Long-read transcriptome sequencing reveals isoform signatures in preeclamptic placentas

Preeclampsia is a major pregnancy-specific multisystem disorder that affects a substantial proportion of pregnancies globally and is a significant contributor to maternal and neonatal mortality. The molecular pathogenesis of this complex disease, however, remains elusive. Long-read sequencing technologies, with their ability to produce long, continuous reads, offer enhanced resolution for genomic studies. This study utilizes this technology to reveal novel insights at the isoform level in preeclamptic placentas.

In this study, we enrolled six participants, including three with normotensive pregnancies and three with preeclamptic pregnancies. By integrating Oxford Nanopore Technologies (ONT) long-read sequencing, Illumina short-read RNA-Seq, ATAC-seq, and Whole-Genome Bisulfite Sequencing (WGBS) of placental tissues, we generated an isoform-resolved transcriptome. We identified a total of 48,175 isoforms, encompassing 19,584 previously unannotated splice variants from known genes and 2,744 novel isoforms from the newly identified loci. Furthermore, we found that epigenetic modifications in promoter regions trigger alternative first exon usage, leading to additional novel isoforms of key preeclampsia regulators (e.g., ADARG1).

This study expands the known transcriptomic landscape of the human placenta, revealing tens of thousands of previously unannotated isoforms. Integration of cross-platform validation and multi-omics datasets not only confirmed the robustness of these findings but also provided insights into their potential biological functions. The resources generated here establish a valuable foundation for future investigations into placental development and the molecular mechanisms of preeclampsia.