Comprehensive Multi-omics Analysis Reveals Mitochondrial Stress as a Central Biological Hub for Spaceflight Impact

Spaceflight is known to impose changes on human physiology with unknown molecular etiologies. To reveal these causes, we used a multi-omics, systems biology analytical approach using biomedical profiles from fifty-nine astronauts and data from NASA's GeneLab derived from hundreds of samples flown in space to determine transcriptomic, proteomic, metabolomic, and epigenetic responses to spaceflight. Overall pathway analyses on the multi-omics datasets showed significant enrichment for mitochondrial processes, as well as innate immunity, chronic inflammation, cell cycle, circadian rhythm, and olfactory functions. Importantly, NASA's Twin Study provided a platform to confirm several of our principal findings. Evidence of altered mitochondrial function and DNA damage was also found in the urine and blood metabolic data compiled from the astronaut cohort and NASA Twin Study data, indicating mitochondrial stress as a consistent phenotype of spaceflight.

[1]  E. Paschetta,et al.  Bioactive Lipid Species and Metabolic Pathways in Progression and Resolution of Nonalcoholic Steatohepatitis. , 2018, Gastroenterology.

[2]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[3]  A. Hevener,et al.  New mitochondrial DNA synthesis enables NLRP3 inflammasome activation , 2018, Nature.

[4]  M. Singer,et al.  Diabetes Worsens Skeletal Muscle Mitochondrial Function, Oxidative Stress, and Apoptosis After Lower-Limb Ischemia-Reperfusion: Implication of the RISK and SAFE Pathways? , 2018, Front. Physiol..

[5]  P. Puigserver,et al.  ER and Nutrient Stress Promote Assembly of Respiratory Chain Supercomplexes through the PERK-eIF2α Axis. , 2019, Molecular cell.

[6]  M. Chang,et al.  Sarcopenia is an independent risk factor for non-alcoholic steatohepatitis and significant fibrosis. , 2017, Journal of hepatology.

[7]  Francine E. Garrett-Bakelman,et al.  methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles , 2012, Genome Biology.

[8]  N. Braidy,et al.  NAD+ metabolism and oxidative stress: the golden nucleotide on a crown of thorns , 2012, Redox report : communications in free radical research.

[9]  T. Shimazu,et al.  Genes down-regulated in spaceflight are involved in the control of longevity in Caenorhabditis elegans , 2012, Scientific Reports.

[10]  M. Punter,et al.  Diagnosis and management of cerebral venous thrombosis , 2018, Clinical medicine.

[11]  D. Klimchuk Structural and functional features of mitochondria in statocytes of soybean root under microgravity conditions , 2007, Cytology and Genetics.

[12]  L. Brady,et al.  Regulation of the long‐chain carnitine acyltransferases , 1993, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[13]  R. Day,et al.  Cell Proliferation, Reactive Oxygen and Cellular Glutathione , 2005, Dose-response : a publication of International Hormesis Society.

[14]  Homer Fogle,et al.  Multi-omics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver , 2019, Scientific Reports.

[15]  Mila Ljujic,et al.  The integrated stress response , 2016, EMBO reports.

[16]  Paolo Sassone-Corsi,et al.  The NAD+-Dependent Deacetylase SIRT1 Modulates CLOCK-Mediated Chromatin Remodeling and Circadian Control , 2008, Cell.

[17]  W. Junger,et al.  Circulating Mitochondrial DAMPs Cause Inflammatory Responses to Injury , 2009, Nature.

[18]  M. Koenig,et al.  Mitochondrial cardiomyopathy: pathophysiology, diagnosis, and management. , 2013, Texas Heart Institute journal.

[19]  P. Chang,et al.  Urinary 8-OHdG: a marker of oxidative stress to DNA and a risk factor for cancer, atherosclerosis and diabetics. , 2004, Clinica chimica acta; international journal of clinical chemistry.

[20]  Marina A Gritsenko,et al.  Proteomic profiling of human liver biopsies: Hepatitis C virus–induced fibrosis and mitochondrial dysfunction , 2007, Hepatology.

[21]  V. Velagapudi,et al.  Fibroblast Growth Factor 21 Drives Dynamics of Local and Systemic Stress Responses in Mitochondrial Myopathy with mtDNA Deletions. , 2019, Cell metabolism.

[22]  Helga Thorvaldsdóttir,et al.  Molecular signatures database (MSigDB) 3.0 , 2011, Bioinform..

