Human endometrial cell-type-specific RNA sequencing provides new insights into the embryo-endometrium interplay

Mariann Koel; Kaarel Krjutškov; Merli Saare; Külli Samuel; Dmitri Lubenets; Shintaro Katayama; Elisabet Einarsdottir; Eva Vargas; Alberto Sola-Leyva; Parameswaran Grace Lalitkumar; Kristina Gemzell-Danielsson; David Blesa; Carlos Simon; Fredrik Lanner; Juha Kere; Andres Salumets; Signe Altmäe

doi:10.1093/hropen/hoac043

Human endometrial cell-type-specific RNA sequencing provides new insights into the embryo-endometrium interplay

Hum Reprod Open. 2022 Oct 13;2022(4):hoac043. doi: 10.1093/hropen/hoac043. eCollection 2022.

Authors

Mariann Koel^{1

2}, Kaarel Krjutškov^{1

3}, Merli Saare^{1

3}, Külli Samuel¹, Dmitri Lubenets², Shintaro Katayama^{4

5}, Elisabet Einarsdottir^{4

6}, Eva Vargas^{7

8

9}, Alberto Sola-Leyva^{7

8}, Parameswaran Grace Lalitkumar¹⁰, Kristina Gemzell-Danielsson¹⁰, David Blesa¹¹, Carlos Simon^{12

13}, Fredrik Lanner^{14

15}, Juha Kere^{4

5}, Andres Salumets^{1

3

14}, Signe Altmäe^{1

7

8

14}

Affiliations

¹ Competence Centre on Health Technologies, Tartu, Estonia.
² Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
³ Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.
⁴ Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, and Folkhälsan Research Center, Helsinki, Finland.
⁵ Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
⁶ Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of Technology, Solna, Sweden.
⁷ Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain.
⁸ Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain.
⁹ Systems Biology Unit, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Jaén, Spain.
¹⁰ Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet, and Karolinska Univeristy Hospital, Stockholm, Sweden.
¹¹ Department of Product Development, IGENOMIX, Valencia, Spain.
¹² Department of Obstetrics and Gynecology, Valencia University and INCLIVA in Valencia, Valencia, Spain.
¹³ Department of Obstetrics and Gynecology, BIDMC, Harvard University, Boston, MA, USA.
¹⁴ Department of Clinical Science, Intervention and Technology, Division of Obstetrics and Gynecology, Karolinska Institutet, Stockholm, Sweden.
¹⁵ Ming Wai Lau Center for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden.

Abstract

Study question: Which genes regulate receptivity in the epithelial and stromal cellular compartments of the human endometrium, and which molecules are interacting in the implantation process between the blastocyst and the endometrial cells?

Summary answer: A set of receptivity-specific genes in the endometrial epithelial and stromal cells was identified, and the role of galectins (LGALS1 and LGALS3), integrin β1 (ITGB1), basigin (BSG) and osteopontin (SPP1) in embryo-endometrium dialogue among many other protein-protein interactions were highlighted.

What is known already: The molecular dialogue taking place between the human embryo and the endometrium is poorly understood due to ethical and technical reasons, leaving human embryo implantation mostly uncharted.

Study design size duration: Paired pre-receptive and receptive phase endometrial tissue samples from 16 healthy women were used for RNA sequencing. Trophectoderm RNA sequences were from blastocysts.

Participants/materials setting methods: Cell-type-specific RNA-seq analysis of freshly isolated endometrial epithelial and stromal cells using fluorescence-activated cell sorting (FACS) from 16 paired pre-receptive and receptive tissue samples was performed. Endometrial transcriptome data were further combined in silico with trophectodermal gene expression data from 466 single cells originating from 17 blastocysts to characterize the first steps of embryo implantation. We constructed a protein-protein interaction network between endometrial epithelial and embryonal trophectodermal cells, and between endometrial stromal and trophectodermal cells, thereby focusing on the very first phases of embryo implantation, and highlighting the molecules likely to be involved in the embryo apposition, attachment and invasion.

Main results and the role of chance: In total, 499 epithelial and 581 stromal genes were up-regulated in the receptive phase endometria when compared to pre-receptive samples. The constructed protein-protein interactions identified a complex network of 558 prioritized protein-protein interactions between trophectodermal, epithelial and stromal cells, which were grouped into clusters based on the function of the involved molecules. The role of galectins (LGALS1 and LGALS3), integrin β1 (ITGB1), basigin (BSG) and osteopontin (SPP1) in the embryo implantation process were highlighted.

Large scale data: RNA-seq data are available at www.ncbi.nlm.nih.gov/geo under accession number GSE97929.

Limitations reasons for caution: Providing a static snap-shot of a dynamic process and the nature of prediction analysis is limited to the known interactions available in databases. Furthermore, the cell sorting technique used separated enriched epithelial cells and stromal cells but did not separate luminal from glandular epithelium. Also, the use of biopsies taken from non-pregnant women and using spare IVF embryos (due to ethical considerations) might miss some of the critical interactions characteristic of natural conception only.

Wider implications of the findings: The findings of our study provide new insights into the molecular embryo-endometrium interplay in the first steps of implantation process in humans. Knowledge about the endometrial cell-type-specific molecules that coordinate successful implantation is vital for understanding human reproduction and the underlying causes of implantation failure and infertility. Our study results provide a useful resource for future reproductive research, allowing the exploration of unknown mechanisms of implantation. We envision that those studies will help to improve the understanding of the complex embryo implantation process, and hopefully generate new prognostic and diagnostic biomarkers and therapeutic approaches to target both infertility and fertility, in the form of new contraceptives.

Study funding/competing interests: This research was funded by the Estonian Research Council (grant PRG1076); Horizon 2020 innovation grant (ERIN, grant no. EU952516); Enterprise Estonia (grant EU48695); the EU-FP7 Marie Curie Industry-Academia Partnerships and Pathways (IAPP, grant SARM, EU324509); Spanish Ministry of Economy, Industry and Competitiveness (MINECO) and European Regional Development Fund (FEDER) (grants RYC-2016-21199, ENDORE SAF2017-87526-R, and Endo-Map PID2021-127280OB-100); Programa Operativo FEDER Andalucía (B-CTS-500-UGR18; A-CTS-614-UGR20), Junta de Andalucía (PAIDI P20_00158); Margarita Salas program for the Requalification of the Spanish University system (UJAR01MS); the Knut and Alice Wallenberg Foundation (KAW 2015.0096); Swedish Research Council (2012-2844); and Sigrid Jusélius Foundation; Academy of Finland. A.S.-L. is funded by the Spanish Ministry of Science, Innovation and Universities (PRE2018-085440). K.G.-D. has received consulting fees and/or honoraria from RemovAid AS, Norway Bayer, MSD, Gedeon Richter, Mithra, Exeltis, MedinCell, Natural cycles, Exelgyn, Vifor, Organon, Campus Pharma and HRA-Pharma and NIH support to the institution; D.B. is an employee of IGENOMIX. The rest of the authors declare no conflict of interest.

Keywords: blastocyst; embryo implantation; endometrial epithelium; endometrial receptivity; endometrial stroma; interactome.