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Mingo Barba S, Lobo-Cerna F, Krawczyk PM, Lattuada M, Füchslin RM, Petri-Fink A, Scheidegger S. The Use of Survival Dose-Rate Dependencies as Theoretical Discrimination Criteria for In-Silico Dynamic Radiobiological Models. Dose Response 2024; 22:15593258241279906. [PMID: 39224699 PMCID: PMC11367615 DOI: 10.1177/15593258241279906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/05/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction Cell repair dynamics are crucial in optimizing anti-cancer therapies. Various assays (eg, comet assay and γ-H2AX) assess post-radiation repair kinetics, but interpreting such data is challenging and model-based data analyses are required. However, ambiguities in parameter calibration remain an unsolved challenge. To address this, we propose combining survival dose-rate effects with computer simulations to gain knowledge about repair kinetics. Methods After a literature review, theoretical discriminators based on common fractionation/dose-rate-related effects were defined to discard unrealistic model dynamics. The Multi-Hit Repair (MHR) model was calibrated with canine osteosarcoma Abrams cell line data to study the discriminators' efficacy in scenarios with limited survival data. Additionally, survival dose-rate-dependent data from the human SiHa cervical cancer cell line were used to illustrate the survival behavior at diverse dose-rates and the capability of the MHR to model these data. Results SiHa data confirmed the validity of the proposed discriminators. The discriminators filtered 99% of parameter sets, improving the calibration of Abrams cells data. Furthermore, results from both cell lines may hint universal aspects of cellular repair. Conclusions Dose-rate theoretical discrimination criteria are an effective method to understand repair kinetics and improve radiobiological model calibration. Moreover, this methodology may be used to analyze diverse biological data using dynamic models in-silico.
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Affiliation(s)
- Sergio Mingo Barba
- School of Engineering, Zürich University of Applied Sciences (ZHAW), Winterthur, Switzerland
- Chemistry Department, University of Fribourg, Fribourg, Switzerland
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Fernando Lobo-Cerna
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Przemek M. Krawczyk
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Marco Lattuada
- Chemistry Department, University of Fribourg, Fribourg, Switzerland
| | - Rudolf M. Füchslin
- School of Engineering, Zürich University of Applied Sciences (ZHAW), Winterthur, Switzerland
- European Centre for Living Technology, Venice, Italy
| | - Alke Petri-Fink
- Chemistry Department, University of Fribourg, Fribourg, Switzerland
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Stephan Scheidegger
- School of Engineering, Zürich University of Applied Sciences (ZHAW), Winterthur, Switzerland
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2
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Cao Y, Zhou X, Nie Q, Zhang J. Inhibition of the thioredoxin system for radiosensitization therapy of cancer. Eur J Med Chem 2024; 268:116218. [PMID: 38387331 DOI: 10.1016/j.ejmech.2024.116218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/28/2024] [Accepted: 02/04/2024] [Indexed: 02/24/2024]
Abstract
Radiotherapy (RT) stands as a cornerstone in the clinical armamentarium against various cancers due to its proven efficacy. However, the intrinsic radiation resistance exhibited by cancer cells, coupled with the adverse effects of RT on normal tissues, often compromises its therapeutic potential and leads to unwanted side effects. This comprehensive review aims to consolidate our understanding of how radiosensitizers inhibit the thioredoxin (Trx) system in cellular contexts. Notable radiosensitizers, including gold nanoparticles (GNPs), gold triethylphosphine cyanide ([Au(SCN) (PEt3)]), auranofin, ceria nanoparticles (CONPs), curcumin and its derivatives, piperlongamide, indolequinone derivatives, micheliolide, motexafin gadolinium, and ethane selenide selenidazole derivatives (SeDs), are meticulously elucidated in terms of their applications in radiotherapy. In this review, the sensitization mechanisms and the current research progress of these radiosensitizers are discussed in detail, with the overall aim of providing valuable insights for the judicious application of Trx system inhibitors in the field of cancer radiosensitization therapy.
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Affiliation(s)
- Yisheng Cao
- School of Pharmacy, State Key Laboratory of Applied Organic Chemistry, and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Xiedong Zhou
- School of Pharmacy, State Key Laboratory of Applied Organic Chemistry, and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Qiuying Nie
- School of Pharmacy, State Key Laboratory of Applied Organic Chemistry, and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Junmin Zhang
- School of Pharmacy, State Key Laboratory of Applied Organic Chemistry, and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China.
