Evolutionary multispecies transcriptomics to reveal genes that govern fungal spore germination and pathogenesis

进化多物种转录组学揭示控制真菌孢子萌发和发病机制的基因

基本信息

批准号：
10612374
负责人：
Anita Sil
金额：
$ 73.37万
依托单位：
YALE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-05-16 至 2025-04-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10612374
关键词：
Aspergillus fumigatus Aspergillus nidulans Biological Assay Biology Candidate Disease Gene Chaetomium Coccidioides Coccidioides posadasii Data Development Developmental Biology Diagnostic Disease Disease Progression Disparate Environment Event Evolution Fungal Genes Fungal Genome Fungal Spores Fungal Vaccines Fusarium Gene Expression Genes Genomics Germination Goals Growth Histoplasma Histoplasma capsulatum Human Infection Intervention Knock-out Knowledge Macrophage Mammals Modeling Mycoses Neurospora crassa Organism Pathogenesis Pathogenicity Pattern Phenotype Phylogenetic Analysis Plants Publications Publishing Reproduction spores Research Role Sexual Development Technology Temperature Time Vaccines Work comparative comparative genomics diagnostic tool dimorphism experimental study fungus gene function host colonization human pathogen innovation interest knockout gene novel diagnostics opportunistic pathogen pathogen pathogenic fungus prophylactic trait transcriptome sequencing transcriptomics vector-borne

项目摘要

Project Summary Fungal pathogens of humans are prevalent in the environment, and commonly come into contact with hosts via dispersal of vegetative spores. Although spore germination and subsequent development are recognized as critical to the initiation of fungal-host interactions, little is known about the fungal genes that govern these events. Our goal is to leverage comparative genomics, evolutionary biology and fungal pathogenesis to define genes that are essential for spore germination, subsequent growth, and host colonization in an evolutionarily diverse group of fungi. We have chosen fungi with a range of abilities to cause disease upon interaction of spores with mammalian hosts, including primary, opportunistic, and nonpathogenic species. We will take advantage of a highly effective and innovative pipeline that reveals genes whose evolving roles have led to phenotypic differences among these species. PIs Trail and Townsend have defined a paradigm that brings together comparative genomics, developmental biology, and transcriptomics into a single, unified phylogenetic framework that will identify key genes that govern spore germination and outgrowth in these fungi. The linchpin of our approach is use of the evolutionary relationship between the fungi to infer genes whose expression has been altered during evolution from their ancestral state to each present-day lineage, thus allowing specific traits (such as pathogenesis) to evolve. In our recently published work and preliminary data, this approach was immensely powerful for identifying genes whose evolving role led to developmental and phenotypic differences among species during (1) fungal sexual development and (2) spore germination and early infection during fungal pathogenesis of plants. We will use a common medium to germinate spores from the following fungi: the primary pathogens Histoplasma capsulatum and Coccidioides posadasii, the opportunistic pathogens Aspergillus fumigatus, Fusarium oxysporum, and Chaetomium elatum, the infrequent opportunistic pathogen Aspergillus nidulans, and the non-pathogenic Neurospora crassa. We will subject these fungi to transcriptomics over a time-course of germination and subsequent development under temperature conditions relevant to germination in the environment vs. in a mammalian host. We will reconstruct evolutionary changes of gene expression across these multiple species to identify genes that have undergone recent shifts in gene expression, in particular shifts that occurred along the shared ancestral branches where key traits (such as the ability to colonize mammals) have evolved. These experiments will yield a high-confidence set of candidate genes whose function is expected to be critical for spore germination and development in each organism. We will use gene knock-out technology to interrogate the function of these candidate genes in spore germination and development. These studies will identify potential targets for diagnostic, prophylactic, and vaccine interventions for ubiquitous fungal infections of humans.

项目摘要人类的真菌病原体在环境中普遍存在，并且通常与宿主接触通过分散营养孢子。尽管孢子发芽和随后的发展被认为是对于启动真菌 - 宿主相互作用至关重要的是，对控制这些事件的真菌基因知之甚少。我们的目标是利用比较基因组学，进化生物学和真菌发病机理来定义基因这对于在进化上多样化的孢子发芽，随后的增长和宿主定植至关重要真菌组。我们选择了具有一系列能力的真菌，可在孢子相互作用时引起疾病哺乳动物的宿主，包括原发性，机会性和非致病性物种。我们将利用一个高效和创新的管道揭示了其不断发展的作用导致表型的基因这些物种之间的差异。 PIS Trail和Townsend定义了一个范式比较基因组学，发育生物学和转录组学成一个单一的统一系统发育框架这将确定这些真菌中孢子发芽和产物的主要基因。我们的关键方法是使用真菌之间的进化关系来推断其表达一直在的基因在从祖先状态到每个当今血统的进化过程中发生了变化，从而允许特定特征（这种特征作为发病机理）要进化。在我们最近发布的工作和初步数据中，这种方法非常强大的用于识别其不断发展的作用导致发展和表型差异的基因（1）真菌性发育和（2）真菌性发芽和早期感染期间的物种植物的发病机理。我们将使用常见培养基从以下真菌发芽：主要病原体组织囊肿囊肿和球虫剂Posadasii，机会性病原体曲霉曲霉，富马图斯， fusarium oxysporum和Chaetomium Elatum，不频繁的机会性病原曲霉，以及非致病性神经孢子骨。我们将使这些真菌的转录组学在一个时间顺序的情况下进行在温度条件下的发芽和随后的发展与发芽有关环境与在哺乳动物宿主中。我们将重建基因表达的进化变化多种物种鉴定基因表达最近发生转移的基因，特别是转移发生在共享祖先分支的情况下，关键特征（例如定植哺乳动物的能力）具有进化。这些实验将产生一组高信任的候选基因，其功能有望对于每个生物体的孢子发芽和发育至关重要。我们将使用基因敲除技术来询问这些候选基因在孢子发芽和发育中的功能。这些研究会确定潜在的诊断，预防性和疫苗干预措施的潜在靶标的无处不在的真菌感染人类。