1
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HDAC6 inhibitors sensitize non-mesenchymal triple-negative breast cancer cells to cysteine deprivation. Sci Rep 2021; 11:10956. [PMID: 34040090 PMCID: PMC8155140 DOI: 10.1038/s41598-021-90527-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/12/2021] [Indexed: 12/24/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly malignant type of breast cancer and lacks effective therapy. Targeting cysteine-dependence is an emerging strategy to treat the mesenchymal TNBC. However, many TNBC cells are non-mesenchymal and unresponsive to cysteine deprivation. To overcome such resistance, three selective HDAC6 inhibitors (Tubacin, CAY10603, and Tubastatin A), identified by epigenetic compound library screening, can synergize with cysteine deprivation to induce cell death in the non-mesenchymal TNBC. Despite the efficacy of HDAC6 inhibitor, knockout of HDAC6 did not mimic the synthetic lethality induced by its inhibitors, indicating that HDAC6 is not the actual target of HDAC6 inhibitor in this context. Instead, transcriptomic profiling showed that tubacin triggers an extensive gene transcriptional program in combination with erastin, a cysteine transport blocker. Notably, the zinc-related gene response along with an increase of labile zinc was induced in cells by the combination treatment. The disturbance of zinc homeostasis was driven by PKCγ activation, which revealed that the PKCγ signaling pathway is required for HDAC6 inhibitor-mediated synthetic lethality. Overall, our study identifies a novel function of HDAC6 inhibitors that function as potent sensitizers of cysteine deprivation and are capable of abolishing cysteine-independence in non-mesenchymal TNBC.
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2
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Chyr J, Zhang Z, Chen X, Zhou X. PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines. Comput Struct Biotechnol J 2021; 19:2870-2880. [PMID: 34093998 PMCID: PMC8142020 DOI: 10.1016/j.csbj.2021.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 10/26/2022] Open
Abstract
Topologically associating domains, or TADs, play important roles in genome organization and gene regulation; however, they are often altered in diseases. High-throughput chromatin conformation capturing assays, such as Hi-C, can capture domains of increased interactions, and TADs and boundaries can be identified using well-established analytical tools. However, generating Hi-C data is expensive. In our study, we addressed the relationship between multi-omics data and higher-order chromatin structures using a newly developed machine-learning model called PredTAD. Our tool uses already-available and cost-effective datatypes such as transcription factor and histone modification ChIPseq data. Specifically, PredTAD utilizes both epigenetic and genetic features as well as neighboring information to classify the entire human genome as boundary or non-boundary regions. Our tool can predict boundary changes between normal and breast cancer genomes. Among the most important features for predicting boundary alterations were CTCF, subunits of cohesin (RAD21 and SMC3), and chromosome number, suggesting their roles in conserved and dynamic boundaries formation. Upon further analysis, we observed that genes near altered TAD boundaries were found to be involved in several important breast cancer signaling pathways such as Ras, Jak-STAT, and estrogen signaling pathways. We also discovered a TAD boundary alteration that contributes to RET oncogene overexpression. PredTAD can also successfully predict TAD boundary changes in other conditions and diseases. In conclusion, our newly developed machine learning tool allowed for a more complete understanding of the dynamic 3D chromatin structures involved in signaling pathway activation, altered gene expression, and disease state in breast cancer cells.
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Affiliation(s)
- Jacqueline Chyr
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77054, USA
| | - Zhigang Zhang
- School of Information Management and Statistics, Hubei University of Economics, Wuhan, Hubei 430205 China
| | - Xi Chen
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77054, USA
| | - Xiaobo Zhou
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77054, USA
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3
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Cystatin M/E (Cystatin 6): A Janus-Faced Cysteine Protease Inhibitor with Both Tumor-Suppressing and Tumor-Promoting Functions. Cancers (Basel) 2021; 13:cancers13081877. [PMID: 33919854 PMCID: PMC8070812 DOI: 10.3390/cancers13081877] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 01/08/2023] Open
Abstract
Alongside its contribution in maintaining skin homeostasis and its probable involvement in fetal and placental development, cystatin M/E (also known as cystatin 6) was first described as a tumor suppressor of breast cancer. This review aims to provide an update on cystatin M/E with particular attention paid to its role during tumorigenesis. Cystatin M/E, which is related to type 2 cystatins, displays the unique property of being a dual tight-binding inhibitor of both legumain (also known as asparagine endopeptidase) and cysteine cathepsins L, V and B, while its expression level is epigenetically regulated via the methylation of the CST6 promoter region. The tumor-suppressing role of cystatin M/E was further reported in melanoma, cervical, brain, prostate, gastric and renal cancers, and cystatin M/E was proposed as a biomarker of prognostic significance. Contrariwise, cystatin M/E could have an antagonistic function, acting as a tumor promoter (e.g., oral, pancreatic cancer, thyroid and hepatocellular carcinoma). Taking into account these apparently divergent functions, there is an urgent need to decipher the molecular and cellular regulatory mechanisms of the expression and activity of cystatin M/E associated with the safeguarding homeostasis of the proteolytic balance as well as its imbalance in cancer.
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4
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To B, Isaac D, Andrechek ER. Studying Lymphatic Metastasis in Breast Cancer: Current Models, Strategies, and Clinical Perspectives. J Mammary Gland Biol Neoplasia 2020; 25:191-203. [PMID: 33034778 DOI: 10.1007/s10911-020-09460-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/24/2020] [Indexed: 03/23/2023] Open
Abstract
Breast cancer is the most commonly diagnosed cancer in women and the second most common cause of cancer-related deaths in the United States. Although early detection has significantly decreased breast cancer mortality, patients diagnosed with distant metastasis still have a very poor prognosis. The most common site that breast cancer spreads to are local lymph nodes. Therefore, the presence of lymph node metastasis remains one of most important prognostic factors in breast cancer patients. Given its significant clinical implications, increased efforts have been dedicated to better understand the molecular mechanism governing lymph node metastasis in breast cancer. The identification of lymphatic-specific biomarkers, including podoplanin and LYVE-1, has propelled the field of lymphatic metastasis forward. In addition, several animal models such as cell line-derived xenografts, patient-derived xenografts, and spontaneous tumor models have been developed to recreate the process of lymphatic metastasis. Moreover, the incorporation of various -omic platforms have provided further insight into the genetic drivers facilitating lymphatic metastasis, as well as potential biomarkers and therapeutic targets. Here, we highlight various models of lymphatic metastasis, their potential pitfalls, and other tools available to study lymphatic metastasis including imaging modalities and -omic studies.
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Affiliation(s)
- Briana To
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Daniel Isaac
- Division of Hematology and Oncology, MSU Breslin Cancer Center, Lansing, MI, USA
| | - Eran R Andrechek
- Department of Physiology, Michigan State University, East Lansing, MI, USA.
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5
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Li X, Li X, He S, Zhao M. MeCP2-421-mediated RPE epithelial-mesenchymal transition and its relevance to the pathogenesis of proliferative vitreoretinopathy. J Cell Mol Med 2020; 24:9420-9427. [PMID: 32638535 PMCID: PMC7417696 DOI: 10.1111/jcmm.15602] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/13/2020] [Indexed: 12/17/2022] Open
Abstract
Proliferative vitreoretinopathy (PVR) is a blinding eye disease. Epithelial‐mesenchymal transition (EMT) of RPE cells plays an important role in the pathogenesis of PVR. In the current study, we sought to investigate the role of the methyl‐CpG‐binding protein 2 (MeCP2), especially P‐MeCP2‐421 in the pathogenesis of PVR. The expressions of P‐MeCP2‐421, P‐MeCP2‐80, PPAR‐γ and the double labelling of P‐MeCP2‐421 with α‐SMA, cytokeratin, TGF‐β and PPAR‐γ in human PVR membranes were analysed by immunohistochemistry. The effect of knocking down MeCP2 using siRNA on the expressions of α‐SMA, phospho‐Smad2/3, collagen I, fibronectin and PPAR‐γ; the expression of α‐SMA stimulated by recombinant MeCP2 in ARPE‐19; and the effect of TGF‐β and 5‐AZA treatment on PPAR‐γ expression were analysed by Western blot. Chromatin immunoprecipitation was used to determine the binding of MeCP2 to TGF‐β. Our results showed that P‐MeCP2‐421 was highly expressed in PVR membranes and was double labelled with α‐SMA, cytokeratin and TGF‐β, knocking down MeCP2 inhibited the activation of Smad2/3 and the expression of collagen I and fibronectin induced by TGF‐β. TGF‐β inhibited the expression of PPAR‐γ, silence of MeCP2 by siRNA or using MeCP2 inhibitor (5‐AZA) increased the expression of PPAR‐γ. α‐SMA was up‐regulated by the treatment of recombinant MeCP2. Importantly, we found that MeCP2 bound to TGF‐β as demonstrated by Chip assay. The results suggest that MeCP2 especially P‐MeCP2‐421 may play a significant role in the pathogenesis of PVR and targeting MeCP2 may be a potential therapeutic approach for the treatment of PVR.
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Affiliation(s)
- Xiaohua Li
- Henan Provincial People's Hospital, Zhengzhou, China.,Henan Eye Hospital, Henan Eye Institute, Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, China.,People's Hospital of Zhengzhou University, Zhengzhou, China.,People's Hospital of Henan University, Zhengzhou, China
| | - Xue Li
- Henan Provincial People's Hospital, Zhengzhou, China.,Henan Eye Hospital, Henan Eye Institute, Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, China.,People's Hospital of Zhengzhou University, Zhengzhou, China.,People's Hospital of Henan University, Zhengzhou, China
| | - Shikun He
- Ophthalmology Optometry Centre, Peking University People's Hospital, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, Beijing, China.,Departments of Pathology, USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mingwei Zhao
- Ophthalmology Optometry Centre, Peking University People's Hospital, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, Beijing, China
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6
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Yang Z, Zhang Y, Wang X, Huang J, Guo W, Wei P, Li G, Wang Z, Huang Z, Zhang L. Putative biomarkers of malignant transformation of sinonasal inverted papilloma into squamous cell carcinoma. J Int Med Res 2019; 47:2371-2380. [PMID: 30991875 PMCID: PMC6567723 DOI: 10.1177/0300060519838385] [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] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE To compare genome-wide DNA methylation between samples of sinonasal inverted papilloma (SNIP) and squamous cell carcinoma (SCC) samples in order to identify aberrantly methylated genes that might be involved in malignant transformation. METHODS Tissue samples were collected from patients. DNA methylation in C-phosphate-G islands and gene promoters was analysed using a DNA methylation microarray kit. The levels of mRNA or protein from aberrantly methylated genes were measured using real-time polymerase chain reaction or Western blot analysis. RESULTS A total of 27 tissue samples were included in this study; 15 SNIP samples and 12 SCCs arising in SNIPs. A total of 11 201 nominally differentially methylated sites were observed between SNIP and SCC arising in SNIPs. Six sites were significantly different at P < 0.01 and contained three genes ( MIR661, PLEC and OPA3). These three genes were hypermethylated. In addition, the levels of mature miR-661 mRNA and PLEC protein were significantly upregulated in SCC tissues compared with SNIP samples. The levels of OPA3 protein were downregulated in SCC tissues compared with SNIP samples. CONCLUSIONS This study demonstrated hypermethylation and abnormal expression of the MIR661, PLEC and OPA3 genes, suggesting a role for their involvement in the malignant transformation of SNIP.
