Constitutive gene expression profile segregates toxicity in locally advanced breast cancer patients treated with high-dose hyperfractionated radical radiotherapy
© Henríquez Hernández et al; licensee BioMed Central Ltd. 2009
Received: 10 March 2009
Accepted: 04 June 2009
Published: 04 June 2009
Breast cancer patients show a wide variation in normal tissue reactions after radiotherapy. The individual sensitivity to x-rays limits the efficiency of the therapy. Prediction of individual sensitivity to radiotherapy could help to select the radiation protocol and to improve treatment results. The aim of this study was to assess the relationship between gene expression profiles of ex vivo un-irradiated and irradiated lymphocytes and the development of toxicity due to high-dose hyperfractionated radiotherapy in patients with locally advanced breast cancer. Raw data from microarray experiments were uploaded to the Gene Expression Omnibus Database http://www.ncbi.nlm.nih.gov/geo/ (GEO accession GSE15341). We obtained a small group of 81 genes significantly regulated by radiotherapy, lumped in 50 relevant pathways. Using ANOVA and t-test statistical tools we found 20 and 26 constitutive genes (0 Gy) that segregate patients with and without acute and late toxicity, respectively. Non-supervised hierarchical clustering was used for the visualization of results. Six and 9 pathways were significantly regulated respectively. Concerning to irradiated lymphocytes (2 Gy), we founded 29 genes that separate patients with acute toxicity and without it. Those genes were gathered in 4 significant pathways. We could not identify a set of genes that segregates patients with and without late toxicity. In conclusion, we have found an association between the constitutive gene expression profile of peripheral blood lymphocytes and the development of acute and late toxicity in consecutive, unselected patients. These observations suggest the possibility of predicting normal tissue response to irradiation in high-dose non-conventional radiation therapy regimens. Prospective studies with higher number of patients are needed to validate these preliminary results.
Radiation is an effective therapy in patients with local advanced breast cancer (LABC) [1, 2]. Tumor control by radiotherapy (RT) requires the use of maximum dose that can be delivered while maintaining a tolerance risk of normal tissue toxicity . Better local control outcomes with an acceptable toxicity have been obtained by using high total doses radiation administered in two small fractions per day compared with standard RT protocols . Some patients treated with RT will develop early or late reactions limiting the efficacy of RT. Knowledge of individual variations of normal tissue toxicities determining tolerance would be of great value in patients treated with high-dose radiation protocol . Microarray technology is a high throughput method that allows large scale genomic studies. Because intrinsic radiosensitivity is genetically determined, different cells from the patient can be used to measure sensitivity to radiation . Few studies have been published with regard to radiation induced toxicity and microarrays [2, 7–10]. Patients were previously selected according to the clinical toxicity observed and only three publications included breast cancer patients [see Additional file 1].
The aim of this study was to assess the relation of the gene expression profile from un-irradiated and irradiated lymphocytes and the development of toxicity due to RT in patients with LABC.
Patients and methods
Characteristics of the patients included in the study. Age, menopause status, characteristics of the tumor and systemic treatment were added.
≥ 60 years
Tumor size (T)
Grade of acute and late toxicity of patients included in the study.
Comparison of gene expression profiles from 0 Gy and 2 Gy-treated lymphocytes, using two-class paired test in SAM program, identified a total of 81 genes significantly regulated by RT [see Additional file 2]. We could not cluster these genes in order to segregate patients with acute or late toxicity. PE was used to explore biological pathways significantly regulated by radiation. Fifty seven genes were mapped and PE identified 50 pathways significantly regulated (p < 0.01). Among the RT modulated pathways there were cell cycle, nucleotide excision repair, DNA replication, mismatch repair; MAPK, erbB, and VEGF signaling, ubiquitination mediated proteolysis, notch and Wnt [see Additional file 3]. A functional classification of 81 regulated genes was made using OE. Forty-five genes were classified according to the BP and several processes were modified by RT [see Additional file 4].
Summary of results obtained after non-supervised hierarchical clustering.
