Comparative Analysis of the Transcriptomes of M1 and M2 Macrophages

Comparative Analysis of the Transcriptomes of M1 and M2 Macrophages

Bibliographic Details
Main Author: Atolagbe, Oluwatomisin Toluwanimi
Language:English
Published: University of Toledo Health Science Campus / OhioLINK 2017
Subjects:
Bioinformatics
Biomedical Research
Macrophage
M1
M2
Atherosclerosis
Transcriptomics
RNA Sequencing
Microarray
Circular RNA
Noncoding RNA
Online Access:http://rave.ohiolink.edu/etdc/view?acc_num=mco150166566713963
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spelling ndltd-OhioLink-oai-etd.ohiolink.edu-mco1501665667139632021-08-03T07:03:46Z Comparative Analysis of the Transcriptomes of M1 and M2 Macrophages Atolagbe, Oluwatomisin Toluwanimi Bioinformatics Biomedical Research Macrophage M1 M2 Atherosclerosis Transcriptomics RNA Sequencing Microarray Circular RNA Noncoding RNA Macrophages are critical cells in the immune system implicated in various diseases with a chronic inflammatory component, such as atherosclerosis. The dominant macrophage types, M1 and M2, play key roles in progression and regression of atherosclerotic plaques. In this study, we profiled the transcriptomes of these macrophage subsets using RNA-Seq and microarray to examine molecular signatures and distinctive pathways for each subset. RNA-Seq analysis revealed a total of 2,127 differentially expressed genes (including coding and non-coding transcripts) between the M1 and M2 subsets. Validation by qRT-PCR of 10 top differentially expressed genes showed that 8 of the upregulated and 9 of the downregulated genes followed the expected trend based on the RNA-Seq analysis. Subsequently, pathway analysis of the upregulated and downregulated gene sets showed M1 and M2 macrophages to be enriched in pathways such as the Th1 and glioma signaling respectively. Microarray analysis revealed a total of 163 differentially expressed circRNAs between the two macrophage subsets and predictions of circRNA/miRNA interactions. From these circRNA/miRNA interactions, a number of the differentially expressed circRNAs were predicted to target athero-relevant miRNAs. As examples, circRNA_41878 (gene Ankrd42) was predicted to target miR-382-5p while circRNA_19794 (gene Lmbrd1) was predicted to target miR-124-3p, miRNAs of recognized effects in atherosclerosis. Overall, this work provides insight into distinctive molecular signatures and pathways enriched in bone-marrow derived M1 and M2 macrophages, and reveals the presence and contribution of non-protein-coding RNAs to their transcriptomes. In addition, our circRNA results provide the basis for future studies on the function of circRNAs in the context of macrophage functions in atherosclerosis. 2017 English text University of Toledo Health Science Campus / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=mco150166566713963 http://rave.ohiolink.edu/etdc/view?acc_num=mco150166566713963 unrestricted This thesis or dissertation is protected by copyright: all rights reserved. It may not be copied or redistributed beyond the terms of applicable copyright laws.
collection NDLTD
language English
sources NDLTD
topic Bioinformatics
Biomedical Research
Macrophage
M1
M2
Atherosclerosis
Transcriptomics
RNA Sequencing
Microarray
Circular RNA
Noncoding RNA
spellingShingle Bioinformatics
Biomedical Research
Macrophage
M1
M2
Atherosclerosis
Transcriptomics
RNA Sequencing
Microarray
Circular RNA
Noncoding RNA
Atolagbe, Oluwatomisin Toluwanimi
Comparative Analysis of the Transcriptomes of M1 and M2 Macrophages
author Atolagbe, Oluwatomisin Toluwanimi
author_facet Atolagbe, Oluwatomisin Toluwanimi
author_sort Atolagbe, Oluwatomisin Toluwanimi
title Comparative Analysis of the Transcriptomes of M1 and M2 Macrophages
title_short Comparative Analysis of the Transcriptomes of M1 and M2 Macrophages
title_full Comparative Analysis of the Transcriptomes of M1 and M2 Macrophages
title_fullStr Comparative Analysis of the Transcriptomes of M1 and M2 Macrophages
title_full_unstemmed Comparative Analysis of the Transcriptomes of M1 and M2 Macrophages
title_sort comparative analysis of the transcriptomes of m1 and m2 macrophages
publisher University of Toledo Health Science Campus / OhioLINK
publishDate 2017
url http://rave.ohiolink.edu/etdc/view?acc_num=mco150166566713963
work_keys_str_mv AT atolagbeoluwatomisintoluwanimi comparativeanalysisofthetranscriptomesofm1andm2macrophages
_version_ 1719452715262672896

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