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 (GWAS), the molecular determinants underlying PTB remain elusive. This stems in part from an incomplete availability of comprehensive functional genomic annotations in human cell types relevant to pregnancy and PTB. Here, we generated extensive transcriptional and chromatin annotations of cultured primary deciduaderived mesenchymal stromal/stem cells (MSCs) and in vitro differentiated decidual stromal cells (DSCs) and developed a computational framework to integrate these functional annotations with results from a GWAS of gestational duration in 56,384 women. This resulted in a significant enrichment of heritability estimates in functional noncoding regions in stromal cells, as well as in the discovery of additional loci associated with gestational duration and target genes of associated loci. Our strategy illustrates how systematic functional annotations in pregnancyrelevant cell types aid in the experimental follow-up of GWAS for PTB and, likely, other pregnancy-related conditions.

Evolutionary transcriptomics implicatesHAND2in the origins of implantation and regulation of gestation length

“…Additionally, it is bound by transcription factors that establish endometrial stromal cell-type identity and mediate decidualization, including the progesterone receptor (PR), 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 PR, 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 up-regulated 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 down-regulated by siRNAs targeting PR (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 used ORA to identify enriched terms for three pathway databases (KEGG, Reactome, and Wikipathway), the Human Phenotype Ontology database, and a custom database of genes implicated in preterm birth by GWAS. The preterm birth gene set was assembled from the NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog), including genes implicated in GWAS with either the ontology terms “Preterm Birth” (EFO_0003917) or “Spontaneous Preterm Birth” (EFO_0006917), as well as two recent preterm birth GWAS (Warrington et al ., 2019; Sakabe et al ., 2020).…”

“…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). • Lastly, it is important to emphasize that advanced, genomewide approaches and the more traditional analysis of individual candidate genes supplement each other and pursuing them in combination can result in optimal outcomes.…”

“…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.…”