Dynamic molecular changes during the first week of human life follow a robust developmental trajectory
Amy H Lee, Casey P Shannon, Nelly Amenyogbe, Tue B Bennike, Joann Diray-Arce, Olubukola T Idoko, Erin E Gill, Rym Ben-Othman, William S Pomat, Simon D van Haren, Kim-Anh Lê Cao, Momoudou Cox, Alansana Darboe, Reza Falsafi, Davide Ferrari, Daniel J Harbeson, Daniel He, Cai Bing, Samuel J Hinshaw, Jorjoh Ndure, Jainaba Njie-Jobe, Matthew A Pettengill, Peter C Richmond, Rebecca Ford, Gerard Saleu, Geraldine Masiria, John Paul Matlam, Wendy Kirarock, Elishia Roberts, Mehrnoush Malek, Guzmán Sanchez-Schmitz, Amrit Singh, Asimenia Angelidou, Kinga K Smolen, EPIC Consortium, Ryan R Brinkman, Al Ozonoff, Robert E W Hancock, Anita H J van den Biggelaar, Hanno Steen, Scott J Tebbutt, Beate Kampmann, Ofer Levy, Tobias R Kollmann, Diana Vo, Ken Kraft, Kerry McEnaney, Sofia Vignolo, Arnaud Marchant, Amy H Lee, Casey P Shannon, Nelly Amenyogbe, Tue B Bennike, Joann Diray-Arce, Olubukola T Idoko, Erin E Gill, Rym Ben-Othman, William S Pomat, Simon D van Haren, Kim-Anh Lê Cao, Momoudou Cox, Alansana Darboe, Reza Falsafi, Davide Ferrari, Daniel J Harbeson, Daniel He, Cai Bing, Samuel J Hinshaw, Jorjoh Ndure, Jainaba Njie-Jobe, Matthew A Pettengill, Peter C Richmond, Rebecca Ford, Gerard Saleu, Geraldine Masiria, John Paul Matlam, Wendy Kirarock, Elishia Roberts, Mehrnoush Malek, Guzmán Sanchez-Schmitz, Amrit Singh, Asimenia Angelidou, Kinga K Smolen, EPIC Consortium, Ryan R Brinkman, Al Ozonoff, Robert E W Hancock, Anita H J van den Biggelaar, Hanno Steen, Scott J Tebbutt, Beate Kampmann, Ofer Levy, Tobias R Kollmann, Diana Vo, Ken Kraft, Kerry McEnaney, Sofia Vignolo, Arnaud Marchant
Abstract
Systems biology can unravel complex biology but has not been extensively applied to human newborns, a group highly vulnerable to a wide range of diseases. We optimized methods to extract transcriptomic, proteomic, metabolomic, cytokine/chemokine, and single cell immune phenotyping data from <1 ml of blood, a volume readily obtained from newborns. Indexing to baseline and applying innovative integrative computational methods reveals dramatic changes along a remarkably stable developmental trajectory over the first week of life. This is most evident in changes of interferon and complement pathways, as well as neutrophil-associated signaling. Validated across two independent cohorts of newborns from West Africa and Australasia, a robust and common trajectory emerges, suggesting a purposeful rather than random developmental path. Systems biology and innovative data integration can provide fresh insights into the molecular ontogeny of the first week of life, a dynamic developmental phase that is key for health and disease.
Conflict of interest statement
O.L. is a named inventor on patents regarding bactericidal/permeability increasing protein (BPI), including “Therapeutic uses of BPI protein products in BPI-deficient humans” (WO2000059531A3) and “BPI and its congeners as radiation mitigators and radiation protectors” (WO2012138839A1). R.R.B. has ownership interest in Cytapex Bioinformatics Inc. The remaining authors declare no competing interests.
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