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Guo Q, Jin Y, Lin M, Zeng C, Zhang J. NF-κB signaling in therapy resistance of breast cancer: Mechanisms, approaches, and challenges. Life Sci 2024; 348:122684. [PMID: 38710275 DOI: 10.1016/j.lfs.2024.122684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/19/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024]
Abstract
Breast cancer is the most common type of cancer and is the second leading cause of cancer-related mortality in women. Chemotherapy, targeted therapy, endocrine therapy, and radiotherapy are all effective in destroying tumor cells, but they also activate the defense and protection systems of cancer cells, leading to treatment resistance. Breast cancer is characterized by a highly inflammatory tumor microenvironment. The NF-κB pathway is essential for connecting inflammation and cancer, as well as for tumor growth and therapy resistance. An increase in NF-κB signaling boosts the growth potential of breast cancer cells and facilitates the spread of tumors to bone, lymph nodes, lungs, and liver. This review focuses on the mechanisms by which chemotherapy, targeted therapy, endocrine therapy, and radiotherapy induce breast cancer resistance through NF-κB signaling. Additionally, we investigate therapeutic regimens, including single agents or in combination with target inhibitors, plant extracts, nanomedicines, and miRNAs, that have been reported in clinical trials, in vivo, and in vitro to reverse resistance. In particular, NF-κB inhibitors combined with tamoxifen were shown to significantly increase the sensitivity of breast cancer cells to tamoxifen. Combination therapy of miRNA-34a with doxorubicin was also found to synergistically inhibit the progression of doxorubicin-resistant breast cancer by inhibiting Notch/NF-κB signaling.
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Affiliation(s)
- Qing Guo
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, No. 270, Dong'an Road, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yizi Jin
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, No. 270, Dong'an Road, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Mingxi Lin
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, No. 270, Dong'an Road, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cheng Zeng
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, No. 270, Dong'an Road, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jian Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, No. 270, Dong'an Road, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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2
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Shoukat I, Mueller CR. Searching for DNA methylation in patients triple-negative breast cancer: a liquid biopsy approach. Expert Rev Mol Diagn 2023; 23:41-51. [PMID: 36715539 DOI: 10.1080/14737159.2023.2173579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Liquid biopsies are proving to have diagnostic and prognostic value in many different cancers, and in breast cancer they have the potential to improve outcomes by providing valuable information throughout a patient's cancer journey. However, patients with triple negative breast cancer (TNBC) have received little benefit from such liquid biopsies due to underlying limitations in the discovery and utility of robust biomarkers. Here, we examine the development of DNA methylation-based liquid biopsy assays for breast cancer and how they pertain to TNBC. AREAS COVERED We conducted a systematic review of liquid biopsy assays for breast cancer and analyzed their relevance in TNBC. We show that the utility of DNA mutation-based assays is poor for TNBC due to the low mutational frequencies across the genome in this subtype. We offer a detailed review of mDETECT - a liquid biopsy specifically designed for assessing tumor burden in TNBC patients. EXPERT OPINION DNA methylation are foundational and robust events that occur in cancer evolution and may differentiate almost all forms of cancer, including TNBC. Longitudinal patient monitoring using DNA methylation-based liquid biopsies offers great potential for improving the detection and management of TNBC.
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Affiliation(s)
- Irsa Shoukat
- Queen's Cancer Research Institute, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Christopher R Mueller
- Queen's Cancer Research Institute, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
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3
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Bousset L, Gil J. Targeting senescence as an anticancer therapy. Mol Oncol 2022; 16:3855-3880. [PMID: 36065138 PMCID: PMC9627790 DOI: 10.1002/1878-0261.13312] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/12/2022] [Accepted: 08/21/2022] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence is a stress response elicited by different molecular insults. Senescence results in cell cycle exit and is characterised by multiple phenotypic changes such as the production of a bioactive secretome. Senescent cells accumulate during ageing and are present in cancerous and fibrotic lesions. Drugs that selectively kill senescent cells (senolytics) have shown great promise for the treatment of age-related diseases. Senescence plays paradoxical roles in cancer. Induction of senescence limits cancer progression and contributes to therapy success, but lingering senescent cells fuel progression, recurrence, and metastasis. In this review, we describe the intricate relation between senescence and cancer. Moreover, we enumerate how current anticancer therapies induce senescence in tumour cells and how senolytic agents could be deployed to complement anticancer therapies. "One-two punch" therapies aim to first induce senescence in the tumour followed by senolytic treatment to target newly exposed vulnerabilities in senescent tumour cells. "One-two punch" represents an emerging and promising new strategy in cancer treatment. Future challenges of "one-two punch" approaches include how to best monitor senescence in cancer patients to effectively survey their efficacy.
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Affiliation(s)
- Laura Bousset
- MRC London Institute of Medical Sciences (LMS)UK
- Faculty of Medicine, Institute of Clinical Sciences (ICS)Imperial College LondonUK
| | - Jesús Gil
- MRC London Institute of Medical Sciences (LMS)UK
- Faculty of Medicine, Institute of Clinical Sciences (ICS)Imperial College LondonUK
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4
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Kim Y, Inoue Y, Hasegawa H, Yoshida Y, Sakata T. In Situ Electrical Monitoring of Methylated DNA Based on Its Conformational Change to G-Quadruplex Using a Solution-Gated Field-Effect Transistor. Anal Chem 2021; 93:16709-16717. [PMID: 34859677 DOI: 10.1021/acs.analchem.1c04466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methylated DNA is not only a diagnostic but also a prognostic biomarker for early-stage cancer. However, sodium bisulfite sequencing as a "gold standard" method for detection of methylation markers has some drawbacks such as its time-consuming and labor-intensive procedures. Therefore, simple and reliable methods are required to analyze DNA sequences with or without methylated residues. Herein, we propose a simple and direct method for detecting DNA methylation through its conformation transition to G-quadruplex using a solution-gated field-effect transistor (SG-FET) without using labeled materials. The BCL-2 gene, which is involved in the development of various human tumors, contains G-rich segments and undergoes a conformational change to G-quadruplex depending on the K+ concentration. Stacked G-quadruplex strands move close to the SG-FET sensor surface, resulting in large electrical signals based on intrinsic molecular charges. In addition, a dense hydrophilic polymer brush is grafted using surface-initiated atom transfer radical polymerization onto the SG-FET sensor surface to reduce electrical noise based on nonspecific adsorption of interfering species. In particular, control of the polymer brush thickness induces electrical signals based on DNA molecular charges in the diffusion layer, according to the Debye length limit. A platform based on the SG-FET sensor with a well-defined polymer brush is suitable for in situ monitoring of methylated DNA and realizes a point-of-care device with a high signal-to-noise ratio and without the requirement for additional processes such as bisulfite conversion and polymerase chain reaction.
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Affiliation(s)
- Yeji Kim
- Advanced Technology Research Dept., LG Japan Lab Inc., Glass Cube Shinagawa, 4-13-14 Higashi Shinagawa, Shinagawa-ku, Tokyo 140-0002, Japan
| | - Yuuki Inoue
- Advanced Technology Research Dept., LG Japan Lab Inc., Glass Cube Shinagawa, 4-13-14 Higashi Shinagawa, Shinagawa-ku, Tokyo 140-0002, Japan
| | - Hijiri Hasegawa
- Advanced Technology Research Dept., LG Japan Lab Inc., Glass Cube Shinagawa, 4-13-14 Higashi Shinagawa, Shinagawa-ku, Tokyo 140-0002, Japan
| | | | - Toshiya Sakata
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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5
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Guo L, Lee YT, Zhou Y, Huang Y. Targeting epigenetic regulatory machinery to overcome cancer therapy resistance. Semin Cancer Biol 2021; 83:487-502. [PMID: 33421619 PMCID: PMC8257754 DOI: 10.1016/j.semcancer.2020.12.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023]
Abstract
Drug resistance, either intrinsic or acquired, represents a major hurdle to achieving optimal therapeutic outcomes during cancer treatment. In addition to acquisition of resistance-conferring genetic mutations, accumulating evidence suggests an intimate involvement of the epigenetic machinery in this process as well. Recent studies have revealed that epigenetic reprogramming, such as altered expression or relocation of DNA/histone modulators accompanied with chromatin structure remodeling, can lead to transcriptional plasticity in tumor cells, thereby driving their transformation towards a persistent state. These "persisters" represent a pool of slow-growing cells that can either re-expand when treatment is discontinued or acquire permanent resistance. Targeting epigenetic reprogramming or plasticity represents a new strategy to prevent the emergence of drug-refractory populations and to enable more consistent clinical responses. With the growing numbers of drugs or drug candidates developed to target epigenetic regulators, more and more epigenetic therapies are under preclinical evaluation, early clinical trials or approved by FDA as single agent or in combination with existing antitumor drugs. In this review, we highlight latest discoveries in the mechanistic understanding of epigenetically-induced drug resistance. In parallel, we discuss the potential of combining epigenetic drugs with existing anticancer regimens as a promising strategy for overcoming cancer drug resistance.
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Affiliation(s)
- Lei Guo
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA; Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Yi-Tsang Lee
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA; Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, 77030, USA.
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA; Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, 77030, USA.
