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All sourcesNASA NTRSDOE OSTI
NASA NTRS2016

BioSentinel: Biosensors for Deep-Space Radiation Study

The BioSentinel mission will be deployed on NASA's Exploration Mission 1 (EM-1) in 2018. We will use the budding yeast, Saccharomyces cerevisiae, as a biosensor to study the effect of deep-space radiation on living cells. The BioSentinel mission will be the first investigation of a biological response to space radiation outside Low Earth Orbit (LEO) in over 40 years. Radiation can cause damage such as double stand breaks (DSBs) on DNA. The yeast cell was chosen for this mission because it is genetically controllable, shares homology with human cells in its DNA repair pathways, and can be stored in a desiccated state for long durations. Three yeast strains will be stored dry in multiple microfluidic cards: a wild type control strain, a mutant defective strain that cannot repair DSBs, and a biosensor strain that can only grow if it gets DSB-and-repair events occurring near a specific gene. Growth and metabolic activity of each strain will be measured by a 3-color LED optical detection system. Parallel experiments will be done on the International Space Station and on Earth so that we can compare the results to that of deep space. One of our main objectives is to characterize the microfluidic card activation sequence before the mission. To increase the sensitivity of yeast cells as biosensors, desiccated yeast in each card will be resuspended in a rehydration buffer. After several weeks, the rehydration buffer will be exchanged with a growth medium in order to measure yeast growth and metabolic activity. We are currently working on a time-course experiment to better understand the effects of the rehydration buffer on the response to ionizing radiation. We will resuspend the dried yeast in our rehydration medium over a period of time; then each week, we will measure the viability and ionizing radiation sensitivity of different yeast strains taken from this rehydration buffer. The data obtained in this study will be useful in finalizing the card activation sequence for this mission.

Yeast↗
NASA NTRS2017

Machine Learning Approaches to Increasing Value of Spaceflight Omics Databases

The number of spaceflight bioscience mission opportunities is too small to allow all relevant biological and environmental parameters to be experimentally identified. Simulated spaceflight experiments in ground-based facilities (GBFs), such as clinostats, are each suitable only for particular investigations -- a rotating-wall vessel may be 'simulated microgravity' for cell differentiation (hours), but not DNA repair (seconds) -- and introduce confounding stimuli, such as motor vibration and fluid shear effects. This uncertainty over which biological mechanisms respond to a given form of simulated space radiation or gravity, as well as its side effects, limits our ability to baseline spaceflight data and validate mission science. Machine learning techniques autonomously identify relevant and interdependent factors in a data set given the set of desired metrics to be evaluated: to automatically identify related studies, compare data from related studies, or determine linkages between types of data in the same study. System-of-systems (SoS) machine learning models have the ability to deal with both sparse and heterogeneous data, such as that provided by the small and diverse number of space biosciences flight missions; however, they require appropriate user-defined metrics for any given data set. Although machine learning in bioinformatics is rapidly expanding, the need to combine spaceflight/GBF mission parameters with omics data is unique. This work characterizes the basic requirements for implementing the SoS approach through the System Map (SM) technique, a composite of a dynamic Bayesian network and Gaussian mixture model, in real-world repositories such as the GeneLab Data System and Life Sciences Data Archive. The three primary steps are metadata management for experimental description using open-source ontologies, defining similarity and consistency metrics, and generating testing and validation data sets. Such approaches to spaceflight and GBF omics data may soon enable unique insight into which measured phenomena correlate to biological mechanisms that are truly affected by spaceflight conditions; which are most likely to be confounded by other variables; and which are insufficiently characterized, significantly increasing existing and future science return from ISS and spaceflight missions.