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3
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Scott RT, Sanders LM, Antonsen EL, Hastings JJA, Park SM, Mackintosh G, Reynolds RJ, Hoarfrost AL, Sawyer A, Greene CS, Glicksberg BS, Theriot CA, Berrios DC, Miller J, Babdor J, Barker R, Baranzini SE, Beheshti A, Chalk S, Delgado-Aparicio GM, Haendel M, Hamid AA, Heller P, Jamieson D, Jarvis KJ, Kalantari J, Khezeli K, Komarova SV, Komorowski M, Kothiyal P, Mahabal A, Manor U, Garcia Martin H, Mason CE, Matar M, Mias GI, Myers JG, Nelson C, Oribello J, Parsons-Wingerter P, Prabhu RK, Qutub AA, Rask J, Saravia-Butler A, Saria S, Singh NK, Snyder M, Soboczenski F, Soman K, Van Valen D, Venkateswaran K, Warren L, Worthey L, Yang JH, Zitnik M, Costes SV. Biomonitoring and precision health in deep space supported by artificial intelligence. NAT MACH INTELL 2023. [DOI: 10.1038/s42256-023-00617-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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4
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Cekanaviciute E, Tran D, Nguyen H, Lopez Macha A, Pariset E, Langley S, Babbi G, Malkani S, Penninckx S, Schisler JC, Nguyen T, Karpen GH, Costes SV. Mouse genomic associations with in vitro sensitivity to simulated space radiation. LIFE SCIENCES IN SPACE RESEARCH 2023; 36:47-58. [PMID: 36682829 DOI: 10.1016/j.lssr.2022.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 06/17/2023]
Abstract
Exposure to ionizing radiation is considered by NASA to be a major health hazard for deep space exploration missions. Ionizing radiation sensitivity is modulated by both genomic and environmental factors. Understanding their contributions is crucial for designing experiments in model organisms, evaluating the risk of deep space (i.e. high-linear energy transfer, or LET, particle) radiation exposure in astronauts, and also selecting therapeutic irradiation regimes for cancer patients. We identified single nucleotide polymorphisms in 15 strains of mice, including 10 collaborative cross model strains and 5 founder strains, associated with spontaneous and ionizing radiation-induced in vitro DNA damage quantified based on immunofluorescent tumor protein p53 binding protein (53BP1) positive nuclear foci. Statistical analysis suggested an association with pathways primarily related to cellular signaling, metabolism, tumorigenesis and nervous system damage. We observed different genomic associations in early (4 and 8 h) responses to different LET radiation, while later (24 hour) DNA damage responses showed a stronger overlap across all LETs. Furthermore, a subset of pathways was associated with spontaneous DNA damage, suggesting 53BP1 positive foci as a potential biomarker for DNA integrity in mouse models. Our results suggest several mouse strains as new models to further study the impact of ionizing radiation and validate the identified genetic loci. We also highlight the importance of future human in vitro studies to refine the association of genes and pathways with the DNA damage response to ionizing radiation and identify targets for space travel countermeasures.
