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Manem VSK. Development and validation of genomic predictors of radiation sensitivity using preclinical data. BMC Cancer 2021; 21:937. [PMID: 34416855 PMCID: PMC8377977 DOI: 10.1186/s12885-021-08652-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/25/2021] [Indexed: 11/19/2022] Open
Abstract
Background Radiation therapy is among the most effective and commonly used therapeutic modalities of cancer treatments in current clinical practice. The fundamental paradigm that has guided radiotherapeutic regimens are ‘one-size-fits-all’, which are not in line with the dogma of precision medicine. While there were efforts to build radioresponse signatures using OMICS data, their ability to accurately predict in patients is still limited. Methods We proposed to integrate two large-scale radiogenomics datasets consisting of 511 with 23 tissues and 60 cancer cell lines with 9 tissues to build and validate radiation response biomarkers. We used intrinsic radiation sensitivity, i.e., surviving fraction of cells (SF2) as the radiation response indicator. Gene set enrichment analysis was used to examine the biological determinants driving SF2. Using SF2 as a continuous variable, we used five different approaches, univariate, rank gene ensemble, rank gene multivariate, mRMR and elasticNet to build genomic predictors of radiation response through a cross-validation framework. Results Through the pathway analysis, we found 159 pathways to be statistically significant, out of which 54 and 105 were positively and negatively enriched with SF2. More importantly, we found cell cycle and repair pathways to be enriched with SF2, which are inline with the fundamental aspects of radiation biology. With regards to the radiation response gene signature, we found that all multivariate models outperformed the univariate model with a ranking based approach performing well compared to other models, indicating complex biological processes underpinning radiation response. Conclusion To summarize, we found biological processes underpinning SF2 and systematically compared different machine learning approaches to develop and validate predictors of radiation response. With more patient data available in the future, the clinical value of these biomarkers can be assessed that would allow for personalization of radiotherapy.
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Affiliation(s)
- Venkata S K Manem
- Quebec Heart & Lung Institute Research Center, Quebec City, Quebec, G1V 4G5, Canada. .,Faculty of Pharmacy, Laval University, Quebec City, Quebec, G1V 0A6, Canada.
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Manem VSK, Dhawan A. Modelling recurrence and second cancer risks induced by proton therapy. MATHEMATICAL MEDICINE AND BIOLOGY : A JOURNAL OF THE IMA 2018; 35:347-361. [PMID: 29106564 PMCID: PMC6132082 DOI: 10.1093/imammb/dqx006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 04/09/2017] [Accepted: 06/05/2017] [Indexed: 12/30/2022]
Abstract
In the past few years, proton therapy has taken the centre stage in treating various tumour types. The primary contribution of this study is to investigate the tumour control probability (TCP), relapse time and the corresponding secondary cancer risks induced by proton beam radiation therapy. We incorporate tumour relapse kinetics into the TCP framework and calculate the associated second cancer risks. To calculate proton therapy-induced secondary cancer induction, we used the well-known biologically motivated mathematical model, initiation-inactivation-proliferation formalism. We used the available in vitro data for the linear energy transfer (LET) dependence of cell killing and mutation induction parameters. We evaluated the TCP and radiation-induced second cancer risks for protons in the clinical range of LETs, i.e. approximately 8 $\mathrm{keV/\mu m}$ for the tumour volume and 1-3 $\mathrm{keV/\mu m}$ for the organs at risk. This study may serve as a framework for further work in this field and elucidates proton-induced TCP and the associated secondary cancer risks, not previously reported in the literature. Although studies with a greater number of cell lines would reduce uncertainties within the model parameters, we argue that the theoretical framework presented within is a sufficient rationale to assess proton radiation TCP, relapse and carcinogenic effects in various treatment plans. We show that compared with photon therapy, proton therapy markedly reduces the risk of secondary malignancies and for equivalent dosing regimens achieves better tumour control as well as a reduced primary recurrence outcome, especially within a hypo-fractionated regimen.
