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Fanizzi A, Bove S, Comes MC, Di Benedetto EF, Latorre A, Giotta F, Nardone A, Rizzo A, Soranno C, Zito A, Massafra R. Prediction of breast cancer Invasive Disease Events using transfer learning on clinical data as image-form. PLoS One 2024; 19:e0312036. [PMID: 39570983 PMCID: PMC11581389 DOI: 10.1371/journal.pone.0312036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 09/30/2024] [Indexed: 11/25/2024] Open
Abstract
BACKGROUND AND OBJECTIVE Detecting patients at high risk of occurrence of an Invasive Disease Event after a first diagnosis of breast cancer, such as recurrence, distant metastasis, contralateral tumor and second tumor, could support clinical decision-making processes in the treatment of this malignancy. Though several machine learning models analyzing both clinical and histopathological information have been developed in literature to address this task, these approaches turned out to be unsuitable for describing this problem. METHODS In this study, we designed a novel artificial intelligence-based approach which converts clinical information into an image-form to be analyzed through Convolutional Neural Networks. Specifically, we predicted the occurrence of an Invasive Disease Event at both 5-year and 10-year follow-ups of 696 female patients with a first invasive breast cancer diagnosis enrolled at IRCCS "Giovanni Paolo II" in Bari, Italy. After transforming each patient, represented by a vector of clinical information, to an image form, we extracted low-level quantitative imaging features by means of a pre-trained Convolutional Neural Network, namely, AlexNET. Then, we classified breast cancer patients in the two classes, namely, Invasive Disease Event and non-Invasive Disease Event, via a Support Vector Machine classifier trained on a subset of significative features previously identified. RESULTS Both 5-year and 10-year models resulted particularly accurate in predicting breast cancer recurrence event, achieving an AUC value of 92.07% and 92.84%, an accuracy of 88.71% and 88.82%, a sensitivity of 86.83% and 88.06%, a specificity of 89.55% and 89.3%, a precision of 71.93% and 84.82%, respectively. CONCLUSIONS This is the first study proposing an approach which converts clinical information into an image-form to develop a decision support system for identifying patients at high risk of occurrence of an Invasive Disease Event, and then defining personalized oncological therapeutic treatments for breast cancer patients.
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Affiliation(s)
| | - Samantha Bove
- I.R.C.C.S. Istituto Tumori “Giovanni Paolo II”, Bari, Italy
| | | | | | - Agnese Latorre
- I.R.C.C.S. Istituto Tumori “Giovanni Paolo II”, Bari, Italy
| | | | | | | | - Clara Soranno
- I.R.C.C.S. Istituto Tumori “Giovanni Paolo II”, Bari, Italy
| | - Alfredo Zito
- I.R.C.C.S. Istituto Tumori “Giovanni Paolo II”, Bari, Italy
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2
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Wu R, Jia Y, Li N, Lu X, Yao Z, Ma Y, Nie F. Evaluation of Breast Cancer Tumor-Infiltrating Lymphocytes on Ultrasound Images Based on a Novel Multi-Cascade Residual U-Shaped Network. ULTRASOUND IN MEDICINE & BIOLOGY 2023; 49:2398-2406. [PMID: 37634979 DOI: 10.1016/j.ultrasmedbio.2023.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/30/2023] [Accepted: 08/04/2023] [Indexed: 08/29/2023]
Abstract
OBJECTIVE Breast cancer has become the leading cancer of the 21st century. Tumor-infiltrating lymphocytes (TILs) have emerged as effective biomarkers for predicting treatment response and prognosis in breast cancer. The work described here was aimed at designing a novel deep learning network to assess the levels of TILs in breast ultrasound images. METHODS We propose the Multi-Cascade Residual U-Shaped Network (MCRUNet), which incorporates a gray feature enhancement (GFE) module for image reconstruction and normalization to achieve data synergy. Additionally, multiple residual U-shaped (RSU) modules are cascaded as the backbone network to maximize the fusion of global and local features, with a focus on the tumor's location and surrounding regions. The development of MCRUNet is based on data from two hospitals and uses a publicly available ultrasound data set for transfer learning. RESULTS MCRUNet exhibits excellent performance in assessing TILs levels, achieving an area under the receiver operating characteristic curve of 0.8931, an accuracy of 85.71%, a sensitivity of 83.33%, a specificity of 88.64% and an F1 score of 86.54% in the test group. It outperforms six state-of-the-art networks in terms of performance. CONCLUSION The MCRUNet network based on breast ultrasound images of breast cancer patients holds promise for non-invasively predicting TILs levels and aiding personalized treatment decisions.
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Affiliation(s)
- Ruichao Wu
- School of Information Science and Engineering, Lanzhou University, Lanzhou, China
| | - Yingying Jia
- Ultrasound Medical Center, Lanzhou University Second Hospital, Lanzhou, China; Gansu Province Medical Engineering Research Center for Intelligence Ultrasound, Lanzhou, China; Gansu Province Clinical Research Center for Ultrasonography, Lanzhou, China
| | - Nana Li
- Ultrasound Medical Center, Lanzhou University Second Hospital, Lanzhou, China; Gansu Province Medical Engineering Research Center for Intelligence Ultrasound, Lanzhou, China; Gansu Province Clinical Research Center for Ultrasonography, Lanzhou, China
| | - Xiangyu Lu
- School of Information Science and Engineering, Lanzhou University, Lanzhou, China
| | - Zihuan Yao
- School of Information Science and Engineering, Lanzhou University, Lanzhou, China
| | - Yide Ma
- School of Information Science and Engineering, Lanzhou University, Lanzhou, China.
| | - Fang Nie
- Ultrasound Medical Center, Lanzhou University Second Hospital, Lanzhou, China; Gansu Province Medical Engineering Research Center for Intelligence Ultrasound, Lanzhou, China; Gansu Province Clinical Research Center for Ultrasonography, Lanzhou, China
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3
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Neves Rebello Alves L, Dummer Meira D, Poppe Merigueti L, Correia Casotti M, do Prado Ventorim D, Ferreira Figueiredo Almeida J, Pereira de Sousa V, Cindra Sant'Ana M, Gonçalves Coutinho da Cruz R, Santos Louro L, Mendonça Santana G, Erik Santos Louro T, Evangelista Salazar R, Ribeiro Campos da Silva D, Stefani Siqueira Zetum A, Silva Dos Reis Trabach R, Imbroisi Valle Errera F, de Paula F, de Vargas Wolfgramm Dos Santos E, Fagundes de Carvalho E, Drumond Louro I. Biomarkers in Breast Cancer: An Old Story with a New End. Genes (Basel) 2023; 14:1364. [PMID: 37510269 PMCID: PMC10378988 DOI: 10.3390/genes14071364] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Breast cancer is the second most frequent cancer in the world. It is a heterogeneous disease and the leading cause of cancer mortality in women. Advances in molecular technologies allowed for the identification of new and more specifics biomarkers for breast cancer diagnosis, prognosis, and risk prediction, enabling personalized treatments, improving therapy, and preventing overtreatment, undertreatment, and incorrect treatment. Several breast cancer biomarkers have been identified and, along with traditional biomarkers, they can assist physicians throughout treatment plan and increase therapy success. Despite the need of more data to improve specificity and determine the real clinical utility of some biomarkers, others are already established and can be used as a guide to make treatment decisions. In this review, we summarize the available traditional, novel, and potential biomarkers while also including gene expression profiles, breast cancer single-cell and polyploid giant cancer cells. We hope to help physicians understand tumor specific characteristics and support decision-making in patient-personalized clinical management, consequently improving treatment outcome.
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Affiliation(s)
- Lyvia Neves Rebello Alves
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Débora Dummer Meira
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Luiza Poppe Merigueti
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
| | - Matheus Correia Casotti
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Diego do Prado Ventorim
- Instituto Federal de Educação, Ciência e Tecnologia do Espírito Santo (Ifes), Cariacica 29150-410, ES, Brazil
| | - Jucimara Ferreira Figueiredo Almeida
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
| | - Valdemir Pereira de Sousa
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Marllon Cindra Sant'Ana
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
| | - Rahna Gonçalves Coutinho da Cruz
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
| | - Luana Santos Louro
- Centro de Ciências da Saúde, Curso de Medicina, Universidade Federal do Espírito Santo (UFES), Vitória 29090-040, ES, Brazil
| | - Gabriel Mendonça Santana
- Centro de Ciências da Saúde, Curso de Medicina, Universidade Federal do Espírito Santo (UFES), Vitória 29090-040, ES, Brazil
| | - Thomas Erik Santos Louro
- Escola Superior de Ciências da Santa Casa de Misericórdia de Vitória (EMESCAM), Vitória 29027-502, ES, Brazil
| | - Rhana Evangelista Salazar
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Danielle Ribeiro Campos da Silva
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Aléxia Stefani Siqueira Zetum
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Raquel Silva Dos Reis Trabach
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
| | - Flávia Imbroisi Valle Errera
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Flávia de Paula
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Eldamária de Vargas Wolfgramm Dos Santos
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Elizeu Fagundes de Carvalho
- Instituto de Biologia Roberto Alcântara Gomes (IBRAG), Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20551-030, RJ, Brazil
| | - Iúri Drumond Louro
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
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Massafra R, Comes MC, Bove S, Didonna V, Diotaiuti S, Giotta F, Latorre A, La Forgia D, Nardone A, Pomarico D, Ressa CM, Rizzo A, Tamborra P, Zito A, Lorusso V, Fanizzi A. A machine learning ensemble approach for 5- and 10-year breast cancer invasive disease event classification. PLoS One 2022; 17:e0274691. [PMID: 36121822 PMCID: PMC9484691 DOI: 10.1371/journal.pone.0274691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/02/2022] [Indexed: 12/24/2022] Open
Abstract
Designing targeted treatments for breast cancer patients after primary tumor removal is necessary to prevent the occurrence of invasive disease events (IDEs), such as recurrence, metastasis, contralateral and second tumors, over time. However, due to the molecular heterogeneity of this disease, predicting the outcome and efficacy of the adjuvant therapy is challenging. A novel ensemble machine learning classification approach was developed to address the task of producing prognostic predictions of the occurrence of breast cancer IDEs at both 5- and 10-years. The method is based on the concept of voting among multiple models to give a final prediction for each individual patient. Promising results were achieved on a cohort of 529 patients, whose data, related to primary breast cancer, were provided by Istituto Tumori "Giovanni Paolo II" in Bari, Italy. Our proposal greatly improves the performances returned by the baseline original model, i.e., without voting, finally reaching a median AUC value of 77.1% and 76.3% for the IDE prediction at 5-and 10-years, respectively. Finally, the proposed approach allows to promote more intelligible decisions and then a greater acceptability in clinical practice since it returns an explanation of the IDE prediction for each individual patient through the voting procedure.
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Affiliation(s)
| | | | - Samantha Bove
- I.R.C.C.S. Istituto Tumori “Giovanni Paolo II”, Bari, Italy
| | | | | | | | - Agnese Latorre
- I.R.C.C.S. Istituto Tumori “Giovanni Paolo II”, Bari, Italy
| | | | | | - Domenico Pomarico
- Dipartimento di Fisica and MECENAS, Università di Bari, Bari, Italy
- INFN, Sezione di Bari, Bari, Italy
| | | | | | | | - Alfredo Zito
- I.R.C.C.S. Istituto Tumori “Giovanni Paolo II”, Bari, Italy
| | - Vito Lorusso
- I.R.C.C.S. Istituto Tumori “Giovanni Paolo II”, Bari, Italy
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5
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Understanding Breast Cancers through Spatial and High-Resolution Visualization Using Imaging Technologies. Cancers (Basel) 2022; 14:cancers14174080. [PMID: 36077616 PMCID: PMC9454728 DOI: 10.3390/cancers14174080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Breast cancer is the most common cancer affecting women worldwide. Although many analyses and treatments have traditionally targeted the breast cancer cells themselves, recent studies have focused on investigating entire cancer tissues, including breast cancer cells. To understand the structure of breast cancer tissues, including breast cancer cells, it is necessary to investigate the three-dimensional location of the cells and/or proteins comprising the tissues and to clarify the relationship between the three-dimensional structure and malignant transformation or metastasis of breast cancers. In this review, we aim to summarize the methods for analyzing the three-dimensional structure of breast cancer tissue, paying particular attention to the recent technological advances in the combination of the tissue-clearing method and optical three-dimensional imaging. We also aimed to identify the latest methods for exploring the relationship between the three-dimensional cell arrangement in breast cancer tissues and the gene expression of each cell. Finally, we aimed to describe the three-dimensional imaging features of breast cancer tissues using noninvasive photoacoustic imaging methods.
