Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth

Abstract

While a genetic component of preterm birth (PTB) has long been recognized and recently mapped by genome-wide association studies (GWASs), the molecular determinants underlying PTB remain elusive. This stems in part from an incomplete availability of functional genomic annotations in human cell types relevant to pregnancy and PTB. We generated transcriptome (RNA-seq), epigenome (ChIP-seq of H3K27ac, H3K4me1, and H3K4me3 histone modifications), open chromatin (ATAC-seq), and chromatin interaction (promoter capture Hi-C) annotations of cultured primary decidua-derived mesenchymal stromal/stem cells and in vitro differentiated decidual stromal cells and developed a computational framework to integrate these functional annotations with results from a GWAS of gestational duration in 56,384 women. Using these resources, we uncovered additional loci associated with gestational duration and target genes of associated loci. Our strategy illustrates how functional annotations in pregnancy-relevant cell types aid in the experimental follow-up of GWAS for PTB and, likely, other pregnancy-related conditions.

Evolutionary transcriptomics implicates HAND2 in the origins of implantation and regulation of gestation length

“…HAND2 expression was almost entirely restricted to cell populations in the endometrial stromal fibroblast lineage (see Materials and methods for cell type naming convention), with particularly high expression in ESF2s and DSCs ( Figure 2A ). Interestingly, while it is generally thought that ESFs are not present in the pregnant endometrium, previous studies have demonstrated that ESFs retain a presence in the endometrium from the first trimester all the way to term ( Richards et al, 1995 ; Suryawanshi et al, 2018 ; Muñoz-Fernández et al, 2019 ; Sakabe et al, 2020 ).…”

“…Additionally, it is bound by transcription factors that establish endometrial stromal cell type identity and mediate decidualization, including the progesterone receptor (PGR), NR2F2 (COUP-TFII), GATA2, FOSL2, FOXO1, as well as polymerase II ( Figure 2C ). The HAND2 promoter loops to several distal enhancers, as assessed by H3K27ac HiChIP data generated from a normal hTERT-immortalized endometrial cell line (E6E7hTERT), including a region bound by PGR, NR2F2, GATA2, FOSL2, and FOXO1, that also contains SNPs associated with gestation length in recent GWAS ( Warrington et al, 2019 ; Sakabe et al, 2020 ; Figure 2C ). HAND2 was significantly upregulated by decidualization of human ESFs into DSCs by cAMP/progesterone treatment (Log 2 FC = 1.28, p = 2.62×10 −26 , FDR = 1.16×10 −24 ), and significantly downregulated by siRNAs targeting PGR (Log 2 FC = −0.90, p = 7.05×10 −15 , FDR = 2.03×10 −13 ) and GATA2 (Log 2 FC = −2.73, p = 0.01, FDR = 0.19) ( Figure 2D ).…”

“…We determined that HAND2 expression at the first trimester maternal-fetal interface was almost entirely restricted to cell types in ESF lineage and is regulated by multiple transcription factors that control progesterone responsiveness. Moreover, the HAND2 promoter loops to an enhancer with single-nucleotide polymorphisms (SNPs) that have been implicated by GWAS in the regulation of gestation length ( Warrington et al, 2019 ; Sakabe et al, 2020 ). Furthermore, we showed that HAND2 regulates interleukin 15 ( IL15 ) expression in ESFs, and that ESF-derived IL15 influences the migration of natural killer and trophoblast cells.…”

Fetal Membrane Epigenetics

“…Inclusion of transcriptomic, chromatin accessibility ( Buenrostro et al, 2015 ) and chromatin conformation capture ( Kempfer and Pombo, 2020 ) data in the integrative analyses are expected to inform about the functional impact of chromatin modification changes. These approaches are technically complex and computationally demanding, but also extremely informative, as has been demonstrated recently with decidual cells ( Sakabe et al, 2020 ).…”

“…Nuclear accumulation of the H3K27me3 demethylase, lysine demethylase 6A (KDM6A), has been detected concomitantly with this process, which suggests that epigenetic mechanisms, including the removal of the suppressive H3K27me3 mark, take part in the transition ( Nancy et al, 2018 ). Very recently, a comprehensive analysis of chromatin landscape changes has been reported in endometrial fibroblasts decidualized in vitro ( Sakabe et al, 2020 ). Chromatin accessibility using the ATAC-seq technique, ChIP-seq with H3K4me1, H3K27ac, and H3K4me3 antibodies, and promoter capture Hy-C to detect distant regulatory elements, were integrated and matched with RNA-seq data in this large-scale genome-wide study.…”