Longitudinal transcriptomic and epigenetic analysis in astronauts reveals dynamic immune response to spaceflight
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PROVIDER: PRJNA1156627 | ENA |
REPOSITORIES: ENA
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Project description:The space industry has made significant strides in recent years, leading to an era of commercial spaceflight. Meanwhile, understanding the molecular responses to spaceflight becomes crucial for astronaut safety in harsh space conditions. To this end, we conducted a study to examine the transcriptomic and epigenetic changes in two astronauts' blood samples at three timepoints: two weeks before spaceflight (T0), 24 hours after spaceflight (T2), and three months after spaceflight (T3). Transcriptomic analysis pinpointed two gene clusters with opposing transient expression trends post-flight (T2) which was normalized at T3: one upregulated and the other downregulated. Pathway analysis of these gene clusters showed enrichment in the protein modification, cell cycle, and regulation of autophagy pathways, suggesting autophagy’s role in monocyte differentiation. Epigenetic analysis identified four methylation patterns that showed transient and persistent changes immediately after the spaceflight, enriched in the nervous system development and cell apoptosis pathways. Methylation changes at specific regions implicated genes associated with bone disorders, including FBLIM1, IHH, and SCAMP2. Further, eQTM analysis suggested a link between RNA transcriptional activity and DNA methylation through a transcriptional regulator ZNF684. In conclusion, our longitudinal study offers a detailed perspective of spaceflight’s physiological effects on human biology, revealing both significant short-term transcriptional and methylation and profound long-term methylation impacts on bodily functions.
2025-07-30 | GSE276323 | GEO
Project description:The space industry has made significant strides in recent years, leading to an era of commercial spaceflight. Meanwhile, understanding the molecular responses to spaceflight becomes crucial for astronaut safety in harsh space conditions. To this end, we conducted a study to examine the transcriptomic and epigenetic changes in two astronauts' blood samples at three timepoints: two weeks before spaceflight (T0), 24 hours after spaceflight (T2), and three months after spaceflight (T3). Transcriptomic analysis pinpointed two gene clusters with opposing transient expression trends post-flight (T2) which was normalized at T3: one upregulated and the other downregulated. Pathway analysis of these gene clusters showed enrichment in the protein modification, cell cycle, and regulation of autophagy pathways, suggesting autophagy’s role in monocyte differentiation. Epigenetic analysis identified four methylation patterns that showed transient and persistent changes immediately after the spaceflight, enriched in the nervous system development and cell apoptosis pathways. Methylation changes at specific regions implicated genes associated with bone disorders, including FBLIM1, IHH, and SCAMP2. Further, eQTM analysis suggested a link between RNA transcriptional activity and DNA methylation through a transcriptional regulator ZNF684. In conclusion, our longitudinal study offers a detailed perspective of spaceflight’s physiological effects on human biology, revealing both significant short-term transcriptional and methylation and profound long-term methylation impacts on bodily functions.
2025-07-30 | GSE276490 | GEO
Project description:Longitudinal transcriptomic and epigenetic analysis in astronauts reveals dynamic immune response to spaceflight [RNA-seq]
| PRJNA1157458 | ENA
Project description:Astronauts are exposed to a unique combination of stressors during spaceflight, which leads to alterations in their physiology and potentially increases their susceptibility to infectious pathogens. Here we report the first microarray evaluation of any astronaut tissue sample, specifically whole blood, before and after spaceflight using an array comprising 234 well-characterized stress response genes. Differentially regulated genes included those important for DNA repair, oxidative stress, and protein folding/degradation. Microarrays comprising 234 well characterized stress-related genes were used to profile transcriptomic changes in six astronauts before and after short-duration spaceflight. Blood samples were collected for analysis from each eastronaut 10 days prior and 2-3 hours after return from spaceflight. Data submitted for platform GPL140 contain genes that have been pre-filtered by the analytical software to remove values of low certainty, resulting in missing values for some samples. Unfortunately, these original data are no longer available due to physical damage at Tulane University during hurricane Katrina, but the processed values were retained in redundant locations and these are submitted for upload to GEO.
2013-10-15 | E-GEOD-47126 | biostudies-arrayexpress
Project description:Astronauts are exposed to a unique combination of stressors during spaceflight, which leads to alterations in their physiology and potentially increases their susceptibility to infectious pathogens. Here we report the first microarray evaluation of any astronaut tissue sample, specifically whole blood, before and after spaceflight using an array comprising 234 well-characterized stress response genes. Differentially regulated genes included those important for DNA repair, oxidative stress, and protein folding/degradation.
2013-10-15 | GSE47126 | GEO
Project description:This study aimed to determine whether the spaceflight-induced snoRNA changes in plasma extracellular vesicles (EV) and astronauts' peripheral blood mononuclear cells (PBMCs) can be utilized as potential biomarkers. Using unbiased small RNA sequencing, we evaluated the EV snoRNA changes in peripheral blood (PB) plasma of astronauts (n=5/group) who underwent median 12-day long Shuttle missions between 1998-2001. Using stringent cutoff (> log 2-fold change, FDR < 0.05), we detected 21 down-regulated snoRNAs and 9 upregulated in PB-EVs at three days after return (R+3) compared to ten days before launch (L-10). Our findings unveiled that spaceflight induced changes in EV and PBMCs snoRNA expression, thus suggesting snoRNAs may serve as novel biomarkers for monitoring astronauts' health.
