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

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

doi:10.1016/j.crmeth.2022.100325

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

Cell Rep Methods. 2022 Oct 31;2(11):100325. doi: 10.1016/j.crmeth.2022.100325. eCollection 2022 Nov 21.

Authors

Eliah G Overbey^{1

2}, Saswati Das³, Henry Cope⁴, Pedro Madrigal⁵, Zaneta Andrusivova⁶, Solène Frapard⁶, Rebecca Klotz⁷, Daniela Bezdan^{8

9

10}, Anjali Gupta¹¹, Ryan T Scott⁷, Jiwoon Park¹, Dawn Chirko¹, Jonathan M Galazka¹², Sylvain V Costes¹², Christopher E Mason^{1

2

13

14}, Raul Herranz¹⁵, Nathaniel J Szewczyk^{4

16}, Joseph Borg¹⁷, Stefania Giacomello⁶

Affiliations

¹ Weill Cornell Medicine, New York, NY, USA.
² Institute for Computational Biomedicine, New York, NY, USA.
³ Department of Biochemistry, Atal Bihari Vajpayee Institute of Medical Sciences & Dr. Ram Manohar Lohia Hospital, New Delhi, India.
⁴ School of Medicine, University of Nottingham, Derby DE22 3DT, UK.
⁵ European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK.
⁶ Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
⁷ KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
⁸ Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany.
⁹ NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, German.
¹⁰ yuri GmbH, Meckenbeuren, Germany.
¹¹ Axiom Space, Houston, TX, USA.
¹² Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
¹³ The Feil Family Brain and Mind Research Institute, New York, NY, USA.
¹⁴ The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA.
¹⁵ Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid 28040, Spain.
¹⁶ Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA.
¹⁷ Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta.

Abstract

Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have experienced rapid development in recent years. The findings of spaceflight-based scRNA-seq and SRT investigations are likely to improve our understanding of life in space and our comprehension of gene expression in various cell systems and tissue dynamics. However, compared to their Earth-based counterparts, gene expression experiments conducted in spaceflight have not experienced the same pace of development. Out of the hundreds of spaceflight gene expression datasets available, only a few used scRNA-seq and SRT. In this perspective piece, we explore the growing importance of scRNA-seq and SRT in space biology and discuss the challenges and considerations relevant to robust experimental design to enable growth of these methods in the field.

Keywords: RNA-sequencing; single-cell; spaceflight; spatial; spatially resolved transcriptomics; transcriptomics.

Publication types

Review
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Gene Expression Profiling / methods
Sequence Analysis, RNA / methods
Single-Cell Analysis / methods
Space Flight*
Transcriptome* / genetics