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pp 1-43 | Cite as

Transcriptome Sequencing Approaches to Elucidate Host–Microbe Interactions in Opportunistic Human Fungal Pathogens

  • Hrant Hovhannisyan
  • Toni Gabaldón
Chapter
Part of the Current Topics in Microbiology and Immunology book series

Abstract

Infections caused by opportunistic human fungal pathogens are a source of increasing medical concern, due to their growing incidence, the emergence of novel pathogenic species, and the lack of effective diagnostics tools. Fungal pathogens are phylogenetically diverse, and their virulence mechanisms can differ widely across species. Despite extensive efforts, the molecular bases of virulence in pathogenic fungi and their interactions with the human host remain poorly understood for most species. In this context, next-generation sequencing approaches hold the promise of helping to close this knowledge gap. In particular, high-throughput transcriptome sequencing (RNA-Seq) enables monitoring the transcriptional profile of both host and microbes to elucidate their interactions and discover molecular mechanisms of virulence and host defense. Here, we provide an overview of transcriptome sequencing techniques and approaches, and survey their application in studying the interplay between humans and fungal pathogens. Finally, we discuss novel RNA-Seq approaches in studying host–pathogen interactions and their potential role in advancing the clinical diagnostics of fungal infections.

Notes

Acknowledgements

TG group acknowledges support from the Spanish Ministry of Economy, Industry, and Competitiveness (MEIC) for the EMBL partnership and grants “Centro de Excelencia Severo Ochoa 2013–2017” SEV-2012-0208, and BFU2015-67107 cofounded by European Regional Development Fund (ERDF), from the CERCA Programme/Generalitat de Catalunya, from the Catalan Research Agency (AGAUR) SGR857, and grant from the European Union’s Horizon 2020 research and innovation programme under the grant agreement ERC-2016-724173 the Marie Sklodowska-Curie grant agreement No. H2020-MSCA-ITN-2014-642095.

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© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelonaSpain
  2. 2.Universitat Pompeu FabraBarcelonaSpain
  3. 3.Institució Catalana de Recerca i Estudis AvançatsBarcelonaSpain

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