51
|
Waraya M, Yamashita K, Katoh H, Ooki A, Kawamata H, Nishimiya H, Nakamura K, Ema A, Watanabe M. Cancer specific promoter CpG Islands hypermethylation of HOP homeobox (HOPX) gene and its potential tumor suppressive role in pancreatic carcinogenesis. BMC Cancer 2012; 12:397. [PMID: 22958219 PMCID: PMC3488580 DOI: 10.1186/1471-2407-12-397] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2011] [Accepted: 08/31/2012] [Indexed: 12/25/2022] Open
Abstract
Background We have recently identified HOP hoemobox (HOPX) as a tumor suppressor gene candidate, characterized by tumor-specific promoter DNA hypermethylation in human cancers, and it can remarkably inhibit tumors’ aggressive phenotypes. In this current study, we for the first time examined methylation level of HOPX and tested the functional relevance in pancreatic cancer (PC). Methods Clinical features of HOPX promoter hypermethylation was investigated in 89 PC tissues, and immunohistochemistry was added. We also examined its functional relevance in phenotype assays such as soft agar, proliferation, invasion, and cell cycle analysis. Results PC tissues had HOPX gene hypermethylation as compared to the corresponding normal pancreas tissues, and its uniqueness was robust to discriminate tumor from normal tissues (AUC = 0.85, P < 0.0001). Unexpectedly, HOPX was increased in expression in tumor tissues, and immunohistochemistry revealed its predominant expression in the Langerhans islet cells, where HOPX was reduced in expression for PC cells with promoter hypermethylation. HOPX transfectants exhibited G1 arrest with subG1 accumulation, and inhibited tumor forming and invasive ability. Conclusion Defective expression of HOPX which is consistent with promoter DNA hypermethylation may explain aggressive phenotype of pancreatic cancer, and intense expression of HOPX in the Langerhans cells may in turn uniquely contribute to pancreatic carcinogenesis.
Collapse
Affiliation(s)
- Mina Waraya
- Department of Surgery, Kitasato University Hospital, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0375, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
52
|
Gaykalova D, Vatapalli R, Glazer CA, Bhan S, Shao C, Sidransky D, Ha PK, Califano JA. Dose-dependent activation of putative oncogene SBSN by BORIS. PLoS One 2012; 7:e40389. [PMID: 22792300 PMCID: PMC3390376 DOI: 10.1371/journal.pone.0040389] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 06/06/2012] [Indexed: 11/18/2022] Open
Abstract
Testis-specific transcription factor BORIS (Brother of the Regulator of Imprinted Sites), a paralog and proposed functional antagonist of the widely expressed CTCF, is abnormally expressed in multiple tumor types and has been implicated in the epigenetic activation of cancer-testis antigens (CTAs). We have reported previously that suprabasin (SBSN), whose expression is restricted to the epidermis, is epigenetically derepressed in lung cancer. In this work, we establish that SBSN is a novel non-CTA target of BORIS epigenetic regulation. With the use of a doxycycline-inducible BORIS expressing vector, we demonstrate that relative BORIS dosage is critical for SBSN activation. At lower concentrations, BORIS induces demethylation of the SBSN CpG island and disruption and activation of chromatin around the SBSN transcription start site (TSS), resulting in a 35-fold increase in SBSN expression in the H358 human lung cancer cell line. Interestingly, increasing BORIS concentrations leads to a subsequent reduction in SBSN expression via chromatin repression. In a similar manner, increase in BORIS concentrations leads to eventual decrease of cell growth and colony formation. This is the first report demonstrating that different amount of BORIS defines its varied effects on the expression of a target gene via chromatin structure reorganization.
Collapse
Affiliation(s)
- Daria Gaykalova
- Department of Otolaryngology–Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Rajita Vatapalli
- Department of Otolaryngology–Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Chad A. Glazer
- Department of Otolaryngology–Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Sheetal Bhan
- Department of Otolaryngology–Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Chunbo Shao
- Department of Otolaryngology–Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - David Sidransky
- Department of Otolaryngology–Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland, United States of America
| | - Patrick K. Ha
- Department of Otolaryngology–Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland, United States of America
| | - Joseph A. Califano
- Department of Otolaryngology–Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland, United States of America
- * E-mail:
| |
Collapse
|
53
|
Li JS, Ying JM, Wang XW, Wang ZH, Tao Q, Li LL. Promoter methylation of tumor suppressor genes in esophageal squamous cell carcinoma. CHINESE JOURNAL OF CANCER 2012; 32:3-11. [PMID: 22572016 PMCID: PMC3845589 DOI: 10.5732/cjc.011.10381] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) is a prevalent and fatal cancer in China and other Asian countries. Epigenetic silencing of key tumor suppressor genes (TSGs) is critical to ESCC initiation and progression. Recently, many novel TSGs silenced by promoter methylation have been identified in ESCC, and these genes further serve as potential tumor markers for high-risk group stratification, early detection, and prognosis prediction. This review summarizes recent discoveries on aberrant promoter methylation of TSGs in ESCC, providing better understanding of the role of disrupted epigenetic regulation in tumorigenesis and insight into diagnostic and prognostic biomarkers for this malignancy.
Collapse
Affiliation(s)
- Ji-Sheng Li
- Department of Chemotherapy, Shandong University, Jinan, Shandong, People's Republic of China
| | | | | | | | | | | |
Collapse
|
54
|
Chen B, Chen J, House MG, Cullen KJ, Nephew KP, Guo Z. Role of neurofilament light polypeptide in head and neck cancer chemoresistance. Mol Cancer Res 2012; 10:305-15. [PMID: 22246235 DOI: 10.1158/1541-7786.mcr-11-0300] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Resistance to cisplatin-based chemotherapy is responsible for therapeutic failure of many common human cancers including cancer of head and neck (HNC). Mechanisms underlying cisplatin resistance remain unclear. In this study, we identified neurofilament light polypeptide (NEFL) as a novel hypermethylated gene associated with resistance to cisplatin-based chemotherapy in HNC. Analysis of 14 HNC cell lines revealed that downregulation of NEFL expression significantly correlated with increased resistance to cisplatin. Hypermethylation of NEFL promoter CpG islands was observed in cell lines as examined by bisulfite DNA sequencing and methylation-specific PCR (MSP) and tightly correlated with reduced NEFL mRNA and protein expression. Furthermore, in patient samples with HNC (n = 51) analyzed by quantitative MSP, NEFL promoter hypermethylation was associated with resistance to cisplatin-based chemotherapy [relative risk (RR), 3.045; 95% confidence interval (CI), 1.459-6.355; P = 0.007] and predicted diminished overall and disease-free survival for patients treated with cisplatin-based chemotherapy. Knockdown of NEFL by siRNA in the highly cisplatin-sensitive cell line PCI13 increased (P < 0.01) resistance to cisplatin. In cisplatin-resistant O11 and SCC25cp cells, restored expression of NEFL significantly increased sensitivity to the drug. Furthermore, NEFL physically associated with tuberous sclerosis complex 1 (TSC1), a known inhibitor of the mTOR pathway, and NEFL downregulation led to functional activation of mTOR pathway and consequentially conferred cisplatin resistance. This is the first study to show a role for NEFL in HNC chemoresistance. Our findings suggest that NEFL methylation is a novel mechanism for HNC chemoresistance and may represent a candidate biomarker predictive of chemotherapeutic response and survival in patients with HNC.