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6
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Jiang M, Wu X, Bao S, Wang X, Qu F, Liu Q, Huang X, Li W, Tang J, Yin Y. Immunometabolism characteristics and a potential prognostic risk model associated with TP53 mutations in breast cancer. Front Immunol 2022; 13:946468. [PMID: 35935965 PMCID: PMC9353309 DOI: 10.3389/fimmu.2022.946468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
TP53, a gene with high-frequency mutations, plays an important role in breast cancer (BC) development through metabolic regulation, but the relationship between TP53 mutation and metabolism in BC remains to be explored. Our study included 1,066 BC samples from The Cancer Genome Atlas (TCGA) database, 415 BC cases from the Gene Expression Omnibus (GEO) database, and two immunotherapy cohorts. We identified 92 metabolic genes associated with TP53 mutations by differential expression analysis between TP53 mutant and wild-type groups. Univariate Cox analysis was performed to evaluate the prognostic effects of 24 TP53 mutation-related metabolic genes. By unsupervised clustering and other bioinformatics methods, the survival differences and immunometabolism characteristics of the distinct clusters were illustrated. In a training set from TCGA cohort, we employed the least absolute shrinkage and selection operator (LASSO) regression method to construct a metabolic gene prognostic model associated with TP53 mutations, and the GEO cohort served as an external validation set. Based on bioinformatics, the connections between risk score and survival prognosis, tumor microenvironment (TME), immunotherapy response, metabolic activity, clinical characteristics, and gene characteristics were further analyzed. It is imperative to note that our model is a powerful and robust prognosis factor in comparison to other traditional clinical features and also has high accuracy and clinical usefulness validated by receiver operating characteristic (ROC) and decision curve analysis (DCA). Our findings deepen our understanding of the immune and metabolic characteristics underlying the TP53 mutant metabolic gene profile in BC, laying a foundation for the exploration of potential therapies targeting metabolic pathways. In addition, our model has promising predictive value in the prognosis of BC.
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Affiliation(s)
- Mengping Jiang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Xiangyan Wu
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, China
| | - Shengnan Bao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Xi Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Fei Qu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Qian Liu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Xiang Huang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Jinhai Tang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Yongmei Yin, ; Jinhai Tang,
| | - Yongmei Yin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Yongmei Yin, ; Jinhai Tang,
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7
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Ren X, Cui H, Wu J, Zhou R, Wang N, Liu D, Xie X, Zhang H, Liu D, Ma X, Dang C, Kang H, Lin S. Identification of a combined apoptosis and hypoxia gene signature for predicting prognosis and immune infiltration in breast cancer. Cancer Med 2022; 11:3886-3901. [PMID: 35441810 PMCID: PMC9582692 DOI: 10.1002/cam4.4755] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/11/2022] [Accepted: 04/01/2022] [Indexed: 11/26/2022] Open
Abstract
Background Breast cancer (BC) is the most common malignant tumor worldwide. Apoptosis and hypoxia are involved in the progression of BC, but reliable biomarkers for these have not been developed. We hope to explore a gene signature that combined apoptosis and hypoxia‐related genes (AHGs) to predict BC prognosis and immune infiltration. Methods We collected the mRNA expression profiles and clinical data information of BC patients from The Cancer Genome Atlas database. The gene signature based on AHGs was constructed using the univariate Cox regression, least absolute shrinkage and selection operator, and multivariate Cox regression analysis. The associations between risk scores, immune infiltration, and immune checkpoint gene expression were studied using single‐sample gene set enrichment analysis. Besides, gene signature and independent clinicopathological characteristics were combined to establish a nomogram. Finally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed on the potential functions of AHGs. Results We identified a 16‐AHG signature (AGPAT1, BTBD6, EIF4EBP1, ERRFI1, FAM114A1, GRIP1, IRF2, JAK1, MAP2K6, MCTS1, NFKBIA, NFKBIZ, NUP43, PGK1, RCL1, and SGCE) that could independently predict BC prognosis. The median score of the risk model divided the patients into two subgroups. By contrast, patients in the high‐risk group had poorer prognosis, less abundance of immune cell infiltration, and expression of immune checkpoint genes. The gene signature and nomogram had good predictive effects on the overall survival of BC patients. GO and KEGG analyses revealed that the differential expression of AHGs may be closely related to tumor immunity. Conclusion We established and verified a 16‐AHG BC signature which may help predict prognosis, assess potential immunotherapy benefits, and provide inspiration for future research on the functions and mechanisms of AHGs in BC.
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Affiliation(s)
- Xueting Ren
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hanxiao Cui
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jianhua Wu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ruina Zhou
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Nan Wang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Dandan Liu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xin Xie
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hao Zhang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Di Liu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiaobin Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Chengxue Dang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shuai Lin
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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8
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Correlation of ER, PR, and HER2 at protein and mRNA levels in the Asian patients with operable breast cancer. Biosci Rep 2022; 42:230628. [PMID: 35006257 PMCID: PMC8766827 DOI: 10.1042/bsr20211706] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 12/21/2021] [Accepted: 01/07/2022] [Indexed: 11/17/2022] Open
Abstract
Breast cancer is the most common cancer and the leading cause of cancer-related deaths in women. The estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) are the important biomarkers in the prognosis of breast cancer, and their expression is used to categorize breast cancer into subtypes. We aimed to analyze the concordance among ER, PR, and HER2 expression levels and breast cancer subtyping results obtained by immunohistochemistry (IHC, for protein) and reverse transcriptase-polymerase chain reaction (RT-PCR, for mRNA) and to assess the recurrence-free survival (RFS) of the different subtypes as determined by the two methods. We compared biomarker expression by IHC and RT-PCR in 397 operable breast cancer patients and categorized all patients into luminal, HER2, and triple-negative (TN) subtypes. The concordance of biomarker expression between the two methods was 81.6% (κ = 0.4075) for ER, 87.2% (κ = 0.5647) for PR, and 79.1% (κ = 0.2767) for HER2. The κ-statistic was 0.3624 for the resulting luminal, HER2, and TN subtypes. The probability of 5-year RFS was 0.78 for the luminal subtype versus 0.77 for HER2 and 0.51 for TN, when determined by IHC (P=0.007); and 0.80, 0.71, and 0.61, respectively, when determined by the RT-PCR method (P=0.008). Based on the current evidence, subtyping by RT-PCR performs similar to conventional IHC with regard to the 5-year prognosis. The PCR method may thus provide a complementary means of subtyping when IHC results are ambiguous.
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9
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Pellegrini M. Accurate prediction of breast cancer survival through coherent voting networks with gene expression profiling. Sci Rep 2021; 11:14645. [PMID: 34282236 PMCID: PMC8289832 DOI: 10.1038/s41598-021-94243-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/07/2021] [Indexed: 02/06/2023] Open
Abstract
For a patient affected by breast cancer, after tumor removal, it is necessary to decide which adjuvant therapy is able to prevent tumor relapse and formation of metastases. A prediction of the outcome of adjuvant therapy tailored for the patient is hard, due to the heterogeneous nature of the disease. We devised a methodology for predicting 5-years survival based on the new machine learning paradigm of coherent voting networks, with improved accuracy over state-of-the-art prediction methods. The 'coherent voting communities' metaphor provides a certificate justifying the survival prediction for an individual patient, thus facilitating its acceptability in practice, in the vein of explainable Artificial Intelligence. The method we propose is quite flexible and applicable to other types of cancer.
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Affiliation(s)
- Marco Pellegrini
- Institute of Informatics and Telematics (IIT), CNR, 56124, Pisa, Italy.
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10
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Sivakumar R, Lee NY. Recent progress in smartphone-based techniques for food safety and the detection of heavy metal ions in environmental water. CHEMOSPHERE 2021; 275:130096. [PMID: 33677270 DOI: 10.1016/j.chemosphere.2021.130096] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/10/2021] [Accepted: 02/21/2021] [Indexed: 05/14/2023]
Abstract
Emerging smartphone-based point-of-care tests (POCTs) are cost-effective, precise, and easy to implement in resource-limited areas. Thus, they are considered a potential alternative to conventional diagnostic testing. This review explores food safety and the detection of metal ions in environmental water based on unprecedented smartphone technology. Specifically, we provide an overview of various methods used for target analyte detection (antibiotics, enzymes, mycotoxins, pathogens, pesticides, small molecules, and metal ions), such as colorimetric, fluorescence, microscopic imaging, and electrochemical methods. This paper performs a comprehensive review of smartphone-based POCTs developed in the last three years (2018-2020) and evaluates their relative advantages and limitations. Moreover, we discuss the imperative role of new technology in the progress of POCTs. Sensor materials (metal nanoparticles, carbon dots, quantum dots, organic substrates, etc.) and detection techniques (paper-based, later flow assay, microfluidic platform, etc.) involved in POCTs based on smartphones, and the challenges faced by these techniques, are addressed.
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Affiliation(s)
- Rajamanickam Sivakumar
- Department of Industrial Environmental Engineering, College of Industrial Environmental Engineering, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, South Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, South Korea.
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11
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Qi A, Ju M, Liu Y, Bi J, Wei Q, He M, Wei M, Zhao L. Development of a Novel Prognostic Signature Based on Antigen Processing and Presentation in Patients with Breast Cancer. Pathol Oncol Res 2021; 27:600727. [PMID: 34257557 PMCID: PMC8262234 DOI: 10.3389/pore.2021.600727] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/10/2021] [Indexed: 01/02/2023]
Abstract
Background: Complex antigen processing and presentation processes are involved in the development and progression of breast cancer (BC). A single biomarker is unlikely to adequately reflect the complex interplay between immune cells and cancer; however, there have been few attempts to find a robust antigen processing and presentation-related signature to predict the survival outcome of BC patients with respect to tumor immunology. Therefore, we aimed to develop an accurate gene signature based on immune-related genes for prognosis prediction of BC. Methods: Information on BC patients was obtained from The Cancer Genome Atlas. Gene set enrichment analysis was used to confirm the gene set related to antigen processing and presentation that contributed to BC. Cox proportional regression, multivariate Cox regression, and stratified analysis were used to identify the prognostic power of the gene signature. Differentially expressed mRNAs between high- and low-risk groups were determined by KEGG analysis. Results: A three-gene signature comprising HSPA5 (heat shock protein family A member 5), PSME2 (proteasome activator subunit 2), and HLA-F (major histocompatibility complex, class I, F) was significantly associated with OS. HSPA5 and PSME2 were protective (hazard ratio (HR) < 1), and HLA-F was risky (HR > 1). Risk score, estrogen receptor (ER), progesterone receptor (PR) and PD-L1 were independent prognostic indicators. KIT and ACACB may have important roles in the mechanism by which the gene signature regulates prognosis of BC. Conclusion: The proposed three-gene signature is a promising biomarker for estimating survival outcomes in BC patients.
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Affiliation(s)
- Aoshuang Qi
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation China Medical University, Shenyang, China
| | - Mingyi Ju
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation China Medical University, Shenyang, China
| | - Yinfeng Liu
- Department of Breast Surgery, The First Hospital of Qinhuangdao, Qinhuangdao, China
| | - Jia Bi
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation China Medical University, Shenyang, China
| | - Qian Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation China Medical University, Shenyang, China
| | - Miao He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation China Medical University, Shenyang, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation China Medical University, Shenyang, China
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation China Medical University, Shenyang, China
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12
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Rahaman S, Li X, Yu J, Wong KC. CancerEMC: frontline non-invasive cancer screening from circulating protein biomarkers and mutations in cell-free DNA. Bioinformatics 2021; 37:3319-3327. [PMID: 33515231 DOI: 10.1093/bioinformatics/btab044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/19/2020] [Accepted: 01/20/2021] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION The early detection of cancer through accessible blood tests can foster early patient interventions. Although there are developments in cancer detection from cell-free DNA (cfDNA), its accuracy remains speculative. Given its central importance with broad impacts, we aspire to address the challenge. METHODS A bagging Ensemble Meta Classifier (CancerEMC) is proposed for early cancer detection based on circulating protein biomarkers and mutations in cfDNA from the blood. CancerEMC is generally designed for both binary cancer detection and multi-class cancer type localization. It can address the class imbalance problem in multi-analyte blood test data based on robust oversampling and adaptive synthesis techniques. RESULTS Based on the clinical blood test data, we observe that the proposed CancerEMC has outperformed other algorithms and state-of-the-arts studies (including CancerSEEK published in Science, 2018) for cancer detection. The results reveal that our proposed method (i.e., CancerEMC) can achieve the best performance result for both binary cancer classification with 99.1748% accuracy (AUC = 0.999) and localized multiple cancer detection with 74.1214% accuracy (AUC = 0.938). For addressing the data imbalance issue with oversampling techniques, the accuracy can be increased to 91.4966% (AUC = 0.992), where the state-of-the-art method can only be estimated at 69.64% (AUC = 0.921). Similar results can also be observed on independent and isolated testing data. AVAILABILITY https://github.com/saifurcubd/Cancer-Detection.
