Last updated: 2024-02-08
Checks: 2 0
Knit directory: Treg_uNK/1_analysis/
This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 8da2e31. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for
the analysis have been committed to Git prior to generating the results
(you can use wflow_publish or
wflow_git_commit). workflowr only checks the R Markdown
file, but you know if there are other scripts or data files that it
depends on. Below is the status of the Git repository when the results
were generated:
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: 2_plots/4_GSEA/
Untracked files:
Untracked: .gitignore
Untracked: 0_data/functions/compColour.rds
Untracked: 0_data/rawData/DTvsPBS_upstream regulators.xls
Untracked: 0_data/rawData/IPA Diseases and Functions.xlsx
Untracked: 0_data/rawData/IPA pathways.xlsx
Untracked: 0_data/rawData/IPA upstream regulators.xlsx
Untracked: 0_data/rawData/Treg vs DT_diseases and functions.xls
Untracked: 0_data/rawData/Treg vs DT_pathways.xls
Untracked: 0_data/rawData/Treg vs DT_upstream regulators.xls
Untracked: 0_data/rawData/Treg vs PBS_diseases and functions.xls
Untracked: 0_data/rawData/Treg vs PBS_pathways.xls
Untracked: 0_data/rawData/Treg vs PBS_upstream regulators.xls
Untracked: 0_data/rds_objects/disease_function_sig.rds
Untracked: 0_data/rds_objects/ipa_pathways.rds
Untracked: 0_data/rds_objects/upstream_sig.rds
Untracked: 0_data/rds_plots/
Untracked: 2_plots/2_DE/heat_DT vs veh.svg
Untracked: 2_plots/2_DE/heat_DT+Treg vs DT.svg
Untracked: 2_plots/2_DE/heat_DT+Treg vs veh.svg
Untracked: 2_plots/2_DE/hist_DT vs veh.svg
Untracked: 2_plots/2_DE/hist_DT+Treg vs DT.svg
Untracked: 2_plots/2_DE/hist_DT+Treg vs veh.svg
Untracked: 2_plots/2_DE/ma_DT vs veh.png
Untracked: 2_plots/2_DE/ma_DT+Treg vs DT.png
Untracked: 2_plots/2_DE/ma_DT+Treg vs veh.png
Untracked: 2_plots/2_DE/venn_2comp.png
Untracked: 2_plots/2_DE/venn_2comp.png.2024-02-02_16-30-41.893776.log
Untracked: 2_plots/2_DE/venn_2comp.png.2024-02-02_16-31-08.009748.log
Untracked: 2_plots/2_DE/vol_DT vs veh.png
Untracked: 2_plots/2_DE/vol_DT+Treg vs DT.png
Untracked: 2_plots/2_DE/vol_DT+Treg vs veh.png
Untracked: 2_plots/3_FA/go/dot_DT vs veh.svg
Untracked: 2_plots/3_FA/go/dot_DT+Treg vs DT.svg
Untracked: 2_plots/3_FA/go/dot_DT+Treg vs veh.svg
Untracked: 2_plots/3_FA/go/parTerm_dot_DT vs veh.svg
Untracked: 2_plots/3_FA/go/parTerm_dot_DT+Treg vs DT.svg
Untracked: 2_plots/3_FA/go/parTerm_dot_DT+Treg vs veh.svg
Untracked: 2_plots/3_FA/go/semSim_dendrogram_DT vs veh.svg
Untracked: 2_plots/3_FA/go/semSim_dendrogram_DT+Treg vs DT.svg
Untracked: 2_plots/3_FA/go/semSim_dendrogram_DT+Treg vs veh.svg
Untracked: 2_plots/3_FA/go/semSim_scatter_DT vs veh.svg
Untracked: 2_plots/3_FA/go/semSim_scatter_DT+Treg vs DT.svg
Untracked: 2_plots/3_FA/go/semSim_scatter_DT+Treg vs veh.svg
Untracked: 2_plots/3_FA/go/upset_DT vs veh.svg
Untracked: 2_plots/3_FA/go/upset_DT+Treg vs DT.svg
Untracked: 2_plots/3_FA/go/upset_DT+Treg vs veh.svg
Untracked: 2_plots/3_FA/ipa/
Untracked: 2_plots/3_FA/kegg/heat_Antigen processing and presentation.svg