[23]  J. Morrow,et al.  Urinary Prostaglandin F2α Is Generated from the Isoprostane Pathway and Not the Cyclooxygenase in Humans* , 2007, Journal of Biological Chemistry.

[24]  Alexey Sergushichev,et al.  An algorithm for fast preranked gene set enrichment analysis using cumulative statistic calculation , 2016 .

[25]  Keisuke Ito,et al.  Metabolic requirements for the maintenance of self-renewing stem cells , 2014, Nature Reviews Molecular Cell Biology.

[26]  Francine E. Garrett-Bakelman,et al.  The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight , 2019, Science.

[27]  Kevin D Cooper,et al.  Hair follicle stem cell-specific PPARgamma deletion causes scarring alopecia. , 2009, The Journal of investigative dermatology.

[28]  I. Nonaka,et al.  Skeletal muscle gene expression in space‐flown rats , 2004, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[29]  Scott M Smith,et al.  The nutritional status of astronauts is altered after long-term space flight aboard the International Space Station. , 2005, The Journal of nutrition.

[30]  D. Wallace A mitochondrial bioenergetic etiology of disease. , 2013, The Journal of clinical investigation.

[31]  A. Suomalainen,et al.  Mitochondrial diseases: the contribution of organelle stress responses to pathology , 2017, Nature Reviews Molecular Cell Biology.

[32]  C. Glembotski,et al.  Integrating ER and Mitochondrial Proteostasis in the Healthy and Diseased Heart , 2020, Frontiers in Cardiovascular Medicine.

[33]  J. Kobayashi,et al.  Severe mitochondrial damage associated with low-dose radiation sensitivity in ATM- and NBS1-deficient cells , 2016, Cell cycle.

[34]  P. Reddy,et al.  Mitochondrial dysfunction and oxidative stress in metabolic disorders - A step towards mitochondria based therapeutic strategies. , 2017, Biochimica et biophysica acta. Molecular basis of disease.

[35]  M. Illario,et al.  GRKs and β-Arrestins: “Gatekeepers” of Mitochondrial Function in the Failing Heart , 2019, Front. Pharmacol..

[36]  P. Scott,et al.  Solute Diffusion in Nonionic Liquids—Effects of Gravity , 2009, Annals of the New York Academy of Sciences.

[37]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[38]  Joshua A. Lerman,et al.  COBRApy: COnstraints-Based Reconstruction and Analysis for Python , 2013, BMC Systems Biology.

[39]  Tytus D. Mak,et al.  MetaboLyzer: a novel statistical workflow for analyzing Postprocessed LC-MS metabolomics data. , 2014, Analytical chemistry.

[40]  C. Aranow Vitamin D and the Immune System , 2011, Journal of Investigative Medicine.

[41]  N. Ohashi,et al.  Circadian rhythm of blood pressure and the renin–angiotensin system in the kidney , 2017, Hypertension Research.

[42]  Jing He,et al.  Dysfunction of mitochondria in human skeletal muscle in type 2 diabetes. , 2002, Diabetes.

[43]  Lei He,et al.  Inhibition of GPR35 Preserves Mitochondrial Function After Myocardial Infarction by Targeting Calpain 1/2 , 2020, Journal of cardiovascular pharmacology.

[44]  James M. Pattarini,et al.  Venous Thrombosis during Spaceflight. , 2020 .

[45]  Kanika Jain,et al.  Role of Platelet Mitochondria: Life in a Nucleus-Free Zone , 2019, Front. Cardiovasc. Med..

[46]  F. Ferrari,et al.  Genetics, Dyslipidemia, and Cardiovascular Disease: New Insights , 2019, Current Cardiology Reports.

[47]  Marni J. Falk,et al.  Nutritional interventions in primary mitochondrial disorders: Developing an evidence base. , 2016, Molecular genetics and metabolism.

[48]  G. vanRossum Python reference manual , 1995 .

[49]  Scott M Smith,et al.  Vitamin K Status in Spaceflight and Ground-Based Models of Spaceflight , 2010, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research.

[50]  J. Vernikos,et al.  Recent Progress in Space Physiology and Aging , 2018, Front. Physiol..

[51]  Scott M Smith,et al.  Arterial Structure and Function during and after Long-Duration Spaceflight. , 2020, Journal of applied physiology.

[52]  Francine E. Garrett-Bakelman,et al.  Multi-omic, Single-Cell, and Biochemical Profiles of Astronauts Guide Pharmacological Strategies for Returning to Gravity , 2020, Cell Reports.