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Affiliation(s)
- Saifur Rahaman
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR
| | - Xiangtao Li
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR
| | - Jun Yu
- Institute of Digestive Diseases and The Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR
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13
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Yu F, Quan F, Xu J, Zhang Y, Xie Y, Zhang J, Lan Y, Yuan H, Zhang H, Cheng S, Xiao Y, Li X. Breast cancer prognosis signature: linking risk stratification to disease subtypes. Brief Bioinform 2020; 20:2130-2140. [PMID: 30184043 DOI: 10.1093/bib/bby073] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 07/14/2018] [Accepted: 07/28/2018] [Indexed: 01/29/2023] Open
Abstract
Breast cancer is a very complex and heterogeneous disease with variable molecular mechanisms of carcinogenesis and clinical behaviors. The identification of prognostic risk factors may enable effective diagnosis and treatment of breast cancer. In particular, numerous gene-expression-based prognostic signatures were developed and some of them have already been applied into clinical trials and practice. In this study, we summarized several representative gene-expression-based signatures with significant prognostic value and separately assessed their ability of prognosis prediction in their originally targeted populations of breast cancer. Notably, many of the collected signatures were originally designed to predict the outcomes of estrogen receptor positive (ER+) patients or the whole breast cancer cohort; there are no typical signatures used for the prognostic prediction in a specific population of patients with the intrinsic subtype. We thus attempted to identify subtype-specific prognostic signatures via a computational framework for analyzing multi-omics profiles and patient survival. For both the discovery and an independent data set, we confirmed that subtype-specific signature is a strong and significant independent prognostic factor in the corresponding cohort. These results indicate that the subtype-specific prognostic signature has a much higher resolution in the risk stratification, which may lead to improved therapies and precision medicine for patients with breast cancer.
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Affiliation(s)
- Fulong Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Fei Quan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jinyuan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yi Xie
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jingyu Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Huating Yuan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Hongyi Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Shujun Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.,State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Cancer Institute and Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
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14
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Cardoso F, Kyriakides S, Ohno S, Penault-Llorca F, Poortmans P, Rubio IT, Zackrisson S, Senkus E. Early breast cancer: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up†. Ann Oncol 2020; 30:1194-1220. [PMID: 31161190 DOI: 10.1093/annonc/mdz173] [Citation(s) in RCA: 1318] [Impact Index Per Article: 263.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- F Cardoso
- Breast Unit, Champalimaud Clinical Center/Champalimaud Foundation, Lisbon, Portugal
| | | | - S Ohno
- Breast Oncology Center, Cancer Institute Hospital, Tokyo, Japan
| | - F Penault-Llorca
- Department of Pathology, Centre Jean Perrin, Clermont-Ferrand; .,UMR INSERM 1240, IMoST Université d'Auvergne, Clermont-Ferrand
| | - P Poortmans
- Department of Radiation Oncology, Institut Curie, Paris;,Paris Sciences & Lettres – PSL University, Paris, France
| | - I T Rubio
- Breast Surgical Oncology Unit, Clinica Universidad de Navarra, Madrid, Spain
| | - S Zackrisson
- Department of Translational Medicine, Diagnostic Radiology, Lund University and Skåne University Hospital Malmö, Malmö, Sweden
| | - E Senkus
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, Gdańsk, Poland
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15
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Kang J, Yu Y, Jeong S, Lee H, Heo HJ, Park JJ, Na HS, Ko DS, Kim YH. Prognostic role of high cathepsin D expression in breast cancer: a systematic review and meta-analysis. Ther Adv Med Oncol 2020; 12:1758835920927838. [PMID: 32550865 PMCID: PMC7281710 DOI: 10.1177/1758835920927838] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/27/2020] [Indexed: 12/21/2022] Open
Abstract
Background: High cathepsin D has been associated with poor prognosis in breast cancer;
however, the results of many studies are controversial. Here, we assessed
the association between high cathepsin D levels and worse breast cancer
prognosis by conducting a meta-analysis. Methods: A comprehensive search strategy was used to search relevant literature in
PUBMED and EMBASE by September 2018. The meta-analysis was performed in
Review Manager 5.3 using hazard ratios (HRs) with 95% confidence intervals
(CIs). Results: A total of 15,355 breast cancer patients from 26 eligible studies were
included in this meta-analysis. Significant associations between elevated
high cathepsin D and poor overall survival (OS) (HR = 1.61, 95% CI:
1.35–1.92, p < 0.0001) and disease-free survival (DFS)
(HR = 1.52, 95% CI: 1.31–2.18, p < 0.001) were observed.
In the subgroup analysis for DFS, high cathepsin D was significantly
associated with poor prognosis in node-positive patients (HR = 1.38, 95% CI:
1.25–1.71, p < 0.00001), node-negative patients
(HR = 1.78, 95% CI: 1.39–2.27, p < 0.0001), early stage
patients (HR = 1.73, 95% CI: 1.34–2.23, p < 0.0001), and
treated with chemotherapy patients (HR = 1.60, 95% CI: 1.21–2.12,
p < 0.001). Interestingly, patients treated with
tamoxifen had a low risk of relapse when their cathepsin D levels were high
(HR = 0.71, 95% CI: 0.52–0.98, p = 0.04) and a high risk of
relapse when their cathepsin D levels were low (HR = 1.50, 95% CI:
1.22–1.85, p = 0.0001). Conclusions: Our meta-analysis suggests that high expression levels of cathepsin D are
associated with a poor prognosis in breast cancer. Based on our subgroup
analysis, we believe that cathepsin D can act as a marker for poor breast
cancer prognosis and also as a therapeutic target for breast cancer.
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Affiliation(s)
- Junho Kang
- Interdisciplinary Program of Genomic Data Science, Pusan National University, Yangsan, Republic of Korea
| | - Yeuni Yu
- Interdisciplinary Program of Genomic Data Science, Pusan National University, Yangsan, Republic of Korea
| | - Seongdo Jeong
- Interdisciplinary Program of Genomic Data Science, Pusan National University, Yangsan, Republic of Korea
| | - Hansong Lee
- Interdisciplinary Program of Genomic Data Science, Pusan National University, Yangsan, Republic of Korea
| | - Hye Jin Heo
- Departmment of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Jeong Jun Park
- Departemt of Anesthesiology and Pain Medicine, Korea University College of Medicine, Anam Hospital, Seoul, Republic of Korea
| | - Hee Sam Na
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, Republic of Korea
| | - Dai Sik Ko
- Division of Vascular Surgery, Department of Surgery, Gachon University Gil Medical Center, Incheon, Republic of Korea
| | - Yun Hak Kim
- Department of Anatomy and Department of Biomedical Informatics, Pusan National University, 49 Busandaehak-ro, Yangsan 50612, Republic of Korea
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16
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Lee J, Park A, Mun S, Kim HJ, Son H, Choi H, Kim D, Lee SJ, Kim JG, Kang HG. Proteomics-Based Identification of Diagnostic Biomarkers Related to Risk Factors and Pathogenesis of Ischemic Stroke. Diagnostics (Basel) 2020; 10:diagnostics10050340. [PMID: 32466277 PMCID: PMC7278009 DOI: 10.3390/diagnostics10050340] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 12/04/2022] Open
Abstract
Ischemic stroke is caused by blood clot formation and consequent vessel blockage. Proteomic approaches provide a cost-effective alternative to current diagnostic methods, including computerized tomography (CT) scans and magnetic resonance imaging (MRI). To identify diagnostic biomarkers associated with ischemic stroke risk factors, we performed individual proteomic analysis of serum taken from 20 healthy controls and 20 ischemic stroke patients. We then performed SWATH analysis, a data-independent method, to assess quantitative changes in protein expression between the two experimental conditions. Our analysis identified several candidate protein biomarkers, 11 of which were validated by multiple reaction monitoring (MRM) analysis as novel diagnostic biomarkers associated with ischemic stroke risk factors. Our study identifies new biomarkers associated with the risk factors and pathogenesis of ischemic stroke which, to the best of our knowledge, were previously unknown. These markers may be effective in not only the diagnosis but also the prevention and management of ischemic stroke.
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Affiliation(s)
- Jiyeong Lee
- Department of Biomedical Laboratory Science, School of Medicine, Eulji University, Daejeon 34824, Korea;
| | - Arum Park
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Seongnam 13135, Korea; (A.P.); (S.M.); (H.-J.K.); (H.S.); (H.C.)
| | - Sora Mun
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Seongnam 13135, Korea; (A.P.); (S.M.); (H.-J.K.); (H.S.); (H.C.)
| | - Hyo-Jin Kim
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Seongnam 13135, Korea; (A.P.); (S.M.); (H.-J.K.); (H.S.); (H.C.)
| | - Hyunsong Son
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Seongnam 13135, Korea; (A.P.); (S.M.); (H.-J.K.); (H.S.); (H.C.)
| | - Hyebin Choi
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Seongnam 13135, Korea; (A.P.); (S.M.); (H.-J.K.); (H.S.); (H.C.)
| | - Doojin Kim
- Department of Laboratory Medicine, Seongnam Central Hospital, Seongnam 13161, Korea;
| | - Soo Joo Lee
- Department of Neurology, Eulji University Hospital, School of Medicine, Eulji University, Daejeon 35233, Korea; (S.J.L.); (J.G.K.)
| | - Jae Guk Kim
- Department of Neurology, Eulji University Hospital, School of Medicine, Eulji University, Daejeon 35233, Korea; (S.J.L.); (J.G.K.)
| | - Hee-Gyoo Kang
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Seongnam 13135, Korea; (A.P.); (S.M.); (H.-J.K.); (H.S.); (H.C.)
- Department of Biomedical Laboratory Science, School of Medicine, Eulji University, Seongnam 13135, Korea
- Seongnam Senior Industry Innovation Center, Eulji University, Seongnam 13503, Korea
- Correspondence: ; Tel.: +82-31-740-7315; Fax: +82-31-740-7448
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17
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Chen G, Cao Y, Tang Y, Yang X, Liu Y, Huang D, Zhang Y, Li C, Wang Q. Advanced Near-Infrared Light for Monitoring and Modulating the Spatiotemporal Dynamics of Cell Functions in Living Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903783. [PMID: 32328436 PMCID: PMC7175256 DOI: 10.1002/advs.201903783] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/06/2020] [Indexed: 05/07/2023]
Abstract
Light-based technique, including optical imaging and photoregulation, has become one of the most important tools for both fundamental research and clinical practice, such as cell signal sensing, cancer diagnosis, tissue engineering, drug delivery, visual regulation, neuromodulation, and disease treatment. In particular, low energy near-infrared (NIR, 700-1700 nm) light possesses lower phototoxicity and higher tissue penetration depth in living systems as compared with ultraviolet/visible light, making it a promising tool for in vivo applications. Currently, the NIR light-based imaging and photoregulation strategies have offered a possibility to real-time sense and/or modulate specific cellular events in deep tissues with subcellular accuracy. Herein, the recent progress with respect to NIR light for monitoring and modulating the spatiotemporal dynamics of cell functions in living systems are summarized. In particular, the applications of NIR light-based techniques in cancer theranostics, regenerative medicine, and neuroscience research are systematically introduced and discussed. In addition, the challenges and prospects for NIR light-based cell sensing and regulating techniques are comprehensively discussed.
