Periodic Reporting for period 2 - OPATHY (From Omics to Patient: Improving Diagnostics of Pathogenic Yeasts)
Okres sprawozdawczy: 2017-09-01 do 2019-08-31
The specific scientific and technical objectives for the project are:
1. Study the genomic, transcriptomic and proteomic diversity of yeast pathogens, focusing on the discovery of specific biomarkers with diagnostic potential.
2. Advance our understanding of the dynamics of host-pathogen interactions during the course of infection and colonization and how this varies across species.
3. Develop novel analysis tools that exploit recently developed high-throughput (-omics) techniques and that enable faster and more efficient diagnostics of fungal pathogens, resistance traits, and infection stages.
With respect to objective 1. (Study the genomic, transcriptomic and proteomic diversity of yeast pathogens, focusing on the discovery of specific biomarkers with diagnostic potential.). The different work packages have obtained a) whole genome sequences b) transcriptomic profiling of host-pathogen interactions, and c) proteomics surveys from which candidate biomarkers have been prioritized for further development. A protein antibody for one such biomarkes have resulted in a filed patent, and several multiplex systems to detect several DNA-based biomarkers are currently being developed.
With respect to objective 2: A first time-course experiment has been successfully performed, in which the transcriptomes from both the host and the pathogen are traced and provide a detailed view of host-pathogen interactions. A manuscript is in preparation.
Objective 3 heavily relied on the above ones. Several computational tools and databases to ease the processing, analysis and interpretation of diverse types of omics data have been developed, including Candidamine (www.candidamine.org) focused on Omics-related data for the main Candida pathogens. Several potential novel diagnostic tools, derived from investigations within OPATHY have been explored and some of them are advancing towards patenting, valorization, and validation in the clinical settings. As indicated above a patent has been filed and several other diagnostic markers are being explored in the clinical setting.
The main results of the project are:
– A cartography of genomic, transcriptomic and proteomic resources have been produced for the main Candida pathogens, as well as for some rare (emerging species). This resource has been mined for the finding of novel diagnostic markers and has been put available for the whole community through http://candidamine.org database.
- Several new tools have been developed in the framework of this project which have been made available to the community, these include new proteomics based test for anti-fungal resistance (MBT-ASTRA), specific multiplex PCR probes for detecting different Candida species, as well as several bioinfomatics pipelines and tools for genome, transcriptome, and proteome analysis. These have been published in peer-reviewed journals and bioinformatics tools have been made accessible to the research community in an open-code format, or stand-alone programs.
- Several biomarkers have been selected for further development into tools or kits that are ready-to-use in the clinic. This has resulted in a patent filled by some of the partners and in further development by some of the companies involved in the consortium.
Through its many communication actions OPATHY has contributed to increase the awareness on fungal diseases and on the research that is needed to combat them. The many scientific findings published and the methods developed by the consortium that are already available are already contributing to accelerate the research in fungal diseases. Finally, some of the biomarkers identified are proceeding to further stages of developments into tools or kits that will likely have an impact in the clinics, thereby helping to improve the lives of people suffering from fungal infections.