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6
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Zeng H, Li T, He X, Cai S, Luo H, Chen P, Chen Y. Oxidative stress mediates the apoptosis and epigenetic modification of the Bcl-2 promoter via DNMT1 in a cigarette smoke-induced emphysema model. Respir Res 2020; 21:229. [PMID: 32883320 PMCID: PMC7469342 DOI: 10.1186/s12931-020-01495-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
Background Emphysema is a crucial pathological characteristic of chronic obstructive pulmonary disease (COPD). Oxidative stress, apoptosis and epigenetic mechanisms contribute to the pathogenesis of emphysema. However, an attempt to accurately identify whether these mechanisms interact with each other and how they are triggered has never been conducted. Method The total reactive oxygen species (ROS) level, pulmonary apoptosis and B-cell lymphoma/leukemia-2 (Bcl-2) expression, an apoptosis regulator, were detected in samples from COPD patients. Bisulfite sequencing PCR (BSP) was conducted to observe the alterations in the methylation of the Bcl-2 promoter in specimens. The dysregulation of DNA methyltransferase enzyme 1 (DNMT1), a vital DNA methyltransferase enzyme, in the lungs of patients was confirmed through western blotting. To find out interactions between oxidative stress and DNA methylation in emphysema, mouse models were built with antioxidant treatment and DNMT1 silencing, and were examined with the pulmonary apoptosis, Bcl-2 and DNMT1 levels, and epigenetic alterations of Bcl-2. Results Higher ROS levels and pulmonary apoptosis were observed in COPD patients than in healthy controls. Downregulated Bcl-2 expression with increased promoter methylation and DNMT1 protein expression was found in COPD patients. Antioxidant treatment reduced the level of ROS, DNMT1 protein and emphysematous progression in the smoking models. Following DNMT1 blockade, smoking models showed improved lung function, pulmonary apoptosis, emphysematous progression, and increased Bcl-2 protein level with less promoter methylation than emphysema mice. Conclusion Cigarette-induced oxidative stress mediates pulmonary apoptosis and hypermethylation of the Bcl-2 promoter in emphysema models through DNMT1.
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Affiliation(s)
- Huihui Zeng
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, No. 139 Renmin Road, Changsha, 410011, Hunan, China.,Research Unit of Respiratory Diseases, Central South University, No. 139 Renmin Road, Changsha, 410011, Hunan, China.,Hunan Centre for Evidence-based Medicine, No. 139 Renmin Road, Changsha, 410011, Hunan, China
| | - Tiao Li
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, No. 139 Renmin Road, Changsha, 410011, Hunan, China.,Research Unit of Respiratory Diseases, Central South University, No. 139 Renmin Road, Changsha, 410011, Hunan, China.,Hunan Centre for Evidence-based Medicine, No. 139 Renmin Road, Changsha, 410011, Hunan, China
| | - Xue He
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, No. 139 Renmin Road, Changsha, 410011, Hunan, China.,Research Unit of Respiratory Diseases, Central South University, No. 139 Renmin Road, Changsha, 410011, Hunan, China.,Hunan Centre for Evidence-based Medicine, No. 139 Renmin Road, Changsha, 410011, Hunan, China
| | - Shan Cai
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, No. 139 Renmin Road, Changsha, 410011, Hunan, China.,Research Unit of Respiratory Diseases, Central South University, No. 139 Renmin Road, Changsha, 410011, Hunan, China.,Hunan Centre for Evidence-based Medicine, No. 139 Renmin Road, Changsha, 410011, Hunan, China
| | - Hong Luo
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, No. 139 Renmin Road, Changsha, 410011, Hunan, China.,Research Unit of Respiratory Diseases, Central South University, No. 139 Renmin Road, Changsha, 410011, Hunan, China.,Hunan Centre for Evidence-based Medicine, No. 139 Renmin Road, Changsha, 410011, Hunan, China
| | - Ping Chen
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, No. 139 Renmin Road, Changsha, 410011, Hunan, China.,Research Unit of Respiratory Diseases, Central South University, No. 139 Renmin Road, Changsha, 410011, Hunan, China.,Hunan Centre for Evidence-based Medicine, No. 139 Renmin Road, Changsha, 410011, Hunan, China
| | - Yan Chen
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, No. 139 Renmin Road, Changsha, 410011, Hunan, China. .,Research Unit of Respiratory Diseases, Central South University, No. 139 Renmin Road, Changsha, 410011, Hunan, China. .,Hunan Centre for Evidence-based Medicine, No. 139 Renmin Road, Changsha, 410011, Hunan, China.
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7
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Wu MS, Chien CC, Jargalsaikhan G, Ilsan NA, Chen YC. Activation of PERK Contributes to Apoptosis and G 2/M Arrest by Microtubule Disruptors in Human Colorectal Carcinoma Cells ‡. Cancers (Basel) 2019; 12:cancers12010097. [PMID: 31906029 PMCID: PMC7017320 DOI: 10.3390/cancers12010097] [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: 11/29/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 01/01/2023] Open
Abstract
Microtubule-targeting agents (MTAs) are widely used in cancer chemotherapy, but the therapeutic responses significantly vary among different tumor types. Protein kinase RNA-like endoplasmic reticular (ER) kinase (PERK) is an ER stress kinase, and the role of PERK in the anticancer effects of MTAs is still undefined. In the present study, taxol (TAX) and nocodazole (NOC) significantly induced apoptosis with increased expression of phosphorylated PERK (pPERK; Tyr980) in four human colon cancer cell lines, including HCT-15, COLO205, HT-20, and LOVO cells. Induction of G2/M arrest by TAX and NOC with increases in phosphorylated Cdc25C and cyclin B1 protein were observed in human colon cancer cells. Application of the c-Jun N-terminal kinase (JNK) inhibitors SP600125 (SP) and JNK inhibitor V (JNKI) significantly reduced TAX- and NOC-induced apoptosis and G2/M arrest of human colon cancer cells. Interestingly, TAX- and NOC-induced pPERK (Tyr980) protein expression was inhibited by adding the JNK inhibitors, SP and JNKI, and application of the PERK inhibitor GSK2606414 (GSK) significantly reduced apoptosis and G2/M arrest by TAX and NOC, with decreased pPERK (Tyr980) and pJNK, phosphorylated Cdc25C, and Cyc B1 protein expressions in human colon cancer cells. Decreased viability by TAX and NOC was inhibited by knockdown of PERK using PERK siRNA in COLO205 and HCT-15 cells. Disruption of the mitochondrial membrane potential and an increase in B-cell lymphoma-2 (Bcl-2) protein phosphorylation (pBcl-2; Ser70) by TAX and NOC were prevented by adding the PERK inhibitor GSK and JNK inhibitor SP and JNKI. A cross-activation of JNK and PERK by TAX and NOC leading to anti-CRC actions including apoptosis and G2/M arrest was first demonstrated herein.
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Affiliation(s)
- Ming-Shun Wu
- Division of Gastroenterology, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan;
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Integrative Therapy Center for Gastroenterologic Cancers, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
| | - Chih-Chiang Chien
- Department of Nephrology, Chi-Mei Medical Center, Tainan City 710, Taiwan;
- Department of Food Nutrition, Chung Hwa University of Medical Technology, Tainan 71703, Taiwan
| | - Ganbolor Jargalsaikhan
- International MS/PhD Program in Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (G.J.); (N.A.I.)
- Liver Center, Ulaanbaatar 14230, Mongolia
| | - Noor Andryan Ilsan
- International MS/PhD Program in Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (G.J.); (N.A.I.)
- Department of Medical Laboratory Technology, STIKes Mitra Keluarga, Bekasi 17113, West Java, Indonesia
| | - Yen-Chou Chen
- International MS/PhD Program in Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (G.J.); (N.A.I.)
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Cancer Research Center and Orthopedics Research Center, Taipei Medical University Hospital, Taipei 11031, Taiwan
- Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
- Correspondence: ; Tel.: +886-2-2736-1661 (ext. 3421); Fax: +886-2-2377-8620
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8
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Huang S, Chen Y, Liang ZM, Li NN, Liu Y, Zhu Y, Liao D, Zhou XZ, Lu KP, Yao Y, Luo ML. Targeting Pin1 by All-Trans Retinoic Acid (ATRA) Overcomes Tamoxifen Resistance in Breast Cancer via Multifactorial Mechanisms. Front Cell Dev Biol 2019; 7:322. [PMID: 31867329 PMCID: PMC6908472 DOI: 10.3389/fcell.2019.00322] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/22/2019] [Indexed: 12/18/2022] Open
Abstract
Breast cancer is the most prevalent tumor in women worldwide and about 70% patients are estrogen receptor positive. In these cancer patients, resistance to the anticancer estrogen receptor antagonist tamoxifen emerges to be a major clinical obstacle. Peptidyl-prolyl isomerase Pin1 is prominently overexpressed in breast cancer and involves in tamoxifen-resistance. Here, we explore the mechanism and effect of targeting Pin1 using its chemical inhibitor all-trans retinoic acid (ATRA) in the treatment of tamoxifen-resistant breast cancer. We found that Pin1 was up-regulated in tamoxifen-resistant human breast cancer cell lines and tumor tissues from relapsed patients. Pin1 overexpression increased the phosphorylation of ERα on S118 and stabilized ERα protein. ATRA treatment, resembling the effect of Pin1 knockdown, promoted ERα degradation in tamoxifen-resistant cells. Moreover, ATRA or Pin1 knockdown decreased the activation of ERK1/2 and AKT pathways. ATRA also reduced the nuclear expression and transcriptional activity of ERα. Importantly, ATRA inhibited cell viability and proliferation of tamoxifen-resistant human breast cancer cells in vitro. Slow-releasing ATRA tablets reduced the growth of tamoxifen-resistant human breast cancer xenografts in vivo. In conclusion, ATRA-induced Pin1 ablation inhibits tamoxifen-resistant breast cancer growth by suppressing multifactorial mechanisms of tamoxifen resistance simultaneously, which demonstrates an attractive strategy for treating aggressive and endocrine-resistant tumors.