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Affiliation(s)
- Zheng Yang
- 1 Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,2 Key Laboratory of Otolaryngology Head and Neck Surgery of the Ministry of Education, Beijing, China
| | - Yang Zhang
- 1 Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,2 Key Laboratory of Otolaryngology Head and Neck Surgery of the Ministry of Education, Beijing, China
| | - Xiangdong Wang
- 1 Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,2 Key Laboratory of Otolaryngology Head and Neck Surgery of the Ministry of Education, Beijing, China
| | - Junwei Huang
- 1 Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,2 Key Laboratory of Otolaryngology Head and Neck Surgery of the Ministry of Education, Beijing, China
| | - Wei Guo
- 1 Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,2 Key Laboratory of Otolaryngology Head and Neck Surgery of the Ministry of Education, Beijing, China
| | - Peng Wei
- 3 Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guojun Li
- 4 Department of Head and Neck Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,5 Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ziqiao Wang
- 3 Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhigang Huang
- 1 Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,2 Key Laboratory of Otolaryngology Head and Neck Surgery of the Ministry of Education, Beijing, China
| | - Luo Zhang
- 1 Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,2 Key Laboratory of Otolaryngology Head and Neck Surgery of the Ministry of Education, Beijing, China
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7
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Nicolini A, Ferrari P, Rossi G, Carpi A. Tumour growth and immune evasion as targets for a new strategy in advanced cancer. Endocr Relat Cancer 2018; 25:R577–R604. [PMID: 30306784 DOI: 10.1530/erc-18-0142] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
It has become clearer that advanced cancer, especially advanced breast cancer, is an entirely displayed pathological system that is much more complex than previously considered. However, the direct relationship between tumour growth and immune evasion can represent a general rule governing the pathological cancer system from the initial cancer cells to when the system is entirely displayed. Accordingly, a refined pathobiological model and a novel therapeutic strategy are proposed. The novel therapeutic strategy is based on therapeutically induced conditions (undetectable tumour burden and/or a prolonged tumour ‘resting state’), which enable an efficacious immune response in advanced breast and other types of solid cancers.
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Affiliation(s)
- Andrea Nicolini
- Department of Oncology, Transplantations and New Technologies in Medicine, University of Pisa, Pisa, Italy
| | - Paola Ferrari
- Department of Oncology, Transplantations and New Technologies in Medicine, University of Pisa, Pisa, Italy
| | - Giuseppe Rossi
- Unit of Epidemiology and Biostatistics, Institute of Clinical Physiology, National Council of Research, Pisa, Italy
| | - Angelo Carpi
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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8
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Kalinkova L, Zmetakova I, Smolkova B, Minarik G, Sedlackova T, Horvathova Kajabova V, Cierna Z, Mego M, Fridrichova I. Decreased methylation in the SNAI2 and ADAM23 genes associated with de-differentiation and haematogenous dissemination in breast cancers. BMC Cancer 2018; 18:875. [PMID: 30189837 PMCID: PMC6127923 DOI: 10.1186/s12885-018-4783-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/29/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND In breast cancer (BC), deregulation of DNA methylation leads to aberrant expressions and functions of key regulatory genes. In our study, we investigated the relationship between the methylation profiles of genes associated with cancer invasivity and clinico-pathological parameters. In detail, we studied differences in the methylation levels between BC patients with haematogenous and lymphogenous cancer dissemination. METHODS We analysed samples of primary tumours (PTs), lymph node metastases (LNMs) and peripheral blood cells (PBCs) from 59 patients with sporadic disseminated BC. Evaluation of the DNA methylation levels of six genes related to invasivity, ADAM23, uPA, CXCL12, TWIST1, SNAI1 and SNAI2, was performed by pyrosequencing. RESULTS Among the cancer-specific methylated genes, we found lower methylation levels of the SNAI2 gene in histologic grade 3 tumours (OR = 0.61; 95% CI, 0.39-0.97; P = 0.038) than in fully or moderately differentiated cancers. We also evaluated the methylation profiles in patients with different cancer cell dissemination statuses (positivity for circulating tumour cells (CTCs) and/or LNMs). We detected the significant association between reduced DNA methylation of ADAM23 in PTs and presence of CTCs in the peripheral blood of patients (OR = 0.45; 95% CI, 0.23-0.90; P = 0.023). CONCLUSION The relationships between the decreased methylation levels of the SNAI2 and ADAM23 genes and cancer de-differentiation and haematogenous dissemination, respectively, indicate novel functions of those genes in the invasive processes. After experimental validation of the association between the lower values of SNAI2 and ADAM23 methylation and clinical features of aggressive BCs, these methylation profiles could improve the management of metastatic disease.
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Affiliation(s)
- Lenka Kalinkova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, v.v.i., Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Iveta Zmetakova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, v.v.i., Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Bozena Smolkova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, v.v.i., Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Gabriel Minarik
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08, Bratislava, Slovak Republic
| | - Tatiana Sedlackova
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08, Bratislava, Slovak Republic
| | - Viera Horvathova Kajabova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, v.v.i., Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Zuzana Cierna
- Institute of Pathological Anatomy, Faculty of Medicine, Comenius University, University Hospital, Sasinkova 4, 811 08, Bratislava, Slovak Republic
| | - Michal Mego
- 2nd Department of Oncology, Faculty of Medicine, Comenius University, National Cancer Institute, Klenova 1, 83310, Bratislava, Slovak Republic
| | - Ivana Fridrichova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, v.v.i., Dubravska cesta 9, 845 05, Bratislava, Slovak Republic.
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Altered DNA Methylation of Long Noncoding RNA uc.167 Inhibits Cell Differentiation in Heart Development. BIOMED RESEARCH INTERNATIONAL 2018; 2018:4658024. [PMID: 30003100 PMCID: PMC5998154 DOI: 10.1155/2018/4658024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 04/03/2018] [Accepted: 04/10/2018] [Indexed: 12/15/2022]
Abstract
In previous studies, we have demonstrated the function of uc.167 in the heart development. DNA methylation plays a crucial role in regulating the expression of developmental genes during embryonic development. In this study, the methylomic landscape was investigated in order to identify the DNA methylation alterations. Methylated DNA immunoprecipitation (MeDIP) was performed to examine the differences in methylation status of overexpressed uc.167 in P19 cells. GO and KEGG pathway analyses of differentially methylated genes were also conducted. We found that the distribution of differentially methylated regions (DMRs) peaks in different components of genome was mainly located in intergenic regions and intron. The biological process associated with uc.167 was focal adhesion and Rap1 signaling pathway. MEF2C was significantly decreased in uc.167 overexpressed group, suggesting that uc.167 may influence the P19 differentiation through MEF2C reduction. Taken together, our findings revealed that the effect of uc.167 on P19 differentiation may be attributed to the altered methylation of specific genes.
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10
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Changes in DNA methylation in naïve T helper cells regulate the pathophysiological state in minimal-change nephrotic syndrome. BMC Res Notes 2017; 10:480. [PMID: 28915836 PMCID: PMC5603023 DOI: 10.1186/s13104-017-2719-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 07/29/2017] [Indexed: 11/13/2022] Open
Abstract
Background DNA methylation plays a crucial role in regulating transcription, and changes in DNA methylation affect gene expression and disease development. Minimal change nephrotic syndrome (MCNS) has been reported to involve immunological disturbances. Since the characteristic features of the disease include recurrent relapse and sex and age preference, the disease pathogenesis may be partly related to epigenetic changes. However, little is known about these changes. Methods We analyzed genome-wide DNA methylation using the microarray-based integrated analysis of methylation by isoschizomers method. This method was used to evaluate methylation in monocytes (patient number; n = 6) and naïve T helper cells (n = 4) from the peripheral blood of MCNS patients both in relapse and following remission and that of healthy controls (n = 5). Results In total, 85 co-occurring genes were identified in naïve T helper cells, while 4 such genes were identified in monocytes, which were common among the 3 following comparisons for changes in DNA methylation using sample pairs: (1) relapse versus remission, (2) relapse versus controls, and (3) remission versus controls. In 82 of 85 co-occurring genes (96.5%) in naïve T helper cells, the level of DNA methylation was altered according to disease activity, but was not related to disease activity in the 4 genes detected in monocytes. Conclusions Therefore, in 82 co-occurring genes in naïve T helper cells, the regulation of DNA methylation was well correlated with the clinical and pathophysiological state. Our genome-wide approach to analyze DNA methylation provides further insight into the pathogenesis of MCNS and indicates potential prediction and diagnostic tool for the disease. Electronic supplementary material The online version of this article (doi:10.1186/s13104-017-2719-1) contains supplementary material, which is available to authorized users.
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11
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Yoon J, Kim SB, Ahmed G, Shay JW, Terman JR. Amplification of F-Actin Disassembly and Cellular Repulsion by Growth Factor Signaling. Dev Cell 2017; 42:117-129.e8. [PMID: 28689759 PMCID: PMC5564210 DOI: 10.1016/j.devcel.2017.06.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 04/10/2017] [Accepted: 06/06/2017] [Indexed: 01/09/2023]
Abstract
Extracellular cues that regulate cellular shape, motility, and navigation are generally classified as growth promoting (i.e., growth factors/chemoattractants and attractive guidance cues) or growth preventing (i.e., repellents and inhibitors). Yet, these designations are often based on complex assays and undefined signaling pathways and thus may misrepresent direct roles of specific cues. Here, we find that a recognized growth-promoting signaling pathway amplifies the F-actin disassembly and repulsive effects of a growth-preventing pathway. Focusing on Semaphorin/Plexin repulsion, we identified an interaction between the F-actin-disassembly enzyme Mical and the Abl tyrosine kinase. Biochemical assays revealed Abl phosphorylates Mical to directly amplify Mical Redox-mediated F-actin disassembly. Genetic assays revealed that Abl allows growth factors and Semaphorin/Plexin repellents to combinatorially increase Mical-mediated F-actin disassembly, cellular remodeling, and repulsive axon guidance. Similar roles for Mical in growth factor/Abl-related cancer cell behaviors further revealed contexts in which characterized positive effectors of growth/guidance stimulate such negative cellular effects as F-actin disassembly/repulsion.
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Affiliation(s)
- Jimok Yoon
- Departments of Neuroscience and Pharmacology, Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sang Bum Kim
- Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Giasuddin Ahmed
- Departments of Neuroscience and Pharmacology, Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jerry W Shay
- Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jonathan R Terman
- Departments of Neuroscience and Pharmacology, Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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12
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Yoon J, Hung RJ, Terman JR. Characterizing F-actin Disassembly Induced by the Semaphorin-Signaling Component MICAL. Methods Mol Biol 2017; 1493:119-128. [PMID: 27787846 DOI: 10.1007/978-1-4939-6448-2_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The MICALs are a family of phylogenetically conserved cytoplasmic proteins that modulate numerous cellular behaviors and play critical roles in semaphorin-plexin signaling. Our recent results have revealed that the MICALs are an unusual family of actin regulatory proteins that use actin filaments (F-actin) as a direct substrate-controlling F-actin dynamics via stereospecific oxidation of conserved methionine (Met44 and Met47) residues within actin. In particular, the MICALs have a highly conserved flavoprotein monooxygenase (redox) enzymatic domain in their N-terminus that directly oxidizes and destabilizes F-actin. Here, we describe methods to characterize MICAL-mediated F-actin disassembly using in vitro assays with purified proteins.