Gentry, Diana↗
NASA NTRS2018

Radiation and the Immune System

Radiation has profound effects on the immune system. This makes it particularly important to study in order to protect astronauts venturing into deep space and cancer patients considering radiotherapy treatments. Beyond the Earth's magentic field lies galactic cosmic radiation, which contains heavy ion based rays. Immune alterations in response to radiation depends on factors such as the type and amount of radiation, and potentially even the genes of the individual being exposed. In order to study the effects of cosmic radiation on the immune system, we are exposing primary human immune cells to various types and amounts of radiation. To measure sensitivity to radiation, we are quantifying the DNA damage within the cells before irradiation, 4 hours after irradiation, and 24 hours after irradiation. DNA damage is visualized by fluorescently staining for known DNA repair proteins, which get recruited to the site of damage within a cell. These results will be analyzed to search for correlations between immune cell responses and the type of radiation, amount of radiation, or any genetic markers present in the human blood donors. We will also be attempting to determine which specific immune cells are most suspectible to radiation damage. These correlations and discoveries will contribute to making long duration human deep space exploration a possibility, and can even be used to design more personalized and effective radiation treatments for cancer patients.

Malkani, Sherina S.↗
NASA NTRS2018

BioSentinel: An Adaptable Platform for Studying the Biological Effects of Deep Space Radiation

NASA's BioSentinel mission is a 6U nanosatellite with autonomous life support that will utilize the budding yeast Saccharomyces cerevisiae to study the DNA damage response to the deep space radiation environment. BioSentinel is planned to launch in 2019 as a secondary payload on the Space Launch System's first Exploration Mission (EM-1), and will undergo a lunar fly-by and enter heliocentric orbit after deployment. As the first biological mission beyond Low Earth Orbit (LEO) in nearly half a century, this mission will help fill critical gaps in knowledge about the effects of uniquely composed, chronic, low-flux deep space radiation on biological systems. Yeast is well-suited for this mission due to its desiccation tolerance and space-flight heritage. As a eukaryotic model organism, it also serves as a robust analog for human cells. Data gathered on this mission will thus inform us of the hazards involved in long-duration human exploration in deep space, and the protections necessary to mitigate them. Due to its low-cost, flexible and advanced technology, the 4U BioSensor payload contained within the nanosatellite is adaptable to other model microorganisms, exploration platforms and environments relevant to human exploration, such as the ISS, the Lunar Orbital Platform - Gateway and future lunar landers. In order to query the DNA damage response to deep space radiation, BioSentinel contains a wild type yeast strain as a positive control, and a radiation sensitive rad51 mutant strain that is defective for DNA repair. Yeast cells are desiccated in microfluidic cards, and rehydrated with growth medium and metabolic indicator dye at the desired time points during the mission. A thermal control system supports these stasis and growth states, and an optical system continuously measures cell growth and metabolism. An onboard radiation spectrometer and dosimeter allows us to correlate the dose, energy and particle-type of deep space radiation to the biological response. Data received from the deep space biosensor will be compared to control payloads on Earth and the ISS. Ongoing science testing for the BioSentinel project includes optimization for cell viability, desiccation tolerance, and long-term biocompatibility, as well as radiation experiments to understand the sensitivity and responsiveness of cells to varying radiation doses and particle types.

BioSentinel↗
NASA NTRS2019

Using DNA Damage to Investigate the Individual Variability of Human Sensitivity to Ionizing Radiation