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Affiliation(s)
- Songyin Huang
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yang Chen
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhi-Mei Liang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Na-Na Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yujie Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yinghua Zhu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dingzhun Liao
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiao Zhen Zhou
- Division of Translational Therapeutics, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Kun Ping Lu
- Division of Translational Therapeutics, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Yandan Yao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Man-Li Luo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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9
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The prognostic association of SPAG5 gene expression in breast cancer patients with systematic therapy. BMC Cancer 2019; 19:1046. [PMID: 31690268 PMCID: PMC6833211 DOI: 10.1186/s12885-019-6260-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/14/2019] [Indexed: 01/13/2023] Open
Abstract
Background Despite much effort on the treatment of breast cancer over the decades, a great uncertainty regarding the appropriate molecular biomarkers and optimal therapeutic strategy still exists. This research was performed to analyze the association of SPAG5 gene expression with clinicopathological factors and survival outcomes. Methods We used a breast cancer database including 5667 patients with a mean follow-up of 69 months. Kaplan-Meier survival analyses for relapse free survival (RFS), overall survival (OS), and distant metastasis-free survival (DMFS) were performed. In addition, ROC analysis was performed to validate SPAG5 as a prognostic candidate gene. Results Mean SPAG5 expression value was significantly higher with some clinicopathological factors that resulted in tumor promotion and progression, including poor differentiated type, HER2 positive or TP53 mutated breast cancer. Based on ROC-analysis SPAG 5 is a suitable prognostic marker of poor survival. In patients who received chemotherapy alone, SPAG5 had only a moderate and not significant predictive impact on survival outcomes. However, in hormonal therapy, high SPAG5 expression could strongly predict prognosis with detrimental RFS (HR = 1.57, 95% CI 1.2–2.06, p = 0.001), OS (HR = 2, 95% CI 1.05–3.8, p = 0.03) and DMFS (HR = 2.36, 95% CI 1.57–3.54, p < 0.001), respectively. In addition, SPAG5 could only serve as a survival predictor in ER+, but not ER- breast cancer patients. Patients might also be at an increased risk of relapse despite being diagnosed with a lower grade cancer (well differentiated type). Conclusions SPAG5 could be used as an independent prognostic and predictive biomarker that might have clinical utility, especially in ER+ breast cancer patients who received hormonal therapy.
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Gómez-Miragaya J, Morán S, Calleja-Cervantes ME, Collado-Sole A, Paré L, Gómez A, Serra V, Dobrolecki LE, Lewis MT, Diaz-Lagares A, Eroles P, Prat A, Esteller M, González-Suárez E. The Altered Transcriptome and DNA Methylation Profiles of Docetaxel Resistance in Breast Cancer PDX Models. Mol Cancer Res 2019; 17:2063-2076. [PMID: 31320385 DOI: 10.1158/1541-7786.mcr-19-0040] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 06/05/2019] [Accepted: 07/10/2019] [Indexed: 11/16/2022]
Abstract
Taxanes are standard therapy in clinical practice for metastatic breast cancer; however, primary or acquired chemoresistance are a common cause of mortality. Breast cancer patient-derived xenografts (PDX) are powerful tools for the study of cancer biology and drug treatment response. Specific DNA methylation patterns have been associated to different breast cancer subtypes but its association with chemoresistance remains unstudied. Aiming to elucidate docetaxel resistance mechanisms, we performed genome-wide DNA methylation in breast cancer PDX models, including luminal and triple-negative breast cancer (TNBC) models sensitive to docetaxel, their matched models after emergence of chemoresistance and residual disease after short-term docetaxel treatment. We found that DNA methylation profiles from breast cancer PDX models maintain the subtype-specific methylation patterns of clinical samples. Two main DNA methylation clusters were found in TNBC PDX and remain stable during the emergence of docetaxel resistance; however, some genes/pathways were differentially methylated according to docetaxel response. A DNA methylation signature of resistance able to segregate TNBC based on chemotherapy response was identified. Transcriptomic profiling of selected sensitive/resistant pairs and integrative analysis with methylation data demonstrated correlation between some differentially methylated and expressed genes in docetaxel-resistant TNBC PDX models. Multiple gene expression changes were found after the emergence of docetaxel resistance in TNBC. DNA methylation and transcriptional changes identified between docetaxel-sensitive and -resistant TNBC PDX models or residual disease may have predictive value for chemotherapy response in TNBC. IMPLICATIONS: Subtype-specific DNA methylation patterns are maintained in breast cancer PDX models. While no global methylation changes were found, we uncovered differentially DNA methylated and expressed genes/pathways associated with the emergence of docetaxel resistance in TNBC.
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Affiliation(s)
- Jorge Gómez-Miragaya
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Sebastián Morán
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | | | - Alejandro Collado-Sole
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Laia Paré
- Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Antonio Gómez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Violeta Serra
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Lacey E Dobrolecki
- Departments of Molecular and Cellular Biology and Radiology, The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Michael T Lewis
- Departments of Molecular and Cellular Biology and Radiology, The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Angel Diaz-Lagares
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), CIBERONC, Santiago de Compostela, Spain
| | - Pilar Eroles
- Biomedical Research Institute (INCLIVA), Valencia, Spain. CIBERONC, Spain
| | - Aleix Prat
- Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain.,Josep Carreras Leukaemia Research Institute, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Eva González-Suárez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.
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11
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Yuan L, Huang DS. A Network-guided Association Mapping Approach from DNA Methylation to Disease. Sci Rep 2019; 9:5601. [PMID: 30944378 PMCID: PMC6447594 DOI: 10.1038/s41598-019-42010-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/12/2019] [Indexed: 01/11/2023] Open
Abstract
Aberrant DNA methylation may contribute to development of cancer. However, understanding the associations between DNA methylation and cancer remains a challenge because of the complex mechanisms involved in the associations and insufficient sample sizes. The unprecedented wealth of DNA methylation, gene expression and disease status data give us a new opportunity to design machine learning methods to investigate the underlying associated mechanisms. In this paper, we propose a network-guided association mapping approach from DNA methylation to disease (NAMDD). Compared with existing methods, NAMDD finds methylation-disease path associations by integrating analysis of multiple data combined with a stability selection strategy, thereby mining more information in the datasets and improving the quality of resultant methylation sites. The experimental results on both synthetic and real ovarian cancer data show that NAMDD substantially outperforms former disease-related methylation site research methods (including NsRRR and PCLOGIT) under false positive control. Furthermore, we applied NAMDD to ovarian cancer data, identified significant path associations and provided hypothetical biological path associations to explain our findings.
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Affiliation(s)
- Lin Yuan
- Institute of Machine Learning and Systems Biology, College of Electronic and Information Engineering, Tongji University, Shanghai, 201804, P.R. China
| | - De-Shuang Huang
- Institute of Machine Learning and Systems Biology, College of Electronic and Information Engineering, Tongji University, Shanghai, 201804, P.R. China.
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12
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Calderón-Aparicio A, Orue A. Precision oncology in Latin America: current situation, challenges and perspectives. Ecancermedicalscience 2019; 13:920. [PMID: 31281417 PMCID: PMC6546257 DOI: 10.3332/ecancer.2019.920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Anti-cancer cytotoxic treatments like platinum-derived compounds often show low therapeutic efficacy, high-risk side effects and resistance. Hence, targeted treatments designed to attack only tumour cells avoiding these harmful side effects are highly needed in clinical practice. Due to this, precision oncology has arisen as an approach to specifically target alterations present only in cancer cells, minimising side effects for patients. It involves the use of molecular biomarkers present in each kind of tumour for diagnosis, prognosis and treatment. Since these biomarkers are specific for each cancer type, physicians use them to stratify, diagnose or take the best therapeutic options for each patient depending on the features of the specific tumour. AIM This review aims to describe the current situation, limitations, advantages and perspectives about precision oncology in Latin America. MAIN BODY For many years, many biomarkers have been used in a clinical setting in developed countries. However, in Latin American countries, their broad application has not been affordable partially due to financial and technical limitations associated with precarious health systems and poor access of low-income populations to quality health care. Furthermore, the genetic mixture in Latin American populations could generate differences in treatment responses from one population to another (pharmacoethnicity) and this should be evaluated before establishing precision therapy in particular populations. Some research groups in the region have done a lot of work in this field and these data should be taken as a starting point to establish networks oriented to finding clinically useful cancer biomarkers in Latin American populations. CONCLUSION Latin America must create policies allowing excluded populations to gain access to health systems and next generation anti-cancer drugs, i.e. high-cost targeted therapies to improve survival. Also, cancer clinical research must be oriented to establish cancer biomarkers adapted to specific populations with different ethnicity, allowing the improvement of patient outcomes.
