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Cristalli C, Scotlandi K. Targeting DNA Methylation Machinery in Pediatric Solid Tumors. Cells 2024; 13:1209. [PMID: 39056791 PMCID: PMC11275080 DOI: 10.3390/cells13141209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
DNA methylation is a key epigenetic regulatory mechanism that plays a critical role in a variety of cellular processes, including the regulation of cell fate during development, maintenance of cell identity, and genome stability. DNA methylation is tightly regulated by enzymatic reactions and its deregulation plays an important role in the development of cancer. Specific DNA methylation alterations have been found in pediatric solid tumors, providing new insights into the development of these tumors. In addition, DNA methylation profiles have greatly contributed to tune the diagnosis of pediatric solid tumors and to define subgroups of patients with different risks of progression, leading to the reduction in unwanted toxicity and the improvement of treatment efficacy. This review highlights the dysregulated DNA methylome in pediatric solid tumors and how this information provides promising targets for epigenetic therapies, particularly inhibitors of DNMT enzymes (DNMTis). Opportunities and limitations are considered, including the ability of DNMTis to induce viral mimicry and immune signaling by tumors. Besides intrinsic action against cancer cells, DNMTis have the potential to sensitize immune-cold tumors to immunotherapies and may represent a remarkable option to improve the treatment of challenging pediatric solid tumors.
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Affiliation(s)
- Camilla Cristalli
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
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Ding L, Luo J, Du J, Zhao B, Luo J, Pan S, Zhang L, Yan X, Li J, Liu L. Upregulated SPAG6 correlates with increased STAT1 and is associated with reduced sensitivity of interferon-α response in BCR::ABL1 negative myeloproliferative neoplasms. Cancer Sci 2023; 114:4445-4458. [PMID: 37681349 PMCID: PMC10637088 DOI: 10.1111/cas.15950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/06/2023] [Accepted: 08/16/2023] [Indexed: 09/09/2023] Open
Abstract
Sperm-associated antigen 6 (SPAG6) has been identified as an oncogene or tumor suppressor in various types of human cancer. However, the role of SPAG6 in BCR::ABL1 negative myeloproliferative neoplasms (MPNs) remains unclear. Herein, we found that SPAG6 was upregulated at the mRNA level in primary MPN cells and MPN-derived leukemia cell lines. The SPAG6 protein was primarily located in the cytoplasm around the nucleus and positively correlated with β-tubulin expression. In vitro, forced expression of SPAG6 increased cell clone formation and promoted G1 to S cell cycle progression. Downregulation of SPAG6 promoted apoptosis, reduced G1 to S phase transition, and impaired cell proliferation and cytokine release accompanied by downregulated signal transducer and activator of transcription 1 (STAT1) expression. Furthermore, the inhibitory effect of interferon-α (INF-α) on the primary MPN cells with high SPAG6 expression was decreased. Downregulation of SPAG6 enhanced STAT1 induction, thus enhancing the proapoptotic and cell cycle arrest effects of INF-α both in vitro and in vivo. Finally, a decrease in SPAG6 protein expression was noted when the STAT1 signaling was blocked. Chromatin immunoprecipitation assays indicated that STAT1 protein could bind to the SPAG6 promoter, while the dual-luciferase reporter assay indicated that STAT1 could promote the expression of SPAG6. Our results substantiate the relationship between upregulated SPAG6, increased STAT1, and reduced sensitivity to INF-α response in MPN.
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Affiliation(s)
- Li Ding
- Department of HematologyThe First Affiliated Hospital of Chongqing Medical UniversityChongqingChina
- Department of HematologyThe Affiliated Hospital of Southwest Medical UniversityLuzhouChina
| | - Jie Luo
- Department of HematologyThe First Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Juan Du
- Department of HematologyThe Affiliated Hospital of Southwest Medical UniversityLuzhouChina
| | - Beibei Zhao
- Department of HematologyThe First Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Jin Luo
- Department of HematologyThe First Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Shirui Pan
- Department of HematologyThe First Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Linyi Zhang
- Department of HematologyThe First Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Xinyu Yan
- Department of HematologyThe First Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Junnan Li
- Department of HematologyThe First Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Lin Liu
- Department of HematologyThe First Affiliated Hospital of Chongqing Medical UniversityChongqingChina
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Sugino RP, Ohira M, Mansai SP, Kamijo T. Comparative epigenomics by machine learning approach for neuroblastoma. BMC Genomics 2022; 23:852. [PMID: 36572864 PMCID: PMC9793522 DOI: 10.1186/s12864-022-09061-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/02/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Neuroblastoma (NB) is the second most common pediatric solid tumor. Because the number of genetic mutations found in tumors are small, even in some patients with unfavorable NB, epigenetic variation is expected to play an important role in NB progression. DNA methylation is a major epigenetic mechanism, and its relationship with NB prognosis has been a concern. One limitation with the analysis of variation in DNA methylation is the lack of a suitable analytical model. Therefore, in this study, we performed a random forest (RF) analysis of the DNA methylome data of NB from multiple databases. RESULTS RF is a popular machine learning model owing to its simplicity, intuitiveness, and computational cost. RF analysis identified novel intermediate-risk patient groups with characteristic DNA methylation patterns within the low-risk group. Feature selection analysis based on probe annotation revealed that enhancer-annotated regions had strong predictive power, particularly for MYCN-amplified NBs. We developed a gene-based analytical model to identify candidate genes related to disease progression, such as PRDM8 and FAM13A-AS1. RF analysis revealed sufficient predictive power compared to other machine learning models. CONCLUSIONS RF is a useful tool for DNA methylome analysis in cancer epigenetic studies, and has potential to identify a novel cancer-related genes.
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Affiliation(s)
- Ryuichi P. Sugino
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan
| | - Miki Ohira
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan
| | - Sayaka P. Mansai
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan
| | - Takehiko Kamijo
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan ,grid.263023.60000 0001 0703 3735Laboratory of Tumor Molecular Biology, Department of Graduate School of Science and Engineering, Saitama University, Kita-Urawa, Saitama, Japan
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Mu J, Yuan P, Luo J, Chen Y, Tian Y, Ding L, Zhao B, Wang X, Wang B, Liu L. Upregulated SPAG6 promotes acute myeloid leukemia progression through MYO1D that regulates the EGFR family expression. Blood Adv 2022; 6:5379-5394. [PMID: 35667090 PMCID: PMC9631693 DOI: 10.1182/bloodadvances.2021006920] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/02/2022] [Indexed: 11/20/2022] Open
Abstract
Chromosomal aberrations and gene mutations have been considered to be the major reasons for high recurrence rates and poor survival among acute myeloid leukemia (AML) patients. However, the underlying molecular mechanism of AML gene mutation remains largely unclear. Here, we show that SPAG6 (sperm-associated antigen 6), one of the most markedly increased SPAG genes in AML, significantly contributed to the proliferation and migration of leukemic cells. SPAG6 was highly expressed in AML, and its upregulation was negatively correlated with the prognosis of the disease. In vitro, SPAG6 promoted the proliferation and migration of leukemia cells and promoted cell cycle progression from the G1 phase to the S phase. In vivo, low expression of SPAG6 reduced the proliferation and infiltration of leukemia cells and prolonged the survival of xenograft tumor mice. Furthermore, immunoprecipitation and mass spectrometry analysis showed that SPAG6 interacts with MYO1D (myosin 1D). Specifically, overexpression of SPAG6 promoted the translocation of MYO1D into the cell membrane, thus upgrading the expression level of the EGFR family and thereby promoting the progression of AML. Overall, our study found that SPAG6 combined with MYO1D and translocated MYO1D from the cytosol to the cytomembrane, which induced the PI3K (phosphoinositide 3-kinase)/AKT (protein kinase B) signaling and ERK (extracellular signal-regulated kinase) signaling pathway to regulate the growth and prognosis of AML. SPAG6 may become a new target gene for the treatment of AML.
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Affiliation(s)
- Jiao Mu
- Department of Hematology, and
- Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Yuan
- Department of Interventional Radiology and Pain Treatment, Tangdu Hospital, Air Force Medical University, Xi’an, China
| | - Jie Luo
- Department of Hematology, and
- Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yafan Chen
- Department of Human Movement Science, Xi’an Physical Education University, Xi’an, China
| | - Yiyuan Tian
- Department of Physiology, Medical College of Yan’an University, Yan’an, China; and
| | - Li Ding
- Department of Hematology, and
- Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Beibei Zhao
- Department of Hematology, and
- Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaocheng Wang
- Center of Clinical Aerospace Medicine, School of Aerospace Medicine, Key Laboratory of Aerospace Medicine of Ministry of Education
- Department of Aviation Medicine, The First Affiliated Hospital, and
| | - Bao Wang
- Tangdu Hospital, Department of Neurosurgery, Air Force Medical University, Xi’an, China
| | - Lin Liu
- Department of Hematology, and
- Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Bao Z, Zhu R, Fan H, Ye Y, Li T, Chai D. Aberrant expression of SPAG6 and NM23 predicts poor prognosis of human osteosarcoma. Front Genet 2022; 13:1012548. [PMID: 36199573 PMCID: PMC9527292 DOI: 10.3389/fgene.2022.1012548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: To investigate the expression and clinical significance of sperm-associated antigen 6 and NM23 proteins in human osteosarcoma.Methods: The specimens of conventional osteosarcoma with follow-up from 42 Chinese patients were analyzed in this study, and 12 cases of osteochondroma were considered controls. The expression of SPAG6 and NM23 was inspected using immunohistochemical staining, qRT-PCR, and Western blotting methods.Results: The positive expression rate of SPAG6 protein (71.43%) in 42 cases of osteosarcoma tissue was significantly higher than that (33.33%) in 12 cases of osteochondroma tissues (p < 0.05), while the positive rate of NM23 protein (35.71%) in osteosarcoma tissue was lower than that (58.33%) in osteochondroma tissue (p < 0.05). The mRNA and protein levels of SPAG6 were significantly higher than those of the adjacent normal tissues, while the expression of NM23 was lower in osteosarcoma tissues than that in the controls (p < 0.05 for all). There was a positive relationship between the expression of SPAG6 and pathological grade, metastasis, and Enneking stage (p < 0.05 for all). The overall survival rate of osteosarcoma patients with SPAG6 positive expression was significantly lower than that with SPAG6 negative expression. The relationship between the expression of NM23 and pathological grade, metastasis, and Enneking stage was negative (p < 0.05 for all). The overall survival rate of the osteosarcoma patients with NM23 positive expression was higher than that of the patients with NM23 negative expression (p < 0.05).Conclusion: Overexpression of SPAG6 and low expression of NM23 are negatively related to pathological grade, metastasis, and Enneking stage and prognosis of osteosarcoma patients. This suggested that SPAG6 and NM23 should be considered candidate prognostic biomarkers for patients with osteosarcoma.
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Affiliation(s)
- Zhengqi Bao
- Department of Orthopedics, The First Affiliated Hospital of Bengbu Medical University, Bengbu, China
- Anhui Province Key Laboratory of Tissue Transplantation, Bengbu Medical University, Bengbu, China
- *Correspondence: Zhengqi Bao, ; Tian Li, ; Damin Chai,
| | - Ruizhi Zhu
- Department of Orthopedics, The First Affiliated Hospital of Bengbu Medical University, Bengbu, China
| | - Huagang Fan
- Department of Orthopedics, The First Affiliated Hospital of Bengbu Medical University, Bengbu, China
| | - Yuchen Ye
- Department of Orthopedics, The First Affiliated Hospital of Bengbu Medical University, Bengbu, China
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, Xi’an, China
- *Correspondence: Zhengqi Bao, ; Tian Li, ; Damin Chai,
| | - Damin Chai
- Department of Pathology, The First Affiliated Hospital of Bengbu Medical University, Bengbu, China
- *Correspondence: Zhengqi Bao, ; Tian Li, ; Damin Chai,
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Xia Y, Li X, Tian X, Zhao Q. Identification of a Five-Gene Signature Derived From MYCN Amplification and Establishment of a Nomogram for Predicting the Prognosis of Neuroblastoma. Front Mol Biosci 2021; 8:769661. [PMID: 34950701 PMCID: PMC8691574 DOI: 10.3389/fmolb.2021.769661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/15/2021] [Indexed: 12/29/2022] Open
Abstract
Background: Neuroblastoma (NB), the most common solid tumor in children, exhibits vastly different genomic abnormalities and clinical behaviors. While significant progress has been made on the research of relations between clinical manifestations and genetic abnormalities, it remains a major challenge to predict the prognosis of patients to facilitate personalized treatments. Materials and Methods: Six data sets of gene expression and related clinical data were downloaded from the Gene Expression Omnibus (GEO) database, ArrayExpress database, and Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. According to the presence or absence of MYCN amplification, patients were divided into two groups. Differentially expressed genes (DEGs) were identified between the two groups. Enrichment analyses of these DEGs were performed to dig further into the molecular mechanism of NB. Stepwise Cox regression analyses were used to establish a five-gene prognostic signature whose predictive performance was further evaluated by external validation. Multivariate Cox regression analyses were used to explore independent prognostic factors for NB. The relevance of immunity was evaluated by using algorithms, and a nomogram was constructed. Results: A five-gene signature comprising CPLX3, GDPD5, SPAG6, NXPH1, and AHI1 was established. The five-gene signature had good performance in predicting survival and was demonstrated to be superior to International Neuroblastoma Staging System (INSS) staging and the MYCN amplification status. Finally, a nomogram based on the five-gene signature was established, and its clinical efficacy was demonstrated. Conclusion: Collectively, our study developed a novel five-gene signature and successfully built a prognostic nomogram that accurately predicted survival in NB. The findings presented here could help to stratify patients into subgroups and determine the optimal individualized therapy.