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Affiliation(s)
- Jimok Yoon
- Departments of Neuroscience and Pharmacology and Neuroscience Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ruei-Jiun Hung
- Departments of Neuroscience and Pharmacology and Neuroscience Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jonathan R Terman
- Departments of Neuroscience and Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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13
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Development and validation of a multiplex methylation specific PCR-coupled liquid bead array for liquid biopsy analysis. Clin Chim Acta 2016; 461:156-64. [DOI: 10.1016/j.cca.2016.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/06/2016] [Accepted: 08/03/2016] [Indexed: 12/21/2022]
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14
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Noubissi FK, Ogle BM. Cancer Cell Fusion: Mechanisms Slowly Unravel. Int J Mol Sci 2016; 17:ijms17091587. [PMID: 27657058 PMCID: PMC5037852 DOI: 10.3390/ijms17091587] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/26/2016] [Accepted: 09/12/2016] [Indexed: 01/15/2023] Open
Abstract
Although molecular mechanisms and signaling pathways driving invasion and metastasis have been studied for many years, the origin of the population of metastatic cells within the primary tumor is still not well understood. About a century ago, Aichel proposed that cancer cell fusion was a mechanism of cancer metastasis. This hypothesis gained some support over the years, and recently became the focus of many studies that revealed increasing evidence pointing to the possibility that cancer cell fusion probably gives rise to the metastatic phenotype by generating widespread genetic and epigenetic diversity, leading to the emergence of critical populations needed to evolve resistance to the treatment and development of metastasis. In this review, we will discuss the clinical relevance of cancer cell fusion, describe emerging mechanisms of cancer cell fusion, address why inhibiting cancer cell fusion could represent a critical line of attack to limit drug resistance and to prevent metastasis, and suggest one new modality for doing so.
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Affiliation(s)
| | - Brenda M Ogle
- Department of Biomedical Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA.
- Stem Cell Institute, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA.
- Masonic Cancer Center, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA.
- Lillehei Heart Institute, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA.
- Institute for Engineering and Medicine, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA.
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15
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Li Z, Guo X, Tang L, Peng L, Chen M, Luo X, Wang S, Xiao Z, Deng Z, Dai L, Xia K, Wang J. Methylation analysis of plasma cell-free DNA for breast cancer early detection using bisulfite next-generation sequencing. Tumour Biol 2016; 37:13111-13119. [PMID: 27449045 DOI: 10.1007/s13277-016-5190-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 07/13/2016] [Indexed: 12/15/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) has been considered as a potential biomarker for non-invasive cancer detection. To evaluate the methylation levels of six candidate genes (EGFR, GREM1, PDGFRB, PPM1E, SOX17, and WRN) in plasma cfDNA as biomarkers for breast cancer early detection, quantitative analysis of the promoter methylation of these genes from 86 breast cancer patients and 67 healthy controls was performed by using microfluidic-PCR-based target enrichment and next-generation bisulfite sequencing technology. The predictive performance of different logistic models based on methylation status of candidate genes was investigated by means of the area under the ROC curve (AUC) and odds ratio (OR) analysis. Results revealed that EGFR, PPM1E, and 8 gene-specific CpG sites showed significantly hypermethylation in cancer patients' plasma and significantly associated with breast cancer (OR ranging from 2.51 to 9.88). The AUC values for these biomarkers were ranging from 0.66 to 0.75. Combinations of multiple hypermethylated genes or CpG sites substantially improved the predictive performance for breast cancer detection. Our study demonstrated the feasibility of quantitative measurement of candidate gene methylation in cfDNA by using microfluidic-PCR-based target enrichment and bisulfite next-generation sequencing, which is worthy of further validation and potentially benefits a broad range of applications in clinical oncology practice. Quantitative analysis of methylation pattern of plasma cfDNA by next-generation sequencing might be a valuable non-invasive tool for early detection of breast cancer.
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Affiliation(s)
- Zibo Li
- The State Key Laboratory of Medical Genetics and School of Life Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China
| | - Xinwu Guo
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
| | - Lili Tang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Limin Peng
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
| | - Ming Chen
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
| | - Xipeng Luo
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
| | - Shouman Wang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Zhi Xiao
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Zhongping Deng
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
- Research Center for Technologies in Nucleic Acid-Based Diagnostics, Changsha, Hunan, 410205, China
- Research Center for Technologies in Nucleic Acid-Based Diagnostics and Therapeutics, Changsha, Hunan, 410205, China
| | - Lizhong Dai
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
- Research Center for Technologies in Nucleic Acid-Based Diagnostics, Changsha, Hunan, 410205, China
- Research Center for Technologies in Nucleic Acid-Based Diagnostics and Therapeutics, Changsha, Hunan, 410205, China
| | - Kun Xia
- The State Key Laboratory of Medical Genetics and School of Life Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China
| | - Jun Wang
- The State Key Laboratory of Medical Genetics and School of Life Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China.
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16
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Longacre M, Snyder NA, Housman G, Leary M, Lapinska K, Heerboth S, Willbanks A, Sarkar S. A Comparative Analysis of Genetic and Epigenetic Events of Breast and Ovarian Cancer Related to Tumorigenesis. Int J Mol Sci 2016; 17:E759. [PMID: 27213343 PMCID: PMC4881580 DOI: 10.3390/ijms17050759] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/02/2016] [Accepted: 05/12/2016] [Indexed: 01/02/2023] Open
Abstract
Breast cancer persists as the most common cause of cancer death in women worldwide. Ovarian cancer is also a significant source of morbidity and mortality, as the fifth leading cause of cancer death among women. This reflects the continued need for further understanding and innovation in cancer treatment. Though breast and ovarian cancer usually present as distinct clinical entities, the recent explosion of large-scale -omics research has uncovered many overlaps, particularly with respect to genetic and epigenetic alterations. We compared genetic, microenvironmental, stromal, and epigenetic changes common between breast and ovarian cancer cells, as well as the clinical relevance of these changes. Some of the most striking commonalities include genetic alterations of BRCA1 and 2, TP53, RB1, NF1, FAT3, MYC, PTEN, and PIK3CA; down regulation of miRNAs 9, 100, 125a, 125b, and 214; and epigenetic alterations such as H3K27me3, H3K9me2, H3K9me3, H4K20me3, and H3K4me. These parallels suggest shared features of pathogenesis. Furthermore, preliminary evidence suggests a shared epigenetic mechanism of oncogenesis. These similarities, warrant further investigation in order to ultimately inform development of more effective chemotherapeutics, as well as strategies to circumvent drug resistance.
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Affiliation(s)
| | - Nicole A Snyder
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Genevieve Housman
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA.
| | - Meghan Leary
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Karolina Lapinska
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Sarah Heerboth
- School of Medicine, Vanderbilt University, Nashville, TN 37240, USA.
| | - Amber Willbanks
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Sibaji Sarkar
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
- Genome Science Institute, Boston University School of Medicine, Boston, MA 02118, USA.
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17
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Guerrero-Bosagna C, Jensen P. Optimized method for methylated DNA immuno-precipitation. MethodsX 2015; 2:432-9. [PMID: 26740923 PMCID: PMC4678308 DOI: 10.1016/j.mex.2015.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/14/2015] [Indexed: 11/04/2022] Open
Abstract
Methylated DNA immunoprecipitation (MeDIP) is one of the most widely used methods to evaluate DNA methylation on a whole genome scale, and involves the capture of the methylated fraction of the DNA by an antibody specific to methyl-cytosine. MeDIP was initially coupled with microarray hybridization to detect local DNA methylation enrichments along the genome. More recently, MeDIP has been coupled with next generation sequencing, which highlights its current and future applicability. In previous studies in which MeDIP was applied, the protocol took around 3 days to be performed. Given the importance of MeDIP for studies involving DNA methylation, it was important to optimize the method in order to deliver faster turnouts. The present article describes optimization steps of the MeDIP method. The length of the procedure was reduced in half without compromising the quality of the results. This was achieved by:Reduction of the number of washes in different stages of the protocol, after a careful evaluation of the number of indispensable washes. Reduction of reaction times for detaching methylated DNA fragments from the complex agarose beads:antibody. Modification of the methods to purify methylated DNA, which incorporates new devices and procedures, and eliminates a lengthy phenol and chloroform:isoamyl alcohol extraction.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Avian Behavioral Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 58 183, Sweden
| | - Per Jensen
- Avian Behavioral Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 58 183, Sweden
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18
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Lai J, Nie W, Zhang W, Wang Y, Xie R, Wang Y, Gu J, Xu J, Song W, Yang F, Huang G, Cao P, Guan X. Transcriptional regulation of the p73 gene by Nrf-2 and promoter CpG methylation in human breast cancer. Oncotarget 2015; 5:6909-22. [PMID: 25071010 PMCID: PMC4196172 DOI: 10.18632/oncotarget.2230] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
To understand the transcriptional regulation of p73 by promoter methylation and Nrf-2 in breast carcinogenesis, ChIP assay indicated that Nrf-2 can bind to both promoters and can activate the transcription of TAp73 and ΔΝp73 in MCF-7 cell line, knockdown of Nrf-2 gene resulted in an abrogation of TAp73 and ΔΝp73 expression in the cells transfected with sh-Nrf-2 as well as Nrf-2 knock out mouse model. However, we found Nrf-2 induced ΔΝp73 expression was abolished with 5-aza-dC treatment, thus lead to a down-regulated ΔΝp73 and an up-regulated TAp73 expression in breast cancer cells lines. Consistent with this model, we detected decreased TAp73 and increased ΔNp73 expression in breast cancer tissue, along with increased TAp73 but decreased ΔNp73 expression in corresponding surrounding noncancerous tissues (NCTs) in a breast cancer tissue assay. A significant inverse correlation was found between TAp73 and ΔNp73 expression in the above tissue-array (P = 0.047) and validated in another set consisting of 128 breast cancer tumor tissue (P = 0.034). Taken together, our findings suggest that Nrf-2 and promoter methylation cooperatively govern the transcriptional regulation of p73, and unbalanced expression of TAp73 and ΔNp73 expression plays a critical role in breast cancer development.
