Space Omics and Medical Atlas (SOMA) across orbits

New studies on astronauts and space biology bring humanity one step closer to the final frontier

Time-lapse video taken by the Expedition 28 crew on board the International Space Station during a night pass over North and South America. Credit: Earth Science and Remote Sensing Unit, NASA Johnson Space Center.

Time-lapse video taken by the Expedition 28 crew on board the International Space Station during a night pass over North and South America. Credit: Earth Science and Remote Sensing Unit, NASA Johnson Space Center.

The Space Omics and Medical Atlas (SOMA) package of manuscripts, data, protocols, and code represents the largest-ever compendium of data for aerospace medicine and space biology. Over 100 institutions from >25 countries worked together for a coordinated 2024 release of molecular, cellular, physiological, phenotypic, and spaceflight data.

Notably, this includes analysis of samples collected from the first all-civilian crew of the Inspiration4 mission, which consisted of commercial astronauts who embarked on a short-term mission to a high-altitude orbit (575 km), farther than the International Space Station (ISS). This data is distinct from the longer-duration missions of ISS-based astronauts, who typically stay 120, 180, or 365 days. While in orbit, the Inspiration4 crew performed an extensive battery of scientific experiments, which have now been processed, sequenced, and analyzed, contributing to most of the 44 papers in the SOMA package, some of which are highlighted below. Embracing the spirit of Open Science at NASA and data accessibility, all raw and processed data acquired from the crew during and after their missions have been made available in NASA’s Open Science Data Repository an expansion of NASA GeneLab. Additionally, four new data portals have been created for browsing results from the mission, which also include linked data from the NASA Twins Study, enhancing our understanding of human health in space.

Earth from space with diagram overlay showing the orbits of the International Space Station at 420 km, the Hubble Space Telescope at 540 km, and SpaceX Inspiration4 at 575 km.

Samples from different orbits (i.e. ISS and Inspiration4) have now been analyzed and integrated. Photo credit: Inspiration4 crew

Samples from different orbits (i.e. ISS and Inspiration4) have now been analyzed and integrated. Photo credit: Inspiration4 crew

The SOMA package represents a milestone in several other respects. It features a >10-fold increase in the number of next-generation sequencing (NGS) data from spaceflight, a 4-fold increase in the number of single-cells processed from spaceflight, the launch of the first aerospace medicine biobank (Weill Cornell Medicine’s CAMbank), the first-ever direct RNA sequencing data from astronauts, the largest number of processed biological samples from a mission (2,911), and the first ever spatially-resolved transcriptome data from astronauts.

Working across borders and teams, between companies and governments, and spanning myriad international laboratories enabled the greatest amount of science and erudition to be gained in this package. These data can serve as a springboard for new experiments, hypotheses, and follow-up studies, as well as guide future mission planning and countermeasure development. Finally, this package shows how the modern tools of molecular biology and precision medicine can help guide humanity into more challenging missions, which will be critical for a permanent presence on the moon, Mars, and beyond.

Transcriptome changes

Four astronauts in a row in front of rocket at launch site

The civillian crew for Inspiration4 and the Dragon spacecraft Resillience atop the Falcon 9 rocket. Credit: Inspiration4 / John Kraus

The civillian crew for Inspiration4 and the Dragon spacecraft Resillience atop the Falcon 9 rocket. Credit: Inspiration4 / John Kraus

Communications Biology: Spaceflight induces changes in gene expression profiles linked to insulin and estrogen

Nature Communications: Cosmic kidney disease: An integrated pan-omic, physiological and morphological study into spaceflight-induced renal dysfunction

Green fluorescence histological cross-section of kidney and transcriptome maps showing the location of cell types in two areas of the tissue section.

Spatial transcriptome data from the kidney profiles show the impact of spaceflight on the kidney structure and kidney cells’ gene expression. Cell types are shown as colors, and labeled sections of the kidney are highlighted by arrows.

Spatial transcriptome data from the kidney profiles show the impact of spaceflight on the kidney structure and kidney cells’ gene expression. Cell types are shown as colors, and labeled sections of the kidney are highlighted by arrows.

Stained cross-section of a mouse kidney 6-month post exposure to radiation, analysed for detection of kidney damage and impact of spaceflight. Zoomed in areas of the cross-section shows labelled structure and different cell types of kidney cells'.

