IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-34422-2.html
   My bibliography  Save this article

Multi-omics signatures of the human early life exposome

Author

Listed:
  • Léa Maitre

    (Institute for Global Health (ISGlobal)
    Universitat Pompeu Fabra (UPF)
    Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP))

  • Mariona Bustamante

    (Institute for Global Health (ISGlobal)
    Universitat Pompeu Fabra (UPF)
    Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP)
    Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology)

  • Carles Hernández-Ferrer

    (Institute for Global Health (ISGlobal)
    Universitat Pompeu Fabra (UPF)
    Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP))

  • Denise Thiel

    (Imperial College London)

  • Chung-Ho E. Lau

    (Imperial College London
    Imperial College London)

  • Alexandros P. Siskos

    (Imperial College London)

  • Marta Vives-Usano

    (Institute for Global Health (ISGlobal)
    Universitat Pompeu Fabra (UPF)
    Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP)
    Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology)

  • Carlos Ruiz-Arenas

    (Institute for Global Health (ISGlobal)
    Universitat Pompeu Fabra (UPF)
    Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP))

  • Dolors Pelegrí-Sisó

    (Institute for Global Health (ISGlobal)
    Universitat Pompeu Fabra (UPF)
    Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP))

  • Oliver Robinson

    (Imperial College London)

  • Dan Mason

    (Bradford Teaching Hospitals NHS Foundation Trust)

  • John Wright

    (Bradford Teaching Hospitals NHS Foundation Trust)

  • Solène Cadiou

    (Inserm, CNRS, Université Grenoble Alpes)

  • Rémy Slama

    (Inserm, CNRS, Université Grenoble Alpes)

  • Barbara Heude

    (Inserm, Université de Paris)

  • Maribel Casas

    (Institute for Global Health (ISGlobal)
    Universitat Pompeu Fabra (UPF)
    Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP))

  • Jordi Sunyer

    (Institute for Global Health (ISGlobal)
    Universitat Pompeu Fabra (UPF)
    Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP)
    Hospital del Mar Medical Research Institute (IMIM))

  • Eleni Z. Papadopoulou

    (Norwegian Institute of Public Health)

  • Kristine B. Gutzkow

    (Norwegian Institute of Public Health)

  • Sandra Andrusaityte

    (Vytautas Magnus University)

  • Regina Grazuleviciene

    (Vytautas Magnus University)

  • Marina Vafeiadi

    (Faculty of Medicine, University of Crete)

  • Leda Chatzi

    (University of Southern California)

  • Amrit K. Sakhi

    (Norwegian Institute of Public Health)

  • Cathrine Thomsen

    (Norwegian Institute of Public Health)

  • Ibon Tamayo

    (CIMA-University of Navarra)

  • Mark Nieuwenhuijsen

    (Institute for Global Health (ISGlobal)
    Universitat Pompeu Fabra (UPF)
    Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP))

  • Jose Urquiza

    (Institute for Global Health (ISGlobal)
    Universitat Pompeu Fabra (UPF)
    Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP))

  • Eva Borràs

    (Universitat Pompeu Fabra (UPF)
    Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology)

  • Eduard Sabidó

    (Universitat Pompeu Fabra (UPF)
    Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology)

  • Inés Quintela

    (University of Santiago de Compostela, CIMUS)

  • Ángel Carracedo

    (University of Santiago de Compostela, CIMUS
    Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Servicio Gallego de Salud (SERGAS))

  • Xavier Estivill

    (Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology)

  • Muireann Coen

    (Imperial College London
    AstraZeneca)

  • Juan R. González

    (Institute for Global Health (ISGlobal)
    Universitat Pompeu Fabra (UPF)
    Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP))

  • Hector C. Keun

    (Imperial College London
    Imperial College London)

  • Martine Vrijheid

    (Institute for Global Health (ISGlobal)
    Universitat Pompeu Fabra (UPF)
    Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP))

Abstract

Environmental exposures during early life play a critical role in life-course health, yet the molecular phenotypes underlying environmental effects on health are poorly understood. In the Human Early Life Exposome (HELIX) project, a multi-centre cohort of 1301 mother-child pairs, we associate individual exposomes consisting of >100 chemical, outdoor, social and lifestyle exposures assessed in pregnancy and childhood, with multi-omics profiles (methylome, transcriptome, proteins and metabolites) in childhood. We identify 1170 associations, 249 in pregnancy and 921 in childhood, which reveal potential biological responses and sources of exposure. Pregnancy exposures, including maternal smoking, cadmium and molybdenum, are predominantly associated with child DNA methylation changes. In contrast, childhood exposures are associated with features across all omics layers, most frequently the serum metabolome, revealing signatures for diet, toxic chemical compounds, essential trace elements, and weather conditions, among others. Our comprehensive and unique resource of all associations ( https://helixomics.isglobal.org/ ) will serve to guide future investigation into the biological imprints of the early life exposome.