Collapse
Affiliation(s)
- Baishen Chen
- Medical Sciences Program, Indiana University School of Medicine, Jordan Hall 104, 1001 E. Third St., Bloomington, IN 47405, USA
| | | | | | | | | | | |
Collapse
|
55
|
Brigati C, Saccuman MC, Banelli B, Di Vinci A, Casciano I, Borzì L, Forlani A, Allemanni G, Romani M. Toward an epigenetic view of our musical mind. Front Genet 2012; 2:111. [PMID: 22303405 PMCID: PMC3268383 DOI: 10.3389/fgene.2011.00111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Accepted: 12/26/2011] [Indexed: 11/13/2022] Open
Abstract
We are transient beings, in a world of constantly changing culture. At home in the fields of Art and Science, seemingly capable of magnificent abstractions, humans have an intense need to externalize their insights. Music is an art and a highly transmissible cultural product, but we still have an incomplete understanding of how our musical experience shapes and is vividly retained within our brain, and how it affects our behavior. However, the developing field of social epigenetics is now helping us to describe how communication and emotion, prime hallmarks of music, can be linked to a transmissible, biochemical change.
Collapse
Affiliation(s)
- Claudio Brigati
- Laboratory of Tumor Genetics, National Cancer Institute Genova, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
56
|
Tamura H, Suzuki M, Moriya Y, Hoshino H, Okamoto T, Yoshida S, Yoshino I. Aberrant methylation of N-methyl-D-aspartate receptor type 2B (NMDAR2B) in non-small cell carcinoma. BMC Cancer 2011; 11:220. [PMID: 21639937 PMCID: PMC3149028 DOI: 10.1186/1471-2407-11-220] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 06/05/2011] [Indexed: 11/10/2022] Open
Abstract
Background N-methyl-D-aspartate receptors (NMDAR) act as tumor suppressors of digestive malignancies. The expression and genetic methylation patterns of NMDAR2B in non-small cell lung cancer (NSCLC) are unknown. Methods The relationship between gene methylation and expression of NMDAR2B was analyzed in NSCLC cell lines (N = 9) and clinical tissues (N = 216). The cell lines were studied using RT-PCR and 5-aza-2'-deoxycytidine treatment, while the clinical tissues were examined by methylation specific real-time quantitative PCR and immunohistochemistry. Retrospective investigation of patient records was used to determine the clinical significance of NMDAR2B methylation. Results NMDAR2B was silenced in five of the nine cell lines; 5-aza-2'-deoxycytidine treatment restored expression, and was inversely correlated with methylation. Aberrant methylation of NMDAR2B, detected in 61% (131/216) of clinical NSCLC tissues, was inversely correlated with the status of protein expression in 20 randomly examined tumors. Aberrant methylation was not associated with clinical factors such as gender, age, histological type, or TNM stage. However, aberrant methylation was an independent prognostic factor in squamous cell carcinoma cases. Conclusions Aberrant methylation of the NMDAR2B gene is a common event in NSCLC. The prognosis was significantly better for cases of squamous cell carcinoma in which NMDAR2B was methylated. It may have different roles in different histological types.
Collapse
Affiliation(s)
- Hajime Tamura
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuoh-Ku, Chiba 280-8670, Japan
| | | | | | | | | | | | | |
Collapse
|
57
|
Rotter A, Asemann R, Decker A, Kornhuber J, Biermann T. Orexin expression and promoter-methylation in peripheral blood of patients suffering from major depressive disorder. J Affect Disord 2011; 131:186-92. [PMID: 21211849 DOI: 10.1016/j.jad.2010.12.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 12/01/2010] [Accepted: 12/01/2010] [Indexed: 11/16/2022]
Abstract
Orexins are endogenous neuropeptides synthesized in hypothalamic neurones; they play a major role in the regulation of feeding, drinking, endocrine function and sleep/wakefulness that is often disturbed in major depression. The aim of this study was to explore Orexin A expression and promotermethylation in peripheral blood cells of 29 patients (14 male and 15 female patients at three different time points during antidepressive treatment) suffering from major depressive disorder (MDD) by quantitative RT-PCR and bisulfite sequencing. There was a measurable difference between Orexin A expression on admission in comparison to the Orexin mRNA expression in the healthy control group (T=1.53; df=39; p=0.135) that failed to reach statistical significance. An inverse correlation between Orexin A mRNA expression on admission and the HAMD scores at all measurement dates each week over 6 weeks could be detected. A cluster of methylated CPG sites within the promoter region of the Orexin A gene could be identified that was positively correlated with Delta CT values of the mRNA expression 14 days after hospital admission (r=0.625; p=0.072) and 4 weeks afterwards (r=0.582; p=0.1). Considering only the methylation of the 7 CPGs within the CPG island in the promoter 4 weeks after treatment onset a statistically significant relation between the cluster of CPG sites within the island and body weight (r=0.55; p=0.034) as well as BMI (r=0.474; p=0.074) could be detected. Furthermore, this methylation pattern 4 weeks after treatment onset was positively associated with mRNA expression on admission, 2 and 4 weeks afterwards. In sum, these results are an indicator of a link between social stresses, disruptions in energy homeostasis and changes in body weight in relation to depressive disorders that are possibly linked to Orexin dysregulation.
Collapse
Affiliation(s)
- Andrea Rotter
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-University, Erlangen-Nuremberg, Germany
| | | | | | | | | |
Collapse
|
58
|
Hennessey PT, Ochs MF, Mydlarz WW, Hsueh W, Cope L, Yu W, Califano JA. Promoter methylation in head and neck squamous cell carcinoma cell lines is significantly different than methylation in primary tumors and xenografts. PLoS One 2011; 6:e20584. [PMID: 21637785 PMCID: PMC3102742 DOI: 10.1371/journal.pone.0020584] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 05/05/2011] [Indexed: 12/31/2022] Open
Abstract
Studies designed to identify novel methylation events related to cancer often employ cancer cell lines in the discovery phase of the experiments and have a relatively low rate of discovery of cancer-related methylation events. An alternative algorithm for discovery of novel methylation in cancer uses primary tumor-derived xenografts instead of cell lines as the primary source of nucleic acid for evaluation. We evaluated DNA extracted from primary head and neck squamous cell carcinomas (HNSCC), xenografts grown from these primary tumors in nude mice, HNSCC-derived cell lines, normal oral mucosal samples, and minimally transformed oral keratinocyte-derived cell lines using Illumina Infinum Humanmethylation 27 genome-wide methylation microarrays. We found >2,200 statistically significant methylation differences between cancer cell lines and primary tumors and when comparing normal oral mucosa to keratinocyte cell lines. We found no statistically significant promoter methylation differences between primary tumor xenografts and primary tumors. This study demonstrates that tumor-derived xenografts are highly accurate representations of promoter methylation in primary tumors and that cancer derived cell lines have significant drawbacks for discovery of promoter methylation alterations in primary tumors. These findings also support use of primary tumor xenografts for the study of methylation in cancer, drug discovery, and the development of personalized cancer treatments.
