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Liang Y, Feng G, Zhong S, Gao X, Tong Y, Cui W, Huang G, Zhang Z, Zhou X. An Inflammation-Immunity Classifier of 11 Chemokines for Prediction of Overall Survival in Head and Neck Squamous Cell Carcinoma. Med Sci Monit 2019; 25:4485-4494. [PMID: 31203306 PMCID: PMC6592142 DOI: 10.12659/msm.915248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Chemokines are important in inflammation, immunity, tumor progression, and metastasis. The purpose of this research was to find an integrated-RNA signature of chemokine family genes to predict the survival prognosis in head and neck squamous carcinoma (HNSC) patients. MATERIAL AND METHODS Relevant data of 504 HNSC patients were extracted from The Cancer Genome Atlas (TCGA) database. Through analyzing RNA sequencing data, the univariate Cox model was used to identify chemokine family genes associated with survival and then to develop a multiple-RNA signature in the training set. The prediction value of this multiple-RNA signature was further verified in the validation and entire sets. The receiver operating characteristic curves were used to assess the predictive value of this multiple-RNA signature. RESULTS Eleven chemokines were included in this prognostic signature. Based on this 11-chemokine signature, we further categorized patients as high or low risk. Compared with low-risk patients, high-risk patients had shorter overall survival (OS) time in the training set [hazard ratio (HR)=3.497, 95% confidence interval (CI)=2.142-5.711, p<0.001], validation set (HR=3.575, 95% CI=1.988-6.390, p<0.001), and entire set (HR=3.416, 95% CI=2.363-4.939, p<0.001). This 11-chemokine signature was an independent prognostic factor for OS in these datasets (p<0.05). The AUC values for predicting overall survival within 48 months in the training, validation, and entire sets were 0.71, 0.69, and 0.69, respectively. CONCLUSIONS This 11-chemokine signature could serve as a reliable prognostic tool for HNSC patients and might be useful to guide individualized treatment or even gene target therapy for high-risk patients.
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Affiliation(s)
- Yushan Liang
- Department of Otolaryngology Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Guofei Feng
- Department of Otolaryngology Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Suhua Zhong
- Department of Otolaryngology Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Xiaoyu Gao
- Department of Otolaryngology Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Yan Tong
- Department of Otolaryngology Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Wanmeng Cui
- Department of Otolaryngology Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Guangwu Huang
- Department of Otolaryngology Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Zhe Zhang
- Department of Otolaryngology Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Xiaoying Zhou
- Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China (mainland)
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Integrative Network Analysis Reveals a MicroRNA-Based Signature for Prognosis Prediction of Epithelial Ovarian Cancer. BIOMED RESEARCH INTERNATIONAL 2019; 2019:1056431. [PMID: 31275959 PMCID: PMC6582839 DOI: 10.1155/2019/1056431] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/18/2019] [Indexed: 01/08/2023]
Abstract
Background Epithelial ovarian cancer (EOC) is a heterogeneous disease, which has been recently classified into four molecular subtypes, of which the mesenchymal subtype exhibited the worst prognosis. We aimed to identify a microRNA- (miRNA-) based signature by incorporating the molecular modalities involved in the mesenchymal subtype for risk stratification, which would allow the identification of patients who might benefit from more rigorous treatments. Method We characterized the regulatory mechanisms underlying the mesenchymal subtype using network analyses integrating gene and miRNA expression profiles from The Cancer Genome Atlas (TCGA) cohort to identify a miRNA signature for prognosis prediction. Results We identified four miRNAs as the master regulators of the mesenchymal subtype and developed a risk score model. The 4-miRNA signature significantly predicted overall survival (OS) and progression-free survival (PFS) in discovery (p=0.004 and p=0.04) and two independent public datasets (GSE73582: OS, HR: 2.26 (1.26-4.05), p=0.005, PFS, HR: 2.03 (1.34-3.09), p<0.001; GSE25204: OS, HR: 3.07 (1.73-5.46), p<0.001, PFS, HR: 2.59 (1.72-3.88), p<0.001). Moreover, in multivariate analyses, the miRNA signature maintained as an independent prognostic predictor and achieved superior efficiency compared to the currently used clinical factors. Conclusions In conclusion, our network analysis identified a 4-miRNA signature which has prognostic value superior to currently reported clinical covariates. This signature warrants further testing and validation for use in clinical practice.
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Hao D, Li J, Wang J, Meng Y, Zhao Z, Zhang C, Miao K, Deng C, Tsang BK, Wang L, Di LJ. Non-classical estrogen signaling in ovarian cancer improves chemo-sensitivity and patients outcome. Theranostics 2019; 9:3952-3965. [PMID: 31281524 PMCID: PMC6587348 DOI: 10.7150/thno.30814] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 03/29/2019] [Indexed: 12/15/2022] Open
Abstract
Deficiency in homologous recombination repair (HRR) is frequently associated with hormone-responsive cancers, especially the epithelial ovarian cancer (EOC) which shows defects of HRR in up to half of cases. However, whether there are molecular connections between estrogen signaling and HRR deficiency in EOC remains unknown. Methods: We analyzed the estrogen receptor α (ERα) binding profile in EOC cell lines and investigated its association with genome instability, HRR deficiency and sensitivity to chemotherapy using extensive public datasets and in vitro/in vivo experiments. Results: We found an inverse correlation between estrogen signaling and HRR activity in EOC, and the genome-wide collaboration between ERα and the co-repressor CtBP. Though the non-classical AP-1-mediated ERα signaling, their targets were highly enriched by HRR genes. We found that depleting ERα in EOC cells up-regulates HRR activity and HRR gene expression. Consequently, estrogen signaling enhances the sensitivity of ovarian cancer cells to chemotherapy agents in vitro and in vivo. Large-scale analyses further indicate that estrogen replacement and ESR1 expression are associated with chemo-sensitivity and the favorable survival of EOC patients. Conclusion: These findings characterize a novel role of ERα in mediating the molecular connection between hormone and HRR in EOC and encourage hormone replacement therapy for EOC patients.
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Sun J, Zhao H, Lin S, Bao S, Zhang Y, Su J, Zhou M. Integrative analysis from multi-centre studies identifies a function-derived personalized multi-gene signature of outcome in colorectal cancer. J Cell Mol Med 2019; 23:5270-5281. [PMID: 31140730 PMCID: PMC6653159 DOI: 10.1111/jcmm.14403] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 04/25/2019] [Accepted: 05/06/2019] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer (CRC) is highly heterogeneous leading to variable prognosis and treatment responses. Therefore, it is necessary to explore novel personalized and reproducible prognostic signatures to aid clinical decision‐making. The present study combined large‐scale gene expression profiles and clinical data of 1828 patients with CRC from multi‐centre studies and identified a personalized gene prognostic signature consisting of 46 unique genes (called function‐derived personalized gene signature [FunPGS]) from an integrated statistics and function‐derived perspective. In the meta‐training and multiple independent validation cohorts, the FunPGS effectively discriminated patients with CRC with significantly different prognosis at the individual level and remained as an independent factor upon adjusting for clinical covariates in multivariate analysis. Furthermore, the FunPGS demonstrated superior performance for risk stratification with respect to other recently reported signatures and clinical factors. The complementary value of the molecular signature and clinical factors was further explored, and it was observed that the composite signature called IMCPS greatly improved the predictive performance of survival estimation relative to molecular signatures or clinical factors alone. With further prospective validation in clinical trials, the FunPGS may become a promising and powerful personalized prognostic tool for stratifying patients with CRC in order to achieve an optimal systemic therapy.
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Affiliation(s)
- Jie Sun
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, P. R. China
| | - Hengqiang Zhao
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, P. R. China
| | - Shuting Lin
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, P. R. China
| | - Siqi Bao
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, P. R. China
| | - Yan Zhang
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, P. R. China
| | - Jianzhong Su
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, P. R. China
| | - Meng Zhou
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, P. R. China
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Qiu Y, Jiang H, Ching WK, Ng MK. On predicting epithelial mesenchymal transition by integrating RNA-binding proteins and correlation data via L1/2-regularization method. Artif Intell Med 2019; 95:96-103. [DOI: 10.1016/j.artmed.2018.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 09/20/2018] [Accepted: 09/30/2018] [Indexed: 01/06/2023]
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Abstract
Fanconi anemia (FA) is a complex genetic disorder characterized by bone marrow failure (BMF), congenital defects, inability to repair DNA interstrand cross-links (ICLs), and cancer predisposition. FA presents two seemingly opposite characteristics: (a) massive cell death of the hematopoietic stem and progenitor cell (HSPC) compartment due to extensive genomic instability, leading to BMF, and (b) uncontrolled cell proliferation leading to FA-associated malignancies. The canonical function of the FA proteins is to collaborate with several other DNA repair proteins to eliminate clastogenic (chromosome-breaking) effects of DNA ICLs. Recent discoveries reveal that the FA pathway functions in a critical tumor-suppressor network to preserve genomic integrity by stabilizing replication forks, mitigating replication stress, and regulating cytokinesis. Homozygous germline mutations (biallelic) in 22 FANC genes cause FA, whereas heterozygous germline mutations in some of the FANC genes (monoallelic), such as BRCA1 and BRCA2, do not cause FA but significantly increase cancer susceptibility sporadically in the general population. In this review, we discuss our current understanding of the functions of the FA pathway in the maintenance of genomic stability, and we present an overview of the prevalence and clinical relevance of somatic mutations in FA genes.
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Affiliation(s)
- Joshi Niraj
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA;
| | - Anniina Färkkilä
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA;
| | - Alan D D'Andrea
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA;
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57
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High-Grade Serous Ovarian Cancer: Basic Sciences, Clinical and Therapeutic Standpoints. Int J Mol Sci 2019. [PMID: 30813239 DOI: 10.3390/ijms20040952] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Among a litany of malignancies affecting the female reproductive tract, that of the ovary is the most frequently fatal. Moreover, while the steady pace of scientific discovery has fuelled recent ameliorations in the outcomes of many other cancers, the rates of mortality for ovarian cancer have been stagnant since around 1980. Yet despite the grim outlook, progress is being made towards better understanding the fundamental biology of this disease and how its biology in turn influences clinical behaviour. It has long been evident that ovarian cancer is not a unitary disease but rather a multiplicity of distinct malignancies that share a common anatomical site upon presentation. Of these, the high-grade serous subtype predominates in the clinical setting and is responsible for a disproportionate share of the fatalities from all forms of ovarian cancer. This review aims to provide a detailed overview of the clinical-pathological features of ovarian cancer with a particular focus on the high-grade serous subtype. Along with a description of the relevant clinical aspects of this disease, including novel trends in treatment strategies, this text will inform the reader of recent updates to the scientific literature regarding the origin, aetiology and molecular-genetic basis of high-grade serous ovarian cancer (HGSOC).
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High-Grade Serous Ovarian Cancer: Basic Sciences, Clinical and Therapeutic Standpoints. Int J Mol Sci 2019. [PMID: 30813239 DOI: 10.3390/ijms20040952]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Among a litany of malignancies affecting the female reproductive tract, that of the ovary is the most frequently fatal. Moreover, while the steady pace of scientific discovery has fuelled recent ameliorations in the outcomes of many other cancers, the rates of mortality for ovarian cancer have been stagnant since around 1980. Yet despite the grim outlook, progress is being made towards better understanding the fundamental biology of this disease and how its biology in turn influences clinical behaviour. It has long been evident that ovarian cancer is not a unitary disease but rather a multiplicity of distinct malignancies that share a common anatomical site upon presentation. Of these, the high-grade serous subtype predominates in the clinical setting and is responsible for a disproportionate share of the fatalities from all forms of ovarian cancer. This review aims to provide a detailed overview of the clinical-pathological features of ovarian cancer with a particular focus on the high-grade serous subtype. Along with a description of the relevant clinical aspects of this disease, including novel trends in treatment strategies, this text will inform the reader of recent updates to the scientific literature regarding the origin, aetiology and molecular-genetic basis of high-grade serous ovarian cancer (HGSOC).
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High-Grade Serous Ovarian Cancer: Basic Sciences, Clinical and Therapeutic Standpoints. Int J Mol Sci 2019; 20:ijms20040952. [PMID: 30813239 PMCID: PMC6412907 DOI: 10.3390/ijms20040952] [Citation(s) in RCA: 342] [Impact Index Per Article: 68.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/13/2019] [Accepted: 02/19/2019] [Indexed: 02/07/2023] Open
Abstract
Among a litany of malignancies affecting the female reproductive tract, that of the ovary is the most frequently fatal. Moreover, while the steady pace of scientific discovery has fuelled recent ameliorations in the outcomes of many other cancers, the rates of mortality for ovarian cancer have been stagnant since around 1980. Yet despite the grim outlook, progress is being made towards better understanding the fundamental biology of this disease and how its biology in turn influences clinical behaviour. It has long been evident that ovarian cancer is not a unitary disease but rather a multiplicity of distinct malignancies that share a common anatomical site upon presentation. Of these, the high-grade serous subtype predominates in the clinical setting and is responsible for a disproportionate share of the fatalities from all forms of ovarian cancer. This review aims to provide a detailed overview of the clinical-pathological features of ovarian cancer with a particular focus on the high-grade serous subtype. Along with a description of the relevant clinical aspects of this disease, including novel trends in treatment strategies, this text will inform the reader of recent updates to the scientific literature regarding the origin, aetiology and molecular-genetic basis of high-grade serous ovarian cancer (HGSOC).