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Affiliation(s)
- Egle Cekanaviciute
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Duc Tran
- Department of Computer Science and Engineering, University of Nevada, Reno, NV 89557, USA
| | - Hung Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, NV 89557, USA
| | - Alejandra Lopez Macha
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Blue Marble Space Institute of Science, 600 1st Avenue, 1st Floor, Seattle, WA 98104, USA
| | - Eloise Pariset
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Universities Space Research Association, 615 National Avenue, Mountain View, CA 94043, USA
| | - Sasha Langley
- Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA, and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Giulia Babbi
- Bologna Biocomputing Group, FABIT, University of Bologna, Via Belmeloro 6, Bologna, Italy
| | - Sherina Malkani
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Blue Marble Space Institute of Science, 600 1st Avenue, 1st Floor, Seattle, WA 98104, USA
| | - Sébastien Penninckx
- Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA, and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA; Medical Physics Department, Jules Bordet Institute, Université Libre de Bruxelles, 90 Rue Meylemeersch, 1070 Brussels, Belgium
| | - Jonathan C Schisler
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, NC 27599, USA
| | - Tin Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, NV 89557, USA
| | - Gary H Karpen
- Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA, and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
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Ternad I, Penninckx S, Lecomte V, Vangijzegem T, Conrard L, Lucas S, Heuskin AC, Michiels C, Muller RN, Stanicki D, Laurent S. Advances in the Mechanistic Understanding of Iron Oxide Nanoparticles' Radiosensitizing Properties. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:201. [PMID: 36616111 PMCID: PMC9823929 DOI: 10.3390/nano13010201] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/16/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Among the plethora of nanosystems used in the field of theranostics, iron oxide nanoparticles (IONPs) occupy a central place because of their biocompatibility and magnetic properties. In this study, we highlight the radiosensitizing effect of two IONPs formulations (namely 7 nm carboxylated IONPs and PEG5000-IONPs) on A549 lung carcinoma cells when exposed to 225 kV X-rays after 6 h, 24 h and 48 h incubation. The hypothesis that nanoparticles exhibit their radiosensitizing effect by weakening cells through the inhibition of detoxification enzymes was evidenced by thioredoxin reductase activity monitoring. In particular, a good correlation between the amplification effect at 2 Gy and the residual activity of thioredoxin reductase was observed, which is consistent with previous observations made for gold nanoparticles (NPs). This emphasizes that NP-induced radiosensitization does not result solely from physical phenomena but also results from biological events.
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Affiliation(s)
- Indiana Ternad
- General, Organic and Biomedical Chemistry Unit, NMR and Molecular Imaging Laboratory, University of Mons (UMONS), B-7000 Mons, Belgium
| | - Sebastien Penninckx
- Medical Physics Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), B-1070 Brussels, Belgium
| | - Valentin Lecomte
- General, Organic and Biomedical Chemistry Unit, NMR and Molecular Imaging Laboratory, University of Mons (UMONS), B-7000 Mons, Belgium
| | - Thomas Vangijzegem
- General, Organic and Biomedical Chemistry Unit, NMR and Molecular Imaging Laboratory, University of Mons (UMONS), B-7000 Mons, Belgium
| | - Louise Conrard
- Center for Microscopy and Molecular Imaging (CMMI), B-6041 Gosselies, Belgium
| | - Stéphane Lucas
- Namur Research Institute for Life Sciences (NARILIS), University of Namur, B-5000 Namur, Belgium
| | - Anne-Catherine Heuskin
- Namur Research Institute for Life Sciences (NARILIS), University of Namur, B-5000 Namur, Belgium
| | - Carine Michiels
- Namur Research Institute for Life Sciences (NARILIS), University of Namur, B-5000 Namur, Belgium
| | - Robert N. Muller
- General, Organic and Biomedical Chemistry Unit, NMR and Molecular Imaging Laboratory, University of Mons (UMONS), B-7000 Mons, Belgium
- Center for Microscopy and Molecular Imaging (CMMI), B-6041 Gosselies, Belgium
| | - Dimitri Stanicki
- General, Organic and Biomedical Chemistry Unit, NMR and Molecular Imaging Laboratory, University of Mons (UMONS), B-7000 Mons, Belgium
| | - Sophie Laurent
- General, Organic and Biomedical Chemistry Unit, NMR and Molecular Imaging Laboratory, University of Mons (UMONS), B-7000 Mons, Belgium
- Center for Microscopy and Molecular Imaging (CMMI), B-6041 Gosselies, Belgium
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6
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Zaharieva EK, Sasatani M, Kamiya K. Kinetics of DNA Repair Under Chronic Irradiation at Low and Medium Dose Rates in Repair Proficient and Repair Compromised Normal Fibroblasts. Radiat Res 2021; 197:332-349. [PMID: 34958666 DOI: 10.1667/rade-21-00158.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 11/17/2021] [Indexed: 11/03/2022]
Abstract
We present time and dose dependencies for the formation of 53BP1 and γH2AX DNA damage repair foci after chronic radiation exposure at dose rates of 140, 250 and 450 mGy/day from 3 to 96 h, in human and mouse repair proficient and ATM or DNA-PK deficient repair compromised cell models. We describe the time/dose-response curves using a mathematical equation which contains a linear component for the induction of DNA damage repair foci after irradiation, and an exponential component for their resolution. We show that under conditions of chronic irradiation at low and medium dose rates, the processes of DNA double-strand breaks (DSBs) induction and repair establish an equilibrium, which in repair proficient cells manifests as a plateau-shaped dose-response where the plateau is reached within the first 24 h postirradiation, and its height is proportionate to the radiation dose rate. In contrast, in repair compromised cells, where the rate of repair may be exceeded by the DSB induction rate, DNA damage accumulates with time of exposure and total absorbed dose. In addition, we discuss the biological meaning of the observed dependencies by presenting the frequency of micronuclei formation under the same irradiation conditions as a marker of radiation-induced genomic instability. We believe that the data and analysis presented here shed light on the kinetics of DNA repair under chronic radiation and are useful for future studies in the low-to-medium dose rate range.
