GSE111731
Revealing parallel host-pathogen transcriptional dynamics using sorted subpopulations and single, Candida albicans infected macrophages
Purpose: The purpose of this study was to simulataneously examine the host and fungal pathogen transcriptional profiles of four distinct infection fates during macrophage and Candida albicans interactions Methods: Membrane stained (Deep Red),primary, bone marrow derived, murine macrophages and Candida albicans expressing GFP and mCherry were exposed to each other over a four hour time course. Samples were collected at 0, 1, 2 and 4 hours and sorted for four infection subpopulations: 1. Macrophages which phagocytosed live C. albicans  (GFP+ /mCherry+ /Deep Red +), 2. Macrophages which phagocytosed dead C. albicans  (GFP- /mCherry+ /Deep Red +), 3. Uninfected macrophages(GFP- /mCherry- /Deep Red +) and 4. Unengulfed C. albicans (GFP+ /mCherry + /Deep Red -). Unexposed controls were also collected for some time points (i.e. macrophages never exposed to C. albicans and C. albicans never exposed to macrophages). Single macrophages infected with live or dead C. albicans were also sorted. Smart-seq2 was used to create libraries for both infection subpopulation and single, infected cell samples that were sequenced on Illumina's Miseqand Nextseq. Basic quality assessment of Illumina reads and sample demultiplexing was done with Picard version 1.107 and Trimmomatic. Samples profiling exclusively the mouse transcriptional response were aligned to the mouse transcriptome generated from the v. Dec. 2011 GRCm38/mm10 and a collection of mouse rRNA sequences from the UCSC genome website. Samples profiling exclusively the yeast transcriptional response were aligned to the C. albicans transcriptome strain SC5314 version A21-s02-m09-r10 downloaded from Candida Genome Database. Samples containing both macrophages and C. albicans were aligned to a “composite transcriptome” made by combining the mouse transcriptome and C. albicans transcriptomes described above and alignment was done via BWA (version 0.7.10-r789.) Multi-reads (reads that aligned to both host and pathogen transcripts) were discarded. Then, each host or pathogen sample file were aligned to its corresponding reference using Bowtie2 and RSEM (v.1.2.21). Transcript abundance was estimated using transcripts per million (TPM). For subpopulation samples, TPM was calculated using edgeR, all as implemented in the Trinity package version 2.1.. Genes were considered differentially expressed only if they had a 4-fold change difference (> 4 FC) in TPM values and a false discovery rate below or equal to 0.001 (FDR < 0.001), unless specified otherwise.  For single macrophages infected with C. albicans, samples were aligned to the combined transcriptome as described above and RSEM was used to calculate TPM. Results:  We were able to simultaneously measure the host and fungal pathogen transcriptional profiles of four distinct infection fates during macrophage and Candida albicans interactions Conclusions: Our study represents an analysis of both distinct infection populations of macrophages and fungus. Overall design: stained, primary, bone derived macrophages were exposed to GFP and mCherry expressing C. albicans. Four distinct subpopulations were collected at 0, 1, 2 and 4 hours and gene expression was measured. Single macrophages infected with Candida albicans were also collected and gene expression was measured at 2 and 4 hours