Search NASA⌕ Search

SEARCH · Search NASA

Results for “transcriptomic analyses”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7

Spaceflight Biospecimen Sharing in Support of Science Discovery and Exploration

For decades, NASA and international partners have flown non-human biological experiments in space to understand the effects of spaceflight and address potential biological hazards. Sending organisms into space is a costly endeavor which makes space-flown biological specimens a valuable resource. To enable maximum scientific return, samples not required by the Principal Investigators are harvested and collected mostly by NASA’s Space Biology Biospecimen Sharing Program. These specimens are collected according to well-established SOPs that maintain quality and integrity. The specimens are then preserved, archived, and made available to the international scientific community through NASA’s Institutional Scientific Collection (ISC) at Ames Research Center (ARC). The ISC-ARC biospecimens and descriptive metadata are findable and accessible for request through the Life Sciences Data Archive (LSDA). The NASA ISC-ARC currently stores over 32,000 specimens from Shuttle, International Space Station, and ground-based investigations (spaceflight analog experiments involving either hindlimb unloading, centrifugation, or partial weight-bearing study designs). Tissues are predominantly from mice and rats, though samples are also available from bacteria and quail. The specimens include tissues from many physiological systems including musculoskeletal, neurosensory, reproductive, respiratory, circulatory, and digestive. Tissues are stored at -80°C, -20°C, +4°C, or ambient and preserved in various fixatives. Descriptive metadata is available for all samples. Historically, these tissues have been used for a wide range of analyses, including histology, genomics, and transcriptomics. Plans are underway to expand the ISC-ARC beyond the mostly-rodent contents, to include a space-relevant microbial culture collection including bacteria, fungi, and yeast. This expansion of the ISC-ARC will now involve identifying and standardizing best practices for microbial curations. To ensure safe long-term storage of microbial isolates, a microbiology laboratory will be dedicated for identification, cell culture, and lyophilization. Awarding of tissue to public science investigators has resulted in 33 publications since 2011, with 48 requests being submitted since 2016. Of note, NASA GeneLab has been awarded ISC-ARC biospecimens in the past few years. GeneLab processes the biospecimens to generate various levels of ‘omics’ data, which are published on GeneLab’s open access online platform for bioinformatics analysis and visualization. This has helped a systems biology community grow around the processed-biospecimens’ datasets, resulting in many new publications and insights. Websites: https://www.nasa.gov/ames/research/space-biosciences/isc-bsp ; https://lsda.jsc.nasa.gov/Biospecimen

Ryan T. Scott↗

Multidimensional quantitative phenotypic and molecular analysis reveals neomorphic behaviors of p53 missense mutants

Abstract Mutations in the TP53 tumor suppressor gene occur in >80% of the triple-negative or basal-like breast cancer. To test whether neomorphic functions of specific TP53 missense mutations contribute to phenotypic heterogeneity, we characterized phenotypes of non-transformed MCF10A-derived cell lines expressing the ten most common missense mutant p53 proteins and observed a wide spectrum of phenotypic changes in cell survival, resistance to apoptosis and anoikis, cell migration, invasion and 3D mammosphere architecture. The p53 mutants R248W, R273C, R248Q, and Y220C are the most aggressive while G245S and Y234C are the least, which correlates with survival rates of basal-like breast cancer patients. Interestingly, a crucial amino acid difference at one position—R273C vs. R273H—has drastic changes on cellular phenotype. RNA-Seq and ChIP-Seq analyses show distinct DNA binding properties of different p53 mutants, yielding heterogeneous transcriptomics profiles, and MD simulation provided structural basis of differential DNA binding of different p53 mutants. Integrative statistical and machine-learning-based pathway analysis on gene expression profiles with phenotype vectors across the mutant cell lines identifies quantitative association of multiple pathways including the Hippo/YAP/TAZ pathway with phenotypic aggressiveness. Further, comparative analyses of large transcriptomics datasets on breast cancer cell lines and tumors suggest that dysregulation of the Hippo/YAP/TAZ pathway plays a key role in driving the cellular phenotypes towards basal-like in the presence of more aggressive p53 mutants. Overall, our study describes distinct gain-of-function impacts on protein functions, transcriptional profiles, and cellular behaviors of different p53 missense mutants, which contribute to clinical phenotypic heterogeneity of triple-negative breast tumors.

