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Identification of DEGs in B cells of patients with common variable immunodeficiency and healthy donors
University of Skövde, School of Bioscience.
2019 (English)Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
Abstract [en]

Common variable immunodeficiency (CVID) is a rare primary immune deficiency (1:25000) in which patients have a reduction in antibody production and very low titres in one or more of their Ig isotypes, (IgG, IgA and sometimes IgM). This disease can cause different symptoms such as: bronchiectasis, chronic lung disease and even autoimmunity, polyclonal lymphocytic infiltration, lymphoma and death. The underlying causes of CVID are still largely unknown but studies show that different factors like primary B-cell dysfunctions, defects in T cells and antigen-presenting cells are involved. Quantitative analysis of gene expression is of high importance in understanding the molecular mechanisms underlying this diseases´ genome regulation. Next-generation RNA-seq has enabled researchers to analyse both coding and non-coding regions of RNA, and therefore has made it possible to identify differentially expressed genes in large-scale data, especially in polygenic diseases like CVID. The aim for this study was to identify the differentially expressed genes between CVID patients and healthy donors to identify important genes and molecular mechanisms underlying this diseases´ genome regulation. For this matter, whole genome RNA-seq analysis was performed on RNA isolated from sorted peripheral blood naïve and CD27bright memory B cells from healthy donors (n=7) and CVID patients (n=5). The RNA-seq data for the samples was collected and undergone several bioinformatical and analytical steps to be processed. After quality control and trimming, the data files were assembled to the human genome. Then, the transcriptomic data of the CVID patients was compared with the healthy donors to identify differentially expressed genes (DEGs). From this study, it was found that PAX5, ETS1, POU2AF1, SPIB, BACH 2, EBF1 and PRDM1 play an important role on regulation of the B cells and especially this disease. Also, the Ikaros family, toll-like receptors and a number of chemokine and cytokine receptors were found out to have high importance regarding CVID.

Place, publisher, year, edition, pages
2019. , p. 43
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:his:diva-18370OAI: oai:DiVA.org:his-18370DiVA, id: diva2:1422745
External cooperation
Ola Grimsholm, University of Gothenburg
Subject / course
Systems Biology
Educational program
Molecular Biotechnology - Master's Programme, 120 ECTS
Supervisors
Examiners
Available from: 2020-04-08 Created: 2020-04-08 Last updated: 2020-04-08Bibliographically approved

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School of Bioscience
Bioinformatics and Systems Biology

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