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Original Articles

Construction of dose prediction model and identification of sensitive genes for space radiation based on single-sample networks under spaceflight conditions

ORCID Icon, , ORCID Icon & ORCID Icon
Pages 777-790 | Received 22 Aug 2023, Accepted 01 Mar 2024, Published online: 12 Mar 2024

References

  • Abruzzese V, Matera I, Martinelli F, Carmosino M, Koshal P, Milella L, Bisaccia F, Ostuni A. 2021. Effect of quercetin on ABCC6 transporter: implication in HepG2 migration. Int J Mol Sci. 22(8):3871. doi:10.3390/ijms22083871
  • Andersson B, Langen B, Liu P, Dávila López M. 2023. Development of a machine learning framework for radiation biomarker discovery and absorbed dose prediction. Front Oncol. 13:1156009. doi:10.3389/fonc.2023.1156009
  • Berrios DC, Galazka J, Grigorev K, Gebre S, Costes SV. 2021. NASA GeneLab: interfaces for the exploration of space omics data. Nucleic Acids Res. 49(D1):D1515–D1522. doi:10.1093/nar/gkaa887
  • Boswell-Casteel RC, Fukuda Y, Schuetz JD. 2017. ABCB6, an ABC transporter impacting drug response and disease. AAPS J. 20(1):8. doi:10.1208/s12248-017-0165-6
  • Cannell IG, Merrick KA, Morandell S, Zhu CQ, Braun CJ, Grant RA, Cameron ER, Tsao MS, Hemann MT, Yaffe MB. 2015. A pleiotropic RNA-binding protein controls distinct cell cycle checkpoints to drive resistance of p53-defective tumors to chemotherapy. Cancer Cell. 28(5):623–637. doi:10.1016/j.ccell.2015.09.009
  • Chastkofsky MI, Bie W, Ball-Kell SM, He YY, Tyner AL. 2015. Protein tyrosine kinase 6 regulates UVB-induced signaling and tumorigenesis in mouse skin. J Invest Dermatol. 135(10):2492–2501. doi:10.1038/jid.2015.166
  • Chen YK, Tan YY, Yao M, Lin HC, Tsai MH, Li YY, Hsu YJ, Huang TT, Chang CW, Cheng CM, et al. 2021. Bisphenol A-induced DNA damages promote to lymphoma progression in human lymphoblastoid cells through aberrant CTNNB1 signaling pathway. iScience. 24(8):102888. doi:10.1016/j.isci.2021.102888
  • Cheng C, Cai Y, Liu X, Wu Y, Cheng Q, Wu Y, Wu Z. 2022. KHSRP modulated cell proliferation and cell cycle via regulating PPP2CA and p27 expression in Wilms tumor. Cell Signal. 100:110447. doi:10.1016/j.cellsig.2022.110447
  • Crucian B, Lee P, Stowe R, Jones J, Effenhauser R, Widen R, Sams C. 2007. Immune system changes during simulated planetary exploration on Devon Island, high arctic. BMC Immunol. 8(1):7. doi:10.1186/1471-2172-8-7
  • Cucinotta FA, Kim MH, Willingham V, George KA. 2008. Physical and biological organ dosimetry analysis for International Space Station astronauts. Radiat Res. 170(1):127–138. doi:10.1667/RR1330.1
  • Farrell AW, Halliday GM, Lyons JG. 2018. Brahma deficiency in keratinocytes promotes UV carcinogenesis by accelerating the escape from cell cycle arrest and the formation of DNA photolesions. J Dermatol Sci. 92(3):254–263. doi:10.1016/j.jdermsci.2018.11.006
  • Garrett-Bakelman FE, Darshi M, Green SJ, Gur RC, Lin L, Macias BR, McKenna MJ, Meydan C, Mishra T, Nasrini J, et al. 2019. The NASA Twins Study: a multidimensional analysis of a year-long human spaceflight. Science. 364(6436):eaau8650. doi:10.1126/science.aau8650
  • GeneLab. 2024. Environmental data for spaceflight experiments; [accessed 2024 Jan 15]. https://genelab.nasa.gov/environmental/radiation.
  • Gómez X, Sanon S, Zambrano K, Asquel S, Bassantes M, Morales JE, Otáñez G, Pomaquero C, Villarroel S, Zurita A, et al. 2021. Key points for the development of antioxidant cocktails to prevent cellular stress and damage caused by reactive oxygen species (ROS) during manned space missions. NPJ Microgravity. 7(1):35. doi:10.1038/s41526-021-00162-8
  • Guo WF, Yu X, Shi QQ, Liang J, Zhang SW, Zeng T. 2021. Performance assessment of sample-specific network control methods for bulk and single-cell biological data analysis. PLoS Comput Biol. 17(5):e1008962. doi:10.1371/journal.pcbi.1008962