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Affiliation(s)
- V S K Manem
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - A Dhawan
- Department of Oncology, University of Oxford, Oxford, UK
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Stokkevåg CH, Schneider U, Muren LP, Newhauser W. Radiation-induced cancer risk predictions in proton and heavy ion radiotherapy. Phys Med 2017; 42:259-262. [DOI: 10.1016/j.ejmp.2017.04.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/01/2017] [Accepted: 04/19/2017] [Indexed: 12/20/2022] Open
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Predicting Organ-Specific Risk Interactions between Radiation and Chemotherapy in Secondary Cancer Survivors. Cancers (Basel) 2017; 9:cancers9090119. [PMID: 28878202 PMCID: PMC5615334 DOI: 10.3390/cancers9090119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/29/2017] [Accepted: 09/04/2017] [Indexed: 01/09/2023] Open
Abstract
Several studies have shown that pediatric patients have an increased risk of developing a secondary malignancy several decades after treatment with radiotherapy and chemotherapy. In this work, we use a biologically motivated mathematical formalism to estimate the relative risks of breast, lung and thyroid cancers in childhood cancer survivors due to concurrent therapy regimen. This model specifically includes possible organ-specific interaction between radiotherapy and chemotherapy. The model predicts relative risks for developing secondary cancers after chemotherapy in breast, lung and thyroid tissues, and compared with the epidemiological data. For a concurrent therapy protocol, our model predicted relative risks of 3.2, 9.3, 4.5 as compared to the clinical data, i.e., 1.4, 8.0, 2.3 for secondary breast, lung and thyroid cancer risks, respectively. The extracted chemotherapy mutation induction rates for breast, lung and thyroid are 10−9, 0.5 × 10−6, 0.9 × 10−7 respectively. We found that there exists no synergistic interaction between radiation and chemotherapy for neither mutation induction nor cell kill in lung tissue, but there is an interaction in cell kill for the breast and thyroid organs. These findings help understand the risks of current clinical protocols and might provide rational guidance to develop future multi-modality treatment protocols to minimize secondary cancer risks.
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Manem VSK, Kohandel M, Hodgson DC, Sivaloganathan S. Predictive modeling of therapy induced secondary thyroid malignancies in childhood cancer survivors. CONVERGENT SCIENCE PHYSICAL ONCOLOGY 2017. [DOI: 10.1088/2057-1739/aa7dec] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Eley JG, Friedrich T, Homann KL, Howell RM, Scholz M, Durante M, Newhauser WD. Comparative Risk Predictions of Second Cancers After Carbon-Ion Therapy Versus Proton Therapy. Int J Radiat Oncol Biol Phys 2016; 95:279-286. [PMID: 27084647 DOI: 10.1016/j.ijrobp.2016.02.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 02/02/2016] [Accepted: 02/09/2016] [Indexed: 02/08/2023]
Abstract
PURPOSE This work proposes a theoretical framework that enables comparative risk predictions for second cancer incidence after particle beam therapy for different ion species for individual patients, accounting for differences in relative biological effectiveness (RBE) for the competing processes of tumor initiation and cell inactivation. Our working hypothesis was that use of carbon-ion therapy instead of proton therapy would show a difference in the predicted risk of second cancer incidence in the breast for a sample of Hodgkin lymphoma (HL) patients. METHODS AND MATERIALS We generated biologic treatment plans and calculated relative predicted risks of second cancer in the breast by using two proposed methods: a full model derived from the linear quadratic model and a simpler linear-no-threshold model. RESULTS For our reference calculation, we found the predicted risk of breast cancer incidence for carbon-ion plans-to-proton plan ratio, <Rc/Rp>, to be 0.75 ± 0.07 but not significantly smaller than 1 (P=.180). CONCLUSIONS Our findings suggest that second cancer risks are, on average, comparable between proton therapy and carbon-ion therapy.
