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All sourcesNASA NTRSDOE OSTI
NASA NTRSDate not supplied

Elevating the Quality of Space Omics Sequencing Data: Innovations and Methodologies from NASA GeneLab Sample Processing Laboratory

NASA’s GeneLab, part of the NASA Open Science Data Repository, is a space-related database that hosts a diverse range of transcriptomics, proteomics, epigenomics and genomics data. The NASA GeneLab Sample Processing Laboratory (SPL) generates omics data from biological experiments conducted aboard the International Space Station, Space Shuttle and space related ground experiments, this omics data then hosted on the GeneLab repository. Samples generated such experiments pose numerous technical challenges such as small experimental sample size, variance in dissection times, limited tissue preservation methods, prolonged storage time, and more. GeneLab SPL team had developed specialized expertise in nucleic acid extraction, library preparation and sequencing of such biological samples via extensive training and years of experience. In order to ensure data accuracy and consistency across experiments, SPL has developed standardized protocols for each species and tissue type. These protocols in conjunction with quality control metrics and data standards are crucial in generating of high-quality data. SPL protocols and standards have been developed in collaboration with the scientific community and had been made publicly available on the GeneLab portal, guaranteeing comparability of datasets across spaceflight experiments. To ensure reliability of data generation, SPL leverages cutting-edge innovations in laboratory automation for sample processing. By leveraging these state-of-the-art platforms, SPL achieves high levels of data reproducibility while significantly minimizing sources of bias and variability, especially across experiments with large numbers of samples. Over the past few years, the space biology investigator community has accessed SPL-generated data from the Open Science Data Repository for a myriad of data re-analysis and re-use studies. We observe a trend that in-house SPL-generated data consistently outperforms outsourced sequencing data in terms of technical standards, quality control metrics, timeliness of data delivery, and sequencing and reagent efficiency. Superior data generation has and will continue to enable discoveries in disease, diagnostic tools, and the biological effects of long duration spaceflight.

GeneLab↗
NASA NTRSDate not supplied

NASA Open Science Data Repository: Biomedical FAIR Data, Analysis Tools, User Communities, and Discoveries for Deep Space Missions

Increased biomedical risks and challenges associated with deep space missions require new knowledge discovery, new health countermeasures, and development of novel ecosystems, life support, crop production, and biomedical support capabilities. To meet NASA’s Moon to Mars strategic program goals for Human and Biological Sciences, findable, accessible, interoperable, reusable (FAIR), and maximally open-access data is going to be required to enable humanity to thrive in deep space. Indeed, this cornerstone perspective on FAIR and maximally open access data was also recommended in the recent 2023-2032 Decadal Survey from the National Academies of Sciences, Engineering, and Medicine. The NASA Open Science Data Repository (OSDR) is a maximally open access and FAIR database, and meets various scientific, technical, and operational spaceflight needs. It offers public users and submitters the ability to upload, download, search, share, analyze, and visualize data across ‘omics, physiological, phenotypic, behavioral, bioimaging, video, and environmental monitoring telemetry datasets. OSDR includes NASA GeneLab, NASA Ames Life Sciences Data Archive, and the NASA Biological Institutional Scientific Collection. OSDR has >455 studies with datasets from model organisms and non-NASA human astronauts. There are ~12 datasets from the Inspiration 4 (I4) mission, spanning metagenomics, comprehensive metabolic panels, clonal hematopoiesis, spatial transcriptomics, proteomics, and cytokine panels. In the interest of data privacy, two I4 datasets have raw FASTQ and FASTA files relating to the epitranscriptome, and a new request feature is live in OSDR (with a backend review process established) which was developed based on industry norms. OSDR also recently began a collaboration with the European Space Agency (ESA) to scientifically curate and make available >200 terabytes of human and model organism space-relevant data. The OSDR submission portal is designed to ingest and curate ~25 ‘omics assay data types, and ~50 physiological-phenotypic-imaging assay data types, spanning ultrasonography, micro-computed tomography, histology, morphometric photography, rebound tonometry, gait analysis, optical coherence tomography, novel object recognition, flow cytometry, and immunohistochemistry. A suite of analysis tools are available for OSDR users including: 1) an Environmental Data Application to compare radiation, CO2, relative humidity, temperature, and other telemetry across missions and subjects, 2) the RadLab database, a collaboration between NASA, ESA, the German and Italian Space Agencies, and the Bulgarian Academy of Sciences, which compiles radiation measurements relevant to human spaceflight and provides tools for accessing and manipulating the data, and 3) a Multi-study visualization tool which enables users to look across and combine GeneLab’s omics datasets across different experiments and missions. There are ~600 volunteer OSDR Analysis Working Group (AWG) members who: 1) provide feedback on scientific standards for reuse (subject and assay metadata; processing pipelines; dataset formats and uniformed structures for machine-readability), and 2) collaborate to mine-reuse OSDR data conducting scientific analysis. OSDR has enabled 60 publications as of September 2023, many directly from AWG collaborations most notably the Cell Press package in 2020. Lastly, there are at least 15 articles which mine OSDR data part of a package of ~50 articles across Nature Portfolio with research stemming from I4, the Japan Aerospace Exploration Agency, NASA Space Biology, and the NASA Human Research Program.