N° of pathways
Acute 0 Gy
Late 0 Gy
Acute 2 Gy
Late 2 Gy
Constitutive gene expression pattern from un-irradiated lymphocytes can segregates LABC patients with acute and late toxicity from patients without toxicity after hyperfractionated radiation therapy treatment. Using 2 Gy irradiated lymphocytes from the same patients we could only observe association related to acute toxicity. Few series were published to explore the relation of radiation induced toxicity and microarray, and only three were referred to breast cancer [7, 9, 10]. The paper published by Svensson et al. is similar to the present work in relation to the experimental design, but was assessed in prostate cancer patients . Recently, Rødningen et al. published two relevant papers [10, 23]. Our results were not similar related to genes involved in late toxicity. Anyhow, we coincided in relation to some BP. Differences in cell type, microarray platform, experimental design, RT protocol and statistical strategy could explain those differences. Compared with previously available studies, this is the first work in which: i) patients were consecutive and non-previously selected, ii) patients were treated with high-dose radiation protocol with altered fractionation, iii) the complete human genome was analyzed and iv) comparative studies of constitutive gene expression profiles of LABC patients and toxicity were made.
Pak1 seems to have an important role in late toxicity in our study. Pak1 overexpression is related to apoptosis-resistance in normal and tumour cells . An appropriate apoptotic response seems to protect normal tissue against radiation late toxicity . Therefore, over-expression of Pak1 observed in our patients would be related to resistance to late toxicity. The role of PAK1 in late toxicity should be explored.
This long term study makes a novel contribution to shed light to the relationship between the constitutive gene expression profile of peripheral blood lymphocytes and toxicity after RT. This analysis opens the possibility that the different constitutive expression levels of a selected group of genes would predict acute and late toxicity caused by RT. The feasibility and cost effectiveness of this assay would encourage clinical application in larger series of patients. Further prospective experiments are needed to validate those genomic profiles.
Local Advanced Breast Cancer
False Discovery Rate
Significant Analysis for Microarray.
This work was supported by a grant from Canary Institute for Cancer Research, ICIC (ISCiii, RTICCC 10/2004). We appreciate the help and guide in the use, comprehension and learning of Onto-tools of Dr. Sorin Draghici and his team at The Intelligent Systems and Bioinformatics Laboratory (ISBL), Wayne University (Detroit, MI).
- Shenkier T, Weir L, Levine M, Olivotto I, Whelan T, Reyno L: Clinical practice guidelines for the care and treatment of breast cancer: 15. Treatment for women with stage III or locally advanced breast cancer. Cmaj 2004, 170: 983-994.PubMed CentralView ArticlePubMedGoogle Scholar
- Svensson JP, Stalpers LJ, Esveldt-van Lange RE, Franken NA, Haveman J, Klein B, Turesson I, Vrieling H, Giphart-Gassler M: Analysis of gene expression using gene sets discriminates cancer patients with and without late radiation toxicity. PLoS Med 2006, 3: e422. 10.1371/journal.pmed.0030422PubMed CentralView ArticlePubMedGoogle Scholar
- Bedwinek J, Rao DV, Perez C, Lee J, Fineberg B: Stage III and localized stage IV breast cancer: irradiation alone vs irradiation plus surgery. Int J Radiat Oncol Biol Phys 1982, 8: 31-36.View ArticlePubMedGoogle Scholar
- Budach W, Hehr T, Budach V, Belka C, Dietz K: A meta-analysis of hyperfractionated and accelerated radiotherapy and combined chemotherapy and radiotherapy regimens in unresected locally advanced squamous cell carcinoma of the head and neck. BMC Cancer 2006, 6: 28. 10.1186/1471-2407-6-28PubMed CentralView ArticlePubMedGoogle Scholar
- Johansson S, Svensson H, Denekamp J: Timescale of evolution of late radiation injury after postoperative radiotherapy of breast cancer patients. Int J Radiat Oncol Biol Phys 2000, 48: 745-750.View ArticlePubMedGoogle Scholar
- Gatti RA: The inherited basis of human radiosensitivity. Acta Oncol 2001, 40: 702-711. 10.1080/02841860152619115View ArticlePubMedGoogle Scholar
