GSE189581_BAL_hcmv
2024-12-31
GSE189581-The molecular principles governing HCMV infection outcome. samples: Bronchoalveolar lavage (BAL) cells, infected with TB40/E-GFP strain of HCMV at 20 and 70 hours post infectionpools.
Public on Jan 05, 2023
Infection with Human cytomegalovirus (HCMV) can result in either productive or non-productive infection, the latter potentially leading to establishment of latency, but the molecular factors that dictate these different infection outcomes are elusive. Macrophages are known targets of HCMV and considered to be permissive for productive infection, while monocytes, their precursors, are thought to support latent infection. Here we reveal that infection of macrophages is more complex than previously appreciated and can result in either productive or non-productive infection. By analyzing the progression of HCMV infection in c and macrophages using single cell transcriptomics, we uncover that the key characteristics that define productive and non-productive cells are the onset of viral gene expression, and activation of Interferon-stimulated genes (ISGs), respectively. We show that the level of viral gene expression, and specifically the expression of the major immediate early factor, IE1, is the principle barrier for establishing productive infection. On the cellular side, induction of ISGs in response to infection surprisingly does not dictate infection outcome, but we find that the cell intrinsic ISG levels is a main determinant of infection outcome. Indeed, intrinsic ISG level is downregulated with monocyte differentiation. We further show that, compared to monocytes, non-productive macrophages maintain slightly higher levels of viral transcripts and are able to reactivate, raising the possibility that they can serve as latency reservoirs in tissues. Moreover, we find that productive infection perturbs macrophage identity and function, likely affecting their immunological role during active infection. Overall, by harnessing the tractable system of monocyte differentiation we decipher the underlying principles that control HCMV infection outcome, and propose macrophages as a new potential HCMV reservoir in tissues.
10X Genomics Chromium Single Cell 3’
Weizmann Institute
Schwartz, M., Shnayder, M., Nachshon, A. et al. Molecular characterization of human cytomegalovirus infection with single-cell transcriptomics. Nat Microbiol 8, 455–468 (2023). https://doi.org/10.1038/s41564-023-01325-x
Illumina NovaSeq 6000 (Homo sapiens)
All raw fastq files were downloaded from NCBI and aligned in cellranger with assembly: hg38 + TB40/E (NCBI accession EF999921.1)
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## JS## [1] 14589 26813List of HCMV viral gene transcripts:
## [1] "US7-hcmv" "US8-hcmv" "US9-hcmv"
## [4] "US10-hcmv" "US11-hcmv" "US12-hcmv"
## [7] "US13-hcmv" "US14-hcmv" "US15-hcmv"
## [10] "US16-hcmv" "US17-hcmv" "US18-hcmv"
## [13] "US19-hcmv" "US20-hcmv" "US21-hcmv"
## [16] "US22-hcmv" "US23-hcmv" "US24-hcmv"
## [19] "US26-hcmv" "US27-hcmv" "US28-hcmv"
## [22] "US29-hcmv" "US30-hcmv" "US31-hcmv"
## [25] "US32-hcmv" "US33-hcmv" "US34-hcmv"
## [28] "US34A-hcmv" "RL1-hcmv" "RL10-hcmv"
## [31] "RL11-hcmv" "RL12-hcmv" "RL13-TRL14-hcmv"
## [34] "UL1-hcmv" "UL2-hcmv" "UL3-hcmv"
## [37] "UL4-hcmv" "UL5-hcmv" "UL6-hcmv"
## [40] "UL7-hcmv" "UL8-hcmv" "UL9-hcmv"
