IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-41159-z.html
   My bibliography  Save this article

Comprehensive proteomics and meta-analysis of COVID-19 host response

Author

Listed:
  • Haris Babačić

    (Karolinska Institutet)

  • Wanda Christ

    (Karolinska Institutet)

  • José Eduardo Araújo

    (Karolinska Institutet)

  • Georgios Mermelekas

    (Karolinska Institutet)

  • Nidhi Sharma

    (Karolinska Institutet)

  • Janne Tynell

    (Karolinska Institutet)

  • Marina García

    (Karolinska Institutet)

  • Renata Varnaite

    (Karolinska Institutet)

  • Hilmir Asgeirsson

    (Karolinska University Hospital
    Karolinska Institutet)

  • Hedvig Glans

    (Karolinska Institutet
    Karolinska University Hospital)

  • Janne Lehtiö

    (Karolinska Institutet)

  • Sara Gredmark-Russ

    (Karolinska Institutet
    Karolinska University Hospital
    The Laboratory for Molecular Infection Medicine Sweden (MIMS))

  • Jonas Klingström

    (Karolinska Institutet
    Linköping University)

  • Maria Pernemalm

    (Karolinska Institutet)

Abstract

COVID-19 is characterised by systemic immunological perturbations in the human body, which can lead to multi-organ damage. Many of these processes are considered to be mediated by the blood. Therefore, to better understand the systemic host response to SARS-CoV-2 infection, we performed systematic analyses of the circulating, soluble proteins in the blood through global proteomics by mass-spectrometry (MS) proteomics. Here, we show that a large part of the soluble blood proteome is altered in COVID-19, among them elevated levels of interferon-induced and proteasomal proteins. Some proteins that have alternating levels in human cells after a SARS-CoV-2 infection in vitro and in different organs of COVID-19 patients are deregulated in the blood, suggesting shared infection-related changes.The availability of different public proteomic resources on soluble blood proteome alterations leaves uncertainty about the change of a given protein during COVID-19. Hence, we performed a systematic review and meta-analysis of MS global proteomics studies of soluble blood proteomes, including up to 1706 individuals (1039 COVID-19 patients), to provide concluding estimates for the alteration of 1517 soluble blood proteins in COVID-19. Finally, based on the meta-analysis we developed CoViMAPP, an open-access resource for effect sizes of alterations and diagnostic potential of soluble blood proteins in COVID-19, which is publicly available for the research, clinical, and academic community.

Suggested Citation

  • Haris Babačić & Wanda Christ & José Eduardo Araújo & Georgios Mermelekas & Nidhi Sharma & Janne Tynell & Marina García & Renata Varnaite & Hilmir Asgeirsson & Hedvig Glans & Janne Lehtiö & Sara Gredma, 2023. "Comprehensive proteomics and meta-analysis of COVID-19 host response," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41159-z
    DOI: 10.1038/s41467-023-41159-z
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-41159-z
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-41159-z?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. Philipp Doebler & Heinz Holling, 2015. "Meta-analysis of Diagnostic Accuracy and ROC Curves with Covariate Adjusted Semiparametric Mixtures," Psychometrika, Springer;The Psychometric Society, vol. 80(4), pages 1084-1104, December.
    2. Alexey Stukalov & Virginie Girault & Vincent Grass & Ozge Karayel & Valter Bergant & Christian Urban & Darya A. Haas & Yiqi Huang & Lila Oubraham & Anqi Wang & M. Sabri Hamad & Antonio Piras & Fynn M., 2021. "Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV," Nature, Nature, vol. 594(7862), pages 246-252, June.
    3. Bates, Douglas & Mächler, Martin & Bolker, Ben & Walker, Steve, 2015. "Fitting Linear Mixed-Effects Models Using lme4," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 67(i01).
    4. Sangtae Kim & Pavel A. Pevzner, 2014. "MS-GF+ makes progress towards a universal database search tool for proteomics," Nature Communications, Nature, vol. 5(1), pages 1-10, December.
    5. Clemens Gutmann & Kaloyan Takov & Sean A. Burnap & Bhawana Singh & Hashim Ali & Konstantinos Theofilatos & Ella Reed & Maria Hasman & Adam Nabeebaccus & Matthew Fish & Mark JW. McPhail & Kevin O’Galla, 2021. "SARS-CoV-2 RNAemia and proteomic trajectories inform prognostication in COVID-19 patients admitted to intensive care," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    6. Xiaonan Zhang & Yun Tan & Yun Ling & Gang Lu & Feng Liu & Zhigang Yi & Xiaofang Jia & Min Wu & Bisheng Shi & Shuibao Xu & Jun Chen & Wei Wang & Bing Chen & Lu Jiang & Shuting Yu & Jing Lu & Jinzeng Wa, 2020. "Viral and host factors related to the clinical outcome of COVID-19," Nature, Nature, vol. 583(7816), pages 437-440, July.
    Full references (including those not matched with items on IDEAS)

