bioRxiv preprint doi: https://doi.org/10.1101/680181; this version posted June 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Transcriptional and Progesterone Receptor Binding Profiles of the Human 2 Endometrium Reveal Important Pathways and Regulators in the Epithelium During 3 the Window of Implantation 4 5 Ru-pin Alicia Chi1, Tianyuan Wang2, Nyssa Adams3, San-pin Wu1, Steven L. Young4, 6 Thomas E. Spencer5,6, and Francesco DeMayo1 7 8 1 Reproductive and Developmental Biology Laboratory, National Institute of 9 Environmental Health Sciences, Research Triangle Park, North Carolina, USA 10 2 Integrative Bioinformatics Support Group, National Institute of Environmental Health 11 Sciences, Research Triangle Park, North Carolina, USA 12 3 Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor 13 College of Medicine, Houston, Texas, USA 14 4 Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, 15 Chapel Hill, North Carolina, USA 16 5 Division of Animal Sciences and 6Department of Obstetrics, Gynecology and Women’s 17 Health, University of Missouri, Columbia, Missouri, USA 18 19 1 bioRxiv preprint doi: https://doi.org/10.1101/680181; this version posted June 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 20 ABSTRACT 21 22 The endometrium undergoes highly dynamic modifications in a time and compartment specific 23 manner during each menstrual cycle resulting in full receptivity to embryo implantation during a 24 discrete temporal window of implantation (WOI). Attainment of normal receptivity is strictly 25 governed by the steroid hormone progesterone, which acts via the two isoforms of the nuclear 26 Progesterone Receptor (PGR). In order to define the molecular mechanisms regulated by PGR 27 in uterine receptivity, we conducted RNA-sequencing and PGR ChIP-sequencing (ChIP-seq) in 28 endometrial biopsies taken from fertile women during the proliferative (P) and mid-secretory (MS) 29 phases. Overlaying the genes with altered PGR binding and differential expression (DEGs) during 30 the phase transition identified 653 genes, which are involved in inflammatory response signaling, 31 xenobiotic metabolism, epithelial-mesenchymal transition (EMT), cell death regulation, 32 interleukin/STAT signaling, estrogen response, as well as MTORC1 response. RNA-sequencing 33 conducted using epithelium-derived RNA identified 3,052 DEGs in the epithelium, of which 658 34 were uniquely regulated in the epithelium. Transcription factors IRF8 and MEF2C were selected 35 for validation and found to be regulated in the epithelium during the WOI at the protein level, 36 suggesting potentially important functions that are previously unrecognized. In summary, we 37 present herein data that expands our understanding of the progesterone action in human 38 endometrium during the WOI. 39 2 bioRxiv preprint doi: https://doi.org/10.1101/680181; this version posted June 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 40 Introduction 41 42 The human endometrium is a highly complex tissue. The functionalis layer consists of the stromal 43 compartment which makes up significant portion of the endometrium; the glandular epithelium 44 which is responsible for secreting an array of growth factors and cytokines [1]; and the luminal 45 epithelium which lines the stromal compartment and is the first maternal cell type with which the 46 embryo interacts inside the uterus. In order to maximize the chances of a successful pregnancy, 47 the uterus prepares for embryo implantation after each menstruation by the generation and 48 differentiation of the endometrial functionalis, a process known as the menstrual cycle [2, 3]. This 49 is orchestrated by the interplay of two steroid hormones, estrogen and progesterone. During the 50 proliferative (P) phase, estrogen promotes proliferation of both the stromal and epithelial cells, 51 steadily increasing the thickness of the functionalis [4, 5]. Upon ovulation, the ovary begins 52 secreting significant amounts of progesterone, halting estrogen-induced proliferation and initiating 53 a dramatic pattern of differentiation of stromal cells (decidualization) and epithelial cells. These 54 include depolarization, altered surface morphology, expression of specific adhesion proteins, 55 altered steroid receptor expression, and secretion of glycogen [5, 6]. Without a successful 56 implantation, the levels of both steroid hormones decrease during the late secretory phase, 57 leading to endometrial involution and subsequently endometrial shedding (menstruation), 58 initiating another cycle [7]. 