High-LET ionizing radiation is a major occupational health hazard for astronauts, but risk assessment remains elusive due to limited epidemiological data. Identifying genetic factors modulating the individual radiation response may be the most effective strategy to provide individualized risk management for long-duration high-radiation missions. We have started tackling the challenge of predicting individual risks by identifying human genetic loci associated with various radiation sensitivity phenotypes in primary blood mononuclear cells from a relatively large healthy human cohort. To date, we have performed the isolation of PBMCs from 768 subjects of the same ethnicity, and irradiated PBMCs from 576 subjects with 1 and 3 particles/100µm2 of 600 MeV/n 56Fe, 350 MeV/n 40Ar and 350 MeV/n 28Si ions. The phenotypes of interest were: number of radiation-induced foci (or RIFs), CellROX oxidative stress responses and cell death, at 4h and 24h following irradiation. We have observed a significant inter-individual variability at 0 Gy between the 576 studied subjects, with a mean fold difference between the 10% lowest and highest responders of 5.6 of RIFs/cell, 7.9 in mean CellRox intensity, and 9.3 in percentage of dead cells. In order to better assess genetic factors influencing DNA repair, we used a metric previously introduced by our group to sort out radiation sensitivity phenotypes in mice: i.e. the ratio of the first to the second slope of RIFs/cell (between 0 and 1, and between 1 and 3 particle/100µm2). Preliminary data on 192 individuals showed a distribution of low-dose responders (ratio > 1) to high-dose responders (ratio < 1) at 4h of 12%, 55% and 52% respectively for Fe, Ar and Si. The average value for the first and the second slopes was very similar for the two lowest LET (0.10 [-0.26;0.58] and 0.09 [-0.45;0.41] for Ar, 0.07 [-0.27;0.38] and 0.08 [-0.19;0.42] for Si), indicating a linear dose response across both fluence. Fe showed clear saturation for the highest dose with a slope of -0.09 [-0.86;1.51] against 0.68 [-2.21;2.20] for the low dose range, which probably reflects that many PBMCs are beyond repair at the high dose. Note that other significances were found for additional factors such as BMI and age whereas none were found for sex. GWAS will be performed on all phenotypes upon completion of measurements.

Pariset, E.↗
NASA NTRS2019

Using DNA Damage to Investigate the Individual Variability of Human Sensitivity to Ionizing Radiation

High-LET ionizing radiation is a major occupational health hazard for astronauts, but risk assessment remains elusive due to limited epidemiological data. Identifying genetic factors modulating the individual radiation response may be the most effective strategy to provide individualized risk management for long-duration high-radiation missions. We have started tackling the challenge of predicting individual risks by identifying human genetic loci associated with various radiation sensitivity phenotypes in primary blood mononuclear cells from a relatively large healthy human cohort. To date, we have performed the isolation of PBMCs from 768 subjects of the same ethnicity, and irradiated PBMCs from 576 subjects with 1 and 3 particles/100µm2 of 600 MeV/n 56Fe, 350 MeV/n 40Ar and 350 MeV/n 28Si ions. The phenotypes of interest were: number of radiation-induced foci (or RIFs), CellROX oxidative stress responses and cell death, at 4h and 24h following irradiation. We have observed a significant inter-individual variability at 0 Gy between the 576 studied subjects, with a mean fold difference between the 10% lowest and highest responders of 5.6 of RIFs/cell, 7.9 in mean CellRox intensity, and 9.3 in percentage of dead cells. In order to better assess genetic factors influencing DNA repair, we used a metric previously introduced by our group to sort out radiation sensitivity phenotypes in mice: i.e. the ratio of the first to the second slope of RIFs/cell (between 0 and 1, and between 1 and 3 particle/100µm2). Preliminary data on 192 individuals showed a distribution of ?low-dose responders? (ratio > 1) to ?high-dose responders? (ratio < 1) at 4h of 12%, 55% and 52% respectively for Fe, Ar and Si. The average value for the first and the second slopes was very similar for the two lowest LET (0.10 [-0.26;0.58] and 0.09 [-0.45;0.41] for Ar, 0.07 [-0.27;0.38] and 0.08 [-0.19;0.42] for Si), indicating a linear dose response across both fluence. Fe showed clear saturation for the highest dose with a slope of -0.09 [-0.86;1.51] against 0.68 [-2.21;2.20] for the low dose range, which probably reflects that many PBMCs are beyond repair at the high dose. Note that other significances were found for additional factors ? such as BMI and age ? whereas none were found for sex. GWAS will be performed on all phenotypes upon completion of measurements.

