Global transcriptomic analysis suggests carbon dioxide as an environmental stressor in spaceflight: A systems biology GeneLab case study

Beheshti, Afshin; Cekanaviciute, Egle; Smith, David J.; Costes, Sylvain V.

doi:10.1038/s41598-018-22613-1

Cited by 46 publications

(42 citation statements)

References 53 publications

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“…These primary results suggest that plant mitochondria and cell energy production may play a role in the cellular response to altered gravity conditions. The same relationship was observed in other microgravity studies in plants [52], but also in Drosophila [53], rodents [54], cultured human lymphocyte [55] or human ocular tissue [56]. Furthermore, recent studies support this role during abiotic/biotic stress response [57][58][59][60][61].…”

Section: Discussionsupporting

confidence: 83%

Differential transcriptional profile through cell cycle progression in Arabidopsis cultures under simulated microgravity

et al. 2019

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Plant cell proliferation is affected by microgravity during spaceflight, but involved molecular mechanisms, key for space agronomy goals, remain unclear. To investigate transcriptomic changes in cell cycle phases caused by simulated microgravity, an Arabidopsis immobilized synchronous suspension culture was incubated in a Random Positioning Machine. After simulation, a transcriptomic analysis was performed with two subpopulations of cells (G2/M and G1 phases enriched) and an asynchronous culture sample. Differential expression was found at cell proliferation, energy/redox and stress responses, plus unknown biological processes gene ontology groups. Overall expression inhibition was a common response to simulated microgravity, but differences peak at the G2/M phase and stress response components change dramatically from G2/M to the G1 subpopulation suggesting a differential adaptation response to simulated microgravity through the cell cycle. Cell cycle adaptation using both known stress mechanisms and unknown function genes may cope with reduced gravity as an evolutionary novel environment.

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Section: Discussionsupporting

confidence: 83%

Differential transcriptional profile through cell cycle progression in Arabidopsis cultures under simulated microgravity

et al. 2019

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“…There was a total of 25 GeneLab datasets (GLDS) with 30 experimental comparisons from RNA-sequencing or microarray platforms (Table 1). Data pre-processing was performed as previously published to obtain normalized expression values for the majority of the datasets [32,33,42]. For GLDS-73, human bronchial epithelial cells (HBECs) were exposed to gamma-rays (1 Gy or 3 Gy), iron ( 56 Fe), or silicon ( 26 Si) particles (0.5 Gy or 1 Gy each).…”

Section: Bioinformatics Gene Set Enrichment Analysis and Visulizatimentioning

confidence: 99%

NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models

McDonald¹,

Stainforth

Cahill

et al. 2020

Cancers

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Background: Ionizing radiation from galactic cosmic rays (GCR) is one of the major risk factors that will impact the health of astronauts on extended missions outside the protective effects of the Earth’s magnetic field. The NASA GeneLab project has detailed information on radiation exposure using animal models with curated dosimetry information for spaceflight experiments. Methods: We analyzed multiple GeneLab omics datasets associated with both ground-based and spaceflight radiation studies that included in vivo and in vitro approaches. A range of ions from protons to iron particles with doses from 0.1 to 1.0 Gy for ground studies, as well as samples flown in low Earth orbit (LEO) with total doses of 1.0 mGy to 30 mGy, were utilized. Results: From this analysis, we were able to identify distinct biological signatures associating specific ions with specific biological responses due to radiation exposure in space. For example, we discovered changes in mitochondrial function, ribosomal assembly, and immune pathways as a function of dose. Conclusions: We provided a summary of how the GeneLab’s rich database of omics experiments with animal models can be used to generate novel hypotheses to better understand human health risks from GCR exposures.

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“…1. Find the following datasets related to a previous publication 36 as instructed above and copy over to the local workspace: GLDS-21, GLDS-111, GLDS-25, and GLDS-63.…”

Section: Notementioning

confidence: 99%

“…We discuss the configuration of the Rodent Habitats used for space missions, and how spaceflight tissues are processed. We also describe how spaceflight omics data can be discovered and accessed on GeneLab and how key factors driving the overall response to spaceflight can be identified 36 . The specific example we will present on how this protocol is implemented will be comparing the biological differences occurring in rodents housed in Rodent Habitat and the vivarium controls that were published by Beheshti et al…”

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confidence: 99%

Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform

Beheshti

Shirazi‐Fard

Choi

et al. 2019

JoVE

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Performing biological experiments in space requires special accommodations and procedures to ensure that these investigations are performed effectively and efficiently. Moreover, given the infrequency of these experiments it is imperative that their impacts be maximized. The rapid advancement of omics technologies offers an opportunity to dramatically increase the volume of data produced from precious spaceflight specimens. To capitalize on this, NASA has developed the GeneLab platform to provide unrestricted access to spaceflight omics data and encourage its widespread analysis. Rodents (both rats and mice) are common model organisms used by scientists to investigate space-related biological impacts. The enclosure that house rodents during spaceflight are called Rodent Habitats (formerly Animal Enclosure Modules), and are substantially different from standard vivarium cages in their dimensions, air flow, and access to water and food. In addition, due to environmental and atmospheric conditions on the International Space Station (ISS), animals are exposed to a higher CO 2 concentration. We recently reported that mice in the Rodent Habitats experience large changes in their transcriptome irrespective of whether animals were on the ground or in space. Furthermore, these changes were consistent with a hypoxic response, potentially driven by higher CO 2 concentrations. Here we describe how a typical rodent experiment is performed in space, how omics data from these experiments can be accessed through the GeneLab platform, and how to identify key factors in this data. Using this process, any individual can make critical discoveries that could change the design of future space missions and activities.

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Global transcriptomic analysis suggests carbon dioxide as an environmental stressor in spaceflight: A systems biology GeneLab case study

Cited by 46 publications

References 53 publications

Differential transcriptional profile through cell cycle progression in Arabidopsis cultures under simulated microgravity

Differential transcriptional profile through cell cycle progression in Arabidopsis cultures under simulated microgravity

NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models

Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform

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