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Affiliation(s)
- Jing Lai
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Southern Medical University, Guangzhou, China; These authors contributed equally to this work
| | - Weiwei Nie
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Southern Medical University, Guangzhou, China; These authors contributed equally to this work
| | - Wenwen Zhang
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, China; These authors contributed equally to this work
| | - Yucai Wang
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Ruilian Xie
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Southern Medical University, Guangzhou, China
| | - Yanru Wang
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Southern Medical University, Guangzhou, China
| | - Jun Gu
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jing Xu
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Wei Song
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Southern Medical University, Guangzhou, China
| | - Fang Yang
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Guichun Huang
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Peng Cao
- Laboratory of Cellular and Molecular Biology, Jiangsu Province Institute of Chinese Medicine, Nanjing, China
| | - Xiaoxiang Guan
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Southern Medical University, Guangzhou, China; Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
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19
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Zhao H, Cai W, Su S, Zhi D, Lu J, Liu S. Screening genes crucial for pediatric pilocytic astrocytoma using weighted gene coexpression network analysis combined with methylation data analysis. Cancer Gene Ther 2014; 21:448-55. [PMID: 25257306 DOI: 10.1038/cgt.2014.49] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/18/2014] [Accepted: 08/19/2014] [Indexed: 12/25/2022]
Abstract
To identify novel genes associated with pediatric pilocytic astrocytoma (PA) for better understanding the molecular mechanism underlying the pediatric PA pathogenesis. Gene expression profile data of GSE50161 and GSE44971 and the methylation data of GSE44684 were downloaded from Gene Expression Omnibus. The differentially expressed genes (DEGs) between PA and normal control samples were screened using the limma package in R, and then used to construct weighted gene coexpression network (WGCN) using the WGCN analysis (WGCNA) package in R. Significant modules of DEGs were selected using the clustering analysis. Function enrichment analysis of the DEGs in significant modules were performed using the WGCNA package and clusterprofiler package in R. Correlation between methylation sites of DEGs and PA was analyzed using the CpGassoc package in R. Totally, 3479 DEGs were screened in PA samples. Thereinto, 3424 DEGs were used to construct the WGCN. Several significant modules of DEGs were selected based on the WGCN, in which the turquoise module was positively related to PA, whereas blue module was negatively related to PA. DEGs (for example, DOCK2 (dedicator of cytokinesis 2), DOCK8 and FCGR2A (Fc fragment of IgG, low affinity IIa)) in blue module were mainly involved in Fc gamma R-mediated phagocytosis pathway and natural killer cell-mediated cytotoxicity pathway. Methylations of 14 DEGs among the top 30 genes in blue module were related to PA. Our data suggest that DOCK2, DOCK8 and FCGR2A may represent potential therapeutic targets in PA that merits further investigation.
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Affiliation(s)
- H Zhao
- Department of Neurosurgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - W Cai
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, China
| | - S Su
- Department of Neurosurgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - D Zhi
- Department of Neurosurgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - J Lu
- Department of Neurosurgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - S Liu
- Department of Neurosurgery, Shengjing Hospital, China Medical University, Shenyang, China
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20
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Wang F, Yang Y, Fu Z, Xu N, Chen F, Yin H, Lu X, Shen R, Lu C. Differential DNA methylation status between breast carcinomatous and normal tissues. Biomed Pharmacother 2014; 68:699-707. [PMID: 25070394 DOI: 10.1016/j.biopha.2014.07.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 07/08/2014] [Indexed: 12/31/2022] Open
Abstract
Breast cancer has been considered to be a multifactorial disease with a wide array of well-characterized gene mutations and chromosomal abnormalities. However, it is becoming evident that the onset or development of breast cancer also depends on epigenetic factors, although the mechanisms have not been fully elucidated. We performed a genome-wide analysis of DNA methylation of breast carcinomatous tissues and paired normal tissues to examine the differences in methylation between them. Methylation-specific polymerase chain reaction (MSP) was used to validate the hypermethylated genes screened out by DNA methylation microarray. We found that hypomethylation and hypermethylation occurred in 2753 and 1795 genes, respectively, in breast carcinomatous tissues. Meanwhile, gene ontology analysis and ingenuity pathway analysis revealed the function and pathway of several genes whose methylation status was altered in breast carcinomatous tissues. In addition, we investigated the promoter methylation status of four genes in breast carcinomatous tissue and paired normal tissues (n=30) by MSP. Promoter hypermethylation of CRABP1, HOXB13, IFNGR2, and PIK3C3 was found in 37% (11/30), 23% (7/30), 17% (5/30), and 2% (2/30) of the carcinomas, respectively. Mutation of these four important genes was critical to many types of cancer. Our results suggest that DNA methylation mechanisms may be involved in regulating the occurrence and development of breast cancer.
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Affiliation(s)
- Fengliang Wang
- Department of Breast Surgery, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, China
| | - Yafang Yang
- Department of Radiology, the Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Ziyi Fu
- Department of Breast Surgery, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, China
| | - Nan Xu
- First Clinical Medicine College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Fei Chen
- Department of Breast Surgery, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, China
| | - Hong Yin
- Department of Breast Surgery, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, China
| | - Xun Lu
- Jinling High School, Nanjing, China
| | - Rong Shen
- Department of Breast Surgery, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, China
| | - Cheng Lu
- Department of Breast Surgery, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, China.
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21
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Tania M, Khan MA, Fu J. Epithelial to mesenchymal transition inducing transcription factors and metastatic cancer. Tumour Biol 2014; 35:7335-42. [PMID: 24880591 DOI: 10.1007/s13277-014-2163-y] [Citation(s) in RCA: 203] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 05/27/2014] [Indexed: 12/14/2022] Open
Abstract
The epithelial to mesenchymal transition (EMT) is an important step for the developmental process. Recent evidences support that EMT allows the tumor cells to acquire invasive properties and to develop metastatic growth characteristics. Some of the transcription factors, which are actively involved in EMT process, have a significant role in the EMT-metastasis linkage. A number of studies have reported that EMT-inducing transcription factors (EMT-TFs), such as Twist, Snail, Slug, and Zeb, are directly or indirectly involved in cancer cell metastasis through a different signaling cascades, including the Akt, signal transducer and activator of transcription 3 (STAT3), mitogen-activated protein kinase (MAPK) and Wnt pathways, with the ultimate consequence of the downregulation of E-cadherin and upregulation of metastatic proteins, such as N-cadherin, vimentin, matrix metalloproteinase (MMP)-2, etc. This review summarizes the update information on the association of EMT-TFs with cancer metastasis and the possible cancer therapeutics via targeting the EMT-TFs.
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Affiliation(s)
- Mousumi Tania
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Luzhou Medical College, Luzhou, 646000, Sichuan, China,
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22
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Marsan M, Van den Eynden G, Limame R, Neven P, Hauspy J, Van Dam PA, Vergote I, Dirix LY, Vermeulen PB, Van Laere SJ. A core invasiveness gene signature reflects epithelial-to-mesenchymal transition but not metastatic potential in breast cancer cell lines and tissue samples. PLoS One 2014; 9:e89262. [PMID: 24586640 PMCID: PMC3931724 DOI: 10.1371/journal.pone.0089262] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 01/15/2014] [Indexed: 01/07/2023] Open
Abstract
Introduction Metastases remain the primary cause of cancer-related death. The acquisition of invasive tumour cell behaviour is thought to be a cornerstone of the metastatic cascade. Therefore, gene signatures related to invasiveness could aid in stratifying patients according to their prognostic profile. In the present study we aimed at identifying an invasiveness gene signature and investigated its biological relevance in breast cancer. Methods & Results We collected a set of published gene signatures related to cell motility and invasion. Using this collection, we identified 16 genes that were represented at a higher frequency than observed by coincidence, hereafter named the core invasiveness gene signature. Principal component analysis showed that these overrepresented genes were able to segregate invasive and non-invasive breast cancer cell lines, outperforming sets of 16 randomly selected genes (all P<0.001). When applied onto additional data sets, the expression of the core invasiveness gene signature was significantly elevated in cell lines forced to undergo epithelial-mesenchymal transition. The link between core invasiveness gene expression and epithelial-mesenchymal transition was also confirmed in a dataset consisting of 2420 human breast cancer samples. Univariate and multivariate Cox regression analysis demonstrated that CIG expression is not associated with a shorter distant metastasis free survival interval (HR = 0.956, 95%C.I. = 0.896–1.019, P = 0.186). Discussion These data demonstrate that we have identified a set of core invasiveness genes, the expression of which is associated with epithelial-mesenchymal transition in breast cancer cell lines and in human tissue samples. Despite the connection between epithelial-mesenchymal transition and invasive tumour cell behaviour, we were unable to demonstrate a link between the core invasiveness gene signature and enhanced metastatic potential.
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Affiliation(s)
- Melike Marsan
- Translational Cancer Research Unit, Oncology Center, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
- Department of oncology, KU Leuven, Leuven, Belgium
- * E-mail:
| | - Gert Van den Eynden
- Translational Cancer Research Unit, Oncology Center, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Ridha Limame
- Laboratory for Cancer Research and Clinical Oncology, University of Antwerp, Antwerp, Belgium
| | | | - Jan Hauspy
- Translational Cancer Research Unit, Oncology Center, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | | | | | - Luc Y. Dirix
- Translational Cancer Research Unit, Oncology Center, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Peter B. Vermeulen
- Translational Cancer Research Unit, Oncology Center, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Steven J. Van Laere
- Translational Cancer Research Unit, Oncology Center, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
- Department of oncology, KU Leuven, Leuven, Belgium
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23
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Brglez V, Pucer A, Pungerčar J, Lambeau G, Petan T. Secreted phospholipases A₂are differentially expressed and epigenetically silenced in human breast cancer cells. Biochem Biophys Res Commun 2014; 445:230-5. [PMID: 24508801 DOI: 10.1016/j.bbrc.2014.01.182] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 01/29/2014] [Indexed: 02/06/2023]
Abstract
Secreted phospholipases A2 (sPLA2s) have recently been associated with several cancers, but their role in breast cancer is unknown. Here we demonstrate that mRNA expression of group IIA, III and X sPLA2s differs both in vivo in tumour biopsies and in breast cancer cells in vitro. Their expression is differentially regulated by DNA methylation and histone acetylation and, significantly, all three genes are silenced in aggressive triple negative cells due to both mechanisms. The transcription start site promoter region and the upstream CpG islands, exclusive to the group X sPLA2 gene, have variable roles in the regulation of sPLA2 expression. Our results suggest that the differential expression of hGIIA, hGIII and hGX sPLA2s in breast cancer cells is a consequence of various degrees of epigenetic silencing due to DNA hypermethylation and histone deacetylation.
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Affiliation(s)
- Vesna Brglez
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Anja Pucer
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Jože Pungerčar
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Gérard Lambeau
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS et Université de Nice Sophia Antipolis, UMR 6097, Sophia Antipolis, Valbonne, France
| | - Toni Petan
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia.
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24
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Tamagawa S, Beder LB, Hotomi M, Gunduz M, Yata K, Grenman R, Yamanaka N. Role of miR-200c/miR-141 in the regulation of epithelial-mesenchymal transition and migration in head and neck squamous cell carcinoma. Int J Mol Med 2014; 33:879-86. [PMID: 24424572 DOI: 10.3892/ijmm.2014.1625] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 12/17/2013] [Indexed: 11/06/2022] Open
Abstract
Epithelial-mesenchymal-transition (EMT) is a critical step in tumor invasion and metastasis, while its fate is mainly defined by the balanced expression between the miR-200 family and ZEB transcription factors. In this study, we observed a reciprocal correlation between miR-200c/mir-141 and ZEB1, as well as between ZEB2 and E-cadherin expression in a panel of 13 head and neck squamous cell carcinoma (HNSCC) cell lines. We also confirmed that the enforced expression of miR-200c and miR-141 significantly reduced the migration capacity of HNSCC cells. Accordingly, the enforced expression of miR-200c and mir-141 resulted in a significant upregulation in E-cadherin expression, contrary to the significant downregulation in ZEB1 expression in 3 cell lines (UTSCC-24A, UTSCC-24B and UTSCC-6A cells). Another pair of cell lines, UTSCC-60A and UTSCC‑ 60B failed to show a significant change in the expression of E-cadherin or ZEB1/ZEB2 during the enforced expression of miR-200c/miR-141. To address the issue, we focused on the hypermethylation status of the ZEB1/2 promoters, which have both been shown to include wide CpG islands. We observed a marked upregulation in both ZEB1 and ZEB2 mRNA expression following treatment with a demethylating agent in both pairs of UTSCC cell lines. In conclusion, our findings confirm the existence of a reciprocal correlation between the mir-200 family and the ZEB family, and demonstrate the role of the miR-200 family in EMT, as well as in the migration and invasion ability of HNSCC cells. Furthermore, our data suggest that the promoter hypermethylation of ZEB1 and ZEB2 may play an essential role and may overshadow the effects of the miR-200 family in the regulation of EMT during carcinogenesis.
