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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

ABSTRACT: 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

PROVIDER: PRJNA667461 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12774644_1.fastq.gz	Fastqsanger.gz
	SRR12774644_2.fastq.gz	Fastqsanger.gz
	SRR12774645_1.fastq.gz	Fastqsanger.gz
	SRR12774645_2.fastq.gz	Fastqsanger.gz
	SRR12774646_1.fastq.gz	Fastqsanger.gz

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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

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 | GSE159035 | GEO

Whole-transcriptome in PBMCs from patients with LS-OCMB characterization reveals 4 RNAs as 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.

Project description: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 peripheral blood mononuclear cells (PBMCs) from patients with lipid-specific oligoclonal IgM band characterization. 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. 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. The expression of hsa_circ_0000478, hsa_circ_0116639, IRF5 and MTRNR2L8 might serve as minimally invasive biomarkers of highly active disease.

| S-EPMC7759842 | biostudies-literature

Non-coding RNA analysis in IgM monoclonal gammopathies: an underrecognized role of microRNA and long non-coding RNA differentiating Waldenström macroglobulinemia from IgM-MGUS

Project description:Waldenström macroglobulinemia (WM), is a rare non-Hodgkin lymphoma preceded by a clinically asymptomatic benign monoclonal gammopathy of undetermined significance (IgM-MGUS). The factors underlying the malignant progression between these two IgM-monoclonal gammopathies remain poorly understood. The non-coding genome is increasingly recognized as an important driver of disease pathogenesis, and there remains a lack of exploration of the influence of non-coding RNAs within the IgM-monoclonal gammopathy disease spectrum. The present study explores the role of microRNA (miRNA) and long non-coded RNA (lncRNA) in IgM-gammopathies and specifically elucidates potentially regulated protein-coding genes and pathways. A comprehensive analysis of miRNA, lncRNA and protein-coding coding genes was conducted on 28 subjects, 17 patients with WM, 6 patients with IgM-MGUS, and 5 normal controls. Differential expression analysis revealed a number of dysregulated miRNA and lncRNA between IgM-gammopathies compared to normal controls and specifically between IgM-MGUS and WM. Pathway analysis was conducted utilizing differentially expressed mRNA with correlated biological expression of targeting miRNA. Here, a number of pathways were implicated influencing a gamut of cellular functions, including cell signaling, metabolism, replication, and immune regulation in both WM compared to IgM-MGUS and IgM-gammopathies compared to controls. This report is additionally one of the first published analyses of lncRNAs in WM, where we demonstrate a number of lncRNA associated with transcription and apoptosis regulation genes in WM compared to IgM-MGUS. This study highlights the role of non-coding RNA in IgM-gammopathies and the potential to recognize novel targets which may halt or slow the malignant progression between these two diseases.

2023-12-08 | GSE232995 | GEO

Identification of target antigens of CSF OCB-derived monoclonal antibodies

Project description:The identification of target antigens recognized by monoclonal antibodies that have been derived from oligoclonal band IgG of CSF samples from multiple sclerosis patients.

2016-06-06 | GSE72789 | GEO

B cell response to Anti-IgM and CD40 treatment

Project description:Temporal analysis (60, 180, 360 min) of B cells treated with Anti-IgM alone, CD40 alone or Anti-IgM and CD40 (all in triplicates). Keywords: other

2004-02-13 | GSE1019 | GEO

B cell response to Anti-IgM and terbutaline treatment

Project description:Temporal analysis (60, 180, 360 min) of B cells treated with Anti-IgM alone, terbutaline alone or Anti-IgM and terbutaline (all in triplicates). Keywords: other

2004-02-13 | GSE1021 | GEO

B cell response to Anti-IgM and ELC treatment

Project description:Temporal analysis (60, 180, 360 min) of B cells treated with Anti-IgM alone, ELC alone or Anti-IgM and ELC (all in triplicates). Keywords: other

2004-02-13 | GSE1020 | GEO

25 kDa band from HSPA1A immunoprecipitation

Project description:HSPA1A was immunoprecipitated from WT and TorsinKO HeLa cells. A band around 27 kDa was identified uniquely in TorsinKO samples and for identification, this band was extracted.

2022-08-25 | PXD036266 | Pride

B cell response to CD40, Anti-IgM, ELC, IL4, terbutaline and lipopolysaccharide treatment

Project description:Temporal analysis (60, 180, 360 min) of B cells treated with either: CD40 Anti-IgM ELC IL4 Lipopolysaccharide Terbutaline CD40 and IL4 CD40 and Lipopolysaccharide CD40 and Anti-IgM Anti-IgM and ELC Anti-IgM and Terbutaline ELC and Lipopolysaccharide This SuperSeries is composed of the SubSeries listed below.

2004-02-16 | GSE1014 | GEO

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