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Affiliation(s)
- Yuren Xia
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Xin Li
- Tianjin Cancer Hospital Airport Hospital, Tianjin, China
| | - Xiangdong Tian
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Qiang Zhao
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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Ding L, Luo J, Zhang JP, Wang J, Li ZQ, Huang J, Chai L, Mu J, Zhao B, Zhong YR, Zhang LY, Liu L. Aberrant expression of SPAG6 may affect the disease phenotype and serve as a tumor biomarker in BCR/ABL1-negative myeloproliferative neoplasms. Oncol Lett 2021; 23:10. [PMID: 34820009 PMCID: PMC8607346 DOI: 10.3892/ol.2021.13128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/15/2021] [Indexed: 11/28/2022] Open
Abstract
Sperm-associated antigen 6 (SPAG6) is a newly identified cancer-testis antigen that has been revealed to contribute to the occurrence and development of various types of human cancer, such as ovarian, bladder, breast and lung cancer. However, to the best of our knowledge, the expression levels of SPAG6 in breakpoint cluster region (BCR)/ABL1-negative myeloproliferative neoplasms (MPNs) have not been investigated previously. Using reverse transcription-quantitative PCR and different tissue staining techniques, the present study revealed that SPAG6 was expressed by MPN cells, both at the mRNA and protein levels, and that nucleated erythroid precursors and megakaryocytes expressed the highest levels of SPAG6. In addition, SPAG6, which is known as a microtubule-associated protein, was found to exhibit nucleic, cytoplasmic or both cytoplasmic and nucleic subcellular localization patterns within the same patient or cell type; however, it did not always co-localize with β-tubulin. Furthermore, SPAG6 expression was revealed to be associated with fewer splenomegaly [P=0.015 for polycythemia vera (PV) and essential thrombocythemia (ET); and P=0.012 for primary myelofibrosis (PMF)] and myelofibrosis events (P=0.014 for PV and ET; and P=0.004 for PMF). In patients with PMF, upregulated expression levels of SPAG6 were also found to be associated with lower white blood cell counts (P=0.042) and lactate dehydrogenase levels (P=0.012), and higher hemoglobin levels (P=0.031) and platelet counts (P=0.025). In addition, the receiver operating characteristic curve analysis indicated that SPAG6 may be a potential biomarker for distinguishing MPN cases from healthy individuals. In conclusion, to the best of our knowledge, the present study is the first to report that aberrant SPAG6 expression may affect the disease phenotype and serve as a tumor biomarker in BCR/ABL1-negative MPNs.
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Affiliation(s)
- Li Ding
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China.,Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jie Luo
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| | - Jing Ping Zhang
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Ji Wang
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Zhao Quan Li
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| | - Juan Huang
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Li Chai
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jiao Mu
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| | - Beibei Zhao
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| | - Yi Rui Zhong
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| | - Lin Yi Zhang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| | - Lin Liu
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
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Hattori N, Asada K, Miyajima N, Mori A, Nakanishi Y, Kimura K, Wakabayashi M, Takeshima H, Nitani C, Hara J, Ushijima T. Combination of a synthetic retinoid and a DNA demethylating agent induced differentiation of neuroblastoma through retinoic acid signal reprogramming. Br J Cancer 2021; 125:1647-1656. [PMID: 34635821 DOI: 10.1038/s41416-021-01571-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/16/2021] [Accepted: 09/29/2021] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The CpG island methylator phenotype of neuroblastoma (NBL) is strongly associated with poor prognosis and can be targeted by 5-aza-2'-deoxycytidine (5-aza-dC). Differentiation therapy is a standard maintenance therapy for high-risk NBLs. However, the in vivo effect of tamibarotene, a synthetic retinoic acid, and the efficacy of its combination with 5-aza-dC have not been studied. Here, we conducted a preclinical study to assess the in vivo tamibarotene effect and the combination. METHODS Treatment effects were analysed by in vitro cell growth and differentiation state and by in vivo xenograft suppression. Demethylated genes were analysed by DNA methylation microarrays and geneset enrichment. RESULTS Tamibarotene monotherapy induced neural extension and upregulation of differentiation markers of NBL cells in vitro, and tumour regression without severe side effects in vivo. 5-Aza-dC monotherapy suppressed tumour growth both in vitro and in vivo, and induced demethylation of genes related to nervous system development and function. Pre-treatment with 5-aza-dC in vitro enhanced upregulation of differentiation markers and genes involved in retinoic acid signaling. Pre-treatment with 5-aza-dC in vivo significantly suppressed tumour growth and reduced the variation in tumour sizes. CONCLUSIONS Epigenetic drug-based differentiation therapy using 5-aza-dC and TBT is a promising strategy for refractory NBLs.
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Affiliation(s)
- Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.
| | - Kiyoshi Asada
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Nozomu Miyajima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akiko Mori
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoko Nakanishi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kana Kimura
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Mika Wakabayashi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Chika Nitani
- Department of Pediatric Hematology and Oncology, Osaka City General Hospital, Osaka, Japan
| | - Junichi Hara
- Department of Pediatric Hematology and Oncology, Osaka City General Hospital, Osaka, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.
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Nitani C, Hara J, Kawamoto H, Taguchi T, Kimura T, Yoshimura K, Hamada A, Kitano S, Hattori N, Ushijima T, Ono H, Nakamoto M, Higuchi T, Sato A. Phase I study of tamibarotene monotherapy in pediatric and young adult patients with recurrent/refractory solid tumors. Cancer Chemother Pharmacol 2021; 88:99-107. [PMID: 33829292 DOI: 10.1007/s00280-021-04271-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/26/2021] [Indexed: 11/24/2022]
Abstract
PURPOSE Tamibarotene is a synthetic retinoid that inhibits proliferation and induces differentiation of malignant cells by binding to the retinoic acid receptor α/β. Previous in vitro studies have shown that some pediatric solid tumors with retinoic acid receptors differentiate in response to retinoic acid. We conducted a phase I dose-escalation study to determine the recommended dose of tamibarotene for further study in pediatric and young adult patients with recurrent/refractory solid tumors. METHODS Pediatric and young adult patients with recurrent/refractory solid tumors were administered tamibarotene at 4, 6, 8, 10, and 12 mg/m2/day for 14 or 21 days of a 28 day cycle. Safety, efficacy, and pharmacokinetics of tamibarotene were evaluated. RESULTS Twenty-two patients (median age 8 years) were enrolled in this study. No dose-limiting toxicity (DLT) was encountered, and tamibarotene was generally well tolerated. Two patients experienced severe adverse events (AEs), leading to discontinuation of the treatment. One grade 4 venous thrombosis and one grade 2 erythema multiforme were observed, which promptly resolved after tamibarotene discontinuance. The grade 4 venous thrombosis was a severe AE but not DLT because it occurred after the evaluation period. Pharmacokinetic analyses showed a dose-dependent increase in the maximum drug concentration (Cmax) and area under the concentration-time curve (AUC). None of the patients achieved a complete response or partial response. Seven patients had stable disease lasting longer than 18 weeks. CONCLUSIONS The recommended dose for phase II study of tamibarotene in pediatric and young adult patients with refractory solid tumors is 12 mg/m2/day for 21 days in a 28 day cycle.
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Affiliation(s)
- Chika Nitani
- Department of Pediatric Hematology and Oncology, Osaka City General Hospital, 2-13-22 Miyakojima-hondori, Miyakojima-ku, Osaka, 534-0021, Japan.
| | - Junichi Hara
- Department of Pediatric Hematology and Oncology, Osaka City General Hospital, 2-13-22 Miyakojima-hondori, Miyakojima-ku, Osaka, 534-0021, Japan
| | - Hiroshi Kawamoto
- Department of Pediatric Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Tomoaki Taguchi
- Department of Pediatric Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Toshimi Kimura
- Department of Pharmacy, Tokyo Women's Medical University Hospital, Tokyo, Japan
| | - Kenichi Yoshimura
- Center for Integrated Medical Research, Hiroshima University Hospital, Hiroshima, Japan
| | - Akinobu Hamada
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Shigehisa Kitano
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
| | - Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiromi Ono
- Clinical Research Support Office, National Cancer Center Hospital East, Chiba, Japan
| | - Masako Nakamoto
- Clinical Research Support Office, National Cancer Center Hospital East, Chiba, Japan
| | - Tsukiko Higuchi
- Clinical Research Support Office, National Cancer Center Hospital East, Chiba, Japan
| | - Akihiro Sato
- Clinical Research Support Office, National Cancer Center Hospital East, Chiba, Japan
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Li X, Zhang D, Xu L, Han Y, Liu W, Li W, Fan Z, Costanzo RM, Strauss Iii JF, Zhang Z, Wang H. Planar cell polarity defects and hearing loss in sperm-associated antigen 6 ( Spag6)-deficient mice. Am J Physiol Cell Physiol 2021; 320:C132-C141. [PMID: 33175573 PMCID: PMC7846974 DOI: 10.1152/ajpcell.00166.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Spag6 encodes an axoneme central apparatus protein that is required for normal flagellar and cilia motility. Recent findings suggest that Spag6 also plays a role in ciliogenesis, orientation of cilia basal feet, and planar polarity. Sensory cells of the inner ear display unique structural features that underlie their mechanosensitivity. They represent a distinctive form of cellular polarity, known as planar cell polarity (PCP). However, a role for Spag6 in the inner ear has not yet been explored. In the present study, the function of Spag6 in the inner ear was examined using Spag6-deficient mice. Our results demonstrate hearing loss in the Spag6 mutants, associated with abnormalities in cellular patterning, cell shape, stereocilia bundles, and basal bodies, as well as abnormally distributed Frizzled class receptor 6 (FZD6), suggesting that Spag6 participates in PCP regulation. Moreover, we found that the subapical microtubule meshwork was disrupted. Our observations suggest new functions for Spag6 in hearing and PCP in the inner ear.
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Affiliation(s)
- Xiaofei Li
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Daogong Zhang
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Lei Xu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Yuechen Han
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Wenwen Liu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Wei Li
- Department of Physiology, Wayne State University, Detroit, Michigan
| | - Zhaomin Fan
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Richard M Costanzo
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia
| | - Jerome F Strauss Iii
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, Virginia
| | - Zhibing Zhang
- Department of Physiology, Wayne State University, Detroit, Michigan
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan
| | - Haibo Wang
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
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11
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Pancho A, Aerts T, Mitsogiannis MD, Seuntjens E. Protocadherins at the Crossroad of Signaling Pathways. Front Mol Neurosci 2020; 13:117. [PMID: 32694982 PMCID: PMC7339444 DOI: 10.3389/fnmol.2020.00117] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/08/2020] [Indexed: 12/25/2022] Open
Abstract
Protocadherins (Pcdhs) are cell adhesion molecules that belong to the cadherin superfamily, and are subdivided into clustered (cPcdhs) and non-clustered Pcdhs (ncPcdhs) in vertebrates. In this review, we summarize their discovery, expression mechanisms, and roles in neuronal development and cancer, thereby highlighting the context-dependent nature of their actions. We furthermore provide an extensive overview of current structural knowledge, and its implications concerning extracellular interactions between cPcdhs, ncPcdhs, and classical cadherins. Next, we survey the known molecular action mechanisms of Pcdhs, emphasizing the regulatory functions of proteolytic processing and domain shedding. In addition, we outline the importance of Pcdh intracellular domains in the regulation of downstream signaling cascades, and we describe putative Pcdh interactions with intracellular molecules including components of the WAVE complex, the Wnt pathway, and apoptotic cascades. Our overview combines molecular interaction data from different contexts, such as neural development and cancer. This comprehensive approach reveals potential common Pcdh signaling hubs, and points out future directions for research. Functional studies of such key factors within the context of neural development might yield innovative insights into the molecular etiology of Pcdh-related neurodevelopmental disorders.
