The enhancer RNA lnc-SLC4A1-1 epigenetically regulates unexplained recurrent pregnancy loss (URPL) by activating CXCL8 and NF-kB pathway

Abstract

BackgroundEnhancer RNAs (eRNAs) are a group of lncRNAs transcribed from enhancers, whose regulatory effects on gene expression are an emerging area of interest. However, the role of eRNAs in regulating trophoblast cells and unexplained recurrent pregnancy loss (URPL) remains elusive.MethodsWe profiled eRNAs in villi from URPL patients and matched controls by RNA-seq. Functions of URPL-related eRNAs were further investigated in vitro.ResultsWe identified lnc-SLC4A1-1, which was transcribed from an active enhancer marked with H3K27ac and H3K4me1 and so-called eRNA, highly expressed in URPL patients. Gain-of-function experiments indicated that lnc-SLC4A1-1 facilitated trophoblast cell migration and apoptosis. Mechanistically, as an eRNA, lnc-SLC4A1-1 was retained in the nuclei and recruited transcription factor NF-κB to bind to CXCL8, resulting in increased H3K27ac in the CXCL8 promoter and subsequent elevation of CXCL8 expression. Activation of CXCL8 exacerbated inflammatory reactions in trophoblast cells by inducing TNF-α and IL-1β, which could be blocked by an antagonist of lnc-SLC4A1-1.InterpretationThese findings indicate that an eRNA, lnc-SLC4A1-1, alters trophoblast function via activation of immune responses and by regulating the NF-κB/CXCL8 axis. Our study provides new insights in understanding lncRNA/eRNA function in pathological pregnancy, potentially informing on therapeutic strategies for URPL.FundNational Natural Science Foundation of China, Natural Science Foundation of Jiangsu Province, National Key Research and Development Program, the Priority Academic Program for the Development of Jiangsu Higher Education Institutions.

Diversity and Emerging Roles of Enhancer RNA in Regulation of Gene Expression and Cell Fate

“…In addition to promoter-enhancer looping and histone modifications, eRNAs interact with transcriptional machinery such as transcription factors, BRD4, and RNAP II. eRNA knockdown decreases binding of transcription factors at respective promoter and enhancer loci, perhaps due to loss of the "transcription factor trapping" mechanism previously discussed (Sigova et al, 2015;Spurlock et al, 2017;Huang Z. et al, 2018). Additionally, the bromodomains of BRD4 have been shown to directly interact with eRNA.…”

“…RNAs tethered near enhancer loci were shown to increase the presence of YY1 specifically at those loci, perhaps due to "transcription factor trapping" wherein nascent RNA from enhancers and promoters increase the affinity of otherwise weak DNA-TF interactions creating a kinetic sink that would "trap" escaped transcription factors (Sigova et al, 2015). Such a model may explain observations that eRNA increases the binding of transcription factors such as c-Jun and NF-κB to target loci (Shii et al, 2017;Spurlock et al, 2017;Huang Z. et al, 2018). An emerging idea for how eRNAs may interact with large numbers of proteins is through phase separation.…”

“…Multiple genome-wide association studies have found that most disease associated mutations occur outside the coding genome, and that a majority of those occur in enhancers or their transcribed RNAs (Farh et al, 2014;Aune et al, 2017). Accordingly, eRNAs are beginning to be utilized to map specific disease states and show the ability to identify disease-specific variants in a broad range of diseases including autoimmunity, cancer, infectious disease, cardiac hypertrophy, recurrent pregnancy loss, psychiatric, and neurological disorders (Farh et al, 2014;Witte et al, 2015;Liang et al, 2016;Aune et al, 2017;Le Gras et al, 2017;Ren et al, 2017;Hauberg et al, 2018;Huang Z. et al, 2018;Imamura et al, 2018;Jiao et al, 2018;Gu et al, 2019;Kyzar et al, 2019;Mirtschink et al, 2019;Tan et al, 2019). The therapeutic potential of these studies was demonstrated when knockdown of the HERNA1 eRNA, which promotes pathological cardiac hypertrophy, protected mice from disease and reversed pathology in mice that had already developed the disease (Mirtschink et al, 2019).…”

The role of CXC chemokine ligand 16 in physiological and pathological pregnancies

“…However, URM is currently considered to be mainly associated with immune factors . Studies have shown that abnormal expression of chemokines may be associated with miscarriage . A series of studies have shown that the abnormal expression of chemokines and their receptors at the maternal‐fetal interface may be associated with URM, such as CCL2, CXCL12, and CXCL13 .…”

“…1,95 Studies have shown that abnormal expression of chemokines may be associated with miscarriage. 27,96,97 A series of studies have shown that the abnormal expression of chemokines and their receptors at the maternal-fetal interface may be associated with URM, such as CCL2, CXCL12, and CXCL13. 27,96,98,99 Other studies have also reported, through immunohistochemistry and immunoblotting, that CXCL16 expression of the villus was decreased in patients who had undergone spontaneous miscarriage compared with normal pregnant women.…”