Epigenomic changes

Rocket lifts off from launch site

Liftoff of Inspiration4 from Kennedy Space Center at 8:02 pm (local time) on 16 September 2021. Credit: Inspiration4 / John Kraus

Liftoff of Inspiration4 from Kennedy Space Center at 8:02 pm (local time) on 16 September 2021. Credit: Inspiration4 / John Kraus

T-cells and monocyte cells showed the largest degree of chromatin changes in the immune system after spaceflight and female crew members had a faster return to baseline across all cell types for their chromatin landscape (ATAC-seq) than male astronauts (Kim et al.). These data can also now be visualized in the SOMA browser.

Two female astronauts smiling with Earth in the background

Sian Procter (left) and Hayley Arceneaux enjoying a flowing hair moment in zero gravity, analogous to the unwinding of DNA from chromatin observed in their monocytes. Credit: Inspiration4 crew

Sian Procter (left) and Hayley Arceneaux enjoying a flowing hair moment in zero gravity, analogous to the unwinding of DNA from chromatin observed in their monocytes. Credit: Inspiration4 crew

Scientific Reports: Chromosomal positioning and epigenetic architecture influence DNA methylation patterns triggered by galactic cosmic radiation

Nature Communications: Single-cell multi-ome and immune profiles of the Inspiration4 crew reveal conserved, cell-type, and sex-specific responses to spaceflight 

Communications Biology: Telomeric RNA (TERRA) increases in response to spaceflight and high-altitude climbing

Flow diagram summarising the effects of chronic exposure to space radiation on telomere length encircles a photograph of the Inspiration4 crew

Radiation impacts the genome and epigenome. Average telomere length in all Inspiration4 civilian crew members increased during spaceflight, similar to observations from the NASA Twins Study. Also, RNA-seq data revealed significantly increased telomeric RNA, or TERRA, during spaceflight for all astronauts, highlighing a unique response of telomeres to DNA damage, with protective telomeric DNA:RNA hybrids forming to facilitate RNA templated/HR-directed repair and transient activation of ALT/ALT-like phenotype, which likely contribute to the telomere elongation observed during spaceflight.

Radiation impacts the genome and epigenome. Average telomere length in all Inspiration4 civilian crew members increased during spaceflight, similar to observations from the NASA Twins Study. Also, RNA-seq data revealed significantly increased telomeric RNA, or TERRA, during spaceflight for all astronauts, highlighing a unique response of telomeres to DNA damage, with protective telomeric DNA:RNA hybrids forming to facilitate RNA templated/HR-directed repair and transient activation of ALT/ALT-like phenotype, which likely contribute to the telomere elongation observed during spaceflight.

Diagram summarising the effects of chronic exposure to space radiation on astronauts and the cellular mechanisms involved in repairing telomeres. The presented model suggest a telomere-specific DNA damage response associated with chronic exposure to the space radiation environment and elevated levels of oxidative stress. This acts to continuously damage telomeres, thereby triggering increased transcription of TERRA and hybridization at broken telomeres, forming protective telomeric DNA:RNA hybrids and facilitating RNA templated/HR-directed repair and transient activation of ALT/ALT-like phenotypes that possibly contribute to the telomere elongation observed during spaceflight.

Cellular states and dynamics

Trajectory of rocket in sky captured by long exposure

The reusable Falcon 9 rocket separates at an altitude of 80 km. Credit: Inspiration4 / John Kraus

The reusable Falcon 9 rocket separates at an altitude of 80 km. Credit: Inspiration4 / John Kraus

Each cell type exhibited both conserved and distinct disruptions across cell types, species, and missions, with changes in gene expression, chromatin accessibility, and transcription factor motif accessibility observed after spaceflight and during recovery. Novel, single-cell approaches were used to delineate sex-dependent changes in gene networks, cytokines/chemokines (e.g. fibrinogen and CXCL8/IL-8), and radiation response.