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60
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Ruffalo M, Thomas R, Chen J, Lee AV, Oesterreich S, Bar-Joseph Z. Network-guided prediction of aromatase inhibitor response in breast cancer. PLoS Comput Biol 2019; 15:e1006730. [PMID: 30742607 PMCID: PMC6386390 DOI: 10.1371/journal.pcbi.1006730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 02/22/2019] [Accepted: 12/19/2018] [Indexed: 01/07/2023] Open
Abstract
Prediction of response to specific cancer treatments is complicated by significant heterogeneity between tumors in terms of mutational profiles, gene expression, and clinical measures. Here we focus on the response of Estrogen Receptor (ER)+ post-menopausal breast cancer tumors to aromatase inhibitors (AI). We use a network smoothing algorithm to learn novel features that integrate several types of high throughput data and new cell line experiments. These features greatly improve the ability to predict response to AI when compared to prior methods. For a subset of the patients, for which we obtained more detailed clinical information, we can further predict response to a specific AI drug. Breast cancer is the second most common type of cancer in women, with an incidence rate of over 250,000 cases per year, and breast cancer cases show significant heterogeneity in clinical and omic measures. Estrogen receptor positive (ER+) tumors typically grow in response to estrogen, and in post menopausal women, estrogen is only produced in peripheral tissues via the aromatase enzyme. Inhibition of aromatase is often an effective treatment for ER+ tumors, but aromatase inhibitor therapy is not effective for all tumors, and causes of this heterogeneity in response are largely not known. In this work, we present a feature construction and classification method to predict response to aromatase inhibitor therapy. We use network smoothing techniques to combine tumor omic data into predictive features, which we use as input to standard machine learning algorithms. We train predictive models using clinical data, including high-quality clinical data from UPMC patients, and show that our method outperforms previous approaches in predicting response to aromatase inhibitor therapy.
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Affiliation(s)
- Matthew Ruffalo
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Roby Thomas
- Women’s Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, Pennsylvania, United States of America
| | - Jian Chen
- Women’s Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, Pennsylvania, United States of America
| | - Adrian V. Lee
- Women’s Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, Pennsylvania, United States of America
| | - Steffi Oesterreich
- Women’s Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, Pennsylvania, United States of America
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Romeo M, Pardo JC, Martínez-Cardús A, Martínez-Balibrea E, Quiroga V, Martínez-Román S, Solé F, Margelí M, Mesía R. Translational Research Opportunities Regarding Homologous Recombination in Ovarian Cancer. Int J Mol Sci 2018; 19:ijms19103249. [PMID: 30347758 PMCID: PMC6214122 DOI: 10.3390/ijms19103249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 09/29/2018] [Accepted: 10/16/2018] [Indexed: 02/07/2023] Open
Abstract
Homologous recombination (HR) is a DNA repair pathway that is deficient in 50% of high-grade serous ovarian carcinomas (HGSOC). Deficient HR (DHR) constitutes a therapeutic opportunity for these patients, thanks to poly (ADP-ribose) polymerases (PARP) inhibitors (PARPi; olaparib, niraparib, and rucaparib are already commercialized). Although initially, PARPi were developed for patients with BRCA1/2 mutations, robust clinical data have shown their benefit in a broader population without DHR. This breakthrough in daily practice has raised several questions that necessitate further research: How can populations that will most benefit from PARPi be selected? At which stage of ovarian cancer should PARPi be used? Which strategies are reasonable to overcome PARPi resistance? In this paper, we present a summary of the literature and discuss the present clinical research involving PARPi (after reviewing ClinicalTrials.gov) from a translational perspective. Research into the functional biomarkers of DHR and clinical trials testing PARPi benefits as first-line setting or rechallenge are currently ongoing. Additionally, in the clinical setting, only secondary restoring mutations of BRCA1/2 have been identified as events inducing resistance to PARPi. The clinical frequency of this and other mechanisms that have been described in preclinics is unknown. It is of great importance to study mechanisms of resistance to PARPi to guide the clinical development of drug combinations.
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Affiliation(s)
- Margarita Romeo
- Medical Oncology Department, B-ARGO Group, Institut Català d'Oncologia Badalona, Carretera del Canyet s/n, 08916 Badalona, Spain.
- Campus de la UAB, Universitat Autónoma de Barcelona, Plaça Cívica, 08193 Bellaterra, Spain.
| | - Juan Carlos Pardo
- Medical Oncology Department, B-ARGO Group, Institut Català d'Oncologia Badalona, Carretera del Canyet s/n, 08916 Badalona, Spain.
| | - Anna Martínez-Cardús
- Health Sciences Research Institute of the Germans Trias i Pujol Foundation (IGTP), B-ARGO Group, Carretera del Canyet s/n, 08916 Badalona, Spain.
| | - Eva Martínez-Balibrea
- Program against Cancer Therapeutic Resistance (ProCURE), Institut Català d'Oncologia Badalona, Program for Predictive and Personalized Cancer Medicine (PMPPC), Health Sciences Research Institute Germans Trias i Pujo (IGTP), Carretera de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Spain.
| | - Vanesa Quiroga
- Medical Oncology Department, B-ARGO Group, Institut Català d'Oncologia Badalona, Carretera del Canyet s/n, 08916 Badalona, Spain.
| | - Sergio Martínez-Román
- Gynecology Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain.
| | - Francesc Solé
- Institut de Recerca contra la Leucemia Josep Carreras, 08916 Badalona, Spain.
| | - Mireia Margelí
- Medical Oncology Department, B-ARGO Group, Institut Català d'Oncologia Badalona, Carretera del Canyet s/n, 08916 Badalona, Spain.
| | - Ricard Mesía
- Medical Oncology Department, B-ARGO Group, Institut Català d'Oncologia Badalona, Carretera del Canyet s/n, 08916 Badalona, Spain.
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Xu G, Zhou Y, Zhou F. Development and validation of an immunity-related classifier of nine chemokines for predicting recurrence in stage I-III patients with colorectal cancer after operation. Cancer Manag Res 2018; 10:4051-4064. [PMID: 30323661 PMCID: PMC6173492 DOI: 10.2147/cmar.s174452] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Introduction Chemokines are closely related with tumor immunity, progression, and metastasis. We aimed to construct a multi-RNA classifier of chemokine family genes for predicting tumor recurrence in stage I-III patients with colorectal cancer (CRC) after operation. Patients and methods By analyzing microarray data, the Cox regression analysis was conducted to determine survival-related chemokine family genes and develop a multi-RNA classifier in the training set. The prognostic value of this multi-RNA classifier was further validated in the internal validation and external independent sets. Receiver operating characteristic curves were used to compare the prediction ability of the combined model of this multi-RNA classifier and stage, and this multi-RNA classifier and stage alone. Results Nine survival-related chemokines were identified in the training set. We identified a nine-chemokine classifier and classified the patients as high-risk or low-risk. Compared with CRC patients with high-risk scores, CRC patients with low-risk scores had longer disease-free survival in the training (HR=2.353, 95% CI=1.480-3.742, P<0.001), internal validation (HR=2.389, 95% CI=1.428-3.996, P<0.001), and external independent (HR=3.244, 95% CI=1.813-5.807, P<0.001) sets. This nine-chemokine classifier was an independent prognostic factor in these datasets (P<0.05). The combined model of this nine-chemokine classifier and tumor stage may tend to have higher accuracy than stage alone in the training (area under curve 0.727 vs 0.626, P<0.01), internal validation (0.668 vs 0.584, P=0.03), and external independent (0.704 vs 0.678, P>0.05) sets. This nine-chemokine classifier may only be applied in Marisa's C2, C5, and C6 subtypes patients. Conclusion Our nine-chemokine classifier is a reliable prognostic tool for some specific biological subtypes of CRC patients. It might contribute to guide the personalized treatment for high-risk patients.
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Affiliation(s)
- Guozeng Xu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China, .,Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan, China,
| | - Yuehan Zhou
- Department of Pharmacology, Guilin Medical University, Guilin 541004, Guangxi, China
| | - Fuxiang Zhou
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China, .,Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan, China,
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Toward A variable RBE for proton beam therapy. Radiother Oncol 2018; 128:68-75. [PMID: 29910006 DOI: 10.1016/j.radonc.2018.05.019] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/09/2018] [Accepted: 05/17/2018] [Indexed: 12/19/2022]
Abstract
In the clinic, proton beam therapy (PBT) is based on the use of a generic relative biological effectiveness (RBE) of 1.1 compared to photons in human cancers and normal tissues. However, the experimental basis for this RBE lacks any significant number of representative tumor models and clinically relevant endpoints for dose-limiting organs at risk. It is now increasingly appreciated that much of the variations of treatment responses in cancers are due to inter-tumoral genomic heterogeneity. Indeed, recently it has been shown that defects in certain DNA repair pathways, which are found in subsets of many cancers, are associated with a RBE increase in vitro. However, there currently exist little in vivo or clinical data that confirm the existence of similarly increased RBE values in human cancers. Furthermore, evidence for variable RBE values for normal tissue toxicity has been sparse and conflicting to date. If we could predict variable RBE values in patients, we would be able to optimally use and personalize PBT. For example, predictive tumor biomarkers may facilitate selection of patients with proton-sensitive cancers previously ineligible for PBT. Dose de-escalation may be possible to reduce normal tissue toxicity, especially in pediatric patients. Knowledge of increased tumor RBE may allow us to develop biologically optimized therapies to enhance local control while RBE biomarkers for normal tissues could lead to a better understanding and prevention of unusual PBT-associated toxicity. Here, we will review experimental data on the repair of proton damage to DNA that impact both RBE values and biophysical modeling to predict RBE variations. Experimental approaches for studying proton sensitivity in vitro and in vivo will be reviewed as well and recent clinical findings discussed. Ultimately, therapeutically exploiting the understudied biological advantages of protons and developing approaches to limit treatment toxicity should fundamentally impact the clinical use of PBT.
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Tumiati M, Hietanen S, Hynninen J, Pietilä E, Färkkilä A, Kaipio K, Roering P, Huhtinen K, Alkodsi A, Li Y, Lehtonen R, Erkan EP, Tuominen MM, Lehti K, Hautaniemi SK, Vähärautio A, Grénman S, Carpén O, Kauppi L. A Functional Homologous Recombination Assay Predicts Primary Chemotherapy Response and Long-Term Survival in Ovarian Cancer Patients. Clin Cancer Res 2018; 24:4482-4493. [PMID: 29858219 DOI: 10.1158/1078-0432.ccr-17-3770] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/25/2018] [Accepted: 05/25/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Homologous recombination deficiency (HRD) correlates with platinum sensitivity in patients with ovarian cancer, which clinically is the most useful predictor of sensitivity to PARPi. To date, there are no reliable diagnostic tools to anticipate response to platinum-based chemotherapy, thus we aimed to develop an ex vivo functional HRD detection test that could predict both platinum-sensitivity and patient eligibility to targeted drug treatments.Experimental Design: We obtained a functional HR score by quantifying homologous recombination (HR) repair after ionizing radiation-induced DNA damage in primary ovarian cancer samples (n = 32). Samples clustered in 3 categories: HR-deficient, HR-low, and HR-proficient. We analyzed the HR score association with platinum sensitivity and treatment response, platinum-free interval (PFI) and overall survival (OS), and compared it with other clinical parameters. In parallel, we performed DNA-sequencing of HR genes to assess if functional HRD can be predicted by currently offered genetic screening.Results: Low HR scores predicted primary platinum sensitivity with high statistical significance (P = 0.0103), associated with longer PFI (HR-deficient vs. HR-proficient: 531 vs. 53 days), and significantly correlated with improved OS (HR score <35 vs. ≥35, hazard ratio = 0.08, P = 0.0116). At the genomic level, we identified a few unclear mutations in HR genes and the mutational signature associated with HRD, but, overall, genetic screening failed to predict functional HRD.Conclusions: We developed an ex vivo assay that detects tumor functional HRD and an HR score able to predict platinum sensitivity, which holds the clinically relevant potential to become the routine companion diagnostic in the management of patients with ovarian cancer. Clin Cancer Res; 24(18); 4482-93. ©2018 AACR.
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Affiliation(s)
- Manuela Tumiati
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland.
| | - Sakari Hietanen
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Elina Pietilä
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Anniina Färkkilä
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Katja Kaipio
- Department of Pathology, University of Turku and Turku University Hospital, Finland
| | - Pia Roering
- Department of Pathology, University of Turku and Turku University Hospital, Finland
| | - Kaisa Huhtinen
- Department of Pathology, University of Turku and Turku University Hospital, Finland
| | - Amjad Alkodsi
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Yilin Li
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Rainer Lehtonen
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Erdogan Pekcan Erkan
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Minna M Tuominen
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Kaisa Lehti
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sampsa K Hautaniemi
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Anna Vähärautio
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Seija Grénman
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Olli Carpén
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Pathology, University of Turku and Turku University Hospital, Finland
| | - Liisa Kauppi
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland.
