The Cryptococcus neoformans transcriptome at the site of human meningitis.
The Cryptococcus neoformans transcriptome at the site of human meningitis.
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DOI：
10.1128/mbio.01087-13
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发表时间：
2014-02-04
期刊：
影响因子：
6.4
通讯作者：
Perfect JR
中科院分区：
文献类型：
--
作者：
Chen Y;Toffaletti DL;Tenor JL;Litvintseva AP;Fang C;Mitchell TG;McDonald TR;Nielsen K;Boulware DR;Bicanic T;Perfect JR
新型隐球菌是全球真菌性脑膜炎的主要病因。先前的研究已经表征了各种应激条件下的隐球菌转录组，但尚未尝试对人类宿主中的新型隐球菌转录组进行全面的分析。在这里，我们提取RNA酵母细胞直接从脑脊液（CSF）的两个艾滋病患者隐球菌脑膜炎抗真菌治疗前。患者感染了新型隐球菌变种菌株。分子类型VNI和VNII的Grubii。使用RNA-seq，我们比较了这些菌株在三种环境条件下（体内CSF，离体CSF和酵母提取物-蛋白胨-葡萄糖[YPD]）的转录谱。虽然我们确定了一些差异表达的基因，单核苷酸变异，和新的基因是独特的每一个菌株，两个菌株的整体表达模式是相似的，在相同的环境条件下。具体地，直接从每个患者的CSF获得的酵母细胞比在CSF中离体孵育的细胞更具有代谢活性。与在YPD中的生长相比，一些基因被鉴定为在体内和离体CSF中显著上调，并且它们与先前被认为有助于致病性的基因相关。例如，具有已知应激反应功能的基因，如RIM 101、ENA 1和CFO 1，在两种临床菌株中受到类似的调控。相反，两种菌株之间差异调节的许多基因似乎是转运蛋白。这些发现为进一步研究这种酵母如何生存和产生疾病建立了平台。新型隐球菌是一种环境机会性酵母菌，每年造成约100万例脑膜炎和60多万人死亡，其中大多数是撒哈拉以南非洲和亚洲的艾滋病毒感染者。使用RNA-seq，我们分析了从感染患者的脑脊液（CSF）中获得的两种新型隐球菌菌株的基因表达，从而创建了人体内酵母菌遗传反应的全面快照。通过比较三种条件（体内CSF、离体CSF和实验室培养）下每种临床菌株的基因表达，我们鉴定了受CSF暴露独特调控的基因和途径，这些基因和途径可能对新生隐球菌在中枢神经系统中的存活至关重要。进一步的分析揭示了菌株之间的遗传多样性，为隐球菌的进化和菌株特异性提供了证据。这种表征体内转录的能力使得能够阐明促进疾病产生和进展的特定遗传反应。
Cryptococcus neoformans is the leading cause of fungal meningitis worldwide. Previous studies have characterized the cryptococcal transcriptome under various stress conditions, but a comprehensive profile of the C. neoformans transcriptome in the human host has not been attempted. Here, we extracted RNA from yeast cells taken directly from the cerebrospinal fluid (CSF) of two AIDS patients with cryptococcal meningitis prior to antifungal therapy. The patients were infected with strains of C. neoformans var. grubii of molecular type VNI and VNII. Using RNA-seq, we compared the transcriptional profiles of these strains under three environmental conditions (in vivo CSF, ex vivo CSF, and yeast extract-peptone-dextrose [YPD]). Although we identified a number of differentially expressed genes, single nucleotide variants, and novel genes that were unique to each strain, the overall expression patterns of the two strains were similar under the same environmental conditions. Specifically, yeast cells obtained directly from each patient’s CSF were more metabolically active than cells that were incubated ex vivo in CSF. Compared with growth in YPD, some genes were identified as significantly upregulated in both in vivo and ex vivo CSF, and they were associated with genes previously recognized for contributing to pathogenicity. For example, genes with known stress response functions, such as RIM101, ENA1, and CFO1, were regulated similarly in the two clinical strains. Conversely, many genes that were differentially regulated between the two strains appeared to be transporters. These findings establish a platform for further studies of how this yeast survives and produces disease. Cryptococcus neoformans, an environmental, opportunistic yeast, is annually responsible for an estimated million cases of meningitis and over 600,000 deaths, mostly among HIV-infected patients in sub-Saharan Africa and Asia. Using RNA-seq, we analyzed the gene expression of two strains of C. neoformans obtained from the cerebrospinal fluid (CSF) of infected patients, thus creating a comprehensive snapshot of the yeasts’ genetic responses within the human body. By comparing the gene expression of each clinical strain under three conditions (in vivo CSF, ex vivo CSF, and laboratory culture), we identified genes and pathways that were uniquely regulated by exposure to CSF and likely crucial for the survival of C. neoformans in the central nervous system. Further analyses revealed genetic diversity between the strains, providing evidence for cryptococcal evolution and strain specificity. This ability to characterize transcription in vivo enables the elucidation of specific genetic responses that promote disease production and progression.