Collapse
Affiliation(s)
- Patrick T. Hennessey
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Michael F. Ochs
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Division of Biostatistics and Bioinformatics, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Wojciech W. Mydlarz
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Wayne Hsueh
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Leslie Cope
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Division of Biostatistics and Bioinformatics, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Wayne Yu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Joseph A. Califano
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland, United States of America
- * E-mail:
| |
Collapse
|
59
|
Promoter methylation of leukemia inhibitory factor receptor gene in colorectal carcinoma. Int J Oncol 2011; 39:337-44. [PMID: 21617854 DOI: 10.3892/ijo.2011.1050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 01/20/2011] [Indexed: 12/31/2022] Open
Abstract
Aberrant methylation of gene promoters and corresponding loss of gene expression plays a critical role in the initiation and progression of colorectal cancer. An IL-6-type cytokine receptor, leukemia inhibitory factor receptor (LIFR), is a component of cell-surface receptor complexes for multifunctional cytokines such as LIF. Herein, we report that LIFR is methylated in human colon cancer. LIFR promoter was methylated in primary tumor tissues with high frequency (65%, 52/80). Quantitative methylation-specific PCR (TaqMan-MSP) demonstrated differential promoter methylation of LIFR in primary colorectal cancer tissues as compared to normal colon tissues (5%, 4/80). LIFR methylation was not detectable in 13 normal colon mucosa samples obtained from patients without cancer. The mRNA expression of LIFR was significantly down-regulated in colon cancer tissues as compared to corresponding normal tissues. A strong expression of LIFR protein was observed in all non-malignant normal and adjacent normal colon mucosa tissues whereas down-regulated LIFR protein expression was observed in primary tumors. These results demonstrate that cancer-specific methylation and a specific decrease of LIFR expression are a common inactivation event in colon cancer development.
Collapse
|
60
|
Huang Y, Chang X, Lee J, Cho YG, Zhong X, Park IS, Liu JW, Califano JA, Ratovitski EA, Sidransky D, Kim MS. Cigarette smoke induces promoter methylation of single-stranded DNA-binding protein 2 in human esophageal squamous cell carcinoma. Int J Cancer 2011; 128:2261-73. [PMID: 20658532 PMCID: PMC3206631 DOI: 10.1002/ijc.25569] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) is the sixth most frequent cause of cancer death in the world, and cigarette smoke is a key factor in esophageal carcinogenesis. To identify molecular changes during cigarette smoke-induced ESCC, we examined the methylation status of 13 gene promoters in the human immortalized, nontumorigenic esophageal epithelial cell line (Het-1A) that were exposed to mainstream (MSE) or sidestream cigarette smoke extract (SSE) for 6 months in culture. The promoter of sequence-specific single-stranded DNA-binding protein 2 (SSBP2) was methylated in the Het-1A cells exposed to MSE (MSE-Het-1A). Promoter methylation (86%, 56/70) and downregulation of SSBP2 expression were frequently detected in tumor tissues from ESCC patients. In addition, reintroduction of SSBP2 in an ESCC cell line (TE1) that does not express SSBP2 and in the MSE-Het-1A cells inhibited expression of LRP6 and Dvl3, which are mediators of the Wnt signaling pathway. SSBP2 expression markedly decreased the colony-forming ability of ESCC cell lines and significantly inhibited cell growth of the MSE-Het-1A cells. Our results indicate that cigarette smoking is a cause of SSBP2 promoter methylation and that SSBP2 harbors a tumor suppressive role in ESCC through inhibition of the Wnt signaling pathway.
Collapse
Affiliation(s)
- Yiping Huang
- Department of Dermatology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Xiaofei Chang
- Department of Otolaryngology – Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Juna Lee
- Department of Otolaryngology – Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Yong Gu Cho
- Department of Otolaryngology – Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Xiaoli Zhong
- Department of Otolaryngology – Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Il-Seok Park
- Department of Otolaryngology, Head and Neck Surgery, Ilsong Memorial Institute of Head and Neck Cancer, Hallym University, College of Medicine, Seoul, Korea
| | - Jun-Wei Liu
- Department of Otolaryngology – Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Joseph A. Califano
- Department of Otolaryngology – Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Edward A. Ratovitski
- Department of Dermatology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - David Sidransky
- Department of Otolaryngology – Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Myoung Sook Kim
- Department of Otolaryngology – Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| |
Collapse
|
61
|
Shao C, Sun W, Tan M, Glazer CA, Bhan S, Zhong X, Fakhry C, Sharma R, Westra WH, Hoque MO, Moskaluk CA, Sidransky D, Califano JA, Ha PK. Integrated, genome-wide screening for hypomethylated oncogenes in salivary gland adenoid cystic carcinoma. Clin Cancer Res 2011; 17:4320-30. [PMID: 21551254 DOI: 10.1158/1078-0432.ccr-10-2992] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PURPOSE Salivary gland adenoid cystic carcinoma (ACC) is a rare malignancy that is poorly understood. To look for relevant oncogene candidates under the control of promoter methylation, an integrated, genome-wide screen was conducted. EXPERIMENTAL DESIGN Global demethylation of normal salivary gland cell strains using 5-aza-2'-deoxycytidine (5-aza-dC) and trichostatin A (TSA), followed by expression array analysis was conducted. ACC-specific expression profiling was generated using expression microarray analysis of primary ACC and normal samples. Next, the two profiles were integrated to identify a subset of genes for further validation of promoter demethylation in ACC versus normal. Finally, promising candidates were further validated for mRNA, protein, and promoter methylation levels in larger ACC cohorts. Functional validation was then conducted in cancer cell lines. RESULTS We found 159 genes that were significantly re-expressed after 5-aza-dC/TSA treatment and overexpressed in ACC. After initial validation, eight candidates showed hypomethylation in ACC: AQP1, CECR1, C1QR1, CTAG2, P53AIP1, TDRD12, BEX1, and DYNLT3. Aquaporin 1 (AQP1) showed the most significant hypomethylation and was further validated. AQP1 hypomethylation in ACC was confirmed with two independent cohorts. Of note, there was significant overexpression of AQP1 in both mRNA and protein in the paraffin-embedded ACC cohort. Furthermore, AQP1 was upregulated in 5-aza-dC/TSA-treated SACC83. Finally, AQP1 promoted cell proliferation and colony formation in SACC83. CONCLUSIONS Our integrated, genome-wide screening method proved to be an effective strategy for detecting novel oncogenes in ACC. AQP1 is a promising oncogene candidate for ACC and is transcriptionally regulated by promoter hypomethylation.
