RNAseq analysis of rodent spaceflight experiments is confounded by sample collection techniques

Polo, San-Huei Lai; Saravia-Butler, Amanda; Boyko, Valery; Dinh, Marie; Chen, Yi‐Chun; Fogle, Homer; Reinsch, Sigrid; Ray, Shayoni; Chakravarty, Kaushik; Marcu, Oana; Chen, Rick B.; Costes, Sylvain V.; Galazka, Jonathan M.

doi:10.1101/2020.07.18.209775

Cited by 4 publications

(4 citation statements)

References 30 publications

(25 reference statements)

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“…As well we combined different controls and ight cohorts to increase our sample size which was not ideal. It is also worth mentioning that previous studies examining physiological changes in mice sent to the ISS found challenges associated with sample collection in space and the confounding factors it introduces [52]. This includes changes in the transcriptome due to preservation methods, which can overshadow differences between space ight and ground samples, suggesting the need for careful consideration of these factors in future space research.…”

Section: Discussionmentioning

confidence: 99%

Intergalactic Interactions - Network Biology in Rodents from Spaceflight and Terra Firma

Hacking,

Sargin

2023

Preprint

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This study, utilizing data from the NASA Gene Lab Data Repository, investigates the impact of spaceflight on rodents, analyzing changes in lung, colorectal, and skin tissues. We examined RNA-seq data from rodents that had experienced space flight, comparing them with control groups that remained on Earth. Our focus was to better decipher the molecular alterations induced by the unique conditions of space. A comprehensive initial cohort of rodents was selected, ensuring the integrity and completeness of genomic data. We employed Proteinarium, a sophisticated multi-sample analysis tool, to explore and compare protein-protein interaction (PPI) networks between space flight-exposed and control rodents. This approach allowed us to identify significant clusters and distinct PPI networks in the space flight group, which were not present in the control group. Our results revealed that space flight leads to unique molecular changes, with certain genes becoming upregulated in response to the extraterrestrial environment. These changes were tissue-specific, indicating varied physiological responses across different organ systems. We also identified distinct gene hub targets for drug repurposing, which could be evaluated in future studies. The present study contributes to a deeper understanding of how spaceflight affects living organisms at the molecular level, providing insights that could inform future space missions and enhance our knowledge of biological systems in spaceflight environments.

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Section: Discussionmentioning

confidence: 99%

Intergalactic Interactions - Network Biology in Rodents from Spaceflight and Terra Firma

Hacking,

Sargin

2023

Preprint

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“…Most experimentation in space is expensive, time-consuming and not automated. This results in small experiments with few samples and replicates, and high levels of variability due to differing sample-handling procedures [53][54][55] . This makes AI and time in space and distance from Earth 1,6 .…”

Section: Automated Experiments In Space Supported By Aimentioning

confidence: 99%

Biological research and self-driving labs in deep space supported by artificial intelligence

et al. 2023

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Space biology research aims to understand fundamental spaceflight effects on organisms, develop foundational knowledge to support deep space exploration and, ultimately, bioengineer spacecraft and habitats to stabilize the ecosystem of plants, crops, microbes, animals and humans for sustained multi-planetary life. To advance these aims, the field leverages experiments, platforms, data and model organisms from both spaceborne and ground-analogue studies. As research is extended beyond low Earth orbit, experiments and platforms must be maximally automated, light, agile and intelligent to accelerate knowledge discovery. Here we present a summary of decadal recommendations from a workshop organized by the National Aeronautics and Space Administration on artificial intelligence, machine learning and modelling applications that offer solutions to these space biology challenges. The integration of artificial intelligence into the field of space biology will deepen the biological understanding of spaceflight effects, facilitate predictive modelling and analytics, support maximally automated and reproducible experiments, and efficiently manage spaceborne data and metadata, ultimately to enable life to thrive in deep space.Space biology research focuses on answering fundamental mechanistic questions about how molecular, cellular, tissue and whole organismal life responds to the space environment. Biological stressors of spaceflight include ionizing radiation, altered gravitational fields, accelerated day-night cycles, confined isolation, hostile closed environments, distance-duration from Earth 1 , planetary dust regolith 2,3 , and extreme temperatures and atmospheres 4,5 . Moreover, spaceflight stressors are probably compounded and amplified with increasing

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“…This appeared to be exacerbated by the use of poly(A) enrichment-based RNA sequencing (RNA-seq) protocol, and could be alleviated by the use of a ribodepletion-based approach and by snap-freezing carcasses in liquid nitrogen. 60 As a result, the Rapid Freeze hardware was recently developed for use on the ISS. The device can freeze mouse tissues (Glovebox freezer) and whole carcasses (Cryochiller) at rates similar to those attained with liquid nitrogen immersion.…”

Section: Sample Preservationmentioning

confidence: 99%

A New Era for Space Life Science: International Standards for Space Omics Processing

et al. 2020

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Space agencies have announced plans for human missions to the Moon to prepare for Mars. However, the space environment presents stressors that include radiation, microgravity, and isolation. Understanding how these factors affect biology is crucial for safe and effective crewed space exploration. There is a need to develop countermeasures, to adapt plants and microbes for nutrient sources and bioregenerative life support, and to limit pathogen infection. Scientists across the world are conducting space omics experiments on model organisms and, more recently, on humans. Optimal extraction of actionable scientific discoveries from these precious datasets will only occur at the collective level with improved standardization. To address this shortcoming, we established ISSOP (International Standards for Space Omics Processing), an international consortium of THE BIGGER PICTURE With the rise of commercial spaceflight and prospective human missions to Mars, a wider health range of humans will enter space for longer spans and at higher exposure to environmental stressors than ever before. Numerous adverse health effects have been observed in space, including bone demineralization and skeletal muscle atrophy, among others. Scientists across the world are conducting space omics studies to develop countermeasures for safe and effective crewed space missions. However, optimal extraction of scientific insight from such data is contingent on improved standardization. In response, we founded ISSOP (International Standards for Space Omics Processing), an international consortium of scientists who aim to enhance guidelines between space biologists globally. This paper informs scientists and data scientists from many fields about the challenges and future avenues of space omics and can serve as an introductory reference for new members in the space biology discipline. Concept: Basic principles of a new data science output observed and reported ll

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RNAseq analysis of rodent spaceflight experiments is confounded by sample collection techniques

Cited by 4 publications

References 30 publications

Intergalactic Interactions - Network Biology in Rodents from Spaceflight and Terra Firma

Intergalactic Interactions - Network Biology in Rodents from Spaceflight and Terra Firma

Biological research and self-driving labs in deep space supported by artificial intelligence

A New Era for Space Life Science: International Standards for Space Omics Processing

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