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GNPS - Comparative genomics metabolomics analysis of Streptomyces species

ABSTRACT: Various MeOH and PBS extracts from Streptomyces species analyzed by LC-MS/MS analyzed in both positive and negative ionisation using a Vanquish UHPLC System coupled to a Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Scientific, United States). Chromatographic separation was performed in mixed mode (allowing weak anion/cation exchange) on a Scherzo SM-C18 column. Inclusion list was used for the positive mode, and background ions were excluded.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Streptomyces

SUBMITTER: Pieter Dorrestein Kapil Tahlan

PROVIDER: MSV000084595 | GNPS | Mon Nov 18 16:48:00 GMT 2019

REPOSITORIES: GNPS

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Project description:Background: There is emerging evidence for the role of the immune system in osteoarthritis (OA) pathophysiology; however, little is known about how immune cells and the synovial transcriptome are altered in naturally occurring equine OA. Objectives: To evaluate synovial fluid (SF) and synovial membrane (SM) immune cell populations and the SM transcriptome in racehorses with fetlock osteoarthritis. Methods: Fetlock joints from racehorses euthanized on NY racetracks were considered for inclusion. SF and SM were analyzed by flow cytometry using T-cell (CD3, CD4, CD8) and macrophage (CD14, CD86, CD206) surface markers. OA severity was characterized by gross joint evaluation and SM histology. Bulk RNA-sequencing of SM was performed to identify differentially expressed genes. Flow cytometry data was analyzed with mixed linear modeling, including OA severity as a fixed effect and horse as a random effect. RNA-sequencing was evaluated with mixed linear and quadratic modeling using DREAMSeq method to capture differential gene expression over the range of OA severity. Results: Twenty-four fetlocks from 12 horses met inclusion criteria. CD8+ T-cells (R2 = 0.25 for SM, 0.35 for SF) and CD86+ macrophages (R2 = 0.14 for SM) were positively correlated with OA severity, while CD4+ T-cells (R2 = 0.17 for SM, 0.31 for SF) were negatively correlated. Macrophages co-expressing CD86 and CD206 correlated with OA severity in SM (R2 = 0.31). Pathways including those associated with TNF-α signaling, connective tissue development, and cell and neuron projection organization/development were differentially regulated in SM with greater OA scores. Main Limitations: Limited sample size, particularly of horses with severe OA. Conclusions: CD8+ T-cells, CD86+ macrophages, and macrophages co-expressing CD206 and CD86 are enriched in horses with more advanced OA. Gene set analysis suggests the importance of TNF-α signaling and disinhibition of neuron and cell projection development in OA pathogenesis.

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GNPS - Comparative genomics metabolomics analysis of Streptomyces species

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