[53]  Hiroshi Kori,et al.  Circadian regulation of intracellular G-protein signalling mediates intercellular synchrony and rhythmicity in the suprachiasmatic nucleus , 2011, Nature communications.

[54]  R. Hughson,et al.  Heart in space: effect of the extraterrestrial environment on the cardiovascular system , 2018, Nature Reviews Cardiology.

[55]  Bernhard O. Palsson,et al.  Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways , 2015, PLoS Comput. Biol..

[56]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[57]  S. Cassel,et al.  Mitochondria in innate immune signaling. , 2018, Translational research : the journal of laboratory and clinical medicine.

[58]  Chris Bielow,et al.  Proteomics Quality Control: Quality Control Software for MaxQuant Results. , 2016, Journal of proteome research.

[59]  Nimrod D. Rubinstein,et al.  eIF2B activator prevents neurological defects caused by a chronic integrated stress response , 2018, bioRxiv.

[60]  Marco Y. Hein,et al.  The Perseus computational platform for comprehensive analysis of (prote)omics data , 2016, Nature Methods.

[61]  Scott M Smith,et al.  Nutritional status assessment before, during, and after long-duration head-down bed rest. , 2009, Aviation, space, and environmental medicine.

[62]  D. Guttridge,et al.  Inflammation induced loss of skeletal muscle. , 2015, Bone.

[63]  J. García-Ojalvo,et al.  Species-specific segmentation clock periods are due to differential biochemical reaction speeds , 2020, Science.

[64]  Ming-Ling Chang,et al.  Metabolic Signature of Hepatic Fibrosis: From Individual Pathways to Systems Biology , 2019, Cells.

[65]  R. Deberardinis,et al.  Mitochondrial Reactive Oxygen Species Promote Epidermal Differentiation and Hair Follicle Development , 2013, Science Signaling.

[66]  K. Jarrod Millman,et al.  Array programming with NumPy , 2020, Nat..

[67]  N. Jha,et al.  Linking mitochondrial dysfunction, metabolic syndrome and stress signaling in Neurodegeneration. , 2017, Biochimica et biophysica acta. Molecular basis of disease.

[68]  Johan Auwerx,et al.  The metabolic footprint of aging in mice , 2011, Scientific reports.

[69]  Pornpimol Charoentong,et al.  ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks , 2009, Bioinform..

[70]  Hong-Qiang Wang,et al.  SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures , 2011, Bioinform..

[71]  P. A. Peterson,et al.  Proteasomes are regulated by interferon gamma: implications for antigen processing. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[72]  Sui Huang,et al.  Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles , 2003, Bioinform..

[73]  S. Servidei,et al.  Nutritional support in mitochondrial diseases: the state of the art. , 2018, European review for medical and pharmacological sciences.

[74]  P. Stacpoole,et al.  Sleep disorders associated with primary mitochondrial diseases. , 2014, Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine.

[75]  Scott M Smith,et al.  Plasma cytokine concentrations indicate that in vivo hormonal regulation of immunity is altered during long-duration spaceflight. , 2014, Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research.

[76]  Barbara Uszczynska-Ratajczak,et al.  Mitochondrial stress-dependent regulation of cellular protein synthesis , 2019, Journal of Cell Science.

[77]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[78]  S. Capaccioli,et al.  The Coenzyme Q10 as an antiapoptotic countermeasure for retinal lesions onboard the International Space Station , 2018 .

[79]  David S. Wishart,et al.  MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis , 2018, Nucleic Acids Res..

[80]  Francine E. Garrett-Bakelman,et al.  Cell-free DNA (cfDNA) and Exosome Profiling from a Year-Long Human Spaceflight Reveals Circulating Biomarkers , 2020, iScience.

[81]  Aleksey V. Belikov,et al.  T cells and reactive oxygen species , 2015, Journal of Biomedical Science.

[82]  Larry N. Singh,et al.  Regulation of nuclear epigenome by mitochondrial DNA heteroplasmy , 2019, Proceedings of the National Academy of Sciences.

[83]  et al.,et al.  Jupyter Notebooks - a publishing format for reproducible computational workflows , 2016, ELPUB.

[84]  Martina Heer,et al.  Bone metabolism and renal stone risk during International Space Station missions. , 2015, Bone.

[85]  F. Tarantini,et al.  Skeletal muscle: an endocrine organ. , 2013, Clinical cases in mineral and bone metabolism : the official journal of the Italian Society of Osteoporosis, Mineral Metabolism, and Skeletal Diseases.

