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Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy.

  • Author(s): Ghaemi, Mohammad Sajjad
  • DiGiulio, Daniel B
  • Contrepois, Kévin
  • Callahan, Benjamin
  • Ngo, Thuy TM
  • Lee-McMullen, Brittany
  • Lehallier, Benoit
  • Robaczewska, Anna
  • Mcilwain, David
  • Rosenberg-Hasson, Yael
  • Wong, Ronald J
  • Quaintance, Cecele
  • Culos, Anthony
  • Stanley, Natalie
  • Tanada, Athena
  • Tsai, Amy
  • Gaudilliere, Dyani
  • Ganio, Edward
  • Han, Xiaoyuan
  • Ando, Kazuo
  • McNeil, Leslie
  • Tingle, Martha
  • Wise, Paul
  • Maric, Ivana
  • Sirota, Marina
  • Wyss-Coray, Tony
  • Winn, Virginia D
  • Druzin, Maurice L
  • Gibbs, Ronald
  • Darmstadt, Gary L
  • Lewis, David B
  • Partovi Nia, Vahid
  • Agard, Bruno
  • Tibshirani, Robert
  • Nolan, Garry
  • Snyder, Michael P
  • Relman, David A
  • Quake, Stephen R
  • Shaw, Gary M
  • Stevenson, David K
  • Angst, Martin S
  • Gaudilliere, Brice
  • Aghaeepour, Nima
  • et al.
Abstract

Motivation:Multiple biological clocks govern a healthy pregnancy. These biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy. Modeling the chronology of these adaptations during full-term pregnancy provides the frameworks for future studies examining deviations implicated in pregnancy-related pathologies including preterm birth and preeclampsia. Results:We performed a multiomics analysis of 51 samples from 17 pregnant women, delivering at term. The datasets included measurements from the immunome, transcriptome, microbiome, proteome and metabolome of samples obtained simultaneously from the same patients. Multivariate predictive modeling using the Elastic Net (EN) algorithm was used to measure the ability of each dataset to predict gestational age. Using stacked generalization, these datasets were combined into a single model. This model not only significantly increased predictive power by combining all datasets, but also revealed novel interactions between different biological modalities. Future work includes expansion of the cohort to preterm-enriched populations and in vivo analysis of immune-modulating interventions based on the mechanisms identified. Availability and implementation:Datasets and scripts for reproduction of results are available through: https://nalab.stanford.edu/multiomics-pregnancy/. Supplementary information:Supplementary data are available at Bioinformatics online.

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