Untracked: 2_plots/3_FA/kegg/heat_Epstein-Barr virus infection.svg
Untracked: 2_plots/3_FA/kegg/heat_Natural killer cell mediated cytotoxicity.svg
Untracked: 2_plots/3_FA/kegg/heat_Phagosome.svg
Untracked: 2_plots/3_FA/kegg/kegg_dot_DT vs veh.svg
Untracked: 2_plots/3_FA/kegg/kegg_dot_DT+Treg vs DT.svg
Untracked: 2_plots/3_FA/kegg/kegg_dot_DT+Treg vs veh.svg
Untracked: 2_plots/3_FA/kegg/kegg_upset_DT vs veh.svg
Untracked: 2_plots/3_FA/kegg/kegg_upset_DT+Treg vs DT.svg
Untracked: 2_plots/3_FA/kegg/kegg_upset_DT+Treg vs veh.svg
Untracked: 2_plots/3_FA/kegg/mmu04145.png
Untracked: 2_plots/3_FA/kegg/mmu04145.xml
Untracked: 2_plots/3_FA/kegg/mmu04612.png
Untracked: 2_plots/3_FA/kegg/mmu04612.xml
Untracked: 2_plots/3_FA/kegg/mmu04650.png
Untracked: 2_plots/3_FA/kegg/mmu04650.xml
Untracked: 2_plots/3_FA/kegg/mmu05169.png
Untracked: 2_plots/3_FA/kegg/mmu05169.xml
Untracked: 2_plots/3_FA/kegg/pv_mmu04145.png
Untracked: 2_plots/3_FA/kegg/pv_mmu04612.png
Untracked: 2_plots/3_FA/kegg/pv_mmu04650.png
Untracked: 2_plots/3_FA/kegg/pv_mmu05169.png
Untracked: 2_plots/3_FA/reactome/combine_react_dot.svg
Untracked: 2_plots/3_FA/reactome/react_dot_DT vs veh.svg
Untracked: 2_plots/3_FA/reactome/react_dot_DT+Treg vs DT.svg
Untracked: 2_plots/3_FA/reactome/react_dot_DT+Treg vs veh.svg
Untracked: 2_plots/3_FA/reactome/react_upset_DT vs veh.svg
Untracked: 2_plots/3_FA/reactome/react_upset_DT+Treg vs DT.svg
Untracked: 2_plots/3_FA/reactome/react_upset_DT+Treg vs veh.svg
Untracked: 2_plots/3_FA/reactome/venn_react.png
Unstaged changes:
Modified: 0_data/functions/bossTheme.rds
Modified: 0_data/functions/bossTheme_bar.rds
Modified: 0_data/functions/groupColour.rds
Modified: 0_data/functions/groupColour_dark.rds
Modified: 0_data/rds_objects/comp.rds
Modified: 0_data/rds_objects/dge.rds
Modified: 0_data/rds_objects/enrichGO.rds
Modified: 0_data/rds_objects/enrichGO_sig.rds
Modified: 0_data/rds_objects/enrichKEGG.rds
Modified: 0_data/rds_objects/enrichKEGG_all.rds
Modified: 0_data/rds_objects/enrichKEGG_sig.rds
Modified: 0_data/rds_objects/lm.rds
Modified: 0_data/rds_objects/lm_all.rds
Modified: 0_data/rds_objects/lm_sig.rds
Modified: 0_data/rds_objects/pathway_details.rds
Modified: 0_data/rds_objects/rawCount.rds
Modified: 0_data/rds_objects/reactome.rds
Modified: 0_data/rds_objects/reactome_all.rds
Modified: 0_data/rds_objects/reactome_sig.rds
Modified: 0_data/rds_objects/reducedTerms_all.rds
Modified: 0_data/rds_objects/reducedTerms_ora.rds
Modified: 0_data/rds_objects/reduced_semSim_df.rds
Modified: 0_data/rds_objects/scores_ora.rds
Modified: 0_data/rds_objects/semSim_df.rds
Modified: 0_data/rds_objects/simMatrix_ora.rds
Modified: 140_treg_uNK.Rproj
Modified: 1_analysis/_site.yml
Modified: 2_plots/1_QC/PC1_PC2.svg
Modified: 2_plots/1_QC/PC1_PC3.svg
Modified: 2_plots/1_QC/PC2_PC3.svg
Modified: 2_plots/1_QC/counts_after_filtering.svg
Modified: 2_plots/1_QC/counts_before_after_filtering.svg
Modified: 2_plots/1_QC/counts_before_filtering.svg
Modified: 2_plots/1_QC/library_size.svg
Deleted: 2_plots/2_DE/heat_DT vs PBS.svg