Suggested Citation

  • Léa Maitre & Mariona Bustamante & Carles Hernández-Ferrer & Denise Thiel & Chung-Ho E. Lau & Alexandros P. Siskos & Marta Vives-Usano & Carlos Ruiz-Arenas & Dolors Pelegrí-Sisó & Oliver Robinson & Dan, 2022. "Multi-omics signatures of the human early life exposome," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34422-2
    DOI: 10.1038/s41467-022-34422-2
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-34422-2
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-34422-2?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. van Buuren, Stef & Groothuis-Oudshoorn, Karin, 2011. "mice: Multivariate Imputation by Chained Equations in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 45(i03).
    2. Carsten Sticht & Carolina De La Torre & Alisha Parveen & Norbert Gretz, 2018. "miRWalk: An online resource for prediction of microRNA binding sites," PLOS ONE, Public Library of Science, vol. 13(10), pages 1-6, October.
    3. Giacomo Cavalli & Edith Heard, 2019. "Advances in epigenetics link genetics to the environment and disease," Nature, Nature, vol. 571(7766), pages 489-499, July.
    4. Regina Grazuleviciene & Asta Danileviciute & Ruta Nadisauskiene & Jone Vencloviene, 2009. "Maternal Smoking,GSTM1 and GSTT1 Polymorphism and Susceptibility to Adverse Pregnancy Outcomes," IJERPH, MDPI, vol. 6(3), pages 1-16, March.
    5. Michael Coryell & Mark McAlpine & Nicholas V. Pinkham & Timothy R. McDermott & Seth T. Walk, 2018. "The gut microbiome is required for full protection against acute arsenic toxicity in mouse models," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Silvia Rodrigues Jardim & Lucila Marieta Perrotta de Souza & Heitor Siffert Pereira de Souza, 2023. "The Rise of Gastrointestinal Cancers as a Global Phenomenon: Unhealthy Behavior or Progress?," IJERPH, MDPI, vol. 20(4), pages 1-23, February.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Abhilash Bandam & Eedris Busari & Chloi Syranidou & Jochen Linssen & Detlef Stolten, 2022. "Classification of Building Types in Germany: A Data-Driven Modeling Approach," Data, MDPI, vol. 7(4), pages 1-23, April.
    2. Boonstra Philip S. & Little Roderick J.A. & West Brady T. & Andridge Rebecca R. & Alvarado-Leiton Fernanda, 2021. "A Simulation Study of Diagnostics for Selection Bias," Journal of Official Statistics, Sciendo, vol. 37(3), pages 751-769, September.
    3. Christopher J Greenwood & George J Youssef & Primrose Letcher & Jacqui A Macdonald & Lauryn J Hagg & Ann Sanson & Jenn Mcintosh & Delyse M Hutchinson & John W Toumbourou & Matthew Fuller-Tyszkiewicz &, 2020. "A comparison of penalised regression methods for informing the selection of predictive markers," PLOS ONE, Public Library of Science, vol. 15(11), pages 1-14, November.
    4. Norah Alyabs & Sy Han Chiou, 2022. "The Missing Indicator Approach for Accelerated Failure Time Model with Covariates Subject to Limits of Detection," Stats, MDPI, vol. 5(2), pages 1-13, May.
    5. Qiang Zhang & Sai Ma & Zhengzhi Liu & Bohan Zhu & Zirui Zhou & Gaoshan Li & J. Javier Meana & Javier González-Maeso & Chang Lu, 2023. "Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    6. Ida Kubiszewski & Kenneth Mulder & Diane Jarvis & Robert Costanza, 2022. "Toward better measurement of sustainable development and wellbeing: A small number of SDG indicators reliably predict life satisfaction," Sustainable Development, John Wiley & Sons, Ltd., vol. 30(1), pages 139-148, February.
    7. Georges Steffgen & Philipp E. Sischka & Martha Fernandez de Henestrosa, 2020. "The Quality of Work Index and the Quality of Employment Index: A Multidimensional Approach of Job Quality and Its Links to Well-Being at Work," IJERPH, MDPI, vol. 17(21), pages 1-31, October.