Collapse
Affiliation(s)
- Chunbo Shao
- Department of Otolaryngology-Head and Neck Surgery and Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
62
|
Ye J, Su X, Hsueh EC, Zhang Y, Koenig JM, Hoft DF, Peng G. Human tumor-infiltrating Th17 cells have the capacity to differentiate into IFN-γ+ and FOXP3+ T cells with potent suppressive function. Eur J Immunol 2011; 41:936-51. [PMID: 21381020 DOI: 10.1002/eji.201040682] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 11/29/2010] [Accepted: 01/05/2011] [Indexed: 12/18/2022]
Abstract
Accumulating evidence suggests that Th17 cells and Tregs may exhibit development plasticity and that CD4(+) Tregs can differentiate into IL-17-producing T cells; however, whether Th17 cells can reciprocally convert into Tregs has not been described. In this study, we generated Th17 clones from tumor-infiltrating T lymphocytes (TILs). We showed that Th17 clones generated from TILs can differentiate into IFN-γ-producing and FOXP3(+) cells after in vitro stimulation with OKT3 and allogeneic peripheral blood mononuclear cells. We further demonstrated that T-cell receptor (TCR) engagement was responsible for this conversion, and that this differentiation was due to the epigenetic modification and reprogramming of gene expression profiles, including lineage-specific transcriptional factor and cytokine genes. In addition to expressing IFN-γ and FOXP3, we showed that these differentiated Th17 clones mediated potent suppressive function after repetitive stimulation with OKT3, suggesting that these Th17 clones had differentiated into functional Tregs. We further demonstrated that the Th17-derived Tregs, unlike naturally occurring CD4(+) CD25(+) Tregs, did not reconvert back into Th17 cells even under Th17-biasing cytokine conditions. These results provide the critical evidence that human tumor-infiltrating Th17 cells can differentiate into Tregs and indicate a substantial developmental plasticity of Th17 cells.
Collapse
Affiliation(s)
- Jian Ye
- Division of Immunobiology, Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, MO 63104, USA
| | | | | | | | | | | | | |
Collapse
|
63
|
Haas HS, Linecker A, Pfragner R, Sadjak A. Peripheral glutamate signaling in head and neck areas. Head Neck 2011; 32:1554-72. [PMID: 20848447 DOI: 10.1002/hed.21438] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The major excitatory neurotransmitter glutamate is also found in the periphery in an increasing number of nonexcitable cells. In line with this it became apparent that glutamate can regulate a broad array of peripheral biological responses, as well. Of particular interest is the discovery that glutamate receptor reactive reagents can influence tumor biology. However, the knowledge of glutamate signaling in peripheral tissues is still incomplete and, in the case of head and neck areas, is almost lacking. The roles of glutamate signaling pathways in these regions are manifold and include orofacial pain, periodontal bone production, skin and airway inflammation, as well as salivation. Furthermore, the interrelations between glutamate and cancers in the oral cavity, thyroid gland, and other regions are discussed. In summary, this review shall strengthen the view that glutamate receptor reagents may also be promising targets for novel therapeutic concepts suitable for a number of diseases in peripheral tissues. The contents of this review cover the following sections: Introduction; The "Glutamate System"; The Taste of Glutamate; Glutamate Signaling in Dental Regions; Glutamate Signaling in Head and Neck Areas; Glutamate Signaling in Head and Neck Cancer; A Brief Overview of Glutamate Signaling in Other Cancers; and Conclusion.
Collapse
Affiliation(s)
- Helga Susanne Haas
- Department of Pathophysiology and Immunology, Center of Molecular Medicine, Medical University of Graz, Graz, Austria.
| | | | | | | |
Collapse
|
64
|
Chang X, Yamashita K, Sidransky D, Kim MS. Promoter methylation of heat shock protein B2 in human esophageal squamous cell carcinoma. Int J Oncol 2011; 38:1129-35. [PMID: 21258768 DOI: 10.3892/ijo.2011.918] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 11/03/2010] [Indexed: 11/06/2022] Open
Abstract
Hypermethylation of gene promoters and the corresponding loss of gene expression are recognized as a hallmark of human cancer, and DNA methylation has emerged as a promising biomarker for the detection of human esophageal squamous cell carcinoma (ESCC). To identify novel genes methylated in ESCC, we screened 35 candidate genes identified from an oligonucleotide microarray. Among them, the heat shock protein B2 (HSPB2) was methylated in 95.7% (67/70) of primary ESCCs, whereas no methylation was found in normal esophageal tissues from ESCC patients (0%, 0/20). RT-PCR analysis revealed that HSPB2 expression was silenced or weakly expressed in most ESCC cell lines, and re-activated by the demethylating agent 5-aza-2'-deoxy-cytidine. These results indicate that promoter methylation of HSPB2 is one of the causal factors for loss or down-regulation of HSPB2 expression. mRNA expression of HSPB2 in ESCC tissues was significantly down-regulated compared to normal tissues. Our data suggest that promoter methylation of HSPB2 deserves further attention as a novel molecular biomarker in human ESCC.
Collapse
Affiliation(s)
- Xiaofei Chang
- Department of Otolaryngology, Head and Neck Cancer Research Division, The Johns Hopkins University, School of Medicine, 1550 Orleans Street, CRB II-5M, Baltimore, MD 21231, USA
| | | | | | | |
Collapse
|
65
|
Genomic and epigenetic profiles of gastric cancer: Potential diagnostic and therapeutic applications. Surg Today 2010; 41:24-38. [DOI: 10.1007/s00595-010-4370-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 04/22/2010] [Indexed: 02/07/2023]
|
66
|
Wu CS, Lu YJ, Li HP, Hsueh C, Lu CY, Leu YW, Liu HP, Lin KH, Hui-Ming Huang T, Chang YS. Glutamate receptor, ionotropic, kainate 2 silencing by DNA hypermethylation possesses tumor suppressor function in gastric cancer. Int J Cancer 2010; 126:2542-52. [PMID: 19824040 DOI: 10.1002/ijc.24958] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aberrant DNA methylation is considered a major mechanism for silencing tumor suppressor genes in gastric cancer. We used CpG microarray and differential methylation hybridization strategies to identify potential tumor suppressor genes and recovered glutamate receptor, ionotropic, kainate 2 (GRIK2) as a novel epigenetic target in gastric cancer. Additional experiments showed that the promoter region of GRIK2 was hypermethylated in 3 of the 4 tested gastric cancer cell lines, and its expression was restored by treatment of cells with the DNA methylation inhibitor, 5'-aza-dC. In clinical samples, the GRIK2 promoter was differentially hypermethylated in tumor tissues compared with adjacent normal tissues (p < 0.001), and this methylation was inversely correlated with the expression level of GRIK2 mRNA (r = -0.44). Functional studies further showed that GRIK2-expressing gastric cancer cell lines showed decreased colony formation and cell migration. Taken together, these results suggest that GRIK2 may play a tumor-suppressor role in gastric cancer. Future studies are warranted to examine whether DNA hypermethylation of the GRIK2 promoter can be used as a potential tumor marker for gastric cancer.
Collapse
Affiliation(s)
- Chi-Sheng Wu
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
67
|
Abstract
Colorectal cancer (CRC) arises as a consequence of the accumulation of genetic and epigenetic alterations in colonic epithelial cells during neoplastic transformation. Epigenetic modifications, particularly DNA methylation in selected gene promoters, are recognized as common molecular alterations in human tumors. Substantial efforts have been made to determine the cause and role of aberrant DNA methylation ("epigenomic instability") in colon carcinogenesis. In the colon, aberrant DNA methylation arises in tumor-adjacent, normal-appearing mucosa. Aberrant methylation also contributes to later stages of colon carcinogenesis through simultaneous methylation in key specific genes that alter specific oncogenic pathways. Hypermethylation of several gene clusters has been termed CpG island methylator phenotype and appears to define a subgroup of colon cancer distinctly characterized by pathological, clinical, and molecular features. DNA methylation of multiple promoters may serve as a biomarker for early detection in stool and blood DNA and as a tool for monitoring patients with CRC. DNA methylation patterns may also be predictors of metastatic or aggressive CRC. Therefore, the aim of this review is to understand DNA methylation as a driving force in colorectal neoplasia and its emerging value as a molecular marker in the clinic.
