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Leberle J, Perona M, Choudhury A, Bellora N, Ibañez IL, Biolatti LV. Alternative splicing in human cells exposed to ionizing radiation: a comprehensive review of ex vivo and in vivo studies. Int J Radiat Biol 2025:1-10. [PMID: 40402085 DOI: 10.1080/09553002.2025.2505524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Revised: 03/02/2025] [Accepted: 05/02/2025] [Indexed: 05/23/2025]
Abstract
PURPOSE This study reviews how ionizing radiation (IR) induces alternative splicing (AS) in non-tumor and tumor cells under both ex vivo and in vivo irradiation conditions. The relevance and limitations of IR-induced AS in identifying potential biomarkers are highlighted for two main applications: biodosimetry and radiotherapy. CONCLUSIONS Radiation promotes alterations in AS, which may differentially affect the response in both tumor and non-tumor cells. This response can occur in genes that change their overall expression as well as in those that remain unaltered in response to IR. Although cis-regulators modulate AS, trans-regulators like splicing factors are more involved in the IR response. Variants of key genes involved in the DNA damage response (DDR) are regulated in non-tumor cells while they are often deregulated in tumor cells favoring radioresistance. Identifying IR-induced AS variants could enhance the sensitivity of biodosimeters for dose estimation and biomarkers for radiosensitivity, offering potential strategies to personalize radiotherapy and improve outcomes. New and advanced sequencing technologies will allow variant identification important for the field of radiobiological research.
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Affiliation(s)
- Jerónimo Leberle
- Laboratory of Radiobiology and Biodosimetry, Nuclear Medicine and Radiotherapy Center, Institute of Nuclear Technologies for Health (INTECNUS), National Atomic Energy Commission (CNEA), S.C. de Bariloche, Río Negro, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
| | - Marina Perona
- National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
- Department of Radiobiology, Nuclear Biochemistry Division, National Atomic Energy Commission (CNEA), San Martín, Buenos Aires, Argentina
| | - Ananya Choudhury
- Division of Cancer Sciences, The University of Manchester, The Christie Hospital NHS Foundation Trust, Manchester, UK
| | - Nicolas Bellora
- National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
- Laboratory of Computational Genomics, Nuclear Medicine and Radiotherapy Center, Institute of Nuclear Technologies for Health (INTECNUS), National Atomic Energy Commission (CNEA), S.C. de Bariloche, Río Negro, Argentina
| | - Irene L Ibañez
- Technology and Applications of Accelerators Assistant Management, Research and Applications Management, National Atomic Energy Commission (CNEA), Constituyentes Atomic Center, San Martín, Buenos Aires, Argentina
- Institute of Nanosciences and Nanotechnology (INN), National Atomic Energy Commission (CNEA) - National Scientific and Technical Research Council (CONICET), San Martín, Buenos Aires, Argentina
| | - Luisa V Biolatti
- Division of Cancer Sciences, The University of Manchester, The Christie Hospital NHS Foundation Trust, Manchester, UK
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Guardia GDA, Correa BR, Araujo PR, Qiao M, Burns S, Penalva LOF, Galante PAF. Proneural and mesenchymal glioma stem cells display major differences in splicing and lncRNA profiles. NPJ Genom Med 2020; 5:2. [PMID: 31969990 PMCID: PMC6965107 DOI: 10.1038/s41525-019-0108-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
Therapy resistance and recurrence in high-grade gliomas are driven by their populations of glioma stem cells (GSCs). Thus, detailed molecular characterization of GSCs is needed to develop more effective therapies. We conducted a study to identify differences in the splicing profile and expression of long non-coding RNAs in proneural and mesenchymal GSC cell lines. Genes related to cell cycle, DNA repair, cilium assembly, and splicing showed the most differences between GSC subgroups. We also identified genes distinctly associated with survival among patients of mesenchymal or proneural subgroups. We determined that multiple long non-coding RNAs with increased expression in mesenchymal GSCs are associated with poor survival of glioblastoma patients. In summary, our study established critical differences between proneural and mesenchymal GSCs in splicing profiles and expression of long non-coding RNA. These splicing isoforms and lncRNA signatures may contribute to the uniqueness of GSC subgroups, thus contributing to cancer phenotypes and explaining differences in therapeutic responses.
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Affiliation(s)
- Gabriela D A Guardia
- 1Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil
| | - Bruna R Correa
- 1Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil.,4Present Address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003 Catalonia Spain
| | - Patricia Rosa Araujo
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Mei Qiao
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Suzanne Burns
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Luiz O F Penalva
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA.,Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Pedro A F Galante
- 1Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil
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Wahba A, Ryan MC, Shankavaram UT, Camphausen K, Tofilon PJ. Radiation-induced alternative transcripts as detected in total and polysome-bound mRNA. Oncotarget 2017; 9:691-705. [PMID: 29416646 PMCID: PMC5787501 DOI: 10.18632/oncotarget.21672] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/16/2017] [Indexed: 12/20/2022] Open
Abstract
Alternative splicing is a critical event in the posttranscriptional regulation of gene expression. To investigate whether this process influences radiation-induced gene expression we defined the effects of ionizing radiation on the generation of alternative transcripts in total cellular mRNA (the transcriptome) and polysome-bound mRNA (the translatome) of the human glioblastoma stem-like cell line NSC11. For these studies, RNA-Seq profiles from control and irradiated cells were compared using the program SpliceSeq to identify transcripts and splice variations induced by radiation. As compared to the transcriptome (total RNA) of untreated cells, the radiation-induced transcriptome contained 92 splice events suggesting that radiation induced alternative splicing. As compared to the translatome (polysome-bound RNA) of untreated cells, the radiation-induced translatome contained 280 splice events of which only 24 were overlapping with the radiation-induced transcriptome. These results suggest that radiation not only modifies alternative splicing of precursor mRNA, but also results in the selective association of existing mRNA isoforms with polysomes. Comparison of radiation-induced alternative transcripts to radiation-induced gene expression in total RNA revealed little overlap (about 3%). In contrast, in the radiation-induced translatome, about 38% of the induced alternative transcripts corresponded to genes whose expression level was affected in the translatome. This study suggests that whereas radiation induces alternate splicing, the alternative transcripts present at the time of irradiation may play a role in the radiation-induced translational control of gene expression and thus cellular radioresponse.