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Affiliation(s)
- Guangcun Chen
- CAS Key Laboratory of Nano‐Bio InterfaceDivision of Nanobiomedicine and i‐LabCAS Center for Excellence in Brain ScienceSuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- Suzhou Key Laboratory of Functional Molecular Imaging TechnologySuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- School of Nano‐Tech and Nano‐BionicsUniversity of Science and Technology of ChinaHefei230026China
| | - Yuheng Cao
- CAS Key Laboratory of Nano‐Bio InterfaceDivision of Nanobiomedicine and i‐LabCAS Center for Excellence in Brain ScienceSuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- Suzhou Key Laboratory of Functional Molecular Imaging TechnologySuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
| | - Yanxing Tang
- CAS Key Laboratory of Nano‐Bio InterfaceDivision of Nanobiomedicine and i‐LabCAS Center for Excellence in Brain ScienceSuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- Suzhou Key Laboratory of Functional Molecular Imaging TechnologySuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
| | - Xue Yang
- CAS Key Laboratory of Nano‐Bio InterfaceDivision of Nanobiomedicine and i‐LabCAS Center for Excellence in Brain ScienceSuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- Suzhou Key Laboratory of Functional Molecular Imaging TechnologySuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- School of Nano‐Tech and Nano‐BionicsUniversity of Science and Technology of ChinaHefei230026China
| | - Yongyang Liu
- CAS Key Laboratory of Nano‐Bio InterfaceDivision of Nanobiomedicine and i‐LabCAS Center for Excellence in Brain ScienceSuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- Suzhou Key Laboratory of Functional Molecular Imaging TechnologySuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- School of Nano‐Tech and Nano‐BionicsUniversity of Science and Technology of ChinaHefei230026China
| | - Dehua Huang
- CAS Key Laboratory of Nano‐Bio InterfaceDivision of Nanobiomedicine and i‐LabCAS Center for Excellence in Brain ScienceSuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- Suzhou Key Laboratory of Functional Molecular Imaging TechnologySuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- School of Nano‐Tech and Nano‐BionicsUniversity of Science and Technology of ChinaHefei230026China
| | - Yejun Zhang
- CAS Key Laboratory of Nano‐Bio InterfaceDivision of Nanobiomedicine and i‐LabCAS Center for Excellence in Brain ScienceSuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- Suzhou Key Laboratory of Functional Molecular Imaging TechnologySuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- School of Nano‐Tech and Nano‐BionicsUniversity of Science and Technology of ChinaHefei230026China
| | - Chunyan Li
- CAS Key Laboratory of Nano‐Bio InterfaceDivision of Nanobiomedicine and i‐LabCAS Center for Excellence in Brain ScienceSuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- Suzhou Key Laboratory of Functional Molecular Imaging TechnologySuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- School of Nano‐Tech and Nano‐BionicsUniversity of Science and Technology of ChinaHefei230026China
| | - Qiangbin Wang
- CAS Key Laboratory of Nano‐Bio InterfaceDivision of Nanobiomedicine and i‐LabCAS Center for Excellence in Brain ScienceSuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- Suzhou Key Laboratory of Functional Molecular Imaging TechnologySuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
- School of Nano‐Tech and Nano‐BionicsUniversity of Science and Technology of ChinaHefei230026China
- College of Materials Sciences and Opto‐Electronic TechnologyUniversity of Chinese Academy of SciencesBeijing100049China
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18
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Mendaza S, Fernández-Irigoyen J, Santamaría E, Zudaire T, Guarch R, Guerrero-Setas D, Vidal A, Santos-Salas J, Matias-Guiu X, Ausín K, Díaz de Cerio MJ, Martín-Sánchez E. Absence of Nuclear p16 Is a Diagnostic and Independent Prognostic Biomarker in Squamous Cell Carcinoma of the Cervix. Int J Mol Sci 2020; 21:ijms21062125. [PMID: 32204550 PMCID: PMC7139571 DOI: 10.3390/ijms21062125] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/11/2020] [Accepted: 03/18/2020] [Indexed: 12/19/2022] Open
Abstract
The tumor-suppressor protein p16 is paradoxically overexpressed in cervical cancer (CC). Despite its potential as a biomarker, its clinical value and the reasons for its failure in tumor suppression remain unclear. Our purpose was to determine p16 clinical and biological significance in CC. p16 expression pattern was examined by immunohistochemistry in 78 CC cases (high-grade squamous intraepithelial lesions (HSILs) and squamous cell carcinomas of the cervix –SCCCs). CC cell proliferation and invasion were monitored by real-time cell analysis and Transwell® invasion assay, respectively. Cytoplasmic p16 interactors were identified from immunoprecipitated extracts by liquid chromatography-tandem mass spectrometry, and colocalization was confirmed by double-immunofluorescence. We observed that SCCCs showed significantly more cytoplasmic than nuclear p16 expression than HSILs. Importantly, nuclear p16 absence significantly predicted poor outcome in SCCC patients irrespective of other clinical parameters. Moreover, we demonstrated that cytoplasmic p16 interacted with CDK4 and other unreported proteins, such as BANF1, AKAP8 and AGTRAP, which could sequester p16 to avoid nuclear translocation, and then, impair its anti-tumor function. Our results suggest that the absence of nuclear p16 could be a diagnostic biomarker between HSIL and SCCC, and an independent prognostic biomarker in SCCC; and explain why p16 overexpression fails to stop CC growth.
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Affiliation(s)
- Saioa Mendaza
- Molecular Pathology of Cancer Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
| | - Enrique Santamaría
- Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
| | - Tamara Zudaire
- Department of Pathology, Complejo Hospitalario de Navarra (CHN), Irunlarrea 3, 31008 Pamplona, Spain
| | - Rosa Guarch
- Department of Pathology, Complejo Hospitalario de Navarra (CHN), Irunlarrea 3, 31008 Pamplona, Spain
| | - David Guerrero-Setas
- Molecular Pathology of Cancer Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
- Department of Pathology, Complejo Hospitalario de Navarra (CHN), Irunlarrea 3, 31008 Pamplona, Spain
| | - August Vidal
- Department of Pathology, Hospital Universitari de Bellvitge, IDIBELL, Carrer de la Feixa Llarga, 08907 L’Hospitalet de Llobregat, Spain
| | - José Santos-Salas
- Department of Pathology, Complejo Asistencial Universitario, Altos de Nava, 24071 León, Spain
| | - Xavier Matias-Guiu
- Department of Pathology, Hospital Universitari de Bellvitge, IDIBELL, Carrer de la Feixa Llarga, 08907 L’Hospitalet de Llobregat, Spain
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova, University of Lleida, Alcalde Rovira Roure 80, 25198 Lleida, Spain
| | - Karina Ausín
- Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
| | - María José Díaz de Cerio
- Department of Pathology, Complejo Hospitalario de Navarra (CHN), Irunlarrea 3, 31008 Pamplona, Spain
| | - Esperanza Martín-Sánchez
- Molecular Pathology of Cancer Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
- Correspondence:
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19
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Yang PS, Lee YH, Chung CF, Chang YC, Wang MY, Lo C, Tsai LW, Shih KH, Lei J, Yu BL, Cheng SH, Huang CS. A preliminary report of head-to-head comparison of 18-gene-based clinical-genomic model and oncotype DX 21-gene assay for predicting recurrence of early-stage breast cancer. Jpn J Clin Oncol 2020; 49:1029-1036. [PMID: 31287883 PMCID: PMC6918807 DOI: 10.1093/jjco/hyz102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/13/2019] [Accepted: 06/19/2019] [Indexed: 12/25/2022] Open
Abstract
Background The information of Oncotype DX applied in Asian breast cancer patients is limited. A recurrence index for distant recurrence (RI-DR) has been developed for early-stage breast cancer (EBC) from tumor samples in Chinese patients. In this study, we compared the prognostic performance of the Oncotype DX (ODx) recurrence score (RS) with the RI-DR for any recurrence risk type. Materials and methods One hundred thirty-eight (138) patients with hormone receptor-positive and human epidermal growth factor receptor 2-negative EBC who were previously tested with ODx were included for testing with the RI-DR. The cutoff score to partition the low- and high-risk patients was 26 for RS and 36 for RI-DR. The primary endpoint was recurrence-free survival (RFS). Results The concordance between the RI-DR and RS was 83% in N0 patients and 81% in node-positive patients when the RS score cutoff was set at 26. With a median follow-up interval of 36.8 months, the 4-year RFS for the high- and low-risk groups categorized by the RS were 61.9% and 95.0%, respectively (hazard ratio: 10.6, 95.0% confidence interval [CI]: 1.8–62.9). The 4-year RFS in the high- and low-risk groups categorized by the RI-DR were 72.6% and 98.5%, respectively (hazard ratio: 18.9, 95% CI: 1.8–138.8). Conclusion This paper illustrated the performance of RI-DR and ODx RS in breast cancer women in Taiwan. There was high concordance between the RI-DR and RS. The RI-DR is not inferior to the RS in predicting RFS in EBC patients. This study will fill the gap between the current and best practice in Chinese patients.
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Affiliation(s)
- Po-Sheng Yang
- Department of Medicine, MacKay Medical College, New Taipei, Taiwan.,Department of General Surgery, MacKay Memorial Hospital, Taipei, Taiwan
| | - Yi-Hsuan Lee
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chi-Feng Chung
- Department of Hematology Oncology, Koo Foundation Sun Yat-Sen Cancer Center, Taipei, Taiwan
| | - Yuan-Ching Chang
- Department of Medicine, MacKay Medical College, New Taipei, Taiwan.,Department of General Surgery, MacKay Memorial Hospital, Taipei, Taiwan
| | - Ming-Yang Wang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Chiao Lo
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Li Wei Tsai
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Kuan-Hui Shih
- Department of Research and Product Development, Amwise Diagnostics Pte. Ltd., Singapore
| | - Jason Lei
- Department of Research and Product Development, Amwise Diagnostics Pte. Ltd., Singapore
| | - Ben-Long Yu
- Department of Surgery, Koo Foundation Sun Yat-Sen Cancer Center, Taipei, Taiwan
| | - Skye H Cheng
- Department of Radiation Oncology, Koo Foundation Sun Yat-Sen Cancer Center, Taipei, Taiwan
| | - Chiun-Sheng Huang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
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20
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Probabilistic cost-utility analysis and expected value of perfect information for the Oncotype multigenic test: a discrete event simulation model. GACETA SANITARIA 2020; 34:61-68. [DOI: 10.1016/j.gaceta.2018.07.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/06/2018] [Accepted: 07/14/2018] [Indexed: 01/01/2023]
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21
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Abstract
Introduction: Breast cancer is heterogeneous with distinct clinical outcomes. Diverse types of markers are available on the market for breast cancer prognosis, diagnosis, and therapeutics, with distinct assay approaches. These, though they enlarge our selection pool for characterizing breast cancer patients and help improve the precision on the therapeutics, they can complicate our understanding and choice of marker panels. Areas covered: This review aims at classifying the commonly used marker panels according to their functionalities and detection approaches, comparing their advantages and disadvantages, and identifying their shared features to gain a comprehensive understanding of the diversified molecular profiles that drive breast cancer heterogeneity. Expert opinion: Our effort will contribute as a guidebook for clinicians on the use of breast cancer signature panels for disease management, and for researchers on the establishment of novel marker panels with improved precision and reduced complexity. We propose that collectively analyzing all available marker panels is equally important as investigating on entirely novel marker panels. Advances in technologies capturing signals from multiple levels are of practical importance in breaking through limitations on translating markers into clinical use.
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Affiliation(s)
- Zhen Wang
- Wuxi School of Medicine, Jiangnan University , Wuxi , China
| | - Xuanhao Zhang
- School of Biotechnology, Jiangnan University , Wuxi , China
| | - Shuo Zhang
- School of Biotechnology, Jiangnan University , Wuxi , China
| | - Xiaofeng Dai
- Wuxi School of Medicine, Jiangnan University , Wuxi , China
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22
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Wong KC, Chen J, Zhang J, Lin J, Yan S, Zhang S, Li X, Liang C, Peng C, Lin Q, Kwong S, Yu J. Early Cancer Detection from Multianalyte Blood Test Results. iScience 2019; 15:332-341. [PMID: 31103852 PMCID: PMC6548890 DOI: 10.1016/j.isci.2019.04.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/18/2019] [Accepted: 04/29/2019] [Indexed: 12/18/2022] Open
Abstract
The early detection of cancers has the potential to save many lives. A recent attempt has been demonstrated successful. However, we note several critical limitations. Given the central importance and broad impact of early cancer detection, we aspire to address those limitations. We explore different supervised learning approaches for multiple cancer type detection and observe significant improvements; for instance, one of our approaches (i.e., CancerA1DE) can double the existing sensitivity from 38% to 77% for the earliest cancer detection (i.e., Stage I) at the 99% specificity level. For Stage II, it can even reach up to about 90% across multiple cancer types. In addition, CancerA1DE can also double the existing sensitivity from 30% to 70% for detecting breast cancers at the 99% specificity level. Data and model analysis are conducted to reveal the underlying reasons. A website is built at http://cancer.cs.cityu.edu.hk/. We propose an approach (CancerA1DE) to detect early cancers from blood CancerA1DE doubles the existing sensitivity for the stage I cancer detection For stage II cancers, it can reach up to 90% across multiple cancer types The related software is opened and released for future follow-up works
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Affiliation(s)
- Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR.
| | - Junyi Chen
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Jiao Zhang
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Jiecong Lin
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Shankai Yan
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Shxiong Zhang
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Xiangtao Li
- School of Information Science and Technology, Northeast Normal University, Jilin, China
| | - Cheng Liang
- School of Information Science and Engineering, Shandong Normal University, Shandong, China
| | - Chengbin Peng
- Ningbo Institute of Industrial Technology, Chinese Academy of Sciences, Ningbo, China
| | - Qiuzhen Lin
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Sam Kwong
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR
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23
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Jakubowicz E, Martin B, Hoffmann R, Kröncke T, Jung T, Steierl R, Steinfeld D, Schenkirsch G, Kriegsmann J, Märkl B. EndoPredict versus uPA/PAI-1 in breast cancer: Comparison of markers and association with clinicopathological parameters. Breast J 2019; 25:450-454. [PMID: 31001905 DOI: 10.1111/tbj.13258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 08/16/2018] [Accepted: 08/22/2018] [Indexed: 11/30/2022]
Abstract
We retrospectively investigated concordance of EndoPredict (EPclin) with urokinase plasminogen activator and plasminogen activator inhibitor-1 (uPA/PAI-1) in 72 breast cancer patients and compared the results with grading, molecular subtype and chemotherapy recommendation. Compared to uPA/PAI-1, EPclin proved to be more conservative concerning correlation with clinicopathological parameters and was significantly associated with the recommendation of adjuvant chemotherapy.