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Affiliation(s)
- Anna Pancho
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Tania Aerts
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Manuela D Mitsogiannis
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
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12
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The Emerging Role of Sperm-Associated Antigen 6 Gene in the Microtubule Function of Cells and Cancer. MOLECULAR THERAPY-ONCOLYTICS 2019; 15:101-107. [PMID: 31660426 PMCID: PMC6807308 DOI: 10.1016/j.omto.2019.08.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Accumulated evidence shows that sperm-associated antigen 6 (SPAG6) gene has multiple biological functions. It maintains the normal function of a variety of cells including ciliary/flagellar biogenesis and polarization, neurogenesis, and neuronal migration. Moreover, SPAG6 is found to be critically involved in auditory transduction and the fibroblast life cycle. Furthermore, SPAG6 plays an essential role in immuno-regulation. Notably, SPAG6 has been demonstrated to participate in the occurrence and progression of a variety of human cancers. New evidence shows that SPAG6 gene regulates tumor cell proliferation, apoptosis, invasion, and metastasis. Therefore, in this review, we describe the physiological function and mechanism of SPAG6 in human normal cells and cancer cells. We also highlight that SPAG6 gene may be an effective biomarker for the diagnosis of human cancer. Taken together, targeting SPAG6 could be a novel strategy for the treatment of human diseases including cancer.
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13
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Yang CM, Chang HS, Chen HC, You JJ, Liou HH, Ting SC, Ger LP, Li SC, Tsai KW. Low C6orf141 Expression is Significantly Associated with a Poor Prognosis in Patients with Oral Cancer. Sci Rep 2019; 9:4520. [PMID: 30872783 PMCID: PMC6418188 DOI: 10.1038/s41598-019-41194-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 02/26/2019] [Indexed: 12/21/2022] Open
Abstract
C6orf141 (Chromosome 6 open reading frame 141) is a novel gene, and its role in oral cancer progression remains unclear. C6orf141 expression in oral squamous cell carcinoma (OSCC) and adjacent normal tissues from 428 patients was examined through immunohistochemistry (IHC). Our results revealed that C6orf141 expression was significantly reduced in OSCC compared with adjacent normal tissues. Low C6orf141 expression was significantly associated with a poor American Joint Committee on Cancer pathological stage (P < 0.001), T classification (P = 0.002), and pN stage (P = 0.032). Kaplan-Meier curves revealed that low C6orf141 expression was significantly associated with shorter disease-specific survival (DSS) in patients with OSCC (log-rank P = 0.007). Multivariate analysis indicated that low C6orf141 expression was an independent prognostic biomarker for DSS (adjusted hazard ratio = 1.34; 95% confidence interval = 1.10-1.81; P = 0.05). Additionally, ectopic C6orf141 expression could significantly suppress oral cancer cell proliferation, colony formation, and migratory and invasive abilities. Xenograft tumor growth assay revealed that C6orf141 could significantly suppress oral tumor growth in vivo. Our results suggest that C6orf141 plays a novel tumor-suppressive role in oral cancer cell growth and motility. Furthermore, C6orf141 dysfunction could be a potential prognostic biomarker for OSCC and provide new therapeutic strategies in the future.
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Affiliation(s)
- Cheng-Mei Yang
- Department of Stomatology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Dental Technology, Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan
| | - Hao-Sheng Chang
- Department of Stomatology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Dental Technology, Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan
| | - Hung-Chih Chen
- Department of Stomatology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Dental Technology, Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan
| | - Jyun-Jie You
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Huei-Han Liou
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Su-Chen Ting
- Planning Office of Kaohsiung Municipal United Hospital, Kaohsiung, Taiwan
| | - Luo-Ping Ger
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Sung-Chou Li
- Genomics & Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.
| | - Kuo-Wang Tsai
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan. .,Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan. .,Department of Chemical Biology, National Pingtung University of Education, Pingtung, Taiwan.
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14
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Pineda B, Diaz-Lagares A, Pérez-Fidalgo JA, Burgués O, González-Barrallo I, Crujeiras AB, Sandoval J, Esteller M, Lluch A, Eroles P. A two-gene epigenetic signature for the prediction of response to neoadjuvant chemotherapy in triple-negative breast cancer patients. Clin Epigenetics 2019; 11:33. [PMID: 30786922 PMCID: PMC6381754 DOI: 10.1186/s13148-019-0626-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/31/2019] [Indexed: 01/14/2023] Open
Abstract
Background Pathological complete response (pCR) after neoadjuvant chemotherapy (NAC) in triple-negative breast cancer (TNBC) varies between 30 and 40% approximately. To provide further insight into the prediction of pCR, we evaluated the role of an epigenetic methylation-based signature. Methods Epigenetic assessment of DNA extracted from biopsy archived samples previous to NAC from TNBC patients was performed. Patients included were categorized according to previous response to NAC in responder (pCR or residual cancer burden, RCB = 0) or non-responder (non-pCR or RCB > 0) patients. A methyloma study was performed in a discovery cohort by the Infinium HumanMethylation450 BeadChip (450K array) from Illumina. The epigenetic silencing of those methylated genes in the discovery cohort were validated by bisulfite pyrosequencing (PyroMark Q96 System version 2.0.6, Qiagen) and qRT-PCR in an independent cohort of TN patients and in TN cell lines. Results Twenty-four and 30 patients were included in the discovery and validation cohorts, respectively. In the discovery cohort, nine genes were differentially methylated: six presented higher methylation in non-responder patients (LOC641519, LEF1, HOXA5, EVC2, TLX3, CDKL2) and three greater methylation in responder patients (FERD3L, CHL1, and TRIP10). After validation, a two-gene (FER3L and TRIP10) epigenetic score predicted RCB = 0 with an area under the ROC curve (AUC) = 0.905 (95% CI = 0.805–1.000). Patients with a positive epigenetic two-gene score showed 78.6% RCB = 0 versus only 10.7% RCB = 0 if signature were negative. Conclusions These results suggest that pCR in TNBC could be accurately predicted with an epigenetic signature of FERD3L and TRIP10 genes. Further prospective validation of these findings is warranted. Electronic supplementary material The online version of this article (10.1186/s13148-019-0626-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Begoña Pineda
- Biomedical Research Institute (INCLIVA), Valencia, Spain.,Department of Physiology, Faculty of Medicine, University of Valencia, Valencia, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Angel Diaz-Lagares
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.,Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Present Address: Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), CIBERONC, Santiago de Compostela, Spain
| | - José Alejandro Pérez-Fidalgo
- Biomedical Research Institute (INCLIVA), Valencia, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.,Oncology Department, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Octavio Burgués
- Biomedical Research Institute (INCLIVA), Valencia, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.,Pathology Department, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | | | - Ana B Crujeiras
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Present Address: Laboratory of Epigenomics in Endocrinology and Nutrition, Instituto de Investigacion Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS), Santiago de Compostela University (USC) and CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain
| | - Juan Sandoval
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Biomarkers and Precision Medicne Unit (UByMP), Instituto de Investigación Sanitaria La Fe (IISLaFeValencia), Valencia, Spain
| | - Manel Esteller
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.,Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Badalona, Barcelona, Catalonia, Spain
| | - Ana Lluch
- Biomedical Research Institute (INCLIVA), Valencia, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.,Oncology Department, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Pilar Eroles
- Biomedical Research Institute (INCLIVA), Valencia, Spain. .,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain. .,COST action, CA15204, Brussels, Belgium.
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15
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Li X, Xu L, Sun G, Wu X, Bai X, Li J, Strauss JF, Zhang Z, Wang H. Spag6 Mutant Mice Have Defects in Development and Function of Spiral Ganglion Neurons, Apoptosis, and Higher Sensitivity to Paclitaxel. Sci Rep 2017; 7:8638. [PMID: 28819108 PMCID: PMC5561245 DOI: 10.1038/s41598-017-08739-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/17/2017] [Indexed: 12/20/2022] Open
Abstract
Mammalian Sperm Associated Antigen 6 (SPAG6) is the orthologue of Chlamydomonas PF16, a protein localized in the axoneme central apparatus. Recent studies showed that Spag6 has a role in brain neuronal proliferation and differentiation. The mammalian spiral ganglion neurons (SGNs) are specialzed bipolar neurons in the inner ear. However, the role of SPAG6 in SGN has not been elucidated. Therefore, We hypothesized that a Spag6 knockout would affect the development and function of SGNs. We utilized Spag6-deficient mice and SGN explants to define the role of SPAG6. On postnatal day 30 (P30) mutant mice had lower SGN density compared to their wild-type littermates, and more apoptosis was evident in the mutants. Increased Bax expression, a disturbed distribution of cytochrome c, and cleaved caspase-3 positive staining indicated that increased apoptosis involved a mitochondrial pathway. Transmission electron microscopy revealed abnormalities in the ultrastructure of mutant SGNs as early as P7. In vitro, lack of SPAG6 affected the growth of neurites and growth cones. Additionally, SPAG6 deficiency decreased synapse density in SGN explants. Finally, Spag6 mutant SGNs were more sensitive to the microtubule stabilizing agent, paclitaxel. These findings suggest that Spag6 plays a crucial role in SGN development and function.
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Affiliation(s)
- Xiaofei Li
- Otolaryngology-Head and Neck Surgery, Provincial Hospital Affiliated to Shandong University, Jinan, PR China
- Shandong Provincial Key Laboratory of Otology, Jinan, PR China
| | - Lei Xu
- Otolaryngology-Head and Neck Surgery, Provincial Hospital Affiliated to Shandong University, Jinan, PR China
| | - Gaoying Sun
- Shandong Provincial Key Laboratory of Otology, Jinan, PR China
| | - Xianmin Wu
- Otolaryngology-Head and Neck Surgery, Provincial Hospital Affiliated to Shandong University, Jinan, PR China
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Xiaohui Bai
- Shandong Provincial Key Laboratory of Otology, Jinan, PR China
| | - Jianfeng Li
- Shandong Provincial Key Laboratory of Otology, Jinan, PR China
| | - Jerome F Strauss
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, 23298, USA
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Zhibing Zhang
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, 23298, USA.
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, 23298, USA.
| | - Haibo Wang
- Otolaryngology-Head and Neck Surgery, Provincial Hospital Affiliated to Shandong University, Jinan, PR China.
- Shandong Provincial Key Laboratory of Otology, Jinan, PR China.
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16
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Chang WL, Lai WW, Kuo IY, Lin CY, Lu PJ, Sheu BS, Wang YC. A six-CpG panel with DNA methylation biomarkers predicting treatment response of chemoradiation in esophageal squamous cell carcinoma. J Gastroenterol 2017; 52:705-714. [PMID: 27671002 DOI: 10.1007/s00535-016-1265-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 09/13/2016] [Indexed: 02/04/2023]
Abstract
BACKGROUND Prognosis of esophageal squamous cell carcinoma (ESCC) patients remains poor, and the chemoradiotherapy (CRT) applied to ESCC patients often failed. Therefore, development of biomarkers to predict CRT response is immensely important for choosing the best treatment strategy of an individual patient. METHODS The methylation array and pyrosequencing methylation assay were performed in pre-treatment endoscopic biopsies to identify probes with differential CpG methylation levels between good and poor CRT responders in a cohort of 12 ESCC patients. Receiver operating characteristic curves and multivariate logistic regressions were conducted to build the risk score equation of selected CpG probes in another cohort of 91 ESCC patients to predict CRT response. Kaplan-Meier analysis was used to estimate progression-free survival or time-to-progression of patients predicted with good and poor CRT responses. RESULTS Nine differentially methylated CpG probes were identified to be associated with CRT response. A risk score equation comprising six CpG probes located in IFNGR2, KCNK4, NOTCH4, NPY, PAX6, and SOX17 genes were built. The risk score was derived from the sum of each probe multiplied by its corresponding coefficient. Such a risk score has a good prediction performance in discriminating poor CRT responders from good responders (AUC: 0.930). Moreover, poor CRT responders predicted by risk score significantly had poorer prognosis in terms of shorter progression-free survival and time-to-progression (p = 0.004-0.008). CONCLUSION We established a proof-of-concept CRT response prediction panel consisting of six-CpG methylation biomarkers in identifying ESCC patients who are at high risk of CRT failure and need intensive care.
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Affiliation(s)
- Wei-Lun Chang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Wu-Wei Lai
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - I-Ying Kuo
- Department of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Chien-Yu Lin
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Pei-Jung Lu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Bor-Shyang Sheu
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan. .,Department of Internal Medicine, Tainan Hospital, Ministry of Health and Welfare, Tainan, 700, Taiwan.
| | - Yi-Ching Wang
- Department of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan. .,Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan.