Collapse
Affiliation(s)
- Myoung Sook Kim
- Department of Otolaryngology, Head and Neck Surgery, The Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB II-5M, Baltimore, MD, 21231, USA
| | | | | |
Collapse
|
68
|
Kang S, Dong SM, Park NH. Frequent promoter hypermethylation of TGFBI in epithelial ovarian cancer. Gynecol Oncol 2010; 118:58-63. [PMID: 20421128 DOI: 10.1016/j.ygyno.2010.03.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 03/30/2010] [Accepted: 03/31/2010] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Using pharmacologic unmasking and genome-wide differential methylation analysis, we identified a novel methylated gene in ovarian cancers. METHODS Two ovarian cancer cells (OVCAR-3, ES-2) that showed synergistic growth inhibition by 5-aza-dC and cisplatin were selected. After treatment with 5-aza-dC, differential expression profiles were compared using microarray that contained 38,500 genes. Reactivation of candidate genes and their promoter methylation were validated by real-time RT-PCR, MS-PCR and bisulfite sequencing. Methylation status was tested by MS-PCR in 56 patients with epithelial ovarian cancer and compared to the 38 normal ovarian tissues. RESULTS We identified 103 candidate genes that were reactivated by 5-aza-dC treatment. Among those, SFN and TGFBI were commonly reactivated in both cells. Since SFN is a well known methylated marker, we selected TGFBI for further validation. Bisulfite sequencing revealed complete promoter methylation in ES-2 and partial methylation in OVCAR-3. In addition, silencing of TGFBI at the transcription level was reversed by 5-aza-dC treatment. TGFBI methylation was observed in 23 out of 38 (60.5%) cases of ovarian cancer, in no normal ovarian tissues (0 of 38, P=0.001), and in 5 out of 18 (27.8%) borderline tumors (P=0.044). In our cohort, we did not observe any association between methylation of TGFBI and clinicopathologic variables or clinical outcomes. CONCLUSION Our results confirm that TGFBI is frequently methylated in ovarian cancer. Its methylation can be used as a novel epigenetic biomarker in discriminating ovarian cancer from non-cancer or borderline tumors.
Collapse
Affiliation(s)
- Sokbom Kang
- Research Institute and Hospital, National Cancer Center, Goyang, Republic of Korea
| | | | | |
Collapse
|
69
|
Kim MS, Chang X, LeBron C, Nagpal JK, Lee J, Huang Y, Yamashita K, Trink B, Ratovitski EA, Sidransky D. Neurofilament heavy polypeptide regulates the Akt-beta-catenin pathway in human esophageal squamous cell carcinoma. PLoS One 2010; 5:e9003. [PMID: 20140245 PMCID: PMC2815775 DOI: 10.1371/journal.pone.0009003] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 12/31/2009] [Indexed: 11/18/2022] Open
Abstract
Aerobic glycolysis and mitochondrial dysfunction are common features of aggressive cancer growth. We observed promoter methylation and loss of expression in neurofilament heavy polypeptide (NEFH) in a significant proportion of primary esophageal squamous cell carcinoma (ESCC) samples that were of a high tumor grade and advanced stage. RNA interference-mediated knockdown of NEFH accelerated ESCC cell growth in culture and increased tumorigenicity in vivo, whereas forced expression of NEFH significantly inhibited cell growth and colony formation. Loss of NEFH caused up-regulation of pyruvate kinase-M2 type and down-regulation of pyruvate dehydrogenase, via activation of the Akt/beta-catenin pathway, resulting in enhanced aerobic glycolysis and mitochondrial dysfunction. The acceleration of glycolysis and mitochondrial dysfunction in NEFH-knockdown cells was suppressed in the absence of beta-catenin expression, and was decreased by the treatment of 2-Deoxyglucose, a glycolytic inhibitor, or API-2, an Akt inhibitor. Loss of NEFH activates the Akt/beta-catenin pathway and increases glycolysis and mitochondrial dysfunction. Cancer cells with methylated NEFH can be targeted for destruction with specific inhibitors of deregulated downstream pathways.
Collapse
Affiliation(s)
- Myoung Sook Kim
- Head and Neck Cancer Research Division, Department of Otolaryngology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Xiaofei Chang
- Head and Neck Cancer Research Division, Department of Otolaryngology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Cynthia LeBron
- Head and Neck Cancer Research Division, Department of Otolaryngology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jatin K. Nagpal
- Head and Neck Cancer Research Division, Department of Otolaryngology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Juna Lee
- Head and Neck Cancer Research Division, Department of Otolaryngology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Yiping Huang
- Department of Dermatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Keishi Yamashita
- Department of Surgery, Kitasato University Hospital, Sagamihara, Kanagawa, Japan
| | - Barry Trink
- Head and Neck Cancer Research Division, Department of Otolaryngology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Edward A. Ratovitski
- Department of Dermatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - David Sidransky
- Head and Neck Cancer Research Division, Department of Otolaryngology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| |
Collapse
|
70
|
Kim MS, Louwagie J, Carvalho B, Terhaar sive Droste JS, Park HL, Chae YK, Yamashita K, Liu J, Ostrow KL, Ling S, Guerrero-Preston R, Demokan S, Yalniz Z, Dalay N, Meijer GA, Van Criekinge W, Sidransky D. Promoter DNA methylation of oncostatin m receptor-beta as a novel diagnostic and therapeutic marker in colon cancer. PLoS One 2009; 4:e6555. [PMID: 19662090 PMCID: PMC2717211 DOI: 10.1371/journal.pone.0006555] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Accepted: 06/30/2009] [Indexed: 12/16/2022] Open
Abstract
In addition to genetic changes, the occurrence of epigenetic alterations is associated with accumulation of both genetic and epigenetic events that promote the development and progression of human cancer. Previously, we reported a set of candidate genes that comprise part of the emerging “cancer methylome”. In the present study, we first tested 23 candidate genes for promoter methylation in a small number of primary colon tumor tissues and controls. Based on these results, we then examined the methylation frequency of Oncostatin M receptor-β (OSMR) in a larger number of tissue and stool DNA samples collected from colon cancer patients and controls. We found that OSMR was frequently methylated in primary colon cancer tissues (80%, 80/100), but not in normal tissues (4%, 4/100). Methylation of OSMR was also detected in stool DNA from colorectal cancer patients (38%, 26/69) (cut-off in TaqMan-MSP, 4). Detection of other methylated markers in stool DNA improved sensitivity with little effect on specificity. Promoter methylation mediated silencing of OSMR in cell lines, and CRC cells with low OSMR expression were resistant to growth inhibition by Oncostatin M. Our data provide a biologic rationale for silencing of OSMR in colon cancer progression and highlight a new therapeutic target in this disease. Moreover, detection and quantification of OSMR promoter methylation in fecal DNA is a highly specific diagnostic biomarker for CRC.