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Affiliation(s)
- Elena K Zaharieva
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Megumi Sasatani
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Kenji Kamiya
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
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7
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Penninckx S, Pariset E, Cekanaviciute E, Costes SV. Quantification of radiation-induced DNA double strand break repair foci to evaluate and predict biological responses to ionizing radiation. NAR Cancer 2021; 3:zcab046. [PMID: 35692378 PMCID: PMC8693576 DOI: 10.1093/narcan/zcab046] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/08/2021] [Accepted: 12/17/2021] [Indexed: 08/08/2023] Open
Abstract
Radiation-induced foci (RIF) are nuclear puncta visualized by immunostaining of proteins that regulate DNA double-strand break (DSB) repair after exposure to ionizing radiation. RIF are a standard metric for measuring DSB formation and repair in clinical, environmental and space radiobiology. The time course and dose dependence of their formation has great potential to predict in vivo responses to ionizing radiation, predisposition to cancer and probability of adverse reactions to radiotherapy. However, increasing complexity of experimentally and therapeutically setups (charged particle, FLASH …) is associated with several confounding factors that must be taken into account when interpreting RIF values. In this review, we discuss the spatiotemporal characteristics of RIF development after irradiation, addressing the common confounding factors, including cell proliferation and foci merging. We also describe the relevant endpoints and mathematical models that enable accurate biological interpretation of RIF formation and resolution. Finally, we discuss the use of RIF as a biomarker for quantification and prediction of in vivo radiation responses, including important caveats relating to the choice of the biological endpoint and the detection method. This review intends to help scientific community design radiobiology experiments using RIF as a key metric and to provide suggestions for their biological interpretation.
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Affiliation(s)
- Sébastien Penninckx
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Medical Physics Department, Jules Bordet Institute, Université Libre de Bruxelles, 1 Rue Héger-Bordet, 1000 Brussels, Belgium
| | - Eloise Pariset
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Universities Space Research Association, 615 National Avenue, Mountain View, CA 94043, USA
| | - Egle Cekanaviciute
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Sylvain V Costes
- To whom correspondence should be addressed. Tel: +1 650 604 5343;
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8
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Afshinnekoo E, Scott RT, MacKay MJ, Pariset E, Cekanaviciute E, Barker R, Gilroy S, Hassane D, Smith SM, Zwart SR, Nelman-Gonzalez M, Crucian BE, Ponomarev SA, Orlov OI, Shiba D, Muratani M, Yamamoto M, Richards SE, Vaishampayan PA, Meydan C, Foox J, Myrrhe J, Istasse E, Singh N, Venkateswaran K, Keune JA, Ray HE, Basner M, Miller J, Vitaterna MH, Taylor DM, Wallace D, Rubins K, Bailey SM, Grabham P, Costes SV, Mason CE, Beheshti A. Fundamental Biological Features of Spaceflight: Advancing the Field to Enable Deep-Space Exploration. Cell 2021; 183:1162-1184. [PMID: 33242416 DOI: 10.1016/j.cell.2020.10.050] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022]
Abstract
Research on astronaut health and model organisms have revealed six features of spaceflight biology that guide our current understanding of fundamental molecular changes that occur during space travel. The features include oxidative stress, DNA damage, mitochondrial dysregulation, epigenetic changes (including gene regulation), telomere length alterations, and microbiome shifts. Here we review the known hazards of human spaceflight, how spaceflight affects living systems through these six fundamental features, and the associated health risks of space exploration. We also discuss the essential issues related to the health and safety of astronauts involved in future missions, especially planned long-duration and Martian missions.