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Affiliation(s)
- Shunji Tamagawa
- Department of Otolaryngology - Head and Neck Surgery, Wakayama Medical University, Wakayama, Japan
| | - Levent Bekir Beder
- Department of Otolaryngology - Head and Neck Surgery, Wakayama Medical University, Wakayama, Japan
| | - Muneki Hotomi
- Department of Otolaryngology - Head and Neck Surgery, Wakayama Medical University, Wakayama, Japan
| | - Mehmet Gunduz
- Department of Otolaryngology, Turgut Ozal University, Faculty of Medicine, Ankara, Turkey
| | - Kazuya Yata
- Department of Otolaryngology - Head and Neck Surgery, Wakayama Medical University, Wakayama, Japan
| | - Reidar Grenman
- Department of Otorhinolaryngology - Head and Neck Surgery, Turku University Central Hospital, Turku, Finland
| | - Noboru Yamanaka
- Department of Otolaryngology - Head and Neck Surgery, Wakayama Medical University, Wakayama, Japan
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The RON receptor tyrosine kinase promotes metastasis by triggering MBD4-dependent DNA methylation reprogramming. Cell Rep 2014; 6:141-54. [PMID: 24388747 PMCID: PMC5312658 DOI: 10.1016/j.celrep.2013.12.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/25/2013] [Accepted: 12/04/2013] [Indexed: 12/14/2022] Open
Abstract
Metastasis is the major cause of death in cancer patients, yet the genetic and epigenetic programs that drive metastasis are poorly understood. Here, we report an epigenetic reprogramming pathway that is required for breast cancer metastasis. Concerted differential DNA methylation is initiated by the activation of the RON receptor tyrosine kinase by its ligand, macrophage stimulating protein (MSP). Through PI3K signaling, RON/MSP promotes expression of the G:T mismatch-specific thymine glycosylase MBD4. RON/MSP and MBD4-dependent aberrant DNA methylation results in the misregulation of a specific set of genes. Knockdown of MBD4 reverses methylation at these specific loci and blocks metastasis. We also show that the MBD4 glycosylase catalytic residue is required for RON/MSP-driven metastasis. Analysis of human breast cancers revealed that this epigenetic program is significantly associated with poor clinical outcome. Furthermore, inhibition of Ron kinase activity with a pharmacological agent blocks metastasis of patient-derived breast tumor grafts in vivo.
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Stewart PA, Luks J, Roycik MD, Sang QXA, Zhang J. Differentially expressed transcripts and dysregulated signaling pathways and networks in African American breast cancer. PLoS One 2013; 8:e82460. [PMID: 24324792 PMCID: PMC3853650 DOI: 10.1371/journal.pone.0082460] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 10/23/2013] [Indexed: 12/24/2022] Open
Abstract
African Americans (AAs) have higher mortality rate from breast cancer than that of Caucasian Americans (CAs) even when socioeconomic factors are accounted for. To better understand the driving biological factors of this health disparity, we performed a comprehensive differential gene expression analysis, including subtype- and stage-specific analysis, using the breast cancer data in the Cancer Genome Atlas (TCGA). In total, 674 unique genes and other transcripts were found differentially expressed between these two populations. The numbers of differentially expressed genes between AA and CA patients increased in each stage of tumor progression: there were 26 in stage I, 161 in stage II, and 223 in stage III. Resistin, a gene that is linked to obesity, insulin resistance, and breast cancer, was expressed more than four times higher in AA tumors. An uncharacterized, long, non-coding RNA, LOC90784, was down-regulated in AA tumors, and its expression was inversely related to cancer stage and was the lowest in triple negative AA breast tumors. Network analysis showed increased expression of a majority of components in p53 and BRCA1 subnetworks in AA breast tumor samples, and members of the aurora B and polo-like kinase signaling pathways were also highly expressed. Higher gene expression diversity was observed in more advanced stage breast tumors suggesting increased genomic instability during tumor progression. Amplified resistin expression may indicate insulin-resistant type II diabetes and obesity are associated with AA breast cancer. Expression of LOC90784 may have a protective effect on breast cancer patients, and its loss, particularly in triple negative breast cancer, could be having detrimental effects. This work helps elucidate molecular mechanisms of breast cancer health disparity and identifies putative biomarkers and therapeutic targets such as resistin, and the aurora B and polo-like kinase signaling pathways for treating AA breast cancer patients.
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Affiliation(s)
- Paul A. Stewart
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, United States of America
| | - Jennifer Luks
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, United States of America
| | - Mark D. Roycik
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, United States of America
| | - Qing-Xiang Amy Sang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, United States of America
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, United States of America
- * E-mail: (QXS); (JZ)
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, Florida, United States of America
- * E-mail: (QXS); (JZ)
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Diede SJ, Yao Z, Keyes CC, Tyler AE, Dey J, Hackett CS, Elsaesser K, Kemp CJ, Neiman PE, Weiss WA, Olson JM, Tapscott SJ. Fundamental differences in promoter CpG island DNA hypermethylation between human cancer and genetically engineered mouse models of cancer. Epigenetics 2013; 8:1254-60. [PMID: 24107773 DOI: 10.4161/epi.26486] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Genetic and epigenetic alterations are essential for the initiation and progression of human cancer. We previously reported that primary human medulloblastomas showed extensive cancer-specific CpG island DNA hypermethylation in critical developmental pathways. To determine whether genetically engineered mouse models (GEMMs) of medulloblastoma have comparable epigenetic changes, we assessed genome-wide DNA methylation in three mouse models of medulloblastoma. In contrast to human samples, very few loci with cancer-specific DNA hypermethylation were detected, and in almost all cases the degree of methylation was relatively modest compared with the dense hypermethylation in the human cancers. To determine if this finding was common to other GEMMs, we examined a Burkitt lymphoma and breast cancer model and did not detect promoter CpG island DNA hypermethylation, suggesting that human cancers and at least some GEMMs are fundamentally different with respect to this epigenetic modification. These findings provide an opportunity to both better understand the mechanism of aberrant DNA methylation in human cancer and construct better GEMMs to serve as preclinical platforms for therapy development.
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Affiliation(s)
- Scott J Diede
- Division of Clinical Research; Fred Hutchinson Cancer Research Center; Seattle, WA USA; Department of Pediatrics; University of Washington School of Medicine; Seattle, WA USA
| | - Zizhen Yao
- Division of Human Biology; Fred Hutchinson Cancer Research Center; Seattle, WA USA
| | - C Chip Keyes
- Division of Human Biology; Fred Hutchinson Cancer Research Center; Seattle, WA USA
| | - Ashlee E Tyler
- Division of Human Biology; Fred Hutchinson Cancer Research Center; Seattle, WA USA
| | - Joyoti Dey
- Division of Clinical Research; Fred Hutchinson Cancer Research Center; Seattle, WA USA
| | - Christopher S Hackett
- Department of Neurological Surgery; University of California at San Francisco; San Francisco, CA USA; Department of Neurology; University of California at San Francisco; San Francisco, CA USA; Department of Pediatrics; University of California at San Francisco; San Francisco, CA USA
| | - Katrina Elsaesser
- Division of Basic Sciences; Fred Hutchinson Cancer Research Center; Seattle, WA USA
| | - Christopher J Kemp
- Division of Basic Sciences; Fred Hutchinson Cancer Research Center; Seattle, WA USA; Division of Public Health Sciences; Fred Hutchinson Cancer Research Center; Seattle, WA USA
| | - Paul E Neiman
- Division of Basic Sciences; Fred Hutchinson Cancer Research Center; Seattle, WA USA; Department of Medicine; University of Washington School of Medicine; Seattle, WA USA
| | - William A Weiss
- Department of Neurological Surgery; University of California at San Francisco; San Francisco, CA USA; Department of Neurology; University of California at San Francisco; San Francisco, CA USA; Department of Pediatrics; University of California at San Francisco; San Francisco, CA USA
| | - James M Olson
- Division of Clinical Research; Fred Hutchinson Cancer Research Center; Seattle, WA USA; Department of Pediatrics; University of Washington School of Medicine; Seattle, WA USA
| | - Stephen J Tapscott
- Division of Clinical Research; Fred Hutchinson Cancer Research Center; Seattle, WA USA; Division of Human Biology; Fred Hutchinson Cancer Research Center; Seattle, WA USA; Department of Neurology; University of Washington School of Medicine; Seattle, WA USA
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Kumar R, Sharma A, Tiwari RK. Application of microarray in breast cancer: An overview. J Pharm Bioallied Sci 2013; 4:21-6. [PMID: 22368395 PMCID: PMC3283953 DOI: 10.4103/0975-7406.92726] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 09/06/2011] [Accepted: 09/17/2011] [Indexed: 01/07/2023] Open
Abstract
There are more than 1.15 million cases of breast cancer diagnosed worldwide annually. At present, only small numbers of accurate prognostic and predictive factors are used clinically for managing the patients with breast cancer. DNA microarrays have the potential to assess the expression of thousands of genes simultaneously. Recent preliminary researches indicate that gene expression profiling based on DNA microarray can offer potential and independent prognostic information in patients with newly diagnosed breast cancer. In this paper, an overview upon the applications of microarray techniques in breast cancer is presented.
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Affiliation(s)
- Rajnish Kumar
- Amity Institute of Biotechnology (AIB), Amity University Uttar Pradesh (AUUP), Lucknow, Uttar Pradesh, India
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Bollig-Fischer A, Michelhaugh S, Ali-Fehmi R, Mittal S. The molecular genomics of metastatic brain tumours. ACTA ACUST UNITED AC 2013; 1. [PMID: 25400938 DOI: 10.13172/2052-9635-1-1-759] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Metastatic brain tumours remain an intractable clinical problem despite notable advances in the treatment of the primary cancers. It is estimated that 30-40% of breast and lung cancer patients will develop brain metastases. Typically, brain lesions are not diagnosed until patients exhibit neurological symptoms because there are currently no tests that can predict which patients will be afflicted. Brain metastases are resistant to current chemotherapies, and despite surgical resection and radiotherapy, the prognosis for these patients remains very poor with an average survival of only 6-9 months. Cancer is ultimately a genetic disease, involving patient genetics and aberrant tumour genomics; therefore the pursuit of an explanation for why or how brain metastases occur requires investigation of the associated somatic mutations. In this article, we review the current literature surrounding the molecular and genome-based mechanistic evidence to indicate driver oncogenes that hold potential biomarkers for risk, or therapeutic targets for treatment of brain metastases. CONCLUSION Patients afflicted with metastatic brain tumours are in dire need of more effective therapies, and clinicians need predictive laboratory tests to identify patients at risk of developing metastatic brain tumours. The as yet unrealized comprehensive analysis of metastatic brain tumour genomics is necessary to meet these needs. Moreover, without improved understanding of the genomic aberrations that drive metastatic brain tumours, development of biomarkers and molecularly targeted therapies will remain stalled and patient outcomes will continue to be dismal.