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17
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Decock A, Ongenaert M, Cannoodt R, Verniers K, De Wilde B, Laureys G, Van Roy N, Berbegall AP, Bienertova-Vasku J, Bown N, Clément N, Combaret V, Haber M, Hoyoux C, Murray J, Noguera R, Pierron G, Schleiermacher G, Schulte JH, Stallings RL, Tweddle DA, De Preter K, Speleman F, Vandesompele J. Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma. Oncotarget 2016; 7:1960-72. [PMID: 26646589 PMCID: PMC4811509 DOI: 10.18632/oncotarget.6477] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/16/2015] [Indexed: 12/12/2022] Open
Abstract
Accurate assessment of neuroblastoma outcome prediction remains challenging. Therefore, this study aims at establishing novel prognostic tumor DNA methylation biomarkers. In total, 396 low- and high-risk primary tumors were analyzed, of which 87 were profiled using methyl-CpG-binding domain (MBD) sequencing for differential methylation analysis between prognostic patient groups. Subsequently, methylation-specific PCR (MSP) assays were developed for 78 top-ranking differentially methylated regions and tested on two independent cohorts of 132 and 177 samples, respectively. Further, a new statistical framework was used to identify a robust set of MSP assays of which the methylation score (i.e. the percentage of methylated assays) allows accurate outcome prediction. Survival analyses were performed on the individual target level, as well as on the combined multimarker signature. As a result of the differential DNA methylation assessment by MBD sequencing, 58 of the 78 MSP assays were designed in regions previously unexplored in neuroblastoma, and 36 are located in non-promoter or non-coding regions. In total, 5 individual MSP assays (located in CCDC177, NXPH1, lnc-MRPL3-2, lnc-TREX1-1 and one on a region from chromosome 8 with no further annotation) predict event-free survival and 4 additional assays (located in SPRED3, TNFAIP2, NPM2 and CYYR1) also predict overall survival. Furthermore, a robust 58-marker methylation signature predicting overall and event-free survival was established. In conclusion, this study encompasses the largest DNA methylation biomarker study in neuroblastoma so far. We identified and independently validated several novel prognostic biomarkers, as well as a prognostic 58-marker methylation signature.
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Affiliation(s)
- Anneleen Decock
- Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium
| | - Maté Ongenaert
- Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium
| | - Robrecht Cannoodt
- Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium.,Bioinformatics Institute Ghent From Nucleotides to Networks (BIG N2N), De Pintelaan, Ghent, Belgium.,DAMBI, VIB Inflammation Research Center, Technologiepark, Ghent, Belgium.,Department of Respiratory Medicine, Ghent University, De Pintelaan, Ghent, Belgium
| | - Kimberly Verniers
- Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium
| | - Bram De Wilde
- Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium.,Department of Pediatric Hematology and Oncology, Ghent University Hospital, De Pintelaan, Ghent, Belgium
| | - Geneviève Laureys
- Department of Pediatric Hematology and Oncology, Ghent University Hospital, De Pintelaan, Ghent, Belgium
| | - Nadine Van Roy
- Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium
| | - Ana P Berbegall
- Department of Pathology, Medical School, University of Valencia, and Health Research Institute INCLIVA, Blasco Ibañez, Valencia, Spain
| | - Julie Bienertova-Vasku
- Department of Pathological Physiology, Department of Pediatric Oncology, Masaryk University, Černopolní, Brno, Czech Republic
| | - Nick Bown
- Northern Genetics Service, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Nathalie Clément
- Department of Pediatric Oncology, Institut Curie, rue d'Ulm, Paris, France
| | - Valérie Combaret
- Centre Léon Bérard, Laboratoire de Recherche Translationnelle, rue Laennec, Lyon, France
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick NSW, Australia
| | - Claire Hoyoux
- Pediatric Hemato-oncology, CHR Citadelle, Liège, Belgium
| | - Jayne Murray
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick NSW, Australia
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia, and Health Research Institute INCLIVA, Blasco Ibañez, Valencia, Spain
| | - Gaelle Pierron
- Unité de Génétique Somatique, Institut Curie, rue d'Ulm, Paris, France
| | - Gudrun Schleiermacher
- U830 INSERM, Recherche Translationelle en Oncologie Pédiatrique (RTOP) and Department of Pediatric Oncology, Institut Curie, rue d'Ulm, Paris, France
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, Hufelandstraße, Essen, Germany
| | - Ray L Stallings
- National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland.,Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, York House, Dublin, Ireland
| | - Deborah A Tweddle
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
| | | | - Katleen De Preter
- Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium.,Bioinformatics Institute Ghent From Nucleotides to Networks (BIG N2N), De Pintelaan, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium.,Bioinformatics Institute Ghent From Nucleotides to Networks (BIG N2N), De Pintelaan, Ghent, Belgium
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Epigenetic dysregulation in neuroblastoma: A tale of miRNAs and DNA methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1502-1514. [PMID: 27751904 DOI: 10.1016/j.bbagrm.2016.10.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 09/19/2016] [Accepted: 10/13/2016] [Indexed: 12/11/2022]
Abstract
In neuroblastoma, the epigenetic landscape is more profoundly altered in aggressive compared to lower grade tumors and the concomitant hypermethylation of many genes, defined as "methylator phenotype", has been associated with poor outcome. DNA methylation can interfere with gene expression acting at distance through the methylation or demethylation of the regulatory regions of miRNAs. The multiplicity of miRNA targets may result in the simultaneous alteration of many biological pathways like cell proliferation, apoptosis, migration and differentiation. We have analyzed the methylation status of a set of miRNAs in a panel of neuroblastoma cell lines and identified a subset of hypermethylated and down-regulated miRNAs (miRNA 34b-3p, miRNA 34b-5p, miRNA34c-5p, and miRNA 124-2-3p) involved in the regulation of cell cycle, apoptosis and in the control of MYCN expression. These miRNAs share, in part, some of the targets whose expression is inversely correlated to the methylation and expression of the corresponding miRNA. To simulate the effect of the demethylation of miRNAs, we transfected the corresponding miRNA-mimics in the same cell lines and observed the down-regulation of a set of their target genes as well as the partial block of the cell cycle and the activation of the apoptotic pathway. The epigenetic alterations of miRNAs described in the present study were found also in a subset of patients at high risk of progression. Our data disclosed a complex network of interactions between epigenetically altered miRNAs and target genes, that could interfere at multiple levels in the control of cell homeostasis.
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Henrich KO, Bender S, Saadati M, Dreidax D, Gartlgruber M, Shao C, Herrmann C, Wiesenfarth M, Parzonka M, Wehrmann L, Fischer M, Duffy DJ, Bell E, Torkov A, Schmezer P, Plass C, Höfer T, Benner A, Pfister SM, Westermann F. Integrative Genome-Scale Analysis Identifies Epigenetic Mechanisms of Transcriptional Deregulation in Unfavorable Neuroblastomas. Cancer Res 2016; 76:5523-37. [PMID: 27635046 DOI: 10.1158/0008-5472.can-15-2507] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 05/29/2016] [Indexed: 11/16/2022]
Abstract
The broad clinical spectrum of neuroblastoma ranges from spontaneous regression to rapid progression despite intensive multimodal therapy. This diversity is not fully explained by known genetic aberrations, suggesting the possibility of epigenetic involvement in pathogenesis. In pursuit of this hypothesis, we took an integrative approach to analyze the methylomes, transcriptomes, and copy number variations in 105 cases of neuroblastoma, complemented by primary tumor- and cell line-derived global histone modification analyses and epigenetic drug treatment in vitro We found that DNA methylation patterns identify divergent patient subgroups with respect to survival and clinicobiologic variables, including amplified MYCN Transcriptome integration and histone modification-based definition of enhancer elements revealed intragenic enhancer methylation as a mechanism for high-risk-associated transcriptional deregulation. Furthermore, in high-risk neuroblastomas, we obtained evidence for cooperation between PRC2 activity and DNA methylation in blocking tumor-suppressive differentiation programs. Notably, these programs could be re-activated by combination treatments, which targeted both PRC2 and DNA methylation. Overall, our results illuminate how epigenetic deregulation contributes to neuroblastoma pathogenesis, with novel implications for its diagnosis and therapy. Cancer Res; 76(18); 5523-37. ©2016 AACR.
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Affiliation(s)
- Kai-Oliver Henrich
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany. k.henrich@dkfz
| | - Sebastian Bender
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany & Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Germany
| | - Maral Saadati
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Daniel Dreidax
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany
| | - Moritz Gartlgruber
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany
| | - Chunxuan Shao
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany
| | - Carl Herrmann
- Division of Theoretical Bioinformatics, German Cancer Research Center, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Germany
| | - Manuel Wiesenfarth
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Martha Parzonka
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany
| | - Lea Wehrmann
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany
| | - Matthias Fischer
- Department of Pediatric Oncology, University Children's Hospital, and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - David J Duffy
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Emma Bell
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Alica Torkov
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany
| | - Peter Schmezer
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany & Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Germany
| | - Frank Westermann
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany. k.henrich@dkfz
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Abe M, Yamashita S, Mori Y, Abe T, Saijo H, Hoshi K, Ushijima T, Takato T. High-risk oral leukoplakia is associated with aberrant promoter methylation of multiple genes. BMC Cancer 2016; 16:350. [PMID: 27255271 PMCID: PMC4891845 DOI: 10.1186/s12885-016-2371-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 05/19/2016] [Indexed: 01/26/2023] Open
Abstract
Background Early detection of oral squamous cell carcinomas (OSCCs) is urgently needed to improve the prognosis and quality of life (QOL) of patients. Oral leukoplakias (OLs), known as the most common premalignant lesions in the oral cavity, often precede OSCCs. Especially, OLs with dysplasia are known to have a high risk of malignant transformation. Here, we searched for the promoter methylation characteristic of high-risk OLs. Methods To identify methylation-silenced genes, a combined analysis of methylated DNA immunoprecipitation (MeDIP) − CpG island (CGI) microarray analysis and expression microarray analysis after treatment with a demethylating agent was performed in two OSCC cell lines (Ca9–22 and HSC-2). The methylation statuses of each gene were examined by methylation-specific PCR. Results A total of 52 genes were identified as candidates for methylation-silenced genes in Ca9-22 or HSC-2. The promoter regions of 13 genes among the 15 genes randomly selected for further analysis were confirmed to be methylated in one or more of five cell lines. In OSCC tissues (n = 26), 8 of the 13 genes, TSPYL5, EGFLAM, CLDN11, NKX2-3, RBP4, CMTM3, TRPC4, and MAP6, were methylated. In OL tissues (n = 24), seven of the eight genes, except for EGFLAM, were found to be methylated in their promoter regions. There were significantly greater numbers of methylated genes in OLs with dysplasia than in those without dysplasia (p < 0.0001). Conclusions OLs at high risk for malignant transformation were associated with aberrant promoter methylation of multiple genes. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2371-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Masanobu Abe
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan. .,Division for Health Service Promotion, University of Tokyo, Tokyo, Japan.
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoshiyuki Mori
- Department of Dentistry, Oral & Maxillofacial Surgery, Jichi Medical University, Tochigi, Japan
| | - Takahiro Abe
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hideto Saijo
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Kazuto Hoshi
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tsuyoshi Takato
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
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Kanth P, Bronner MP, Boucher KM, Burt RW, Neklason DW, Hagedorn CH, Delker DA. Gene Signature in Sessile Serrated Polyps Identifies Colon Cancer Subtype. Cancer Prev Res (Phila) 2016; 9:456-65. [PMID: 27026680 DOI: 10.1158/1940-6207.capr-15-0363] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 03/22/2016] [Indexed: 02/06/2023]
Abstract
Sessile serrated colon adenoma/polyps (SSA/P) are found during routine screening colonoscopy and may account for 20% to 30% of colon cancers. However, differentiating SSA/Ps from hyperplastic polyps (HP) with little risk of cancer is challenging and complementary molecular markers are needed. In addition, the molecular mechanisms of colon cancer development from SSA/Ps are poorly understood. RNA sequencing (RNA-Seq) was performed on 21 SSA/Ps, 10 HPs, 10 adenomas, 21 uninvolved colon, and 20 control colon specimens. Differential expression and leave-one-out cross-validation methods were used to define a unique gene signature of SSA/Ps. Our SSA/P gene signature was evaluated in colon cancer RNA-Seq data from The Cancer Genome Atlas (TCGA) to identify a subtype of colon cancers that may develop from SSA/Ps. A total of 1,422 differentially expressed genes were found in SSA/Ps relative to controls. Serrated polyposis syndrome (n = 12) and sporadic SSA/Ps (n = 9) exhibited almost complete (96%) gene overlap. A 51-gene panel in SSA/P showed similar expression in a subset of TCGA colon cancers with high microsatellite instability. A smaller 7-gene panel showed high sensitivity and specificity in identifying BRAF-mutant, CpG island methylator phenotype high, and MLH1-silenced colon cancers. We describe a unique gene signature in SSA/Ps that identifies a subset of colon cancers likely to develop through the serrated pathway. These gene panels may be utilized for improved differentiation of SSA/Ps from HPs and provide insights into novel molecular pathways altered in colon cancer arising from the serrated pathway. Cancer Prev Res; 9(6); 456-65. ©2016 AACR.