[86]  D. Bikle,et al.  Vitamin D metabolism, mechanism of action, and clinical applications. , 2014, Chemistry & biology.

[87]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[88]  R. Simpson,et al.  Alterations in hematologic indices during long-duration spaceflight , 2017, BMC Hematology.

[89]  Louis S Stodieck,et al.  Is spaceflight-induced immune dysfunction linked to systemic changes in metabolism? , 2017, PloS one.

[90]  G. Demontis,et al.  Human Pathophysiological Adaptations to the Space Environment , 2017, Front. Physiol..

[91]  E. White,et al.  Quantitative Analysis of NAD Synthesis-Breakdown Fluxes. , 2018, Cell metabolism.

[92]  R. Banerjee,et al.  Redox remodeling as an immunoregulatory strategy. , 2010, Biochemistry.

[93]  V. Velagapudi,et al.  mTORC1 Regulates Mitochondrial Integrated Stress Response and Mitochondrial Myopathy Progression. , 2017, Cell metabolism.

[94]  Brent S. Pedersen,et al.  Fast and accurate alignment of long bisulfite-seq reads , 2014, 1401.1129.

[95]  Rhianna Williams,et al.  A Mitochondrial Stress-Specific Form of HSF1 Protects against Age-Related Proteostasis Collapse. , 2020, Developmental cell.

[96]  A. West,et al.  Mitochondrial DNA in innate immune responses and inflammatory pathology , 2017, Nature Reviews Immunology.

[97]  Janan T. Eppig,et al.  The mouse Gene Expression Database (GXD): 2017 update , 2016, Nucleic Acids Res..

[98]  Chaohui Yu,et al.  Relationship between relative skeletal muscle mass and nonalcoholic fatty liver disease: a systematic review and meta-analysis , 2019, Hepatology International.

[99]  L. Rodríguez-Mañas,et al.  Skeletal Muscle Regulates Metabolism via Interorgan Crosstalk: Roles in Health and Disease. , 2016, Journal of the American Medical Directors Association.

[100]  Amina A. Qutub,et al.  Reconstruction of Tissue-Specific Metabolic Networks Using CORDA , 2016, PLoS Comput. Biol..

[101]  A. Lerman,et al.  Interferon Gamma Induces Reversible Metabolic Reprogramming of M1 Macrophages to Sustain Cell Viability and Pro-Inflammatory Activity , 2018, EBioMedicine.

[102]  Clarence Sams,et al.  Immune System Dysregulation During Spaceflight: Potential Countermeasures for Deep Space Exploration Missions , 2018, Front. Immunol..

[103]  Jüergen Cox,et al.  The MaxQuant computational platform for mass spectrometry-based shotgun proteomics , 2016, Nature Protocols.

[104]  Susumu Goto,et al.  Data, information, knowledge and principle: back to metabolism in KEGG , 2013, Nucleic Acids Res..

[105]  Su Guo,et al.  Mechanisms Linking Mitochondrial Dysfunction and Proteostasis Failure. , 2020, Trends in cell biology.

[106]  Dong Liu,et al.  On-orbit sleep problems of astronauts and countermeasures , 2018, Military Medical Research.

[107]  W. Baumgartner,et al.  Mitochondrial Ca2+ mobilization is a key element in olfactory signaling , 2012, Nature Neuroscience.

[108]  C. Cantó,et al.  Circadian Rhythms and Mitochondria: Connecting the Dots , 2018, Front. Genet..

[109]  Liuting Zeng,et al.  Effectiveness of Coenzyme Q10 Supplementation for Type 2 Diabetes Mellitus: A Systematic Review and Meta-Analysis , 2018, International journal of endocrinology.

[110]  S. Bagh,et al.  A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure , 2016, Scientific Reports.

[111]  Y. Wong,et al.  Role of G Protein-Coupled Receptors in the Regulation of Structural Plasticity and Cognitive Function , 2017, Molecules.

[112]  P. Raven,et al.  Interaction between graviception and carotid baroreflex function in humans during parabolic flight-induced microgravity. , 2018, Journal of applied physiology.

[113]  S. Jirawatnotai,et al.  Immunomodulatory Roles of Cell Cycle Regulators , 2019, Front. Cell Dev. Biol..

[114]  U. Saikia,et al.  Alterations in Mitochondrial Oxidative Stress and Mitophagy in Subjects with Prediabetes and Type 2 Diabetes Mellitus , 2017, Front. Endocrinol..