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Mijnes J, Veeck J, Gaisa NT, Burghardt E, de Ruijter TC, Gostek S, Dahl E, Pfister D, Schmid SC, Knüchel R, Rose M. Promoter methylation of DNA damage repair (DDR) genes in human tumor entities: RBBP8/ CtIP is almost exclusively methylated in bladder cancer. Clin Epigenetics 2018; 10:15. [PMID: 29445424 PMCID: PMC5802064 DOI: 10.1186/s13148-018-0447-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/22/2018] [Indexed: 01/18/2023] Open
Abstract
Background Genome-wide studies identified pan-cancer genes and shared biological networks affected by epigenetic dysregulation among diverse tumor entities. Here, we systematically screened for hypermethylation of DNA damage repair (DDR) genes in a comprehensive candidate-approach and exemplarily identify and validate candidate DDR genes as targets of epigenetic inactivation unique to bladder cancer (BLCA), which may serve as non-invasive biomarkers. Methods Genome-wide DNA methylation datasets (2755 CpG probes of n = 7819 tumor and n = 659 normal samples) of the TCGA network covering 32 tumor entities were analyzed in silico for 177 DDR genes. Genes of interest were defined as differentially methylated between normal and cancerous tissues proximal to transcription start sites. The lead candidate gene was validated by methylation-specific PCR (MSP) and/or bisulfite-pyrosequencing in different human cell lines (n = 36), in primary BLCA tissues (n = 43), and in voided urine samples (n = 74) of BLCA patients. Urines from healthy donors and patients with urological benign and malignant diseases were included as controls (n = 78). mRNA expression was determined using qRT-PCR in vitro before (n = 5) and after decitabine treatment (n = 2). Protein expression was assessed by immunohistochemistry (n = 42). R 3.2.0. was used for statistical data acquisition and SPSS 21.0 for statistical analysis. Results Overall, 39 DDR genes were hypermethylated in human cancers. Most exclusively and frequently methylated (37%) in primary BLCA was RBBP8, encoding endonuclease CtIP. RBBP8 hypermethylation predicted longer overall survival (OS) and was found in 2/4 bladder cancer cell lines but not in any of 33 cancer cell lines from entities with another origin like prostate. RBBP8 methylation was inversely correlated with RBBP8 mRNA and nuclear protein expression while RBBP8 was re-expressed after in vitro demethylation. RBBP8 methylation was associated with histological grade in primary BLCA and urine samples. RBBP8 methylation was detectable in urine samples of bladder cancer patients achieving a sensitivity of 52%, at 91% specificity. Conclusions RBBP8 was identified as almost exclusively hypermethylated in BLCA. RBBP8/CtIP has a proven role in homologous recombination-mediated DNA double-strand break repair known to sensitize cancer cells for PARP1 inhibitors. Since RBBP8 methylation was detectable in urines, it may be a complementary marker of high specificity in urine for BLCA detection.
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Affiliation(s)
- Jolein Mijnes
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Jürgen Veeck
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany.,2Division of Medical Oncology, Maastricht University Medical Centre, Maastricht, The Netherlands.,3GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands.,4RWTH Centralized Biomaterial Bank (RWTH cBMB), Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Nadine T Gaisa
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Eduard Burghardt
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Tim C de Ruijter
- 2Division of Medical Oncology, Maastricht University Medical Centre, Maastricht, The Netherlands.,3GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Sonja Gostek
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Edgar Dahl
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany.,4RWTH Centralized Biomaterial Bank (RWTH cBMB), Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - David Pfister
- 5Department of Urology, RWTH Aachen University, Aachen, Germany.,6Department of Urology, Uro-Oncology, Robot Assisted and Reconstructive Urologic Surgery, University Hospital Cologne, Cologne, Germany
| | - Sebastian C Schmid
- 7Department of Urology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Ruth Knüchel
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Michael Rose
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany.,4RWTH Centralized Biomaterial Bank (RWTH cBMB), Medical Faculty, RWTH Aachen University, Aachen, Germany
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66
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Ovarian Cancers: Genetic Abnormalities, Tumor Heterogeneity and Progression, Clonal Evolution and Cancer Stem Cells. MEDICINES 2018; 5:medicines5010016. [PMID: 29389895 PMCID: PMC5874581 DOI: 10.3390/medicines5010016] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 02/07/2023]
Abstract
Four main histological subtypes of ovarian cancer exist: serous (the most frequent), endometrioid, mucinous and clear cell; in each subtype, low and high grade. The large majority of ovarian cancers are diagnosed as high-grade serous ovarian cancers (HGS-OvCas). TP53 is the most frequently mutated gene in HGS-OvCas; about 50% of these tumors displayed defective homologous recombination due to germline and somatic BRCA mutations, epigenetic inactivation of BRCA and abnormalities of DNA repair genes; somatic copy number alterations are frequent in these tumors and some of them are associated with prognosis; defective NOTCH, RAS/MEK, PI3K and FOXM1 pathway signaling is frequent. Other histological subtypes were characterized by a different mutational spectrum: LGS-OvCas have increased frequency of BRAF and RAS mutations; mucinous cancers have mutation in ARID1A, PIK3CA, PTEN, CTNNB1 and RAS. Intensive research was focused to characterize ovarian cancer stem cells, based on positivity for some markers, including CD133, CD44, CD117, CD24, EpCAM, LY6A, ALDH1. Ovarian cancer cells have an intrinsic plasticity, thus explaining that in a single tumor more than one cell subpopulation, may exhibit tumor-initiating capacity. The improvements in our understanding of the molecular and cellular basis of ovarian cancers should lead to more efficacious treatments.
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Comprehensive analysis of lncRNA expression profiles reveals a novel lncRNA signature to discriminate nonequivalent outcomes in patients with ovarian cancer. Oncotarget 2018; 7:32433-48. [PMID: 27074572 PMCID: PMC5078024 DOI: 10.18632/oncotarget.8653] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/28/2016] [Indexed: 02/01/2023] Open
Abstract
There is growing evidence of dysregulated long non-coding RNAs (lncRNAs) serving as potential biomarkers for cancer prognosis. However, systematic efforts of searching for an expression-based lncRNA signature for prognosis prediction in ovarian cancer (OvCa) have not been made yet. Here, we performed comprehensive analysis for lncRNA expression profiles and clinical data of 544 OvCa patients from The Cancer Genome Atlas (TCGA), and identified an eight-lncRNA signature with ability to classify patients of the training cohort into high-risk group showing poor outcome and low-risk group showing significantly improved outcome, which was further validated in the validation cohort and entire TCGA cohort. Multivariate Cox regression analysis and stratified analysis demonstrated that the prognostic value of this signature was independent of other clinicopathological factors. Associating the outcome prediction with BRCA1 and/or BRCA2 mutation revealed a superior prognosis performance both in BRCA1/2-mutated and BRCA1/2 wild-type tumors. Finally, a significantly correlation was found between the lncRNA signature and the complete response rate of chemotherapy, suggesting that this eight-lncRNA signature may be a measure to predict chemotherapy response and identify platinum-resistant patients who might benefit from other more efficacious therapies. With further prospective validation, this eight-lncRNA signature may have important implications for outcome prediction and therapy decisions.
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68
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You N, He S, Wang X, Zhu J, Zhang H. Subtype classification and heterogeneous prognosis model construction in precision medicine. Biometrics 2018; 74:814-822. [PMID: 29359319 DOI: 10.1111/biom.12843] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 11/28/2022]
Abstract
Common diseases including cancer are heterogeneous. It is important to discover disease subtypes and identify both shared and unique risk factors for different disease subtypes. The advent of high-throughput technologies enriches the data to achieve this goal, if necessary statistical methods are developed. Existing methods can accommodate both heterogeneity identification and variable selection under parametric models, but for survival analysis, the commonly used Cox model is semiparametric. Although finite-mixture Cox model has been proposed to address heterogeneity in survival analysis, variable selection has not been incorporated into such semiparametric models. Using regularization regression, we propose a variable selection method for the finite-mixture Cox model and select important, subtype-specific risk factors from high-dimensional predictors. Our estimators have oracle properties with proper choices of penalty parameters under the regularization regression. An expectation-maximization algorithm is developed for numerical calculation. Simulations demonstrate that our proposed method performs well in revealing the heterogeneity and selecting important risk factors for each subtype, and its performance is compared to alternatives with other regularizers. Finally, we apply our method to analyze a gene expression dataset for ovarian cancer DNA repair pathways. Based on our selected risk factors, the prognosis model accounting for heterogeneity consistently improves the prediction for the survival probability in both training and test datasets.
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Affiliation(s)
- Na You
- School of Mathematics and Southern China Center for Statistical Science, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Shun He
- LMAM, School of Mathematical Sciences, Peking University, Beijing 100871, China
| | - Xueqin Wang
- School of Mathematics and Southern China Center for Statistical Science, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.,Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.,SYSU-CMU Shunde International Joint Research Institute, Shunde, Guangdong 528300, China
| | - Junxian Zhu
- School of Mathematics and Southern China Center for Statistical Science, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Heping Zhang
- Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut 06511, U.S.A
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69
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CONCORD biomarker prediction for novel drug introduction to different cancer types. Oncotarget 2017; 9:1091-1106. [PMID: 29416679 PMCID: PMC5787421 DOI: 10.18632/oncotarget.23124] [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: 11/18/2016] [Accepted: 11/13/2017] [Indexed: 01/21/2023] Open
Abstract
Many cancer therapeutic agents have shown to be effective for treating multiple cancer types. Yet major challenges exist toward introducing a novel drug used in one cancer type to different cancer types, especially when a relatively small number of patients with the other cancer type often benefit from anti-cancer therapy with the drug. Recently, many novel agents were introduced to different cancer types together with companion biomarkers which were obtained or biologically assumed from the original cancer type. However, there is no guarantee that biomarkers from one cancer can directly predict a therapeutic response in another. To tackle this challenging question, we have developed a concordant expression biomarker-based technique ("CONCORD") that overcomes these limitations. CONCORD predicts drug responses from one cancer type to another by identifying concordantly co-expressed biomarkers across different cancer systems. Application of CONCORD to three standard chemotherapeutic agents and two targeted agents demonstrated its ability to accurately predict the effectiveness of a drug against new cancer types and predict therapeutic response in patients.
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70
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The expression of miRNAs is associated with tumour genome instability and predicts the outcome of ovarian cancer patients treated with platinum agents. Sci Rep 2017; 7:14736. [PMID: 29116111 PMCID: PMC5677022 DOI: 10.1038/s41598-017-12259-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 09/04/2017] [Indexed: 12/19/2022] Open
Abstract
miRNAs, a class of short but stable noncoding RNA molecules, have been revealed to play important roles in the DNA damage response (DDR). However, their functions in cancer genome instability and the consequent clinical effect as the response to chemotherapy have not been fully elucidated. In this study, we utilized multidimensional TCGA data and the known miRNAs involved in DDR to identify a miRNA-regulatory network that responds to DNA damage. Additionally, based on the expression of ten miRNAs in this network, we developed a 10-miRNA-score that predicts defects in the homologous recombination (HR) pathway and genome instability in ovarian cancer. Importantly, consistent with the association between HR defects and improved response to chemotherapeutic agents, the 10-miRNA-score predicts the outcome of ovarian cancer patients treated with platinum agents, with a surprisingly better performance than the indexes of DNA damage. Therefore, our study demonstrates the implication of miRNA expression on cancer genome instability and provides an alternative method to identify DDR defects in patients who show the best effect with platinum drug treatment.
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71
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Tian X, Zhu X, Yan T, Yu C, Shen C, Hu Y, Hong J, Chen H, Fang JY. Recurrence-associated gene signature optimizes recurrence-free survival prediction of colorectal cancer. Mol Oncol 2017; 11:1544-1560. [PMID: 28796930 PMCID: PMC5664005 DOI: 10.1002/1878-0261.12117] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/27/2017] [Accepted: 07/29/2017] [Indexed: 12/28/2022] Open
Abstract
High throughput gene expression profiling has showed great promise in providing insight into molecular mechanisms. Metastasis‐related mRNAs may potentially enrich genes with the ability to predict cancer recurrence, therefore we attempted to build a recurrence‐associated gene signature to improve prognostic prediction of colorectal cancer (CRC). We identified 2848 differentially expressed mRNAs by analyzing CRC tissues with or without metastasis. For the selection of prognostic genes, a LASSO Cox regression model (least absolute shrinkage and selection operator method) was employed. Using this method, a 13‐mRNA signature was identified and then validated in two independent Gene Expression Omnibus cohorts. This classifier could successfully discriminate the high‐risk patients in discovery cohort [hazard ratio (HR) = 5.27, 95% confidence interval (CI) 2.30–12.08, P < 0.0001). Analysis in two independent cohorts yielded consistent results (GSE14333: HR = 4.55, 95% CI 2.18–9.508, P < 0.0001; GSE33113: HR = 3.26, 95% CI 2.16–9.16, P = 0.0176). Further analysis revealed that the prognostic value of this signature was independent of tumor stage, postoperative chemotherapy and somatic mutation. Receiver operating characteristic (ROC) analysis showed that the area under ROC curve of this signature was 0.8861 and 0.8157 in the discovery and validation cohort, respectively. A nomogram was constructed for clinicians, and did well in the calibration plots. Furthermore, this 13‐mRNA signature outperformed other known gene signatures, including oncotypeDX colon cancer assay. Single‐sample gene‐set enrichment analysis revealed that a group of pathways related to drug resistance, cancer metastasis and stemness were significantly enriched in the high‐risk patients. In conclusion, this 13‐mRNA signature may be a useful tool for prognostic evaluation and will facilitate personalized management of CRC patients.