Deleted: 2_plots/2_DE/heat_Treg vs DT.svg
Deleted: 2_plots/2_DE/heat_Treg vs PBS.svg
Modified: 2_plots/2_DE/heat_combined.svg
Deleted: 2_plots/2_DE/hist_DT vs PBS.svg
Deleted: 2_plots/2_DE/hist_Treg vs DT.svg
Deleted: 2_plots/2_DE/hist_Treg vs PBS.svg
Deleted: 2_plots/2_DE/ma_DT vs PBS.png
Deleted: 2_plots/2_DE/ma_Treg vs DT.png
Deleted: 2_plots/2_DE/ma_Treg vs PBS.png
Modified: 2_plots/2_DE/venn.png
Deleted: 2_plots/2_DE/venn.png.2024-01-08_19-59-50.400111.log
Deleted: 2_plots/2_DE/vol_DT vs PBS.png
Deleted: 2_plots/2_DE/vol_Treg vs DT.png
Deleted: 2_plots/2_DE/vol_Treg vs PBS.png
Modified: 2_plots/3_FA/go/combine_go_dot.svg
Deleted: 2_plots/3_FA/go/dot_DT vs PBS.svg
Deleted: 2_plots/3_FA/go/dot_Treg vs DT.svg
Deleted: 2_plots/3_FA/go/dot_Treg vs PBS.svg
Modified: 2_plots/3_FA/go/parTerm_BP_venn.png
Modified: 2_plots/3_FA/go/parTerm_CC_venn.png
Modified: 2_plots/3_FA/go/parTerm_MF_venn.png
Deleted: 2_plots/3_FA/go/parTerm_dot_DT vs PBS.svg
Deleted: 2_plots/3_FA/go/parTerm_dot_Treg vs DT.svg
Deleted: 2_plots/3_FA/go/parTerm_dot_Treg vs PBS.svg
Modified: 2_plots/3_FA/go/parentTerm_all.svg
Deleted: 2_plots/3_FA/go/upset_DT vs PBS.svg
Deleted: 2_plots/3_FA/go/upset_Treg vs DT.svg
Deleted: 2_plots/3_FA/go/upset_Treg vs PBS.svg
Modified: 2_plots/3_FA/go/venn.png
Modified: 2_plots/3_FA/kegg/combine_kegg_dot.svg
Deleted: 2_plots/3_FA/kegg/heat_DT vs PBS_Antigen processing and presentation.svg
Deleted: 2_plots/3_FA/kegg/heat_DT vs PBS_Natural killer cell mediated cytotoxicity.svg
Deleted: 2_plots/3_FA/kegg/heat_DT vs PBS_Phagosome.svg
Deleted: 2_plots/3_FA/kegg/heat_DT vs PBS_Th1 and Th2 cell differentiation.svg
Deleted: 2_plots/3_FA/kegg/heat_Treg vs DT_Antigen processing and presentation.svg
Deleted: 2_plots/3_FA/kegg/heat_Treg vs DT_Natural killer cell mediated cytotoxicity.svg
Deleted: 2_plots/3_FA/kegg/heat_Treg vs DT_Phagosome.svg
Deleted: 2_plots/3_FA/kegg/heat_Treg vs DT_Th1 and Th2 cell differentiation.svg
Deleted: 2_plots/3_FA/kegg/heat_Treg vs PBS_Antigen processing and presentation.svg
Deleted: 2_plots/3_FA/kegg/heat_Treg vs PBS_Natural killer cell mediated cytotoxicity.svg
Deleted: 2_plots/3_FA/kegg/heat_Treg vs PBS_Phagosome.svg
Deleted: 2_plots/3_FA/kegg/heat_Treg vs PBS_Th1 and Th2 cell differentiation.svg
Deleted: 2_plots/3_FA/kegg/kegg_dot_DT vs PBS.svg
Deleted: 2_plots/3_FA/kegg/kegg_dot_Treg vs DT.svg
Deleted: 2_plots/3_FA/kegg/kegg_dot_Treg vs PBS.svg
Deleted: 2_plots/3_FA/kegg/kegg_upset_DT vs PBS.svg
Deleted: 2_plots/3_FA/kegg/kegg_upset_Treg vs DT.svg
Deleted: 2_plots/3_FA/kegg/kegg_upset_Treg vs PBS.svg
Modified: 2_plots/3_FA/kegg/venn.png
Deleted: 2_plots/3_FA/reactome/react_dot_DT vs PBS.svg
Deleted: 2_plots/3_FA/reactome/react_dot_Treg vs DT.svg
Deleted: 2_plots/3_FA/reactome/react_dot_Treg vs PBS.svg
Deleted: 2_plots/3_FA/reactome/react_upset_DT vs PBS.svg
Deleted: 2_plots/3_FA/reactome/react_upset_Treg vs DT.svg
Deleted: 2_plots/3_FA/reactome/react_upset_Treg vs PBS.svg
Modified: 2_plots/functionalHeat.svg
Modified: 3_output/GO_sig.xlsx
Modified: 3_output/KEGG_all.xlsx
