Host-pathogen transcriptomics of Mucor circinelloides spores phagocytosed by mouse macrophages

Here, we have studied the first stage of this infection—the interaction of Mucor circinelloides spores with phagocytic cells—from an integrated transcriptomic and functional perspective. Our transcriptomic results showed that a relevant gene network is remodelled in response to phagocytosis, enriched in crucial functions to survive the phagosome, such as nutritional adaptation and response to oxidative stress. An additional transcriptomic analysis of atf1 and atf2 mutants unveiled the complex gene network of secondarily regulated genes involved in the response to phagocytosis. These new insights into the initial phase of mucormycosis define genetic regulators and molecular processes that could serve as pharmacological targets. Overall design: 24 samples are provided and analyzed, comprising 2 replicates (a and b) for each coculture interacting samples and each single culture, which are as follows: Mucor strain R7B cocultured with mouse macrophages (cell line J774A.1) for 5h, strain NRRL cocultured with mouse macrophages (cell line J774A.1) for 5h, wild-type control strain (R7B) cocultured with mouse macrophages (cell line J774A.1) for 5h, Mucor atf1 mutant cocultured with mouse macrophages (cell line J774A.1) for 5h, Mucor atf2 mutant cocultured with mouse macrophages (cell line J774A.1) for 5h, wild-type control strain (R7B) singlecultured in cell media for 5h, Mucor strain NRRL singlecultured in cell media for 5h, mouse macrophages (cell line J774A.1) singlecultured in cell media (4 replicates) for 5h, strain R7B singlecultured in MMC media for 24h, Mucor atf1 mutant singlecultured in MMC media for 24h, Mucor atf2 mutant singlecultured in MMC media for 24h. Libraries were prepared with Illumina TruSeq strand-specific mRNA kits and sequenced with an Illumina HiSeq 2500 system to generate 50-bp, first-strand (or reverse) and single-end reads.

本研究深入探讨了该感染的第一阶段——即 mucor circinelloides 孢子与吞噬细胞相互作用的过程，并从转录组学和功能学相结合的角度进行了全面分析。转录组学研究表明，相关基因网络在吞噬作用的影响下发生了重构，并在适应吞噬体生存的关键功能中富集，例如营养适应和对抗氧化应激的响应。对 atf1 和 atf2 突变体的额外转录组学分析揭示了参与吞噬作用响应的次级调控基因的复杂基因网络。这些关于毛霉菌病初始阶段的新见解，不仅定义了遗传调节因子和分子过程，这些过程有望成为药物靶点，同时也为我们的理解提供了新的维度。总体而言，本研究提供了24个样本进行分析，其中包括每个共培养样本和单培养样本的2个重复（标记为a和b），具体包括：将 mucor 稀释株R7B与小鼠巨噬细胞（细胞系J774A.1）共培养5小时，将稀释株NRRL与小鼠巨噬细胞（细胞系J774A.1）共培养5小时，野生型对照株（R7B）与小鼠巨噬细胞（细胞系J774A.1）共培养5小时，mucor atf1 突变株与小鼠巨噬细胞（细胞系J774A.1）共培养5小时，mucor atf2 突变株与小鼠巨噬细胞（细胞系J774A.1）共培养5小时，野生型对照株（R7B）在细胞培养基中单培养5小时，稀释株NRRL在细胞培养基中单培养5小时，小鼠巨噬细胞（细胞系J774A.1）在细胞培养基中单培养5小时（4个重复），稀释株R7B在MMC培养基中单培养24小时，mucor atf1 突变株在MMC培养基中单培养24小时，mucor atf2 突变株在MMC培养基中单培养24小时。通过使用Illumina TruSeq单链特异性mRNA试剂盒制备文库，并利用Illumina HiSeq 2500系统进行测序，生成了50碱基长的第一链（或反向链）和单端读数。