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Affiliation(s)
- Xianglong Tian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Xiaoqiang Zhu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Tingting Yan
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Chenyang Yu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Chaoqin Shen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Ye Hu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Jie Hong
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Haoyan Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
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Tian X, Zhu X, Yan T, Yu C, Shen C, Hong J, Chen H, Fang JY. Differentially Expressed lncRNAs in Gastric Cancer Patients: A Potential Biomarker for Gastric Cancer Prognosis. J Cancer 2017; 8:2575-2586. [PMID: 28900495 PMCID: PMC5595087 DOI: 10.7150/jca.19980] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/10/2017] [Indexed: 12/16/2022] Open
Abstract
Current studies indicate that long non-coding RNAs (lncRNAs) are frequently aberrantly expressed in cancers and implicated with prognosis in gastric cancer (GC). We intended to generate a multi-lncRNA signature to improve prognostic prediction of GC. By analyzing ten paired GC and adjacent normal mucosa tissues, 339 differentially expressed lncRNAs were identified as the candidate prognostic biomarkers in GC. Then we used LASSO Cox regression method to build a 12-lncRNA signature and validated it in another independent GEO dataset. An innovative 12-lncRNA signature was established, and it was significantly associated with the disease free survival (DFS) in the training dataset. By applying the 12-lncRNA signature, the training cohort patients could be categorized into high-risk or low-risk subgroup with significantly different DFS (HR = 4.52, 95%CI= 2.49-8.20, P < 0.0001). Similar results were obtained in another independent GEO dataset (HR=1.58, 95%CI=1.05 - 2.38, P=0.0270). Further analysis showed that the prognostic value of this 12-lncRNA signature was independent of AJCC stage and postoperative chemotherapy. Receiver operating characteristic (ROC) analysis showed that the area under receiver operating characteristic curve (AUC) of combined model reached 0.869. Additionally, a well-performed nomogram was constructed for clinicians. Moreover, single-sample gene-set enrichment analysis (ssGSEA) showed that a group of pathways related to drug resistance and cancer metastasis significantly enriched in the high risk patients. A useful innovative 12-lncRNA signature was established for prognostic evaluation of GC. It might complement clinicopathological features and facilitate personalized management of GC.
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Affiliation(s)
- Xianglong Tian
- Division of Gastroenterology and Hepatology; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; State Key Laboratory for Oncogenes and Related Genes; Renji Hospital, School of Medicine, Shanghai JiaoTong University; Shanghai Institute of Digestive Disease; 145 Middle Shandong Road, Shanghai 200001, China
| | - Xiaoqiang Zhu
- Division of Gastroenterology and Hepatology; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; State Key Laboratory for Oncogenes and Related Genes; Renji Hospital, School of Medicine, Shanghai JiaoTong University; Shanghai Institute of Digestive Disease; 145 Middle Shandong Road, Shanghai 200001, China
| | - Tingting Yan
- Division of Gastroenterology and Hepatology; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; State Key Laboratory for Oncogenes and Related Genes; Renji Hospital, School of Medicine, Shanghai JiaoTong University; Shanghai Institute of Digestive Disease; 145 Middle Shandong Road, Shanghai 200001, China
| | - Chenyang Yu
- Division of Gastroenterology and Hepatology; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; State Key Laboratory for Oncogenes and Related Genes; Renji Hospital, School of Medicine, Shanghai JiaoTong University; Shanghai Institute of Digestive Disease; 145 Middle Shandong Road, Shanghai 200001, China
| | - Chaoqin Shen
- Division of Gastroenterology and Hepatology; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; State Key Laboratory for Oncogenes and Related Genes; Renji Hospital, School of Medicine, Shanghai JiaoTong University; Shanghai Institute of Digestive Disease; 145 Middle Shandong Road, Shanghai 200001, China
| | - Jie Hong
- Division of Gastroenterology and Hepatology; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; State Key Laboratory for Oncogenes and Related Genes; Renji Hospital, School of Medicine, Shanghai JiaoTong University; Shanghai Institute of Digestive Disease; 145 Middle Shandong Road, Shanghai 200001, China
| | - Haoyan Chen
- Division of Gastroenterology and Hepatology; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; State Key Laboratory for Oncogenes and Related Genes; Renji Hospital, School of Medicine, Shanghai JiaoTong University; Shanghai Institute of Digestive Disease; 145 Middle Shandong Road, Shanghai 200001, China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; State Key Laboratory for Oncogenes and Related Genes; Renji Hospital, School of Medicine, Shanghai JiaoTong University; Shanghai Institute of Digestive Disease; 145 Middle Shandong Road, Shanghai 200001, China
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73
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A molecular portrait of microsatellite instability across multiple cancers. Nat Commun 2017; 8:15180. [PMID: 28585546 PMCID: PMC5467167 DOI: 10.1038/ncomms15180] [Citation(s) in RCA: 415] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/03/2017] [Indexed: 12/30/2022] Open
Abstract
Microsatellite instability (MSI) refers to the hypermutability of short repetitive sequences in the genome caused by impaired DNA mismatch repair. Although MSI has been studied for decades, large amounts of sequencing data now available allows us to examine the molecular fingerprints of MSI in greater detail. Here, we analyse ∼8,000 exomes and ∼1,000 whole genomes of cancer patients across 23 cancer types. Our analysis reveals that the frequency of MSI events is highly variable within and across tumour types. We also identify genes in DNA repair and oncogenic pathways recurrently subject to MSI and uncover non-coding loci that frequently display MSI. Finally, we propose a highly accurate exome-based predictive model for the MSI phenotype. These results advance our understanding of the genomic drivers and consequences of MSI, and our comprehensive catalogue of tumour-type-specific MSI loci will enable panel-based MSI testing to identify patients who are likely to benefit from immunotherapy. Some cancers with DNA mismatch repair deficiency display microsatellite instability. Here the authors analyse twenty three cancer types at the exome and whole-genome level, and identify loci with recurrent microsatellite instability that could be used to identify patients who would benefit from immunotherapy.
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74
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Zhan X, Dong C, Liu G, Li Y, Liu L. Panel of seven long noncoding RNA as a candidate prognostic biomarker for ovarian cancer. Onco Targets Ther 2017; 10:2805-2813. [PMID: 28620265 PMCID: PMC5466362 DOI: 10.2147/ott.s128797] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Ovarian cancer is one of the most common and lethal gynecological malignancies. The diagnosis of ovarian cancer is often at an advanced stage. Accumulated evidence suggests that long noncoding RNAs (lncRNAs) play important roles during ovarian tumorigenesis. In this study, using the lncRNA-mining approach, we analyzed lncRNA expression profiles of 493 ovarian cancer patients from Gene Expression Omnibus datasets, and identified a signature group of seven lncRNAs (BC037530, AK021924, AK094536, AK094536, BC062365, BC004123 and BC007937) associated with patient survival in the training dataset GSE9891. We also formulated a risk score model to divide patients into low-risk and high-risk groups based on the expression of these seven lncRNAs. We further validated the predictive power of our risk score model in two other datasets, GSE26193 and GSE63885. Our analysis showed that the seven-lncRNA signature can serve as an independent predictor apart from Federation of Gynecology and Obstetrics (FIGO) stage and patient age. Further investigation revealed the seven-lncRNA signature correlated with few critical signaling pathways involved in cancer. Combined, all these findings strongly support that the seven-lncRNA signature can serve as a strong prognosis biomarker.
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Affiliation(s)
- Xiaohui Zhan
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai.,University of Chinese Academy of Sciences, Beijing
| | - Chuanpeng Dong
- Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai
| | - Gang Liu
- Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai
| | - Yixue Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai.,University of Chinese Academy of Sciences, Beijing.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, People's Republic of China
| | - Lei Liu
- Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai
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75
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McGrail DJ, Lin CCJ, Garnett J, Liu Q, Mo W, Dai H, Lu Y, Yu Q, Ju Z, Yin J, Vellano CP, Hennessy B, Mills GB, Lin SY. Improved prediction of PARP inhibitor response and identification of synergizing agents through use of a novel gene expression signature generation algorithm. NPJ Syst Biol Appl 2017. [PMID: 28649435 PMCID: PMC5445594 DOI: 10.1038/s41540-017-0011-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Despite rapid advancement in generation of large-scale microarray gene expression datasets, robust multigene expression signatures that are capable of guiding the use of specific therapies have not been routinely implemented into clinical care. We have developed an iterative resampling analysis to predict sensitivity algorithm to generate gene expression sensitivity profiles that predict patient responses to specific therapies. The resultant signatures have a robust capacity to accurately predict drug sensitivity as well as the identification of synergistic combinations. Here, we apply this approach to predict response to PARP inhibitors, and show it can greatly outperforms current clinical biomarkers, including BRCA1/2 mutation status, accurately identifying PARP inhibitor-sensitive cancer cell lines, primary patient-derived tumor cells, and patient-derived xenografts. These signatures were also capable of predicting patient response, as shown by applying a cisplatin sensitivity signature to ovarian cancer patients. We additionally demonstrate how these drug-sensitivity signatures can be applied to identify novel synergizing agents to improve drug efficacy. Tailoring therapeutic interventions to improve patient prognosis is of utmost importance, and our drug sensitivity prediction signatures may prove highly beneficial for patient management.
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Affiliation(s)
- Daniel J McGrail
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Curtis Chun-Jen Lin
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Jeannine Garnett
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Qingxin Liu
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Wei Mo
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Hui Dai
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Yiling Lu
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Qinghua Yu
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Zhenlin Ju
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Jun Yin
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX 77030 USA
| | | | - Bryan Hennessy
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland
| | - Gordon B Mills
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX 77030 USA
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76
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Sun CY, Su TF, Li N, Zhou B, Guo ES, Yang ZY, Liao J, Ding D, Xu Q, Lu H, Meng L, Wang SX, Zhou JF, Xing H, Weng DH, Ma D, Chen G. A chemotherapy response classifier based on support vector machines for high-grade serous ovarian carcinoma. Oncotarget 2016; 7:3245-54. [PMID: 26675546 PMCID: PMC4823103 DOI: 10.18632/oncotarget.6569] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/21/2015] [Indexed: 01/13/2023] Open
Abstract
Long-term outcome of high-grade serous epithelial ovarian carcinoma (HGSOC) remains poor as a result of recurrence and the emergence of drug resistance. Almost all the patients were given the same platinum-based chemotherapy after debulking surgery even though some of them are naturally resistant to the first-line chemotherapy. No method could verify this part of patients right after the surgery currently. In this study, we used 156 paraffin-embedded high-grade HGSOC specimens for immunohistochemical analysis with 37 immunology markers, and association between the expression levels of these markers and the chemoresponse were evaluated. A support vector machine (SVM)-based HGSOC prognostic classifier was then established, and was validated by a 95-patient independent cohort. The classifier was strongly predictive of chemotherapy resistance, and divided patients into low- and high-risk groups with significant differences progression-free survival (PFS) and overall survival (OS). This classifier may provide a potential way to predict the chemotherapy resistance of HGSOC right after the surgery, and then allow clinicians to make optimal clinical decision for those potentially chemoresistant patients. The potential clinical application of this classifier will benefit those patients with primary drug resistance.
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Affiliation(s)
- Chao-Yang Sun
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Tie-Fen Su
- Department of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Na Li
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Bo Zhou
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - En-Song Guo
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Zong-Yuan Yang
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Jing Liao
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Dong Ding
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Qin Xu
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Hao Lu
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Li Meng
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Shi-Xuan Wang
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Jian-Feng Zhou
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Hui Xing
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei 441021, China
| | - Dan-Hui Weng
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Ding Ma
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Gang Chen
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
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Santos JC, Ribeiro ML, Sarian LO, Ortega MM, Derchain SF. Exosomes-mediate microRNAs transfer in breast cancer chemoresistance regulation. Am J Cancer Res 2016; 6:2129-2139. [PMID: 27822407 PMCID: PMC5088281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 09/09/2016] [Indexed: 06/06/2023] Open
Abstract
Breast cancer is the most common and fatal type of cancer in women worldwide due to the metastatic process and resistance to treatment. Despite advances in molecular knowledge, little is known regarding resistance to chemotherapy. One highlighted aspect is the DNA damage response (DDR) pathway that is activated upon genotoxic damage, controlling the cell cycle arrest or DNA repair activation. Recently, studies have showed that cancer stem cells (CSCs) could promote chemoresistance through DDR pathway. Furthermore, it is known that the epithelial-mesenchymal transition (EMT) can generate cells with CSCs characteristics and therefore regulate the chemoresistance process. The exosomes are microvesicles filled with RNAs, proteins and microRNAs (miRNAs) that can be released by many cell types, including tumor cells and CSCs. The exosomes content may be cell-to-cell transferable and it could control a wide range of pathways during tumor development and metastasis. A big challenge for modern medicine is to determine the reasons why patients do not respond to chemotherapy treatments and also guide the most appropriate therapy for each one. Considering that the CSCs are able to stimulate the formation of a more aggressive tumor phenotype with migration and metastasis ability, resistance to treatment and disease recurrence, as well as few studies capable to determine clearly the interaction of breast CSCs with its microenvironment, the present review summarize the possibility that exosomes-mediate miRNAs transfer and regulate chemoresistance in breast tumor cells and CSCs, to clarify the complexity of breast cancer progression and therapy.