Pariset, E.↗
NASA NTRSDate not supplied

Modeling Space-Radiation Induced Chromosome Aberrations

Exposure to ionizing radiation is identified as one of the main hazards of space flight. Galactic cosmic rays (GCRs) are composed of energetic protons (87%), helium nuclei (12%) and high-charge and energy (HZE) ions. At the cellular scale, HZE ions have a pattern of energy deposition that depends on the ion linear energy transfer (LET), with high LET ions favoring the formation of complex DNA damages that induce chromosome aberrations (CAs). Understanding how physical (e.g., ion type and energy) and biological (e.g., cell type) parameters impact CA formation is required to assess space radiation risks such as carcinogenesis. The Monte Carlo tool RITCARD/RITRACKS [1,2] developed by NASA allows simulation of the transport of HZE ions and subsequent energy deposition at the cellular scale and models the creation of DNA double strand breaks (DSBs), DNA repair and formation of CAs. We used this radiation transport code to further understand how radiation quality and cell size affects CA formation.

Floriane Poignant↗
NASA NTRSDate not supplied

Investigating the Molecular Response in Irradiated Yeast in Support of the BioSentinel CubeSat Mission

The BioSentinel CubeSat mission is NASA’s first deep space bioscience mission scheduled to fly as a secondary payload onboard Artemis I. BioSentinel seeks to understand the impacts of deep space radiation on living organisms using the model organism Saccharomyces cerevisiae, or budding yeast. In recent years, the BioSentinel team has conducted ground-based investigations into the effects of ionizing radiation (IR) on budding yeast to better understand spaceflight data. One investigation focuses on the impacts of radiation on budding yeast metabolics using the redox dye alamarBlue, an indicator that will also be used onboard BioSentinel. In this investigation, we have observed metabolic changes in both wild-type and in mutant yeast cells deficient in DNA repair. The focus of our research is to support the ongoing investigation into the molecular mechanisms that explain these observed changes. To do this, we first conducted preliminary research into the metabolic processes of S. cerevisiae to identify any potential vulnerabilities to radiation. We then conducted a statistical kinetic analysis on past experimental metabolic data, in addition to an analysis of data from a multisensor metabolic rig experiment. Ultimately, we identified numerous redox-related changes with increasing doses of radiation in both wild-type and mutant cells. These findings highlight the mitochondrial Electron Transport Chain (ETC) as a potential candidate process to account for these observed changes. Specifically, we are focused on the electron carriers of the ETC, including NADH and FADH2, given their participation in numerous redox mechanisms. We propose future experiments, including NADH assays, an investigation into the glycerol-3-phosphate shuttle, and investigations into other ETC complexes.

BioSentinel↗
NASA NTRS2022

Brain Aging Hallmarks: A Primer for Future Studies on Space Radiation Effects

As humankind endeavors to travel farther away from Earth, many questions remain to be solved to ensure proper preparation for deep space. Multiple spaceflight stressors can elicit adverse health outcomes including exposure to space radiation. Space radiation exposure has been identified by the National Aeronautics and Space Administration (NASA) as an important contributor to cancer, degenerative tissue diseases including cataracts, cardiovascular disease, immune system dysfunction and possible central nervous system decrements. The complexity of the human central nervous system makes it difficult to adequately recapitulate in experimental model systems, which hinders quantitative description of associated decrements. The brain aging hallmarks, as introduced by Mattson and Arumugam in 2018, are measurable cellular and molecular hallmarks that generally contribute to the aging process, describe an aging phenotype, and are part of the etiology of age-related neurodegenerative diseases. These hallmarks include mitochondrial dysfunction, accumulation of oxidatively damaged molecules (oxidative stress), impaired lysosome and proteasome function, dysregulation of neuronal calcium homeostasis, compromised adaptive cellular stress response, aberrant neuronal network activity, impaired deoxyribonucleic acid (DNA) repair, inflammation, impaired neurogenesis and dysregulated energy metabolism. Cellular senescence and telomere attrition may also be considered, though more evidence is needed to regard them as brain-specific hallmarks of aging. Radiation exposure has previously been correlated with aging etiology; therefore, investigating the effects of radiation exposure within the context of the hallmarks of brain aging may provide insights into potential health risks facing NASA astronauts, and may provide a means to identify disease processes that may be important targets for disease prevention or intervention. This work describes the hallmarks of brain aging and serves as a primer for future investigation into how the hallmarks of brain aging may compare and contrast with outcomes associated with exposure to the space radiation environment. Further, it will be useful in future identification of hallmarks that may be appropriate to target for radiation countermeasures specific to the central nervous system.