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Affiliation(s)
- Ali Calderón-Aparicio
- Tumor Cell Biology Laboratory, Instituto Venezolano de Investigaciones Científicas IVIC, Centro de Microbiología, Caracas 1020A, Venezuela
| | - Andrea Orue
- Tumor Cell Biology Laboratory, Instituto Venezolano de Investigaciones Científicas IVIC, Centro de Microbiología, Caracas 1020A, Venezuela
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13
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Ahani-Nahayati M, Solali S, Shams Asenjan K, Movassaghpour Akbari AA, Talebi M, Zadi Heydarabad M, Baharaghdam S, Farshdousti Hagh M. Promoter Methylation Status of Survival-Related Genes in MOLT- 4 Cells Co-Cultured with Bone Marrow Mesenchymal Stem Cells under Hypoxic Conditions. CELL JOURNAL 2018; 20:188-194. [PMID: 29633596 PMCID: PMC5893290 DOI: 10.22074/cellj.2018.5101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/11/2017] [Indexed: 01/15/2023]
Abstract
OBJECTIVES DNA methylation is a well-studied epigenetic mechanism that is a potent arm of the gene expression controlling machinery. Since the hypoxic situation and the various cells of bone marrow microenvironment, e.g. mesenchymal stem cells, play a role in the in vivo and in vitro biology of leukemic cells, we decided to study the effects of hypoxia and mesenchymal stem cells (MSCs) on the promoter methylation pattern of BAX and BCL2 genes. MATERIALS AND METHODS In this experimental study, the co-culture of MOLT-4 cells with MSCs and treatment with CoCl2 was done during 6, 12, and 24 hour periods. Total DNA was extracted using commercial DNA extraction kits, and sodium bisulfite (SBS) treatment was performed on the extracted DNA. Methylation specific polymerase chain reaction (MSP) was used to evaluate the methylation status of the selected genes' promoter regions. RESULTS The BAX and BCL2 promoters of untreated MOLT-4 cells were in partial methylated and fully unmethylated states, respectively. After incubating the cancer cells with CoCl2 and MSCs, the MSP results after 6, 12, and 24 hours were the same as untreated MOLT-4 cells. In other words, the exposure of MOLT-4 cells to the hypoxia-mimicry agent and MSCs in various modes and different time frames showed that these factors have exerted no change on the methylation signature of the studied fragments from the promoter region of the mentioned genes. CONCLUSIONS Hypoxia and MSCs actually have no notable effect on the methylation status of the promoters of BAX and BCL2 in the specifically studied regions. DNA methylation is probably not the main process by which MSCs and CoCl2 induced hypoxia regulate the expression of these genes. Finally, we are still far from discovering the exact functional mechanisms of gene expression directors, but these investigations can provide new insights into this field for upcoming studies.
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Affiliation(s)
- Milad Ahani-Nahayati
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Drug Applied Research Center (DARC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeed Solali
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Karim Shams Asenjan
- Drug Applied Research Center (DARC), Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mehdi Talebi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Sina Baharaghdam
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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14
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Busonero C, Leone S, Klemm C, Acconcia F. A functional drug re-purposing screening identifies carfilzomib as a drug preventing 17β-estradiol: ERα signaling and cell proliferation in breast cancer cells. Mol Cell Endocrinol 2018; 460:229-237. [PMID: 28760601 DOI: 10.1016/j.mce.2017.07.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/27/2017] [Accepted: 07/27/2017] [Indexed: 12/13/2022]
Abstract
Most cases of breast cancer (BC) are estrogen receptor α-positive (ERα+) at diagnosis. The presence of ERα drives the therapeutic approach for this disease, which often consists of endocrine therapy (ET). 4OH-Tamoxifen and faslodex (i.e., fulvestrant - ICI182,780) are two ETs that render tumor cells insensitive to 17β-estradiol (E2)-dependent proliferative stimuli and prevent BC progression. However, ET has limitations and serious failures in different tissues and organs. Thus, there is an urgent need to identify novel drugs to fight BC in the clinic. Re-positioning of old drugs for new clinical purposes is an attractive alternative for drug discovery. For this analysis, we focused on the modulation of intracellular ERα levels in BC cells as target for the screening of about 900 Food and Drug Administration (FDA) approved compounds that would hinder E2:ERα signaling and inhibit BC cell proliferation. We found that carfilzomib induces ERα degradation and prevents E2 signaling and cell proliferation in two ERα+ BC cell lines. Remarkably, the analysis of carfilzomib effects on a cell model system with an acquired resistance to 4OH-tamoxifen revealed that this drug has an antiproliferative effect superior to faslodex in BC cells. Therefore, our results identify carfilzomib as a drug preventing E2:ERα signaling and cell proliferation in BC cells and suggest its possible re-position for the treatment of ERα+ BC as well as for those diseases that have acquired resistance to 4OH-tamoxifen.
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Affiliation(s)
- Claudia Busonero
- Department of Sciences, Section Biomedical Sciences and Technology, University Roma Tre, Viale Guglielmo Marconi, 446, I-00146, Rome, Italy
| | - Stefano Leone
- Department of Sciences, Section Biomedical Sciences and Technology, University Roma Tre, Viale Guglielmo Marconi, 446, I-00146, Rome, Italy
| | - Cinzia Klemm
- Department of Biochemistry and Functional Proteomics, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Filippo Acconcia
- Department of Sciences, Section Biomedical Sciences and Technology, University Roma Tre, Viale Guglielmo Marconi, 446, I-00146, Rome, Italy.
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15
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Fang J, Zhang JG, Deng HW, Wang YP. Joint Detection of Associations between DNA Methylation and Gene Expression from Multiple Cancers. IEEE J Biomed Health Inform 2017; 22:1960-1969. [PMID: 29990049 DOI: 10.1109/jbhi.2017.2784621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA methylation plays an important role in the development of various cancers mainly through the regulation on gene expression. Hence, the study on the relation between DNA methylation and gene expression is of particular interest to understand cancers. Recently, an increasing number of datasets are available from multiple cancers, which makes it possible to study both the similarity and difference of genomic alterations across multiple tumor types. However, most of the existing pan-cancer analysis methods perform simple aggregations, which may overlook the heterogeneity of the interactions. In this paper, we propose a novel method to jointly detect complex associations between DNA methylation and gene expression levels from multiple cancers. The main idea is to apply joint sparse canonical correlation analysis to detect a small set of methylated sites, which are associated with another set of genes either shared across cancers or specific to a particular group (group-specific) of cancers. These methylated sites and genes form a complex module with strong multivariate correlations. We further introduced a joint sparse precision matrix estimation method to identify driver methylation-gene pairs in the module. These pairs are characterized by significant partial correlations, which may imply high functional impacts and contribute to complementary information to the main step. We apply our method to The Cancer Genome Atlas(TCGA) datasets with 1166 samples from four cancers. The results reveal significant shared and groupspecific interactions between DNA methylation and gene expression levels. To promote reproducible research, the Matlab code is available at https://sites.google.com/site/jianfang86/jointTCGA.
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16
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Leverson JD, Sampath D, Souers AJ, Rosenberg SH, Fairbrother WJ, Amiot M, Konopleva M, Letai A. Found in Translation: How Preclinical Research Is Guiding the Clinical Development of the BCL2-Selective Inhibitor Venetoclax. Cancer Discov 2017; 7:1376-1393. [PMID: 29146569 DOI: 10.1158/2159-8290.cd-17-0797] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/12/2017] [Accepted: 10/19/2017] [Indexed: 12/12/2022]
Abstract
Since the discovery of apoptosis as a form of programmed cell death, targeting the apoptosis pathway to induce cancer cell death has been a high-priority goal for cancer therapy. After decades of effort, drug-discovery scientists have succeeded in generating small-molecule inhibitors of antiapoptotic BCL2 family proteins. Innovative medicinal chemistry and structure-based drug design, coupled with a strong fundamental understanding of BCL2 biology, were essential to the development of BH3 mimetics such as the BCL2-selective inhibitor venetoclax. We review a number of preclinical studies that have deepened our understanding of BCL2 biology and facilitated the clinical development of venetoclax.Significance: Basic research into the pathways governing programmed cell death have paved the way for the discovery of apoptosis-inducing agents such as venetoclax, a BCL2-selective inhibitor that was recently approved by the FDA and the European Medicines Agency. Preclinical studies aimed at identifying BCL2-dependent tumor types have translated well into the clinic thus far and will likely continue to inform the clinical development of venetoclax and other BCL2 family inhibitors. Cancer Discov; 7(12); 1376-93. ©2017 AACR.
