Ramathal, C. Y., Bagchi, I. C., Taylor, R. N. & Bagchi, M. K. Endometrial decidualization: of mice and men. Semin. Reprod. Med. 28, 17–26 (2010).
Koopman, L. A. et al. Human decidual natural killer cells are a unique NK cell subset with immunomodulatory potential. J. Exp. Med. 198, 1201–1212 (2003).
Burton, G. J., Watson, A. L., Hempstock, J., Skepper, J. N. & Jauniaux, E. Uterine glands provide histiotrophic nutrition for the human fetus during the first trimester of pregnancy. J. Clin. Endocrinol. Metab. 87, 2954–2959 (2002).
Hempstock, J., Cindrova-Davies, T., Jauniaux, E. & Burton, G. J. Endometrial glands as a source of nutrients, growth factors and cytokines during the first trimester of human pregnancy: a morphological and immunohistochemical study. Reprod. Biol. Endocrinol. 2, 58 (2004).
Burton, G. J., Woods, A. W., Jauniaux, E. & Kingdom, J. C. P. Rheological and physiological consequences of conversion of the maternal spiral arteries for uteroplacental blood flow during human pregnancy. Placenta 30, 473–482 (2009).
Fisher, S. J. Why is placentation abnormal in preeclampsia? Am. J. Obstet. Gynecol. 213, S115–S122 (2015).
Jauniaux, E. & Burton, G. J. Placenta accreta spectrum: a need for more research on its aetiopathogenesis. BJOG 125, 1449–1450 (2018).
Apps, R., Gardner, L. & Moffett, A. A critical look at HLA-G. Trends Immunol. 29, 313–321 (2008).
Apps, R. et al. Human leucocyte antigen (HLA) expression of primary trophoblast cells and placental cell lines, determined using single antigen beads to characterize allotype specificities of anti-HLA antibodies. Immunology 127, 26–39 (2009).
Sharkey, A. M. et al. Killer Ig-like receptor expression in uterine NK cells is biased toward recognition of HLA-C and alters with gestational age. J. Immunol. 181, 39–46 (2008).
Parham, P. & Moffett, A. Variable NK cell receptors and their MHC class I ligands in immunity, reproduction and human evolution. Nat. Rev. Immunol. 13, 133–144 (2013).
Moffett, A. & Colucci, F. Co-evolution of NK receptors and HLA ligands in humans is driven by reproduction. Immunol. Rev. 267, 283–297 (2015).
Zheng, G. X. Y. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).
Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protocols 9, 171–181 (2014).
Burton, G. J. & Watson, A. L. The structure of the human placenta: implications for initiating and defending against virus infections. Rev. Med. Virol. 7, 219–228 (1997).
Tsang, J. C. H. et al. Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics. Proc. Natl Acad. Sci. USA 114, E7786–E7795 (2017).
Liu, Y. et al. Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta. Cell Res. 28, 819–832 (2018).
Madigan, J. et al. Chemokine scavenger D6 is expressed by trophoblasts and aids the survival of mouse embryos transferred into allogeneic recipients. J. Immunol. 184, 3202–3212 (2010).
Mariathasan, S. et al. TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature 554, 544–548 (2018).
Maltepe, E. & Fisher, S. J. Placenta: the forgotten organ. Annu. Rev. Cell Dev. Biol. 31, 523–552 (2015).
Bolnick, J. M. et al. Altered biomarkers in trophoblast cells obtained noninvasively prior to clinical manifestation of perinatal disease. Sci. Rep. 6, 32382 (2016).
Lucas, E. S. et al. Reconstruction of the decidual pathways in human endometrial cells using single-cell RNA-seq. Preprint at https://www.biorxiv.org/content/early/2018/07/13/368829 (2018).
Muñoz-Fernández, R. et al. Human predecidual stromal cells have distinctive characteristics of pericytes: cell contractility, chemotactic activity, and expression of pericyte markers and angiogenic factors. Placenta 61, 39–47 (2018).
Gamliel, M. et al. Trained memory of human uterine NK cells enhances their function in subsequent pregnancies. Immunity 48, 951–962 (2018).
Kozuki, N. et al. The associations of parity and maternal age with small-for-gestational-age, preterm, and neonatal and infant mortality: a meta-analysis. BMC Public Health 13, S2 (2013).
Cichocki, F. et al. ARID5B regulates metabolic programming in human adaptive NK cells. J. Exp. Med. 215, 2379–2395 (2018).
Hanna, J. et al. Decidual NK cells regulate key developmental processes at the human fetal–maternal interface. Nat. Med. 12, 1065–1074 (2006).
Jokhi, P. P., King, A., Boocock, C. & Loke, Y. W. Secretion of colony stimulating factor-1 by human first trimester placental and decidual cell populations and the effect of this cytokine on trophoblast thymidine uptake in vitro. Hum. Reprod. 10, 2800–2807 (1995).
Hamilton, G. S., Lysiak, J. J., Watson, A. J. & Lala, P. K. Effects of colony stimulating factor-1 on human extravillous trophoblast growth and invasion. J. Endocrinol. 159, 69–77 (1998).