Vivian Lu↗
NASA NTRSDate not supplied

Designing Experiments for SpinSat, A Novel Variable-Gravity-and-Radiation Platform for Deep-Space Science

Conducting experiments to measure the effects of deep-space radiation and reduced gravity on biological and physical systems remains challenging. The result is a substantial knowledge gap that poses risks to our ability to sustain life and conduct critical operations in deep space. The SpinSat spacecraft platform is designed to bridge such gaps by providing low-cost, reliable, and frequent access to deep space. A disk-shaped rotating satellite that can provide artificial gravity and exposure to space radiation simultaneously, SpinSat is designed to accommodate payloads in a CubeSat form factor (with at least 48 “U” volume), providing power, communications, and a benign thermal environment. It is orbit-agnostic, enabling access to a variety of radiation environments (Van Allen belts, deep space, cis-lunar); and can be equipped with shielding to mimic planetary radiation environments, for both short- and long-term experiments. Because of its versatility and prioritization of late loading for biological payloads, it is well suited to host a wide range of ranging from human tissues and organoids to microorganisms, plants, chemistry, and regolith. Here, we present examples of potential experiment concepts for SpinSat, and discuss the details of how experimental designs could interact with the platform. Potential SpinSat studies have diverse applications, including fundamental radiation biology and DNA repair; cancer biology and countermeasure development; space agriculture; bioproduction of nutrients and pharmaceuticals; understanding regolith dynamics in low gravity; prebiotic chemistry and panspermia. We will further highlight ideas for SpinSat-compatible experimental hardware, existing and in development, and experiment-relevant details on SpinSat capabilities including artificial gravity, potential radiation environments, data, and power. This presentation will aim to provide investigators with the high-level technical information necessary to inspire experiments for SpinSat. We also seek to stimulate conversation and to gain community input on accommodations needs to help guide the evolving design of this platform.