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Affiliation(s)
| | | | | | | | | | - Martine Amiot
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Nantes, France
| | - Marina Konopleva
- The University of Texas MD Anderson Cancer Center, Houston, Texas
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17
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Lochmann TL, Floros KV, Naseri M, Powell KM, Cook W, March RJ, Stein GT, Greninger P, Maves YK, Saunders LR, Dylla SJ, Costa C, Boikos SA, Leverson JD, Souers AJ, Krystal GW, Harada H, Benes CH, Faber AC. Venetoclax Is Effective in Small-Cell Lung Cancers with High BCL-2 Expression. Clin Cancer Res 2017; 24:360-369. [PMID: 29118061 DOI: 10.1158/1078-0432.ccr-17-1606] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/05/2017] [Accepted: 10/25/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Small-cell lung cancer (SCLC) is an often-fatal neuroendocrine carcinoma usually presenting as extensive disease, carrying a 3% 5-year survival. Despite notable advances in SCLC genomics, new therapies remain elusive, largely due to a lack of druggable targets.Experimental Design: We used a high-throughput drug screen to identify a venetoclax-sensitive SCLC subpopulation and validated the findings with multiple patient-derived xenografts of SCLC.Results: Our drug screen consisting of a very large collection of cell lines demonstrated that venetoclax, an FDA-approved BCL-2 inhibitor, was found to be active in a substantial fraction of SCLC cell lines. Venetoclax induced BIM-dependent apoptosis in vitro and blocked tumor growth and induced tumor regressions in mice bearing high BCL-2-expressing SCLC tumors in vivo BCL-2 expression was a predictive biomarker for sensitivity in SCLC cell lines and was highly expressed in a subset of SCLC cell lines and tumors, suggesting that a substantial fraction of patients with SCLC could benefit from venetoclax. Mechanistically, we uncover a novel role for gene methylation that helped discriminate high BCL-2-expressing SCLCs.Conclusions: Altogether, our findings identify venetoclax as a promising new therapy for high BCL-2-expressing SCLCs. Clin Cancer Res; 24(2); 360-9. ©2017 AACR.
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Affiliation(s)
- Timothy L Lochmann
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Konstantinos V Floros
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Mitra Naseri
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Krista M Powell
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Wade Cook
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Ryan J March
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Giovanna T Stein
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Patricia Greninger
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | | | | | - Scott J Dylla
- AbbVie Stemcentrx LLC, South San Francisco, California
| | - Carlotta Costa
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Sosipatros A Boikos
- Division of Hematology, Oncology, & Palliative Care, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | | | | | - Geoffrey W Krystal
- Department of Internal Medicine, Virginia Commonwealth University, McGuire Veterans Affairs Medical Center, Richmond, Virginia
| | - Hisashi Harada
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia.
| | - Cyril H Benes
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts.
| | - Anthony C Faber
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia.
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18
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Xie H, Tao W, Wu X, Gu J. Genetic variations in apoptosis pathway and the risk of ovarian cancer. Oncotarget 2016; 7:56737-56745. [PMID: 27462919 PMCID: PMC5302949 DOI: 10.18632/oncotarget.10772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/09/2016] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Apoptosis is a highly conserved form of cell death and aberrant regulation of apoptotic cell death mechanisms leads to variety of major human diseases, especially tumor formation. Genetic variations in apoptosis genes may increase susceptibility to ovarian cancer. RESULTS In individual SNP analysis, 12 SNPs in 5 apoptosis pathway genes were significantly associated with ovarian cancer risk after adjustment for multiple comparisons at q-value <0.05. The most significant SNP was rs11152377 in the Bcl-2 gene. The homozygous variant TT genotype was associated with a significantly decreased risk of ovarian cancer (odds ratio [OR] =0.53; 95% confidence interval [CI], 0.37-0.77, P<0.001). Cumulative effect analysis showed joint effects of increased risk of ovarian cancer with increasing number of unfavorable genotypes in patients. Classification and regression tree (CART) analysis further revealed high-order gene-gene interactions and categorized the study subjects into low-, medium-, and high-risk groups. Compared with the low-risk group, medium-risk group and high-risk group conferred 1.76-fold (95% CI: 1.06-2.90) and 3.64-fold (95% CI: 2.37-5.59) increased risk of ovarian cancer (P for trend <0.001)Materials and Methods: In a case-control study of 417 ovarian cancer patients and 417 matched controls, we evaluated the associations of 587 single nucleotide polymorphisms (SNPs) from 65 genes of the apoptosis pathway with the risk of ovarian cancer. CONCLUSIONS Our results suggest that genetic variations in apoptosis pathway genes modulate the risk of ovarian cancer individually and jointly.
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Affiliation(s)
- Hui Xie
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Wade Tao
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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19
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Milevskiy MJG, Al-Ejeh F, Saunus JM, Northwood KS, Bailey PJ, Betts JA, McCart Reed AE, Nephew KP, Stone A, Gee JMW, Dowhan DH, Dray E, Shewan AM, French JD, Edwards SL, Clark SJ, Lakhani SR, Brown MA. Long-range regulators of the lncRNA HOTAIR enhance its prognostic potential in breast cancer. Hum Mol Genet 2016; 25:3269-3283. [PMID: 27378691 PMCID: PMC5179926 DOI: 10.1093/hmg/ddw177] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/05/2016] [Accepted: 06/07/2016] [Indexed: 01/17/2023] Open
Abstract
Predicting response to endocrine therapy and survival in oestrogen receptor positive breast cancer is a significant clinical challenge and novel prognostic biomarkers are needed. Long-range regulators of gene expression are emerging as promising biomarkers and therapeutic targets for human diseases, so we have explored the potential of distal enhancer elements of non-coding RNAs in the prognostication of breast cancer survival. HOTAIR is a long non-coding RNA that is overexpressed, promotes metastasis and is predictive of decreased survival. Here, we describe a long-range transcriptional enhancer of the HOTAIR gene that binds several hormone receptors and associated transcription factors, interacts with the HOTAIR promoter and augments transcription. This enhancer is dependent on Forkhead-Box transcription factors and functionally interacts with a novel alternate HOTAIR promoter. HOTAIR expression is negatively regulated by oestrogen, positively regulated by FOXA1 and FOXM1, and is inversely correlated with oestrogen receptor and directly correlated with FOXM1 in breast tumours. The combination of HOTAIR and FOXM1 enables greater discrimination of endocrine therapy responders and non-responders in patients with oestrogen receptor positive breast cancer. Consistent with this, HOTAIR expression is increased in cell-line models of endocrine resistance. Analysis of breast cancer gene expression data indicates that HOTAIR is co-expressed with FOXA1 and FOXM1 in HER2-enriched tumours, and these factors enhance the prognostic power of HOTAIR in aggressive HER2+ breast tumours. Our study elucidates the transcriptional regulation of HOTAIR, identifies HOTAIR and its regulators as novel biomarkers of patient response to endocrine therapy and corroborates the importance of transcriptional enhancers in cancer.
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Affiliation(s)
- Michael J G Milevskiy
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Fares Al-Ejeh
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jodi M Saunus
- The University of Queensland, UQ Centre for Clinical Research, Herston, Australia
| | - Korinne S Northwood
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,The University of Queensland, UQ Centre for Clinical Research, Herston, Australia
| | - Peter J Bailey
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Joshua A Betts
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Amy E McCart Reed
- The University of Queensland, UQ Centre for Clinical Research, Herston, Australia
| | | | - Andrew Stone
- Epigenetics Research Laboratory, Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Julia M W Gee
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University, Cardiff, UK
| | - Dennis H Dowhan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Eloise Dray
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.,Queensland University of Technology, Brisbane, Australia
| | - Annette M Shewan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Juliet D French
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Stacey L Edwards
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Sunil R Lakhani
- The University of Queensland, UQ Centre for Clinical Research, Herston, Australia.,Pathology Queensland, The Royal Brisbane & Women's Hospital, Herston, Australia.,The University of Queensland School of Medicine, Herston, Australia
| | - Melissa A Brown
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
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20
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Abstract
Aberrant DNA methylation is considered to be one of the most common hallmarks of cancer. Several recent advances in assessing the DNA methylome provide great promise for deciphering the cancer-specific DNA methylation patterns. Herein, we present the current key technologies used to detect high-throughput genome-wide DNA methylation, and the available cancer-associated methylation databases. Additionally, we focus on the computational methods for preprocessing, analyzing and interpreting the cancer methylome data. It not only discusses the challenges of the differentially methylated region calling and the prediction model construction but also highlights the biomarker investigation for cancer diagnosis, prognosis and response to treatment. Finally, some emerging challenges in the computational analysis of cancer methylome data are summarized.
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21
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Matta J, Morales L, Ortiz C, Adams D, Vargas W, Casbas P, Dutil J, Echenique M, Suárez E. Estrogen Receptor Expression Is Associated with DNA Repair Capacity in Breast Cancer. PLoS One 2016; 11:e0152422. [PMID: 27032101 PMCID: PMC4816515 DOI: 10.1371/journal.pone.0152422] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 03/14/2016] [Indexed: 02/07/2023] Open
Abstract
Estrogen-receptor-positive (ER+) tumors employ complex signaling that engages in crosstalk with multiple pathways through genomic and non-genomic regulation. A greater understanding of these pathways is important for developing improved biomarkers that can better determine treatment choices, risk of recurrence and cancer progression. Deficiencies in DNA repair capacity (DRC) is a hallmark of breast cancer (BC); therefore, in this work we tested whether ER signaling influences DRC. We analyzed the association between ER positivity (% receptor activation) and DRC in 270 BC patients, then further stratified our analysis by HER2 receptor status. Our results show that among HER2 negative, the likelihood of having low DRC values among ER- women is 1.92 (95% CI: 1.03, 3.57) times the likelihood of having low DRC values among ER+ women, even adjusting for different potential confounders (p<0.05); however, a contrary pattern was observed among HER2 positives women. In conclusion, there is an association between DRC levels and ER status, and this association is modified by HER2 receptor status. Adding a DNA repair capacity test to hormone receptor testing may provide new information on defective DNA repair phenotypes, which could better stratify BC patients who have ER+ tumors. ER+/HER2- tumors are heterogeneous, incompletely defined, and clinically challenging to treat; the addition of a DRC test could better characterize and classify these patients as well as help clinicians select optimal therapies, which could improve outcomes and reduce recurrences.