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Affiliation(s)
- Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ryan T Scott
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Matthew J MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Eloise Pariset
- Universities Space Research Association (USRA), Mountain View, CA 94043, USA; Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Egle Cekanaviciute
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Richard Barker
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Simon Gilroy
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | | | - Scott M Smith
- Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX 77058, USA
| | - Sara R Zwart
- Department of Preventive Medicine and Community Health, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mayra Nelman-Gonzalez
- KBR, Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX 77058, USA
| | - Brian E Crucian
- Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX 77058, USA
| | - Sergey A Ponomarev
- Institute for the Biomedical Problems, Russian Academy of Sciences, 123007 Moscow, Russia
| | - Oleg I Orlov
- Institute for the Biomedical Problems, Russian Academy of Sciences, 123007 Moscow, Russia
| | - Dai Shiba
- JEM Utilization Center, Human Spaceflight Technology Directorate, Japan Aerospace Exploration Agency (JAXA), Ibaraki 305-8505, Japan
| | - Masafumi Muratani
- Transborder Medical Research Center, and Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Masayuki Yamamoto
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan; Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Stephanie E Richards
- Bionetics, NASA Kennedy Space Center, Kennedy Space Center, Merritt Island, FL 32899, USA
| | - Parag A Vaishampayan
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jacqueline Myrrhe
- European Space Agency, Research and Payloads Group, Data Exploitation and Utilisation Strategy Office, 2200 AG Noordwijk, the Netherlands
| | - Eric Istasse
- European Space Agency, Research and Payloads Group, Data Exploitation and Utilisation Strategy Office, 2200 AG Noordwijk, the Netherlands
| | - Nitin Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - Jessica A Keune
- Space Medicine Operations Division, NASA Johnson Space Center, Houston, TX 77058, USA
| | - Hami E Ray
- ASRC Federal Space and Defense, Inc., Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Mathias Basner
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jack Miller
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Martha Hotz Vitaterna
- Center for Sleep and Circadian Biology, Northwestern University, Evanston, IL 60208, USA; Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Deanne M Taylor
- Department of Biomedical Informatics, The Children's Hospital of Philadelphia, PA 19104, USA; Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Douglas Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathleen Rubins
- Astronaut Office, NASA Johnson Space Center, Houston, TX 77058, USA
| | - Susan M Bailey
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - Peter Grabham
- Center for Radiological Research, Department of Oncology, College of Physicians and Surgeons, Columbia University, New York, NY 10027, USA.
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA; The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, NY 10021, USA.
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Rad-Bio-App: a discovery environment for biologists to explore spaceflight-related radiation exposures. NPJ Microgravity 2021; 7:15. [PMID: 33976230 PMCID: PMC8113475 DOI: 10.1038/s41526-021-00143-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 03/29/2021] [Indexed: 02/07/2023] Open
Abstract
In addition to microgravity, spaceflight simultaneously exposes biology to a suite of other stimuli. For example, in space, organisms experience ionizing radiation environments that significantly differ in both quality and quantity from those normally experienced on Earth. However, data on radiation exposure during space missions is often complex to access and to understand, limiting progress towards defining how radiation affects organisms against the unique background of spaceflight. To help address this challenge, we have developed the Rad-Bio-App. This web-accessible database imports radiation metadata from experiments archived in NASA’s GeneLab data repository, and then allows the user to explore these experiments both in the context of their radiation exposure and through their other metadata and results. Rad-Bio-App provides an easy-to-use, graphically-driven environment to enable both radiation biologists and non-specialist researchers to visualize, and understand the impact of ionizing radiation on various biological systems in the context of spaceflight.