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Affiliation(s)
- A Bollig-Fischer
- Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA ; Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sk Michelhaugh
- Department of Neurosurgery, Wayne State University School of Medicine, Detroit, MI, USA
| | - R Ali-Fehmi
- Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA ; Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA
| | - S Mittal
- Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA ; Department of Neurosurgery, Wayne State University School of Medicine, Detroit, MI, USA
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Chimonidou M, Tzitzira A, Strati A, Sotiropoulou G, Sfikas C, Malamos N, Georgoulias V, Lianidou E. CST6 promoter methylation in circulating cell-free DNA of breast cancer patients. Clin Biochem 2013; 46:235-40. [DOI: 10.1016/j.clinbiochem.2012.09.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 09/12/2012] [Accepted: 09/13/2012] [Indexed: 02/06/2023]
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Gene-expression profiling to identify genes related to spontaneous tumor regression in a canine cancer model. Vet Immunol Immunopathol 2013; 151:207-16. [DOI: 10.1016/j.vetimm.2012.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 11/15/2012] [Accepted: 11/15/2012] [Indexed: 02/07/2023]
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Smad interacting protein 1 (SIP1) is associated with peritoneal carcinomatosis in intestinal type gastric cancer. Clin Exp Metastasis 2012; 30:417-29. [PMID: 23143680 DOI: 10.1007/s10585-012-9547-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 10/26/2012] [Indexed: 12/13/2022]
Abstract
Smad interacting protein 1 (SIP1) is an epithelial-mesenchymal transition (EMT)-inducible gene that plays a key role in tumor progression in various cancers. This study seeks to clarify the clinical and biological significance of SIP1 expression, especially in intestinal type gastric cancer. We analyzed the mRNA levels of SIP1 and other EMT regulators by real-time reverse transcription PCR in gastric tissue samples of 134 gastric cancer patients, and in five gastric cancer cell lines. SIP1 gene knockdown by siRNA transfection was performed to evaluate SIP1 function in gastric cancer cells. Expression of the SIP1 gene was significantly higher in cancerous tissue than in adjacent normal mucosa. Although the mRNA expression of the other EMT regulators tested (Snail, Slug, and Twist) was not correlated with clinicopathological factors, increased SIP1 expression was an independent prognostic factor and an independent risk factor for peritoneal dissemination. In addition, SIP1 expression was significantly positive and correlated with vimentin expression. For intestinal type gastric cancer in particular, elevated SIP1 expression was significantly correlated with peritoneal dissemination and poor prognosis (p < 0.05). In vitro, cell proliferation, migration, invasion, and resistance to anoikis were significantly inhibited in SIP1 siRNA-transfected MKN7 cells compared to control siRNA. SIP1 appears to play an important role in progression to peritoneal carcinomatosis and may be a therapeutic target for patients with intestinal type gastric cancer.
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Dimitrakopoulos L, Vorkas PA, Georgoulias V, Lianidou ES. A closed-tube methylation-sensitive high resolution melting assay (MS-HRMA) for the semi-quantitative determination of CST6 promoter methylation in clinical samples. BMC Cancer 2012; 12:486. [PMID: 23088560 PMCID: PMC3495665 DOI: 10.1186/1471-2407-12-486] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 09/23/2012] [Indexed: 12/12/2022] Open
Abstract
Background CST6 promoter is highly methylated in cancer, and its detection can provide important prognostic information in breast cancer patients. The aim of our study was to develop a Methylation-Sensitive High Resolution Melting Analysis (MS-HRMA) assay for the investigation of CST6 promoter methylation. Methods We designed primers that amplify both methylated and unmethylated CST6 sequences after sodium bisulfate (SB) treatment and used spiked control samples of fully methylated to unmethylated SB converted genomic DNA to optimize the assay. We first evaluated the assay by analyzing 36 samples (pilot training group) and further analyzed 80 FFPES from operable breast cancer patients (independent group). MS-HRMA assay results for all 116 samples were compared with Methylation-Specific PCR (MSP) and the results were comparable. Results The developed assay is highly specific and sensitive since it can detect the presence of 1% methylated CST6 sequence and provides additionally a semi-quantitative estimation of CST6 promoter methylation. CST6 promoter was methylated in 39/80 (48.75%) of FFPEs with methylation levels being very different among samples. MS-HRMA and MSP gave comparable results when all samples were analyzed by both assays. Conclusions The developed MS-HRMA assay for CST6 promoter methylation is closed tube, highly sensitive, cost-effective, rapid and easy-to-perform. It gives comparable results to MSP in less time, while it offers the advantage of additionally providing an estimation of the level of methylation.
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Affiliation(s)
- Lampros Dimitrakopoulos
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, 15771, Greece
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Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression. Genome Res 2012; 22:1197-211. [PMID: 22613842 PMCID: PMC3396362 DOI: 10.1101/gr.132662.111] [Citation(s) in RCA: 394] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Lung cancer is the leading cause of cancer death worldwide, and adenocarcinoma is its most common histological subtype. Clinical and molecular evidence indicates that lung adenocarcinoma is a heterogeneous disease, which has important implications for treatment. Here we performed genome-scale DNA methylation profiling using the Illumina Infinium HumanMethylation27 platform on 59 matched lung adenocarcinoma/non-tumor lung pairs, with genome-scale verification on an independent set of tissues. We identified 766 genes showing altered DNA methylation between tumors and non-tumor lung. By integrating DNA methylation and mRNA expression data, we identified 164 hypermethylated genes showing concurrent down-regulation, and 57 hypomethylated genes showing increased expression. Integrated pathways analysis indicates that these genes are involved in cell differentiation, epithelial to mesenchymal transition, RAS and WNT signaling pathways, and cell cycle regulation, among others. Comparison of DNA methylation profiles between lung adenocarcinomas of current and never-smokers showed modest differences, identifying only LGALS4 as significantly hypermethylated and down-regulated in smokers. LGALS4, encoding a galactoside-binding protein involved in cell–cell and cell–matrix interactions, was recently shown to be a tumor suppressor in colorectal cancer. Unsupervised analysis of the DNA methylation data identified two tumor subgroups, one of which showed increased DNA methylation and was significantly associated with KRAS mutation and to a lesser extent, with smoking. Our analysis lays the groundwork for further molecular studies of lung adenocarcinoma by identifying novel epigenetically deregulated genes potentially involved in lung adenocarcinoma development/progression, and by describing an epigenetic subgroup of lung adenocarcinoma associated with characteristic molecular alterations.
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Majumder M, Tutunea-Fatan E, Xin X, Rodriguez-Torres M, Torres-Garcia J, Wiebe R, Timoshenko AV, Bhattacharjee RN, Chambers AF, Lala PK. Co-expression of α9β1 integrin and VEGF-D confers lymphatic metastatic ability to a human breast cancer cell line MDA-MB-468LN. PLoS One 2012; 7:e35094. [PMID: 22545097 PMCID: PMC3335831 DOI: 10.1371/journal.pone.0035094] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 03/12/2012] [Indexed: 01/26/2023] Open
Abstract
Introduction and Objectives Lymphatic metastasis is a common occurrence in human breast cancer, mechanisms remaining poorly understood. MDA-MB-468LN (468LN), a variant of the MDA-MB-468GFP (468GFP) human breast cancer cell line, produces extensive lymphatic metastasis in nude mice. 468LN cells differentially express α9β1 integrin, a receptor for lymphangiogenic factors VEGF-C/-D. We explored whether (1) differential production of VEGF-C/-D by 468LN cells provides an autocrine stimulus for cellular motility by interacting with α9β1 and a paracrine stimulus for lymphangiogenesis in vitro as measured with capillary-like tube formation by human lymphatic endothelial cells (HMVEC-dLy); (2) differential expression of α9 also promotes cellular motility/invasiveness by interacting with macrophage derived factors; (3) stable knock-down of VEGF-D or α9 in 468LN cells abrogates lymphangiogenesis and lymphatic metastasis in vivo in nude mice. Results A comparison of expression of cyclo-oxygenase (COX)-2 (a VEGF-C/-D inducer), VEGF-C/-D and their receptors revealed little COX-2 expression by either cells. However, 468LN cells showed differential VEGF-D and α9β1 expression, VEGF-D secretion, proliferative, migratory/invasive capacities, latter functions being stimulated further with VEGF-D. The requirement of α9β1 for native and VEGF-D-stimulated proliferation, migration and Erk activation was demonstrated by treating with α9β1 blocking antibody or knock-down of α9. An autocrine role of VEGF-D in migration was shown by its impairment by silencing VEGF-D and restoration with VEGF-D. 468LN cells and their soluble products stimulated tube formation, migration/invasiveness of HMVEC-dLy cell in a VEGF-D dependent manner as indicated by the loss of stimulation by silencing VEGF-D in 468LN cells. Furthermore, 468LN cells showed α9-dependent stimulation of migration/invasiveness by macrophage products. Finally, capacity for intra-tumoral lymphangiogenesis and lymphatic metastasis in nude mice was completely abrogated by stable knock-down of either VEGF-D or α9 in 468LN cells. Conclusion Differential capacity for VEGF-D production and α9β1 integrin expression by 468LN cells jointly contributed to their lymphatic metastatic phenotype.
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Affiliation(s)
- Mousumi Majumder
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, Canada
| | - Elena Tutunea-Fatan
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, Canada
| | - Xiping Xin
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, Canada
| | | | - Jose Torres-Garcia
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, Canada
| | - Ryan Wiebe
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, Canada
| | - Alexander V. Timoshenko
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, Canada
- Department of Biology, The University of Western Ontario, London, Ontario, Canada
| | | | - Ann F. Chambers
- Department of Medical Biophysics, The University of Western Ontario, London, Ontario, Canada
- Department of Oncology, The University of Western Ontario, London, Ontario, Canada
| | - Peeyush K. Lala
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, Canada
- Department of Oncology, The University of Western Ontario, London, Ontario, Canada
- * E-mail:
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Abstract
DNA hypomethylation was the initial epigenetic abnormality recognized in human tumors. However, for several decades after its independent discovery by two laboratories in 1983, it was often ignored as an unwelcome complication, with almost all of the attention on the hypermethylation of promoters of genes that are silenced in cancers (e.g., tumor-suppressor genes). Because it was subsequently shown that global hypomethylation of DNA in cancer was most closely associated with repeated DNA elements, cancer linked-DNA hypomethylation continued to receive rather little attention. DNA hypomethylation in cancer can no longer be considered an oddity, because recent high-resolution genome-wide studies confirm that DNA hypomethylation is the almost constant companion to hypermethylation of the genome in cancer, just usually (but not always) in different sequences. Methylation changes at individual CpG dyads in cancer can have a high degree of dependence not only on the regional context, but also on neighboring sites. DNA demethylation during carcinogenesis may involve hemimethylated dyads as intermediates, followed by spreading of the loss of methylation on both strands. In this review, active demethylation of DNA and the relationship of cancer-associated DNA hypomethylation to cancer stem cells are discussed. Evidence is accumulating for the biological significance and clinical relevance of DNA hypomethylation in cancer, and for cancer-linked demethylation and de novo methylation being highly dynamic processes.