open access↗
NASA NTRSDate not supplied

Enabling Model Organism and Commercial Astronaut Data Access Through the NASA Open Science Data Repository

NASA’s Open Science Data Repository (OSDR) brings together omics data from NASA’s GeneLab project and non-omics data, including physiological, phenotypic, imaging, and behavioral data from NASA’s Ames Life Sciences Data Archive (ALSDA) collected from decades of space biology research, providing open and FAIR (findable, accessible, interoperable, and reusable) access of these precious data to scientists world-wide. This rich source of meticulously curated metadata and data from spaceflight and analog studies has been mined by the scientific community resulting in dozens of high impact scientific publications that reveals a complex network of molecular and physiological effects of spaceflight across living systems, from microbes to plants, to mammals. Understanding how these effects translate to the human condition is critical as we move deeper into the era of commercial space travel. However, the integration of data, specifically omics data, from astronauts is particularly challenging due to their sensitive nature. OSDR has risen to this challenge by developing a mechanism to control access to identifiable levels of omics data, such as raw sequence data, while enabling public access to processed, unidentifiable, data and associated metadata that will allow the scientific community to interrogate human astronaut data alongside data from model organisms to begin answering these critical questions. The 2021 SpaceX Inspiration4 (I4) mission collected a comprehensive atlas of biological measurements from four civilian astronauts, providing a wealth of data to characterize the effects of spaceflight on the human body. These data include both non-omics and omics assays such as direct RNA sequencing (RNA-seq), single nuclei ATAC-seq and RNA-seq, metagenomics, proteomics, and comprehensive metabolic and cytokine panels, all of which have been integrated into the OSDR system across no less than 9 studies. Each study has been carefully curated using community-backed OSDR standards for sample and assay level metadata ensuring these data are findable and accessible. In addition to hosting both raw and processed data from the principal investigator team for each assay type, the GeneLab team plans to re-process the I4 omics data using GeneLab’s standard processing pipelines. The GeneLab processed data outputs will allow for comparisons across studies on OSDR and enable visualization of these data through the OSDR data visualization platform thereby enabling data reusability and interoperability. Here we describe the robust privacy and security protocols implemented by OSDR to safeguard sensitive health data from astronauts while facilitating metadata and processed data sharing for research purposes. We further provide a road map for navigating the vast amount of data provided for each I4 study on the OSDR, including experimental design, associated experiments, payloads, and missions, data generation and analysis protocols, and associated scientific articles. Additionally, we illustrate how to interrogate the standardized metadata provided in the sample and assay tables as well as instructions for how to download and access the data. The I4 datasets described here re present the first ever comprehensive collection of commercial astronaut data.