experiment design↗
NASA NTRSDate not supplied

Cleanroom Microbes Survive Drying, Vacuum, and Proton Irradiation

Introduction : The goal of planetary protection at NASA is to mitigate the risk of contaminating sensitive target bodies with biological life. While many cleaning procedures have been put in place to reduce bioburden on spacecraft, microbes are experts at evolving to survive harsh conditions. Specifically, the dry, low-nutrient environment of a cleanroom (commonly used for assembly of spacecraft) can represent an environment where extremophiles can survive. Methods : Scientists at NASA MSFC wished to gather a snapshot of the microbial population within a variety of cleanrooms on site. A study was undertaken to collect air, surface, and floor samples from clean-rooms and isolate unique morphologies. From this study, 95 isolates were collected and saved in a microbial library. About 86% of these were identified at least to a genus level. Following identification, 24 microbes were selected, based on a literature review, as potential extremophiles. These were grown in liquid cultures, diluted to a set optical density, washed with water, and then applied to a sterilized Kapton coupon. Droplets were allowed to dry overnight in a biosafety cabinet. Coupons were then installed in a pelletron and pumped down to high vacuum (~1E-6 Torr). Samples were then subjected 100 keV protons at a fluence of 2x10 15 p+/cm 2 up to 4x10 15 p+/cm 2 . Following exposure, samples were returned to the microbiology lab where they were pro-cessed by submerging in water, vortexing, and then plating either droplets or spread plates. Recovery data collected was qualitative with a ranking or +, minor, or – for growth. Some selected radiotolerant strains were sequenced using the Illumina sequencing platform. The resulting genomes were annotated with the Rapid Annotations using Subsystems Technology (RAST) server and analyzed for conserved and unique stress response relevant genomic signatures to identify clues related to specific tolerances. Results and Discussion : After five rounds of proton radiation, we narrowed our isolates to five, non-spore forming bacteria that demonstrated survival: Arthrobacter koreensis, Paenarthrobacter nitroguajacolicus, Mycetocola manganoxydans , and an Erwinia sp. Furthermore, we exposed these four microbes to 254 nm wavelength light at an intensity of 80 W/m 2 at a distance of ~18 cm for 10 minutes. Only A. koreensis demonstrated survival following UV exposure. Finally, we performed whole genome sequencing on the four strains to look for genetic markers of stress resistance. When we compared the genomes of the four strains, we found that genes coding for GGDEF and EAL domains with PAS/PAC sensors were only found in A. koreensis . These domains, modulated by PAS/PAC sensors, are hypothesized to facilitate survival under drying, desiccation, and proton irradiation. Drying and Desiccation : PAS domains sense hydration changes and modulate GGDEF and EAL domain activity to adjust c-di-GMP levels, enhancing resistance to desiccation. For instance, in Pseudomonas aeruginosa , the PAS domain of RbdA modulates activity under varying hydration conditions, affecting stress responses [1]. Proton Irradiation : Proton irradiation causes oxidative stress, leading to ROS generation. PAS domains detect this stress and modulate GGDEF and EAL domains to manage oxidative stress responses. In Shewanella , EAL domain proteins modulated by PAS sensors help bacteria adapt to extreme conditions [2]. These genes upregulate other stress response genes, protecting membrane function, protein stability, DNA repair, and antioxidant defenses. The modulation of c-di-GMP by PAS domains is crucial for bacterial adaptation to stress conditions, enabling dynamic physio-logical adjustments [3]. Understanding these mechanisms provides insights into bacterial stress responses and strategies for controlling bacterial growth [4]. Conclusions : These findings indicate that clean-rooms harbor extremophile microbes that may be able to survive conditions in deep space. Furthermore, while we identified certain stress-response genes that may be at least partly responsible for the phenotypes observed in this study, there are likely unidentified genes or characteristics about A. koreensis , and other bacteria, that may allow them to survive in harsh environments. Future studies will focus on identifying these unknown genes and characteristics, further elucidating the mechanisms of extremophile survival and potentially informing the development of new biotechnologies for space exploration and other extreme environments.

Chelsi Cassilly↗
NASA NTRSDate not supplied

Microbial Responses to Radiation at the Single-Cell Level

Exploring the biological effects of deep space radiation is crucial for developing protective protocols for humans traveling beyond Earth’s magnetosphere. Saccharomyces cerevisiae, or budding yeast, is an ideal model organism to study the effects of radiation on eukaryotes as it shares several pathways with humans, including DNA repair mechanisms. Here, we used time-lapse imaging of colony growth on agar plates to monitor the effects of radiation exposure on individual yeast cells and their progeny.

Paola J. Maldonado Martinez↗
DOE OSTI2021

DNA asymmetry promotes SUMO modification of the single-stranded DNA-binding protein RPA

Repair of DNA double-stranded breaks by homologous recombination (HR) is dependent on DNA end resection and on post-translational modification of repair factors. In budding yeast, single-stranded DNA is coated by replication protein A (RPA) following DNA end resection, and DNA–RPA complexes are then SUMO-modified by the E3 ligase Siz2 to promote repair. Here, we show using enzymatic assays that DNA duplexes containing 3' single-stranded DNA overhangs increase the rate of RPA SUMO modification by Siz2. The SAP domain of Siz2 binds DNA duplexes and makes a key contribution to this process as highlighted by models and a crystal structure of Siz2 and by assays performed using protein mutants. Enzymatic assays performed using DNA that can accommodate multiple RPA proteins suggest a model in which the SUMO-RPA signal is amplified by successive rounds of Siz2-dependent SUMO modification of RPA and dissociation of SUMO-RPA at the junction between single- and double-stranded DNA. Our results provide insights on how DNA architecture scaffolds a substrate and E3 ligase to promote SUMO modification in the context of DNA repair.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1998