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Affiliation(s)
- Juliana Carvalho Santos
- Women’s Health Hospital “Prof Dr José Aristodemo Pinotti” (CAISM), State University of Campinas (UNICAMP)Campinas, SP, Brazil
| | - Marcelo Lima Ribeiro
- Clinical Pharmacology and Gastroenterology Unit, São Francisco University, São Francisco UniversityBragança Paulista, SP, Brazil
| | - Luis Otávio Sarian
- Women’s Health Hospital “Prof Dr José Aristodemo Pinotti” (CAISM), State University of Campinas (UNICAMP)Campinas, SP, Brazil
| | - Manoela Marques Ortega
- Clinical Pharmacology and Gastroenterology Unit, São Francisco University, São Francisco UniversityBragança Paulista, SP, Brazil
| | - Sophie Françoise Derchain
- Women’s Health Hospital “Prof Dr José Aristodemo Pinotti” (CAISM), State University of Campinas (UNICAMP)Campinas, SP, Brazil
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78
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Stover EH, Konstantinopoulos PA, Matulonis UA, Swisher EM. Biomarkers of Response and Resistance to DNA Repair Targeted Therapies. Clin Cancer Res 2016; 22:5651-5660. [PMID: 27678458 DOI: 10.1158/1078-0432.ccr-16-0247] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 09/02/2016] [Accepted: 09/06/2016] [Indexed: 11/16/2022]
Abstract
Drugs targeting DNA damage repair (DDR) pathways are exciting new agents in cancer therapy. Many of these drugs exhibit synthetic lethality with defects in DNA repair in cancer cells. For example, ovarian cancers with impaired homologous recombination DNA repair show increased sensitivity to poly(ADP-ribose) polymerase (PARP) inhibitors. Understanding the activity of different DNA repair pathways in individual tumors, and the correlations between DNA repair function and drug response, will be critical to patient selection for DNA repair targeted agents. Genomic and functional assays of DNA repair pathway activity are being investigated as potential biomarkers of response to targeted therapies. Furthermore, alterations in DNA repair function generate resistance to DNA repair targeted agents, and DNA repair states may predict intrinsic or acquired drug resistance. In this review, we provide an overview of DNA repair targeted agents currently in clinical trials and the emerging biomarkers of response and resistance to these agents: genetic and genomic analysis of DDR pathways, genomic signatures of mutational processes, expression of DNA repair proteins, and functional assays for DNA repair capacity. We review biomarkers that may predict response to selected DNA repair targeted agents, including PARP inhibitors, inhibitors of the DNA damage sensors ATM and ATR, and inhibitors of nonhomologous end joining. Finally, we introduce emerging categories of drugs targeting DDR and new strategies for integrating DNA repair targeted therapies into clinical practice, including combination regimens. Generating and validating robust biomarkers will optimize the efficacy of DNA repair targeted therapies and maximize their impact on cancer treatment. Clin Cancer Res; 22(23); 5651-60. ©2016 AACR.
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79
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Liu C, Rohart F, Simpson PT, Khanna KK, Ragan MA, Lê Cao KA. Integrating Multi-omics Data to Dissect Mechanisms of DNA repair Dysregulation in Breast Cancer. Sci Rep 2016; 6:34000. [PMID: 27666291 PMCID: PMC5036051 DOI: 10.1038/srep34000] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/01/2016] [Indexed: 12/20/2022] Open
Abstract
DNA repair genes and pathways that are transcriptionally dysregulated in cancer provide the first line of evidence for the altered DNA repair status in tumours, and hence have been explored intensively as a source for biomarker discovery. The molecular mechanisms underlying DNA repair dysregulation, however, have not been systematically investigated in any cancer type. In this study, we performed a statistical analysis to dissect the roles of DNA copy number alteration (CNA), DNA methylation (DM) at gene promoter regions and the expression changes of transcription factors (TFs) in the differential expression of individual DNA repair genes in normal versus tumour breast samples. These gene-level results were summarised at pathway level to assess whether different DNA repair pathways are affected in distinct manners. Our results suggest that CNA and expression changes of TFs are major causes of DNA repair dysregulation in breast cancer, and that a subset of the identified TFs may exert global impacts on the dysregulation of multiple repair pathways. Our work hence provides novel insights into DNA repair dysregulation in breast cancer. These insights improve our understanding of the molecular basis of the DNA repair biomarkers identified thus far, and have potential to inform future biomarker discovery.
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Affiliation(s)
- Chao Liu
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4067, Australia
| | - Florian Rohart
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Peter T Simpson
- UQ Centre for Clinical Research and School of Medicine, The University of Queensland, Herston, QLD 4101, Australia
| | - Kum Kum Khanna
- QIMR-Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4067, Australia
| | - Kim-Anh Lê Cao
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
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80
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Zhu X, Tian X, Yu C, Shen C, Yan T, Hong J, Wang Z, Fang JY, Chen H. A long non-coding RNA signature to improve prognosis prediction of gastric cancer. Mol Cancer 2016; 15:60. [PMID: 27647437 PMCID: PMC5029104 DOI: 10.1186/s12943-016-0544-0] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/07/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Increasing evidence suggests long non-coding RNAs (lncRNAs) are frequently aberrantly expressed in cancers, however, few related lncRNA signatures have been established for prediction of cancer prognosis. We aimed at developing alncRNA signature to improve prognosis prediction of gastric cancer (GC). METHODS Using a lncRNA-mining approach, we performed lncRNA expression profiling in large GC cohorts from Gene Expression Ominus (GEO), including GSE62254 data set (N = 300) and GSE15459 data set (N = 192). We established a set of 24-lncRNAs that were significantly associated with the disease free survival (DFS) in the test series. RESULTS Based on this 24-lncRNA signature, the test series patients could be classified into high-risk or low-risk subgroup with significantly different DFS (HR = 1.19, 95 % CI = 1.13-1.25, P < 0.0001). The prognostic value of this 24-lncRNA signature was confirmed in the internal validation series and another external validation series, respectively. Further analysis revealed that the prognostic value of this signature was independent of lymph node ratio (LNR) and postoperative chemotherapy. Gene set enrichment analysis (GSEA) indicated that high risk score group was associated with several cancer recurrence and metastasis associated pathways. CONCLUSIONS The identification of the prognostic lncRNAs indicates the potential roles of lncRNAs in GC biogenesis. Our results may provide an efficient classification tool for clinical prognosis evaluation of GC.
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Affiliation(s)
- Xiaoqiang Zhu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Xianglong Tian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Chenyang Yu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Chaoqin Shen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Tingting Yan
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Jie Hong
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Zheng Wang
- Department of gastrointestinal surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Haoyan Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
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81
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Evans JR, Zhao SG, Chang SL, Tomlins SA, Erho N, Sboner A, Schiewer MJ, Spratt DE, Kothari V, Klein EA, Den RB, Dicker AP, Karnes RJ, Yu X, Nguyen PL, Rubin MA, de Bono J, Knudsen KE, Davicioni E, Feng FY. Patient-Level DNA Damage and Repair Pathway Profiles and Prognosis After Prostatectomy for High-Risk Prostate Cancer. JAMA Oncol 2016; 2:471-80. [PMID: 26746117 DOI: 10.1001/jamaoncol.2015.4955] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
IMPORTANCE A substantial number of patients diagnosed with high-risk prostate cancer are at risk for metastatic progression after primary treatment. Better biomarkers are needed to identify patients at the highest risk to guide therapy intensification. OBJECTIVE To create a DNA damage and repair (DDR) pathway profiling method for use as a prognostic signature biomarker in high-risk prostate cancer. DESIGN, SETTING, AND PARTICIPANTS A cohort of 1090 patients with high-risk prostate cancer who underwent prostatectomy and were treated at 3 different academic institutions were divided into a training cohort (n = 545) and 3 pooled validation cohorts (n = 232, 130, and 183) assembled for case-control or case-cohort studies. Profiling of 9 DDR pathways using 17 gene sets for GSEA (Gene Set Enrichment Analysis) of high-density microarray gene expression data from formalin-fixed paraffin-embedded prostatectomy samples with median 10.3 years follow-up was performed. Prognostic signature development from DDR pathway profiles was studied, and DDR pathway gene mutation in published cohorts was analyzed. MAIN OUTCOMES AND MEASURES Biochemical recurrence-free, metastasis-free, and overall survival. RESULTS Across the training cohort and pooled validation cohorts, 1090 men were studied; mean (SD) age at diagnosis was 65.3 (6.4) years. We found that there are distinct clusters of DDR pathways within the cohort, and DDR pathway enrichment is only weakly correlated with clinical variables such as age (Spearman ρ [ρ], range, -0.07 to 0.24), Gleason score (ρ, range, 0.03 to 0.20), prostate-specific antigen level (ρ, range, -0.07 to 0.10), while 13 of 17 DDR gene sets are strongly correlated with androgen receptor pathway enrichment (ρ, range, 0.33 to 0.82). In published cohorts, DDR pathway genes are rarely mutated. A DDR pathway profile prognostic signature built in the training cohort was significantly associated with biochemical recurrence-free, metastasis-free, and overall survival in the pooled validation cohorts independent of standard clinicopathological variables. The prognostic performance of the signature for metastasis-free survival appears to be stronger in the younger patients (HR, 1.67; 95% CI, 1.12-2.50) than in the older patients (HR, 0.77; 95% CI, 0.29-2.07) on multivariate Cox analysis. CONCLUSIONS AND RELEVANCE DNA damage and repair pathway profiling revealed patient-level variations and the DDR pathways are rarely affected by mutation. A DDR pathway signature showed strong prognostic performance with the long-term outcomes of metastasis-free and overall survival that may be useful for risk stratification of high-risk prostate cancer patients.
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Affiliation(s)
- Joseph R Evans
- Department of Radiation Oncology, University of Michigan, Ann Arbor
| | - Shuang G Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor2Beaumont Hospital - Dearborn, Transitional Year Program, Dearborn, Michigan
| | - S Laura Chang
- Department of Radiation Oncology, University of Michigan, Ann Arbor
| | | | - Nicholas Erho
- GenomeDx Biosciences Inc, Vancouver, British Columbia, Canada
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College and New York Presbyterian Hospitals, New York, New York
| | - Matthew J Schiewer
- Kimmel Cancer Center, Jefferson Medical College of Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor
| | - Vishal Kothari
- Department of Radiation Oncology, University of Michigan, Ann Arbor
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio
| | - Robert B Den
- Department of Radiation Oncology, Jefferson Medical College of Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Adam P Dicker
- Department of Radiation Oncology, Jefferson Medical College of Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | | | - Paul L Nguyen
- Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Department of Radiation Oncology, Harvard Medical School, Boston, Massachusetts
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College and New York Presbyterian Hospitals, New York, New York
| | - Johann de Bono
- Drug Development Unit and Prostate Cancer Targeted Therapy Group, The Royal Marsden NHS Foundation Trust and The Institute of Cancer Research, London, England
| | - Karen E Knudsen
- Kimmel Cancer Center, Jefferson Medical College of Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Elai Davicioni
- GenomeDx Biosciences Inc, Vancouver, British Columbia, Canada
| | - Felix Y Feng
- Department of Radiation Oncology, University of Michigan, Ann Arbor13Michigan Center for Translational Pathology, University of Michigan, Ann Arbor14Comprehensive Cancer Center, University of Michigan, Ann Arbor
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82
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Gong C, Tan W, Chen K, You N, Zhu S, Liang G, Xie X, Li Q, Zeng Y, Ouyang N, Li Z, Zeng M, Zhuang S, Lau WY, Liu Q, Yin D, Wang X, Su F, Song E. Prognostic Value of a BCSC-associated MicroRNA Signature in Hormone Receptor-Positive HER2-Negative Breast Cancer. EBioMedicine 2016; 11:199-209. [PMID: 27566954 PMCID: PMC5049991 DOI: 10.1016/j.ebiom.2016.08.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 08/10/2016] [Accepted: 08/10/2016] [Indexed: 01/16/2023] Open
Abstract
Biology-driven strategy can be used in development of prognostic model. The BCSC-associated miRNA classifier can predict prognosis for HR + HER2 − breast cancer. The BCSC-associated miRNA classifier outperforms IHC4 scoring and 21-gene RS. Chemotherapy can improve DRFS in patients predicted as high-risk.