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Affiliation(s)
- Priyanka Kanth
- Department of Gastroenterology, University of Utah, Salt Lake City, Utah.
| | - Mary P Bronner
- Department of Pathology, University of Utah, Salt Lake City, Utah. Huntsman Cancer Institute, Salt Lake City, Utah
| | - Kenneth M Boucher
- Huntsman Cancer Institute, Salt Lake City, Utah. Division of Epidemiology, University of Utah, Salt Lake City, Utah
| | - Randall W Burt
- Department of Gastroenterology, University of Utah, Salt Lake City, Utah. Huntsman Cancer Institute, Salt Lake City, Utah
| | - Deborah W Neklason
- Division of Genetic Epidemiology, University of Utah, Salt Lake City, Utah
| | - Curt H Hagedorn
- Department of Gastroenterology, University of Utah, Salt Lake City, Utah. The Central Arkansas Veterans Healthcare System and University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Don A Delker
- Department of Gastroenterology, University of Utah, Salt Lake City, Utah
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22
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Olsson M, Beck S, Kogner P, Martinsson T, Carén H. Genome-wide methylation profiling identifies novel methylated genes in neuroblastoma tumors. Epigenetics 2016; 11:74-84. [PMID: 26786290 PMCID: PMC4846113 DOI: 10.1080/15592294.2016.1138195] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Neuroblastoma is a very heterogeneous tumor of childhood. The clinical spectra range from very aggressive metastatic disease to spontaneous regression, even without therapy. Aberrant DNA methylation pattern is a common feature of most cancers. For neuroblastoma, it has been demonstrated both for single genes as well as genome-wide, where a so-called methylator phenotype has been described. Here, we present a study using Illumina 450K methylation arrays on 60 neuroblastoma tumors. We show that aggressive tumors, characterized by International Neuroblastoma Risk Group (INRG) as stage M, are hypermethylated compared to low-grade tumors. On the contrary, INRG stage L tumors display more non-CpG methylation. The genes with the highest number of hypermethylated CpG sites in INRG M tumors are TERT, PCDHGA4, DLX5, and DLX6-AS1. Gene ontology analysis showed a representation of neuronal tumor relevant gene functions among the differentially methylated genes. For validation, we used a set of independent tumors previously analyzed with the Illumina 27K methylation arrays, which confirmed the differentially methylated sites. Top candidate genes with aberrant methylation were analyzed for altered gene expression through the R2 platform (http://r2.amc.nl), and for correlations between methylation and gene expression in a public dataset. Altered expression in nonsurvivors was found for the genes B3GALT4 and KIAA1949, CLIC5, DLX6-AS, TERT, and PIRT, and strongest correlations were found for TRIM36, KIAA0513, and PIRT. Our data indicate that methylation profiling can be used for patient stratification and informs on epigenetically deregulated genes with the potential of increasing our knowledge about the underlying mechanisms of tumor development.
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Affiliation(s)
- Maja Olsson
- a Sahlgrenska Cancer Center , Department of Pathology , Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Sweden
| | - Stephan Beck
- b Department of Cancer Biology , UCL Cancer Institute, University College London , UK
| | - Per Kogner
- c Childhood Cancer Research Unit , Department of Woman and Child Health , Karolinska Institute, Karolinska Hospital , Sweden
| | - Tommy Martinsson
- d Department of Clinical Genetics , Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Sweden
| | - Helena Carén
- a Sahlgrenska Cancer Center , Department of Pathology , Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Sweden
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Li W, Mukherjee A, Wu J, Zhang L, Teves ME, Li H, Nambiar S, Henderson SC, Horwitz AR, Strauss JF, Fang X, Zhang Z. Sperm Associated Antigen 6 (SPAG6) Regulates Fibroblast Cell Growth, Morphology, Migration and Ciliogenesis. Sci Rep 2015; 5:16506. [PMID: 26585507 PMCID: PMC4653743 DOI: 10.1038/srep16506] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/15/2015] [Indexed: 11/09/2022] Open
Abstract
Mammalian Spag6 is the orthologue of Chlamydomonas PF16, which encodes a protein localized in the axoneme central apparatus, and regulates flagella/cilia motility. Most Spag6-deficient mice are smaller in size than their littermates. Because SPAG6 decorates microtubules, we hypothesized that SPAG6 has other roles related to microtubule function besides regulating flagellar/cilia motility. Mouse embryonic fibroblasts (MEFs) were isolated from Spag6-deficient and wild-type embryos for these studies. Both primary and immortalized Spag6-deficient MEFs proliferated at a much slower rate than the wild-type MEFs, and they had a larger surface area. Re-expression of SPAG6 in the Spag6-deficient MEFs rescued the abnormal cell morphology. Spag6-deficient MEFs were less motile than wild-type MEFs, as shown by both chemotactic analysis and wound-healing assays. Spag6-deficient MEFs also showed reduced adhesion associated with a non-polarized F-actin distribution. Multiple centrosomes were observed in the Spag6-deficient MEF cultures. The percentage of cells with primary cilia was significantly reduced compared to the wild-type MEFs, and some Spag6-deficient MEFs developed multiple cilia. Furthermore, SPAG6 selectively increased expression of acetylated tubulin, a microtubule stability marker. The Spag6-deficient MEFs were more sensitive to paclitaxel, a microtubule stabilizer. Our studies reveal new roles for SPAG6 in modulation of cell morphology, proliferation, migration, and ciliogenesis.
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Affiliation(s)
- Wei Li
- Department of Obstetrics &Gynecology, Virginia Commonwealth University, Richmond, VA, 23298
| | - Abir Mukherjee
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, 23298
| | - Jinhua Wu
- Department of Obstetrics &Gynecology, Virginia Commonwealth University, Richmond, VA, 23298
| | - Ling Zhang
- Department of Obstetrics &Gynecology, Virginia Commonwealth University, Richmond, VA, 23298.,School of Public Health, Wuhan University of Science and Technology, Wuhan, Hubei 430065, China
| | - Maria E Teves
- Department of Obstetrics &Gynecology, Virginia Commonwealth University, Richmond, VA, 23298
| | - Hongfei Li
- Department of Obstetrics &Gynecology, Virginia Commonwealth University, Richmond, VA, 23298
| | - Shanti Nambiar
- Department of Obstetrics &Gynecology, Virginia Commonwealth University, Richmond, VA, 23298
| | - Scott C Henderson
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, VA, 23298
| | - Alan R Horwitz
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Jerome F Strauss
- Department of Obstetrics &Gynecology, Virginia Commonwealth University, Richmond, VA, 23298.,Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, 23298
| | - Xianjun Fang
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, 23298
| | - Zhibing Zhang
- Department of Obstetrics &Gynecology, Virginia Commonwealth University, Richmond, VA, 23298.,Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, 23298
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Yáñez Y, Grau E, Rodríguez-Cortez VC, Hervás D, Vidal E, Noguera R, Hernández M, Segura V, Cañete A, Conesa A, Font de Mora J, Castel V. Two independent epigenetic biomarkers predict survival in neuroblastoma. Clin Epigenetics 2015; 7:16. [PMID: 25767620 PMCID: PMC4357365 DOI: 10.1186/s13148-015-0054-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/09/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Neuroblastoma (NB) is the most common extracranial pediatric solid tumor with a highly variable clinical course, ranging from spontaneous regression to life-threatening disease. Survival rates for high-risk NB patients remain disappointingly low despite multimodal treatment. Thus, there is an urgent clinical need for additional biomarkers to improve risk stratification, treatment management, and survival rates in children with aggressive NB. RESULTS Using gene promoter methylation analysis in 48 neuroblastoma tumors with microarray technology, we found a strong association between survival and gene promoter hypermethylation (P = 0.036). Hypermethylation of 70 genes significantly differentiated high-risk survivor patients from those who died during follow-up time. Sixteen genes with relevant roles in cancer biology were further validated in an additional cohort of 83 neuroblastoma tumors by bisulfite pyrosequencing. High promoter methylation rates of these genes were found in patients with metastatic tumors (either stage metastatic (M) or metastatic special (MS)), 18 months or older at first diagnosis, MYCN amplification, relapsed, and dead. Notably, the degree of methylation of retinoblastoma 1 (RB1) and teratocarcinoma-derived growth factor 1 (TDGF1) predicts event-free and overall survival independently of the established risk factors. In addition, low RB1 mRNA expression levels associate with poor prognosis suggesting that promoter methylation could contribute to the transcriptional silencing of this gene in NB. CONCLUSIONS We found a new epigenetic signature predictive for NB patients' outcome: the methylation status of RB1 and TDGF1 associate with poorer survival. This information is useful to assess prognosis and improve treatment selection.
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Affiliation(s)
- Yania Yáñez
- Pediatric Oncology Unit, Hospital Universitari i Politècnic La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
| | - Elena Grau
- Pediatric Oncology Unit, Hospital Universitari i Politècnic La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
| | - Virginia C Rodríguez-Cortez
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC) Bellvitge Biomedical Research Institute (IDIBELL), Gran Via de L'Hospitalet, Barcelona, 08908 Spain
| | - David Hervás
- Biostatistics Unit, Instituto de Investigación Sanitaria La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
| | - Enrique Vidal
- Genomics of Gene Expression Lab, Centro de Investigaciones Príncipe Felipe, Carrer d'Eduardo Primo Yúfera, Valencia, 46012 Spain
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia, Avda Blasco Ibáñez, Valencia, 46010 Spain
| | - Miguel Hernández
- Department of Pathology, Hospital Universitari i Politècnic La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
| | - Vanessa Segura
- Pediatric Oncology Unit, Hospital Universitari i Politècnic La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
| | - Adela Cañete
- Pediatric Oncology Unit, Hospital Universitari i Politècnic La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
| | - Ana Conesa
- Genomics of Gene Expression Lab, Centro de Investigaciones Príncipe Felipe, Carrer d'Eduardo Primo Yúfera, Valencia, 46012 Spain
| | - Jaime Font de Mora
- Laboratory of Cellular and Molecular Biology, Instituto de Investigación Sanitaria La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
| | - Victoria Castel
- Pediatric Oncology Unit, Hospital Universitari i Politècnic La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
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Abe M, Inaki R, Kanno Y, Hoshi K, Takato T. Molecular analysis of a mammary analog secretory carcinoma in the upper lip: Novel search for genetic and epigenetic abnormalities in MASC. Int J Surg Case Rep 2015; 9:8-11. [PMID: 25703106 PMCID: PMC4392290 DOI: 10.1016/j.ijscr.2015.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 02/07/2015] [Indexed: 12/01/2022] Open
Abstract
Mammary analog secretory carcinoma (MASC) is a rare malignancy of the salivary glands characterized by ETV6–NTRK3 fusion gene. We diagnosed a case of MASC by molecular approaches (FISH, RT-PCR and sequencing). Furthermore, we searched novel genetic and epigenetic abnormalities in this MASC.
Introduction Mammary analog secretory carcinoma (MASC) is a newly described rare malignancy of the salivary glands characterized by an ETS variant 6 (ETV6)–neurotrophic tyrosine kinase receptor type 3 (NTRK3) fusion gene (EN fusion gene). Presentation of case We present a case of MASC derived from the left upper lip in a 61-year-old woman. ETV6 rearrangement was detected by fluorescence in situ hybridization (FISH). The presence of EN fusion transcripts was verified by reverse-transcriptase polymerase chain reaction (RT-PCR) and sequencing of the PCR products. Accordingly, this tumor was diagnosed as MASC. Moreover, we performed mutation analysis of the 50 known cancer-related genes using next-generation sequencing. No mutation of cancer-related genes was identified here. Subsequently, the methylation status in promoter region of tumor-suppressor genes, RASSF1A and RARB2, was examined. Both genes have been reported to be methylated in malignant salivary gland tumors, but they were found to be unmethylated. Discussion Recent studies have demonstrated that distinct types of malignant salivary gland carcinomas are driven by specific, highly recurrent genetic alterations. Detection of molecular abnormalities could be powerful diagnostic tools in the field of salivary gland tumors in near future. Conclusion We experienced a rare malignant salivary gland carcinoma, MASC. We diagnosed this tumor by molecular approach and subsequently tried to identify novel molecular abnormalities. Although no novel molecular alteration except for EN fusion gene was identified, this result might represent the favorable prognosis of patients with MASC.