[115]  D. Turnbull,et al.  Consensus-based statements for the management of mitochondrial stroke-like episodes , 2019, Wellcome open research.

[117]  Scott M Smith,et al.  Benefits for bone from resistance exercise and nutrition in long‐duration spaceflight: Evidence from biochemistry and densitometry , 2012, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research.

[118]  Lior Pachter,et al.  Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.

[119]  G. Jagadeesh,et al.  A century old renin-angiotensin system still grows with endless possibilities: AT1 receptor signaling cascades in cardiovascular physiopathology. , 2014, Cellular signalling.

[120]  Karl R. Clauser,et al.  MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins , 2015, Nucleic Acids Res..

[121]  M. Khazaei Chronic Low-grade Inflammation after Exercise: Controversies , 2012, Iranian journal of basic medical sciences.

[122]  Sylvain V Costes,et al.  Global transcriptomic analysis suggests carbon dioxide as an environmental stressor in spaceflight: A systems biology GeneLab case study , 2018, Scientific Reports.

[123]  M. Philpott,et al.  Oxidative stress-associated senescence in dermal papilla cells of men with androgenetic alopecia. , 2015, The Journal of investigative dermatology.

[124]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[125]  Martina Heer,et al.  Long-duration space flight and bed rest effects on testosterone and other steroids. , 2012, The Journal of clinical endocrinology and metabolism.

[126]  Marco Durante,et al.  Heavy ion carcinogenesis and human space exploration , 2008, Nature Reviews Cancer.

[127]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[128]  Scott M Smith,et al.  Iron status and its relations with oxidative damage and bone loss during long-duration space flight on the International Space Station. , 2013, The American journal of clinical nutrition.

[129]  Scott M Smith,et al.  Genotype, B‐vitamin status, and androgens affect spaceflight‐induced ophthalmic changes , 2016, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[130]  R. Mistlberger,et al.  Feeding Time Entrains the Olfactory Bulb Circadian Clock in Anosmic PER2::LUC Mice , 2018, Neuroscience.

[131]  J. M. Fadool,et al.  Mitochondrial Ultrastructure and Glucose Signaling Pathways Attributed to the Kv1.3 Ion Channel , 2016, Front. Physiol..

[132]  Xia Yang,et al.  Extended Multiplexing of Tandem Mass Tags (TMT) Labeling Reveals Age and High Fat Diet Specific Proteome Changes in Mouse Epididymal Adipose Tissue* , 2017, Molecular & Cellular Proteomics.

[133]  Gilles Clément,et al.  Fundamentals of Space Medicine , 2005 .

[134]  Brian E. Granger,et al.  IPython: A System for Interactive Scientific Computing , 2007, Computing in Science & Engineering.

[135]  Eduardo Esteve,et al.  Dyslipidemia and inflammation: an evolutionary conserved mechanism. , 2005, Clinical nutrition.

[136]  Judith A. Blake,et al.  Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse , 2017, Nucleic Acids Res..

[137]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[138]  Bruce M. Spiegelman,et al.  Biological Control through Regulated Transcriptional Coactivators , 2004, Cell.

[139]  A. Papavassiliou,et al.  Mitochondria and cardiovascular diseases-from pathophysiology to treatment. , 2018, Annals of translational medicine.

[140]  Daniel C. Berrios,et al.  GeneLab: Omics database for spaceflight experiments , 2018, Bioinform..

[141]  M. Bhuiyan,et al.  Molecular Perspectives of Mitochondrial Adaptations and Their Role in Cardiac Proteostasis , 2020, Frontiers in Physiology.

[142]  J. P. Castro,et al.  Impaired proteostasis during skeletal muscle aging , 2019, Free radical biology & medicine.

[143]  Xiaojing Ye,et al.  Small G Protein Signaling in Neuronal Plasticity and Memory Formation: The Specific Role of Ras Family Proteins , 2010, Neuron.

[144]  Bernhard O. Palsson,et al.  A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1 , 2010, BMC Systems Biology.

[145]  Gary D Bader,et al.  Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation , 2010, PloS one.

[146]  Arthur Liberzon,et al.  A description of the Molecular Signatures Database (MSigDB) Web site. , 2014, Methods in molecular biology.

[147]  Robert W. Williams,et al.  Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals , 2017, The Journal of cell biology.

[148]  A. Hillmer,et al.  Progressive expression of PPARGC1α is associated with hair miniaturization in androgenetic alopecia , 2019, Scientific Reports.