Repair of clustered DNA damage caused by high LET radiation in human fibroblasts

It has recently been demonstrated experimentally that DNA damage induced by high LET radiation in mammalian cells is non-randomly distributed along the DNA molecule in the form of clusters of various sizes. The sizes of such clusters range from a few base-pairs to at least 200 kilobase-pairs. The high biological efficiency of high LET radiation for induction of relevant biological endpoints is probably a consequence of this clustering, although the exact mechanisms by which the clustering affects the biological outcome is not known. We discuss here results for induction and repair of base damage, single-strand breaks and double-strand breaks for low and high LET radiations. These results are discussed in the context of clustering. Of particular interest is to determine how clustering at different scales affects overall rejoining and fidelity of rejoining of DNA double-strand breaks. However, existing methods for measuring repair of DNA strand breaks are unable to resolve breaks that are close together in a cluster. This causes problems in interpretation of current results from high LET radiation and will require new methods to be developed.

NASA Discipline Radiation Health↗
DOE OSTI2022

Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision Repair

Flap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). It plays a crucial role in maintaining genome stability and integrity. FEN1 is also implicated in RNA processing and biogenesis. A recent study from our group has shown that FEN1 is involved in trinucleotide repeat deletion by processing the RNA strand in R-loops through BER, further suggesting that the enzyme can modulate genome stability by facilitating the resolution of R-loops. However, it remains unknown how FEN1 can process RNA to resolve an R-loop. In this study, we examined the FEN1 cleavage activity on the RNA:DNA hybrid intermediates generated during DNA lagging strand processing and BER in R-loops. We found that both human and yeast FEN1 efficiently cleaved an RNA flap in the intermediates using its endonuclease activity. We further demonstrated that FEN1 was recruited to R-loops in normal human fibroblasts and senataxin-deficient (AOA2) fibroblasts, and its R-loop recruitment was significantly increased by oxidative DNA damage. We showed that FEN1 specifically employed its endonucleolytic cleavage activity to remove the RNA strand in an R-loop during BER. We found that FEN1 coordinated its DNA and RNA endonucleolytic cleavage activity with the 3'-5' exonuclease of APE1 to resolve the R-loop. Our results further suggest that FEN1 employed its unique tracking mechanism to endonucleolytically cleave the RNA strand in an R-loop by coordinating with other BER enzymes and cofactors during BER. Our study provides the first evidence that FEN1 endonucleolytic cleavage can result in the resolution of R-loops via the BER pathway, thereby maintaining genome integrity.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1996

DNA damage and repair in oncogenic transformation by heavy ion radiation

Energetic heavy ions are present in galactic cosmic rays and solar particle events. One of the most important late effects in risk assessment is carcinogenesis. We have studied the carcinogenic effects of heavy ions at the cellular and molecular levels and have obtained quantitative data on dose-response curves and on the repair of oncogenic lesions for heavy particles with various charges and energies. Studies with repair inhibitors and restriction endonucleases indicated that for oncogenic transformation DNA is the primary target. Results from heavy ion experiments showed that the cross section increased with LET and reached a maximum value of about 0.02 micrometer2 at about 500 keV/micrometer. This limited size of cross section suggests that only a fraction of cellular genomic DNA is important in radiogenic transformation. Free radical scavengers, such as DMSO, do not give any effect on induction of oncogenic transformation by 600 MeV/u iron particles, suggesting most oncogenic damage induced by high-LET heavy ions is through direct action. Repair studies with stationary phase cells showed that the amount of reparable oncogenic lesions decreased with an increase of LET and that heavy ions with LET greater than 200 keV/micrometer produced only irreparable oncogenic damage. An enhancement effect for oncogenic transformation was observed in cells irradiated by low-dose-rate argon ions (400 MeV/u; 120 keV/micrometer). Chromosomal aberrations, such as translocation and deletion, but not sister chromatid exchange, are essential for heavy-ion-induced oncogenic transformation. The basic mechanism(s) of misrepair of DNA damage, which form oncogenic lesions, is unknown.