Breast cancer patients with high proportion of cancer stem cells (BCSCs) have poor clinical outcomes. MiRNAs regulate key features of BCSCs as oncogenes or tumor suppressors. Although hormone receptor (HR)-positive, HER2-negative breast cancers are the most common subtype, current methods are inadequate to predict its clinical outcome. In this multicenter study, we identified and validated a 10 BCSC-associated-miRNA classifier that can predict survival for HR + HER2 − patients. Retrospective analysis showed that this classifier outperformed IHC4 scoring and 21-gene Recurrence Score (RS), and chemotherapy could improve survival in high-risk patients determined by this classifier. This model may facilitate personalized clinical decision for HR + HER2 − individuals. Purpose Breast cancer patients with high proportion of cancer stem cells (BCSCs) have unfavorable clinical outcomes. MicroRNAs (miRNAs) regulate key features of BCSCs. We hypothesized that a biology-driven model based on BCSC-associated miRNAs could predict prognosis for the most common subtype, hormone receptor (HR)-positive, HER2-negative breast cancer patients. Patients and Methods After screening candidate miRNAs based on literature review and a pilot study, we built a miRNA-based classifier using LASSO Cox regression method in the training group (n = 202) and validated its prognostic accuracy in an internal (n = 101) and two external validation groups (n = 308). Results In this multicenter study, a 10-miRNA classifier incorporating miR-21, miR-30c, miR-181a, miR-181c, miR-125b, miR-7, miR-200a, miR-135b, miR-22 and miR-200c was developed to predict distant relapse free survival (DRFS). With this classifier, HR + HER2 − patients were scored and classified into high-risk and low-risk disease recurrence, which was significantly associated with 5-year DRFS of the patients. Moreover, this classifier outperformed traditional clinicopathological risk factors, IHC4 scoring and 21-gene Recurrence Score (RS). The patients with high-risk recurrence determined by this classifier benefit more from chemotherapy. Conclusions Our 10-miRNA-based classifier provides a reliable prognostic model for disease recurrence in HR + HER2 − breast cancer patients. This model may facilitate personalized therapy-decision making for HR + HER2 − individuals.
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Affiliation(s)
- Chang Gong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Weige Tan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Kai Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Na You
- Department of Statistical Science, School of Mathematics and Computational Science & Southern China Research Center of Statistical Science, Sun Yat-sen University, Guangzhou 510275 China
| | - Shan Zhu
- Department of Statistical Science, School of Mathematics and Computational Science & Southern China Research Center of Statistical Science, Sun Yat-sen University, Guangzhou 510275 China
| | - Gehao Liang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xinhua Xie
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, 510060, China
| | - Qian Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yunjie Zeng
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Nengtai Ouyang
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Zhihua Li
- Prevention and Cure Center of Breast Disease, Key Laboratory of Breast Disease, the Third Hospital of Nanchang City, Nanchang, Jiangxi 330009, China
| | - Musheng Zeng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, 510060, China
| | - ShiMei Zhuang
- Key Laboratory of Gene Engineering of Ministry of Education, Collaborative Innovation Center for Cancer Medicine, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Wan-Yee Lau
- Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China; Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Qiang Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xueqin Wang
- Department of Statistical Science, School of Mathematics and Computational Science & Southern China Research Center of Statistical Science, Sun Yat-sen University, Guangzhou 510275 China
| | - Fengxi Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Collaborative Innovation Center for Cancer Medicine, China.
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83
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Yin X, Wang X, Shen B, Jing Y, Li Q, Cai MC, Gu Z, Yang Q, Zhang Z, Liu J, Li H, Di W, Zhuang G. A VEGF-dependent gene signature enriched in mesenchymal ovarian cancer predicts patient prognosis. Sci Rep 2016; 6:31079. [PMID: 27498762 PMCID: PMC4976329 DOI: 10.1038/srep31079] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/12/2016] [Indexed: 12/14/2022] Open
Abstract
We have previously reported surrogate biomarkers of VEGF pathway activities with the potential to provide predictive information for anti-VEGF therapies. The aim of this study was to systematically evaluate a new VEGF-dependent gene signature (VDGs) in relation to molecular subtypes of ovarian cancer and patient prognosis. Using microarray profiling and cross-species analysis, we identified 140-gene mouse VDGs and corresponding 139-gene human VDGs, which displayed enrichment of vasculature and basement membrane genes. In patients who received bevacizumab therapy and showed partial response, the expressions of VDGs (summarized to yield VDGs scores) were markedly decreased in post-treatment biopsies compared with pre-treatment baselines. In contrast, VDGs scores were not significantly altered following bevacizumab treatment in patients with stable or progressive disease. Analysis of VDGs in ovarian cancer showed that VDGs as a prognostic signature was able to predict patient outcome. Correlation estimation of VDGs scores and molecular features revealed that VDGs was overrepresented in mesenchymal subtype and BRCA mutation carriers. These findings highlighted the prognostic role of VEGF-mediated angiogenesis in ovarian cancer, and proposed a VEGF-dependent gene signature as a molecular basis for developing novel diagnostic strategies to aid patient selection for VEGF-targeted agents.
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Affiliation(s)
- Xia Yin
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Department of Obstetrics and Gynecology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaojie Wang
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Boqiang Shen
- Department of Obstetrics and Gynecology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Ying Jing
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Li
- Department of Obstetrics and Gynecology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mei-Chun Cai
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhuowei Gu
- Department of Obstetrics and Gynecology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qi Yang
- Lingyun Community Health Service Center of Xuhui District, Shanghai, China
| | - Zhenfeng Zhang
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Liu
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hongxia Li
- Department of Obstetrics and Gynecology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Wen Di
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Department of Obstetrics and Gynecology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guanglei Zhuang
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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84
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Zimmermann MT, Jiang G, Wang C. Single-sample expression-based chemo-sensitivity score improves survival associations independently from genomic mutations for ovarian cancer Patients. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2016; 2016:94-100. [PMID: 27570657 PMCID: PMC5001782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Platinum-based chemotherapies are first-line treatments for ovarian cancer (OC) patients. Although chemotherapy has a high initial response rate, some patients exhibit inherent chemo-resistance. With advancements of molecular and genomic profiling, it is of high interest to identify molecular and genomic signatures predictive of chemo- sensitivity priori to treatment initiation in order to better personalize care decisions. Previous efforts have made use of mRNA expression levels of selected genes responsible for repairing DNA damage, under the hypothesis that chemo efficacy is associated with their proficiency. However, the resulting scores have been difficult to interpret. In this study, we designed a single-sample based approach known as eCARD to investigate chemo-sensitivity in ovarian cancer patients from The Cancer Genome Atlas. We demonstrated that the proposed single-sample based approach can lead to a molecular-based chemo-sensitivity score predictive of prognosis, which validates in 5 independent cohorts, and associates with increasing mutation burden and likelihood of BRCA1/2 mutation.
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Affiliation(s)
- Michael T. Zimmermann
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Guoqian Jiang
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Chen Wang
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA,Corresponding author electronic address:
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85
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Bagnoli M, Canevari S, Califano D, Losito S, Maio MD, Raspagliesi F, Carcangiu ML, Toffoli G, Cecchin E, Sorio R, Canzonieri V, Russo D, Scognamiglio G, Chiappetta G, Baldassarre G, Lorusso D, Scambia G, Zannoni GF, Savarese A, Carosi M, Scollo P, Breda E, Murgia V, Perrone F, Pignata S, De Cecco L, Mezzanzanica D. Development and validation of a microRNA-based signature (MiROvaR) to predict early relapse or progression of epithelial ovarian cancer: a cohort study. Lancet Oncol 2016; 17:1137-1146. [PMID: 27402147 DOI: 10.1016/s1470-2045(16)30108-5] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 04/21/2016] [Accepted: 04/21/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND Risk of relapse or progression remains high in the treatment of most patients with epithelial ovarian cancer, and development of a molecular predictor could be a valuable tool for stratification of patients by risk. We aimed to develop a microRNA (miRNA)-based molecular classifier that can predict risk of progression or relapse in patients with epithelial ovarian cancer. METHODS We analysed miRNA expression profiles in three cohorts of samples collected at diagnosis. We used 179 samples from a Multicenter Italian Trial in Ovarian cancer trial (cohort OC179) to develop the model and 263 samples from two cancer centres (cohort OC263) and 452 samples from The Cancer Genome Atlas epithelial ovarian cancer series (cohort OC452) to validate the model. The primary clinical endpoint was progression-free survival, and we adapted a semi-supervised prediction method to the miRNA expression profile of OC179 to identify miRNAs that predict risk of progression. We assessed the independent prognostic role of the model using multivariable analysis with a Cox regression model. FINDINGS We identified 35 miRNAs that predicted risk of progression or relapse and used them to create a prognostic model, the 35-miRNA-based predictor of Risk of Ovarian Cancer Relapse or progression (MiROvaR). MiROvaR was able to classify patients in OC179 into a high-risk group (89 patients; median progression-free survival 18 months [95% CI 15-22]) and a low-risk group (90 patients; median progression-free survival 38 months [24-not estimable]; hazard ratio [HR] 1·85 [1·29-2·64], p=0·00082). MiROvaR was a significant predictor of progression in the two validation sets (OC263 HR 3·16, 95% CI 2·33-4·29, p<0·0001; OC452 HR 1·39, 95% CI 1·11-1·74, p=0·0047) and maintained its independent prognostic effect when adjusted for relevant clinical covariates using multivariable analyses (OC179: adjusted HR 1·48, 95% CI 1·03-2·13, p=0·036; OC263: adjusted HR 3·09 [2·24-4·28], p<0·0001; and OC452: HR 1·41 [1·11-1·79], p=0·0047). INTERPRETATION MiROvaR is a potential predictor of epithelial ovarian cancer progression and has prognostic value independent of relevant clinical covariates. MiROvaR warrants further investigation for the development of a clinical-grade prognostic assay. FUNDING AIRC and CARIPLO Foundation.
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Affiliation(s)
- Marina Bagnoli
- Molecular Therapies Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvana Canevari
- Functional Genomics, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Daniela Califano
- Functional Genomic Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione G Pascale", IRCCS, Naples, Italy
| | - Simona Losito
- Surgical Pathology Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione G Pascale", IRCCS, Naples, Italy
| | - Massimo Di Maio
- Clinical Trials Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione G Pascale", IRCCS, Naples, Italy
| | - Francesco Raspagliesi
- Unit of Gynaecological Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maria Luisa Carcangiu
- Anatomic Pathology 1 Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico, Istituto Ricovero e Cura Carattere Scientifico (CRO-IRCCS), Aviano, Italy
| | - Erika Cecchin
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico, Istituto Ricovero e Cura Carattere Scientifico (CRO-IRCCS), Aviano, Italy
| | - Roberto Sorio
- Medical Oncology C, Centro di Riferimento Oncologico, Istituto Ricovero e Cura Carattere Scientifico (CRO-IRCCS), Aviano, Italy
| | - Vincenzo Canzonieri
- Unit of Pathology, Centro di Riferimento Oncologico, Istituto Ricovero e Cura Carattere Scientifico (CRO-IRCCS), Aviano, Italy
| | - Daniela Russo
- Functional Genomic Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione G Pascale", IRCCS, Naples, Italy
| | - Giosué Scognamiglio
- Surgical Pathology Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione G Pascale", IRCCS, Naples, Italy
| | - Gennaro Chiappetta
- Functional Genomic Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione G Pascale", IRCCS, Naples, Italy
| | - Gustavo Baldassarre
- Division of Experimental Oncology 2, Centro di Riferimento Oncologico, Istituto Ricovero e Cura Carattere Scientifico (CRO-IRCCS), Aviano, Italy
| | - Domenica Lorusso
- Unit of Gynaecological Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giovanni Scambia
- Department of Obstetrics and Gynecology, Gynecologic Oncology Unit, Catholic University of the Sacred Heart, Rome, Italy
| | - Gian Franco Zannoni
- Department of Human Pathology, Division of Gynecologic Pathology, Catholic University of the Sacred Heart, Rome, Italy
| | - Antonella Savarese
- Division of Medical Oncology 1, Regina Elena Cancer Institute, Rome, Italy
| | | | - Paolo Scollo
- Department of Obstetrics and Gynecology, Azienda Ospedaliera Cannizzaro, Catania, Italy
| | - Enrico Breda
- Medical Oncology Unit Ospedale S Giovanni Calibita Fatebenefratelli, Rome, Italy
| | | | - Francesco Perrone
- Clinical Trials Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione G Pascale", IRCCS, Naples, Italy
| | - Sandro Pignata
- Department of Urogynaecological Oncology, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione G Pascale", IRCCS, Naples, Italy
| | - Loris De Cecco
- Functional Genomics, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Delia Mezzanzanica
- Molecular Therapies Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
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86
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Goh J, Mohan GR, Ladwa R, Ananda S, Cohen PA, Baron-Hay S. Frontline treatment of epithelial ovarian cancer. Asia Pac J Clin Oncol 2016; 11 Suppl 6:1-16. [PMID: 26669253 DOI: 10.1111/ajco.12449] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2015] [Indexed: 11/29/2022]
Abstract
This is a contemporaneous review of the frontline treatment of epithelial ovarian cancer (EOC), specifically on the importance of optimal surgical cytoreductive surgery, the pivotal role of platinum-based adjuvant chemotherapy (which encompasses intraperitoneal and dose-dense regimens) and the emergence of neo-adjuvant chemotherapy. Additionally, the benefit of concurrent and maintenance bevacizumab in the suboptimally debullked stage III and stage IV EOC setting is also reviewed. The article also discusses the increasing importance of prognostic and predictive molecular biomarkers in the future management of EOC.