2022-04-06 | GSE200079 | GEO
Project description:We sought to determine whether the spaceflight environment can induce alterations in small extracellular vesicles (sEV) smallRNA content and their utility as biomarkers. Using small RNA sequencing (sRNAseq), we evaluated the impact of the spaceflight environment on sEV miRNA content in peripheral blood (PB) plasma of 14 astronauts, who flew STS missions between 1998-2001. Samples were collected at three-time points:10 days before the launch (L-10), the day of return (R-0), and three days post-landing (R+3).
2022-01-12 | GSE193331 | GEO
Project description:Spaceflight imposes the risk of skeletal muscle atrophy for astronauts. The understanding of muscle atrophy because of spaceflight is limited, but continued efforts are essential for developing countermeasures of this effect. A distinct difference between spaceflight-induced muscle atrophy and other forms of atrophy is the additional effect of cosmic rays in outer space. To study spaceflight-induced muscle atrophy, we performed two ground-based models of microgravity in a low dose radiation environment and studied transcriptional changes in rat soleus muscle using microarray technology.
2017-01-20 | GSE93838 | GEO
Project description:There are unique stressors in the spaceflight environment. Exposure to such stressors is associated with adverse effects on astronauts' health, including increased cancer and cardiovascular disease risks. Small extracellular vesicles (sEVs, i.e., exosomes) play a vital role in intercellular communication and regulate various biological processes contributing to their role in disease pathogenesis. To assess whether spaceflight alters sEVs transcriptome profile, sEVs were isolated from the blood plasma of 3 astronauts at two different time points: 10 days before launch (L-10) and 3 days after return (R+3) from the Shuttle mission. Human adult ventricular cardiomyocyte cells (AC16) were treated with L-10 and R+3 astronauts-derived exosomes for 24 hours. Total RNA was isolated and analyzed for gene expression profiling using Affymetrix microarrays. Enrichment analysis was performed using Enrichr. Transcription factor enrichment analysis using the ENCODE/ChEA Consensus TF database identified gene sets related to the polycomb repressive complex 2 (PRC2) and Vitamin D receptor (VDR) in AC16 cells treated with R+3 compared to cells treated with L-10 astronauts-derived exosomes. Further analysis of the histone modifications using datasets from the Roadmap Epigenomics Project confirmed enrichment in gene sets related to the H3K27me3 repressive mark. Interestingly, analysis of previously published H3K27me3–chromatin immunoprecipitation sequencing (ChIP-Seq) ENCODE datasets showed enrichment of H3K27me3 in the VDR promoter. Collectively, our results suggest that astronaut-derived sEVs may epigenetically repress the expression of the VDR in human adult cardiomyocytes c by promoting the activation of the PRC2 complex and H3K27me3 levels.
2022-03-12 | GSE198322 | GEO
Project description:Interplanetary human spaceflight represents a formidable medical challenge, but also provides a unique platform for investigating human adaptation to extreme environmental changes. Understanding the long-term effects of isolation has relevance in a range of scenarios and it is well recognized that a better understanding of the relationship between environmental exposure and the epigenome can lead to more effective preventive measures. Here we conduct a longitudinal epigenetic, mood state and biochemical profiling of 6 crew members in an experiment simulating a 520-day mission to Mars. Illumina HumanMethylation450 BeadChip was used to obtain DNA methylation profiles. Firstly, we found that long-term isolation can induce global DNA methylation remodeling, and this change seems to be an active adaptation (rather than a random process or a by-product of the isolation). This study is the first to demonstrate the dynamic relationship between global epigenetic remodeling and isolation-induced mood state and biochemical changes. Secondly, by considering the location of methylation sites within the genome and using gene-pathway annotation, we were able to identify pathways that were significantly enriched in methylation events and consider their association with specific function and the timeline of the mission. Thirdly, via our definition of epi-entropy, a measure of entropy adapted to methylation events, we observed that the methylation remodeling produced a marked reduction in epi-entropy. Results suggest that DNA methylation change is an indicator of change rather than its by-product, i.e., there is a psychology-epigenome-metabolism model of long-term depression; DNA methylation programs the environment signal into the epigenome, which is subsequently transformed into the biochemical output and health outcome. Thus, longitudinal epigenetic profiling could code the effect of isolation and act as early indicators of latent health outcome. A longitudinal epigenetic, mood state and biochemical profiling of 6 crew members in an experiment simulating a 520-day mission to Mars. 36 samples of blood cell DNA methylation profiling were obtained by Illumina HumanMethylation450 BeadChip, across 6 sampling points during the 520 days mission for all of the 6 crew members.
2015-01-14 | E-GEOD-64950 | biostudies-arrayexpress