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Affiliation(s)
- Amy Wahba
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Uma T Shankavaram
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kevin Camphausen
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Philip J Tofilon
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
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Forrester HB, Sprung CN. Intragenic controls utilizing radiation-induced alternative transcript regions improves gene expression biodosimetry. Radiat Res 2014; 181:314-23. [PMID: 24625097 DOI: 10.1667/rr13501.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Ionizing-radiation exposure can be life threatening if given to the whole body. In addition, whole body radiation exposure can affect large numbers of people such as after a nuclear reactor accident, a nuclear explosion or a radiological terrorist attack. In these cases, an accurate biodosimeter is essential for triage management. One of the problems for biodosimetry in general is the interindividual variation before and after exposure, which can make it challenging to assign an accurate dose. To begin to address this challenge, lymphocyte cell lines were exposed to 0, 1, 2 and 5 Gy ionizing radiation from a ¹³⁷Cs source at a dose rate of 0.6 Gy/min. Alternative transcripts with regions showing large differential responses to ionizing radiation were determined from exon array data. Gene expression analysis was then performed on isolated mRNA using qRT-PCR with normalization to intergenic (PGK1, GAPDH) and novel intragenic regions for candidate radiation-responsive genes, PPM1D and MDM2. Our studies show that the use of a cis-associated expression reference improved the potential dose prediction approximately 2.3-8.3 fold and provided an advantage for dose prediction compared to distantly or trans-located control ionizing radiation nonresponsive genes. This approach also provides an alternative gene expression normalization method to potentially reduce interindividual variations when untreated basal gene expression levels are unavailable. Using associated noninduced regions of ionizing radiation-induced genes provides a way to estimate basal gene expression in the irradiated sample. This strategy can be utilized as a biodosimeter on its own or to enhance other gene expression candidates for biodosimetry. This normalization strategy may also be generally applicable for other quantitative PCR strategies where normalization is required for a particular response.
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Affiliation(s)
- Helen B Forrester
- Centre for Innate Immunity and Infectious Diseases, MIMR-PHI Institute of Medical Research and Monash University, Victoria, Australia
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Alternative transcript initiation and splicing as a response to DNA damage. PLoS One 2011; 6:e25758. [PMID: 22039421 PMCID: PMC3198437 DOI: 10.1371/journal.pone.0025758] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 09/11/2011] [Indexed: 12/22/2022] Open
Abstract
Humans are exposed to the DNA damaging agent, ionizing radiation (IR), from background radiation, medical treatments, occupational and accidental exposures. IR causes changes in transcription, but little is known about alternative transcription in response to IR on a genome-wide basis. These investigations examine the response to IR at the exon level in human cells, using exon arrays to comprehensively characterize radiation-induced transcriptional expression products. Previously uncharacterized alternative transcripts that preferentially occur following IR exposure have been discovered. A large number of genes showed alternative transcription initiation as a response to IR. Dose-response and time course kinetics have also been characterized. Interestingly, most genes showing alternative transcript induction maintained these isoforms over the dose range and times tested. Finally, clusters of co-ordinately up- and down-regulated radiation response genes were identified at specific chromosomal loci. These data provide the first genome-wide view of the transcriptional response to ionizing radiation at the exon level. This study provides novel insights into alternative transcripts as a mechanism for response to DNA damage and cell stress responses in general.
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Dahm K, Hübscher U. Colocalization of human Rad17 and PCNA in late S phase of the cell cycle upon replication block. Oncogene 2002; 21:7710-9. [PMID: 12400013 DOI: 10.1038/sj.onc.1205872] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2002] [Revised: 07/11/2002] [Accepted: 07/15/2002] [Indexed: 12/22/2022]
Abstract
In response to replication block or DNA damage in S phase the DNA replication and DNA damage checkpoints are activated. The current model in human predicts, that a Rad17/Replication factor C (RF-C) complex might serve as a recruitment complex for the Rad9/Hus1/Rad1 complex to sites of replication block or DNA damage. In this study we have investigated the fate of the Rad17/RF-C complex after treatment of synchronized Hela cells with the replication inhibitor hydroxyurea. In hydroxyurea treated cells the RF-C p37 subunit became more resistant to extraction. Moreover, co-immunoprecipitation studies with extracts of hydroxyurea treated cells showed an interaction of RF-C p37 with Rad17 and of PCNA with Rad9 and RF-C p37. An enhanced colocalization of Rad17 and PCNA in late S phase after hydroxyurea treatment was observed. Our data suggested, that upon replication block a Rad17/RF-C complex is recruited to sites of DNA lesions in late S phase, binds the Rad9/Hus1/Rad1 complex and enables it to interact with PCNA. An interaction of Rad17/RF-C with PCNA appears to be mediated by the small RF-C p37 subunit, suggesting that PCNA might provide communication between replication checkpoint control and DNA replication and repair.
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Affiliation(s)
- Kirsten Dahm
- Institute of Veterinary Biochemistry and Molecular Biology, University Zürich-Irchel, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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