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Affiliation(s)
- Masanobu Abe
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, Tokyo, Japan; Division for Health Service Promotion, University of Tokyo, Tokyo, Japan.
| | - Ryoko Inaki
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, Tokyo, Japan
| | - Yuki Kanno
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, Tokyo, Japan
| | - Kazuto Hoshi
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, Tokyo, Japan
| | - Tsuyoshi Takato
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, Tokyo, Japan
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Suzuki H, Yamamoto E, Maruyama R, Niinuma T, Kai M. Biological significance of the CpG island methylator phenotype. Biochem Biophys Res Commun 2014; 455:35-42. [PMID: 25016183 DOI: 10.1016/j.bbrc.2014.07.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/25/2014] [Accepted: 07/01/2014] [Indexed: 12/12/2022]
Abstract
Cancers exhibiting the CpG island methylator phenotype (CIMP) are found among a wide variety of human malignancies and represent a subclass of tumors showing concurrent hypermethylation of multiple CpG islands. These CIMP-positive tumors often exhibit characteristic molecular and clinicopathological features, suggesting CIMP represents a distinct carcinogenic pathway. However, marker genes to define CIMP have been largely inconsistent among studies, which has caused results to vary. Nonetheless, recent advances in genome-wide methylation analysis have enabled the existence of CIMP to be confirmed, and large-scale cancer genome analyses have begun to unravel the previously unknown molecular basis of CIMP tumors. CIMP is strongly associated with clinical outcome, suggesting it may be a predictive biomarker.
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Affiliation(s)
- Hiromu Suzuki
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan.
| | - Eiichiro Yamamoto
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Reo Maruyama
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Takeshi Niinuma
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Masahiro Kai
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
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27
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Zhao X, Yang F, Li S, Liu M, Ying S, Jia X, Wang X. CpG island methylator phenotype of myelodysplastic syndrome identified through genome-wide profiling of DNA methylation and gene expression. Br J Haematol 2014; 165:649-58. [PMID: 24601943 DOI: 10.1111/bjh.12811] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 01/10/2014] [Indexed: 12/13/2022]
Abstract
The CpG island methylator phenotype (CIMP) is an epigenetic phenomenon and plays an important role in tumourigenesis in various cancers. The identification of aberrant DNA methylation can be exploited for early diagnosis and risk assessment of patients. We identified a CIMP in myelodysplastic syndrome (MDS). Genes were screened for hypermethylation and transcription downregulation through genome-wide DNA methylation profiling and gene expression microarrays. Methylation-specific, real-time, and bisulfite-sequencing polymerase chain reaction were performed to validate selected genes. The hypermethylation of genes as a diagnostic tool for the detection of MDS was evaluated. Kaplan-Meier survival analysis and Cox regression were performed. A draft of an MDS CIMP was established and revised to 6 genes after validation in 20 patients and 20 controls. Further large-scale analysis showed that the majority of 211 MDS patients were hypermethylated in 6 genes. The area under the curve of CIMP was 0·9768 (95% confidence interval 0·9609-0·9928). A combination of 5 or more of the methylated genes showed a specificity of 95% and sensitivity of 91% for the diagnosis of MDS. We found CIMP positivity to be a significantly unfavourable prognostic factor for MDS. These results indicate that the newly established CIMP may improve diagnostic accuracy and prognosis assessment in MDS.
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Affiliation(s)
- Xiaoli Zhao
- Department of Haematology, Huashan Hospital, Fudan University, Shanghai, China
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Aberrant methylation of NPY, PENK, and WIF1 as a promising marker for blood-based diagnosis of colorectal cancer. BMC Cancer 2013; 13:566. [PMID: 24289328 PMCID: PMC4219483 DOI: 10.1186/1471-2407-13-566] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 11/25/2013] [Indexed: 12/26/2022] Open
Abstract
Background DNA methylation is a well-known epigenetic mechanism involved in epigenetic gene regulation. Several genes were reported hypermethylated in CRC, althought no gene marker was proven to be individually of sufficient sensitivity or specificity in routine clinical practice. Here, we identified novel epigenetic markers and assessed their combined use for diagnostic accuracy. Methods We used methylation arrays on samples from several effluents to characterize methylation profiles in CRC samples and controls, as established by colonoscopy and pathology findings, and selected two differentially methylated candidate epigenetic genes (NPY, PENK). To this gene panel we added WIF, on the basis of being reported in literature as silenced by promoter hypermethylation in several cancers, including CRC. We measured their methylation degrees by quantitative multiplex-methylation specific PCR (QM-MSP) on 15 paired carcinomas and adjacent non-cancerous colorectal tissues and we subsequently performed a clinical validation on two different series of 266 serums, subdivided in 32 CRC, 26 polyps, 47 other cancers and 161 with normal colonoscopy. We assessed the results by receiver operating characteristic curve (ROC), using cumulative methylation index (CMI) as variable threshold. Results We obtained CRC detection on tissues with both sensitivity and specificity of 100%. On serum CRC samples, we obtained sensitivity/specificity values of, e.g., 87%/80%, 78%/90% and 59%/95%, and negative predictive value/positive predictive value figures of 97%/47%, 95%/61% and 92%/70%. On serum samples from other cancers we obtained sensitivity/specificity of, e.g, 89%/25%, 43%/80% and 28%/91%. Conclusions We showed the potential of NPY, PENK, and WIF1 as combined epigenetic markers for CRC diagnosis, both in tissue and serum and tested their use as serum biomarkers in other cancers. We optimized a QM-MSP for simultaneously quantifying their methylation levels. Our assay can be an effective blood test for patients where CRC risk is present but difficult to assess (e.g. mild symptoms with no CRC family history) and who would therefore not necessarily choose to go for further examination. This panel of markers, if validated, can also be a cost effective screening tool for the detection of asymptomatic cancer patients for colonoscopy.
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Histone-lysine methyltransferase EHMT2 is involved in proliferation, apoptosis, cell invasion, and DNA methylation of human neuroblastoma cells. Anticancer Drugs 2013; 24:484-93. [PMID: 23466651 DOI: 10.1097/cad.0b013e32835ffdbb] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Neuroblastoma (NB), a childhood neoplasm arising from neural crest cells, is characterized by a diversity of clinical behaviors ranging from spontaneous remission to rapid tumor progression and death. In addition to genetic abnormalities, recent studies have indicated that epigenetic aberrations also contribute toward NB pathogenesis. However, the epigenetic mechanisms underlying the pathogenesis of NB are largely unknown. Inhibition of euchromatic histone-lysine N-methyltransferase 2 (EHMT2) was evaluated through the measurement of H3K9Me2 levels. Cell proliferation was examined by cell counting in human NB cell lines (LA1-55n, IMR-5, and NMB). The RNA expression of EHMT2, MYCN, and p21 was measured by real-time PCR. The expression of PCNA, MYCN, p53, cyclinD1, H3, H3K27M2, and H3K9Me2 was examined by western blot analysis. In-vitro invasion and the effects of the EHMT2 inhibitor (BIX-01294) were assessed in the Transwell chamber assay. Caspase 3 and 8 activities were measured using a Caspase-Glo assay kit. The level of overall DNA methylation was measured by liquid chromatography-mass spectroscopy. BIX-01294, a specific inhibitor of EHMT2 (a key enzyme for histone H3 dimethylation at lysine-9), specifically decreases the overall H3K9Me2 level but not H3K27Me2. The inhibition of EHMT2 decreased the proliferation of NB cells and induced apoptosis by increasing caspase 8/caspase 3 activity. BIX-01294 inhibited NB cell mobility and invasion. This was accompanied by a decreased expression of the MYCN oncogene. Inhibition of EHMT2 enhanced a doxorubicin-induced inhibitory effect on cell proliferation. Finally, EHMT2 inhibition modulated overall DNA methylation levels in NB cells. Our results show that histone-lysine methylation is involved in cell proliferation, apoptosis, cell invasion, and overall DNA methylation in human NB cells. Further understanding of this mechanism may provide an insight into the pathogenesis of NB progression and lead to novel treatment strategies.
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Asada K, Abe M, Ushijima T. Clinical application of the CpG island methylator phenotype to prognostic diagnosis in neuroblastomas. J Hum Genet 2013; 58:428-33. [DOI: 10.1038/jhg.2013.64] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 05/06/2013] [Accepted: 05/11/2013] [Indexed: 12/21/2022]
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Banelli B, Merlo DF, Allemanni G, Forlani A, Romani M. Clinical potentials of methylator phenotype in stage 4 high-risk neuroblastoma: an open challenge. PLoS One 2013; 8:e63253. [PMID: 23717404 PMCID: PMC3661569 DOI: 10.1371/journal.pone.0063253] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/31/2013] [Indexed: 12/31/2022] Open
Abstract
Approximately 20% of stage 4 high-risk neuroblastoma patients are alive and disease-free 5 years after disease onset while the remaining experience rapid and fatal progression. Numerous findings underline the prognostic role of methylation of defined target genes in neuroblastoma without taking into account the clinical and biological heterogeneity of this disease. In this report we have investigated the methylation of the PCDHB cluster, the most informative member of the “Methylator Phenotype” in neuroblastoma, hypothesizing that if this epigenetic mark can predict overall and progression free survival in high-risk stage 4 neuroblastoma, it could be utilized to improve the risk stratification of the patients, alone or in conjunction with the previously identified methylation of the SFN gene (14.3.3sigma) that can accurately predict outcome in these patients. We have utilized univariate and multivariate models to compare the prognostic power of PCDHB methylation in terms of overall and progression free survival, quantitatively determined by pyrosequencing, with that of other markers utilized for the patients' stratification utilizing methylation thresholds calculated on neuroblastoma at stage 1–4 and only on stage 4, high-risk patients. Our results indicate that PCDHB accurately distinguishes between high- and intermediate/low risk stage 4 neuroblastoma in agreement with the established risk stratification criteria. However PCDHB cannot predict outcome in the subgroup of stage 4 patients at high-risk whereas methylation levels of SFN are suggestive of a “methylation gradient” associated with tumor aggressiveness as suggested by the finding of a higher threshold that defines a subset of patients with an extremely severe disease (OS <24 months). Because of the heterogeneity of neuroblastoma we believe that clinically relevant methylation markers should be selected and tested on homogeneous groups of patients rather than on patients at all stages.
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Affiliation(s)
- Barbara Banelli
- Tumor Genetics and Epigenetics, IRCCS AOU San Martino-IST, Genova, Italy.
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Ogino S, Lochhead P, Chan AT, Nishihara R, Cho E, Wolpin BM, Meyerhardt JA, Meissner A, Schernhammer ES, Fuchs CS, Giovannucci E. Molecular pathological epidemiology of epigenetics: emerging integrative science to analyze environment, host, and disease. Mod Pathol 2013; 26:465-84. [PMID: 23307060 PMCID: PMC3637979 DOI: 10.1038/modpathol.2012.214] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epigenetics acts as an interface between environmental/exogenous factors, cellular responses, and pathological processes. Aberrant epigenetic signatures are a hallmark of complex multifactorial diseases (including neoplasms and malignancies such as leukemias, lymphomas, sarcomas, and breast, lung, prostate, liver, and colorectal cancers). Epigenetic signatures (DNA methylation, mRNA and microRNA expression, etc) may serve as biomarkers for risk stratification, early detection, and disease classification, as well as targets for therapy and chemoprevention. In particular, DNA methylation assays are widely applied to formalin-fixed, paraffin-embedded archival tissue specimens as clinical pathology tests. To better understand the interplay between etiological factors, cellular molecular characteristics, and disease evolution, the field of 'molecular pathological epidemiology (MPE)' has emerged as an interdisciplinary integration of 'molecular pathology' and 'epidemiology'. In contrast to traditional epidemiological research including genome-wide association studies (GWAS), MPE is founded on the unique disease principle, that is, each disease process results from unique profiles of exposomes, epigenomes, transcriptomes, proteomes, metabolomes, microbiomes, and interactomes in relation to the macroenvironment and tissue microenvironment. MPE may represent a logical evolution of GWAS, termed 'GWAS-MPE approach'. Although epigenome-wide association study attracts increasing attention, currently, it has a fundamental problem in that each cell within one individual has a unique, time-varying epigenome. Having a similar conceptual framework to systems biology, the holistic MPE approach enables us to link potential etiological factors to specific molecular pathology, and gain novel pathogenic insights on causality. The widespread application of epigenome (eg, methylome) analyses will enhance our understanding of disease heterogeneity, epigenotypes (CpG island methylator phenotype, LINE-1 (long interspersed nucleotide element-1; also called long interspersed nuclear element-1; long interspersed element-1; L1) hypomethylation, etc), and host-disease interactions. In this article, we illustrate increasing contribution of modern pathology to broader public health sciences, which attests pivotal roles of pathologists in the new integrated MPE science towards our ultimate goal of personalized medicine and prevention.
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Affiliation(s)
- Shuji Ogino
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA 02215, USA.