Collapse
Affiliation(s)
- Myoung Sook Kim
- Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Joost Louwagie
- OncoMethylome Sciences S.A, CHU Niveau +4Tour 4 dePharmacie (bâtiment 36), Liege, Belgium
| | - Beatriz Carvalho
- Department of Pathology, Free University of Amsterdam, Amsterdam, The Netherlands
| | | | - Hannah Lui Park
- Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Young Kwang Chae
- Department of Medicine, Albert Einstein Medical Center, Philadelphia, Pennsylvania, United States of America
| | - Keishi Yamashita
- Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Junwei Liu
- Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Kimberly Laskie Ostrow
- Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Shizhang Ling
- Department of Pathology, The Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Rafael Guerrero-Preston
- Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Semra Demokan
- Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Zubeyde Yalniz
- Oncology institute, Istanbul University, Istanbul, Turkey
| | - Nejat Dalay
- Oncology institute, Istanbul University, Istanbul, Turkey
| | - Gerrit A. Meijer
- Department of Pathology, Free University of Amsterdam, Amsterdam, The Netherlands
| | - Wim Van Criekinge
- OncoMethylome Sciences S.A, CHU Niveau +4Tour 4 dePharmacie (bâtiment 36), Liege, Belgium
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
| |
Collapse
|
71
|
Wang H, Zhong L, Wang JF, Zhang XG. Research and application of tumor markers in esophageal squamous cell carcinoma. Shijie Huaren Xiaohua Zazhi 2009; 17:1842-1848. [DOI: 10.11569/wcjd.v17.i18.1842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC), the main type of esophageal cancer, is one of the most common gastrointestinal malignant cancers. Tumor markers detection are easy, economical, fast and non-invasive. Some tumor markers can be expressed before morphological changes occurred in tissues and organs; therefore, they can be used for the diagnosis of disease in the asymptomatic stage, thus making the research into tumor marker discovery even more meaningful. This paper summarizes several known tumor makers' expression detected in ESCC in recent years, and illustrates them from the aspects of genes, proteins, autoimmune antibodies, antigens and prognostic factors.
Collapse
|
72
|
N-methyl-d-aspartate 2b receptor subtype (NR2B) promoter methylation in patients during alcohol withdrawal. J Neural Transm (Vienna) 2009; 116:615-22. [DOI: 10.1007/s00702-009-0212-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 03/17/2009] [Indexed: 10/20/2022]
|
73
|
|
74
|
Nagar M, Vernitsky H, Cohen Y, Dominissini D, Berkun Y, Rechavi G, Amariglio N, Goldstein I. Epigenetic inheritance of DNA methylation limits activation-induced expression of FOXP3 in conventional human CD25-CD4+ T cells. Int Immunol 2008; 20:1041-55. [PMID: 18567616 DOI: 10.1093/intimm/dxn062] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The transcription factor forkhead box P3 (FOXP3 in humans; Foxp3 in mice) controls the development and function of regulatory T cells (Treg). In mice, CD4(+)CD25(-) T cells do not express Foxp3 following TCR activation. Whether FOXP3 is a common activation-induced molecule in human T cells--hence not Treg restricted--is currently a controversial issue. As FOXP3 can significantly modulate the function of T cells, understanding the mode (and regulation) of FOXP3 expression in human T cells is vital. Here we show that in conventional CD4(+)CD25(-) T cells, the induction of FOXP3 expression following TCR activation is both restricted to a fraction of the progeny and transient. Moreover, FOXP3 expression in vivo is particularly infrequent in activated effector CD4(+) T cells that accumulate within inflamed joints. We next demonstrate that the repression of FOXP3 transcription in resting conventional human CD25(-) T cells is linked to complete methylation of an evolutionarily conserved intronic CpG island. The dense methylation pattern is furthermore inherited after activation by progeny. This intronic CpG island, on the other hand, is frequently unmethylated in CD4(+)CD25(+) T cells. Importantly, blocking maintenance DNA methylation, by pharmacological inhibition of DNA methyltransferase-1, induced significant and stable activation-dependent FOXP3 expression in cycling conventional T cells, which was further amplified by co-treatment with transforming growth factor beta. In contrast to natural Treg, such induced CD4(+)FOXP3(+) T cells could produce pro-inflammatory cytokines upon activation. These results indicate that DNA methylation normally restricts FOXP3 transcription in conventional human T cells.
Collapse
Affiliation(s)
- Meital Nagar
- Sheba Cancer Research Center, The Chaim Sheba Medical Center, Tel Hashomer and Tel Aviv University-Sackler Faculty of Medicine, Israel
| | | | | | | | | | | | | | | |
Collapse
|
75
|
Hoque MO, Kim MS, Ostrow KL, Liu J, Wisman GBA, Park HL, Poeta ML, Jeronimo C, Henrique R, Lendvai A, Schuuring E, Begum S, Rosenbaum E, Ongenaert M, Yamashita K, Califano J, Westra W, van der Zee AGJ, Van Criekinge W, Sidransky D. Genome-wide promoter analysis uncovers portions of the cancer methylome. Cancer Res 2008; 68:2661-70. [PMID: 18413733 DOI: 10.1158/0008-5472.can-07-5913] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
DNA methylation has a role in mediating epigenetic silencing of CpG island genes in cancer and other diseases. Identification of all gene promoters methylated in cancer cells "the cancer methylome" would greatly advance our understanding of gene regulatory networks in tumorigenesis. We previously described a new method of identifying methylated tumor suppressor genes based on pharmacologic unmasking of the promoter region and detection of re-expression on microarray analysis. In this study, we modified and greatly improved the selection of candidates based on new promoter structure algorithm and microarray data generated from 20 cancer cell lines of 5 major cancer types. We identified a set of 200 candidate genes that cluster throughout the genome of which 25 were previously reported as harboring cancer-specific promoter methylation. The remaining 175 genes were tested for promoter methylation by bisulfite sequencing or methylation-specific PCR (MSP). Eighty-two of 175 (47%) genes were found to be methylated in cell lines, and 53 of these 82 genes (65%) were methylated in primary tumor tissues. From these 53 genes, cancer-specific methylation was identified in 28 genes (28 of 53; 53%). Furthermore, we tested 8 of the 28 newly identified cancer-specific methylated genes with quantitative MSP in a panel of 300 primary tumors representing 13 types of cancer. We found cancer-specific methylation of at least one gene with high frequency in all cancer types. Identification of a large number of genes with cancer-specific methylation provides new targets for diagnostic and therapeutic intervention, and opens fertile avenues for basic research in tumor biology.