Sato, Y. et al. Trophoblasts acquire a chemokine receptor, CCR1, as they differentiate towards invasive phenotype. Development 130, 5519–5532 (2003).
Böttcher, J. P. et al. NK cells stimulate recruitment of cDC1 into the tumor microenvironment promoting cancer immune control. Cell 172, 1022–1037 (2018).
Sotiropoulou, G. & Pampalakis, G. Kallikrein-related peptidases: bridges between immune functions and extracellular matrix degradation. Biol. Chem. 391, 321–331 (2010).
Takenaka, M. C., Robson, S. & Quintana, F. J. Regulation of the T cell response by CD39. Trends Immunol. 37, 427–439 (2016).
Vijayan, D., Young, A., Teng, M. W. L. & Smyth, M. J. Targeting immunosuppressive adenosine in cancer. Nat. Rev. Cancer 17, 709–724 (2017).
Smith, G. C. S. First-trimester determination of complications of late pregnancy. J. Am. Med. Assoc. 303, 561–562 (2010).
Pavličev, M. et al. Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal–fetal interface. Genome Res. 27, 349–361 (2017).
Camp, J. G. et al. Multilineage communication regulates human liver bud development from pluripotency. Nature 546, 533–538 (2017).
Puram, S. V. et al. Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer. Cell 171, 1611–1624 (2017).
Skelly, D. A. et al. Single-cell transcriptional profiling reveals cellular diversity and intercommunication in the mouse heart. Cell Reports 22, 600–610 (2018).
Pardoll, D. M. The blockade of immune checkpoints in cancer immunotherapy. Nat. Rev. Cancer 12, 252–264 (2012).
Bulmer, J. N., Morrison, L., Longfellow, M., Ritson, A. & Pace, D. Granulated lymphocytes in human endometrium: histochemical and immunohistochemical studies. Hum. Reprod. 6, 791–798 (1991).
King, A., Wellings, V., Gardner, L. & Loke, Y. W. Immunocytochemical characterization of the unusual large granular lymphocytes in human endometrium throughout the menstrual cycle. Hum. Immunol. 24, 195–205 (1989).
Gerrelli, D., Lisgo, S., Copp, A. J. & Lindsay, S. Enabling research with human embryonic and fetal tissue resources. Development 142, 3073–3076 (2015).
O’Rahilla, R. & Muller, F. Human Embryology and Teratology (Wiley-Liss, New York, 1992).
Hern, W. M. Correlation of fetal age and measurements between 10 and 26 weeks of gestation. Obstet. Gynecol. 63, 26–32 (1984).
Bulmer, J. N., Williams, P. J. & Lash, G. E. Immune cells in the placental bed. Int. J. Dev. Biol. 54, 281–294 (2010).
Trombetta, J. J. et al. Preparation of single-cell RNA-seq libraries for next generation sequencing. Curr. Protoc. Mol. Biol. 107, 4.22.1–4.22.17 (2014).
Villani, A.-C. et al. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 356, eaah4573 (2017).
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
Anders, S., Pyl, P. T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).
Satija, R., Farrell, J. A., Gennert, D., Schier, A. F. & Regev, A. Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol. 33, 495–502 (2015).
Butler, A. & Satija, R. Integrated analysis of single cell transcriptomic data across conditions, technologies, and species. Preprint at https://www.biorxiv.org/content/early/2017/07/18/164889 (2017).
van den Brink, S. C. et al. Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations. Nat. Methods 14, 935–936 (2017).
Qiu, X. et al. Reversed graph embedding resolves complex single-cell trajectories. Nat. Methods 14, 979–982 (2017).
Hiby, S. E. et al. Combinations of maternal KIR and fetal HLA-C genes influence the risk of preeclampsia and reproductive success. J. Exp. Med. 200, 957–965 (2004).
Robinson, J. et al. The IPD and IMGT/HLA database: allele variant databases. Nucleic Acids Res. 43, D423–D431 (2015).
Kang, H. M. et al. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat. Biotechnol. 36, 89–94 (2018).
Stubbington, M. J. T. et al. T cell fate and clonality inference from single-cell transcriptomes. Nat. Methods 13, 329–332 (2016).
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997 (2013).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Mills, R. E. et al. Natural genetic variation caused by small insertions and deletions in the human genome. Genome Res. 21, 830–839 (2011).
1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010).
Van der Auwera, G. A. et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr. Protoc. Bioinformatics 43, 11.10.1–11.10.33 (2013).
Broad Institute. Picard tools https://broadinstitute.github.io/picard/ (Broad Institute, 2018).
Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993 (2011).
Robinson, J., Mistry, K., McWilliam, H., Lopez, R. & Marsh, S. G. E. IPD—the Immuno Polymorphism Database. Nucleic Acids Res. 38, D863–D869 (2010).
Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525–527 (2016).
Turro, E. et al. Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biol. 12, R13 (2011).
Bachelerie, F. et al. International Union of Basic and Clinical Pharmacology. LXXXIX. Update on the extended family of chemokine receptors and introducing a new nomenclature for atypical chemokine receptors. Pharmacol. Rev. 66, 1–79 (2013).
Orchard, S. et al. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. Methods 9, 345–350 (2012).