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Penninckx S, Pariset E, Acuna AU, Lucas S, Costes SV. Considering Cell Proliferation to Optimize Detection of Radiation-Induced 53BP1 Positive Foci in 15 Mouse Strains Ex Vivo. Radiat Res 2021; 195:47-59. [PMID: 33181852 DOI: 10.1667/rade-20-00165.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/05/2020] [Indexed: 11/03/2022]
Abstract
Due to high metabolic activity, proliferating cells continuously generate free radicals, which induce DNA double-strand breaks (DSB). Fluorescently tagged nuclear foci of DNA repair protein 53 binding protein-1 (53BP1) are used as a standard metric for measuring DSB formation at baseline and in response to environmental insults such as radiation. Here we demonstrate that the background level of spontaneous 53BP1+ foci formation can be modeled mathematically as a function of cell confluence, which is a metric of their proliferation rate. This model was validated using spontaneous 53BP1+ foci data from 72 cultures of primary skin fibroblasts derived from 15 different strains of mice, showing a ∼10-fold decrease from low to full confluence that is independent of mouse strain. On the other hand, the baseline level of spontaneous 53BP1+ foci in a fully confluent cell population was strain-dependent, suggesting genomic associations, and correlated with radiation sensitivity based on previous measurements in the same cell lines. Finally, we have developed an online open-access tool to correct for the effect of cell confluence on 53BP1+ foci-based quantification of DSB. This tool provides guidelines for the number of cells required to reach statistical significance for the detection of DSB induced by low doses of ionizing radiation as a function of confluence and time postirradiation.
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Affiliation(s)
- Sébastien Penninckx
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720.,Namur Research Institute for Life Science (NARILIS - LARN), University of Namur, 5000 Namur, Belgium
| | - Eloise Pariset
- Universities Space Research Association (USRA), Mountain View, California 94043.,Space Biosciences Division, NASA Ames Research Center, Mountain View, California 94035
| | - Ana Uriarte Acuna
- Space Biosciences Division, NASA Ames Research Center, Mountain View, California 94035.,Wyle Laboratories, KBR, Inc., Houston, Texas 77002
| | - Stephane Lucas
- Namur Research Institute for Life Science (NARILIS - LARN), University of Namur, 5000 Namur, Belgium
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Mountain View, California 94035
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11
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A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression. Life (Basel) 2021; 11:life11020115. [PMID: 33546472 PMCID: PMC7913660 DOI: 10.3390/life11020115] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/31/2021] [Accepted: 01/31/2021] [Indexed: 12/19/2022] Open
Abstract
The use of high linear energy transfer (LET) ionizing radiation (IR) is progressively being incorporated in radiation therapy due to its precise dose localization and high relative biological effectiveness. At the same time, these benefits of particle radiation become a high risk for astronauts in the case of inevitable cosmic radiation exposure. Nonetheless, DNA Damage Response (DDR) activated via complex DNA damage in healthy tissue, occurring from such types of radiation, may be instrumental in the induction of various chronic and late effects. An approach to elucidating the possible underlying mechanisms is studying alterations in gene expression. To this end, we identified differentially expressed genes (DEGs) in high Z and high energy (HZE) particle-, γ-ray- and X-ray-exposed healthy human tissues, utilizing microarray data available in public repositories. Differential gene expression analysis (DGEA) was conducted using the R programming language. Consequently, four separate meta-analyses were conducted, after DEG lists were grouped depending on radiation type, radiation dose and time of collection post-irradiation. To highlight the biological background of each meta-analysis group, functional enrichment analysis and biological network construction were conducted. For HZE particle exposure at 8–24 h post-irradiation, the most interesting finding is the variety of DNA repair mechanisms that were downregulated, a fact that is probably correlated with complex DNA damage formation. Simultaneously, after X-ray exposure during the same hours after irradiation, DNA repair mechanisms continue to take place. Finally, in a further comparison of low- and high-LET radiation effects, the most prominent result is that autophagy mechanisms seem to persist and that adaptive immune induction seems to be present. Such bioinformatics approaches may aid in obtaining an overview of the cellular response to high-LET particles. Understanding these response mechanisms can consequently aid in the development of countermeasures for future space missions and ameliorate heavy ion treatments.