- Quarmby S, West C, Magee B, Stewart A, Hunter R, Kumar S: Differential expression of cytokine genes in fibroblasts derived from skin biopsies of patients who developed minimal or severe normal tissue damage after radiotherapy. Radiat Res 2002, 157: 243-248. 10.1667/0033-7587(2002)157[0243:DEOCGI]2.0.CO;2View ArticlePubMedGoogle Scholar
- Sonis S, Haddad R, Posner M, Watkins B, Fey E, Morgan TV, Mookanamparambil L, Ramoni M: Gene expression changes in peripheral blood cells provide insight into the biological mechanisms associated with regimen-related toxicities in patients being treated for head and neck cancers. Oral Oncol 2007, 43: 289-300. 10.1016/j.oraloncology.2006.03.014View ArticlePubMedGoogle Scholar
- Rieger KE, Hong WJ, Tusher VG, Tang J, Tibshirani R, Chu G: Toxicity from radiation therapy associated with abnormal transcriptional responses to DNA damage. Proc Natl Acad Sci USA 2004, 101: 6635-6640. 10.1073/pnas.0307761101PubMed CentralView ArticlePubMedGoogle Scholar
- Rodningen OK, Borresen-Dale AL, Alsner J, Hastie T, Overgaard J: Radiation-induced gene expression in human subcutaneous fibroblasts is predictive of radiation-induced fibrosis. Radiother Oncol 2008, 86: 314-320. 10.1016/j.radonc.2007.09.013View ArticlePubMedGoogle Scholar
- Pinar B, Lara PC, Lloret M, Bordon E, Nunez MI, Villalobos M, Guerrero R, Luna JD, Ruiz de Almodovar JM: Radiation-induced DNA damage as a predictor of long-term toxicity in locally advanced breast cancer patients treated with high-dose hyperfractionated radical radiotherapy. Radiat Res 2007, 168: 415-422. 10.1667/RR0746.1View ArticlePubMedGoogle Scholar
- Quackenbush J: Microarray data normalization and transformation. Nat Genet 2002,32(Suppl):496-501. 10.1038/ng1032View ArticlePubMedGoogle Scholar
- Rico-Bautista E, Greenhalgh CJ, Tollet-Egnell P, Hilton DJ, Alexander WS, Norstedt G, Flores-Morales A: Suppressor of cytokine signaling-2 deficiency induces molecular and metabolic changes that partially overlap with growth hormone-dependent effects. Mol Endocrinol 2005, 19: 781-793. 10.1210/me.2004-0040View ArticlePubMedGoogle Scholar
- Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98: 5116-5121. 10.1073/pnas.091062498PubMed CentralView ArticlePubMedGoogle Scholar
- Pan W: A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 2002, 18: 546-554. 10.1093/bioinformatics/18.4.546View ArticlePubMedGoogle Scholar
- Zar JH: Biostatistical analysis. 4th edition. Upper Saddle River, N.J.: Prentice Hall; 1999.Google Scholar
- Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95: 14863-14868. 10.1073/pnas.95.25.14863PubMed CentralView ArticlePubMedGoogle Scholar
- Draghici S, Khatri P, Bhavsar P, Shah A, Krawetz SA, Tainsky MA: Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res 2003, 31: 3775-3781. 10.1093/nar/gkg624PubMed CentralView ArticlePubMedGoogle Scholar
- Draghici S, Khatri P, Tarca AL, Amin K, Done A, Voichita C, Georgescu C, Romero R: A systems biology approach for pathway level analysis. Genome Res 2007, 17: 1537-1545. 10.1101/gr.6202607PubMed CentralView ArticlePubMedGoogle Scholar
- Khatri P, Bhavsar P, Bawa G, Draghici S: Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. Nucleic Acids Res 2004, 32: W449-456. 10.1093/nar/gkh409PubMed CentralView ArticlePubMedGoogle Scholar
- Khatri P, Sellamuthu S, Malhotra P, Amin K, Done A, Draghici S: Recent additions and improvements to the Onto-Tools. Nucleic Acids Res 2005, 33: W762-765. 10.1093/nar/gki472PubMed CentralView ArticlePubMedGoogle Scholar
- Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, Kim CJ, Kusanovic JP, Romero R: A novel signaling pathway impact analysis. Bioinformatics 2009, 25: 75-82. 10.1093/bioinformatics/btn577PubMed CentralView ArticlePubMedGoogle Scholar
- Alsner J, Rodningen OK, Overgaard J: Differential gene expression before and after ionizing radiation of subcutaneous fibroblasts identifies breast cancer patients resistant to radiation-induced fibrosis. Radiother Oncol 2007, 83: 261-266. 10.1016/j.radonc.2007.05.001View ArticlePubMedGoogle Scholar
- Friedland JC, Lakins JN, Kazanietz MG, Chernoff J, Boettiger D, Weaver VM: alpha6beta4 integrin activates Rac-dependent p21-activated kinase 1 to drive NF-kappaB-dependent resistance to apoptosis in 3D mammary acini. J Cell Sci 2007, 120: 3700-3712. 10.1242/jcs.03484View ArticlePubMedGoogle Scholar
- Nuyten DS, Vijver MJ: Using microarray analysis as a prognostic and predictive tool in oncology: focus on breast cancer and normal tissue toxicity. Semin Radiat Oncol 2008, 18: 105-114. 10.1016/j.semradonc.2007.10.007View ArticlePubMedGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.