60 APPLIED LIFE SCIENCES↗

A deep generative model for deciphering cellular dynamics and in silico drug discovery in complex diseases

Human diseases are characterized by intricate cellular dynamics. Single-cell transcriptomics provides critical insights, yet a persistent gap remains in computational tools for detailed disease progression analysis and targeted in silico drug interventions. Here we introduce UNAGI, a deep generative neural network tailored to analyse time-series single-cell transcriptomic data. This tool captures the complex cellular dynamics underlying disease progression, enhancing drug perturbation modelling and screening. When applied to a dataset from patients with idiopathic pulmonary fibrosis, UNAGI learns disease-informed cell embeddings that sharpen our understanding of disease progression, leading to the identification of potential therapeutic drug candidates. Validation using proteomics reveals the accuracy of UNAGI’s cellular dynamics analysis, and the use of the fibrotic cocktail-treated human precision-cut lung slices confirms UNAGI’s predictions that nifedipine, an antihypertensive drug, may have anti-fibrotic effects on human tissues. UNAGI’s versatility extends to other diseases, including COVID, demonstrating adaptability and confirming its broader applicability in decoding complex cellular dynamics beyond idiopathic pulmonary fibrosis, amplifying its use in the quest for therapeutic solutions across diverse pathological landscapes.

Neural Network↗

Endogenous Retroviral Elements Generate Pathologic Neutrophils in Pulmonary Arterial Hypertension

Rationale: The role of neutrophils and their extracellular vesicles (EVs) in the pathogenesis of pulmonary arterial hypertension is unclear. Objectives: To relate functional abnormalities in pulmonary arterial hypertension neutrophils and their EVs to mechanisms uncovered by proteomic and transcriptomic profiling. Methods: Production of elastase, release of extracellular traps, adhesion, and migration were assessed in neutrophils from patients with pulmonary arterial hypertension and control subjects. Proteomic analyses were applied to explain functional perturbations, and transcriptomic data were used to find underlying mechanisms. CD66b-specific neutrophil EVs were isolated from plasma of patients with pulmonary arterial hypertension, and we determined whether they produce pulmonary hypertension in mice. Measurements and Main Results: Neutrophils from patients with pulmonary arterial hypertension produce and release increased neutrophil elastase, associated with enhanced extracellular traps. They exhibit reduced migration and increased adhesion attributed to elevated β1-integrin and vinculin identified by proteomic analysis and previously linked to an antiviral response. This was substantiated by a transcriptomic IFN signature that we related to an increase in human endogenous retrovirus K envelope protein. Transfection of human endogenous retrovirus K envelope in a neutrophil cell line (HL-60) increases neutrophil elastase and IFN genes, whereas vinculin is increased by human endogenous retrovirus K deoxyuridine triphosphate diphosphatase that is elevated in patient plasma. Neutrophil EVs from patient plasma contain increased neutrophil elastase and human endogenous retrovirus K envelope and induce pulmonary hypertension in mice, mitigated by elafin, an elastase inhibitor. Conclusions: Elevated human endogenous retroviral elements and elastase link a neutrophil innate immune response to pulmonary arterial hypertension.

60 APPLIED LIFE SCIENCES↗

Omics-Lethal Human Viruses, Interferon-Stimulated Response Experiment IFNFB001

The purpose of this experiment was to evaluate the human host cellular response to interferon alpha/beta (IFNα/β) or interferon gamma (IFNγ) treatment. Sample data was obtained from primary human lung fibroblast (FB) cells inoculated with IFNα/β or IFNγ for transcriptome analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset download have a direct relationship to a primary sample submission corresponding to a specific interferon response to viral infection.

59 BASIC BIOLOGICAL SCIENCES↗

Omics-Lethal Human Viruses, Ebola Experiment EHUH001

The purpose of this experiment was to evaluate the human host response to Zaire Ebola wild-type virus and mutant virus infection. Samples were obtained from human hepatoma carcinoma cells (HUH-7) infected with Zaire Ebola ΔVP30-WT background, in addition to mutant viruses Ebola-ΔsGP (eliminating expression of soluble glycoprotein ssGP) and Ebola-Δmucin (encoding a glycoprotein lacking the mucin domain) for mRNA and miRNA transcriptome expression analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset downloads have a direct relationship to a primary sample submission corresponding to a specific Ebola virus infection.