## [43] "UL10-hcmv" "UL11-hcmv" "UL12-hcmv"
## [46] "UL13-hcmv" "UL14-hcmv" "UL15A-hcmv"
## [49] "UL16-hcmv" "UL17-hcmv" "UL18-hcmv"
## [52] "UL19-hcmv" "UL20-hcmv" "UL21A-hcmv"
## [55] "UL22A-hcmv" "UL23-hcmv" "UL24-hcmv"
## [58] "UL25-hcmv" "UL26-hcmv" "UL27-hcmv"
## [61] "UL28-hcmv" "UL29-hcmv" "UL30-hcmv"
## [64] "UL31-hcmv" "UL32-hcmv" "UL33-hcmv"
## [67] "UL34-hcmv" "UL35-hcmv" "UL36-hcmv"
## [70] "UL37-hcmv" "UL38-hcmv" "vMIA-hcmv"
## [73] "UL40-hcmv" "UL41A-hcmv" "UL42-hcmv"
## [76] "UL43-hcmv" "UL44-hcmv" "UL44-hcmv"
## [79] "UL46-hcmv" "UL47-hcmv" "UL48-hcmv"
## [82] "UL48A-hcmv" "UL49-hcmv" "UL50-hcmv"
## [85] "UL51-hcmv" "UL52-hcmv" "UL53-hcmv"
## [88] "UL54-hcmv" "UL55-hcmv" "UL56-hcmv"
## [91] "UL57-hcmv" "UL59-hcmv" "UL60-hcmv"
## [94] "UL69-hcmv" "UL70-hcmv" "UL71-hcmv"
## [97] "UL72-hcmv" "UL73-hcmv" "UL74"
## [100] "UL75-hcmv" "UL76-hcmv" "UL77-hcmv"
## [103] "UL78-hcmv" "UL79-hcmv" "UL80-hcmv"
## [106] "UL80-5-hcmv" "UL82-hcmv" "UL83-hcmv"
## [109] "UL84-hcmv" "UL85-hcmv" "UL86-hcmv"
## [112] "UL87-hcmv" "UL88-hcmv" "UL89-hcmv"
## [115] "UL90-hcmv" "UL91-hcmv" "UL92-hcmv"
## [118] "UL93-hcmv" "UL94-hcmv" "UL95-hcmv"
## [121] "UL96-hcmv" "UL97-hcmv" "UL98-hcmv"
## [124] "UL99-hcmv" "UL100-hcmv" "UL102-hcmv"
## [127] "UL103-hcmv" "UL104-hcmv" "UL105-hcmv"
## [130] "UL112-hcmv" "UL114-hcmv" "UL115-hcmv"
## [133] "UL116-hcmv" "UL117-hcmv" "UL119-hcmv"
## [136] "UL120-hcmv" "UL121-hcmv" "UL122-hcmv"
## [139] "UL123-hcmv" "UL124-hcmv" "UL127-hcmv"
## [142] "UL128-hcmv" "UL130-hcmv" "UL131A-hcmv"
## [145] "UL132-hcmv" "UL148-hcmv" "UL147A-hcmv"
## [148] "UL147-hcmv" "UL146-hcmv" "UL145-hcmv"
## [151] "UL144-hcmv" "UL142-hcmv" "trunc-UL141-hcmv"
## [154] "UL140-hcmv" "UL139-hcmv" "UL138-hcmv"
## [157] "UL137-hcmv" "UL136-hcmv" "UL135-hcmv"
## [160] "UL134-hcmv" "UL133-hcmv" "UL148A-hcmv"
## [163] "UL148B-hcmv" "UL148C-hcmv" "UL148D-hcmv"
## [166] "UL149-hcmv" "UL150-hcmv" "US2-hcmv"## Warning: The following requested variables were not found (10 out of 72 shown):
## US9-hcmv, US14-hcmv, US15-hcmv, US17-hcmv, US19-hcmv, US20-hcmv, US21-hcmv,
## US27-hcmv, US29-hcmv, US31-hcmv## used (Mb) gc trigger (Mb) max used (Mb)
## Ncells 10544440 563.2 16766051 895.5 12725974 679.7
## Vcells 599525429 4574.1 868642010 6627.3 788073158 6012.6## [1] 14589 26813Shown are heatmaps of human immune and cytomegalovirus gene expressions in 5k BAL cells 20hpi and 5k BAL cells 70hpi. HCMV expressions are elevated in macrophages when compared to other immune compartments.
HCMV glycoprotein UL22A is highly expressed in BAL macrophages.
## Warning: Groups with fewer than two datapoints have been dropped.
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PDL1 and UL22A gene expressions are upregulated at 70hpi when compared to 20hpi.
## p_val avg_log2FC pct.1 pct.2 p_val_adj
## CD274 1.751047e-239 0.6061593 0.624 0.419 2.554602e-235
## UL22A-hcmv 2.260972e-23 0.9633393 0.083 0.052 3.298531e-19Shown are infected cells only, defined by expression of 1 or more viral genes. HCMV genes are upregulated after 70hpi when compared to 20hpi, the majority within the macrophage compartment.
##
## BAL_hcmv_20hpi BAL_hcmv_70hpi
## 2691 2691
PDL1 expression and HCMV viral transcripts increase after 20hpi and were found to be highly expressed in macrophages, a potential HCMV reservoir in tissues.
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