NASA Discipline Number 45-10↗
NASA NTRS1999

Determination of human DNA polymerase utilization for the repair of a model ionizing radiation-induced DNA strand break lesion in a defined vector substrate

Human DNA polymerase and DNA ligase utilization for the repair of a major class of ionizing radiation-induced DNA lesion [DNA single-strand breaks containing 3'-phosphoglycolate (3'-PG)] was examined using a novel, chemically defined vector substrate containing a single, site-specific 3'-PG single-strand break lesion. In addition, the major human AP endonuclease, HAP1 (also known as APE1, APEX, Ref-1), was tested to determine if it was involved in initiating repair of 3'-PG-containing single-strand break lesions. DNA polymerase beta was found to be the primary polymerase responsible for nucleotide incorporation at the lesion site following excision of the 3'-PG blocking group. However, DNA polymerase delta/straightepsilon was also capable of nucleotide incorporation at the lesion site following 3'-PG excision. In addition, repair reactions catalyzed by DNA polymerase beta were found to be most effective in the presence of DNA ligase III, while those catalyzed by DNA polymerase delta/straightepsilon appeared to be more effective in the presence of DNA ligase I. Also, it was demonstrated that the repair initiating 3'-PG excision reaction was not dependent upon HAP1 activity, as judged by inhibition of HAP1 with neutralizing HAP1-specific polyclonal antibody.

Non-NASA Center↗
NASA NTRSDate not supplied

Genomic and Phenotypic Predictors of Human Ex Vivo Sensitivity to Simulated Deep Space Radiation

High-linear energy transfer (LET) ionizing radiation is a major health hazard for astronauts who will be exposed to galactic cosmic rays during upcoming lunar and Mars missions. Predicting and mitigating this risk requires understanding the factors underlying individual radiation sensitivity. We started to address this challenge by identifying the genomic and phenotypic associations with sensitivity to low and high-LET ionizing radiation ex vivo in over 750 healthy human donors. We exposed primary human blood mononuclear cells to simulated galactic cosmic ray components: 350 MeV/n 28Si, 350 MeV/n 40Ar and 600 MeV/n 56Fe particles, at 1.1 and 3 particles/100 sq.m fluences, as well as 0.1 Gy and 1 Gy doses of gamma rays, and analyzed the outcomes at 4 and 24 hours post-irradiation. We quantified DNA damage and repair responses based on 53BP1+ radiation-induced foci formation, together with oxidative stress and changes in secreted factors including immune cytokines and exosomes. We also analyzed phenotypic associations with spontaneous DNA repair foci at baseline prior to irradiation. We identified an increase in spontaneous DNA repair associated with age and latent viral infection, and observed that human spontaneous DNA repair foci at baseline can serve as a negative predictor of DNA repair and immunoregulatory cytokine production after irradiation. Furthermore, we observed a wide variability of subject- and LET-dependent radiation responses, with radiation-induced DNA repair foci increasing by dose and LET, and high-LET particle radiation resulting in more residual DNA damage compared to low-LET particles and gamma rays. We have developed multiple metrics to quantify human radiosensitivity across the spectrum of conditions. Here we present their dependence on radiation quality and phenotypic variables, including an age-dependent decrease in DNA repair after irradiation, and genomic associations with radiosensitivity based on low-coverage whole genome sequencing. We anticipate that our work will pave the way for understanding the spectrum of human radiosensitivity and identifying targets for countermeasure development to reduce DNA and cellular damage and radiation carcinogenesis during deep space exploration.

GWAS↗