Characterisation of transcript expression in placenta across early gestation reveals variable transcript usage

Konstantinos Bogias⁰, Stephen Pederson¹, Qianhui Wan², Melanie Smith⁰, James Breen³, Claire Roberts²
(0) Robinson Research Institute, University of Adelaide, Adelaide SA
(1) Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide SA
(2) Flinders Health and Medical Research Institute, Flinders University, Bedford Park SA
(3) South Australian Health & Medical Research Institute, Adelaide SA

Find me on Wed Nov 25th, 1:30-2:50pm AEDT in Remo, table 92

Abstract
The human placenta is a rapidly developing, highly specialised organ that plays a central role in pregnancy and is essential to the development of the fetus. The myriad functions of the placenta include exchange of nutrients and wastes between mother and fetus, mediation of maternal immune system activity, regulation of maternal insulin sensitivity and protection of the fetus against xenobiotics. In early gestation, the placenta develops in a physiological but low oxygen environment until approximately 10 weeks’ gestation at which time maternal blood flow into the placenta is initiated and oxygenation occurs. Recent work in our lab has shown differential gene expression (DGE) in placenta from 6-10 weeks’ versus 11-23 weeks’ gestation, where striking changes in expression of immune system genes were evident. Identification of individual isoform expression associated with developmental processes in early gestation, and with pregnancy complications, have been previously reported in the literature. To assess the impact of individual transcript isoforms at a genome-wide scale, we initially used selective alignment implemented in Salmon to quantify transcript abundances from 96 placenta samples throughout 6-23 weeks’ gestation. Comparing 6-10 weeks’ and 11-23 weeks’ gestation placenta, differential transcript expression (DTE) was performed using edgeR and differential transcript usage (DTU) analysis using DRIMSeq. Subsequent validation and increased FDR control of DTU results were performed using StageR and gene ontology (GO) enrichment analysis using goseq. Both the DTE and DTU analyses were subsequently compared with each other, along with DGE data. A total of 1,005 DE transcripts were identified from 853 genes, with transcripts more likely to be upregulated at 11-23 weeks’ gestation. In the DTE results, 501 genes were also detected in DGE analysis while 352 genes had observable differential expression in transcripts without any detectable changes in gene-level expression. In DTU analysis, 1441 transcripts from 611 genes were found to have changing proportions from early to mid-gestation. Of the DTU genes, 55 also showed DTE in the absence of any detectable change in gene expression. GO enrichment for DTE genes revealed enrichment in cell surface receptor signalling, cellular migration and inflammatory response, while DTU genes were enriched for intracellular protein transport, positive regulation of splicing, and cadherin binding. The most significant DTU genes (FDR < 1.0e-23), ADAM10, VMP1, MTUS1, ASAH1, and GPR126, exhibited variable usage of transcripts coding for functional protein domains associated with processes including autophagy, embryogenesis, angiogenesis and apoptotic resistance. Overall, this study presents the most comprehensive genome-wide profile of transcript usage in early to mid-gestation placenta to date. It highlights the diversity and plasticity of transcript expression during early placental development. Future studies will examine functional implications.