59 60 Abnormal embryo implantation and implantation failure is a major cause of infertility and early 61 pregnancy loss and is linked to other pregnancy complications [8-12]. Attainment of human 62 endometrial receptivity occurs in the mid-secretory phase (MS) after sufficient time and 63 concentration of progesterone exposure as seen in other placental mammals [13-18]. In women 3 bioRxiv preprint doi: https://doi.org/10.1101/680181; this version posted June 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 64 without ovaries, sequential treatment with estrogen followed by estrogen plus progesterone, 65 without any other ovarian hormones, is sufficient to achieve high rates of successful implantation 66 of embryos derived from donor oocytes [16, 19], though successful pregnancy establishment 67 largely depends on length of progesterone exposure [20]. 68 69 Abnormal progesterone signaling leads not only to fertility issues but also a spectrum of 70 gynecological diseases [21-23], emphasizing the criticality of progesterone signaling in 71 maintaining normal uterine biology and initiating pregnancy. The impact of progesterone is 72 mediated through its nuclear receptor – the progesterone receptor (PGR), where binding of 73 progesterone induces a conformational change of the receptor, leading to affinity change for 74 target DNA response elements and thereby influencing the gene expression network at the 75 transcriptional level [24]. The PGR itself exhibits the highest expression level during the late P 76 phase, followed by a gradual decrease reaching the lowest expression in the late secretory phase 77 [25]. To date, many PGR-regulated genes have been identified in both animal model systems and 78 human studies as important mediators of implantation, including Indian Hedgehog (IHH) [26-28], 79 Krüpple-like Factor 15 (KLF15) [29, 30], Heart and Neural Crest Derivatives-expressed 2 80 (HAND2) [31], Bone Morphogenesis Protein 2 (BMP2) [32, 33], Homeobox gene HOXA10 [30, 81 34, 35], CCAAT/Enhancer-binding Protein β (CEBPB) [36-38], and many others [14]. Yet, 82 implantation failure remains a great challenge in both natural pregnancies and assisted 83 reproductive interventions. 84 85 Epithelial aspects of PGR actions are important, sometimes underappreciated determinants of 86 implantation and pregnancy outcome. Endometrial epithelial cells line the uterine lumen and 87 glands, with the latter derived from the former [39, 40]. The endometrial epithelium undergoes 4 bioRxiv preprint doi: https://doi.org/10.1101/680181; this version posted June 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 88 dramatic cellular and molecular changes common to both mouse models and humans during the 89 WOI, including adhesion mechanisms enabling the attachment of embryo to the luminal 90 epithelium [41, 42], alterations in nuclear pore complex presentation [43], downregulation of the 91 Serum and Glucocorticoid Regulated Kinase 1 (SGK1) [44], apoptotic cascade [45, 46], and 92 expression of epithelial-specific receptivity markers [47]. The glandular epithelium which is 93 regulated by FOXA2 signaling further facilitates implantation via the production of Leukemia 94 Inhibitory Factor (LIF), which is a critical factor in embryo-uterine communication leading to 95 successful implantation [48-50]. Elaborate cross-talk also exists between the endometrial 96 epithelium and stroma that is indispensable for allowing implantation, adding further complexity 97 to the regulatory mechanisms governing pregnancy establishment. For example, epithelial- 98 stromal cross-talk has been well documented for the IHH pathway, where epithelial derived IHH 99 regulates stromal functions through COUP-TFII and HAND2 prior to implantation in a mouse 100 model [26-28]. These findings further highlight the intricacy of the endometrial mechanisms 101 allowing normal implantation, highlighting the need for understanding the contributions of