases antibiotic sensitivity of <i>P. aeruginosa</i> Open
Significance Pseudomonas aeruginosa is one of the leading causes of hospital-acquired infections worldwide primarily due to its ability to develop antibiotic-resistant biofilms. This report describes a mechanism whereby human airway epithe…
View article: The <i>Candida albicans</i> Cdk8-dependent phosphoproteome reveals repression of hyphal growth through a Flo8-dependent pathway
The <i>Candida albicans</i> Cdk8-dependent phosphoproteome reveals repression of hyphal growth through a Flo8-dependent pathway Open
Ssn3, also known as Cdk8, is a member of the four protein Cdk8 submodule within the multi-subunit Mediator complex involved in the co-regulation of transcription. In Candida albicans , the loss of Ssn3 kinase activity affects multiple phen…
View article: GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses
GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses Open
GEO archives transcriptomic data from over 5,800 microbial experiments and allows researchers to answer questions not directly addressed in published papers. However, less than 4% of the microbial data sets include the sample group annotat…
View article: CF monocyte-derived macrophages have an attenuated response to extracellular vesicles secreted by airway epithelial cells
CF monocyte-derived macrophages have an attenuated response to extracellular vesicles secreted by airway epithelial cells Open
Mutations in CFTR alter macrophage responses, for example, by reducing their ability to phagocytose and kill bacteria. Altered macrophage responses may facilitate bacterial infection and inflammation in the lungs, contributing to morbidity…
View article: Supplemental Table 1
Supplemental Table 1 Open
Monocyte donor characteristics including genotype, age, sex, CFTR mutation, CFTR modulators and FEV1 % predicted.
View article: Supplemental Table 3
Supplemental Table 3 Open
Fold changes and p-values from RNAseq analysis of WT and CF monocyte derived macrophages from 3 donors each exposed to extracellular vesicles from airway epithelial cells (EV) or extracellular vesicles from airway epithelial cells after
View article: Supplemental Table 2
Supplemental Table 2 Open
Fold changes and p-values for baseline cytokine secretion of CF MDM vs. WT MDM.
View article: Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics
Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics Open
Pseudomonas aeruginosa and Candida albicans are opportunistic pathogens whose interactions involve the secreted products ethanol and phenazines. Here, we describe the role of ethanol in mixed-species co-cultures by dual-seq analyses. P. ae…
View article: Selection of reference genes for quantitative PCR: identifying reference genes for airway epithelial cells exposed to <i>Pseudomonas aeruginosa</i>
Selection of reference genes for quantitative PCR: identifying reference genes for airway epithelial cells exposed to <i>Pseudomonas aeruginosa</i> Open
Most quantitative PCR (qPCR) experiments report differential expression relative to the expression of one or more reference genes. Therefore, when experimental conditions alter reference gene expression, qPCR results may be compromised. Li…
View article: Conditional antagonism in co-cultures of<i>Pseudomonas aeruginosa</i>and<i>Candida albicans</i>: an intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics
Conditional antagonism in co-cultures of<i>Pseudomonas aeruginosa</i>and<i>Candida albicans</i>: an intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics Open
Pseudomonas aeruginosa and Candida albicans are opportunistic pathogens whose interactions involve the secreted products ethanol and phenazines. Here we describe the focal role of ethanol in mixed-species co-cultures by dual RNA-seq analys…
View article: Supplemental Table 2
Supplemental Table 2 Open
Fold changes and p-values from RNA-seq analysis of CF MDM and WT MDM exposed to EV or EV-PA.