Collapse
Affiliation(s)
- Mohammad Obaidul Hoque
- Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins School of Medicine, Baltimore, Maryland 21231, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
76
|
Yamashita K, Kim MS, Park HL, Tokumaru Y, Osada M, Inoue H, Mori M, Sidransky D. HOP/OB1/NECC1 promoter DNA is frequently hypermethylated and involved in tumorigenic ability in esophageal squamous cell carcinoma. Mol Cancer Res 2008; 6:31-41. [PMID: 18234960 DOI: 10.1158/1541-7786.mcr-07-0213] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Promoter DNA hypermethylation with gene silencing is a common feature of human cancer, and cancer-prone methylation is believed to be a landmark of tumor suppressor genes (TSG). Identification of novel methylated genes would not only aid in the development of tumor markers but also elucidate the biological behavior of human cancers. We identified several epigenetically silenced candidate TSGs by pharmacologic unmasking of esophageal squamous cell carcinoma (ESCC) cell lines by demethylating agents (5-aza-2'-deoxycitidine and trichostatin A) combined with ESCC expression profiles using expression microarray. HOP/OB1/NECC1 was identified as an epigenetically silenced candidate TSG and further examined for (a) expression status, (b) methylation status, and (c) functional involvement in cancer cell lines. (a) The HOP gene encodes two putative promoters (promoters A and B) associated with two open reading frames (HOPalpha and HOPbeta, respectively), and HOPalpha and HOPbeta were both down-regulated in ESCC independently. (b) Promoter B harbors dense CpG islands, in which we found dense methylation in a cancer-prone manner (55% in tumor tissues by TaqMan methylation-specific PCR), whereas promoter A does not harbor CpG islands. HOPbeta silencing was associated with DNA methylation of promoter B in nine ESCC cell lines tested, and reactivated by optimal conditions of demethylating agents, whereas HOPalpha silencing was not reactivated by such treatments. Forced expression of HOP suppressed tumorigenesis in soft agar in four different squamous cell carcinoma cell lines. More convincingly, RNA interference knockdown of HOP in TE2 cells showed drastic restoration of the oncogenic phenotype. In conclusion, HOP is a putative TSG that harbors tumor inhibitory activity, and we for the first time showed that the final shutdown process of HOP expression is linked to promoter DNA hypermethylation under the double control of the discrete promoter regions in cancer.
Collapse
Affiliation(s)
- Keishi Yamashita
- Department of Otolaryngology, Head and Neck Cancer Research Division, Johns Hopkins University, Baltimore, MD 21231, USA
| | | | | | | | | | | | | | | |
Collapse
|
77
|
Kim MS, Lebron C, Nagpal JK, Chae YK, Chang X, Huang Y, Chuang T, Yamashita K, Trink B, Ratovitski EA, Califano JA, Sidransky D. Methylation of the DFNA5 increases risk of lymph node metastasis in human breast cancer. Biochem Biophys Res Commun 2008; 370:38-43. [PMID: 18346456 DOI: 10.1016/j.bbrc.2008.03.026] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2008] [Accepted: 03/04/2008] [Indexed: 01/12/2023]
Abstract
The pathogenesis of breast cancer involves multiple genetic and epigenetic events. In this study, we report an epigenetic alteration of DFNA5 in human breast cancer. DFNA5 gene was silenced in breast cancer cell lines that were methylated in the DFNA5 promoter, and restored by treatment with the demethylating agent, 5-aza-dC, and gene knock-down of DFNA5 increased cellular invasiveness in vitro. The mRNA expression of DFNA5 in breast cancer tissues was down-regulated as compared to normal tissues. Moreover, the DFNA5 promoter was found to be methylated in primary tumor tissues with high frequency (53%, 18/34). Quantitative methylation-specific PCR of DFNA5 clearly discriminated primary breast cancer tissues from normal breast tissues (15.3%, 2/13). Moreover, methylation status of DFNA5 was correlated with lymph node metastasis in breast cancer patients. Our data implicate DFNA5 promoter methylation as a novel molecular biomarker in human breast cancer.
Collapse
Affiliation(s)
- Myoung Sook Kim
- Department of Otolaryngology, Head and Neck Cancer Research Institute, Johns Hopkins University, 1550 Orleans Street 5N.03, Baltimore, MD 21231, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
78
|
|
79
|
Watanabe K, Kanno T, Oshima T, Miwa H, Tashiro C, Nishizaki T. The NMDA receptor NR2A subunit regulates proliferation of MKN45 human gastric cancer cells. Biochem Biophys Res Commun 2008; 367:487-90. [DOI: 10.1016/j.bbrc.2007.12.167] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 12/22/2007] [Indexed: 10/22/2022]
|
80
|
Kim MS, Yamashita K, Chae YK, Tokumaru Y, Chang X, Zahurak M, Osada M, Park HL, Chuang A, Califano JA, Sidransky D. A promoter methylation pattern in the N-methyl-D-aspartate receptor 2B gene predicts poor prognosis in esophageal squamous cell carcinoma. Clin Cancer Res 2008; 13:6658-65. [PMID: 18006766 DOI: 10.1158/1078-0432.ccr-07-1178] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To investigate whether the promoter methylation pattern in N-methyl-d-aspartate receptor 2B (NMDAR2B) is correlated with clinical features of human esophageal squamous cell carcinoma (ESCC), the methylation status of the gene was examined at three different sites (P1, P2, and P3) where two CpG islands reside within 1 kb upstream of the transcription start site. EXPERIMENTAL DESIGN Three independent modalities for methylation analysis (bisulfite sequencing, combined bisulfite restriction analysis, and TaqMan methylation-specific PCR) were done to analyze total 67 ESCC tissues that included 43 primary tumors with well-characterized clinicopathologic variables including patient outcome. RESULTS Using an optimized cutoff value based on quantitative methylation-specific PCR, we found that patients with higher NMDAR2B methylation ratio in the proximal region (P1) showed a worse 5-year disease-specific survival rate than those without NMDAR2B methylation (P < 0.006). A significant correlation was also seen between NMDAR2B promoter methylation and the presence of vascular permeation (P = 0.03). CONCLUSION NMDAR2B promoter methylation could be a clinically applicable marker in ESCC.
Collapse
Affiliation(s)
- Myoung Sook Kim
- Department of Otolaryngology, Head and Neck Cancer Research Division, Johns Hopkins University, 1550 Orleans Street, Baltimore, MD 21231, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
81
|
Kim MS, Chang X, Yamashita K, Nagpal JK, Baek JH, Wu G, Trink B, Ratovitski EA, Mori M, Sidransky D. Aberrant promoter methylation and tumor suppressive activity of the DFNA5 gene in colorectal carcinoma. Oncogene 2008; 27:3624-34. [PMID: 18223688 DOI: 10.1038/sj.onc.1211021] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To identify novel methylated gene promoters, we compared differential RNA expression profiles of colorectal cancer (CRC) cell lines with or without treatment of 5-aza-2'-deoxycytidine (5-aza-dC). Out of 1776 genes that were initially 'absent (that is, silenced)' by gene expression array analysis, we selected 163 genes that were increased after 5-aza-dC treatment in at least two of three CRC cell lines. The microarray results were confirmed by Reverse Transcription-PCR, and CpG island of the gene promoters were amplified and sequenced for examination of cancer-specific methylation. Among the genes identified, the deafness, autosomal dominant 5 gene, DFNA5, promoter was found to be methylated in primary tumor tissues with high frequency (65%, 65/100). Quantitative methylation-specific PCR of DFNA5 clearly discriminated primary CRC tissues from normal colon tissues (3%, 3/100). The mRNA expression of DFNA5 in four of five colon cancer tissues was significantly downregulated as compared to normal tissues. Moreover, forced expression of full-length DFNA5 in CRC cell lines markedly decreased the cell growth and colony-forming ability whereas knockdown of DFNA5 increased cell growth in culture. Our data implicate DFNA5 as a novel tumor suppressor gene in CRC and a valuable molecular marker for human cancer.
