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Whole-transcriptome in PBMCs from patients with LS-OCMB characterization reveals 4 RNAs as biomarkers of highly active disease

ABSTRACT: Whole-transcriptome in PBMCs from patients with LS-OCMB characterization reveals 4 RNAs as biomarkers of highly active disease

PROVIDER: PRJNA667452 | ENA |

REPOSITORIES: ENA

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Whole-transcriptome in PBMCs from patients with LS-OCMB characterization reveals 4 RNAs as biomarkers of highly active disease

Project description:Background: The presence of anti-myelin lipid specific oligoclonal IgM bands (LS-OCMBs) has been defined as an accurate predictor of an aggressive evolution of multiple sclerosis. However, the detection of this biomarker is performed in cerebrospinal fluid, a quite invasive liquid biopsy. In the present study we aimed at studying the expression profile of miRNA, snoRNA, circRNA and linearRNA in PBMCs from patients with lipid-specific oligoclonal IgM band characterization. Methods: We included a total of 89 MS patients, 47 with negative LS-OCMB status and 42 with positive status. Microarray (miRNA and snoRNA) and RNA-seq (circular and linear RNAs) were used to perform the profiling study in the discovery cohort and candidates were validated by RT-qPCR in the whole cohort. The biomarker potential of the candidates was evaluated by ROC curve analysis. Results: RNA-seq and RT-qPCR validation revealed that two circular (hsa_circ_0000478 and hsa_circ_0116639) and two linear RNAs (IRF5 and MTRNR2L8) are downregulated in PBMCs from patients with positive LS-OCMBs. Finally, those RNAs show a performance of a 70% accuracy in some of the combinations. Conclusion: The expression of hsa_circ_0000478, hsa_circ_0116639, IRF5 and MTRNR2L8 might serve as minimally invasive biomarkers of highly active disease.

2020-12-21 | GSE159033 | GEO

Whole-transcriptome analysis in peripheral blood mononuclear cells from patients with lipid-specific oligoclonal IgM band characterization reveals two circular RNAs and two linear RNAs as biomarkers of highly active disease

2020-12-21 | GSE159035 | GEO

PBMCs from patients with LS-OCMB characterization

Project description:PBMCs from patients with LS-OCMB characterization

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SLIDE analysis of the scRNA-seq data using an interpretable factor-analysis machine learning framework, that moves beyond predictive biomarkers to try and infer latent factors underlying LS pathophysiology.

Project description:Using transcriptomic profiling at single-cell resolution, we investigate cell-intrinsic and cell-extrinsic signatures associated with pathogenesis and inflammation-driven fibrosis in both adult and pediatric localized Scleroderma (LS) patients. We perform scRNA-seq on adult and pediatric LS patients and healthy controls. We then analyze the scRNA-seq data using an interpretable factor-analysis machine learning framework, SLIDE, that moves beyond predictive biomarkers to try and infer latent factors underlying LS pathophysiology. SLIDE is a novel latent factor regression-based framework that comes with rigorous statistical guarantees regarding identifiability of the latent factors, corresponding inference, and FDR control. We find distinct differences in the characteristics and complexity in the molecular signatures between adult and pediatric LS. SLIDE identified cell type-specific determinants of LS associated with age and severity and revealed insights into signaling mechanisms shared between LS and Systemic Sclerosis (SSc), as well as differences in onset of the disease in the pediatric compared with adult population. Our analyses recapitulate known drivers of LS pathology and find previously unidentified cellular signaling modules that stratify LS subtypes and define a shared signaling axis with SSc.In this study we compared 17 healthy and 27 LS samples evaluated by 10X Genomics single cell sequencing. Samples were processed and clustered for DEG analysis.

2025-02-28 | GSE288490 | GEO

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Signature of circular RNAs in peripheral blood mononuclear cells (PBMCs) from patients with active tuberculosis

Project description:The knowledge of circRNAs in tuberculosis (TB) remains limited. Aim of the present study was to characterize the expression profiles and potential function of circRNAs in human peripheral blood mononuclear cells (PBMCs) from patients with active TB.

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A2780 and OVCAR-3 Cells:Control vs. LS-98 treated

Project description:Transcriptional profiling of human ovarian cancer cells comparing control vehicle-treated A2780 and OVCAR-3 (Human ovarian cancer cell lines) cells with A2780 and OVCAR-3 cells treated with 5μM LS-98 for 24 hours.Goal was to determine the effects of LS-98 compound on the global A2780 and OVCAR-3 cells gene expression.

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