59 BASIC BIOLOGICAL SCIENCES↗

Omics-Lethal Human Viruses, Ebola Experiment EHUH003

The purpose of this experiment was to evaluate the human host response to Zaire Ebola wild-type virus infection. Samples were obtained from human hepatoma carcinoma cells (HUH-7) infected with Zaire Ebola ΔVP30-WT background for mRNA and miRNA transcriptome expression analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset downloads have a direct relationship to a primary sample submission corresponding to a specific Ebola virus infection.

59 BASIC BIOLOGICAL SCIENCES↗

Omics-Lethal Human Viruses, Ebola Experiment EHUVEC001

The purpose of this experiment was to evaluate the human host response to Zaire Ebola wild-type virus and mutant virus infection in VP30 expression background. Samples were obtained from human umbilical cord endothelial cells (HUVEC) infected with wild-type Zaire Ebola virus in the ΔVP30 background (deltaVP30-WT) and mutant lacking the mucin domain (deltaVP30-deltamucin) encoding a glycoprotein lacking the mucin domain for mRNA transcriptome expression analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset downloads have a direct relationship to a primary sample submission corresponding to a specific Ebola virus infection.

59 BASIC BIOLOGICAL SCIENCES↗

Omics Lethal Human Viruses, Ebola Experiment EU937001

The purpose of this experiment was to evaluate the human host response to Zaire Ebola wild-type virus and mutant virus infection. Samples were obtained from human histiocytic lymphoma cells (U937), expressing the Ebola VP30 protein, infected with wild-type Zaire Ebola (in ΔVP30 background) and Δmucin mutant virus encoding a glycoprotein lacking the mucin domain for mRNA and miRNA transcriptome expression analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset downloads have a direct relationship to a primary sample submission corresponding to a specific Ebola virus infection.

59 BASIC BIOLOGICAL SCIENCES↗

Omics-Lethal Human Viruses, Interferon-Stimulated Response Experiment IFNaHUH001

The purpose of this experiment was to evaluate the human host cellular response to treatment with and without interferon alpha/beta (IFNα/β) treatment. Sample time course data was obtained from human hepatoma carcinoma cells (HUH-7) expressing transcriptional activation protein VP30, stably transfected with the Ebola VP30 gene for enabling replication of VP30-deficient Ebola virus for transcriptome expression analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset download have a direct relationship to a primary sample submission corresponding to a specific interferon response to viral infection.

59 BASIC BIOLOGICAL SCIENCES↗

Omics-Lethal Human Viruses, Interferon-Stimulated Response Experiment IFNaCL001

The purpose of this experiment was to evaluate the host interferon-stimulated cellular response to interferon alpha (IFNα) treatment. Sample data was obtained from human lung adenocarcinoma cells (Calu-3) treated with or without IFNα for mRNA and miRNA transcriptome expression analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset download have a direct relationship to a primary sample submission corresponding to a specific interferon response to viral infection.

59 BASIC BIOLOGICAL SCIENCES↗

Omics-Lethal Human Viruses, Interferon-Stimulated Response Experiment IFNMVE001

The purpose of this experiment was to evaluate the human host interferon-stimulated cellular response to interferon alpha/beta (IFNα/β) or gamma (INFγ) treatment. Sample data was obtained from primary lung microvascular endothelial cells (MVE) treated with or without human IFNαβ or INFγ for mRNA transcriptome expression analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset download have a direct relationship to a primary sample submission corresponding to a specific interferon response to viral infection.

59 BASIC BIOLOGICAL SCIENCES↗

Omics-Lethal Human Viruses, Influenza A Experiment IM101

The purpose of this experiment was to evaluate the host mouse response to wild-type Influenza A/Vietnam/1203/2004 (H5N1) virus, Influenza A/California/04/2009 (H1N1) virus, and Influenza A/Vietnam/1203/2004 (H5N1; "PB2-627E" and "NS1trunc124") infection. Sample data was obtained from whole mouse lung and processed for transcriptomics expression analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset downloads have a direct relationship to a primary sample submission corresponding to a specific Influenza A virus host infection.

