Published July 19, 2023 | Published + Supplemental Material
Journal Article Open

A spatially resolved timeline of the human maternal–fetal interface

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Abstract

Beginning in the first trimester, fetally derived extravillous trophoblasts (EVTs) invade the uterus and remodel its spiral arteries, transforming them into large, dilated blood vessels. Several mechanisms have been proposed to explain how EVTs coordinate with the maternal decidua to promote a tissue microenvironment conducive to spiral artery remodelling (SAR). However, it remains a matter of debate regarding which immune and stromal cells participate in these interactions and how this evolves with respect to gestational age. Here we used a multiomics approach, combining the strengths of spatial proteomics and transcriptomics, to construct a spatiotemporal atlas of the human maternal–fetal interface in the first half of pregnancy. We used multiplexed ion beam imaging by time-of-flight and a 37-plex antibody panel to analyse around 500,000 cells and 588 arteries within intact decidua from 66 individuals between 6 and 20 weeks of gestation, integrating this dataset with co-registered transcriptomics profiles. Gestational age substantially influenced the frequency of maternal immune and stromal cells, with tolerogenic subsets expressing CD206, CD163, TIM-3, galectin-9 and IDO-1 becoming increasingly enriched and colocalized at later time points. By contrast, SAR progression preferentially correlated with EVT invasion and was transcriptionally defined by 78 gene ontology pathways exhibiting distinct monotonic and biphasic trends. Last, we developed an integrated model of SAR whereby invasion is accompanied by the upregulation of pro-angiogenic, immunoregulatory EVT programmes that promote interactions with the vascular endothelium while avoiding the activation of maternal immune cells.

Additional Information

© The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. M.A. is supported by 5U54CA20997105, 5DP5OD01982205, 1R01CA24063801A1, 5R01AG06827902, 5UH3CA24663303, 5R01CA22952904, 1U24CA22430901, 5R01AG05791504 and 5R01AG05628705 from the NIH, W81XWH2110143 from the DOD, and other funding from the Bill and Malinda Gates Foundation, the Cancer Research Institute, the Parker Center for Cancer Immunotherapy, and the Breast Cancer Research Foundation. S.G. is supported by the Bill and Melinda Gates Foundation (OPP1113682). I.A. is an awardee of the Weizmann Institute of Science–Israel National Postdoctoral Award Program for Advancing Women in Science. E.S. is supported by National Science Scholarship, Agency for Science, Technology, and Research (A*STAR), Singapore. These authors contributed equally: Shirley Greenbaum, Inna Averbukh, Erin Soon. Author contributions. S.G. assembled the tissue cohort, performed tissue staining and MIBI experiments, annotated images, analysed and interpreted MIBI data and wrote the manuscript. I.A. analysed and interpreted MIBI data and NanoString data and wrote the manuscript. E.S. assisted with tissue staining and MIBI experiments, annotated images, performed NanoString experiments, analysed and interpreted MIBI and NanoString data and wrote the manuscript. G.R. advised on the cohort design, assembled the tissue cohort and annotated images. A.B. wrote software for artery digital morphometrics. N.F.G., G.M., M.S., W.G. and D.V.V. developed and wrote software for cell segmentation and clustering. A.K. wrote software for cell–cell spatial-enrichment measurement. M.B. performed two-colour IHC experiments, advised on experimental design and reagent validation. M.G. and A.S. performed IHC experiments. H.P. and V.D.W. advised on experimental design and reagent validation. E.G.J. assembled cohort patient metadata. L.K. advised on computational analyses. Z.K. prepared and validated reagents. S.K. constructed the TMAs. S.W. annotated images. T.H. validated reagents and advised on experimental design. M.v.d.R. oversaw TMA construction. M.A. conceived the study, advised on experimental design and data analyses, interpreted data and wrote the manuscript. Data availability. MIBI data are available at the Human BioMolecular Atlas Program (10.35079/hbm585.qpdv.454). The same MIBI data in a browsable format, along with segmentation masks, extracted features, cell phenotype masks (CPMs), cell–cell and cell–artery spatial-enrichment scores per image, a table enumerating all single cells in this study and provides their location, morphological characteristics (such as size and shape), marker expression, FlowSOM cluster assignment and cell-type assignment, are available at FigShare (10.6084/m9.figshare.16663465). H&E images of tissue blocks from the cohort with annotations are available at Dryad (10.5061/dryad.v15dv41zp). The following public databases were used in this study (see Methods for details): the Gene Ontology Biological Process database (http://geneontology.org/) and the Gene Cards database (https://www.genecards.org/). Source data are provided with this paper. Code availability. The following software were used for analysis in the article: ImageJ, MAUI (https://github.com/angelolab/MAUI) for low-level image processing; DeepCell v.0.5.0 (https://deepcell.readthedocs.io/en/master/index.html) for cell segmentation; Ark Analysis for cell–cell spatial enrichment (https://github.com/angelolab/ark-analysis); and QuPath (v.0.4.0) for two-colour IHC analysis. Custom code for this study is available at FigShare (10.6084/m9.figshare.16663465). Ethics statement. All human samples were acquired and all experiments were approved by Institutional Review Board protocol number 46646 "Assessing normal expression patterns of immune and non-immune markers across tissue types with multiplexed ion beam imaging" at Stanford University. Per this protocol from the Institutional Review Board at Stanford University, the consent to use archival deidentified tissue was not required. All experiments followed all relevant guidelines and regulations. Online content. Any methods, additional references, Nature Portfolio reporting summaries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author contributions and competing interests; and statements of data and code availability are available at 10.1038/s41586-023-06298-9. Competing interests. M.A. and is a named inventor on patent US20150287578A1, which covers the mass spectrometry approach utilized by MIBI-TOF to detect elemental reporters in tissue using secondary ion mass spectrometry. M.A. is a board member and shareholder in IonPath, which develops and manufactures the commercial MIBI-TOF platform. All other authors declare no competing interests.

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Additional details

Created:
August 22, 2023
Modified:
December 22, 2023