  • Houtgraaf JH, Versmissen J, van der Giessen WJ. 2006. A concise review of DNA damage checkpoints and repair in mammalian cells. Cardiovasc Revasc Med. 7(3):165–172. doi:10.1016/j.carrev.2006.02.002
  • Hu Y, Hellweg CE, Baumstark-Khan C, Reitz G, Lau P. 2014. Cell cycle delay in murine pre-osteoblasts is more pronounced after exposure to high-LET compared to low-LET radiation. Radiat Environ Biophys. 53(1):73–81. doi:10.1007/s00411-013-0499-0
  • Huang Y, Chang X, Zhang Y, Chen L, Liu X. 2021. Disease characterization using a partial correlation-based sample-specific network. Brief Bioinform. 22(3):bbaa062. doi:10.1093/bib/bbaa062
  • Jiang Y, Song L, Lin Y, Nowialis P, Gao Q, Li T, Li B, Mao X, Song Q, Xing C, et al. 2023. ROS-mediated SRMS activation confers platinum resistance in ovarian cancer. Oncogene. 42(20):1672–1684. doi:10.1038/s41388-023-02679-6
  • Kuijjer ML, Tung MG, Yuan G, Quackenbush J, Glass K. 2019. Estimating sample-specific regulatory networks. iScience. 14:226–240. doi:10.1016/j.isci.2019.03.021
  • Kumar M, Molkentine D, Molkentine J, Bridges K, Xie T, Yang L, Hefner A, Gao M, Bahri R, Dhawan A, et al. 2021. Inhibition of histone acetyltransferase function radiosensitizes CREBBP/EP300 mutants via repression of homologous recombination, potentially targeting a gain of function. Nat Commun. 12(1):6340. doi:10.1038/s41467-021-26570-8
  • Kumar V, Santhosh Kumar TR, Kartha CC. 2019. Mitochondrial membrane transporters and metabolic switch in heart failure. Heart Fail Rev. 24(2):255–267. doi:10.1007/s10741-018-9756-2
  • Lee M, Daniels MJ, Garnett MJ, Venkitaraman AR. 2011. A mitotic function for the high-mobility group protein HMG20b regulated by its interaction with the BRC repeats of the BRCA2 tumor suppressor. Oncogene. 30(30):3360–3369. doi:10.1038/onc.2011.55
  • Li HH, Wang YW, Chen R, Zhou B, Ashwell JD, Fornace AJJr. 2015. Ionizing radiation impairs T cell activation by affecting metabolic reprogramming. Int J Biol Sci. 11(7):726–736. doi:10.7150/ijbs.12009
  • Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15(12):550. doi:10.1186/s13059-014-0550-8
  • Lundberg SM, Lee S-I. 2017. A unified approach to interpreting model predictions. In: Guyon I, Luxburg UV, Bengio S, Wallach H, Fergus R, Vishwanathan S, Garnett R, editors. 31st Annual Conference on Neural Information Processing Systems (NIPS). Vol. 30. Long Beach (CA): Curran Associates Inc.
  • Macaeva E, Mysara M, De Vos WH, Baatout S, Quintens R. 2019. Gene expression-based biodosimetry for radiological incidents: assessment of dose and time after radiation exposure. Int J Radiat Biol. 95(1):64–75. doi:10.1080/09553002.2018.1511926
  • Martin P. 2015. NASA’s efforts to manage health and human performance risks for space exploration. Office of Inspector General. Report No. IG-16-003. 15.
  • McBride WH, Iwamoto KS, Syljuasen R, Pervan M, Pajonk F. 2003. The role of the ubiquitin/proteasome system in cellular responses to radiation. Oncogene. 22(37):5755–5773. doi:10.1038/sj.onc.1206676
  • McDonald JT, Stainforth R, Miller J, Cahill T, da Silveira WA, Rathi KS, Hardiman G, Taylor D, Costes SV, Chauhan V, et al. 2020. NASA GeneLab platform utilized for biological response to space radiation in animal models. Cancers. 12(2):381. doi:10.3390/cancers12020381
  • Moreno-Oñate M, Herrero-Ruiz AM, García-Dominguez M, Cortés-Ledesma F, Ruiz JF. 2020. RanBP2-mediated SUMOylation promotes human DNA polymerase lambda nuclear localization and DNA repair. J Mol Biol. 432(13):3965–3979. doi:10.1016/j.jmb.2020.03.020
  • Moreno-Villanueva M, Wong M, Lu T, Zhang Y, Wu H. 2017. Interplay of space radiation and microgravity in DNA damage and DNA damage response. NPJ Microgravity. 3(1):14. doi:10.1038/s41526-017-0019-7