Amanda M Saravia-Butler↗
NASA NTRS2024

Metabolic Stress in Space: ROS-Induced Mutations in Mice Hint at A New Path to Cancer

Long-duration spaceflight beyond Earth's magnetosphere poses serious health risks, including muscle atrophy, bone loss, liver and kidney damage, and the Spaceflight-Associated Neuro-ocular Syndrome (SANS). RNA-seq of mice aboard the International Space Station (ISS) for 37 days revealed extraordinary hypermutation in tissue-specific genes, with guanine base conversion predominating, potentially contributing to spaceflight-associated health risks. Our results suggest that the genome-wide accelerated mutation that we measured, seemingly independent of radiation dose, was induced by oxidative damage from higher atmospheric carbon dioxide (CO 2 ) levels and increased reactive oxygen species (ROS) on the ISS. This accelerated mutation, faster via RNA transcription than replication and more numerous than by radiation alone, unveils novel hotspots in the mammalian proteome. Notably, these hotspots correlate with commonly mutated genes across various human cancers, highlighting the ISS as a crucial platform for studying accelerated mutation, genome instability, and the induction of disease-causing mutations in model organisms. Our results suggest that metabolic processes can contribute to somatic mutation, and thus may play a role in the development of cancer. A metabolic link to genetic instability potentially has far-reaching implications for various diseases, with implications for human health on Earth and in space.

mice↗
NASA NTRSDate not supplied

Enabling Open and Interoperable Science: Multi-Omics Data Processing Platform with NASA GeneLab Standardized Bioinformatics Workflows for Space and Earth Research

Multi-omics biological data continues to be generated at an astounding pace. Genomics, transcriptomics, metabolomics, and proteomics, or collectively known as multi-omics data, are used to assess biological functions, and provide invaluable insights into human, animal, plant, and environmental health both on Earth and in Space. Despite the abundance of these valuable data, the need for bioinformatics expertise, particularly as it relates to the niche filed of space biology, and a lack of accessible resources for processing these data limit their usefulness in deriving biological insights. The NASA Open Science Data Repository (OSDR) provides access to omics data from various spaceflight and analog studies. To enhance the accessibility and reusability of these data, GeneLab (part of OSDR) designs and implements standardized, community-driven, open-source bioinformatics workflows to transform raw omics data into standardized processed data. Currently, GeneLab-processed data from hundreds of space studies have been reused for meta-analyses. This has led to new insights and scientific publications that extend beyond the initial research, thereby enriching our understanding of molecular-scale biological responses to the space environment. To make these bioinformatics workflows open and accessible, GeneLab teamed up with DOE-funded initiatives, including the National Microbiome Data Collaborative (NMDC), to create the NASA EDGE [Empowering the Development of Genomics Expertise] Bioinformatics web-based platform. NASA EDGE utilizes shared compute resources to run the GeneLab standardized bioinformatics workflows, which eliminates the need for researchers to have their own high performance computing cluster. The web-based platform makes complicated biological analyses incredibly easy to perform, thus expanding the reach of these analyses to bioinformatics novices, students, and even citizen scientists enabling them to contribute to scientific discoveries and progress. The authors will demonstrate how the NASA EDGE platform can be used to process microbial omics data hosted on OSDR as well as user-generated omics datasets using GeneLab’s standard workflows.

Amanda M. Saravia-Butler↗
NASA NTRS2004

Rapid Protein Separations in Microfluidic Devices

This paper describes fabrication of glass and plastic microfluidic devices for protein separations. Although the long-term goal is to develop a microfluidic device for two-dimensional gel electrophoresis, this paper focuses on the first dimension-isoelectric focusing (IEF). A laser-induced fluorescence (LIF) imaging system has been built for imaging an entire channel in an IEF device. The whole-channel imaging eliminates the need to migrate focused protein bands, which is required if a single-point detector is used. Using the devices and the imaging system, we are able to perform IEF separations of proteins within minutes rather than hours in traditional bench-top instruments.

MICROFLUIDICS↗