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Affiliation(s)
- Jaime Matta
- Department of Basic Sciences, Division of Pharmacology & Toxicology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
- Department of Basic Sciences, Division of Cancer Biology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
- * E-mail:
| | - Luisa Morales
- Public Health Program, Ponce Health Sciences University, Ponce, Puerto Rico, United States of America
| | - Carmen Ortiz
- Department of Basic Sciences, Division of Pharmacology & Toxicology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
- Department of Basic Sciences, Division of Cancer Biology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
| | - Damian Adams
- Department of Basic Sciences, Division of Pharmacology & Toxicology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
- Department of Basic Sciences, Division of Cancer Biology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
| | - Wanda Vargas
- Department of Basic Sciences, Division of Pharmacology & Toxicology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
- Department of Basic Sciences, Division of Cancer Biology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
| | - Patricia Casbas
- Department of Basic Sciences, Division of Cancer Biology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
- Department of Basic Sciences, Division of Biochemistry, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
| | - Julie Dutil
- Department of Basic Sciences, Division of Cancer Biology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
- Department of Basic Sciences, Division of Biochemistry, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
| | - Miguel Echenique
- Auxilio Mutuo Hospital, San Juan, Puerto Rico, United States of America
| | - Erick Suárez
- Department of Biostatistics and Epidemiology, Graduate School of Public Health, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico, United States of America
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22
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Zeng H, Shi Z, Kong X, Chen Y, Zhang H, Peng H, Luo H, Chen P. Involvement of B-cell CLL/lymphoma 2 promoter methylation in cigarette smoke extract-induced emphysema. Exp Biol Med (Maywood) 2016; 241:808-16. [PMID: 26924842 DOI: 10.1177/1535370216635759] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 02/02/2016] [Indexed: 12/26/2022] Open
Abstract
Abnormal apoptotic events play an important role in the pathogenesis of emphysema. The B-cell CLL/lymphoma 2 (Bcl-2) family proteins are essential and critical regulators of apoptosis. We determined whether the anti-apoptotic Bcl-2 play a role in the cigarette smoke extract (CSE)-induced emphysema. Furthermore, given the involvement of epigenetics in chronic obstructive pulmonary disease, we hypothesized that the deregulation of Bcl-2 might be caused by gene methylation. The emphysema in BALB/C mice was established by intraperitoneally injection of CSE. 5-aza-2'-deoxycytidine (AZA; a demethylation reagent) and phosphate-buffered saline were also administered intraperitoneally as CSE. TUNEL assay was used to assess apoptotic index of pulmonary cells. The methylation status of CpG dinucleotides within the Bcl-2 promoter was observed in all groups by bisulfite sequencing PCR. Pulmonary expression of Bcl-2, Bax, and cytochrome C were measured after four weeks of treatment. The apoptotic index of pulmonary cells in CSE injection group was much higher than control ((25.88 ± 7.55)% vs (6.28 ± 2.96)%). Compared to control mice, decreased expression of Bcl-2 and high methylation of Bcl-2 promoter was observed in CSE injected mice (0.88 ± 0.08 vs 0.49 ± 0.11, (3.82 ± 1.34)% vs (35.68 ± 5.99)%, P < 0.01).CSE treatment induced lung cell apoptosis and decreased lung function. AZA treatment increased Bcl-2 expression with Bcl-2 promoter demethylation. AZA also alleviated the lung cell apoptosis and function failure caused by CSE treatment. The decreased expression of anti-apoptotic Bcl-2 might account for the increased apoptosis in CSE induced-emphysema. Apparently, epigenetic alternation played a role in this deregulation of Bcl-2 expression, and it might support the involvement of epigenetic events in the pathogenesis of emphysema.
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Affiliation(s)
- Huihui Zeng
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Zhihui Shi
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Xianglong Kong
- Department of Respiratory Medicine, The First Hospital of Changsha, Changsha, Hunan 410011, China
| | - Yan Chen
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Hongliang Zhang
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Hong Peng
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Hong Luo
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Ping Chen
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
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23
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Zhang Z, Zhang G, Kong C. FOXM1 participates in PLK1-regulated cell cycle progression in renal cell cancer cells. Oncol Lett 2016; 11:2685-2691. [PMID: 27073539 DOI: 10.3892/ol.2016.4228] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 02/04/2016] [Indexed: 12/27/2022] Open
Abstract
The regulation of entry into and progression through mitosis is important for cell proliferation. Polo-like kinase 1 (PLK1) is involved in multiple stages of mitosis. Forkhead box protein M1 (FOXM1) has multiple functions in tumorigenesis and, in elevated levels, is frequently associated with cancer progression. The present study reports that FOXM1, a substrate of PLK1, controls the transcription mechanism that mediates the PLK1-dependent regulation of the cell cycle. The present study investigated the expression of PLK1 and FOXM1 in the clear renal cell carcinoma 769-P and ACHN cell lines, and indicated that the expression of PLK1 and FOXM1 are correlated in human renal cell cancer cell lines and that the suppression of PLK1 may decrease the expression of FOXM1. The knockdown of FOXM1 or PLK1 in renal cell cancer cell lines caused cell cycle progression to be blocked. As a result, the present study indicated the involvement of FOXM1 in PLK1-regulated cell cycle progression.
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Affiliation(s)
- Zhe Zhang
- Department of Urology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Guojun Zhang
- Department of Hematology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110022, P.R. China
| | - Chuize Kong
- Department of Urology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
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24
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Baur B, Bozdag S. A canonical correlation analysis-based dynamic bayesian network prior to infer gene regulatory networks from multiple types of biological data. J Comput Biol 2016; 22:289-99. [PMID: 25844668 DOI: 10.1089/cmb.2014.0296] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
One of the challenging and important computational problems in systems biology is to infer gene regulatory networks (GRNs) of biological systems. Several methods that exploit gene expression data have been developed to tackle this problem. In this study, we propose the use of copy number and DNA methylation data to infer GRNs. We developed an algorithm that scores regulatory interactions between genes based on canonical correlation analysis. In this algorithm, copy number or DNA methylation variables are treated as potential regulator variables, and expression variables are treated as potential target variables. We first validated that the canonical correlation analysis method is able to infer true interactions in high accuracy. We showed that the use of DNA methylation or copy number datasets leads to improved inference over steady-state expression. Our results also showed that epigenetic and structural information could be used to infer directionality of regulatory interactions. Additional improvements in GRN inference can be gleaned from incorporating the result in an informative prior in a dynamic Bayesian algorithm. This is the first study that incorporates copy number and DNA methylation into an informative prior in dynamic Bayesian framework. By closely examining top-scoring interactions with different sources of epigenetic or structural information, we also identified potential novel regulatory interactions.
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Affiliation(s)
- Brittany Baur
- Department of Math, Statistics and Computer Science, Marquette University , Milwaukee, Wisconsin
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25
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Kalmár A, Péterfia B, Hollósi P, Galamb O, Spisák S, Wichmann B, Bodor A, Tóth K, Patai ÁV, Valcz G, Nagy ZB, Kubák V, Tulassay Z, Kovalszky I, Molnár B. DNA hypermethylation and decreased mRNA expression of MAL, PRIMA1, PTGDR and SFRP1 in colorectal adenoma and cancer. BMC Cancer 2015; 15:736. [PMID: 26482433 PMCID: PMC4612409 DOI: 10.1186/s12885-015-1687-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 10/07/2015] [Indexed: 12/18/2022] Open
Abstract
Background Colorectal cancer (CRC) development is accompanied by changes in expression for several genes; but the details of the underlying regulatory procesess remain unknown. Our aims were to assess the role of epigenetic processes in tumour formation and to identify characteristic DNA methylation and miRNA alterations in the colorectal adenoma-carcinoma sequence. Methods Whole genome expression profiling was performed on colonic biopsy samples (49 healthy normal, 49 colorectal adenoma (AD), 49 CRC); on laser capture microdissected (LCM) epithelial and stromal cells from 6 CRC-normal adjacent tissue (NAT) samples pairs, and on demethylated human CRC cell lines using HGU133 Plus 2.0 microarrays (Affymetrix). Methylation status of genes with gradually altering expression along the AD-CRC sequence was further analysed on 10–10 macrodissected and 5–5 LCM samples from healthy colon, from adenoma and from CRC biopsy samples using bisulfite-sequencing PCR (BS-PCR) followed by pyrosequencing. In silico miRNA prediction for the selected genes was performed with miRWALK algorithm, miRNA expression was analysed on 3 CRC-NAT sample pairs and 3 adenoma tissue samples using the Human Panel I + II (Exiqon). SFRP1 immunohistochemistry experiments were performed. Results A set of transcripts (18 genes including MAL, SFRP1, SULT1A1, PRIMA1, PTGDR) showed decreasing expression (p < 0.01) in the biopsy samples along the adenoma-carcinoma sequence. Three of those (COL1A2, SFRP2, SOCS3) showed hypermethylation and THBS2 showed hypomethylation both in AD and in CRC samples compared to NAT, while BCL2, PRIMA1 and PTGDR showed hypermethylation only in the CRC group. miR-21 was found to be significantly (p < 0.01) upregulated in adenoma and tumour samples compared to the healthy colonic tissue controls and could explain the altered expression of genes for which DNA methylation changes do not appear to play role (e.g. BCL2, MAL, PTGS2). Demethylation treatment could upregulate gene expression of genes that were found to be hypermethylated in human CRC tissue samples. Decreasing protein levels of SFRP1 was also observed along the adenoma-carcinoma sequence. Conclusion Hypermethylation of the selected markers (MAL, PRIMA1, PTGDR and SFRP1) can result in reduced gene expression and may contribute to the formation of colorectal cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1687-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandra Kalmár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary. .,Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Bálint Péterfia
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary. .,Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Péter Hollósi
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary. .,Tumour Progression Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Orsolya Galamb
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Sándor Spisák
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Barnabás Wichmann
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | - András Bodor
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary.