    8. Christopher Kath & Florian Ziel, 2018. "The value of forecasts: Quantifying the economic gains of accurate quarter-hourly electricity price forecasts," Papers 1811.08604, arXiv.org.
    9. J M van Niekerk & M C Vos & A Stein & L M A Braakman-Jansen & A F Voor in ‘t holt & J E W C van Gemert-Pijnen, 2020. "Risk factors for surgical site infections using a data-driven approach," PLOS ONE, Public Library of Science, vol. 15(10), pages 1-14, October.
    10. Joost R. Ginkel, 2020. "Standardized Regression Coefficients and Newly Proposed Estimators for $${R}^{{2}}$$R2 in Multiply Imputed Data," Psychometrika, Springer;The Psychometric Society, vol. 85(1), pages 185-205, March.
    11. Gerko Vink & Laurence E. Frank & Jeroen Pannekoek & Stef Buuren, 2014. "Predictive mean matching imputation of semicontinuous variables," Statistica Neerlandica, Netherlands Society for Statistics and Operations Research, vol. 68(1), pages 61-90, February.
    12. Tsai, Tsung-Han, 2016. "A Bayesian Approach to Dynamic Panel Models with Endogenous Rarely Changing Variables," Political Science Research and Methods, Cambridge University Press, vol. 4(3), pages 595-620, September.
    13. Hung Tong & Cristina Tortora, 2022. "Model-based clustering and outlier detection with missing data," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 16(1), pages 5-30, March.
    14. Manuel S. González Canché, 2017. "Financial Benefits of Rapid Student Loan Repayment: An Analytic Framework Employing Two Decades of Data," The ANNALS of the American Academy of Political and Social Science, , vol. 671(1), pages 154-182, May.
    15. Annisa Rahmalia & Michael Holton Price & Yovita Hartantri & Bachti Alisjahbana & Rudi Wisaksana & Reinout van Crevel & Andre J A M van der Ven, 2019. "Are there differences in HIV retention in care between female and male patients in Indonesia? A multi-state analysis of a retrospective cohort study," PLOS ONE, Public Library of Science, vol. 14(6), pages 1-17, June.
    16. Lara Lopez & Fernando L. Vázquez & Ángela J. Torres & Patricia Otero & Vanessa Blanco & Olga Díaz & Mario Páramo, 2020. "Long-Term Effects of a Cognitive Behavioral Conference Call Intervention on Depression in Non-Professional Caregivers," IJERPH, MDPI, vol. 17(22), pages 1-24, November.
    17. Sabine Zinn & Michael Bayer, 2021. "Time Spent on School-Related Activities at Home during the Pandemic: A Longitudinal Analysis of Social Group Inequality among Secondary School Students," SOEPpapers on Multidisciplinary Panel Data Research 1132, DIW Berlin, The German Socio-Economic Panel (SOEP).
    18. Ronald Herrera & Ursula Berger & Ondine S. Von Ehrenstein & Iván Díaz & Stella Huber & Daniel Moraga Muñoz & Katja Radon, 2017. "Estimating the Causal Impact of Proximity to Gold and Copper Mines on Respiratory Diseases in Chilean Children: An Application of Targeted Maximum Likelihood Estimation," IJERPH, MDPI, vol. 15(1), pages 1-15, December.
    19. Graffelman, Jan, 2015. "Exploring Diallelic Genetic Markers: The HardyWeinberg Package," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 64(i03).
    20. Maaz Gardezi & J. Gordon Arbuckle, 2019. "Spatially Representing Vulnerability to Extreme Rain Events Using Midwestern Farmers’ Objective and Perceived Attributes of Adaptive Capacity," Risk Analysis, John Wiley & Sons, vol. 39(1), pages 17-34, January.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34422-2. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.