Challenges and considerations for single-cell and spatially resolved transcriptomics sample collection during spaceflight

Overbey, Eliah; Das, Saswati; Cope, Henry; Madrigal, Pedro; Andrusivová, Žaneta; Frapard, Solène; Klotz, Rebecca; Bezdan, Daniela; Gupta, Anjali; Scott, Ryan T.; Park, Jiwoon; Chirko, Dawn; Galazka, Jonathan M.; Costes, Sylvain V.; Mason, Christopher E.; Herranz, Raúl; Szewczyk, Nathaniel J.; Borg, Joseph; Giacomello, Stefania

doi:10.1016/j.crmeth.2022.100325

Cited by 11 publications

(9 citation statements)

References 132 publications

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“…In the future, it seems necessary (1) to study cellular and molecular events occurring in the vertebrate and human retina and in the visual system in general in response to effects of SF-related factors; (2) study the adaptive and compensatory mechanisms of retinal cells in animals and humans during SF and upon return to Earth; and (3) develop technical potential for conducting research by up-to-date methods, in particular by single-cell RNA sequencing and spatially resolved transcriptomics. The challenges and considerations relevant for robust experimental design to enable the growth of these methods in experiments under SF conditions are already discussed [ 166 ].…”

Section: Discussionmentioning

confidence: 99%

Impact of Microgravity and Other Spaceflight Factors on Retina of Vertebrates and Humans In Vivo and In Vitro

Grigoryan

2023

Life

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Spaceflight (SF) increases the risk of developmental, regenerative, and physiological disorders in animals and humans. Astronauts, besides bone loss, muscle atrophy, and cardiovascular and immune system alterations, undergo ocular disorders affecting posterior eye tissues, including the retina. Few studies revealed abnormalities in the development and changes in the regeneration of eye tissues in lower vertebrates after SF and simulated microgravity. Under microgravity conditions, mammals show disturbances in the retinal vascular system and increased risk of oxidative stress that can lead to cell death in the retina. Animal studies provided evidence of gene expression changes associated with cellular stress, inflammation, and aberrant signaling pathways. Experiments using retinal cells in microgravity-modeling systems in vitro additionally indicated micro-g-induced changes at the molecular level. Here, we provide an overview of the literature and the authors’ own data to assess the predictive value of structural and functional alterations for developing countermeasures and mitigating the SF effects on the human retina. Further emphasis is given to the importance of animal studies on the retina and other eye tissues in vivo and retinal cells in vitro aboard spacecraft for understanding alterations in the vertebrate visual system in response to stress caused by gravity variations.

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Section: Discussionmentioning

confidence: 99%

Impact of Microgravity and Other Spaceflight Factors on Retina of Vertebrates and Humans In Vivo and In Vitro

Grigoryan

2023

Life

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“…To better understand the regulation of gene expression induced by microgravity, the experiments should be investigated more precisely by single cell RNAseq (Overbey et al, 2022; Willis et al, 2020) and localization experiments based on the result of the bulk analysis reported here. In fact, SMG should have different effects on neuronal lineages depending also on the duration of SMG exposure.…”

Section: Discussionmentioning

confidence: 99%

Physical exercise restores adult neurogenesis deficits induced by simulated microgravity

Gros,

Furlan,

Rouglan

et al. 2023

Preprint

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Cognitive impairments have been reported in astronauts during spaceflights and documented in ground-based models of simulated microgravity (SMG) in animals. However, the neuronal causes of these behavioral effects remain largely unknown. We explored whether adult neurogenesis, known to be a crucial plasticity mechanism supporting memory processes, is altered by SMG. Adult male Long-Evans rats were submitted to the hindlimb unloading model of SMG. We studied the proliferation, survival and maturation of newborn cells in the following neurogenic niches: the subventricular zone (SVZ)/olfactory bulb (OB) and the dentate gyrus (DG) of the hippocampus, at different delays following various periods of SMG. SMG exposure for 7 days, but not shorter periods of 6 or 24 hours, resulted in a decrease of newborn cell proliferation restricted to the DG. SMG also induced a decrease in short-term (7 days), but not long-term (21 days), survival of newborn cells in the SVZ/OB and DG. Physical exercise, used as a countermeasure, was able to reverse the decrease in newborn cell survival observed in the SVZ and DG. In addition, depending on the duration of SMG periods, transcriptomic analysis revealed modifications in gene expression involved in neurogenesis. These findings highlight the sensitivity of adult neurogenesis to gravitational environmental factors during a transient period, suggesting that there is a period of adaptation of physiological systems to this new environment.

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“…As a first step, we ensured that the morphological and RNA quality of the samples was preserved well enough for our experimental workflow given that our spaceflown samples had to undergo a specific preservation approach 18 , which was also adopted for the corresponding ground control animals. In brief, to preserve changes induced by the space environment, spaceflown mice were euthanized on-board the ISS and underwent freezing as a whole carcass in a -80°C freezer.…”

Section: Spaceflight Sample Quality Is Suitable For St and Snmultiomi...mentioning

confidence: 99%

Spatially resolved multiomics on the neuronal effects induced by spaceflight

Masarapu

Cekanaviciute²,

Andrusivová

et al. 2023

Preprint

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Impairment of the central nervous system (CNS) functions in astronauts is a major health risk for long-duration space missions. Here, for the first time, we combine single-cell multiomics (transcriptomics and chromatin accessibility) and spatial transcriptomics analyses to discover spaceflight-mediated changes in the mouse brain. By comparing ground control and spaceflight animals, we found that the main processes affected by spaceflight include neurogenesis, synaptogenesis and synaptic transmission in cortex, hippocampus, striatum and neuroendocrine structures as well as astrocyte activation and immune dysfunction. At the pathway level, spaceflight resembles neurodegenerative diseases with oxidative stress and protein misfolding components, such as in Parkinson’s disease. Our integrated spatial multiomics approach reveals both widespread and localized brain impairments and suggests key structures and mechanisms to be targeted for countermeasure development. All datasets can be mined through an interactive data portal as well as the National Aeronautics and Space Administration (NASA) GeneLab repositories.

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Challenges and considerations for single-cell and spatially resolved transcriptomics sample collection during spaceflight

Cited by 11 publications

References 132 publications

Impact of Microgravity and Other Spaceflight Factors on Retina of Vertebrates and Humans In Vivo and In Vitro

Impact of Microgravity and Other Spaceflight Factors on Retina of Vertebrates and Humans In Vivo and In Vitro

Physical exercise restores adult neurogenesis deficits induced by simulated microgravity

Spatially resolved multiomics on the neuronal effects induced by spaceflight

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