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| Author(s): |
Renato Augusto Corrêa dos Santos
Total Authors: 1
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| Document type: | Doctoral Thesis |
| Press: | Campinas, SP. |
| Institution: | Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia |
| Defense date: | 2021-11-22 |
| Examining board members: |
Gustavo Henrique Goldman;
Renato Vicentini;
Benilton de Sá Carvalho;
Pedro Alexandre Favoretto Galante;
Débora Castelo Branco de Souza Collares Maia
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| Advisor: | Marcelo Falsarella Carazzolle; Gustavo Henrique Goldman |
| Abstract | |
Aspergillus fumigatus is an important human pathogen that causes invasive aspergillosis (IA). Additionally, several closely related members of section Fumigati that are morphologically similar to A. fumigatus but differ genetically and phenotypically, so called ‘cryptic species’, also comprise important causal agents of IA. Treatment of patients with aspergillosis is mainly carried out with antifungals, but there is an increasing worldwide concern about the emergency of resistance in several isolates of A. fumigatus and in cryptic species. The increasing availability of fungal genomes and phenotypic information such as antifungal susceptibility and virulence allows us to investigate several genes involved in biological mechanisms of clinical relevance. However, only a few isolates of cryptic species in section Fumigati with associated phenotypic information are currently available. Additionally, the genomic and transcriptomic data that are publicly available are still underexploited in the context of resistance or the response to antifungals, and they could be exploited to raise genetic or evolutionary hypotheses. Previous studies reported that in A. fumigatus, a high phenotypic heterogeneity among different strains has been observed for several traits, indicating that this could also be the case for antifungal susceptibility, and that this might be extended to cryptic species. Regarding the transcriptomic data, even though previous studies analyzed the expression of protein-coding genes in responses to individual drugs such as itraconazole and voriconazole, none have integrated different data sets to understand the general response to azoles, nor have these studies exploited the noncoding genomic elements in the A. fumigatus genome, particularly the long-noncoding RNAs (lncRNAs). Three aims of this project were to (i) study genomic and phenotypic heterogeneity in clinical isolates of A. fumigatus and cryptic species; (ii) identify signatures of positive selection in genes involved in antifungal resistance using genome sequenced isolates of section Fumigati and; (iii) exploit public RNA-Seq data sets to raise novel gene candidates possibly involved in the general responses to azoles, including lncRNAs. Interestingly, we found high heterogeneity in antifungal susceptibility and virulence across strains of A. fumigatus and two cryptic species. Analysing mutations in targets of antifungal drugs, cyp51A (azoles) and fks1 (echinocandins), we identified strains of A. fumigatus with known relevant mutations related to resistance, and mutations exclusive to cryptic species. Comparative genomics and phylogenetics revealed a paralog in A. fumigatiaffinis, cyp51C, which is uncommon in section Fumigati and could be related to resistance. Analysis of signatures of natural selection across important genes in sequenced species of section Fumigati revealed sites that did not overlap known resistance mutations, including cyp51A, suggesting an ancient selective pressure that probably differs from those of current strains and species. On the other hand, the main target of echinocandins, for which analogous natural compounds exist in nature, did present sites under selection (fks1). Transcriptome analysis of A. fumigatus under different azoles revealed novel candidates in response to azoles, both coding genes and lncRNAs. These results improve our understanding of the biology and evolution of A. fumigatus and related species in the clinical context (AU) | |
| FAPESP's process: | 17/21983-3 - Genomic analysis of Aspergillus cryptic species |
| Grantee: | Renato Augusto Corrêa dos Santos |
| Support Opportunities: | Scholarships in Brazil - Doctorate |