Multi-omic integration reveals dynamic changes in human placental metabolism across gestation

Parenti, M.; Rosen, S.; Pettes, M.; Djukovic, D.; Raftery, D.; Glass, I. A.; Birth Defects Research Laboratory (BDRL),; Gray, K. J.; Paquette, A. G.; McCartney, S. A.

doi:10.1101/2025.10.22.683996

bioRxiv · 10.1101/2025.10.22.683996

Multi-omic integration reveals dynamic changes in human placental metabolism across gestation

Parenti, M.·Rosen, S.·Pettes, M.·Djukovic, D.·Raftery, D.·Glass, I. A.·Birth Defects Research Laboratory (BDRL),·Gray, K. J.·Paquette, A. G.·McCartney, S. A.

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Abstract

ObjectivesMetabolic demands of the developing conceptus are highly dynamic during pregnancy. While placental metabolism has been well described at term and in cell lines, changes in the placental metabolome during development remains understudied. We investigated the placental metabolome, metabolite trajectories, and altered pathways across trimesters in normal human pregnancy by integrating metabolomic and transcriptomic data. MethodsTargeted aqueous metabolomic profiling of 372 metabolites was conducted on placental biopsies from samples collected in the first (n=12), second (n=13), and third (n=11) trimesters of normal pregnancy using liquid chromatography-tandem mass spectrometry. Robust linear models identified differentially abundant metabolites across trimesters in models adjusted for fetal sex and total protein. We conducted pathway analysis using a human metabolic reconstruction. To further aid in biological interpretation, we leveraged publicly available transcriptomics data to conduct pathway-level multi-omic integration throughout gestation. ResultsSamples clustered by trimester in principal component analysis and we identified 5 metabolite trajectories. Out of 193 detectable metabolites, 149 (77%) differed by trimester (FDR<0.05). Using pathway-level multi-omic integration, pathways involved in extracellular transport, and pyruvate, amino acid, NAD, and membrane lipid metabolism are up-regulated in the second trimester compared to the first. In the late third trimester, pathways involved in amino acid metabolism, redox balance, mitochondrial transport, and biomolecule synthesis were down-regulated compared to second trimester. ConclusionsPlacental metabolite abundances change substantially across gestation and integration with metabolic gene expression provides insight into dynamic metabolic function during pregnancy. Observed pathway-level changes potentially reflect the metabolic response to invading maternal circulation in the first-to-second trimester transition, as well as changing maternal and fetal metabolic requirements. Differences observed at term may reflect placental senescence and preparation for parturition. These data can inform other molecular analyses of the placenta by providing enhanced resolution of metabolic changes across pregnancy.

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Parenti, M., Rosen, S., Pettes, M., Djukovic, D., Raftery, D., Glass, I. A., Birth Defects Research Laboratory (BDRL),, Gray, K. J., Paquette, A. G., McCartney, S. A.. 2025-10-23. Multi-omic integration reveals dynamic changes in human placental metabolism across gestation. https://doi.org/10.1101/2025.10.22.683996

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