Single-cell Multi-ome and Immune Profiles of the Inspiration4 Crew Reveal Conserved, Cell-type, and Sex-specific Responses to Spaceflight

Spaceflight induces an immune response in astronauts. To better characterize this effect, we generated single-cell, multi-ome, cell-free RNA (cfRNA), biochemical, and hematology data for the SpaceX Inspiration4 (I4) mission crew. We found that 18 cytokines/chemokines related to inflammation, aging, and muscle homeostasis changed after spaceflight. In I4 single-cell multi-omics data, we identified a "spaceflight signature" of gene expression characterized by enrichment in oxidative phosphorylation, UV response, immune function, and TCF21 pathways. We confirmed the presence of this signature in independent datasets, including the NASA Twins Study, the I4 skin spatial transcriptomics, and 817 NASA GeneLab mouse transcriptomes. Finally, we observed that (1) T cells showed an up-regulation of FOXP3, (2) MHC class I genes exhibited long-term suppression, and (3) infection-related immune pathways were associated with microbiome shifts. In summary, this study reveals conserved and distinct immune disruptions occurring and details a roadmap for potential countermeasures to preserve astronaut health.

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References

Overbey E, Kim J, Tierney B, Park J, Houerbi N, Lucaci A . The Space Omics and Medical Atlas (SOMA) and international astronaut biobank. Nature. 2024; 632(8027):1145-1154. PMC: 11357981. DOI: 10.1038/s41586-024-07639-y. View

Xu H, Wu F, Zhang H, Yang C, Li K, Wang H . Actin cytoskeleton mediates BMP2-Smad signaling via calponin 1 in preosteoblast under simulated microgravity. Biochimie. 2017; 138:184-193. DOI: 10.1016/j.biochi.2017.04.015. View

Walker J, McKenzie A . T2 cell development and function. Nat Rev Immunol. 2017; 18(2):121-133. DOI: 10.1038/nri.2017.118. View

Willis S, Tellier J, Liao Y, Trezise S, Light A, ODonnell K . Environmental sensing by mature B cells is controlled by the transcription factors PU.1 and SpiB. Nat Commun. 2017; 8(1):1426. PMC: 5681560. DOI: 10.1038/s41467-017-01605-1. View

Pinto Y, Chakraborty M, Jain N, Bhatt A . Phage-inclusive profiling of human gut microbiomes with Phanta. Nat Biotechnol. 2023; 42(4):651-662. DOI: 10.1038/s41587-023-01799-4. View

Zohorul Islam M, Tran M, Xu T, Tierney B, Patel C, Kostic A . Reproducible and opposing gut microbiome signatures distinguish autoimmune diseases and cancers: a systematic review and meta-analysis. Microbiome. 2022; 10(1):218. PMC: 9733034. DOI: 10.1186/s40168-022-01373-1. View

Mark S, Scott G, Donoviel D, Leveton L, Mahoney E, Charles J . The impact of sex and gender on adaptation to space: executive summary. J Womens Health (Larchmt). 2014; 23(11):941-7. PMC: 4236030. DOI: 10.1089/jwh.2014.4914. View

Hammond T, Lewis F, Goodwin T, Linnehan R, Wolf D, Hire K . Gene expression in space. Nat Med. 1999; 5(4):359. DOI: 10.1038/7331. View

Berrios D, Galazka J, Grigorev K, Gebre S, Costes S . NASA GeneLab: interfaces for the exploration of space omics data. Nucleic Acids Res. 2020; 49(D1):D1515-D1522. PMC: 7778922. DOI: 10.1093/nar/gkaa887. View

10.

Scott R, Grigorev K, Mackintosh G, Gebre S, Mason C, Del Alto M . Advancing the Integration of Biosciences Data Sharing to Further Enable Space Exploration. Cell Rep. 2020; 33(10):108441. DOI: 10.1016/j.celrep.2020.108441. View

11.

Stepanek J, Blue R, Parazynski S . Space Medicine in the Era of Civilian Spaceflight. N Engl J Med. 2019; 380(11):1053-1060. DOI: 10.1056/NEJMra1609012. View

12.

Hayashi T, Kudo T, Fujita R, Fujita S, Tsubouchi H, Fuseya S . Nuclear factor E2-related factor 2 (NRF2) deficiency accelerates fast fibre type transition in soleus muscle during space flight. Commun Biol. 2021; 4(1):787. PMC: 8225765. DOI: 10.1038/s42003-021-02334-4. View

13.

Savary C, Grazziuti M, Przepiorka D, Tomasovic S, McIntyre B, Woodside D . Characteristics of human dendritic cells generated in a microgravity analog culture system. In Vitro Cell Dev Biol Anim. 2001; 37(4):216-22. DOI: 10.1007/BF02577532. View

14.

Marke R, van Leeuwen F, Scheijen B . The many faces of IKZF1 in B-cell precursor acute lymphoblastic leukemia. Haematologica. 2018; 103(4):565-574. PMC: 5865415. DOI: 10.3324/haematol.2017.185603. View

15.

Romswinkel A, Infanger M, Dietz C, Strube F, Kraus A . The Role of C-X-C Chemokine Receptor Type 4 (CXCR4) in Cell Adherence and Spheroid Formation of Human Ewing's Sarcoma Cells under Simulated Microgravity. Int J Mol Sci. 2019; 20(23). PMC: 6929163. DOI: 10.3390/ijms20236073. View

16.

Garrett-Bakelman F, Darshi M, Green S, Gur R, Lin L, Macias B . The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. Science. 2019; 364(6436). PMC: 7580864. DOI: 10.1126/science.aau8650. View

17.

Zhu J, Paul W . Heterogeneity and plasticity of T helper cells. Cell Res. 2009; 20(1):4-12. PMC: 3494736. DOI: 10.1038/cr.2009.138. View

18.

Crucian B, Stowe R, Mehta S, Uchakin P, Quiriarte H, Pierson D . Immune system dysregulation occurs during short duration spaceflight on board the space shuttle. J Clin Immunol. 2012; 33(2):456-65. DOI: 10.1007/s10875-012-9824-7. View

19.

Stratis D, Trudel G, Rocheleau L, Pelchat M, Laneuville O . The transcriptome response of astronaut leukocytes to long missions aboard the International Space Station reveals immune modulation. Front Immunol. 2023; 14:1171103. PMC: 10324659. DOI: 10.3389/fimmu.2023.1171103. View

20.

Mehta S, Laudenslager M, Stowe R, Crucian B, Feiveson A, Sams C . Latent virus reactivation in astronauts on the international space station. NPJ Microgravity. 2017; 3:11. PMC: 5445581. DOI: 10.1038/s41526-017-0015-y. View