Human transcriptomic response to periprosthetic joint infection
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PROVIDER: PRJNA1076519 | ENA |
REPOSITORIES: ENA
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Project description:Periprosthetic joint infection (PJI), a devastating complication of total joint replacement, is of incompletely understood pathogenesis and may sometimes be challenging to clinically distinguish from other causes of arthroplasty failure. We characterized human gene expression in 93 specimens derived from surfaces of resected arthroplasties, comparing transcriptomes of subjects with infection- versus non-infection-associated arthroplasty failure. Differential gene expression analysis confirmed 28 previously reported potential biomarkers of PJI, including bactericidal/permeability increasing protein (BPI), cathelicidin antimicrobial peptide (CAMP), C-C-motif chemokine ligand 3 (CCL3), 4(CCL4), and C-X-C-motif chemokine ligand 2 (CXCL2), colony stimulating factor 2 receptor beta (CSF2RB), colony stimulating factor 3 (CSF3), alpha-defensin (DEFA4), Fc fragment of IgG receptor 1B (CD64B), intercellular adhesion molecule 1 (ICAM1), interferon gamma (IFNG), interleukin 13 receptor subunit alpha 2 (IL13RA2), interleukin 17D (IL17D), interleukin 1 (IL1A, IL1B, IL1RN), interleukin 2 receptors (IL2RA, IL2RG), interleukin 5 receptor (IL5RA), interleukin 6 (IL6), interleukin 8 (IL8), lipopolysaccharide binding protein (LBP), lipocalin (LCN2), lactate dehydrogenase C (LDHC), lactotransferrin (LTF), matrix metallopeptidase 3 (MMP3), peptidase inhibitor 3 (PI3), and vascular endothelial growth factor A (VEGFA), and identified three novel molecules of potential diagnostic use for detection of PJI, namely C-C-motif chemokine ligand CCL20, coagulation factor VII (F7), and B cell receptor FCRL4. Comparative analysis of infections caused by staphylococci versus bacteria other than staphylococci and Staphylococcus aureus versus Staphylococcus epidermidis showed elevated expression of interleukin 13 (IL13), IL17D, and MMP3 in staphylococcal infections, and of IL1B, IL8, and platelet factor PF4V1 in S. aureus compared to S. epidermidis infections. Pathway analysis of over-represented genes suggested activation of host immune response and cellular maintenance and repair functions in response to invasion of infectious agents. The data presented provides new potential targets for diagnosis of PJI and for differentiation of PJI caused by different infectious agents.
2024-02-19 | GSE255786 | GEO
Project description:Little is known about regulation of gene activity of the major pathogen Staphylococcus aureus during actual human infection. Here we characterize the transcriptome using deep RNA sequencing and the metabolome using NMR of S. aureus infected joint fluid derived from an acute human prosthetic joint infection, and compare them with the genome, transcriptome and metabolome of an isolate obtained from the sample grown in vitro (LB medium). The transcriptome indicated that the bacterial infection sustained on a versatile human-cell-based diet consisting of amino acids, glycans and nucleosides, since significant upregulation of genes involved in the catabolic degradation pathways of these compounds were observed in situ. This is consistent with metabolite analysis of the infected joint fluid and of S. aureus culture supernatants where the concentration of most amino acids and some amino sugars were found to be higher in the joint fluid, whereas the concentration of glucose was higher in culture supernatant. Furthermore, presumably because of oxygen limitations in the joint fluid, transcriptomic evidence for fermentation was observed, consistent with the presence of fermentation products (ethanol) in situ. Moreover, many, but not all, of the known virulence factor genes were upregulated in situ as well as the nine genes encoding the iron uptaking siderophore synthesis system.
2015-10-01 | GSE62091 | GEO
Project description:Boreal toad transcriptomic response to Bd infection
| PRJNA1023900 | ENA
Project description:Periprosthetic Joint Metagenome Raw sequence reads
| PRJNA378504 | ENA
Project description:Longitudinal Transcriptomic response to SARS-CoV-2 infection
| PRJNA725173 | ENA
Project description:This study aims to use proteomic profiling of sonicate fluid samples to compare host response during Staphylococcus aureus-associated periprosthetic joint infection (PJI) and non-infected arthroplasty failure (NIAF) and investigate novel biomarkers to increase diagnostic accuracy. In this pilot study, eight sonicate fluid samples (four from NIAF and four from caused by Staphylococcus aureus PJI) were studied. Samples were reduced, alkylated and trypsinized overnight, followed by analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) on a high-resolution Orbitrap Eclipse mass spectrometer. MaxQuant software suite was used for protein identification, filtering, and label free quantitation. Principal component analysis of the identified proteins clearly separated S. aureus PJI and NIAF samples. Overall, 810 proteins were quantified in any three samples from each group and 35 statistically significant differentially abundant proteins (DAPs) were found (2-sample t-test p-values ≤0.05 and log2fold-change values ≥2 or ≤-2). Gene ontology pathway analysis found that microbial defense responses, specifically those related to neutrophil activation, were increased in S. aureus PJI compared to NIAF samples. Proteomic profiling of sonicate fluid using LC-MS/MS, alone or in combination with complementary protein analyses, differentiated S. aureus PJI and NIAF in this pilot study.
2023-10-24 | PXD038928 | Pride
Project description:Boreal toads (Anaxyrus boreas boreas) of the Southern Rocky Mountain population are declining due to the introduction of the chytrid fungus Batrachochytrium dendrobatidis (Bd). Boreal toads in Colorado are generally susceptible to Bd infection, but some Bd-tolerant populations persist in parts of the Southern Rocky Mountain and broader Eastern boreal toad population. We conducted a Bd challenge with lab-reared sibling toads from Bd-susceptible Colorado and purportedly Bd-tolerant Utah populations and report on transcriptomic responses to Bd during late infection in skin and liver tissue. Fewer immune genes were expressed in response to Bd in Colorado toads, but with greater upregulation compared to Utah toads, indicating a dysregulated immune response. Signatures of Bd-tolerance in Utah toads included more moderate upregulation in immune gene expression and a significantly enriched suite of gene functions related to innate and adaptive immune responses. Our transcriptomic results support the notion that Utah toads are tolerant to Bd, rather than resistant, carrying Bd loads similar to Colorado yet having a unique transcriptomic profile and presenting minimal clinical signs of chytridiomycosis. We conclude that closely related populations have divergent transcriptomic responses to Bd with a dysregulated immune response in Bd-susceptible toads.
2023-10-04 | GSE244617 | GEO
Project description:Gene expression profile of joint tissue from C3H and interval specific congenic mouse lines (ISCL) following infection with Borrelia burgdorferi; Congenic lines of mice generated between C3H and C57BL/6 with penetrant arthritis severity phenotype were infected with B. burgdorferi; Joint tissue was collected from uninfected control mice and from mice infected for 1 week, RNA was prepared and gene expressed analyzed by Affymetrix microarray. Experiment Overall Design: Each sample was comprised of pooled RNA from at least 5 female mice of each genotype.
2009-07-01 | E-GEOD-16195 | biostudies-arrayexpress
Project description:Innate Lymphoid Cells Activation and Transcriptomic Changes in Response to Human Dengue Infection
| PRJNA655190 | ENA
Project description:metagenomics NGS for identification of prosthetic joint infection pathogens
| PRJEB36849 | ENA