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Affiliation(s)
- Melanie Ehrlich
- Hayward Genetics Program, Department of Biochemistry, Tulane Cancer Center, Tulane Medical School, 1430 TulaneAvenue, New Orleans, LA 70112, USA.
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Kim JH, Kang S, Kim TW, Yin L, Liu R, Kim SJ. Expression profiling after induction of demethylation in MCF-7 breast cancer cells identifies involvement of TNF-α mediated cancer pathways. Mol Cells 2012; 33:127-33. [PMID: 22228181 PMCID: PMC3887717 DOI: 10.1007/s10059-012-2182-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/18/2011] [Accepted: 11/18/2011] [Indexed: 12/29/2022] Open
Abstract
Epigenetic methylation change is a major process that occurs during cancer development. Even though many tumor-related genes have been identified based on their relationship between methylation and expression, few studies have been conducted to investigate the relevant biological pathways involved in these changes. To identify essential pathways likely to be affected by methylation in breast cancer, we examined a pool of genes in which expression was upregulated after induction of demethylation by 5-Aza-2'-deoxycytidine (Aza) in the MCF-7 breast cancer cell line. Genome-wide demethylation was confirmed by monitoring the demethylation of a previously known gene, SULT1A1. Overall, 210 and 213 genes were found to be upregulated and downregulated (fold change ≥ 2), respectively, in common in cells treated with 5 and 10 μM of Aza. Network analysis of these 423 genes with altered expression patterns identified the involvement of a cancer related network of genes that were heavily regulated by TNF-α in breast tumorigenesis. Our results suggest that epigenetic dysregulation of cellular processes relevant to TNF-α-dependent apoptosis may be intimately involved in tumorigenesis in MCF-7 cells.
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Affiliation(s)
- Ju Hee Kim
- Department of Life Science, Dongguk University-Seoul, Seoul 100-715,
Korea
| | - Seongeun Kang
- Department of Life Science, Dongguk University-Seoul, Seoul 100-715,
Korea
| | - Tae Woo Kim
- Department of Life Science, Dongguk University-Seoul, Seoul 100-715,
Korea
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009,
China
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009,
China
| | - Sun Jung Kim
- Department of Life Science, Dongguk University-Seoul, Seoul 100-715,
Korea
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Differential DNA Methylation Status Between Human Preadipocytes and Mature Adipocytes. Cell Biochem Biophys 2012; 63:1-15. [DOI: 10.1007/s12013-012-9336-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Almiñana C, Fazeli A. Exploring the application of high-throughput genomics technologies in the field of maternal-embryo communication. Theriogenology 2012; 77:717-37. [PMID: 22217573 DOI: 10.1016/j.theriogenology.2011.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/30/2011] [Accepted: 09/02/2011] [Indexed: 01/23/2023]
Abstract
Deciphering the complex molecular dialogue between the maternal tract and embryo is crucial to increasing our understanding of pregnancy failure, infertility problems and in the modulation of embryo development, which has consequences through adulthood. High-throughput genomic technologies have been applied to look for a holistic view of the molecular interactions occurring during this dialogue. Among these technologies, microarrays have been widely used, being one of the most popular tools in maternal-embryo communication. Today, next generation sequencing technologies are dwarfing the capabilities of microarrays. The application of these new technologies has broadened to almost all areas of genomics research, because of their massive sequencing capacity. We review the current status of high-throughput genomic technologies and their application to maternal-embryo communication research. We also survey next generation technologies and their huge potential in many research areas. Given the diversity of unanswered questions in the field of maternal-embryo communication and the wide range of possibilities that these technologies offer, here we discuss future perspectives on the use of these technologies to enhance maternal-embryo research.
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Affiliation(s)
- Carmen Almiñana
- Academic Unit of Reproductive and Development Medicine, University of Sheffield, Sheffield, UK.
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Chimonidou M, Strati A, Tzitzira A, Sotiropoulou G, Malamos N, Georgoulias V, Lianidou ES. DNA methylation of tumor suppressor and metastasis suppressor genes in circulating tumor cells. Clin Chem 2011; 57:1169-77. [PMID: 21700955 DOI: 10.1373/clinchem.2011.165902] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Circulating tumor cells (CTCs) are associated with prognosis in a variety of human cancers and have been proposed as a liquid biopsy for follow-up examinations. We show that tumor suppressor and metastasis suppressor genes are epigenetically silenced in CTCs isolated from peripheral blood of breast cancer patients. METHODS We obtained peripheral blood from 56 patients with operable breast cancer, 27 patients with verified metastasis, and 23 healthy individuals. We tested DNA extracted from the EpCAM-positive immunomagnetically selected CTC fraction for the presence of methylated and unmethylated CST6, BRMS1, and SOX17 promoter sequences by methylation-specific PCR (MSP). All samples were checked for KRT19 (keratin 19, formerly CK-19) expression by reverse-transcription quantitative PCR. RESULTS In CTCs of patients with operable breast cancer, promoter methylation of CST6 was observed in 17.9%, BRMS1 in 32.1%, and SOX17 in 53.6% of patients. In CTCs of patients with verified metastasis, promoter methylation of CST6 was observed in 37.0%, BRMS1 in 44.4%, and SOX17 in 74.1%. In healthy individuals, promoter methylation of CST6 was observed in 4.3%, BRMS1 in 8.7%, and SOX17 in 4.3%. DNA methylation of these genes for both operable and metastatic breast cancer was significantly different from that of the control population. CONCLUSIONS DNA methylation of tumor suppressor and metastasis suppressor genes is a hallmark of CTCs and confirms their heterogeneity. Our findings add a new dimension to the molecular characterization of CTCs and may underlie the acquisition of malignant properties, including their stem-like phenotype.
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Acun T, Oztas E, Yagci T, Yakicier MC. SIP1 is downregulated in hepatocellular carcinoma by promoter hypermethylation. BMC Cancer 2011; 11:223. [PMID: 21645397 PMCID: PMC3118200 DOI: 10.1186/1471-2407-11-223] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 06/06/2011] [Indexed: 12/29/2022] Open
Abstract
Background Smad interacting protein-1 is a transcription factor that is implicated in transforming growth factor-β/bone morphogenetic protein signaling and a repressor of E-cadherin and human telomerase reverse transcriptase. It is also involved in epithelial-mesenchymal transition and tumorigenesis. However, genetic and epigenetic alterations of SIP1 have not been fully elucidated in cancers. In this study, we investigated mutations and promoter hypermethylation of the SIP1 gene in human hepatocellular carcinomas. Methods SIP1 expression was analyzed in HCC cell lines and primary tumors in comparison to normal and non-tumor liver tissues by using semi-quantitative RT-PCR, quantitative real-time RT-PCR and immunohistochemistry. Mutation and deletion screening of the SIP1 gene were performed by direct sequencing in HCC-derived cells. Restoration of SIP1 expression was sought by treating HCC cell lines with the DNA methyl transferase inhibitor, 5-AzaC, and the histone deacetylase inhibitor, TSA. SIP1 promoter methylation was analyzed by the combined bisulfite restriction analysis assay in in silico-predicted putative promoter and CpG island regions. Results We found that the expression of SIP1 was completely lost or reduced in five of 14 (36%) HCC cell lines and 17 of 23 (74%) primary HCC tumors. Immunohistochemical analysis confirmed that SIP1 mRNA downregulation was associated with decreased expression of the SIP1 protein in HCC tissues (82.8%). No somatic mutation was observed in SIP1 exons in any of the 14 HCC cell lines. Combined treatment with DNA methyl transferase and histone deacetylase inhibitors synergistically restored SIP1 expression in SIP1-negative cell lines. Analysis of three putative gene regulatory regions revealed tumor-specific methylation in more than half of the HCC cases. Conclusions Epigenetic mechanisms contribute significantly to the downregulation of SIP1 expression in HCC. This finding adds a new level of complexity to the role of SIP1 in hepatocarcinogenesis.
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Affiliation(s)
- Tolga Acun
- Bilkent University, Department of Molecular Biology and Genetics, Ankara, Turkey
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Targeted extracellular nanoparticles enable intracellular detection of activated epidermal growth factor receptor in living brain cancer cells. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2011; 7:896-903. [PMID: 21683807 DOI: 10.1016/j.nano.2011.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 04/15/2011] [Accepted: 05/02/2011] [Indexed: 01/03/2023]
Abstract
UNLABELLED Mechanistic study of biological processes via Quantum Dots (QDs) remain constrained by inefficient QD delivery methods and consequent altered cell function. Here the authors present a rapid method to label activated receptor populations in live cancer cells derived from medulloblastoma and glioma tumors. The authors used QDs to bind the extracellular domain of Epidermal Growth Factor Receptor (EGF-R) proteins and then induced receptor activation to facilitate specific detection of intracellular, activated EGF-R subpopulations. Such labeling enables rapid identification of biological markers characteristic of tumor type, grade and chemotherapy resistance. FROM THE CLINICAL EDITOR In this paper, a rapid, quantum dot-based method is presented with the goal of labeling activated receptor populations in live cancer cells. More accurate characterization of medulloblastoma and glioma cancer cells using this biomarker detection technique may lead to a more specific targeted therapy.
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Rodenhiser DI, Andrews JD, Vandenberg TA, Chambers AF. Gene signatures of breast cancer progression and metastasis. Breast Cancer Res 2011; 13:201. [PMID: 21345283 PMCID: PMC3109557 DOI: 10.1186/bcr2791] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Breast cancer is a heterogeneous disease. Patient outcome varies significantly, depending on prognostic features of patients and their tumors, including patient age, menopausal status, tumor size and histology, nodal status, and so on. Response to treatment also depends on a series of predictive factors, such as hormone receptor and HER2 status. Current treatment guidelines use these features to determine treatment. However, these guidelines are imperfect, and do not always predict response to treatment or survival. Evolving technologies are permitting increasingly large amounts of molecular data to be obtained from tumors, which may enable more personalized treatment decisions to be made. The challenge is to learn what information leads to improved prognostic accuracy and treatment outcome for individual patients.
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Affiliation(s)
- David I Rodenhiser
- London Regional Cancer Program, Cancer Research Laboratories, London Health Sciences Centre, 790 Commissioners Road East, London, Ontario, N6A 4L6, Canada
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Skinner MK, Manikkam M, Guerrero-Bosagna C. Epigenetic transgenerational actions of endocrine disruptors. Reprod Toxicol 2010; 31:337-43. [PMID: 21055462 DOI: 10.1016/j.reprotox.2010.10.012] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 10/21/2010] [Accepted: 10/26/2010] [Indexed: 12/22/2022]
Abstract
Environmental factors have a significant impact on biology. Therefore, environmental toxicants through similar mechanisms can modulate biological systems to influence physiology and promote disease states. The majority of environmental toxicants do not have the capacity to modulate DNA sequence, but can alter the epigenome. In the event an environmental toxicant such as an endocrine disruptor modifies the epigenome of a somatic cell, this may promote disease in the individual exposed, but not be transmitted to the next generation. In the event a toxicant modifies the epigenome of the germ line permanently, then the disease promoted can become transgenerationaly transmitted to subsequent progeny. The current review focuses on the ability of environmental factors such as endocrine disruptors to promote transgenerational phenotypes.