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Owens C, Irwin M. Neuroblastoma: the impact of biology and cooperation leading to personalized treatments. Crit Rev Clin Lab Sci 2012; 49:85-115. [PMID: 22646747 DOI: 10.3109/10408363.2012.683483] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Neuroblastoma is the most common extra-cranial solid tumor in children. It is a heterogeneous disease, consisting of neural crest-derived tumors with remarkably different clinical behaviors. It can present in a wide variety of ways, including lesions which have the potential to spontaneously regress, or as an extremely aggressive form of metastatic cancer which is resistant to all forms of modern therapy. They can arise anywhere along the sympathetic nervous system. The median age of presentation is approximately 18 months of age. Urinary catecholamines (HVA and VMA) are extremely sensitive and specific tumor markers and are used in diagnosis, treatment response assessment and post-treatment surveillance. The largest national treatment groups from North America, Europe and Japan have formed the International Neuroblastoma Risk Group Task Force (INRG) to identify prognostic factors, to understand the mechanisms of tumorigenesis in this rare disease and to develop multi-modality therapies to improve outcomes and decrease treatment-related toxicities. This international cooperation has resulted in a significant leap in our understanding of the molecular pathogenesis of neuroblastoma. Lower staged disease can be cured if the lesion is resectable. Treatment of unresectable disease (loco-regional and metastatic) is stratified depending on clinical features (age at presentation, staging investigations) and specific tumor biological markers that include histopathological analyses, chromosomal abnormalities and the quantification of expression of an oncogene (MYCN). Modern treatment of high-risk neuroblastoma is the paradigm for the evolution of therapy in pediatric oncology. Outcomes have improved substantially with multi-modality therapy, including chemotherapy, surgery, radiation therapy, myeloablative therapy with stem cell transplant, immunotherapy and differentiation therapy; these comprise the standard of care worldwide. In addition, newer targeted therapies are being tested in phase I/II trials. If successful these agents will be incorporated into mainstream treatment programs.
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Affiliation(s)
- Cormac Owens
- Division of Haematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
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Fu T, Pappou EP, Guzzetta AA, Jeschke J, Kwak R, Dave P, Hooker CM, Morgan R, Baylin SB, Iacobuzio-Donahue CA, Wolfgang CL, Ahuja N. CpG island methylator phenotype-positive tumors in the absence of MLH1 methylation constitute a distinct subset of duodenal adenocarcinomas and are associated with poor prognosis. Clin Cancer Res 2012; 18:4743-52. [PMID: 22825585 DOI: 10.1158/1078-0432.ccr-12-0707] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PURPOSE Little information is available on genetic and epigenetic changes in duodenal adenocarcinomas. The purpose was to identify possible subsets of duodenal adenocarcinomas based on microsatellite instability (MSI), DNA methylation, mutations in the KRAS and BRAF genes, clinicopathologic features, and prognosis. EXPERIMENTAL DESIGN Demographics, tumor characteristics, and survival were available for 99 duodenal adenocarcinoma patients. Testing for KRAS and BRAF mutations, MSI, MLH1 methylation, and CpG island methylator phenotype (CIMP) status was conducted. A Cox proportional hazard model was built to predict survival. RESULTS CIMP(+) was detected in 27 of 99 (27.3%) duodenal adenocarcinomas and was associated with MSI (P = 0.011) and MLH1 methylation (P < 0.001), but not with KRAS mutations (P = 0.114), as compared with CIMP(-) tumors. No BRAF V600E mutation was detected. Among the CIMP(+) tumors, 15 (55.6%) were CIMP(+)/MLH1-unmethylated (MLH1-U). Kaplan-Meier analysis showed that tumors classified by CIMP, CIMP/MLH1 methylation status, or CIMP/MSI status could predict overall survival (OS; P = 0.047, 0.002, and 0.002, respectively), whereas CIMP/MLH1 methylation status could also predict time-to-recurrence (TTR; P = 0.016). In multivariate analysis, CIMP/MLH1 methylation status showed a significant prognostic value in both OS (P < 0.001) and TTR (P = 0.023). Patients with CIMP(+)/MLH1-U tumors had the worst OS and TTR. CONCLUSIONS Our results showed existence of CIMP in duodenal adenocarcinomas. The combination of CIMP(+)/MLH1-U seems to be independently associated with poor prognosis in patients with duodenal adenocarcinomas. This study also suggests that BRAF mutations are not involved in duodenal tumorigenesis, MSI, or CIMP development.
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Affiliation(s)
- Tao Fu
- Department of Surgery, Johns Hopkins University, Baltimore, MD 21287, USA
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Navarro S, Piqueras M, Villamón E, Yáñez Y, Balaguer J, Cañete A, Noguera R. New prognostic markers in neuroblastoma. ACTA ACUST UNITED AC 2012; 6:555-67. [PMID: 23480837 DOI: 10.1517/17530059.2012.704018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION The hallmark of neuroblastoma is its clinical and biological heterogeneity, with the likelihood of cure varying widely according to age at diagnosis, extent of disease and tumor biology. We hope this review will be useful for understanding part of the unfamiliar neuroblastoma codex. AREAS COVERED In the first part of this review, the authors summarize the currently used prognostic factors for risk-adapted therapy, with the focus on clinical management of neuroblastoma patients. In the second part, the authors discuss the evolving prognostic factors for future treatment schemes. A search of online medical research databases was undertaken focusing especially on literature published in the last six years. EXPERT OPINION Harnessing the synergy of the various forms of data, including clinical variables and biomarker profiles, would allow mathematical predictive models to be built for the individual patient, which could eventually become molecular targets of specific therapies.
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Affiliation(s)
- Samuel Navarro
- Department of Pathology, Medical School, University of Valencia , Avda. Blasco Ibañez 15 Valencia 46010 , Spain +34 96 3864146 ; +34 96 3864173 ;
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Zage PE, Louis CU, Cohn SL. New aspects of neuroblastoma treatment: ASPHO 2011 symposium review. Pediatr Blood Cancer 2012; 58:1099-105. [PMID: 22378620 PMCID: PMC4104176 DOI: 10.1002/pbc.24116] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 01/31/2012] [Indexed: 11/10/2022]
Abstract
Neuroblastoma is the most common extracranial solid tumor of childhood, and the outcomes for children with high-risk and relapsed disease remain poor. However, new international strategies for risk stratification and for treatment based on novel tumor targets and including immunotherapy are being employed in attempts to improve the outcomes of children with neuroblastoma. A new international neuroblastoma risk classification system has been developed which is being incorporated into cooperative group clinical trials in North America, Japan, and Europe, resulting in standardized approaches for the initial evaluation and treatment stratification of neuroblastoma patients. Furthermore, novel treatment regimens are being developed based on improved understanding of neuroblastoma biology and on the recruitment of the immune system to specifically target neuroblastoma tumors. These approaches will lead to new therapeutic strategies that likely will improve the outcomes for children with neuroblastoma worldwide.
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Affiliation(s)
- Peter E. Zage
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas,Texas Children’s Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas,Correspondence to: Peter E. Zage, MD, PhD, Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, 1102 Bates, Suite 1220, Houston, TX 77030.
| | - Chrystal U. Louis
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas,Texas Children’s Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas
| | - Susan L. Cohn
- Department of Pediatrics, Comer Children’s Hospital and University of Chicago, Chicago, Illinois
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Arai E, Chiku S, Mori T, Gotoh M, Nakagawa T, Fujimoto H, Kanai Y. Single-CpG-resolution methylome analysis identifies clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas. Carcinogenesis 2012; 33:1487-93. [PMID: 22610075 PMCID: PMC3418891 DOI: 10.1093/carcin/bgs177] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
To clarify the significance of DNA methylation alterations during renal carcinogenesis, methylome analysis using single-CpG-resolution Infinium array was performed on 29 normal renal cortex tissue (C) samples, 107 non-cancerous renal cortex tissue (N) samples obtained from patients with clear cell renal cell carcinomas (RCCs) and 109 tumorous tissue (T) samples. DNA methylation levels at 4830 CpG sites were already altered in N samples compared with C samples. Unsupervised hierarchical clustering analysis based on DNA methylation levels at the 801 CpG sites, where DNA methylation alterations had occurred in N samples and were inherited by and strengthened in T samples, clustered clear cell RCCs into Cluster A (n = 90) and Cluster B (n = 14). Clinicopathologically aggressive tumors were accumulated in Cluster B, and the cancer-free and overall survival rates of patients in this cluster were significantly lower than those of patients in Cluster A. Clear cell RCCs in Cluster B were characterized by accumulation of DNA hypermethylation on CpG islands and considered to be CpG island methylator phenotype (CIMP)-positive cancers. DNA hypermethylation of the CpG sites on the FAM150A, GRM6, ZNF540, ZFP42, ZNF154, RIMS4, PCDHAC1, KHDRBS2, ASCL2, KCNQ1, PRAC, WNT3A, TRH, FAM78A, ZNF671, SLC13A5 and NKX6-2 genes became hallmarks of CIMP in RCCs. On the other hand, Cluster A was characterized by genome-wide DNA hypomethylation. These data indicated that DNA methylation alterations at precancerous stages may determine tumor aggressiveness and patient outcome. Accumulation of DNA hypermethylation on CpG islands and genome-wide DNA hypomethylation may each underlie distinct pathways of renal carcinogenesis. Abbreviations: BAMCAbacterial artificial chromosome array-based methylated CpG island amplification Cnormal renal cortex tissue obtained from patients without any primary renal tumor CIMPCpG island methylator phenotype HCChepatocellular carcinoma Nnon-cancerous renal cortex tissue obtained from patients with clear cell renal cell carcinomas NCBINational Center for Biotechnology Information RCCrenal cell carcinoma Ttumorous tissue TNMTumor-Node-Metastasis
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Affiliation(s)
- Eri Arai
- Division of Molecular Pathology, National Cancer Center Research Institute Tokyo 104-0045, Japan
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Banelli B, Brigati C, Di Vinci A, Casciano I, Forlani A, Borzì L, Allemanni G, Romani M. A pyrosequencing assay for the quantitative methylation analysis of the PCDHB gene cluster, the major factor in neuroblastoma methylator phenotype. J Transl Med 2012; 92:458-65. [PMID: 22157715 DOI: 10.1038/labinvest.2011.169] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Epigenetic alterations are hallmarks of cancer and powerful biomarkers, whose clinical utilization is made difficult by the absence of standardization and of common methods of data interpretation. The coordinate methylation of many loci in cancer is defined as 'CpG island methylator phenotype' (CIMP) and identifies clinically distinct groups of patients. In neuroblastoma (NB), CIMP is defined by a methylation signature, which includes different loci, but its predictive power on outcome is entirely recapitulated by the PCDHB cluster only. We have developed a robust and cost-effective pyrosequencing-based assay that could facilitate the clinical application of CIMP in NB. This assay permits the unbiased simultaneous amplification and sequencing of 17 out of 19 genes of the PCDHB cluster for quantitative methylation analysis, taking into account all the sequence variations. As some of these variations were at CpG doublets, we bypassed the data interpretation conducted by the methylation analysis software to assign the corrected methylation value at these sites. The final result of the assay is the mean methylation level of 17 gene fragments in the protocadherin B cluster (PCDHB) cluster. We have utilized this assay to compare the methylation levels of the PCDHB cluster between high-risk and very low-risk NB patients, confirming the predictive value of CIMP. Our results demonstrate that the pyrosequencing-based assay herein described is a powerful instrument for the analysis of this gene cluster that may simplify the data comparison between different laboratories and, in perspective, could facilitate its clinical application. Furthermore, our results demonstrate that, in principle, pyrosequencing can be efficiently utilized for the methylation analysis of gene clusters with high internal homologies.
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Affiliation(s)
- Barbara Banelli
- Laboratory of Tumor Genetics and Epigenetic, Istituto Nazionale per la Ricerca sul Cancro, Largo Rosanna Benzi, Genova, Italy.
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Qureshi IA, Mehler MF. Epigenetics, nervous system tumors, and cancer stem cells. Cancers (Basel) 2011; 3:3525-56. [PMID: 24212967 PMCID: PMC3759209 DOI: 10.3390/cancers3033525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 08/01/2011] [Accepted: 09/08/2011] [Indexed: 12/11/2022] Open
Abstract
Recent advances have begun to elucidate how epigenetic regulatory mechanisms are responsible for establishing and maintaining cell identity during development and adult life and how the disruption of these processes is, not surprisingly, one of the hallmarks of cancer. In this review, we describe the major epigenetic mechanisms (i.e., DNA methylation, histone and chromatin modification, non-coding RNA deployment, RNA editing, and nuclear reorganization) and discuss the broad spectrum of epigenetic alterations that have been uncovered in pediatric and adult nervous system tumors. We also highlight emerging evidence that suggests epigenetic deregulation is a characteristic feature of so-called cancer stem cells (CSCs), which are thought to be present in a range of nervous system tumors and responsible for tumor maintenance, progression, treatment resistance, and recurrence. We believe that better understanding how epigenetic mechanisms operate in neural cells and identifying the etiologies and consequences of epigenetic deregulation in tumor cells and CSCs, in particular, are likely to promote the development of enhanced molecular diagnostics and more targeted and effective therapeutic agents for treating recalcitrant nervous system tumors.