Nature Communications: Single-cell multi-ome and immune profiles of the Inspiration4 crew reveal conserved, cell-type, and sex-specific responses to spaceflight

npj Microgravity: Influence of the spaceflight environment of macrophage lineages

Communications Biology: Spaceflight induces changes in gene expression profiles linked to insulin and estrogen

Scientific Reports: Sexual dimorphism during integrative endocrine and immune responses to ionizing radiation in mice

npj Women’s Health: Understanding how space travel affects the female reproductive system

Nature Communications: Single-cell analysis identifies conserved features of immune dysfunction in simulated microgravity and spaceflight

Diagram depicting the R&D needed for developing drugs that counter the effects of spaceflight on immune cells.

Using single-cell analysis of human PBMCs exposed to short-term simulated microgravity, the team identified significant transcriptional alterations in immune cells, with monocytes showing the most pathway changes, including increased retroviral and mycobacterial transcripts, providing insights into microgravity-induced immune dysfunction and potential countermeasures like quercetin.

Using single-cell analysis of human PBMCs exposed to short-term simulated microgravity, the team identified significant transcriptional alterations in immune cells, with monocytes showing the most pathway changes, including increased retroviral and mycobacterial transcripts, providing insights into microgravity-induced immune dysfunction and potential countermeasures like quercetin.

Diagram depicting the steps needed for developing drugs that counter the effects of spaceflight on immune cells. Analysis of human PBMCs exposed to simulated microgravity integrated with analysis of data from flight crew allows the identification of key signature changes such as transcriptional alterations in immune cells. Strategies such as gene-compound enrichment analysis followed by compound validation are utilized for drug discovery purposes.

Microbiome modifications and movement

Planet Earth from space

During the 3-day mission, the crew monitored their heart activity, blood oxygen levels and immune function, performed ultrasound exams and took samples for microbiological analysis. Credit: Inspiration4 crew

During the 3-day mission, the crew monitored their heart activity, blood oxygen levels and immune function, performed ultrasound exams and took samples for microbiological analysis. Credit: Inspiration4 crew

Exposed parts of the body showed more transfer from the Dragon spacecraft (figure below). Signatures of response to viruses and T-cell activation was a consistent trend across the crew, and the microbiomes of the crew became more similar to each other over time, as has been observed before in space and in sports.

Nature Communications: Secretome profiling reveals acute changes in oxidative stress, brain homeostasis, and coagulation following short-duration spaceflight

Nature Communications: Single-cell multi-ome and immune profiles of the Inspiration4 crew reveal conserved, cell-type, and sex-specific responses to spaceflight

Nature Microbiology: Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight

Colourful circos plot showing the extent of microbial cross-contamination between all four crew members and the spacecraft

Moving microbes: A circos plot shows number of strain-sharing events across time, where an event is defined as the detection of the same strain between two different swabbing locations, between the crew members (C001,2,3,4) or the SpaceX Dragon capsule. The thickness of each line represents the proportional number of species, and the color indicates origin.

Moving microbes: A circos plot shows number of strain-sharing events across time, where an event is defined as the detection of the same strain between two different swabbing locations, between the crew members (C001,2,3,4) or the SpaceX Dragon capsule. The thickness of each line represents the proportional number of species, and the color indicates origin.

A circos plot showing number of strains sharing events from sequencing data from a longitudinal, multi-omics sampling study of 4 crew members on the SpaceX Inspiration4 mission. The crew collected environmental swabs from the Dragon capsule, skin, nasal and oral swabs at different timepoints during the mission. The plot shows the extent of microbial cross-contamination between all four crew members and the spacecraft during the mid-flight timepoint. From the thickness of each line representing the proportional number of species and the color indicating the origin, it is possible to observe that most strain sharing occurred between sites on the same individual or the spacecraft, with limited exchange between astronauts.

Mitochondrial responses to spaceflight

Earth at night showing the urban lights

Orbiting at an altitude of 590 km and travelling at over 28,000 kph, the spacecraft circled the planet every 90 minutes. Credit: Inspiration4 crew

Orbiting at an altitude of 590 km and travelling at over 28,000 kph, the spacecraft circled the planet every 90 minutes. Credit: Inspiration4 crew

An in-flight spike in mtDNA and mtRNA has been shown for most crews; however, the 3-day i4 mission did not show the same spike, so this indicates the mtDNA phenotype might be age specific or related to the length of the mission. Brain-associated proteins were found in the plasma of crew members after the I4 mission, confirming the brain signature from the JAXA study and prior work in the Twins Study.

