A1 Refereed original research article in a scientific journal
Gene Regulatory Network Analysis of Decidual Stromal Cells and Natural Killer Cells
Authors: Rytkönen, Kalle T.; Adossa, Nigatu; Zúñiga Norman, Sebastián; Lönnberg, Tapio; Poutanen, Matti; Elo, Laura L.
Publisher: Springer Nature
Publication year: 2024
Journal: Reproductive Sciences
Journal name in source: Reproductive sciences (Thousand Oaks, Calif.)
Journal acronym: Reprod Sci
Volume: 31
First page : 3159
Last page: 3174
ISSN: 1933-7191
eISSN: 1933-7205
DOI: https://doi.org/10.1007/s43032-024-01653-1(external)
Web address : https://link.springer.com/article/10.1007/s43032-024-01653-1(external)
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/457463666(external)
Human reproductive success relies on the proper differentiation of the uterine endometrium to facilitate implantation, formation of the placenta, and pregnancy. This process involves two critical types of decidual uterine cells: endometrial/decidual stromal cells (dS) and uterine/decidual natural killer (dNK) cells. To better understand the transcription factors governing the in vivo functions of these cells, we analyzed single-cell transcriptomics data from first-trimester terminations of pregnancy, and for the first time conducted gene regulatory network analysis of dS and dNK cell subpopulations. Our analysis revealed stromal cell populations that corresponded to previously described in vitro decidualized cells and senescent decidual cells. We discovered new decidualization driving transcription factors of stromal cells for early pregnancy, including DDIT3 and BRF2, which regulate oxidative stress protection. For dNK cells, we identified transcription factors involved in the immunotolerant (dNK1) subpopulation, including IRX3 and RELB, which repress the NFKB pathway. In contrast, for the less immunotolerant (dNK3) population we predicted TBX21 (T-bet) and IRF2-mediated upregulation of the interferon pathway. To determine the clinical relevance of our findings, we tested the overrepresentation of the predicted transcription factors target genes among cell type-specific regulated genes from pregnancy disorders, such as recurrent pregnancy loss and preeclampsia. We observed that the predicted decidualized stromal and dNK1-specific transcription factor target genes were enriched with the genes downregulated in pregnancy disorders, whereas the predicted dNK3-specific targets were enriched with genes upregulated in pregnancy disorders. Our findings emphasize the importance of stress tolerance pathways in stromal cell decidualization and immunotolerance promoting regulators in dNK differentiation.
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Funding information in the publication:
Open Access funding provided by University of Turku (including Turku University Central Hospital). This research was supported by Eemil Aaltonen Foundation, Päivi and Sakari Sohlberg Foundation and Yrjö Jahnsson Foundation (K.T.R.), Sigrid Juselius Foundation (M.P.) and Academy of Finland (L.L.E). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