Modified: 3_output/KEGG_sig.xlsx
Modified: 3_output/de_genes_all.xlsx
Modified: 3_output/de_genes_sig.xlsx
Modified: 3_output/reactome_all.xlsx
Modified: 3_output/reactome_sig.xlsx
Modified: functions.Rmd
Deleted: ipa.Rmd
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were
made to the R Markdown (1_analysis/index.Rmd) and HTML
(docs/index.html) files. If you’ve configured a remote Git
repository (see ?wflow_git_remote), click on the hyperlinks
in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 8da2e31 | tranmanhha135 | 2024-02-08 | workflowr::wflow_publish(here::here("1_analysis/*.Rmd")) |
| html | d8d23ee | tranmanhha135 | 2024-01-13 | im on holiday |
| html | 36aeb85 | Ha Manh Tran | 2024-01-13 | Build site. |
| Rmd | 221e2fa | tranmanhha135 | 2024-01-10 | fixed error |
| html | 762020e | tranmanhha135 | 2024-01-09 | Build site. |
| Rmd | f2e3750 | tranmanhha135 | 2024-01-08 | completed DE |
| Rmd | 05fa0b3 | tranmanhha135 | 2024-01-06 | added description |
1 The Robinson Research Institute and Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia. 2 Flinders Health and Medical Research Institute, Flinders University, Adelaide, SA 5042, Australia. 3 Women and Children’s Health Research Institute, Department of Obstetrics and Gynaecology, University of Alberta, Edmonton, AB, T6G 2S2, Canada
* Corresponding author: Dr Alison S. Care, Robinson Research Institute and School of Biomedicine, The University of Adelaide, South Australia, 5001, Australia.
E-mail: alison.care@adelaide.edu.au
Conflict of Interest Statement: The authors have declared that no conflict of interest exists
Regulatory T (Treg) cells are essential for maternal immune tolerance of the fetus and placenta. In preeclampsia, aberrant Treg cell tolerance is implicated, but whether and how Treg cells affect the uterine vascular dysfunction thought to precede placental impairment and maternal vasculopathy is unclear. We utilized Foxp3 DTR mice to test the hypothesis that Treg cells are essential regulators of decidual spiral artery adaptation to pregnancy. Transient Treg cell depletion during early placental morphogenesis caused impaired remodeling of decidual spiral arteries and altered uterine artery function, resulting in late gestation fetal loss and fetal growth restriction. Treg cell depletion impaired acquisition of the activation receptor NKp46 on uterine natural killer (uNK cells) and was associated with reduced decidual synthesis of Treg cell-derived cytokines Il35, Il10 and Tgfb implicated in modulating uNK cell phenotype. When Treg cells were replaced, the adverse impact on uNK cell abundance and phenotype, decidual spiral artery remodeling, uterine artery function, and fetal loss was mitigated. These data implicate Treg cells as essential upstream drivers of uterine vascular adaptation to pregnancy through regulation of uNK cell recruitment and activation. The findings provide a mechanism linking impaired adaptive immune tolerance and altered spiral artery remodeling, two hallmark features of preeclampsia.