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Affiliation(s)
- John G Eley
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas; University of Texas Graduate School of Biomedical Sciences, Houston, Texas; Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, Maryland.
| | - Thomas Friedrich
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
| | - Kenneth L Homann
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas; University of Texas Graduate School of Biomedical Sciences, Houston, Texas
| | - Rebecca M Howell
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas; University of Texas Graduate School of Biomedical Sciences, Houston, Texas
| | - Michael Scholz
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
| | - Marco Durante
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
| | - Wayne D Newhauser
- Department of Physics and Astronomy, Louisiana State University and Agricultural and Mechanical College, Baton Rouge, Louisiana; Mary Bird Perkins Cancer Center, Baton Rouge, Louisiana
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Blyth BJ, Kakinuma S, Sunaoshi M, Amasaki Y, Hirano-Sakairi S, Ogawa K, Shirakami A, Shang Y, Tsuruoka C, Nishimura M, Shimada Y. Genetic Analysis of T Cell Lymphomas in Carbon Ion-Irradiated Mice Reveals Frequent Interstitial Chromosome Deletions: Implications for Second Cancer Induction in Normal Tissues during Carbon Ion Radiotherapy. PLoS One 2015; 10:e0130666. [PMID: 26125582 PMCID: PMC4488329 DOI: 10.1371/journal.pone.0130666] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 05/25/2015] [Indexed: 02/07/2023] Open
Abstract
Monitoring mice exposed to carbon ion radiotherapy provides an indirect method to evaluate the potential for second cancer induction in normal tissues outside the radiotherapy target volume, since such estimates are not yet possible from historical patient data. Here, male and female B6C3F1 mice were given single or fractionated whole-body exposure(s) to a monoenergetic carbon ion radiotherapy beam at the Heavy Ion Medical Accelerator in Chiba, Japan, matching the radiation quality delivered to the normal tissue ahead of the tumour volume (average linear energy transfer = 13 keV.μm-1) during patient radiotherapy protocols. The mice were monitored for the remainder of their lifespan, and a large number of T cell lymphomas that arose in these mice were analysed alongside those arising following an equivalent dose of 137Cs gamma ray-irradiation. Using genome-wide DNA copy number analysis to identify genomic loci involved in radiation-induced lymphomagenesis and subsequent detailed analysis of Notch1, Ikzf1, Pten, Trp53 and Bcl11b genes, we compared the genetic profile of the carbon ion- and gamma ray-induced tumours. The canonical set of genes previously associated with radiation-induced T cell lymphoma was identified in both radiation groups. While the pattern of disruption of the various pathways was somewhat different between the radiation types, most notably Pten mutation frequency and loss of heterozygosity flanking Bcl11b, the most striking finding was the observation of large interstitial deletions at various sites across the genome in carbon ion-induced tumours, which were only seen infrequently in the gamma ray-induced tumours analysed. If such large interstitial chromosomal deletions are a characteristic lesion of carbon ion irradiation, even when using the low linear energy transfer radiation to which normal tissues are exposed in radiotherapy patients, understanding the dose-response and tissue specificity of such DNA damage could prove key to assessing second cancer risk in carbon ion radiotherapy patients.
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Affiliation(s)
- Benjamin J. Blyth
- Radiobiology for Children’s Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
| | - Shizuko Kakinuma
- Radiobiology for Children’s Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
| | - Masaaki Sunaoshi
- Radiobiology for Children’s Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
| | - Yoshiko Amasaki
- Radiobiology for Children’s Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
| | - Shinobu Hirano-Sakairi
- Radiobiology for Children’s Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
| | - Kanae Ogawa
- Radiobiology for Children’s Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
| | - Ayana Shirakami
- Radiobiology for Children’s Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
| | - Yi Shang
- Radiobiology for Children’s Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
| | - Chizuru Tsuruoka
- Radiobiology for Children’s Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
| | - Mayumi Nishimura
- Radiobiology for Children’s Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
| | - Yoshiya Shimada
- Radiobiology for Children’s Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
- * E-mail:
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