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Affiliation(s)
| | - Benedikt Martin
- Institute of Pathology, Universitätsklinikum Augsburg, Augsburg, Germany
| | - Reinhard Hoffmann
- Institute of Laboratory Medicine and Microbiology, Universitätsklinikum Augsburg, Augsburg, Germany
| | - Thomas Kröncke
- Department of Diagnostic and Interventional Radiology, Universitätsklinikum Augsburg, Augsburg, Germany
| | - Thomas Jung
- Clinic for Gynecology and Obstetrics, Universitätsklinikum Augsburg, Augsburg, Germany
| | - Roman Steierl
- Frauenklinik im Josefinum Augsburg, Katholische Jugendfürsorge Fachklinik, Augsburg, Germany
| | | | - Gerhard Schenkirsch
- Tumor Data Management, Interdisciplinary Cancer Center Augsburg, Augsburg, Germany
| | - Jörg Kriegsmann
- Histology, Cytology and Molecular Diagnostics Center Trier, Trier, Germany
| | - Bruno Märkl
- Institute of Pathology, Universitätsklinikum Augsburg, Augsburg, Germany
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24
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Marcos X, Padilla-Beltrán C, Bernad-Bernad MJ, Rosales-Hernández MC, Pérez-Casas S, Correa-Basurto J. Controlled release of N-(2-hydroxyphenyl)-2-propylpentanamide nanoencapsulated in polymeric micelles of P123 and F127 tested as anti-proliferative agents in MDA-MB-231 cells. J Drug Deliv Sci Technol 2018. [DOI: 10.1016/j.jddst.2018.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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25
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Beelen K, Opdam M, Severson T, Koornstra R, Vincent A, Wesseling J, Sanders J, Vermorken J, van Diest P, Linn S. Mitotic count can predict tamoxifen benefit in postmenopausal breast cancer patients while Ki67 score cannot. BMC Cancer 2018; 18:761. [PMID: 30041599 PMCID: PMC6057037 DOI: 10.1186/s12885-018-4516-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 05/18/2018] [Indexed: 12/13/2022] Open
Abstract
Background Controversy exists for the use of Ki67 protein expression as a predictive marker to select patients who do or do not derive benefit from adjuvant endocrine therapy. Whether other proliferation markers, like Cyclin D1, and mitotic count can also be used to identify those estrogen receptor α (ERα) positive breast cancer patients that derive benefit from tamoxifen is not well established. We tested the predictive value of these markers for tamoxifen benefit in ERα positive postmenopausal breast cancer patients. Methods We collected primary tumor blocks from 563 ERα positive patients who had been randomized between tamoxifen (1 to 3 years) vs. no adjuvant therapy (IKA trial) with a median follow-up of 7.8 years. Mitotic count, Ki67 and Cyclin D1 protein expression were centrally assessed by immunohistochemistry on tissue microarrays. In addition, we tested the predictive value of CCND1 gene copy number variation using MLPA technology. Multivariate Cox proportional hazard models including interaction between marker and treatment were used to test the predictive value of these markers. Results Patients with high Ki67 (≥5%) as well as low (< 5%) expressing tumors equally benefitted from adjuvant tamoxifen (adjusted hazard ratio (HR) 0.5 for both groups)(p for interaction 0.97). We did not observe a significant interaction between either Cyclin D1 or Ki67 and tamoxifen, indicating that the relative benefit from tamoxifen was not dependent on the level of these markers. Patients with tumors with low mitotic count derived substantial benefit from tamoxifen (adjusted HR 0.24, p < 0.0001), while patients with tumors with high mitotic count derived no significant benefit (adjusted HR 0.64, p = 0.14) (p for interaction 0.03). Conclusion Postmenopausal breast cancer patients with high Ki67 counts do significantly benefit from adjuvant tamoxifen, while those with high mitotic count do not. Mitotic count is a better selection marker for reduced tamoxifen benefit than Ki67. Electronic supplementary material The online version of this article (10.1186/s12885-018-4516-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karin Beelen
- Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mark Opdam
- Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tesa Severson
- Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rutger Koornstra
- Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andrew Vincent
- Departments of Biometrics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jelle Wesseling
- Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joyce Sanders
- Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jan Vermorken
- Department of Medical Oncology, University Hospital Antwerpen, Edegem, Belgium
| | - Paul van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sabine Linn
- Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands. .,Medical Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands.
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26
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Martínez Del Prado P, Alvarez-López I, Domínguez-Fernández S, Plazaola A, Ibarrondo O, Galve-Calvo E, Ancizar-Lizarraga N, Gutierrez-Toribio M, Lahuerta-Martínez A, Mar J. Clinical and economic impact of the 21-gene recurrence score assay in adjuvant therapy decision making in patients with early-stage breast cancer: pooled analysis in 4 Basque Country university hospitals. CLINICOECONOMICS AND OUTCOMES RESEARCH 2018; 10:189-199. [PMID: 29593426 PMCID: PMC5863711 DOI: 10.2147/ceor.s146095] [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] [Indexed: 01/03/2023] Open
Abstract
Purpose The 21-gene recurrence score (RS) is a genomic test developed as a prognostic and predictive tool to improve the treatment decision making in cases of estrogen receptor-positive and human epidermal growth factor receptor 2-negative early-stage breast cancer. This study examined the clinical and economic impact of its use in 4 Basque Country university hospitals. Methods Taking into consideration the RS result, we recorded the recommended initial systemic adjuvant therapy (endocrine therapy with or without chemotherapy) according to standard clinicopathologic factors and the final decision about chemotherapy. Then, if the RS was high, chemotherapy was recommended; it was not recommended if the RS was low; for those with an intermediate RS, clinicopathologic factors were considered, and the initial recommendation based on those factors was maintained. In addition, the probability of switching treatment was calculated. Then, we developed an economic evaluation by measuring the treatment’s incremental short-term budget impact from both the societal perspective and that of the Basque Health System. Patients’ characteristics and chemotherapy use were analyzed using logistic regressions and receiver operating characteristic curves. Results Without an RS, chemotherapy would have been prescribed to 56% of 401 patients, but, with RS use, that percentage decreased to 25. The overall rate of decision change was 35.4%. Test inclusion led to a reduction in chemotherapy costs of €922 per patient in the total population. Although this reduction did not entirely offset the cost of the test, the productivity loss per patient was reduced by €1,977. Conclusion The 21-gene RS test significantly changed the indication for chemotherapy. As chemotherapy treatments with no benefit were avoided, patients’ quality of life was improved. The short-term economic impact was negative for the Basque Health Service, but savings resulted when sick-leave costs were included.
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Affiliation(s)
| | - Isabel Alvarez-López
- Medical Oncology Service, Donostia University Hospital, Donostia-San Sebastián, Spain.,Biodonostia Health Research Institute, Donostia-San Sebastián, Spain
| | | | - Arrate Plazaola
- Medical Oncology Service, Onkologikoa, Donostia-San Sebastián, Spain
| | - Oliver Ibarrondo
- AP-OSI Research Unit, Alto Deba Integrated Health Care Organization, Mondragon, Spain
| | - Elena Galve-Calvo
- Medical Oncology Service, Basurto University Hospital, Bilbao, Spain
| | - Nerea Ancizar-Lizarraga
- Medical Oncology Service, Donostia University Hospital, Donostia-San Sebastián, Spain.,Biodonostia Health Research Institute, Donostia-San Sebastián, Spain
| | | | | | - Javier Mar
- AP-OSI Research Unit, Alto Deba Integrated Health Care Organization, Mondragon, Spain.,Health Services Research on Chronic Patients Network, Kronikgune Group, Bilbao, Spain
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27
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Aushev VN, Lee E, Zhu J, Gopalakrishnan K, Li Q, Teitelbaum SL, Wetmur J, Degli Esposti D, Hernandez-Vargas H, Herceg Z, Parada H, Santella RM, Gammon MD, Chen J. Novel Predictors of Breast Cancer Survival Derived from miRNA Activity Analysis. Clin Cancer Res 2018; 24:581-591. [PMID: 29138345 PMCID: PMC6103440 DOI: 10.1158/1078-0432.ccr-17-0996] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/21/2017] [Accepted: 11/10/2017] [Indexed: 01/14/2023]
Abstract
Purpose: Breast cancer is among the leading causes of cancer-related death; discovery of novel prognostic markers is needed to improve outcomes. Combining systems biology and epidemiology, we investigated miRNA-associated genes and breast cancer survival in a well-characterized population-based study.Experimental Design: A recently developed algorithm, ActMiR, was used to identify key miRNA "activities" corresponding to target gene degradation, which were predictive of breast cancer mortality in published databases. We profiled miRNA-associated genes in tumors from our well-characterized population-based cohort of 606 women with first primary breast cancer. Cox proportional hazards models were used to estimate HRs and 95% confidence intervals (CI), after 15+ years of follow-up with 119 breast cancer-specific deaths.Results: miR-500a activity was identified as a key miRNA for estrogen receptor-positive breast cancer mortality using public databases. From a panel of 161 miR-500a-associated genes profiled, 73 were significantly associated with breast cancer-specific mortality (FDR < 0.05) in our population, among which two clusters were observed to have opposing directions of association. For example, high level of SUSD3 was associated with reduced breast cancer-specific mortality (HR = 0.3; 95% CI, 0.2-0.4), whereas the opposite was observed for TPX2 (HR = 2.7; 95% CI, 1.8-3.9). Most importantly, we identified set of genes for which associations with breast cancer-specific mortality were independent of known prognostic factors, including hormone receptor status and PAM50-derived risk-of-recurrence scores. These results are validated in independent datasets.Conclusions: We identified novel markers that may improve prognostic efficiency while shedding light on molecular mechanisms of breast cancer progression. Clin Cancer Res; 24(3); 581-91. ©2017 AACR.
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Affiliation(s)
- Vasily N Aushev
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York
- Carcinogenesis Institute of N.N. Blokhin Russian Cancer Research Center, Moscow, Russia
| | - Eunjee Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kalpana Gopalakrishnan
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Qian Li
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Susan L Teitelbaum
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York
| | - James Wetmur
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Humberto Parada
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Regina M Santella
- Department of Environmental Health Sciences, Columbia University, New York, New York
| | - Marilie D Gammon
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York.
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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Liu H, Li J, Koirala P, Ding X, Chen B, Wang Y, Wang Z, Wang C, Zhang X, Mo YY. Long non-coding RNAs as prognostic markers in human breast cancer. Oncotarget 2018; 7:20584-96. [PMID: 26942882 PMCID: PMC4991477 DOI: 10.18632/oncotarget.7828] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 02/18/2016] [Indexed: 02/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been recently shown to play an important role in gene regulation and normal cellular functions, and disease processes. However, despite the overwhelming number of lncRNAs identified to date, little is known about their role in cancer for vast majority of them. The present study aims to determine whether lncRNAs can serve as prognostic markers in human breast cancer. We interrogated the breast invasive carcinoma dataset of the Cancer Genome Atlas (TCGA) at the cBioPortal consisting of ~ 1,000 cases. Among 2,730 lncRNAs analyzed, 577 lncRNAs had alterations ranging from 1% to 32% frequency, which include mutations, alterations of copy number and RNA expression. We found that deregulation of 11 lncRNAs, primarily due to copy number alteration, is associated with poor overall survival. At RNA expression level, upregulation of 4 lncRNAs (LINC00657, LINC00346, LINC00654 and HCG11) was associated with poor overall survival. A third signature consists of 9 lncRNAs (LINC00705, LINC00310, LINC00704, LINC00574, FAM74A3, UMODL1-AS1, ARRDC1-AS1, HAR1A, and LINC00323) and their upregulation can predict recurrence. Finally, we selected LINC00657 to determine their role in breast cancer, and found that LINC00657 knockout significantly suppresses tumor cell growth and proliferation, suggesting that it plays an oncogenic role. Together, these results highlight the clinical significance of lncRNAs, and thus, these lncRNAs may serve as prognostic markers for breast cancer.
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Affiliation(s)
- Hairong Liu
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA.,Department of Oncology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Juan Li
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA.,Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shangdong Province, China
| | - Pratirodh Koirala
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA.,Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS, USA
| | - Xianfeng Ding
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA.,College of Life Science, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Binghai Chen
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA.,Department of Urology, Affiliated Hospital of Jiangsu University, Jiangsu, Zhenjiang, China
| | - Yiheng Wang
- School of Computing, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Zheng Wang
- School of Computing, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Chuanxin Wang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shangdong Province, China
| | - Xu Zhang
- Center of Biostatistics and Bioinformatics, Department of Preventive Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Yin-Yuan Mo
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA.,Department of Pharmacology/Toxicology, University of Mississippi Medical Center, Jackson, MS, USA
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29
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Abstract
BACKGROUND The identification of prognostic biomarkers for cancer patients is essential for cancer research. These days, DNA methylation has been proved to be associated with cancer prognosis. However, there are few methods which identify the prognostic markers based on DNA methylation data systematically, especially considering the interaction among DNA methylation sites. METHODS In this paper, we first evaluated the stabilities of microRNA, mRNA, and DNA methylation data in prognosis of cancer. After that, a rank-based method was applied to construct a DNA methylation interaction network. In this network, nodes with the largest degrees (10% of all the nodes) were selected as hubs. Cox regression was applied to select the hubs as prognostic signature. In this prognostic signature, DNA methylation levels of each DNA methylation site are correlated with the outcomes of cancer patients. After obtaining these prognostic genes, we performed the survival analysis in the training group and the test group to verify the reliability of these genes. RESULTS We applied our method in three cancers (ovarian cancer, breast cancer and Glioblastoma Multiforme). In all the three cancers, there are more common ones of prognostic genes selected from different samples in DNA methylation data, compared with gene expression data and miRNA expression data, which indicates the DNA methylation data may be more stable in cancer prognosis. Power-law distribution fitting suggests that the DNA methylation interaction networks are scale-free. And the hubs selected from the three networks are all enriched by cancer related pathways. The gene signatures were obtained for the three cancers respectively, and survival analysis shows they can distinguish the outcomes of tumor patients in both the training data sets and test data sets, which outperformed the control signatures. CONCLUSIONS A computational method was proposed to construct DNA methylation interaction network and this network could be used to select prognostic signatures in cancer.