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Affiliation(s)
- Irfan A. Qureshi
- Rosyln and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; E-Mail:
- Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Mark F. Mehler
- Rosyln and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; E-Mail:
- Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-718-430-3543; Fax: +1-718-918-7505
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Su H, Hu N, Yang HH, Wang C, Takikita M, Wang QH, Giffen C, Clifford R, Hewitt SM, Shou JZ, Goldstein AM, Lee MP, Taylor PR, Kaempgen E, Van Gool SW, Helms W, Keegan P, Pazdur R. Global gene expression profiling and validation in esophageal squamous cell carcinoma and its association with clinical phenotypes. Clin Cancer Res 2011. [PMID: 29950348 DOI: 10.1158/1078-0432] [Citation(s) in RCA: 402] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE Esophageal squamous cell carcinoma (ESCC) is an aggressive tumor with poor prognosis. Understanding molecular changes in ESCC will enable identification of molecular subtypes and provide potential targets for early detection and therapy. EXPERIMENTAL DESIGN We followed up a previous array study with additional discovery and confirmatory studies in new ESCC cases by using alternative methods. We profiled global gene expression for discovery and confirmation, and validated selected dysregulated genes with additional RNA and protein studies. RESULTS A total of 159 genes showed differences with extreme statistical significance (P < E-15) and 2-fold differences or more in magnitude (tumor/normal RNA expression ratio, N = 53 cases), including 116 upregulated and 43 downregulated genes. Of 41 genes dysregulated in our prior array study, all but one showed the same fold change directional pattern in new array studies, including 29 with 2-fold changes or more. Alternative RNA expression methods validated array results: more than two thirds of 51 new cases examined by real-time PCR (RT-PCR) showed 2-fold differences or more for all seven genes assessed. Immunohistochemical protein expression results in 275 cases which were concordant with RNA for five of six genes. CONCLUSION We identified an expanded panel of genes dysregulated in ESCC and confirmed previously identified differentially expressed genes. Microarray-based gene expression results were confirmed by RT-PCR and protein expression studies. These dysregulated genes will facilitate molecular categorization of tumor subtypes and identification of their risk factors, and serve as potential targets for early detection, outcome prediction, and therapy.
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Affiliation(s)
- Hua Su
- Genetic Epidemiology Branch, DCEG, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Whitney Helms
- Office of Hematology and Oncology Products, Office of New Drugs, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Patricia Keegan
- Office of Hematology and Oncology Products, Office of New Drugs, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Richard Pazdur
- Office of Biostatistics, Office of Translational Sciences, U.S. Food and Drug Administration, Silver Spring, Maryland
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Ohira M, Nakagawara A. Global genomic and RNA profiles for novel risk stratification of neuroblastoma. Cancer Sci 2010; 101:2295-301. [PMID: 20731666 PMCID: PMC11159775 DOI: 10.1111/j.1349-7006.2010.01681.x] [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: 11/27/2022] Open
Abstract
Neuroblastoma is one of the most common solid tumors in children. Its clinical behavior ranges widely from spontaneous regression to life-threatening aggressive growth. The molecular etiology of neuroblastoma is still enigmatic and the overall cure rate of advanced disease is still very poor. Recent microarray-based technology provided us with important information such as comprehensive genomic alterations and gene expression profiles to help us understand the molecular characteristics of each tumor in detail. Several retrospective studies have revealed that these signatures are strongly correlated with patient prognoses and led to the construction of new risk stratification systems, some of which are considered for evaluation in upcoming clinical studies in a prospective way. Large-scale analyses using a variety of genetic tools also discovered a major familial neuroblastoma predisposition gene ALK, as well as new candidate susceptibility genes at 6q22 and 2q35 for sporadic neuroblastoma. Of note, ALK is mutated in 6-9% of sporadic cases, and is either amplified or constitutively activated through mutations mainly within the kinase domain, promoting the possibility of new therapeutic strategies using ALK inhibitors. Additional candidates for outcome predictors such as the methylation phenotype of tumor DNA and expression profiles of microRNA have also been proposed. Such variety of information will help us understand the heterogeneity of neuroblastoma biology and further, the combined use of these signatures will be beneficial in predicting prognosis with high accuracy, as well as choosing a suitable therapy for the individual patient.
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Affiliation(s)
- Miki Ohira
- Division of Biochemistry and Innovative Cancer Therapeutics Laboratory of Cancer Genomics, Chiba Cancer Center Research Institute, Chuoh-ku, Chiba, Japan
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Shin SH, Kim BH, Jang JJ, Suh KS, Kang GH. Identification of novel methylation markers in hepatocellular carcinoma using a methylation array. J Korean Med Sci 2010; 25:1152-9. [PMID: 20676325 PMCID: PMC2908783 DOI: 10.3346/jkms.2010.25.8.1152] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 01/19/2010] [Indexed: 12/17/2022] Open
Abstract
Promoter CpG island hypermethylation has become recognized as an important mechanism for inactivating tumor suppressor genes or tumor-related genes in human cancers of various tissues. Gene inactivation in association with promoter CpG island hypermethylation has been reported to be four times more frequent than genetic changes in human colorectal cancers. Hepatocellular carcinoma is also one of the human cancer types in which aberrant promoter CpG island hypermethylation is frequently found. However, the number of genes identified to date as hypermethylated for hepatocellular carcinoma (HCC) is fewer than that for colorectal cancer or gastric cancer, which can be attributed to fewer attempts to perform genome-wide methylation profiling for HCC. In the present study, we used bead-array technology and coupled methylation-specific PCR to identify new genes showing cancer-specific methylation in HCC. Twenty-four new genes have been identified as hypermethylated at their promoter CpG island loci in a cancer-specific manner. Of these, TNFRSF10C, HOXA9, NPY, and IRF5 were frequently hypermethylated in hepatocellular carcinoma tissue samples and their methylation was found to be closely associated with inactivation of gene expression. Further study will be required to elucidate the clinicopathological implications of these newly found DNA methylation markers in hepatocellular carcinoma.
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Affiliation(s)
- So Hyun Shin
- Laboratory of Epigenetics, Cancer Research Institute and Brain Korea 2nd Stage, Seoul National University, Seoul, Korea
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Yang Q, Tian Y, Ostler KR, Chlenski A, Guerrero LJ, Salwen HR, Godley LA, Cohn SL. Epigenetic alterations differ in phenotypically distinct human neuroblastoma cell lines. BMC Cancer 2010; 10:286. [PMID: 20546602 PMCID: PMC2897803 DOI: 10.1186/1471-2407-10-286] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 06/14/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Epigenetic aberrations and a CpG island methylator phenotype have been shown to be associated with poor outcomes in children with neuroblastoma (NB). Seven cancer related genes (THBS-1, CASP8, HIN-1, TIG-1, BLU, SPARC, and HIC-1) that have been shown to have epigenetic changes in adult cancers and play important roles in the regulation of angiogenesis, tumor growth, and apoptosis were analyzed to investigate the role epigenetic alterations play in determining NB phenotype. METHODS Two NB cell lines (tumorigenic LA1-55n and non-tumorigenic LA1-5s) that differ in their ability to form colonies in soft agar and tumors in nude mice were used. Quantitative RNA expression analyses were performed on seven genes in LA1-5s, LA1-55n and 5-Aza-dC treated LA1-55n NB cell lines. The methylation status around THBS-1, HIN-1, TIG-1 and CASP8 promoters was examined using methylation specific PCR. Chromatin immunoprecipitation assay was used to examine histone modifications along the THBS-1 promoter. Luciferase assay was used to determine THBS-1 promoter activity. Cell proliferation assay was used to examine the effect of 5-Aza-dC on NB cell growth. The soft agar assay was used to determine the tumorigenicity. RESULTS Promoter methylation values for THBS-1, HIN-1, TIG-1, and CASP8 were higher in LA1-55n cells compared to LA1-5s cells. Consistent with the promoter methylation status, lower levels of gene expression were detected in the LA1-55n cells. Histone marks associated with repressive chromatin states (H3K9Me3, H3K27Me3, and H3K4Me3) were identified in the THBS-1 promoter region in the LA1-55n cells, but not the LA1-5s cells. In contrast, the three histone codes associated with an active chromatin state (acetyl H3, acetyl H4, and H3K4Me3) were present in the THBS-1 promoter region in LA1-5s cells, but not the LA1-55n cells, suggesting that an accessible chromatin structure is important for THBS-1 expression. We also show that 5-Aza-dC treatment of LA1-55n cells alters the DNA methylation status and the histone code in the THBS-1 promoter modifies cell morphology, and inhibits their ability to form colonies in soft agar. CONCLUSION Our results suggest that epigenetic aberrations contribute to NB phenotype, and that tumorigenic properties can be inhibited by reversing the epigenetic changes with 5-Aza-dC.
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Affiliation(s)
- Qiwei Yang
- Department of Pediatrics, University of Chicago, 900 Ease 57th Street, KCBD Rm, 5100 Chicago, IL 60637, USA
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Banelli B, Bonassi S, Casciano I, Mazzocco K, Di Vinci A, Scaruffi P, Brigati C, Allemanni G, Borzì L, Tonini GP, Romani M. Outcome prediction and risk assessment by quantitative pyrosequencing methylation analysis of the SFN gene in advanced stage, high-risk, neuroblastic tumor patients. Int J Cancer 2010; 126:656-68. [DOI: 10.1002/ijc.24768] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Epigenetic inactivation of the Sotos overgrowth syndrome gene histone methyltransferase NSD1 in human neuroblastoma and glioma. Proc Natl Acad Sci U S A 2009; 106:21830-5. [PMID: 20018718 DOI: 10.1073/pnas.0906831106] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Sotos syndrome is an autosomal dominant condition characterized by overgrowth resulting in tall stature and macrocephaly, together with an increased risk of tumorigenesis. The disease is caused by loss-of-function mutations and deletions of the nuclear receptor SET domain containing protein-1 (NSD1) gene, which encodes a histone methyltransferase involved in chromatin regulation. However, despite its causal role in Sotos syndrome and the typical accelerated growth of these patients, little is known about the putative contribution of NSD1 to human sporadic malignancies. Here, we report that NSD1 function is abrogated in human neuroblastoma and glioma cells by transcriptional silencing associated with CpG island-promoter hypermethylation. We also demonstrate that the epigenetic inactivation of NSD1 in transformed cells leads to the specifically diminished methylation of the histone lysine residues H4-K20 and H3-K36. The described phenotype is also observed in Sotos syndrome patients with NSD1 genetic disruption. Expression microarray data from NSD1-depleted cells, followed by ChIP analysis, revealed that the oncogene MEIS1 is one of the main NSD1 targets in neuroblastoma. Furthermore, we show that the restoration of NSD1 expression induces tumor suppressor-like features, such as reduced colony formation density and inhibition of cellular growth. Screening a large collection of different tumor types revealed that NSD1 CpG island hypermethylation was a common event in neuroblastomas and gliomas. Most importantly, NSD1 hypermethylation was a predictor of poor outcome in high-risk neuroblastoma. These findings highlight the importance of NSD1 epigenetic inactivation in neuroblastoma and glioma that leads to a disrupted histone methylation landscape and might have a translational value as a prognostic marker.
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Yamashita S, Hosoya K, Gyobu K, Takeshima H, Ushijima T. Development of a novel output value for quantitative assessment in methylated DNA immunoprecipitation-CpG island microarray analysis. DNA Res 2009; 16:275-86. [PMID: 19767598 PMCID: PMC2762412 DOI: 10.1093/dnares/dsp017] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In DNA methylation microarray analysis, quantitative assessment of intermediate methylation levels in samples with various global methylation levels is still difficult. Here, specifically for methylated DNA immunoprecipitation-CpG island (CGI) microarray analysis, we developed a new output value. The signal log ratio reflected the global methylation levels, but had only moderate linear correlation (r = 0.72) with the fraction of DNA molecules immunoprecipitated. By multiplying the signal log ratio using a coefficient obtained from the probability value that took account of signals in neighbouring probes, its linearity was markedly improved (r = 0.94). The new output value, Me value, reflected the global methylation level, had a strong correlation also with the fraction of methylated CpG sites obtained by bisulphite sequencing (r = 0.88), and had an accuracy of 71.8 and 83.8% in detecting completely methylated and unmethylated CGIs. Analysis of gastric cancer cell lines using the Me value showed that methylation of CGIs in promoters and gene bodies was associated with low and high, respectively, gene expression. The degree of demethylation of promoter CGIs after 5-aza-2'-deoxycytidine treatment had no association with that of induction of gene expression. The Me value was considered to be useful for analysis of intermediate methylation levels of CGIs.
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Affiliation(s)
- Satoshi Yamashita
- Carcinogenesis Division, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
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