Small non-coding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology

SND-ID: snd1150-1. Version: 1.0. DOI: https://doi.org/10.5878/c1mq-9r62

Citation

Creator/Principal investigator(s)

Galina Zheleznyakova - Karolinska Institutet, Department of Clinical Neuroscience

Eliane Piket - Karolinska Institutet, Department of Clinical Neuroscience

Maria Needhamsen - Karolinska Institutet, Department of Clinical Neuroscience

Maja Jagodic - Karolinska Institutet, Department of Clinical Neuroscience

Research principal

Karolinska Institutet - Department of Clinical Neuroscience rorId

Description

To improve our understanding of MS pathology and heterogeneity and provide new strategies for biomarkers and treatments development we carried out a genome-wide small non-coding RNA analysis. The analysis was performed in paired peripheral blood mononuclear cells, plasma, cerebrospinal fluid (CSF) cells and cell-free CSF from 29 MS patients and 16 controls using next-generation sequencing. We aimed to detect differentially expressed small non-coding RNAs between MS and controls. The data contains unique molecular identifier (UMI) count information for each transcript.

The small non-coding RNA analysis was performed in paired peripheral blood mononuclear cells, plasma, cerebrospinal fluid (CSF) cells and cell-free CSF from 29 MS patients and 16 controls using next-generation sequencing. One INDC control was missing a CSF cell and cell-free CSF sample and one NINDC control was missing a PBMC and plasma sample.
Small non-coding RNAs were isolated from 300 ul of plasma or CSF using the miRCURY RNA isolation kit for biofluids (Exiqon, Denmark) or from CSF cells and peripheral blood mononuclear cel

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To improve our understanding of MS pathology and heterogeneity and provide new strategies for biomarkers and treatments development we carried out a genome-wide small non-coding RNA analysis. The analysis was performed in paired peripheral blood mononuclear cells, plasma, cerebrospinal fluid (CSF) cells and cell-free CSF from 29 MS patients and 16 controls using next-generation sequencing. We aimed to detect differentially expressed small non-coding RNAs between MS and controls. The data contains unique molecular identifier (UMI) count information for each transcript.

The small non-coding RNA analysis was performed in paired peripheral blood mononuclear cells, plasma, cerebrospinal fluid (CSF) cells and cell-free CSF from 29 MS patients and 16 controls using next-generation sequencing. One INDC control was missing a CSF cell and cell-free CSF sample and one NINDC control was missing a PBMC and plasma sample.
Small non-coding RNAs were isolated from 300 ul of plasma or CSF using the miRCURY RNA isolation kit for biofluids (Exiqon, Denmark) or from CSF cells and peripheral blood mononuclear cells precipitate using the miRNAeasy micro kit (Qiagen, Germany). Small non-coding RNA libraries were prepared as previously described at PMID: 27798564. The libraries were sequenced on eight lanes of HiSeq2500. Preprocessing and alignment were done according to PMID: 30250291.

The "Unique molecular identifier_sncRNAs_analysis_MS" file contains unique molecular identifier count information for each small non-coding RNA transcript as well as other types of transcripts identified in the sequencing libraries from 44 individuals and 4 compartments (PBMCs, CSF cells, plasma, cell-free CSF). Altogether 176 samples.

The metafile contains information about the disease status, sex, age for all MS patients and controls.
The "readme" explains the contents of the data files and contains the variables list. Show less..

Data contains personal data

No

Language

Method and outcome

Population

Multiple Sclerosis patients (29), non-inflammatory neurological disease patients (11), Systemic lupus erythematosus patients (5)

Study design

Observational study

Description of study design

Small non-coding RNAs were isolated from PBMC, plasma, CSF cells and CSF. The libraries were prepared as previously described (PMID: 27798564) and sequenced on two lanes of HiSeq2500. The data analysis was performed as previously described (PMID: 27798564).

Sampling procedure

Biobank is connected to the study

Yes

Variables

4

Number of individuals/objects

176

Data format / data structure

Data collection
  • Mode of collection: Focus group
  • Source of the data: Biological samples
Geographic coverage

Geographic spread

Geographic location: Sweden, Stockholm County, Stockholm Municipality

Administrative information

Responsible department/unit

Department of Clinical Neuroscience

Contributor(s)

Tomas Olsson - Karolinska Institutet, Department of Clinical Neuroscience

Faiez Al Nimer - Karolinska Institutet, Department of Clinical Neuroscience

Patrick Scicluna - Karolinska Institutet, Department of Clinical Neuroscience

Omid Faridani - Karolinska Institutet, Ludwig Institute for Cancer Research

Michael Hagemann-Jensen - Karolinska Institutet, Ludwig Institute for Cancer Research

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Tomas Olsson - Karolinska Institutet, Department of Clinical Neuroscience

Faiez Al Nimer - Karolinska Institutet, Department of Clinical Neuroscience

Patrick Scicluna - Karolinska Institutet, Department of Clinical Neuroscience

Omid Faridani - Karolinska Institutet, Ludwig Institute for Cancer Research

Michael Hagemann-Jensen - Karolinska Institutet, Ludwig Institute for Cancer Research

Fredrik Piehl - Karolinska Institutet, Department of Clinical Neuroscience

Mohsen Khademi - Karolinska Institutet, Department of Clinical Neuroscience

Diana Ekman - National Bioinformatics Infrastructure Sweden

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Funding 1

  • Funding agency: Swedish Association of persons with Neurological disabilities

Funding 2

  • Funding agency: Horizon 2020

Funding 3

  • Funding agency: Swedish Research Council

Funding 4

  • Funding agency: Swedish MS Foundation

Funding 5

  • Funding agency: Swedish Society for Medical Research
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Funding 1

  • Funding agency: Swedish Association of persons with Neurological disabilities

Funding 2

  • Funding agency: Horizon 2020

Funding 3

  • Funding agency: Swedish Research Council

Funding 4

  • Funding agency: Swedish MS Foundation

Funding 5

  • Funding agency: Swedish Society for Medical Research

Funding 6

  • Funding agency: AstraZeneca-Science for Life Laboratory collaboration

Funding 7

  • Funding agency: Stockholm County Council

Funding 8

  • Funding agency: Swedish Brain Foundation
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Ethics Review

Stockholm - Ref. 2009/2107-31/2

Topic and keywords
Publications

Profiling of small non-coding RNAs across cellular and biofluid compartments: implications for multiple sclerosis immunopathology. Galina Yurevna Zheleznyakova, Eliane Piket, Maria Needhamsen, Michael Hagemann-Jensen, Diana Ekman, Mohsen Khademi, Faiez Al Nimer, Patrick Scicluna, Omid R Faridani, Tomas Olsson, Fredrik Piehl, Maja Jagodic. Deposited on bioRxiv.
https://www.biorxiv.org/content/10.1101/2020.05.15.097519v1
DOI: https://doi.org/10.1101/2020.05.15.097519

If you have published anything based on these data, please notify us with a reference to your publication(s). If you are responsible for the catalogue entry, you can update the metadata/data description in DORIS.

Published: 2021-04-08
Last updated: 2021-04-09