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Affiliation(s)
- Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, United States.
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Guerrero-Bosagna C, Settles M, Lucker B, Skinner MK. Epigenetic transgenerational actions of vinclozolin on promoter regions of the sperm epigenome. PLoS One 2010; 5. [PMID: 20927350 PMCID: PMC2948035 DOI: 10.1371/journal.pone.0013100] [Citation(s) in RCA: 289] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 08/31/2010] [Indexed: 12/16/2022] Open
Abstract
Previous observations have demonstrated that embryonic exposure to the endocrine disruptor vinclozolin during gonadal sex determination promotes transgenerational adult onset disease such as male infertility, kidney disease, prostate disease, immune abnormalities and tumor development. The current study investigates genome-wide promoter DNA methylation alterations in the sperm of F3 generation rats whose F0 generation mother was exposed to vinclozolin. A methylated DNA immunoprecipitation with methyl-cytosine antibody followed by a promoter tilling microarray (MeDIP-Chip) procedure was used to identify 52 different regions with statistically significant altered methylation in the sperm promoter epigenome. Mass spectrometry bisulfite analysis was used to map the CpG DNA methylation and 16 differential DNA methylation regions were confirmed, while the remainder could not be analyzed due to bisulfite technical limitations. Analysis of these validated regions identified a consensus DNA sequence (motif) that associated with 75% of the promoters. Interestingly, only 16.8% of a random set of 125 promoters contained this motif. One candidate promoter (Fam111a) was found to be due to a copy number variation (CNV) and not a methylation change, suggesting initial alterations in the germline epigenome may promote genetic abnormalities such as induced CNV in later generations. This study identifies differential DNA methylation sites in promoter regions three generations after the initial exposure and identifies common genome features present in these regions. In addition to primary epimutations, a potential indirect genetic abnormality was identified, and both are postulated to be involved in the epigenetic transgenerational inheritance observed. This study confirms that an environmental agent has the ability to induce epigenetic transgenerational changes in the sperm epigenome.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Matthew Settles
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Ben Lucker
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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Tumor suppressor genes are frequently methylated in lymph node metastases of breast cancers. BMC Cancer 2010; 10:378. [PMID: 20642860 PMCID: PMC2914707 DOI: 10.1186/1471-2407-10-378] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 07/20/2010] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION Metastasis represents a major adverse step in the progression of breast carcinoma. Lymph node invasion is the most relevant prognostic factor; however little is known on the molecular events associated with lymph node metastasis process. This study is to investigate the status and role of methylation in lymph node metastatic tumors. MATERIALS AND METHODS Bisulfite pyrosequencing is used to screen 6 putative tumor suppressor genes (HIN-1, RASSF1A, RIL, CDH13, RARbeta2 and E-cadherin) in 38 pairs of primary breast tumors and lymph node metastases. RESULTS We found that HIN-1, CDH13, RIL, RASSF1A and RARbeta2 were frequently methylated both in primary and metastatic tissues (range: 55.3% approximately 89.5%). E-cadherin was not frequently methylated in either setting (range: 18.4% approximately 23.7%). The methylation status of HIN-1, CDH13, RIL, and RARbeta2 in lymph nodes metastasis were correlated with that in primary tumors. The Pearson correlation values ranged from 0.624 to 0.472 (p values < 0.01 to 0.001). Interestingly, we observed an association between HIN-1 methylation and hormone status in metastatic lymph nodes. Hypermethylation of HIN-1 in metastasis lymph nodes was significantly associated with expression of ER (odds ratio, 1.070; P = 0.024) and with PR (odds ratio, 1.046; P = 0.026). CONCLUSIONS This study suggests that hypermethylation of tumor suppressor genes is extended from primary to metastatic tumors during tumor progression.
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Flanagan JM, Cocciardi S, Waddell N, Johnstone CN, Marsh A, Henderson S, Simpson P, da Silva L, Khanna K, Lakhani S, Boshoff C, Chenevix-Trench G. DNA methylome of familial breast cancer identifies distinct profiles defined by mutation status. Am J Hum Genet 2010; 86:420-33. [PMID: 20206335 DOI: 10.1016/j.ajhg.2010.02.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 02/03/2010] [Accepted: 02/08/2010] [Indexed: 01/21/2023] Open
Abstract
It is now understood that epigenetic alterations occur frequently in sporadic breast carcinogenesis, but little is known about the epigenetic alterations associated with familial breast tumors. We performed genome-wide DNA-methylation profiling on familial breast cancers (n = 33) to identify patterns of methylation specific to the different mutation groups (BRCA1, BRCA2, and BRCAx) or intrinsic subtypes of breast cancer (basal, luminal A, luminal B, HER2-amplified, and normal-like). We used methylated DNA immunoprecipitation (MeDIP) on Affymetrix promoter chips to interrogate methylation profiles across 25,500 distinct transcripts. Using a support vector machine classification algorithm, we demonstrated that genome-wide methylation profiles predicted tumor mutation status with estimated error rates of 19% (BRCA1), 31% (BRCA2), and 36% (BRCAx) but did not accurately predict the intrinsic subtypes defined by gene expression. Furthermore, using unsupervised hierarchical clustering, we identified a distinct subgroup of BRCAx tumors defined by methylation profiles. We validated these findings in the 33 tumors in the test set, as well as in an independent validation set of 47 formalin-fixed, paraffin-embedded familial breast tumors, by pyrosequencing and Epityper. Finally, gene-expression profiling and SNP CGH array previously performed on the same samples allowed full integration of methylation, gene-expression, and copy-number data sets, revealing frequent hypermethylation of genes that also displayed loss of heterozygosity, as well as of genes that show copy-number gains, providing a potential mechanism for expression dosage compensation. Together, these data show that methylation profiles for familial breast cancers are defined by the mutation status and are distinct from the intrinsic subtypes.
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Affiliation(s)
- James M Flanagan
- CRUK Viral Oncology Group, UCL Cancer Institute, London WC1E 6BT, UK.
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Radaelli E, Damonte P, Cardiff RD. Epithelial-mesenchymal transition in mouse mammary tumorigenesis. Future Oncol 2010; 5:1113-27. [PMID: 19852725 DOI: 10.2217/fon.09.93] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Epithelial-mesenchymal transition tumorigenesis in the mouse has been described for over 100 years using various terms and with little comprehension of the underlying mechanisms. Recently, epithelial-mesenchymal transition tumors have been recognized in mammary glands of genetically engineered mice. This review provides a historical perspective and the current observations in the context of some of the key molecular biology. The biology of mouse mammary epithelial-mesenchymal transition tumorigenesis is discussed with comparisons to human breast cancer.
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Affiliation(s)
- Enrico Radaelli
- Department of Veterinary Pathology, Hygiene and Public Health, Section of Veterinary and Avian Pathology, Faculty of Veterinary Medicine, University of Milan, Via Celoria, 10 20133 Milano, Italy
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Andrews J, Kennette W, Pilon J, Hodgson A, Tuck AB, Chambers AF, Rodenhiser DI. Multi-platform whole-genome microarray analyses refine the epigenetic signature of breast cancer metastasis with gene expression and copy number. PLoS One 2010; 5:e8665. [PMID: 20084286 PMCID: PMC2801616 DOI: 10.1371/journal.pone.0008665] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 11/06/2009] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND We have previously identified genome-wide DNA methylation changes in a cell line model of breast cancer metastasis. These complex epigenetic changes that we observed, along with concurrent karyotype analyses, have led us to hypothesize that complex genomic alterations in cancer cells (deletions, translocations and ploidy) are superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes observed in breast cancer metastasis. METHODOLOGY/PRINCIPAL FINDINGS We undertook simultaneous high-resolution, whole-genome analyses of MDA-MB-468GFP and MDA-MB-468GFP-LN human breast cancer cell lines (an isogenic, paired lymphatic metastasis cell line model) using Affymetrix gene expression (U133), promoter (1.0R), and SNP/CNV (SNP 6.0) microarray platforms to correlate data from gene expression, epigenetic (DNA methylation), and combination copy number variant/single nucleotide polymorphism microarrays. Using Partek Software and Ingenuity Pathway Analysis we integrated datasets from these three platforms and detected multiple hypomethylation and hypermethylation events. Many of these epigenetic alterations correlated with gene expression changes. In addition, gene dosage events correlated with the karyotypic differences observed between the cell lines and were reflected in specific promoter methylation patterns. Gene subsets were identified that correlated hyper (and hypo) methylation with the loss (or gain) of gene expression and in parallel, with gene dosage losses and gains, respectively. Individual gene targets from these subsets were also validated for their methylation, expression and copy number status, and susceptible gene pathways were identified that may indicate how selective advantage drives the processes of tumourigenesis and metastasis. CONCLUSIONS/SIGNIFICANCE Our approach allows more precisely profiling of functionally relevant epigenetic signatures that are associated with cancer progression and metastasis.
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Affiliation(s)
- Joseph Andrews
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - Wendy Kennette
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - Jenna Pilon
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Biochemistry, The Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Alexandra Hodgson
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Biochemistry, The Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Alan B. Tuck
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Oncology, The Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Pathology, The Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Ann F. Chambers
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Oncology, The Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Pathology, The Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - David I. Rodenhiser
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Biochemistry, The Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Oncology, The Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Paediatrics, The Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- EpiGenWestern Research Group at the Children's Health Research Institute, London, Ontario, Canada
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Chen X, Cao X, Dong W, Xia M, Luo S, Fan Q, Xie J. Cystatin M expression is reduced in gastric carcinoma and is associated with promoter hypermethylation. Biochem Biophys Res Commun 2009; 391:1070-4. [PMID: 20004178 DOI: 10.1016/j.bbrc.2009.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2009] [Accepted: 12/04/2009] [Indexed: 10/20/2022]
Abstract
Cystatin M is a secreted inhibitor of lysosomal cysteine proteases and increasing evidences indicate that it is a novel target for epigenetic silencing during mammary tumorigenesis. Aberrant promoter methylation is a well-known mechanism that participates in cystatin M silencing in breast cancer. However, the role of cystatin M in the gastric cancer remains to be elucidated. Immunohistochemistry was used to investigate the expression of cystatin M in 60 gastric carcinomas. Hypermethylation of cystatin M promoter was evaluated by the methylation-specific PCR (MSP) method in gastric carcinomas (tumor and paired adjacent non-tumor tissues). Reverse-transcriptase PCR and BSP were also performed on gastric cancer cell lines before and after treatment with 5-aza-2'-deoxycytidine (5-Aza-dC). Lost expression of cystatin M was observed in 42 of 60 (70%) gastric carcinomas. 55% (33 of 60) of primary tumors analyzed displayed cystatin M promoter hypermethylation, indicating that this aberrant characteristic is common in gastric malignancies. Moreover, a statistically significant inverse association was found between cystatin M methylation status and expression of the cystatin M protein in tumor tissues (p=0.027). We also found that patients with cystatin M promoter methylation had a significantly shorter survival time than those without this methylation (p=0.020). These results suggest that cystatin M promoter hypermethylation is one of the molecular mechanisms that accounts for reduced cystatin M gene expression in gastric carcinomas.
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Affiliation(s)
- Xiaobing Chen
- Department of Internal Medicine-Oncology, The First Affiliated Hospital, Zhengzhou University, People's Republic of China
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