Collapse
Affiliation(s)
- M S Kim
- Department of Otolaryngology, Head and Neck Cancer Research Division, Johns Hopkins University, Baltimore, MD 21231, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
82
|
Kim MS, Chang X, Nagpal JK, Yamashita K, Baek JH, Dasgupta S, Wu G, Osada M, Woo JH, Westra WH, Trink B, Ratovitski EA, Moon C, Sidransky D. The N-methyl-D-aspartate receptor type 2A is frequently methylated in human colorectal carcinoma and suppresses cell growth. Oncogene 2007; 27:2045-54. [DOI: 10.1038/sj.onc.1210842] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
83
|
Wu G, Guo Z, Chang X, Kim MS, Nagpal JK, Liu J, Maki JM, Kivirikko KI, Ethier SP, Trink B, Sidransky D. LOXL1 and LOXL4 are epigenetically silenced and can inhibit ras/extracellular signal-regulated kinase signaling pathway in human bladder cancer. Cancer Res 2007; 67:4123-9. [PMID: 17456585 DOI: 10.1158/0008-5472.can-07-0012] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Promoter hypermethylation is one of the common mechanisms leading to gene silencing in various human cancers. Using a combination of pharmacologic unmasking and microarray techniques, we identified 59 candidate hypermethylated genes, including LOXL1, a lysyl oxidase-like gene, in human bladder cancer cells. We further showed that LOXL1 and LOXL4 are commonly silenced genes in human bladder cancer cells, and this silence is predominantly related to promoter methylation. We also found LOXL1 and LOXL4 gene methylation and loss of expression in primary bladder tumors. In addition, somatic mutations were identified in LOXL4, but not in LOXL1 in bladder cancer. Moreover, reintroduction of LOXL1 and LOXL4 genes into human bladder cancer cells leads to a decrease of colony formation ability. Further studies indicated that the overexpression of LOXL1 and LOXL4 could antagonize Ras in activating the extracellular signal-regulated kinase (ERK) signaling pathway. Thus, our current study suggests for the first time that lysyl oxidase-like genes can act as tumor suppressor genes and exert their functions through the inhibition of the Ras/ERK signaling pathway in human bladder cancer.
Collapse
Affiliation(s)
- Guojun Wu
- Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
84
|
Tanaka K, Imoto I, Inoue J, Kozaki K, Tsuda H, Shimada Y, Aiko S, Yoshizumi Y, Iwai T, Kawano T, Inazawa J. Frequent methylation-associated silencing of a candidate tumor-suppressor, CRABP1, in esophageal squamous-cell carcinoma. Oncogene 2007; 26:6456-68. [PMID: 17438526 DOI: 10.1038/sj.onc.1210459] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Epigenetic alterations and the resulting inactivation of tumor suppressor genes often contribute to the development of various cancers. To identify novel candidates that may be silenced by aberrant methylation in esophageal squamous-cell carcinoma (ESCC), we analysed ESCC cell lines by a recently developed method known as bacterial artificial chromosome array-based methylated CpG island amplification (BAMCA), and selected candidates through BAMCA-assisted strategy. In the course of this program, we identified frequent CpG methylation-dependent silencing of the gene encoding cellular retinoic acid binding protein 1 (CRABP1) in our panel of ESCC cell lines. Expression of CRABP1 mRNA was restored in gene-silenced ESCC cells after treatment with 5-aza 2'-deoxycytidine. The DNA methylation status of the CRABP1 CpG island with clear promoter activity correlated inversely with expression of this gene. CpG methylation of CRABP1 was frequently observed in primary ESCC tissues as well. Restoration of CRABP1 expression in ESCC cells lacking the protein reduced cell growth by inducing arrest at G(0)-G(1), whereas knockdown of the gene in cells expressing CRABP1 promoted cell growth. Among 113 primary ESCC tumors, the absence of immunoreactive CRABP1 was significantly associated with de-differentiation of cancer cells and with distant lymph-node metastases in the patients. These results indicate that CRABP1 appears to have a tumor-suppressor function in esophageal epithelium, and its epigenetic silencing may play a pivotal role during esophageal carcinogenesis. Its expression status in biopsies or resected tumors might serve as an index for identifying ESCC patients for whom combined therapeutic modalities would be recommended.
Collapse
MESH Headings
- Azacitidine/pharmacology
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Differentiation
- Cell Proliferation
- DNA Methylation
- Epigenesis, Genetic
- Esophageal Neoplasms/genetics
- Esophageal Neoplasms/metabolism
- Esophageal Neoplasms/pathology
- Female
- Gene Expression Regulation, Neoplastic
- Gene Silencing
- Humans
- Lymphatic Metastasis/pathology
- Male
- Middle Aged
- Promoter Regions, Genetic
- Receptors, Retinoic Acid/genetics
- Receptors, Retinoic Acid/metabolism
Collapse
Affiliation(s)
- K Tanaka
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
85
|
Liu JW, Kim MS, Nagpal J, Yamashita K, Poeta L, Chang X, Lee J, Park HL, Jeronimo C, Westra WH, Mori M, Moon C, Trink B, Sidransky D. Quantitative hypermethylation of NMDAR2B in human gastric cancer. Int J Cancer 2007; 121:1994-2000. [PMID: 17620329 DOI: 10.1002/ijc.22934] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
NMDA receptor Type 2B (NMDAR2B) is a candidate TSG first identified in esophageal squamous cell carcinoma (ESCC). To evaluate NMDAR2B methylation in gastric cancer progression, we performed quantitative methylation-specific PCR (MSP), RT-PCR and immnunohistochemistry (IHC) in primary gastric tissues and colony formation assays in gastric cancer cell lines. We found that the expression of NMDAR2B was reactivated by the demethylating agent, 5-aza-2'-deoxycytidine, with or without trichostatin A in gastric cancer cell lines. Moreover, inactivation of NMDAR2B was found to be closely correlated with promoter methylation status in gastric cell lines and primary gastric tumors. IHC data also showed that NMDAR2B was specifically expressed in gastric epithelial cells and its expression was diminished or absent in gastric cancer epithelium. Quantitative analysis of NMDAR2B promoter methylation showed 61% (17/28) hypermethylation in primary gastric tumors versus 5% (1/20) in normal gastric tissues from nongastric cancer patients. Forced over-expression of NMDAR2B in gastric cancer cell lines significantly inhibited cell colony formation. Taken together, the above results suggest that NMDAR2B methylation is a common and important biologically relevant event in gastric cancer progression.
Collapse
Affiliation(s)
- Jun-Wei Liu
- Department of Otolaryngology, Division of Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Myoung Sook Kim
- Department of Otolaryngology, Division of Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jatin Nagpal
- Department of Otolaryngology, Division of Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Keishi Yamashita
- Department of Otolaryngology, Division of Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Luana Poeta
- Department of Otolaryngology, Division of Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Xiaofei Chang
- Department of Otolaryngology, Division of Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Juna Lee
- Department of Otolaryngology, Division of Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Hannah Lui Park
- Department of Otolaryngology, Division of Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Carmen Jeronimo
- Department of Otolaryngology, Division of Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD
| | - William H Westra
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Masaki Mori
- Department of Surgical Oncology, Medical Institute of Bioregulation, Kyushu University, Tsurumibaru, Beppu, Japan
| | - Chulso Moon
- Department of Otolaryngology, Division of Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Barry Trink
- Department of Otolaryngology, Division of Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD
| | - David Sidransky
- Department of Otolaryngology, Division of Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD
| |
Collapse
|