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12
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Berrios DC, Galazka J, Grigorev K, Gebre S, Costes SV. NASA GeneLab: interfaces for the exploration of space omics data. Nucleic Acids Res 2021; 49:D1515-D1522. [PMID: 33080015 PMCID: PMC7778922 DOI: 10.1093/nar/gkaa887] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/16/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
The mission of NASA's GeneLab database (https://genelab.nasa.gov/) is to collect, curate, and provide access to the genomic, transcriptomic, proteomic and metabolomic (so-called 'omics') data from biospecimens flown in space or exposed to simulated space stressors, maximizing their utilization. This large collection of data enables the exploration of molecular network responses to space environments using a systems biology approach. We review here the various components of the GeneLab platform, including the new data repository web interface, and the GeneLab Online Data Entry (GEODE) web portal, which will support the expansion of the database in the future to include companion non-omics assay data. We discuss our design for GEODE, particularly how it promotes investigators providing more accurate metadata, reducing the curation effort required of GeneLab staff. We also introduce here a new GeneLab Application Programming Interface (API) specifically designed to support tools for the visualization of processed omics data. We review the outreach efforts by GeneLab to utilize the spaceflight data in the repository to generate novel discoveries and develop new hypotheses, including spearheading data analysis working groups, and a high school student training program. All these efforts are aimed ultimately at supporting precision risk management for human space exploration.
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Affiliation(s)
| | | | | | - Samrawit Gebre
- KBR/NASA Ames Research Center, Moffett Field, CA 94035, USA
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13
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DNA Damage Baseline Predicts Resilience to Space Radiation and Radiotherapy. Cell Rep 2020; 33:108434. [PMID: 33242409 PMCID: PMC7784531 DOI: 10.1016/j.celrep.2020.108434] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/22/2020] [Accepted: 11/04/2020] [Indexed: 12/11/2022] Open
Abstract
Deep space exploration will require real-time, minimally invasive monitoring of astronaut health to mitigate the potential health impairments caused by space radiation and microgravity. Genotoxic stress in humans can be monitored by quantifying the amount of DNA double-strand breaks (DSBs) in immune cells from a simple finger prick. In a cohort of 674 healthy donors, we show that the endogenous level of DSBs increases with age and with latent cytomegalovirus infection. To map the range of human responses to space radiation, we then study DSB induction and repair in immune cells from 319 healthy donors after the cells are exposed to galactic cosmic ray components and lymphocytes from 30 cancer patients after radiotherapy. Individuals with low baseline DSB have fewer clinical complications, enhanced DNA damage repair responses, and a functional dose-dependent cytokine response in healthy donor cells. This supports the use of DSB monitoring for health resilience in space.
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14
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Penninckx S, Heuskin AC, Michiels C, Lucas S. Gold Nanoparticles as a Potent Radiosensitizer: A Transdisciplinary Approach from Physics to Patient. Cancers (Basel) 2020; 12:E2021. [PMID: 32718058 PMCID: PMC7464732 DOI: 10.3390/cancers12082021] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 12/14/2022] Open
Abstract
Over the last decade, a growing interest in the improvement of radiation therapies has led to the development of gold-based nanomaterials as radiosensitizer. Although the radiosensitization effect was initially attributed to a dose enhancement mechanism, an increasing number of studies challenge this mechanistic hypothesis and evidence the importance of chemical and biological contributions. Despite extensive experimental validation, the debate regarding the mechanism(s) of gold nanoparticle radiosensitization is limiting its clinical translation. This article reviews the current state of knowledge by addressing how gold nanoparticles exert their radiosensitizing effects from a transdisciplinary perspective. We also discuss the current and future challenges to go towards a successful clinical translation of this promising therapeutic approach.
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Affiliation(s)
- Sébastien Penninckx
- Research Center for the Physics of Matter and Radiation (PMR-LARN), Namur Research Institute For Life Sciences (NARILIS), University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium; (S.P.); (A.-C.H.); (S.L.)
| | - Anne-Catherine Heuskin
- Research Center for the Physics of Matter and Radiation (PMR-LARN), Namur Research Institute For Life Sciences (NARILIS), University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium; (S.P.); (A.-C.H.); (S.L.)
| | - Carine Michiels
- Unité de Recherche en Biologie Cellulaire (URBC), Namur Research Institute For Life Sciences (NARILIS), University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Stéphane Lucas
- Research Center for the Physics of Matter and Radiation (PMR-LARN), Namur Research Institute For Life Sciences (NARILIS), University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium; (S.P.); (A.-C.H.); (S.L.)
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