    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. Heinz Holling & Katrin Jansen & Walailuck Böhning & Dankmar Böhning & Susan Martin & Patarawan Sangnawakij, 2022. "Estimation of Effect Heterogeneity in Rare Events Meta-Analysis," Psychometrika, Springer;The Psychometric Society, vol. 87(3), pages 1081-1102, September.
    2. Jack S. Gisby & Norzawani B. Buang & Artemis Papadaki & Candice L. Clarke & Talat H. Malik & Nicholas Medjeral-Thomas & Damiola Pinheiro & Paige M. Mortimer & Shanice Lewis & Eleanor Sandhu & Stephen , 2022. "Multi-omics identify falling LRRC15 as a COVID-19 severity marker and persistent pro-thrombotic signals in convalescence," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    3. JANSSENS, Jochen & DE CORTE, Annelies & SÖRENSEN, Kenneth, 2016. "Water distribution network design optimisation with respect to reliability," Working Papers 2016007, University of Antwerp, Faculty of Business and Economics.
    4. Raymond Hernandez & Elizabeth A. Pyatak & Cheryl L. P. Vigen & Haomiao Jin & Stefan Schneider & Donna Spruijt-Metz & Shawn C. Roll, 2021. "Understanding Worker Well-Being Relative to High-Workload and Recovery Activities across a Whole Day: Pilot Testing an Ecological Momentary Assessment Technique," IJERPH, MDPI, vol. 18(19), pages 1-17, October.
    5. Elisabeth Beckmann & Lukas Olbrich & Joseph Sakshaug, 2024. "Multivariate assessment of interviewer-related errors in a cross-national economic survey (Lukas Olbrich, Elisabeth Beckmann, Joseph W. Sakshaug)," Working Papers 253, Oesterreichische Nationalbank (Austrian Central Bank).
    6. Valentina Krenz & Arjen Alink & Tobias Sommer & Benno Roozendaal & Lars Schwabe, 2023. "Time-dependent memory transformation in hippocampus and neocortex is semantic in nature," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    7. Morán-Ordóñez, Alejandra & Ameztegui, Aitor & De Cáceres, Miquel & de-Miguel, Sergio & Lefèvre, François & Brotons, Lluís & Coll, Lluís, 2020. "Future trade-offs and synergies among ecosystem services in Mediterranean forests under global change scenarios," Ecosystem Services, Elsevier, vol. 45(C).
    8. Damian M. Herz & Manuel Bange & Gabriel Gonzalez-Escamilla & Miriam Auer & Keyoumars Ashkan & Petra Fischer & Huiling Tan & Rafal Bogacz & Muthuraman Muthuraman & Sergiu Groppa & Peter Brown, 2022. "Dynamic control of decision and movement speed in the human basal ganglia," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    9. Dongyan Liu & Chongran Zhou & John K. Keesing & Oscar Serrano & Axel Werner & Yin Fang & Yingjun Chen & Pere Masque & Janine Kinloch & Aleksey Sadekov & Yan Du, 2022. "Wildfires enhance phytoplankton production in tropical oceans," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    10. Zhaogeng Yang & Yanhui Li & Peijin Hu & Jun Ma & Yi Song, 2020. "Prevalence of Anemia and its Associated Factors among Chinese 9-, 12-, and 14-Year-Old Children: Results from 2014 Chinese National Survey on Students Constitution and Health," IJERPH, MDPI, vol. 17(5), pages 1-10, February.
    11. Marco Lopez-Cruz & Fernando M. Aguate & Jacob D. Washburn & Natalia Leon & Shawn M. Kaeppler & Dayane Cristina Lima & Ruijuan Tan & Addie Thompson & Laurence Willard Bretonne & Gustavo los Campos, 2023. "Leveraging data from the Genomes-to-Fields Initiative to investigate genotype-by-environment interactions in maize in North America," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    12. Baumann, Elias & Kern, Jana & Lessmann, Stefan, 2019. "Usage Continuance in Software-as-a-Service," IRTG 1792 Discussion Papers 2019-005, Humboldt University of Berlin, International Research Training Group 1792 "High Dimensional Nonstationary Time Series".
    13. repec:cup:judgdm:v:16:y:2021:i:1:p:201-237 is not listed on IDEAS
    14. C. Gabriel Hidalgo Pizango & Eurídice N. Honorio Coronado & Jhon del Águila-Pasquel & Gerardo Flores Llampazo & Johan de Jong & César J. Córdova Oroche & José M. Reyna Huaymacari & Steve J. Carver & D, 2022. "Sustainable palm fruit harvesting as a pathway to conserve Amazon peatland forests," Nature Sustainability, Nature, vol. 5(6), pages 479-487, June.
    15. Szefer Elena & Graham Jinko & Lu Donghuan & Beg Mirza Faisal & Nathoo Farouk, 2017. "Multivariate association between single-nucleotide polymorphisms in Alzgene linkage regions and structural changes in the brain: discovery, refinement and validation," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 16(5-6), pages 349-365, December.
    16. Julien Collet & Samantha C Patrick & Henri Weimerskirch, 2017. "A comparative analysis of the behavioral response to fishing boats in two albatross species," Behavioral Ecology, International Society for Behavioral Ecology, vol. 28(5), pages 1337-1347.
    17. Sean Coogan & Zhixian Sui & David Raubenheimer, 2018. "Gluttony and guilt: monthly trends in internet search query data are comparable with national-level energy intake and dieting behavior," Palgrave Communications, Palgrave Macmillan, vol. 4(1), pages 1-9, December.
    18. Darcy Steeg Morris & Kimberly F. Sellers, 2022. "A Flexible Mixed Model for Clustered Count Data," Stats, MDPI, vol. 5(1), pages 1-18, January.
    19. Katrijn Delaruelle, 2023. "Migration-related inequalities in loneliness across age groups: a cross-national comparative study in Europe," European Journal of Ageing, Springer, vol. 20(1), pages 1-17, December.
    20. Christos C Ioannou & Luis Arrochela Braga Carvalho & Chessy Budleigh & Graeme D Ruxton, 2023. "Virtual prey with Lévy motion are preferentially attacked by predatory fish," Behavioral Ecology, International Society for Behavioral Ecology, vol. 34(4), pages 695-699.
    21. Vonneilich, Nico & Lüdecke, Daniel & von dem Knesebeck, Olaf, 2020. "Educational inequalities in self-rated health and social relationships – analyses based on the European Social Survey 2002-2016," Social Science & Medicine, Elsevier, vol. 267(C).

    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:14:y:2023:i:1:d:10.1038_s41467-023-41159-z. 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.