Communications Medicine: Transcriptomics analysis reveals molecular alterations underpinning spaceflight dermatology 

Nature Communications: Space radiation damage rescued by inhibition of key spaceflight associated miRNAs

Nature Communications: Secretome profiling reveals acute changes in oxidative stress, brain homeostasis, and coagulation following short-duration spaceflight

Nature Communications: Release of CD36-associated cell-free mitochondrial DNA and RNA as a hallmark of space environment response

Bubble chart showing the enrichment of mitochondrial RNA is various tissue during spaceflight, and the significance of changes measured

Mitochondrial spikes across tissues. Different tissues (vertical axis) measured for their enrichment of mitochondrial RNA (mtRNA) levels (x-axis) show that the brain, skeletal muscle, and retina are among the most responsive tissues to spaceflight. Fold enrichment is shown in proportion to the size of the circle and the p-value is shown from red to blue for signifiance.

Mitochondrial spikes across tissues. Different tissues (vertical axis) measured for their enrichment of mitochondrial RNA (mtRNA) levels (x-axis) show that the brain, skeletal muscle, and retina are among the most responsive tissues to spaceflight. Fold enrichment is shown in proportion to the size of the circle and the p-value is shown from red to blue for signifiance.

Bubble chart showing the enrichment of mitochondrial RNA in various tissues during spaceflight. Brain, skeletal muscle, retina and heart muscle are the most responsive tissues to spaceflight with a greater mitochondrial gene count with fold enrichment between 0.96 and 2.84 and p value <0.05 compared with liver, testis, pituitary gland, choroid plexus, intestine, kidney, tongue, lymphoid tissue, thyroid gland, oesophagus, skin, parathyroid, placenta, pancreas, adipose tissue, bone marrow.

Artificial intelligence and computational frameworks

View of Earthh from space with bright glare of sun in the ocean

The total amount of sequence data in the Open Science Data Repository has increased almost 14-fold with the addition of Inspiration4 data. Credit: Inspiration4 crew

The total amount of sequence data in the Open Science Data Repository has increased almost 14-fold with the addition of Inspiration4 data. Credit: Inspiration4 crew

As research and missions are extended beyond low Earth orbit, experiments and platforms must be maximally automated, light, agile and intelligent to accelerate knowledge discovery and support mission operations. The integration of artificial intelligence into the fields of space biology and space health has deepened the biological understanding of spaceflight effects. To effectively mitigate health hazards, AI-enabled paradigm shifts in astronaut health systems are necessary to enable Earth-independent healthcare to be predictive, preventative, participatory, and personalized.

npj Microgravity: Explainable machine learning identifies multi-omics signatures of muscle response to spaceflight in mice

Nature Machine Intelligence: Biological research and self-driving labs in deep space supported by artificial intelligence

npj Microgravity: NASA GeneLab derived microarrays studies of Mus musculus and Homo sapiens organisms in altered gravitational conditions

npj Microgravity: Harmonizing heterogeneous transcriptomics datasets for machine learning-based analysis to identify spaceflown murine liver-specific changes

Preprint: Analyzing the relationship between gene expression and phenotype in space-flown mice using a causal inference machine learning ensemble

Nature Machine Intelligence: Biomonitoring and precision health in deep space supported by artificial intelligence

Layered and integrated data acquisition and monitoring for deep-space missions. The integrated biological and health monitoring system is shown as a pyramid, with layers of increasingly invasive and granular monitoring, where data flow from both experimental models as well as astronauts, and are put into the context of environmental monitoring via AI/ML algorithms.

Layered and integrated data acquisition and monitoring for deep-space missions. The integrated biological and health monitoring system is shown as a pyramid, with layers of increasingly invasive and granular monitoring, where data flow from both experimental models as well as astronauts, and are put into the context of environmental monitoring via AI/ML algorithms.

Diagram summarising a plan for multi-layer monitoring with AI algorithms for deep space missions. The monitoring system is shown as a pyramid. The starting layer of monitoring is a continuous environmental sensing of physical, chemical, and biological components. Going up in the pyramid, layers become more invasive with the usage of wearable and point of care devices. At the top of the pyramid, a third layer, more invasive, entails acquisition of molecular physiological biomarkers including usage of swabs and sampling methods. Monitoring data is to be integrated with data from environmental monitoring via AI/ML algorithms.