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Affiliation(s)
- Jeffrey Goh
- Royal Brisbane and Women's Hospital (RBWH), Herston.,University of Queensland, St Lucia.,Greenslopes Private Hospital, Greenslopes, Queensland
| | - G Raj Mohan
- King Edward Memorial Hospital, Subiaco.,St John of God Hospital, Subiaco.,School of Women's and Infants' Health, University of Western Australia, Crawley, Western Australia
| | - Rahul Ladwa
- Royal Brisbane and Women's Hospital (RBWH), Herston
| | | | - Paul A Cohen
- St John of God Hospital, Subiaco.,School of Women's and Infants' Health, University of Western Australia, Crawley, Western Australia
| | - Sally Baron-Hay
- Royal North Shore Hospital, St Leonards, New South Wales, Australia
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87
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An integrated model of clinical information and gene expression for prediction of survival in ovarian cancer patients. Transl Res 2016; 172:84-95.e11. [PMID: 27059002 DOI: 10.1016/j.trsl.2016.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 11/20/2022]
Abstract
Accumulating evidence shows that clinical factors alone are not adequate for predicting the survival of patients with ovarian cancer (OvCa), and many genes have been found to be associated with OvCa prognosis. The objective of this study was to develop a model that integrates clinical information and a gene signature to predict the survival durations of patients diagnosed with OvCa. We constructed mRNA and microRNA expression profiles and gathered the corresponding clinical data of 552 OvCa patients and 8 normal controls from The Cancer Genome Atlas. Using univariate Cox regression followed by a permutation test, elastic net-regulated Cox regression, and ridge regression, we generated a prognosis index consisting of 2 clinical variables, 7 protective mRNAs, 12 risky mRNAs, and 1 protective microRNA. The area under the curve of the receiver operating characteristic of the integrated clinical-and-gene model was 0.756, larger than that of the clinical-alone model (0.686) or the gene-alone model (0.703). OvCa patients in the high-risk group had a significantly shorter overall survival time compared with patients in the low-risk group (hazard ratio = 8.374, 95% confidence interval = 4.444-15.780, P = 4.90 × 10(-11), by the Wald test). The reliability of the gene signature was confirmed by a public external data set from the Gene Expression Omnibus. Our conclusions that we have identified an integrated clinical-and-gene model superior to the traditional clinical-alone model in ascertaining the survival prognosis of patients with OvCa. Our findings may prove valuable for improving the clinical management of OvCa.
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88
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Gene-expression signatures in ovarian cancer: Promise and challenges for patient stratification. Gynecol Oncol 2016; 141:379-385. [DOI: 10.1016/j.ygyno.2016.01.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 01/04/2016] [Accepted: 01/27/2016] [Indexed: 11/22/2022]
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89
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Saunders EJ, Dadaev T, Leongamornlert DA, Olama AAA, Benlloch S, Giles GG, Wiklund F, Grönberg H, Haiman CA, Schleutker J, Nordestgaard BG, Travis RC, Neal D, Pasayan N, Khaw KT, Stanford JL, Blot WJ, Thibodeau SN, Maier C, Kibel AS, Cybulski C, Cannon-Albright L, Brenner H, Park JY, Kaneva R, Batra J, Teixeira MR, Pandha H, Govindasami K, Muir K, Easton DF, Eeles RA, Kote-Jarai Z. Gene and pathway level analyses of germline DNA-repair gene variants and prostate cancer susceptibility using the iCOGS-genotyping array. Br J Cancer 2016; 114:945-52. [PMID: 26964030 PMCID: PMC5379914 DOI: 10.1038/bjc.2016.50] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/05/2016] [Accepted: 02/09/2016] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Germline mutations within DNA-repair genes are implicated in susceptibility to multiple forms of cancer. For prostate cancer (PrCa), rare mutations in BRCA2 and BRCA1 give rise to moderately elevated risk, whereas two of B100 common, low-penetrance PrCa susceptibility variants identified so far by genome-wide association studies implicate RAD51B and RAD23B. METHODS Genotype data from the iCOGS array were imputed to the 1000 genomes phase 3 reference panel for 21 780 PrCa cases and 21 727 controls from the Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome (PRACTICAL) consortium. We subsequently performed single variant, gene and pathway-level analyses using 81 303 SNPs within 20 Kb of a panel of 179 DNA-repair genes. RESULTS Single SNP analyses identified only the previously reported association with RAD51B. Gene-level analyses using the SKAT-C test from the SNP-set (Sequence) Kernel Association Test (SKAT) identified a significant association with PrCa for MSH5. Pathway-level analyses suggested a possible role for the translesion synthesis pathway in PrCa risk and Homologous recombination/Fanconi Anaemia pathway for PrCa aggressiveness, even though after adjustment for multiple testing these did not remain significant. CONCLUSIONS MSH5 is a novel candidate gene warranting additional follow-up as a prospective PrCa-risk locus. MSH5 has previously been reported as a pleiotropic susceptibility locus for lung, colorectal and serous ovarian cancers.
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Affiliation(s)
- Edward J Saunders
- The Institute of Cancer Research
& Royal Marsden NHS Foundation Trust, 123 Old Brompton
Rd, London
SW7 3RP, UK
| | - Tokhir Dadaev
- The Institute of Cancer Research
& Royal Marsden NHS Foundation Trust, 123 Old Brompton
Rd, London
SW7 3RP, UK
| | - Daniel A Leongamornlert
- The Institute of Cancer Research
& Royal Marsden NHS Foundation Trust, 123 Old Brompton
Rd, London
SW7 3RP, UK
| | - Ali Amin Al Olama
- Centre for Cancer Genetic
Epidemiology, Department of Public Health and Primary Care, University of
Cambridge, Strangeways Laboratory, Worts Causeway,
Cambridge
CB1 8RN, UK
| | - Sara Benlloch
- Centre for Cancer Genetic
Epidemiology, Department of Public Health and Primary Care, University of
Cambridge, Strangeways Laboratory, Worts Causeway,
Cambridge
CB1 8RN, UK
| | - Graham G Giles
- Cancer Epidemiology Centre, The
Cancer Council Victoria, 1 Rathdowne Street,
Carlton Victoria, Australia
- Centre for Molecular, Environmental,
Genetic and Analytic Epidemiology, The University of Melbourne
3053, Victoria, Australia
| | - Fredrik Wiklund
- Department of Medical Epidemiology
and Biostatistics, Karolinska Institute, Stockholm
17177, Sweden
| | - Henrik Grönberg
- Department of Medical Epidemiology
and Biostatistics, Karolinska Institute, Stockholm
17177, Sweden
| | - Christopher A Haiman
- Department of Preventive Medicine,
Keck School of Medicine, University of Southern California & Norris
Comprehensive Cancer Center, Los Angeles,
CA
90089, USA
| | - Johanna Schleutker
- Department of Medical Biochemistry
and Genetics, University of Turku, Turku,
Finland
- Institute of Biomedical Technology
and BioMediTech, University of Tampere and FimLab Laboratories,
Tampere
33520, Finland
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry,
Herlev and Gentofte Hospital, Copenhagen University Hospital,
Herlev Ringvej 75
DK-2730, Herlev, Denmark
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield
Department of Population Health, University of Oxford,
Oxford
OX3 7LF, UK
| | - David Neal
- Surgical Oncology (Uro-Oncology:
S4), University of Cambridge, Addenbrooke's Hospital, Hills Road,
Cambridge & Cancer Research UK Cambridge Research Institute, Li Ka
Shing Centre, Cambridge
CB2 2QQ, UK
| | - Nora Pasayan
- University College London,
Department of Applied Health Research, 1-19 Torrington
Place, London
WC1E 7HB, UK
| | - Kay-Tee Khaw
- Cambridge Institute of Public
Health, University of Cambridge, Forvie Site, Robinson
Way, Cambridge
CB2 0SR, UK
| | - Janet L Stanford
- Department of Epidemiology, School
of Public Health, University of Washington & Division of Public
Health Sciences, Fred Hutchinson Cancer Research Center,
Seattle, WA, USA
| | - William J Blot
- International Epidemiology
Institute, 1455 Research Blvd., Suite 550,
Rockville
MD 20850, USA
| | | | - Christiane Maier
- Institute of Human Genetics,
University Hospital Ulm, Ulm
89075, Germany
| | - Adam S Kibel
- Division of Urologic Surgery,
Brigham and Women's Hospital, Dana-Farber Cancer Institute,
45 Francis Street- ASB II-3
Boston, MA, 02245,
USA
| | - Cezary Cybulski
- International Hereditary Cancer
Center, Department of Genetics and Pathology, Pomeranian Medical
University, Szczecin
70-115, Poland
| | - Lisa Cannon-Albright
- Division of Genetic Epidemiology,
Department of Medicine, University of Utah School of Medicine &
George E. Wahlen Department of Veterans Affairs Medical Center,
Salt Lake City, UT
84132, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology
and Aging Research, German Cancer Research Center (DKFZ), Heidelberg
& Division of Preventive Oncology, German Cancer Research Center
(DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg &
German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ),
Heidelberg, Germany
| | - Jong Y Park
- Department of Cancer Epidemiology,
H. Lee Moffitt Cancer Center, 12902 Magnolia Drive,
Tampa, FL
33612, USA
| | - Radka Kaneva
- Molecular Medicine Center and
Department of Medical Chemistry and Biochemistry, Medical University -
Sofia, 2 Zdrave Street, Sofia
1431, Bulgaria
| | - Jyotsna Batra
- Australian Prostate Cancer Research
Centre-Qld, Institute of Health and Biomedical Innovation & School
of Biomedical Science, Queensland University of Technology,
Brisbane
4102, Australia
| | - Manuel R Teixeira
- Biomedical Sciences Institute
(ICBAS), Porto University, Porto, Portugal
- Department of Genetics, Portuguese
Oncology Institute, Porto, Portugal
4200-072, Portugal
| | - Hardev Pandha
- The University of Surrey,
Guildford, Surrey
GU2 7XH, UK
| | - Koveela Govindasami
- The Institute of Cancer Research
& Royal Marsden NHS Foundation Trust, 123 Old Brompton
Rd, London
SW7 3RP, UK
| | - Ken Muir
- Warwick Medical School, University
of Warwick, Coventry
CV4 7AL, UK
| | - Douglas F Easton
- Centre for Cancer Genetic
Epidemiology, Department of Public Health and Primary Care, University of
Cambridge, Strangeways Laboratory, Worts Causeway,
Cambridge
CB1 8RN, UK
| | - Rosalind A Eeles
- The Institute of Cancer Research
& Royal Marsden NHS Foundation Trust, 123 Old Brompton
Rd, London
SW7 3RP, UK
| | - Zsofia Kote-Jarai
- The Institute of Cancer Research
& Royal Marsden NHS Foundation Trust, 123 Old Brompton
Rd, London
SW7 3RP, UK
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90
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Chowanadisai W, Messerli SM, Miller DH, Medina JE, Hamilton JW, Messerli MA, Brodsky AS. Cisplatin Resistant Spheroids Model Clinically Relevant Survival Mechanisms in Ovarian Tumors. PLoS One 2016; 11:e0151089. [PMID: 26986722 PMCID: PMC4795743 DOI: 10.1371/journal.pone.0151089] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 02/23/2016] [Indexed: 12/31/2022] Open
Abstract
The majority of ovarian tumors eventually recur in a drug resistant form. Using cisplatin sensitive and resistant cell lines assembled into 3D spheroids we profiled gene expression and identified candidate mechanisms and biological pathways associated with cisplatin resistance. OVCAR-8 human ovarian carcinoma cells were exposed to sub-lethal concentrations of cisplatin to create a matched cisplatin-resistant cell line, OVCAR-8R. Genome-wide gene expression profiling of sensitive and resistant ovarian cancer spheroids identified 3,331 significantly differentially expressed probesets coding for 3,139 distinct protein-coding genes (Fc >2, FDR < 0.05) (S2 Table). Despite significant expression changes in some transporters including MDR1, cisplatin resistance was not associated with differences in intracellular cisplatin concentration. Cisplatin resistant cells were significantly enriched for a mesenchymal gene expression signature. OVCAR-8R resistance derived gene sets were significantly more biased to patients with shorter survival. From the most differentially expressed genes, we derived a 17-gene expression signature that identifies ovarian cancer patients with shorter overall survival in three independent datasets. We propose that the use of cisplatin resistant cell lines in 3D spheroid models is a viable approach to gain insight into resistance mechanisms relevant to ovarian tumors in patients. Our data support the emerging concept that ovarian cancers can acquire drug resistance through an epithelial-to-mesenchymal transition.
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Affiliation(s)
- Winyoo Chowanadisai
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, Oklahoma, United States of America, 74078
- Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America, 02543
| | - Shanta M. Messerli
- Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America, 02543
| | - Daniel H. Miller
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, 02139
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America, 02142
| | - Jamie E. Medina
- Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America, 02543
- Department of Biological Sciences, Bridgewater State University, Bridgewater, Massachusetts, United States of America, 02325
| | - Joshua W. Hamilton
- Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America, 02543
- Swenson College of Science and Engineering, University of Minnesota, Duluth, Minnesota, United States of America, 55804
| | - Mark A. Messerli
- Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America, 02543
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, United States of America, 57007
- * E-mail: (MAM); (ASB)
| | - Alexander S. Brodsky
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, 02139
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Alpert Medical School of Brown University, Providence, Rhode Island, United States of America, 02903
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America, 02912
- * E-mail: (MAM); (ASB)
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91
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Gu Y, Zhang M, Peng F, Fang L, Zhang Y, Liang H, Zhou W, Ao L, Guo Z. The BRCA1/2-directed miRNA signature predicts a good prognosis in ovarian cancer patients with wild-type BRCA1/2. Oncotarget 2016; 6:2397-406. [PMID: 25537514 PMCID: PMC4385859 DOI: 10.18632/oncotarget.2963] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 12/10/2015] [Indexed: 11/25/2022] Open
Abstract
Ovarian cancer patients carrying alterations (i.e., germline mutations, somatic mutations, hypermethylations and/or deletions) of BRCA1 or BRCA2 (BRCA1/2) have a better prognosis than BRCA1/2 alteration non-carriers. However, patients with wild-type BRCA1/2 may also have a favorable prognosis as a result of other mechanisms that remain poorly elucidated, such as the deregulation of miRNAs. We therefore sought to identify BRCA1/2-directed miRNA signatures that have prognostic value in ovarian cancer patients with wild-type BRCA1/2 and study how the deregulation of miRNAs impacts the prognosis of patients treated with platinum-based chemotherapy. By analyzing multidimensional datasets of ovarian cancer patients from the TCGA data portal, we identified three miRNAs (hsa-miR-146a, hsa-miR-148a and hsa-miR-545) that target BRCA1/2 and were associated with overall survival and progression-free survival in patients with wild-type BRCA1/2. By analyzing the expression profiles and Gene Ontology functional enrichment, we found that carriers of BRCA1/2 alterations and patients with miRNA deregulation shared a common mechanism, regulation of the DNA repair-related pathways, that affects the prognosis of ovarian cancer patients. Our work highlights that a proportion of patients with wild-type BRCA1/2 ovarian cancers benefit from platinum-based chemotherapy and that the patients who benefit could be predicted from BRCA1/2-directed miRNA signature.