| | - Kinga Tóth
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary.
| | - Árpád V Patai
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary.
| | - Gábor Valcz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | | | - Vivien Kubák
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary.
| | - Zsolt Tulassay
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary. .,Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Ilona Kovalszky
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary.
| | - Béla Molnár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary. .,Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
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26
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Prashanth Kumar B, Rajput S, Bharti R, Parida S, Mandal M. BI2536 – A PLK inhibitor augments paclitaxel efficacy in suppressing tamoxifen induced senescence and resistance in breast cancer cells. Biomed Pharmacother 2015; 74:124-32. [DOI: 10.1016/j.biopha.2015.07.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 07/09/2015] [Indexed: 02/02/2023] Open
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DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer. Nat Commun 2015; 6:7758. [PMID: 26169690 PMCID: PMC4510968 DOI: 10.1038/ncomms8758] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/06/2015] [Indexed: 12/15/2022] Open
Abstract
Expression of oestrogen receptor (ESR1) determines whether a breast cancer patient receives endocrine therapy, but does not guarantee patient response. The molecular factors that define endocrine response in ESR1-positive breast cancer patients remain poorly understood. Here we characterize the DNA methylome of endocrine sensitivity and demonstrate the potential impact of differential DNA methylation on endocrine response in breast cancer. We show that DNA hypermethylation occurs predominantly at oestrogen-responsive enhancers and is associated with reduced ESR1 binding and decreased gene expression of key regulators of ESR1 activity, thus providing a novel mechanism by which endocrine response is abated in ESR1-positive breast cancers. Conversely, we delineate that ESR1-responsive enhancer hypomethylation is critical in transition from normal mammary epithelial cells to endocrine-responsive ESR1-positive cancer. Cumulatively, these novel insights highlight the potential of ESR1-responsive enhancer methylation to both predict ESR1-positive disease and stratify ESR1-positive breast cancer patients as responders to endocrine therapy. The molecular factors influencing patient response to endocrine therapy are poorly understood. Here Stone et al. characterize the DNA methylome of endocrine response and show that methylation of oestrogen receptor-associated enhancers underpins endocrine sensitivity in human breast cancer.
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28
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Locke WJ, Zotenko E, Stirzaker C, Robinson MD, Hinshelwood RA, Stone A, Reddel RR, Huschtscha LI, Clark SJ. Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis. Clin Epigenetics 2015; 7:52. [PMID: 25960784 PMCID: PMC4424562 DOI: 10.1186/s13148-015-0086-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 04/16/2015] [Indexed: 01/17/2023] Open
Abstract
Background Dysregulation of the epigenome is a common event in malignancy; however, deciphering the earliest cancer-associated epigenetic events remains a challenge. Cancer epigenome studies to date have primarily utilised cancer cell lines or clinical samples, where it is difficult to identify the initial epigenetic lesions from those that occur over time. Here, we analysed the epigenome of human mammary epithelial cells (HMEC) and a matched variant cell population (vHMEC) that have spontaneously escaped senescence and undergone partial carcinogenic transformation. Using this model of basal-like breast carcinogenesis, we provide striking new insights into the very first epigenetic changes that occur during the initial stages of malignancy. Results The first phase of malignancy is defined by coordinated changes in the epigenome. At the chromatin level, this is embodied in long-range epigenetic deregulation, which involves the concomitant but atypical acquisition or loss of active and repressive histone modifications across large regional blocks. Changes in DNA methylation also occurs in a highly coordinated manner. We identified differentially methylated regions (DMRs) in the very earliest passages of vHMECs. Notably, we find that differential methylation targets loci regulated by key transcription factors including p53, AHR and E2F family members suggesting that epigenetic deregulation of transcription factor binding is a key event in breast carcinogenesis. Interestingly, DMRs identified in vHMEC are extensively methylated in breast cancer, with hypermethylation frequently encroaching into neighbouring regions. A subset of vHMEC DMRs exhibited a strong basal-like cancer specific hypermethylation. Conclusions Here, we generated epigenome-wide maps of the earliest phase of breast malignancy and show long-range epigenetic deregulation and coordinated DNA hypermethylation targets loci regulated by key transcription factors. These findings support a model where induction of breast cancer occurs through epigenetic disruption of transcription factor binding leading to deregulation of cancer-associated transcriptional networks. With their stability and very early occurrence, vHMECs hypermethylated loci could serve as excellent biomarkers for the initial detection of basal breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0086-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Warwick J Locke
- Epigenetic Research Laboratory, Genomics and Epigenetic Division, The Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010 Australia ; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Level 5 deLacy Building, St Vincent's Hospital, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Elena Zotenko
- Epigenetic Research Laboratory, Genomics and Epigenetic Division, The Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010 Australia ; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Level 5 deLacy Building, St Vincent's Hospital, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Clare Stirzaker
- Epigenetic Research Laboratory, Genomics and Epigenetic Division, The Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010 Australia ; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Level 5 deLacy Building, St Vincent's Hospital, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Mark D Robinson
- Swiss Institute of Bioinformatics, University of Zurich, Zurich, and Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, CH-8057 Switzerland
| | - Rebecca A Hinshelwood
- Epigenetic Research Laboratory, Genomics and Epigenetic Division, The Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010 Australia ; Sydney West Cancer Trials Centre, Crown Princess Mary Cancer Centre Westmead, Westmead Hospital, Hawkesbury Road, Westmead, NSW 2145 Australia
| | - Andrew Stone
- Epigenetic Research Laboratory, Genomics and Epigenetic Division, The Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010 Australia ; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Level 5 deLacy Building, St Vincent's Hospital, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, 2145 Hawkesbury Road, Westmead, NSW 2145 Australia ; Sydney Medical School, University of Sydney, Fisher Road, Sydney, NSW 2006 Australia
| | - Lily I Huschtscha
- Cancer Research Unit, Children's Medical Research Institute, 2145 Hawkesbury Road, Westmead, NSW 2145 Australia
| | - Susan J Clark
- Epigenetic Research Laboratory, Genomics and Epigenetic Division, The Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010 Australia ; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Level 5 deLacy Building, St Vincent's Hospital, Victoria Street, Darlinghurst, NSW 2010 Australia
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29
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Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value. Nat Commun 2015; 6:5899. [PMID: 25641231 DOI: 10.1038/ncomms6899] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 11/17/2014] [Indexed: 01/09/2023] Open
Abstract
Epigenetic alterations in the cancer methylome are common in breast cancer and provide novel options for tumour stratification. Here, we perform whole-genome methylation capture sequencing on small amounts of DNA isolated from formalin-fixed, paraffin-embedded tissue from triple-negative breast cancer (TNBC) and matched normal samples. We identify differentially methylated regions (DMRs) enriched with promoters associated with transcription factor binding sites and DNA hypersensitive sites. Importantly, we stratify TNBCs into three distinct methylation clusters associated with better or worse prognosis and identify 17 DMRs that show a strong association with overall survival, including DMRs located in the Wilms tumour 1 (WT1) gene, bi-directional-promoter and antisense WT1-AS. Our data reveal that coordinated hypermethylation can occur in oestrogen receptor-negative disease, and that characterizing the epigenetic framework provides a potential signature to stratify TNBCs. Together, our findings demonstrate the feasibility of profiling the cancer methylome with limited archival tissue to identify regulatory regions associated with cancer.
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Liu MZ, McLeod HL, He FZ, Chen XP, Zhou HH, Shu Y, Zhang W. Epigenetic perspectives on cancer chemotherapy response. Pharmacogenomics 2014; 15:699-715. [PMID: 24798726 DOI: 10.2217/pgs.14.41] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Epigenetic programs are now widely recognized as being critical to the biological processes of cancer genesis. However, it has not been comprehensively understood how and to what degree they can influence anticancer drugs responses. The development of drugs targeting epigenetic regulation has generated great enthusiasm, with a growing number in clinical development. We highlight here that epigenetic modifications can be involved in the regulation of genes responsible for the absorption, distribution, metabolism and excretion of drugs and for the pathological progression of cancer, thereby affecting anticancer drug responses. The major epigenetic regulatory mechanisms are reviewed, including DNA methylation, miRNA regulation and histone modification, with the aim of promoting rational use of anticancer drugs in the clinic and epigenetic drug development.
