Differential Gene Expression Analysis of PMA Treated Pro-monocytic Cell Lines

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dc.contributor.authorKama, Asavela Olona
dc.contributor.co-supervisorMeyer, Vanessa
dc.contributor.supervisorGentle, Nikki
dc.date.accessioned2024-10-25T21:18:43Z
dc.date.available2024-10-25T21:18:43Z
dc.date.issued2023
dc.descriptionA dissertation submitted in fulfilment of the requirements for the degree of Master of Science, top the Faculty of Science, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2023.
dc.description.abstractHL-60, THP-1, and U937 are model cell lines that can undergo myeloid differentiation in vitro, allowing the study of myeloid cell function in drug metabolism, cytotoxicity, and the aetiology of infections. However, the differentiated end-state of these cells is not well characterised. Moreover, cell line-specific differences in the level of gene expression may confound results obtained from such studies. The aim of this study was thus to compare changes in gene expression between HL-60, THP-1, and U937 cells in response to the differentiation agent, phorbol 12-myristate 13-acetate (PMA), 48 hours after treatment. Gene expression profiles were compared across all three cell lines prior to and post-PMA treatment. Differential gene expression analysis between treated and untreated cells was performed using DESeq2 (v 4.2). Gene over-representation analysis was performed using cluster Profiler (v 4.0). HL-60, THP-1, and U937 cells had similar expression profiles prior to PMA treatment, but different sets of genes were significantly differentially expressed in these cell lines 48 h after treatment with PMA. A total of 475 genes were consistently differentially expressed across all cell lines. These genes were found to be involved in phagosome formation and cell cycle transition. HL-60, THP-1, and U937 cells had 944, 1231, and 624 uniquely differentially expressed genes, respectively. These genes were predominantly involved in energy metabolism and pathogen recognition. Overall, THP-1 cells showed greater potential to detect viruses, while U937 cells showed greater potential to detect bacteria. From this, it can be concluded that while all three cell lines did indeed undergo myeloid differentiation, the macrophage-like cell state produced in each case differed between cell lines.
dc.description.sponsorshipNational Research Foundation (NRF).
dc.description.submitterMM2024
dc.facultyFaculty of Science
dc.identifier0000-0003-4627-6232
dc.identifier.citationKama, Asavela Olona. (2023). Differential Gene Expression Analysis of PMA Treated Pro-monocytic Cell Lines. [Master's dissertation, University of the Witwatersrand, Johannesburg]. https://hdl.handle.net/10539/41968
dc.identifier.urihttps://hdl.handle.net/10539/41968
dc.language.isoen
dc.publisherUniversity of the Witwatersrand, Johannesburg
dc.rights©2023 University of the Witwatersrand, Johannesburg. All rights reserved. The copyright in this work vests in the University of the Witwatersrand, Johannesburg. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of University of the Witwatersrand, Johannesburg.
dc.rights.holderUniversity of the Witwatersrand, Johannesburg
dc.schoolSchool of Molecular and Cell Biology
dc.subjectDifferentiation
dc.subjectPMA
dc.subjectCell line
dc.subjectMonocyte
dc.subjectMacrophage
dc.subjectHL-60
dc.subjectTHP-1
dc.subjectU937
dc.subjectRNA-seq
dc.subjectUCTD
dc.subject.otherSDG-3: Good health and well-being
dc.titleDifferential Gene Expression Analysis of PMA Treated Pro-monocytic Cell Lines
dc.typeDissertation
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