59 BASIC BIOLOGICAL SCIENCES↗

Omics-Lethal Human Viruses, MERS-CoV Experiment MCL001

The purpose of this experiment was to evaluate the human host response to wild-type Middle Eastern Respiratory Syndrome coronavirus (icMERS) and icMERS-CoV mutants icMERS-CoV-RFP, icMERS-CoV-dNSP16, icMERS-CoV-d4B, and icMERS-CoV-d3 virus infection. Sample data was obtained from human bronchial epithelial cells (Calu-3 clone 2B4) for mRNA and miRNA transcriptome expression analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific MERS-CoV virus infection.

59 BASIC BIOLOGICAL SCIENCES↗

VEG-05 Tomato Crop Testing on the International Space Station

Production of fresh, nutritious, and tasty produce for astronauts during spaceflight may provide health-promoting, bioavailable nutrients, enhance the dietary experience, and reduce menu fatigue as we move into longer-duration missions. Growing and caring for plants may also reduce the psychological stresses associated with spaceflight and enhance connection to Earth. A diversity of crops will be required to provide nutrition, variety, and resiliency, however requirements for consistent growth under spaceflight environmental conditions remain unclear. VEG-05 is part of a series of experiments with pick-and-eat salad crops to better define best practices for crop production in space. VEG-05 and predecessor experiments VEG-04A and VEG-04B, grew salad crops in the Veggie vegetable production facilities on the International Space Station using different lighting treatments. In VEG-05 we grew ‘Red Robin’ dwarf cherry tomatoes under two different red: blue lighting spectra. Light can impact the growth habit, yield, nutritional composition, microbial levels, and even flavor attributes within crops, and our goal was to assess these characteristics in ‘Red Robin’ tomatoes during VEG-05. Considerable pre-flight verification testing was performed prior to launch in Nov. 2022. Prior to the flight and ground experiments, lighting in both Veggie units on ISS was measured and lights were standardized between flight and ground hardware. VEG-05 flight operations ran between December 2022 and March 2023, with a ground control initially 48 hours delayed. Due to environmental challenges of very low humidity during the first week of the experiment, seed germination was low for both flight and ground plants. The flight experiment ultimately had 4 - 5 plants per treatment out of the planned 6 plants, but the initial ground control had only three plants in one treatment and none in the other, so this ground control was restarted at the beginning of Feb. 2023 and ran through May, with successful growth of all 12 plants. Both flight and ground control ran 100 days, with harvests of fruit at day 83, day 90, and day 100. Flight plants had uneven growth, and following the early drying events, excess water was frequently observed, which led to a variety of plant stress responses including uneven plant growth, excess adventitious root formation, flower and fruit abortion, and visible microbial growth. In total, from the five surviving red-rich lighted plants, only 5 ripe fruit were produced, and from the four surviving blue-rich lighted plants, 10 fruit were produced with only 6 of these ripe by day 100. Because of the small fruit number and the unsatisfactory growth, crew members were not allowed to consume the tomatoes, and all fruit, as well as large branches with leaves, samples of the adventitious roots, two plant rooting pillows from each treatment, microbial sampling swabs, and some water samples were returned for analysis. Because of the small sample sizes and factors affecting growth on the ISS, objectives of assessing light quality effect (red: blue light treatments) will not be achieved. Revised objectives of this study include to compare stressed flight plants with normal ground plants to determine the impact of plant overwatering stress in space on food safety and the plant microbial community, to determine nutrient content changes in fruit and leaves from stressed plants, and to evaluate stress metabolism changes in returned tissue by transcriptomic analysis. Postflight analysis is underway with the following analyses being conducted: A. culturable microbiology and food safety as well as molecular microbial community analysis of 1. ripe fruit, 2. leaves, stems, and adventitious roots, 3. pillow components (roots, wicks, and substrates), 4. swabs, and 5. water samples from root mats before and after growth. B. transcriptomics of leaf tissue and adventitious roots, and C. elemental analysis of leaf tissue. If sufficient tissue remains elemental analyses will also be conducted on fruit. While not generating the desired information on spaceflight growth responses of healthy crops, our team is hopeful that these analyses will shed light on tomato responses to stress in this environment as plant overwatering stress is a mission-relevant condition that could occur in future space crop growth systems. This research was co-funded by the Human Research Program and Space Biology (MTL#1075) in the ILSRA 2015 NRA call.