Countermeasures to risks

Nose cone of Dragon spacecraft in view with Earth in background with sun's reflection between clouds

The data collected on the mission adds to the body of evidence for monitoring countermeasure effectiveness. Credit: Inspiration4 / Hayley Arceneaux

The data collected on the mission adds to the body of evidence for monitoring countermeasure effectiveness. Credit: Inspiration4 / Hayley Arceneaux

To mitigate these reported biological changes and limit the damage caused to the body by spaceflight and space environment, it is key to develop countermeasures. Countermeasures can involve novel drug production, repurposing FDA approved drugs, or genome/epigenome modification systems.

Preprint: Countermeasures for cardiac fibrosis in space travel: It takes more than a towel for a hitchhiker's guide to the galaxy

Nature Communications: Single-cell analysis identifies conserved features of immune dysfunction in simulated microgravity and spaceflight

Nature Communications: Single-cell multi-ome and immune profiles of the Inspiration4 crew reveal conserved, cell-type, and sex-specific responses to spaceflight

Communications Medicine: Transcriptomics analysis reveals molecular alterations underpinning spaceflight dermatology

Nature Communications: Space radiation damage rescued by inhibition of key spaceflight associated miRNAs

Heat map charts showing the changes in several micro RNAs before, during and after spaceflight.

Countermeasures mediated by miRNAs. Data from the JAXA astronaut cell-free RNA study (CFE) shows that a wide range of micro RNAs (miRNAs) can be helpful for guiding countermeasures. The miRNA targets are shown (top), as well as the enrichment (scale from red to blue) during flight or post-flight for the astronauts.

Countermeasures mediated by miRNAs. Data from the JAXA astronaut cell-free RNA study (CFE) shows that a wide range of micro RNAs (miRNAs) can be helpful for guiding countermeasures. The miRNA targets are shown (top), as well as the enrichment (scale from red to blue) during flight or post-flight for the astronauts.

Heatmap chart showing normalized plasma cell-free RNA expression values for 21 key genes over time for the six astronauts over 120 days in space from JAXA cell-free RNA study. Plotting the changes in several micro RNAs before, during and after spaceflight with three miRNA targets being shown at the top (let-7a-5p, miR-125b-5p, miR-16-5p). Most of the 21 antagomir-rescued genes in the JAXA data were downregulated during the flight. Most of the genes show up-regulation post-flight as compared with pre-flight and during flight.

Ethics and perspectives

Artistic representation of Libra constellation in the night sky.

The constellation of Libra (the scales) is a metaphor for the ethical challenges of space exploration. Credit: iStock / Getty Images Plus

The constellation of Libra (the scales) is a metaphor for the ethical challenges of space exploration. Credit: iStock / Getty Images Plus

New spacecraft enable novel missions and a wider array of crews to go into space, but also generate new ethical questions and parameters about data accessibility. Some of these ideas and novel data types are discussed in these perspectives:

Nature Communications: Biological horizons: pioneering open science in the cosmos

npj Microgravity: Inspiration4 data access through the NASA Open Science Data Repository

Nature Communications: Ethical considerations for the age of non-governmental space exploration

Diagram summarising the ethical framework in space human subject research, which comprises three areas: the existing ethical principles and regulations, the implementation of ethical standards, and the emerging ethical challenges in space research.

Human Subjects Research Ethical and Operational Guidelines. The ethical principles currently in place for human subject research and the challenges and new ethical principles and challenges that have to be considered during the second space age.

Human Subjects Research Ethical and Operational Guidelines. The ethical principles currently in place for human subject research and the challenges and new ethical principles and challenges that have to be considered during the second space age.

Diagram showing 14 items that constitute the ethical framework in space human subject research. It is split into three areas: first, the existing ethical principles and regulations, which includes the US Code of Regulations for informed consent, respecting autonomy, the declaration of Helsinki, avoiding harm, risk–benefit balance, Fairness, and the Genetic Information Non-discrimination Act; second, the implementation of ethical standards, which includes the Institutional Review Board, Informed consent, and Genetic Data Protection; and third, the Emerging ethical challenges in space research, which includes secure drug storage, violating favourable risk–benefit balance, participant’s autonomy: withdrawing from research, and avoiding the increased health risks of space.