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Affiliation(s)
- Wei-Lin Hu
- College of Science, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Xiong-Hui Zhou
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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30
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Aapro M, De Laurentiis M, Rea D, Bargallo Rocha JE, Elizalde R, Landherr L, Linderholm B, Mamounas E, Markopoulos C, Neven P, Petrovsky A, Rouzier R, Smit V, Svedman C, Schneider D, Thomssen C, Martin M. The MAGIC survey in hormone receptor positive (HR+), HER2-negative (HER2-) breast cancer: When might multigene assays be of value? Breast 2017; 33:191-199. [PMID: 28441617 DOI: 10.1016/j.breast.2017.01.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 01/15/2017] [Accepted: 01/23/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND A modest proportion of patients with early stage hormone receptor-positive (HR+), HER2-negative (HER2-) breast cancer benefit from adjuvant chemotherapy. Traditionally, treatment recommendations are based on clinical/pathologic criteria that are not predictive of chemotherapy benefit. Multigene assays provide prognostic and predictive information that can help to make more informed treatment decisions. The MAGIC survey evaluated international differences in treatment recommendations, how traditional parameters are used for making treatment choices, and for which patients treating physicians feel most uncertain about their decisions. METHODS The MAGIC survey captured respondents' demographics, practice patterns, relevance of traditional parameters for treatment decisions, and use of or interest in using multigene assays. Using this information, a predictive model was created to simulate treatment recommendations for 672 patient profiles. RESULTS The survey was completed by 911 respondents (879 clinicians, 32 pathologists) from 52 countries. Chemo-endocrine therapy was recommended more often than endocrine therapy alone, but there was substantial heterogeneity in treatment recommendations in 52% of the patient profiles; approximately every fourth physician provided a different treatment recommendation. The majority of physicians indicated they wanted to use multigene assays clinically. Lack of reimbursement/availability were the main reasons for non-usage. CONCLUSIONS The survey reveals substantial heterogeneity in treatment recommendations. Physicians have uncertainty in treatment recommendations in a high proportion of patients with intermediate risk features using traditional parameters. In HR+, HER2- patients with early disease the findings highlight the need for additional markers that are both prognostic and predictive of chemotherapy benefit that may support more-informed treatment decisions.
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Affiliation(s)
- Matti Aapro
- Genolier Breast Center, Clinic of Genolier, Route du Muids 3, 1272 Genolier, Switzerland.
| | - Michelino De Laurentiis
- Department of Senology, National Cancer Institute G. Pascale Foundation, Via Mariano Semmola, 80131 Naples, Italy
| | - Dan Rea
- School of Cancer Sciences, University of Birmingham, Vincent Drive, Edgbaston, B15 2TT Birmingham, United Kingdom
| | - Juan Enrique Bargallo Rocha
- Department of Surgery, Instituto Nacional de Cancerología, Av. San Fernando No. 22, Col. Sección XVI Delegación Tlalpan, 14080 Mexico City, Mexico
| | - Roberto Elizalde
- División Ginecologia y Mastologia, Hospital Dr. I. Pirovano, Av Monroe 3555, 1428 Buenos Aires, Argentina
| | - László Landherr
- Department of Oncoradiology, Uzsoki Teaching Hospital, Uzsoki u. 29-41, 1145 Budapest, Hungary
| | - Barbro Linderholm
- Department of Oncology, Sahlgrenska Academy and University Hospital, Per Dubbsgatan 15, 413 45 Gothenburg, Sweden; Department of Oncology/Pathology, Karolinska Institutet, Karolinska Univ Hospital, Z1:00, 171 76 Stockholm, Sweden
| | - Eleftherios Mamounas
- University of Florida Health Cancer Center at Orlando Health, 1400 S. Orange Avenue, 32806 Orlando, FL, USA
| | - Christos Markopoulos
- Department of Surgery, Athens University Medical School, Iassiou Street 8, 11521 Athens, Greece
| | - Patrick Neven
- Multidisciplinary Breast Centre and Gynaecological Oncology, UZ Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Alexander Petrovsky
- Department of Radiosurgery, Russian Cancer Research Center, 23 Kashirskoye Shosse, Moscow, Russia
| | - Roman Rouzier
- Department of Surgery, Institut Curie-Université Versailles-Saint-Quentin, 35 rue Dailly, 92220 Paris-Saint-Cloud, France
| | - Vincent Smit
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Christer Svedman
- Medical Affairs, Genomic Health, Quai du Sujet 10, Stockholm, Sweden
| | - Daniel Schneider
- International, Genomic Health, Quai du Sujet 10, Geneva, Switzerland
| | - Christoph Thomssen
- Department of Gynaecology, Martin-Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany
| | - Miguel Martin
- Instituto de Investigación Sanitaria Hospital Gregorio Marañón, Universidad Complutense, c/Dr Esquerdo 46, 28007 Madrid, Spain
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31
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Hyams DM, Schuur E, Angel Aristizabal J, Bargallo Rocha JE, Cabello C, Elizalde R, García-Estévez L, Gomez HL, Katz A, Nuñez De Pierro A. Selecting postoperative adjuvant systemic therapy for early stage breast cancer: A critical assessment of commercially available gene expression assays. J Surg Oncol 2017; 115:647-662. [PMID: 28211064 PMCID: PMC5484338 DOI: 10.1002/jso.24561] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 12/15/2016] [Accepted: 12/15/2016] [Indexed: 12/13/2022]
Abstract
Risk stratification of patients with early stage breast cancer may support adjuvant chemotherapy decision-making. This review details the development and validation of six multi-gene classifiers, each of which claims to provide useful prognostic and possibly predictive information for early stage breast cancer patients. A careful assessment is presented of each test's analytical validity, clinical validity, and clinical utility, as well as the quality of evidence supporting its use.
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Affiliation(s)
- David M Hyams
- Desert Surgical Oncology, Eisenhower Medical Center, Rancho Mirage, California
| | | | | | | | | | | | | | - Henry L Gomez
- Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Artur Katz
- Hospital Sírio-Libanes, Sao Paulo, Brazil
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32
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Ricks-Santi LJ, McDonald JT. Low utility of Oncotype DX® in the clinic. Cancer Med 2017; 6:501-507. [PMID: 28145091 PMCID: PMC5345634 DOI: 10.1002/cam4.837] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 12/19/2022] Open
Abstract
Precision medicine tools are currently making their way into the clinic and being utilized to diagnose, prognose, and individualize cancer care. The multi-gene expression-based assay, Oncotype DX® (ODX), is a genomic tumor profiling tool that determines the expression of 21 tumor- associated genes; it helps determine the risk for distant recurrence and whether chemotherapy is an appropriate course of treatment in patients with early stage, estrogen receptor (ER) positive, HER2 negative, and lymph node negative (or 1-3 positive lymph nodes) invasive BCa. The aim of this study was to determine the overall utilization and uptake of the ODX genomic test in a cross-sectional analysis of the Virginia Tumor registry, compare utilization in African Americans (AAs) and Caucasian Americans (CAs), and determine the profile of patients referred for testing. Caucasian (89.7%) patients made up the majority of the ODX testers compared to AAs (10.3%) (P < 0.0001). Those who received ODX testing were less likely to have higher grade and higher stage tumors, and were less likely to be ER negative (RR = 0.21, 95% CI: 0.01-0.31), progesterone receptor (PR) negative (RR = 0.35, 95% CI: 0.27-0.45), HER2 amplified (RR = 0.27, 95% CI: 0.17-0.43), or triple negative (RR = 0.21, 95% CI: 0.14-0.33). Of the patients that were eligible (n = 3924), 10.5% (n = 412) received ODX testing. Specifically, 11.7% of the Caucasian patients and 5.1% of AAs patients received ODX testing (P < 0.001). Our analysis confirmed that the utilization of ODX was low and that AAs were much less likely to receive ODX testing.
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Affiliation(s)
- Luisel J Ricks-Santi
- Cancer Research Center, Hampton University, 100 E. Queen Street, Hampton, Virginia, 23668
| | - John Tyson McDonald
- Cancer Research Center, Hampton University, 100 E. Queen Street, Hampton, Virginia, 23668
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33
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Fortenberry YM, Brandal SM, Carpentier G, Hemani M, Pathak AP. Intracellular Expression of PAI-1 Specific Aptamers Alters Breast Cancer Cell Migration, Invasion and Angiogenesis. PLoS One 2016; 11:e0164288. [PMID: 27755560 PMCID: PMC5068744 DOI: 10.1371/journal.pone.0164288] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 09/22/2016] [Indexed: 02/07/2023] Open
Abstract
Plasminogen activator inhibitor-1 (PAI-1) is elevated in various cancers, where it has been shown to effect cell migration and invasion and angiogenesis. While, PAI-1 is a secreted protein, its intercellular levels are increased in cancer cells. Consequently, intracellular PAI-1 could contribute to cancer progression. While various small molecule inhibitors of PAI-1 are currently being investigated, none specifically target intracellular PAI-1. A class of inhibitors, termed aptamers, has been used effectively in several clinical applications. We previously generated RNA aptamers that target PAI-1 and demonstrated their ability to inhibit extracellular PAI-1. In the current study we explored the effect of these aptamers on intracellular PAI-1. We transiently transfected the PAI-1 specific aptamers into both MDA-MB-231 human breast cancer cells, and human umbilical vein endothelial cells (HUVECs) and studied their effects on cell migration, invasion and angiogenesis. Aptamer expressing MDA-MB-231 cells exhibited a decrease in cell migration and invasion. Additionally, intracellular PAI-1 and urokinase plasminogen activator (uPA) protein levels decreased, while the PAI-1/uPA complex increased. Moreover, a significant decrease in endothelial tube formation in HUVECs transfected with the aptamers was observed. In contrast, conditioned media from aptamer transfected MDA-MB-231 cells displayed a slight pro-angiogenic effect. Collectively, our study shows that expressing functional aptamers inside breast and endothelial cells is feasible and may exhibit therapeutic potential.
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Affiliation(s)
- Yolanda M Fortenberry
- Department of Pediatric Hematology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.,Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Stephanie M Brandal
- Department of Pediatric Hematology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Gilles Carpentier
- Laboratoire CRRET, Faculté des Sciences et Technologie, Université Paris-Est Créteil, 61 avenue du général De Gaulle, 94010 Créteil, France
| | - Malvi Hemani
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Arvind P Pathak
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
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34
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Leung RC, Yau TC, Chan MC, Chan SW, Chan TW, Tsang YY, Wong TT, Chao C, Yoshizawa C, Soong IS, Kwan WH, Kwok CC, Suen JS, Ngan RK, Cheung PS. The Impact of the Oncotype DX Breast Cancer Assay on Treatment Decisions for Women With Estrogen Receptor-Positive, Node-Negative Breast Carcinoma in Hong Kong. Clin Breast Cancer 2016; 16:372-378. [DOI: 10.1016/j.clbc.2016.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 03/06/2016] [Accepted: 03/09/2016] [Indexed: 10/22/2022]
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35
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Muthukaruppan A, Lasham A, Woad KJ, Black MA, Blenkiron C, Miller LD, Harris G, McCarthy N, Findlay MP, Shelling AN, Print CG. Multimodal Assessment of Estrogen Receptor mRNA Profiles to Quantify Estrogen Pathway Activity in Breast Tumors. Clin Breast Cancer 2016; 17:139-153. [PMID: 27756582 DOI: 10.1016/j.clbc.2016.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 08/25/2016] [Accepted: 09/02/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Molecular markers have transformed our understanding of the heterogeneity of breast cancer and have allowed the identification of genomic profiles of estrogen receptor (ER)-α signaling. However, our understanding of the transcriptional profiles of ER signaling remains inadequate. Therefore, we sought to identify the genomic indicators of ER pathway activity that could supplement traditional immunohistochemical (IHC) assessments of ER status to better understand ER signaling in the breast tumors of individual patients. MATERIALS AND METHODS We reduced ESR1 (gene encoding the ER-α protein) mRNA levels using small interfering RNA in ER+ MCF7 breast cancer cells and assayed for transcriptional changes using Affymetrix HG U133 Plus 2.0 arrays. We also compared 1034 ER+ and ER- breast tumors from publicly available microarray data. The principal components of ER activity generated from these analyses and from other published estrogen signatures were compared with ESR1 expression, ER-α IHC, and patient survival. RESULTS Genes differentially expressed in both analyses were associated with ER-α IHC and ESR1 mRNA expression. They were also significantly enriched for estrogen-driven molecular pathways associated with ESR1, cyclin D1 (CCND1), MYC (v-myc avian myelocytomatosis viral oncogene homolog), and NFKB (nuclear factor kappa B). Despite their differing constituent genes, the principal components generated from these new analyses and from previously published ER-associated gene lists were all associated with each other and with the survival of patients with breast cancer treated with endocrine therapies. CONCLUSION A biomarker of ER-α pathway activity, generated using ESR1-responsive mRNAs in MCF7 cells, when used alongside ER-α IHC and ESR1 mRNA expression, could provide a method for further stratification of patients and add insight into ER pathway activity in these patients.
