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Bogias KJ, Pederson SM, Leemaqz S, Smith MD, McAninch D, Jankovic-Karasoulos T, McCullough D, Wan Q, Bianco-Miotto T, Breen J, Roberts CT. Placental Transcription Profiling in 6-23 Weeks' Gestation Reveals Differential Transcript Usage in Early Development. Int J Mol Sci 2022; 23:ijms23094506. [PMID: 35562897 PMCID: PMC9105363 DOI: 10.3390/ijms23094506] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/13/2022] Open
Abstract
The human placenta is a rapidly developing transient organ that is key to pregnancy success. Early development of the conceptus occurs in a low oxygen environment before oxygenated maternal blood begins to flow into the placenta at ~10-12 weeks' gestation. This process is likely to substantially affect overall placental gene expression. Transcript variability underlying gene expression has yet to be profiled. In this study, accurate transcript expression profiles were identified for 84 human placental chorionic villus tissue samples collected across 6-23 weeks' gestation. Differential gene expression (DGE), differential transcript expression (DTE) and differential transcript usage (DTU) between 6-10 weeks' and 11-23 weeks' gestation groups were assessed. In total, 229 genes had significant DTE yet no significant DGE. Integration of DGE and DTE analyses found that differential expression patterns of individual transcripts were commonly masked upon aggregation to the gene-level. Of the 611 genes that exhibited DTU, 534 had no significant DGE or DTE. The four most significant DTU genes ADAM10, VMP1, GPR126, and ASAH1, were associated with hypoxia-responsive pathways. Transcript usage is a likely regulatory mechanism in early placentation. Identification of functional roles will facilitate new insight in understanding the origins of pregnancy complications.
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Affiliation(s)
- Konstantinos J. Bogias
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (K.J.B.); (S.L.); (D.M.); (T.J.-K.)
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia;
| | - Stephen M. Pederson
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia;
| | - Shalem Leemaqz
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (K.J.B.); (S.L.); (D.M.); (T.J.-K.)
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia;
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
| | - Melanie D. Smith
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
| | - Dale McAninch
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (K.J.B.); (S.L.); (D.M.); (T.J.-K.)
| | - Tanja Jankovic-Karasoulos
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (K.J.B.); (S.L.); (D.M.); (T.J.-K.)
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia;
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
| | - Dylan McCullough
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
| | - Qianhui Wan
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
| | - Tina Bianco-Miotto
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia;
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - James Breen
- Indigenous Genomics, Telethon Kids Institute (Adelaide Office), Adelaide, SA 5000, Australia;
- College of Health & Medicine, Australian National University, Canberra, ACT 2600, Australia
| | - Claire T. Roberts
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (K.J.B.); (S.L.); (D.M.); (T.J.-K.)
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia;
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
- Correspondence:
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