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Affiliation(s)
- Yunyan Gu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Mengmeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Fuduan Peng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lei Fang
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuanyuan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haihai Liang
- Department of Pharmacology, Harbin Medical University, Harbin, China
| | - Wenbin Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lu Ao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
| | - Zheng Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
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92
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Ma L, Xun X, Qiao Y, An J, Su M. Predicting efficacies of anticancer drugs using single cell HaloChip assay. Analyst 2016; 141:2454-62. [DOI: 10.1039/c5an02564h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Single cell HaloChip assay can be used to assess DNA repair ability.
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Affiliation(s)
- Liyuan Ma
- Department of Chemical Engineering
- Northeastern University
- Boston
- USA
- Wenzhou Institute of Biomaterials and Engineering
| | - Xiaojie Xun
- Department of Chemical Engineering
- Northeastern University
- Boston
- USA
- Wenzhou Institute of Biomaterials and Engineering
| | - Yong Qiao
- NanoScience Technology Center
- University of Central Florida
- Orlando
- USA
| | - Jincui An
- NanoScience Technology Center
- University of Central Florida
- Orlando
- USA
| | - Ming Su
- Department of Chemical Engineering
- Northeastern University
- Boston
- USA
- Wenzhou Institute of Biomaterials and Engineering
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93
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Zhang S, Jing Y, Zhang M, Zhang Z, Ma P, Peng H, Shi K, Gao WQ, Zhuang G. Stroma-associated master regulators of molecular subtypes predict patient prognosis in ovarian cancer. Sci Rep 2015; 5:16066. [PMID: 26530441 PMCID: PMC4632004 DOI: 10.1038/srep16066] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/06/2015] [Indexed: 02/06/2023] Open
Abstract
High-grade serous ovarian carcinoma (HGS-OvCa) has the lowest survival rate among all gynecologic cancers and is hallmarked by a high degree of heterogeneity. The Cancer Genome Atlas network has described a gene expression-based molecular classification of HGS-OvCa into Differentiated, Mesenchymal, Immunoreactive and Proliferative subtypes. However, the biological underpinnings and regulatory mechanisms underlying the distinct molecular subtypes are largely unknown. Here we showed that tumor-infiltrating stromal cells significantly contributed to the assignments of Mesenchymal and Immunoreactive clusters. Using reverse engineering and an unbiased interrogation of subtype regulatory networks, we identified the transcriptional modules containing master regulators that drive gene expression of Mesenchymal and Immunoreactive HGS-OvCa. Mesenchymal master regulators were associated with poor prognosis, while Immunoreactive master regulators positively correlated with overall survival. Meta-analysis of 749 HGS-OvCa expression profiles confirmed that master regulators as a prognostic signature were able to predict patient outcome. Our data unraveled master regulatory programs of HGS-OvCa subtypes with prognostic and potentially therapeutic relevance, and suggested that the unique transcriptional and clinical characteristics of ovarian Mesenchymal and Immunoreactive subtypes could be, at least partially, ascribed to tumor microenvironment.
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Affiliation(s)
- Shengzhe Zhang
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering &Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Jing
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Meiying Zhang
- Department of Obstetrics and Gynecology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenfeng Zhang
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Pengfei Ma
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huixin Peng
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kaixuan Shi
- School of Biomedical Engineering &Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Wei-Qiang Gao
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering &Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Guanglei Zhuang
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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94
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Konstantinopoulos PA, Ceccaldi R, Shapiro GI, D'Andrea AD. Homologous Recombination Deficiency: Exploiting the Fundamental Vulnerability of Ovarian Cancer. Cancer Discov 2015. [PMID: 26463832 DOI: 10.1158/2159-8290.cd-15-0714] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
UNLABELLED Approximately 50% of epithelial ovarian cancers (EOC) exhibit defective DNA repair via homologous recombination (HR) due to genetic and epigenetic alterations of HR pathway genes. Defective HR is an important therapeutic target in EOC as exemplified by the efficacy of platinum analogues in this disease, as well as the advent of PARP inhibitors, which exhibit synthetic lethality when applied to HR-deficient cells. Here, we describe the genotypic and phenotypic characteristics of HR-deficient EOCs, discuss current and emerging approaches for targeting these tumors, and present challenges associated with these approaches, focusing on development and overcoming resistance. SIGNIFICANCE Defective DNA repair via HR is a pivotal vulnerability of EOC, particularly of the high-grade serous histologic subtype. Targeting defective HR offers the unique opportunity of exploiting molecular differences between tumor and normal cells, thereby inducing cancer-specific synthetic lethality; the promise and challenges of these approaches in ovarian cancer are discussed in this review.
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Affiliation(s)
- Panagiotis A Konstantinopoulos
- Department of Medical Oncology, Medical Gynecologic Oncology Program, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
| | - Raphael Ceccaldi
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medical Oncology, Early Drug Development Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alan D D'Andrea
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
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95
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Konstantinopoulos PA, Ceccaldi R, Shapiro GI, D'Andrea AD. Homologous Recombination Deficiency: Exploiting the Fundamental Vulnerability of Ovarian Cancer. Cancer Discov 2015; 5:1137-54. [PMID: 26463832 DOI: 10.1158/2159-8290.cd-15-0714] [Citation(s) in RCA: 613] [Impact Index Per Article: 68.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/11/2015] [Indexed: 12/14/2022]
Abstract
UNLABELLED Approximately 50% of epithelial ovarian cancers (EOC) exhibit defective DNA repair via homologous recombination (HR) due to genetic and epigenetic alterations of HR pathway genes. Defective HR is an important therapeutic target in EOC as exemplified by the efficacy of platinum analogues in this disease, as well as the advent of PARP inhibitors, which exhibit synthetic lethality when applied to HR-deficient cells. Here, we describe the genotypic and phenotypic characteristics of HR-deficient EOCs, discuss current and emerging approaches for targeting these tumors, and present challenges associated with these approaches, focusing on development and overcoming resistance. SIGNIFICANCE Defective DNA repair via HR is a pivotal vulnerability of EOC, particularly of the high-grade serous histologic subtype. Targeting defective HR offers the unique opportunity of exploiting molecular differences between tumor and normal cells, thereby inducing cancer-specific synthetic lethality; the promise and challenges of these approaches in ovarian cancer are discussed in this review.
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Affiliation(s)
- Panagiotis A Konstantinopoulos
- Department of Medical Oncology, Medical Gynecologic Oncology Program, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
| | - Raphael Ceccaldi
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medical Oncology, Early Drug Development Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alan D D'Andrea
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
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96
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Copur MS, Gauchan D, Brussow K, Clark D, Ramaekers R. Germline BRCA1/2 Mutations: Are They Good Enough to Determine Who Will Respond to Poly(ADP-Ribose) Polymerase Inhibitor Therapy in Advanced Cancer? J Clin Oncol 2015; 33:2582. [PMID: 26124479 DOI: 10.1200/jco.2015.61.0576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Dron Gauchan
- St Francis Cancer Treatment Center, Grand Island, NE
| | | | - Douglas Clark
- St Francis Cancer Treatment Center, Grand Island, NE
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97
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Qi L, Chen L, Li Y, Qin Y, Pan R, Zhao W, Gu Y, Wang H, Wang R, Chen X, Guo Z. Critical limitations of prognostic signatures based on risk scores summarized from gene expression levels: a case study for resected stage I non-small-cell lung cancer. Brief Bioinform 2015; 17:233-42. [PMID: 26254430 DOI: 10.1093/bib/bbv064] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 12/16/2022] Open
Abstract
Most of current gene expression signatures for cancer prognosis are based on risk scores, usually calculated as some summaries of expression levels of the signature genes, whose applications require presetting risk score thresholds and data normalization. In this study, we demonstrate the critical limitations of such type of signatures that the risk scores of samples will change greatly when they are normalized together with different samples, which would induce spurious risk classification and difficulty in clinical settings, and the risk scores of independent samples are incomparable if data normalization is not adopted. To overcome these limitations, we propose a rank-based method to extract a prognostic gene pair signature for overall survival of stage I non-small-cell lung cancer. The prognostic gene pair signature is verified in three integrated data sets detected by different laboratories with different microarray platforms. We conclude that, different from the type of signatures based on risk scores summarized from gene expression levels, the rank-based signatures could be robustly applied at the individualized level to independent clinical samples assessed in different laboratories.
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98
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Chen YC, Chang YC, Ke WC, Chiu HW. Cancer adjuvant chemotherapy strategic classification by artificial neural network with gene expression data: An example for non-small cell lung cancer. J Biomed Inform 2015; 56:1-7. [DOI: 10.1016/j.jbi.2015.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 04/02/2015] [Accepted: 05/11/2015] [Indexed: 10/23/2022]
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99
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Davidson B, Tropé CG. Ovarian cancer: diagnostic, biological and prognostic aspects. ACTA ACUST UNITED AC 2015; 10:519-33. [PMID: 25335543 DOI: 10.2217/whe.14.37] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ovarian cancer remains the most lethal gynecologic malignancy, owing to late detection, intrinsic and acquired chemoresistance and remarkable heterogeneity. Despite optimization of surgical and chemotherapy protocols and initiation of clinical trials incorporating targeted therapy, only modest gains have been achieved in prolonging survival in this cancer. This review provides an update of recent developments in our understanding of the etiology, origin, diagnosis, progression and treatment of this malignancy, with emphasis on clinically relevant genetic classification approaches. In the authors' opinion, focused effort directed at understanding the molecular make-up of recurrent and metastatic ovarian cancer, while keeping in mind the unique molecular character of each of its histological types, is central to our effort to improve patient outcome in this cancer.
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Affiliation(s)
- Ben Davidson
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, N-0310 Oslo, Norway
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100
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Miow QH, Tan TZ, Ye J, Lau JA, Yokomizo T, Thiery JP, Mori S. Epithelial-mesenchymal status renders differential responses to cisplatin in ovarian cancer. Oncogene 2015. [PMID: 24858042 DOI: 10.1038/onc.2014.136] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chemoresistance to platinums, such as cisplatin, is of critical concern in the treatment of ovarian cancer. Recent evidence has linked epithelial-mesenchymal transition (EMT) as a contributing mechanism. The current study explored the connection between cellular responses to cisplatin and EMT in ovarian cancer. Expression microarrays were utilized to estimate the EMT status as a binary phenotype, and the transcriptional responses of 46 ovarian cancer cell lines to cisplatin were measured at dosages equivalent to 50% growth inhibition. Phenotypic responses to cisplatin were quantified with respect to cell number, proliferation rate and apoptosis, and then compared with the epithelial or mesenchymal status. Ovarian cancer cell lines with an epithelial status exhibited higher resistance to cisplatin treatment in the MTS assay than those with a mesenchymal status. Pathway analyses revealed the induction of G1/S- and S-phase genes (P=0.001) and the activation of multiple NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) downstream genes (P=0.0016) by cisplatin selectively in epithelial-like cell lines. BrdU incorporation and Caspase-3/7 release assays confirmed impaired apoptosis in epithelial-like ovarian cancer cells. In clinical samples, we observed resistance to single platinum treatment and the selective activation of the NF-κB pathway by platinum in ovarian cancers with an epithelial status. Overall, our results suggest that, in epithelial-like ovarian cancer cells, NF-κB activation by cisplatin may lead to defective apoptosis, preferential proliferation arrest and a consequential decreased sensitivity to cisplatin.
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Affiliation(s)
- Q H Miow
- 1] Cancer Science Institute of Singapore, National University of Singapore, Singapore [2] NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - T Z Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - J Ye
- Dean's Office, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - J A Lau
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - T Yokomizo
- Division of Cancer Genomics, Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - J-P Thiery
- 1] Cancer Science Institute of Singapore, National University of Singapore, Singapore [2] Institute of Molecular and Cell Biology, A*STAR, Singapore [3] Department of Biochemistry, National University of Singapore, Singapore
| | - S Mori
- 1] Cancer Science Institute of Singapore, National University of Singapore, Singapore [2] Division of Cancer Genomics, Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
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