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Affiliation(s)
- Anita Muthukaruppan
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
| | - Annette Lasham
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Kathryn J Woad
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Cherie Blenkiron
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Gavin Harris
- Canterbury Health Laboratories, Christchurch, New Zealand
| | - Nicole McCarthy
- Discipline of Oncology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Michael P Findlay
- Discipline of Oncology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Andrew N Shelling
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Cristin G Print
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand; New Zealand Bioinformatics Institute, The University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
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36
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Spears M, Yousif F, Lyttle N, Boutros PC, Munro AF, Twelves C, Pritchard KI, Levine MN, Shepherd L, Bartlett JMS. A four gene signature predicts benefit from anthracyclines: evidence from the BR9601 and MA.5 clinical trials. Oncotarget 2016; 6:31693-701. [PMID: 26372731 PMCID: PMC4741633 DOI: 10.18632/oncotarget.5562] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 08/10/2015] [Indexed: 12/21/2022] Open
Abstract
Chromosome instability (CIN) in solid tumours results in multiple numerical and structural chromosomal aberrations and is associated with poor prognosis in multiple tumour types. Recent evidence demonstrated CEP17 duplication, a CIN marker, is a predictive marker of anthracycline benefit. An analysis of the BR9601 and MA.5 clinical trials was performed to test the role of existing CIN gene expression signatures as predictive markers of anthracycline sensitivity in breast cancer. Univariate analysis demonstrated, high CIN25 expression score was associated with improved distant relapse free survival (DRFS) (HR: 0.74, 95% CI 0.54-0.99, p = 0.046). High tumour CIN70 and CIN25 scores were associated with aggressive clinicopathological phenotype and increased sensitivity to anthracycline therapy compared to low CIN scores. However, in a prospectively planned multivariate analysis only pathological grade, nodal status and tumour size were significant predictors of outcome for CIN25/CIN70. A limited gene signature was generated, patients with low tumour CIN4 scores benefited from anthracycline treatment significantly more than those with high CIN4 scores (HR 0.37, 95% CI 0.20-0.56, p = 0.001). In multivariate analyses the treatment by marker interaction for CIN4/anthracyclines demonstrated hazard ratio of 0.35 (95% CI 0.15-0.80, p = 0.012) for DRFS. This data shows CIN4 is independent predictor of anthracycline benefit for DRFS in breast cancer.
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Affiliation(s)
- Melanie Spears
- Transformative Pathology, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada
| | - Fouad Yousif
- Informatics and Bio-Computing, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada
| | - Nicola Lyttle
- Transformative Pathology, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada
| | - Paul C Boutros
- Informatics and Bio-Computing, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Alison F Munro
- Edinburgh Cancer Research UK Centre, MRC IGMM, University of Edinburgh, Crewe Road South, Edinburgh, UK
| | - Chris Twelves
- Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, St James' University Hospital, Leeds, UK
| | - Kathleen I Pritchard
- Sunnybrook Odette Cancer Centre, Toronto, ON, Canada.,University of Toronto, Toronto, ON, Canada
| | - Mark N Levine
- McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada
| | - Lois Shepherd
- NCIC Clinical Trials Group (NCIC CTG] and Queen's University, Kingston, ON, Canada
| | - John M S Bartlett
- Transformative Pathology, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada.,Edinburgh Cancer Research UK Centre, MRC IGMM, University of Edinburgh, Crewe Road South, Edinburgh, UK
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37
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Stefansson IM, Raeder M, Wik E, Mannelqvist M, Kusonmano K, Knutsvik G, Haldorsen I, Trovik J, Øyan AM, Kalland KH, Staff AC, Salvesen HB, Akslen LA. Increased angiogenesis is associated with a 32-gene expression signature and 6p21 amplification in aggressive endometrial cancer. Oncotarget 2016; 6:10634-45. [PMID: 25860936 PMCID: PMC4496381 DOI: 10.18632/oncotarget.3521] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 02/17/2015] [Indexed: 12/14/2022] Open
Abstract
Background Angiogenesis is a hallmark of cancer. The aim of this study was to explore whether microvessel proliferation is associated with gene expression profiles or copy number alterations in endometrial cancer. Methods A prospective series of endometrial carcinomas was studied for angiogenesis markers, gene expression profiles, and gene copy number data. For validation, an independent series of endometrial carcinomas as well as an external cohort of endometrial cancer patients were examined by gene expression microarrays. Results Increased microvessel proliferation (MVP) was associated with aggressive tumor features and reduced survival, and a 32-gene expression signature was found to separate tumors with high versus low MVP. An increased 32-gene signature score was confirmed to associate with high-grade tumor features and reduced survival by independent cohorts. Copy number studies revealed that amplification of the 6p21 region was significantly associated with MVP, a high 32-gene score, as well as reduced survival. Conclusion Increased MVP was significantly associated with aggressive endometrial cancer and reduced survival. Integrated analyses demonstrated significant associations between increased vascular proliferation, amplification of the 6p21 region, VEGF-A mRNA expression, and the 32-gene angiogenesis signature. Our findings indicate amplification of 6p21 as a possible driver of tumor vascular proliferation in endometrial cancer.
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Affiliation(s)
- Ingunn M Stefansson
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Maria Raeder
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway
| | - Elisabeth Wik
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Monica Mannelqvist
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Kanthida Kusonmano
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway
| | - Gøril Knutsvik
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Ingfrid Haldorsen
- Department of Radiology, Haukeland University Hospital, Bergen, Norway.,Section for Radiology, University of Bergen, Bergen, Norway
| | - Jone Trovik
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway
| | - Anne M Øyan
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Karl-H Kalland
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Anne Cathrine Staff
- Department of Obstetrics and Gynaecology, Women and Children's Division, Oslo University Hospital, University of Oslo, Norway
| | - Helga B Salvesen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway
| | - Lars A Akslen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, Bergen, Norway
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38
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Dupont DM, Bjerregaard N, Verpaalen B, Andreasen PA, Jensen JK. Building a Molecular Trap for a Serine Protease from Aptamer and Peptide Modules. Bioconjug Chem 2016; 27:918-26. [PMID: 26926041 DOI: 10.1021/acs.bioconjchem.6b00007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In drug development, molecular intervention strategies are usually based on interference with a single protein function, such as enzyme activity or receptor binding. However, in many cases, protein drug targets are multifunctional, with several molecular functions contributing to their pathophysiological actions. Aptamers and peptides are interesting synthetic building blocks for the design of multivalent molecules capable of modulating multiple functions of a target protein. Here, we report a molecular trap with the ability to interfere with the activation, catalytic activity, receptor binding, etc. of the serine protease urokinase-type plasminogen activator (uPA) by a rational combination of two RNA aptamers and a peptide with different inhibitory properties. The assembly of these artificial inhibitors into one molecule enhanced the inhibitory activity between 10- and 10,000-fold toward several functions of uPA. The study highlights the potential of multivalent designs and illustrates how they can easily be constructed from aptamers and peptides using nucleic acid engineering, chemical synthesis, and bioconjugation chemistry. By aptamer to aptamer and aptamer to peptide conjugation, we created, to the best of our knowledge, the first trivalent molecule which combines three artificial inhibitors binding to three different sites in a protein target. We hypothesize that by simultaneously preventing all of the functional interactions and activities of the target protein, this approach may represent an alternative to siRNA technology for a functional knockout.
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Affiliation(s)
- Daniel M Dupont
- Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Nils Bjerregaard
- Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Ben Verpaalen
- Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Jan K Jensen
- Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
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39
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Barney LE, Jansen LE, Polio SR, Galarza S, Lynch ME, Peyton SR. The Predictive Link between Matrix and Metastasis. Curr Opin Chem Eng 2016; 11:85-93. [PMID: 26942108 DOI: 10.1016/j.coche.2016.01.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cancer spread (metastasis) is responsible for 90% of cancer-related fatalities. Informing patient treatment to prevent metastasis, or kill all cancer cells in a patient's body before it becomes metastatic is extremely powerful. However, aggressive treatment for all non-metastatic patients is detrimental, both for quality of life concerns, and the risk of kidney or liver-related toxicity. Knowing when and where a patient has metastatic risk could revolutionize patient treatment and care. In this review, we attempt to summarize the key work of engineers and quantitative biologists in developing strategies and model systems to predict metastasis, with a particular focus on cell interactions with the extracellular matrix (ECM), as a tool to predict metastatic risk and tropism.
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Affiliation(s)
- L E Barney
- Department of Chemical Engineering, University of Massachusetts, Amherst Amherst, MA 01003
| | - L E Jansen
- Department of Chemical Engineering, University of Massachusetts, Amherst Amherst, MA 01003
| | - S R Polio
- Department of Chemical Engineering, University of Massachusetts, Amherst Amherst, MA 01003
| | - S Galarza
- Department of Chemical Engineering, University of Massachusetts, Amherst Amherst, MA 01003
| | - M E Lynch
- Department of Chemical Engineering, University of Massachusetts, Amherst Amherst, MA 01003; Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst Amherst, MA 01003
| | - S R Peyton
- Department of Chemical Engineering, University of Massachusetts, Amherst Amherst, MA 01003
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Manejo de las muestras para test inmunohistoquímicos, moleculares y genéticos en el cáncer de mama. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.senol.2015.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Sager M, Yeat NC, Pajaro-Van der Stadt S, Lin C, Ren Q, Lin J. Transcriptomics in cancer diagnostics: developments in technology, clinical research and commercialization. Expert Rev Mol Diagn 2015; 15:1589-603. [PMID: 26565429 DOI: 10.1586/14737159.2015.1105133] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Transcriptomic technologies are evolving to diagnose cancer earlier and more accurately to provide greater predictive and prognostic utility to oncologists and patients. Digital techniques such as RNA sequencing are replacing still-imaging techniques to provide more detailed analysis of the transcriptome and aberrant expression that causes oncogenesis, while companion diagnostics are developing to determine the likely effectiveness of targeted treatments. This article examines recent advancements in molecular profiling research and technology as applied to cancer diagnosis, clinical applications and predictions for the future of personalized medicine in oncology.
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Affiliation(s)
- Monica Sager
- a College of Arts and Sciences , Washington University in St. Louis , St. Louis , MO , USA.,b Rare Genomics Institute , Bethesda , MD , USA
| | - Nai Chien Yeat
- b Rare Genomics Institute , Bethesda , MD , USA.,c School of Medicine , Washington University in St. Louis , St. Louis , MO , USA
| | - Stefan Pajaro-Van der Stadt
- a College of Arts and Sciences , Washington University in St. Louis , St. Louis , MO , USA.,b Rare Genomics Institute , Bethesda , MD , USA
| | - Charlotte Lin
- b Rare Genomics Institute , Bethesda , MD , USA.,c School of Medicine , Washington University in St. Louis , St. Louis , MO , USA
| | - Qiuyin Ren
- b Rare Genomics Institute , Bethesda , MD , USA.,d Whiting School of Engineering , Johns Hopkins University , Baltimore , MD , USA
| | - Jimmy Lin
- b Rare Genomics Institute , Bethesda , MD , USA
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Senkus E, Kyriakides S, Ohno S, Penault-Llorca F, Poortmans P, Rutgers E, Zackrisson S, Cardoso F. Primary breast cancer: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. Ann Oncol 2015; 26 Suppl 5:v8-30. [PMID: 26314782 DOI: 10.1093/annonc/mdv298] [Citation(s) in RCA: 1096] [Impact Index Per Article: 109.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- E Senkus
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, Gdańsk, Poland
| | | | - S Ohno
- Breast Oncology Center, Cancer Institute Hospital, Tokyo, Japan
| | - F Penault-Llorca
- Department of Pathology, Centre Jean Perrin, Clermont-Ferrand EA 4677 Université d'Auvergne, Clermont-Ferrand, France
| | - P Poortmans
- Radboud University Medical Center, Nijmegen, The Netherlands
| | - E Rutgers
- Department of Surgery, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - S Zackrisson
- Department of Diagnostic Radiology, Lund University, Malmö, Sweden
| | - F Cardoso
- Breast Unit, Champalimaud Clinical Center, Lisbon, Portugal
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Kimbung S, Loman N, Hedenfalk I. Clinical and molecular complexity of breast cancer metastases. Semin Cancer Biol 2015; 35:85-95. [PMID: 26319607 DOI: 10.1016/j.semcancer.2015.08.009] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/17/2015] [Accepted: 08/21/2015] [Indexed: 12/24/2022]
Abstract
Clinical oncology is advancing toward a more personalized treatment orientation, making the need to understand the biology of metastasis increasingly acute. Dissecting the complex molecular, genetic and clinical phenotypes underlying the processes involved in the development of metastatic disease, which remains the principal cause of cancer-related deaths, could lead to the identification of more effective prognostication and targeted approaches to prevent and treat metastases. The past decade has witnessed significant progress in the field of cancer metastasis research. Clinical and technological milestones have been reached which have tremendously enriched our understanding of the complex pathways undertaken by primary tumors to progress into lethal metastases and how some of these processes might be amenable to therapy. The aim of this review article is to highlight the recent advances toward unraveling the clinical and molecular complexity of breast cancer metastases. We focus on genes mediating breast cancer metastases and organ-specific tropism, and discuss gene signatures for prediction of metastatic disease. The challenges of translating this information into clinically applicable tools for improving the prognostication of the metastatic potential of a primary breast tumor, as well as for therapeutic interventions against latent and active metastatic disease are addressed.
