The genus Aspergillus possesses broad functionality and occupation of ecological niches. Underpinning this are changes in the transcriptome of these species. Transcriptional changes are clinically relevant with respect to understanding triazole resistant isolates of Aspergillus fumigatus. Reverse-transcription quantitative Polymerase Chain Reaction (RT-qPCR) is a highly specific means of measuring changes in gene expression. The most common method of which requires normalization to experimentally validated, stably expressed reference genes. Ideal reference genes are unaffected by differences in the experimental conditions or strains/isolates and are expressed at levels near the target gene(s). The first study reviewed current practices for reference gene selection and validation for RT-qPCR gene expression analysis of the genus, Aspergillus. Information on the species examined, experimental conditions, sample type, normalization strategy, reference gene(s) and their state of validation was obtained from 90 primary studies. Twenty reference genes were used, with the most popular reference genes used encoding beta-tubulin, actin, 18S rRNA and glyceraldehyde-3-phosphate dehydrogenase. Seventeen of the 90 studies experimentally validated the expression stability of the reference genes used, out of which eight used more than one reference gene. The results of three studies conflicted with others described in the literature, with no experimental validation of the reference genes available to aid in interpreting the conflicting findings. In the Genome-Wide Association Study, genes noted to increase in expression in response to itraconazole and/or voriconazole treatment of A. fumigatus were extracted from published RNA-sequencing or RT-qPCR studies. Ten ATP-binding cassette transporters, four major facilitator superfamily transporters and 16 transcription factors were identified. Collectively, the findings of this thesis show a large disparity in experimentally validated reference genes as well as future targets of gene expression analysis in triazole resistant isolates of A. fumigatus. / Thesis / Master of Science (MSc) / Aspergillus is a globally distributed genus of fungi, with some species threatening opportunistic human infection. To combat infection with the opportunistic species, Aspergillus fumigatus, antifungal drugs including: itraconazole, voriconazole and amphotericin B are used. Recent years have seen a rise in antifungal resistance in A. fumigatus. To understand this and other mechanisms in Aspergillus, changes in gene expression must be examined. My thesis aimed to determine how reference genes are selected for reverse-transcription quantitative polymerase chain reaction, a method applied to measure gene expression changes in Aspergillus. It was discovered that very few studies between the years 2001 and 2020 experimentally validated that the reference genes used were stably expressed, with only 17 out of 90 studies providing validation. In part two of my thesis, genes overexpressed in A. fumigatus when exposed to antifungal drugs, from formerly published articles, were summarized to better understand the role of gene expression in antifungal drug resistance.
| Identifer | oai:union.ndltd.org:mcmaster.ca/oai:macsphere.mcmaster.ca:11375/27265 |
| Date | January 2021 |
| Creators | Archer, Meagan |
| Contributors | Xu, Jianping, Biology |
| Source Sets | McMaster University |
| Language | en_US |
| Detected Language | English |
| Type | Thesis |
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