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Affiliation(s)
- Mou-Ze Liu
- Pharmacogenetics Research Institute, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, PR China
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31
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Jeschke J, Collignon E, Fuks F. DNA methylome profiling beyond promoters - taking an epigenetic snapshot of the breast tumor microenvironment. FEBS J 2014; 282:1801-14. [PMID: 25331982 DOI: 10.1111/febs.13125] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 10/06/2014] [Accepted: 10/19/2014] [Indexed: 12/22/2022]
Abstract
Breast cancer, one of the most common and deadliest malignancies in developed countries, is a remarkably heterogeneous disease, which is clinically reflected by patients who display similar pathological features but respond differently to treatments. In the search for mediators of responsiveness, the tumor microenvironment (TME), in particular tumor-associated immune cells, has been pushed into the spotlight as it has become clear that the TME is an active component of breast cancer disease that affects clinical outcomes. Thus, the characterization of the TME in terms of cell identities and their frequencies has generated a great deal of interest. The common methods currently used for this purpose are either limited in accuracy or application, and DNA methylation has recently been proposed as an alternative approach. The aim of this review is to discuss DNA methylation profiling beyond promoters as a potential clinical tool for TME characterization and cell typing within tumors. With respect to this, we review the role of DNA methylation in breast cancer and cell-lineage specification, as well as inform about the composition and clinical relevance of the TME.
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Affiliation(s)
- Jana Jeschke
- Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, Brussels, Belgium
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32
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Stone A, Valdes-Mora F, Clark SJ. Exploring and exploiting the aberrant DNA methylation profile of endocrine-resistant breast cancer. Epigenomics 2014; 5:595-8. [PMID: 24283871 DOI: 10.2217/epi.13.70] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Andrew Stone
- Cancer Epigenetics Program, Garvan Institute of Medical Research, Sydney, NSW, Australia.
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Nakamura J, Tanaka T, Kitajima Y, Noshiro H, Miyazaki K. Methylation-mediated gene silencing as biomarkers of gastric cancer: A review. World J Gastroenterol 2014; 20:11991-12006. [PMID: 25232236 PMCID: PMC4161787 DOI: 10.3748/wjg.v20.i34.11991] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 01/29/2014] [Accepted: 04/09/2014] [Indexed: 02/06/2023] Open
Abstract
Despite a decline in the overall incidence of gastric cancer (GC), the disease remains the second most common cause of cancer-related death worldwide and is thus a significant global health problem. The best means of improving the survival of GC patients is to screen for and treat early lesions. However, GC is often diagnosed at an advanced stage and is associated with a poor prognosis. Current diagnostic and therapeutic strategies have not been successful in decreasing the global burden of the disease; therefore, the identification of reliable biomarkers for an early diagnosis, predictive markers of recurrence and survival and markers of drug sensitivity and/or resistance is urgently needed. The initiation and progression of GC depends not only on genetic alterations but also epigenetic changes, such as DNA methylation and histone modification. Aberrant DNA methylation is the most well-defined epigenetic change in human cancers and is associated with inappropriate gene silencing. Therefore, an increasing number of genes methylated at the promoter region have been targeted as possible biomarkers for different purposes, including early detection, classification, the assessment of the tumor prognosis, the development of therapeutic strategies and patient follow-up. This review article summarizes the current understanding and recent evidence regarding DNA methylation markers in GC with a focus on the clinical potential of these markers.
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Abstract
The comparison of DNA methylation patterns across cancer types (pan-cancer methylome analyses) has revealed distinct subgroups of tumors that share similar methylation patterns. Integration of these data with the wealth of information derived from cancer genome profiling studies performed by large international consortia has provided novel insights into the cellular aberrations that contribute to cancer development. There is evidence that genetic mutations in epigenetic regulators (such as DNMT3, IDH1/2 or H3.3) mediate or contribute to these patterns, although a unifying molecular mechanism underlying the global alterations of DNA methylation has largely been elusive. Knowledge gained from pan-cancer methylome analyses will aid the development of diagnostic and prognostic biomarkers, improve patient stratification and the discovery of novel druggable targets for therapy, and will generate hypotheses for innovative clinical trial designs based on methylation subgroups rather than on cancer subtypes. In this review, we discuss recent advances in the global profiling of tumor genomes for aberrant DNA methylation and the integration of these data with cancer genome profiling data, highlight potential mechanisms leading to different methylation subgroups, and show how this information can be used in basic research and for translational applications. A remaining challenge is to experimentally prove the functional link between observed pan-cancer methylation patterns, the associated genetic aberrations, and their relevance for the development of cancer.
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Affiliation(s)
- Tania Witte
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heid elberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heid elberg, Germany
| | - Clarissa Gerhauser
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heid elberg, Germany
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35
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Positive immunohistochemical expression of bcl-2 in hormone-independent breast carcinomas is associated with a greater lymph node involvement and poor outcome. Med Oncol 2014; 31:105. [PMID: 25008065 DOI: 10.1007/s12032-014-0105-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
Abstract
To study the immunohistochemical expression of bcl-2 in patients with hormone-independent breast infiltrating ductal carcinomas (IDC) and its possible association with other clinico-biological parameters and outcome. Our study group included 72 females with hormone-independent (ER and PgR negative) infiltrating ductal breast carcinomas. Age, tumor size, axillary lymph node involvement (N), distant metastasis and histological grade, as well as the immunohistochemical expression of Ki67, p53 and androgen receptor (AR), were analyzed. We follow up 57 patients during a period of time ranged between 20 and 193 months (80.2 ± 58.3; median 78 months). Of all IDCs included in our study, 18 were ER-/PgR-/bcl-2+ and 54 ER-/PgR-/bcl-2-. The percentages of slightly bcl-2-positive (+) and bcl-2-strong positive (++) cases were 25 and 19 %, respectively, values lower than those observed in ER+/PgR+ tumors (79.3 and 86.8 %, respectively). Breast IDC with positivity (+) for bcl-2 showed, exclusively, greater lymph node involvement higher than 3 nodes (N+ >3) (p 0.021) and a great number of deaths due to the tumor (p 0.011). Same results were obtained when we compared bcl-2-negative and bcl-2-strong positive (++) subgroups. Our results led us to consider that the positive (+ or ++) immunohistochemical expression of bcl-2 in hormone-independent (ER and PgR negative) breast carcinomas is associated with greater axillary lymph node involvement and a greater number of deaths in the follow-up, being these data opposite to that observed in hormone-dependent tumors.
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Oliveira JC, Pezuk JA, Brassesco MS, Morales AG, Queiroz RGP, Scrideli CA, Tone LG. PLK1 expression and BI 2536 effects in childhood acute lymphoblastic leukemia. Pediatr Blood Cancer 2014; 61:1227-31. [PMID: 24519995 DOI: 10.1002/pbc.24978] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/16/2014] [Indexed: 01/22/2023]
Abstract
BACKGROUND Polo-like kinase 1 (PLK1) is a conserved kinase that mediates various mitotic events. Compelling data have repeatedly demonstrated its upregulation in different neoplasia, being frequently associated with poor prognosis. However, in childhood acute lymphoblastic leukemia (ALL), no studies have yet been conducted. PROCEDURE PLK1 expression and association with biological features were evaluated in 65 consecutively diagnosed childhood ALL samples by quantitative real-time PCR. Moreover, the effects of a specific PLK1 inhibitor, BI 2536, was tested against a panel of nine ALL cell lines at nanomolar concentrations (10, 50, 100 nM). RESULTS The mRNA expression of PLK1 showed great variability in pediatric ALL, but no difference was evidenced compared to normal bone marrow. Additionally, no association was found between PLK1 mRNA expression with any clinical or biological features. Alternatively, high mRNA expression of PLK1 was present in ALL cell lines. In vitro treatment with BI 2536 strongly diminished growth, while presenting significant reduction in colony formation capacity and increased apoptosis rates. Moreover, strong G2/M arrest was detected suggesting important impaired proliferation after treatment. CONCLUSIONS PLK1 mRNA expression level is not associated with prognosis in childhood ALL; however, considering the great variability observed in the sample and the in vitro experiments presented herein, BI 2536 treatment might serve as a promising therapeutic to enhance the efficacy of conventional treatment modalities in some childhood ALL cases.
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Affiliation(s)
- J C Oliveira
- Federal University of Alfenas, Minas Gerais, Brazil
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Wang Z, Curry E, Montana G. Network-guided regression for detecting associations between DNA methylation and gene expression. ACTA ACUST UNITED AC 2014; 30:2693-701. [PMID: 24919878 DOI: 10.1093/bioinformatics/btu361] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION High-throughput profiling in biological research has resulted in the availability of a wealth of data cataloguing the genetic, epigenetic and transcriptional states of cells. These data could yield discoveries that may lead to breakthroughs in the diagnosis and treatment of human disease, but require statistical methods designed to find the most relevant patterns from millions of potential interactions. Aberrant DNA methylation is often a feature of cancer, and has been proposed as a therapeutic target. However, the relationship between DNA methylation and gene expression remains poorly understood. RESULTS We propose Network-sparse Reduced-Rank Regression (NsRRR), a multivariate regression framework capable of using prior biological knowledge expressed as gene interaction networks to guide the search for associations between gene expression and DNA methylation signatures. We use simulations to show the advantage of our proposed model in terms of variable selection accuracy over alternative models that do not use prior network information. We discuss an application of NsRRR to The Cancer Genome Atlas datasets on primary ovarian tumours. AVAILABILITY AND IMPLEMENTATION R code implementing the NsRRR model is available at http://www2.imperial.ac.uk/∼gmontana CONTACT giovanni.montana@kcl.ac.uk SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zi Wang
- Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Edward Curry
- Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Giovanni Montana
- Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK
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