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Affiliation(s)
- Siker Kimbung
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden; CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Niklas Loman
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden; Department of Oncology, Skåne University Hospital, Lund/Malmö, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden; CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden.
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Halfter K, Ditsch N, Kolberg HC, Fischer H, Hauzenberger T, von Koch FE, Bauerfeind I, von Minckwitz G, Funke I, Crispin A, Mayer B. Prospective cohort study using the breast cancer spheroid model as a predictor for response to neoadjuvant therapy--the SpheroNEO study. BMC Cancer 2015; 15:519. [PMID: 26169261 PMCID: PMC4501185 DOI: 10.1186/s12885-015-1491-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 06/16/2015] [Indexed: 12/20/2022] Open
Abstract
Background Aim of this prospective study was to predict response to neoadjuvant therapy in breast cancer patients using an in vitro breast cancer spheroid model. Methods Three-dimensional spheroids were directly generated from fresh breast tumor biopsies of 78 patients eligible for neoadjuvant therapy. Cell survival was measured after in vitro exposure to the equivalent therapeutic agents in the breast cancer spheroid model. Treatment results in vitro were correlated with pathological complete response (pCR, i.e. ypT0 ypN0) determined at surgery. Results A mean cell survival of 21.8 % was found in the breast cancer spheroid model for 22 patients with pCR versus 63.8 % in 56 patients without pCR (P = .001). The area under the receiver operator characteristic curve to predict pCR was 0.86 (95 % CI: 0.77 to 0.96) for cell survival in vitro compared to 0.80 (95 % CI: 0.70 to 0.90) for a combined model of conventional factors (hormone- and HER2 receptor, and age). A cutoff at 35 % cell survival for the spheroid model was proposed. Out of the 32 patients with values below this threshold, 21 patients (65.6 %) and one patient (2.2 %) with a cell survival greater than 35 % achieved pCR respectively; (sensitivity 95.5 % (95 % CI: 0.86 to 1.00); specificity 80.4 % (95 % CI: 0.70 to 0.91)). Extent of residual disease positively correlated with increased cell survival (P = .021). Conclusion The breast cancer spheroid model proved to be a highly sensitive and specific predictor for pCR after neoadjuvant chemotherapy in breast cancer patients. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1491-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kathrin Halfter
- Department of General, Visceral, Transplantation, Vascular and Thoraic Surgery, Hospital of the University of Munich, Munich, Germany.
| | - Nina Ditsch
- Department of Obstetrics and Gynecology, Ludwig-Maximilians-University of Munich, Munich, Germany.
| | | | - Holger Fischer
- Evangelische Kliniken Gelsenkirchen, Gelsenkirchen, Germany.
| | | | - Franz Edler von Koch
- Department of Obstetrics and Gynecology, Klinikum Dritter Orden, Munich, Germany.
| | | | - Gunter von Minckwitz
- GBG Forschungs GmbH, Neu-Isenburg and University Women's Hospital Frankfurt, Frankfurt, Germany.
| | | | - Alexander Crispin
- IBE LMU, Department of Obstetrics and Gynecology, Technical University of Munich, Klinikum Starnberg, Leopoldina Krankenhaus der Stadt Schweinfurt, Markus Krankenhaus Frankfurt, Klinikum Nürnberg, Städtisches Klinkum Karlsruhe, Klinikum Harlaching, Munich, Germany.
| | - Barbara Mayer
- Department of General, Visceral, Transplantation, Vascular and Thoraic Surgery, Hospital of the University of Munich, Munich, Germany. .,SpheroTec GmbH, Martinsried, Germany.
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Christgen M, von Ahsen S, Christgen H, Länger F, Kreipe H. The region-of-interest size impacts on Ki67 quantification by computer-assisted image analysis in breast cancer. Hum Pathol 2015. [PMID: 26206765 DOI: 10.1016/j.humpath.2015.05.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Therapeutic decision-making in breast cancer depends on histopathologic biomarkers and is influenced by the Ki67 proliferation index. Computer-assisted image analysis (CAIA) promises to improve Ki67 quantification. Several commercial applications have been developed for semiautomated CAIA-based Ki67 quantification, many of which rely on measurements in user-defined regions of interest (ROIs). Because of intratumoral proliferative heterogeneity, definition of the ROI is an important step in the analytical procedure. This study explores the ROI size impacts on Ki67 quantification. Whole-slide sections of 100 breast cancers were immunostained with the anti-Ki67 antibody 30-9 and were analyzed on the iScan Coreo digital pathology platform using a Food and Drug Administration-cleared Ki67 quantification software version v5.3 (Virtuoso; Ventana, Tucson, TX). For each case, the Ki67 labeling index (LI) was determined in multiple ROIs of gradually increasing size centered around a high-proliferation area. The spatial Ki67 decline was modeled with nonlinear regression. Depending on the ROI size, the median Ki67 LI varied between 55% and 15%. The proportion of tumors classified as Ki67 low according to the St Gallen 2013/2015 cutoff increased from 2% to 56%, as the ROI size increased from 50 to 10,000 cells captured. The interrater reliability of conventional Ki67 assessment versus CAIA-based Ki67 quantification was also dependent on the ROI size and varied between slight and almost perfect agreement (Cohen κ = 0.06-0.85). In conclusion, the ROI size is a critically important parameter for semiautomated Ki67 quantification by CAIA. Ki67 LIs determined on platforms like iScan Coreo/Virtuoso require an ROI size adjustment, for which we offer a downloadable data transformation tool.
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Affiliation(s)
- Matthias Christgen
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany.
| | - Sabrina von Ahsen
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany
| | | | - Florian Länger
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany
| | - Hans Kreipe
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany
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Dupont DM, Thuesen CK, Bøtkjær KA, Behrens MA, Dam K, Sørensen HP, Pedersen JS, Ploug M, Jensen JK, Andreasen PA. Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites. PLoS One 2015; 10:e0119207. [PMID: 25793507 PMCID: PMC4368798 DOI: 10.1371/journal.pone.0119207] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/11/2015] [Indexed: 11/28/2022] Open
Abstract
Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless, there are only a few studies on the molecular basis underlying aptamer-protease interactions and the associated mechanisms of inhibition. In the present study, we use site-directed mutagenesis to delineate the binding sites of two 2´-fluoropyrimidine RNA aptamers (upanap-12 and upanap-126) with therapeutic potential, both binding to the serine protease urokinase-type plasminogen activator (uPA). We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A) controlling uPA activities. One of the aptamers (upanap-126) binds to the area around the C-terminal α-helix in pro-uPA, while the other aptamer (upanap-12) binds to both the β-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro-uPA complex. The results suggest and highlight that the size and shape of an aptamer as well as the domain organization of a multi-domain protein such as uPA, may provide the basis for extensive sterical interference with protein ligand interactions considered distant from the aptamer binding site.
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Affiliation(s)
- Daniel M. Dupont
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Danish-Chinese Centre for Proteases and Cancer, Aarhus University, Aarhus, Denmark
- * E-mail:
| | - Cathrine K. Thuesen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Danish-Chinese Centre for Proteases and Cancer, Aarhus University, Aarhus, Denmark
| | - Kenneth A. Bøtkjær
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Danish-Chinese Centre for Proteases and Cancer, Aarhus University, Aarhus, Denmark
| | - Manja A. Behrens
- iNANO Interdisciplinary Nanoscience Center and Department of Chemistry, Aarhus University, Aarhus, Denmark
- Department of Chemistry, Lund University, Lund, Sweden
| | - Karen Dam
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Hans P. Sørensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Danish-Chinese Centre for Proteases and Cancer, Aarhus University, Aarhus, Denmark
| | - Jan S. Pedersen
- iNANO Interdisciplinary Nanoscience Center and Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Michael Ploug
- Danish-Chinese Centre for Proteases and Cancer, Aarhus University, Aarhus, Denmark
- Finsen Laboratory, Rigshospitalet and Biotech Research & Innovation Centre, Copenhagen, Denmark
| | - Jan K. Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Danish-Chinese Centre for Proteases and Cancer, Aarhus University, Aarhus, Denmark
| | - Peter A. Andreasen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Danish-Chinese Centre for Proteases and Cancer, Aarhus University, Aarhus, Denmark
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Xu C, Wei Q, Guo J, Zhou JC, Mei J, Jiang ZN, Shen JG, Wang LB. FOXA1 Expression Significantly Predict Response to Chemotherapy in Estrogen Receptor-Positive Breast Cancer Patients. Ann Surg Oncol 2015; 22:2034-9. [PMID: 25707489 DOI: 10.1245/s10434-014-4313-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Indexed: 01/09/2023]
Abstract
PURPOSE Most estrogen receptor (ER)-positive breast cancer responds poorly to chemotherapy and no single cost-effective biomarker capable of selecting chemosensitive ones has been found yet. We investigated FOXA1 for its role in predicting chemosensitivity of this subgroup in neoadjuvant chemotherapy settings. METHODS We reviewed pathologic slides of 123 patients who were diagnosed with ER-positive breast cancer on core needle biopsy and underwent neoadjuvant chemotherapy at our institution between 2002 and 2012. FOXA1 expression and pathologic response were evaluated. We then statistically analyzed FOXA1 expression and its relationship with chemosensitivity. RESULTS FOXA1 expression before NAC was correlated with poor chemoresponse in ER-positive as well as luminal A and luminal B breast cancer patients (p = 0.002, 0.001, and 0.049 respectively). Significant association between change of FOXA1 staining position after NAC and chemosensitivity also was observed (p = 0.024). Multivariate analysis identified FOXA1 expression before NAC as an independent predictor of chemosensitivity in ER-positive and luminal A breast cancer patients [p = 0.002; relative risk (RR) 0.163; 95 % confidence interval (CI) 0.053-0.500, and p = 0.002; RR 0.055; 95 % CI 0.008-0.353, respectively]. Additionally, change of FOXA1 staining position after NAC was shown to be an independent predictor of chemoresponse in luminal B subtype breast cancer patients (p = 0.012; RR 0.153; 95 % CI 0.035-0.665). CONCLUSIONS FOXA1 expression can independently predict chemosensitivity of ER-positive breast cancer patients.
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Affiliation(s)
- Chenpu Xu
- Department of Surgical Oncology, Affiliated Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
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Khan SS, Karn T, Symmans WF, Rody A, Müller V, Holtrich U, Becker S, Pusztai L, Hatzis C. Genomic predictor of residual risk of recurrence after adjuvant chemotherapy and endocrine therapy in high risk estrogen receptor-positive breast cancers. Breast Cancer Res Treat 2015; 149:789-97. [PMID: 25651779 DOI: 10.1007/s10549-015-3277-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/16/2015] [Indexed: 01/24/2023]
Abstract
A subset of early stage estrogen receptor (ER)-positive breast cancers considered "high risk" for recurrence with endocrine therapy alone by current genomic prognostic predictors, such as Oncotype DX, is no longer high risk after receiving adjuvant chemotherapy. We hypothesized that a recently described gene expression-based outcome predictor adjuvant chemotherapy and endocrine therapy sensitivity (ACES) could re-stratify these patients into high and low risk groups for relapse when treated with both chemo- and endocrine therapies. ACES involves four separate modules (endocrine sensitivity, chemotherapy sensitivity, chemotherapy resistance, and survival prediction) that yield a prediction for good or poor outcome with current standard of care multimodality therapy. ACES was applied to Affymetrix gene expression data from 2 retrospectively collected ER-positive and HER2-negative patient cohorts that were uniformly treated with adjuvant endocrine and chemotherapy (n = 250). Each sample was first risk stratified by a genomic surrogate of Oncotype DX, and the high risk patients (n = 76) were re-stratified by ACES. Recurrence-free survival (RFS) was evaluated with ACES risk categories. The Oncotype DX high risk but ACES good prognosis patients (n = 24, 32%) had an RFS of 95% compared to 76% in the poor prognosis group (n = 52; log-rank p = 0.033) at 5 years. ACES risk category remained an independent predictor in multivariate analysis after adjusting for age, T-stage, and lymph node involvement at diagnosis (hazard ratio 0.15; p = 0.072). Tertiary risk prediction that takes into account chemotherapy and endocrine sensitivity, and baseline prognosis may help identify high risk ER-positive patients who have excellent survival after chemotherapy.
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Affiliation(s)
- Glen C Jickling
- From the Department of Neurology and the MIND Institute, University of California at Davis, Sacramento.
| | - Frank R Sharp
- From the Department of Neurology and the MIND Institute, University of California at Davis, Sacramento
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