  • Mori N, Matsumoto Y, Okumoto M, Suzuki N, Yamate J. 2001. Variations in Prkdc encoding the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) and susceptibility to radiation-induced apoptosis and lymphomagenesis. Oncogene. 20(28):3609–3619. doi:10.1038/sj.onc.1204497
  • Mountford PJ, Temperton DH. 1992. Recommendations of the International Commission on Radiological Protection (ICRP) 1990. Eur J Nucl Med. 19(2):77–79. doi:10.1007/BF00184120
  • Ohnishi K, Ohnishi T. 2004. The biological effects of space radiation during long stays in space. Biol Sci Space. 18(4):201–205. doi:10.2187/bss.18.201
  • Özelbaykal B, Öğretmenoğlu G, Gedik Ş. 2022. The effects of space radiation and microgravity on ocular structures. Turk J Ophthalmol. 52(1):57–63. doi:10.4274/tjo.galenos.2021.29566
  • Radić M, Šoštar M, Weber I, Ćetković H, Slade N, Herak Bosnar M. 2020. The subcellular localization and oligomerization preferences of NME1/NME2 upon radiation-induced DNA damage. Int J Mol Sci. 21(7):2363. doi:10.3390/ijms21072363
  • Ray S, Gebre S, Fogle H, Berrios DC, Tran PB, Galazka JM, Costes SV. 2019. GeneLab: Omics database for spaceflight experiments. Bioinformatics. 35(10):1753–1759. doi:10.1093/bioinformatics/bty884
  • Roh C. 2018. Metabolomics in radiation-induced biological dosimetry: a mini-review and a polyamine study. Biomolecules. 8(2):34. doi:10.3390/biom8020034
  • Sagkrioti E, Biz GM, Takan I, Asfa S, Nikitaki Z, Zanni V, Kars RH, Hellweg CE, Azzam EI, Logotheti S, et al. 2022. Radiation type- and dose-specific transcriptional responses across healthy and diseased mammalian tissues. Antioxidants. 11(11):2286. doi:10.3390/antiox11112286
  • Schmidt CK, Galanty Y, Sczaniecka-Clift M, Coates J, Jhujh S, Demir M, Cornwell M, Beli P, Jackson SP. 2015. Systematic E2 screening reveals a UBE2D–RNF138–CtIP axis promoting DNA repair. Nat Cell Biol. 17(11):1458–1470. doi:10.1038/ncb3260
  • Tucker JD, Divine GW, Grever WE, Thomas RA, Joiner MC, Smolinski JM, Auner GW. 2013. Gene expression-based dosimetry by dose and time in mice following acute radiation exposure. PLOS One. 8(12):e83390. doi:10.1371/journal.pone.0083390
  • Vaquer S, Cuyàs E, Rabadán A, González A, Fenollosa F, de la Torre R. 2014. Active transmembrane drug transport in microgravity: a validation study using an ABC transporter model. F1000Res. 3:201. doi:10.12688/f1000research.4909.1
  • Wang C, Chan DW, Hendrickson EA. 2023. Kinome-wide screening uncovers a role for bromodomain protein 3 in DNA double-stranded break repair. DNA Repair. 122:103445. doi:10.1016/j.dnarep.2022.103445
  • Waters KM, Tan R, Opresko LK, Quesenberry RD, Bandyopadhyay S, Chrisler WB, Weber TJ. 2009. Cellular dichotomy between anchorage-independent growth responses to bFGF and TPA reflects molecular switch in commitment to carcinogenesis. Mol Carcinog. 48(11):1059–1069. doi:10.1002/mc.20558
  • Wu Y, Zhang Y, Wang F, Ni Q, Li M. 2020. MiR-660-5p promotes the progression of hepatocellular carcinoma by interaction with YWHAH via PI3K/Akt signaling pathway. Biochem Biophys Res Commun. 531(4):480–489. doi:10.1016/j.bbrc.2020.07.034
  • Zhang H, Liu F, Zhou Y, Zhang Z. 2020. A hybrid method integrating an elite genetic algorithm with tabu search for the quadratic assignment problem. Inf Sci. 539:347–374. doi:10.1016/j.ins.2020.06.036
  • Zhao L, Gao Y, Mi D, Sun Y. 2016. Mining potential biomarkers associated with space flight in Caenorhabditis elegans experienced Shenzhou-8 mission with multiple feature selection techniques. Mutat Res. 791–792:27–34. doi:10.1016/j.mrfmmm.2016.08.002
  • Zhao L, Li Z, Huang B, Mi D, Xu D, Sun Y. 2024. Integrating evolutionarily conserved mechanism of response to radiation for exploring novel Caenorhabditis elegans radiation-responsive genes for estimation of radiation dose associated with spaceflight. Chemosphere. 351:141148. doi:10.1016/j.chemosphere.2024.141148

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