Gioia D. Massa↗

Ectomycorrhizal fungi enhance pine growth by stimulating iron‐dependent mechanisms with trade‐offs in symbiotic performance

Iron (Fe) is crucial for metabolic functions of living organisms. Plants access occluded Fe through interactions with rhizosphere microorganisms and symbionts. Yet, the interplay between Fe addition and plant–mycorrhizal interactions, especially the molecular mechanisms underlying mycorrhiza-assisted Fe processing in plants, remains largely unexplored. Here, we conducted mesocosms in Pinus plants inoculated with different ectomycorrhizal fungi (EMF) Suillus species under conditions with and without Fe coatings. Meta-transcriptomic, biogeochemical, and X-ray fluorescence imaging analyses were applied to investigate early-stage mycorrhizal roots. While Fe addition promoted Pinus growth, it concurrently reduced mycorrhiza formation rate, symbiosis-related metabolites in plant roots, and aboveground plant carbon and macronutrient content. This suggested potential trade-offs between Fe-enhanced plant growth and symbiotic performance. However, the extent of this trade-off may depend on interactions between host plants and EMF species. Interestingly, dual EMF species were more effective at facilitating plant Fe uptake by inducing diverse Fe-related functions than single-EMF species. This subsequently triggered various Fe-dependent physiological and biochemical processes in Pinus roots, significantly contributing to Pinus growth. However, this resulted in a greater carbon allocation to roots, relatively reducing the aboveground plant carbon content. Our study offers critical insights into how EMF communities rebalance benefits of Fe-induced effects on symbiotic partners.

36 MATERIALS SCIENCE↗

High-throughput Single-Cell Proteomics and Transcriptomics from the Same Cells with a Nanoliter-Scale Spin-Transfer Approach

Single-cell multiomic platforms provide a comprehensive snapshot of cellular states and cell types by offering critical insights into the spatiotemporal regulation of biomolecular networks at a systems level, thereby defining the basis of multicellularity. Here, we introduce nanoSPINS, an advanced platform that enables high-throughput profiling and integrative analysis of the transcriptome and proteome from the same single cells using RNA sequencing and isobaric labeling LC-MS-based proteomics, respectively. NanoSPINS can efficiently transfer mRNA-containing droplets across two microarrays via a centrifugation-based approach, while proteins are retained on the initial platform. Benchmarking of nanoSPINS on two cell lines demonstrates its ability to generate global proteomic and transcriptomic profiles that align well with previously established methodologies/platforms. The incorporation of isobaric TMTpro labeling into this single-cell multiomics platform significantly enhances the throughput of single-cell proteomic analyses. Through the high-throughput quantification of the proteome and transcriptome, nanoSPINS not only facilitates the identification of molecular features at both mRNA and protein level but also provides larger sample sizes for improved statistical power in clustering and differential abundance. Given the broad applicability of single-cell multiomics in biological research and clinical settings, we believe nanoSPINS represents a powerful platform for the characterization of heterogeneous cell populations.

multi 'omics↗

A tissue‐resolved, network‐based transcriptomic framework for abiotic stress responses in sorghum

Developing climate‐resilient crops requires a detailed understanding of stress‐induced gene expression dynamics, as maladaptive responses can compromise their productivity and survival. Sorghum, a globally important cereal with exceptional tolerance to multiple abiotic stresses, provides a powerful system for investigating these dynamics. However, how stress type, tissue specificity, and temporal progression jointly shape transcriptomic responses in crops remains poorly understood. Here, we present a comparative, time‐resolved transcriptomic atlas of sorghum responses to drought, heat, and salinity stress across shoot and root tissues. Integrative analyses revealed that tissue specificity is the dominant determinant of abiotic stress‐induced gene reprogramming across all three stresses. Building on these global comparisons, we focused on heat stress, as it elicited the most coherent and pronounced transcriptional and regulatory responses, enabling deeper network‐level interrogation. Co‐expression network analysis identified tissue‐specific modules enriched for phytohormone‐responsive genes, while gene regulatory network (GRN) mapping and cistrome analyses uncovered transcription factors (TFs) controlling key hub genes within these modules. Together, this study provides a foundational transcriptomic and network‐based resource for dissecting the regulatory architecture of abiotic stress responses in sorghum and offers prioritized candidates for future functional validation and engineering of climate‐resilient crops.

abiotic stress↗