1
|
Xiang C, Li Y, Wang W, Tao H, Liang N, Wu S, Yu T, Cui X, Xie Y, Zuo H, Lin C, Xu F. Joint analysis of WES and RNA-Seq identify signature genes related to metastasis in prostate cancer. J Cell Mol Med 2023. [PMID: 37378426 DOI: 10.1111/jcmm.17781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 06/29/2023] Open
Abstract
Prostate cancer (PCa) has a certain degree of heritability, and metastasis occurs as cancer progresses. However, its underlying mechanism remains largely unknown. We sequenced four cases of cancer without metastasis, four metastatic cancer, and four benign hyperplasia tissues as controls. A total of 1839 damaging mutations were identified. Pathway analysis, gene clustering, and weighted gene co-expression network analysis were employed to find characteristics associated with metastasis. Chr19 had the most mutation density and 1p36 had the highest mutation frequency across the genome. These mutations occurred in 1630 genes, including the most frequently mutated genes TTN and PLEC, and dozens of metastasis-related genes, such as FOXA1, NCOA1, CD34, and BRCA2. Ras signalling and arachidonic acid metabolism were uniquely enriched in metastatic cancer. Gene programmes 10 and 11 showed the signatures indicating the occurrence of metastasis better. A module (135 genes) was specifically associated with metastasis. Of them, 67.41% reoccurred in program 10, with 26 genes further retained as the signature genes related to PCa metastasis, including AGR3, RAPH1, SOX14, DPEP1, and UBL4A. Our study provides new molecular perspectives on PCa metastasis. The signature genes and pathways could be served as potential therapeutic targets for metastasis or cancer progression.
Collapse
Affiliation(s)
- Chongjun Xiang
- The 2nd Medical College of Binzhou Medical University, Yantai, China
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Yue Li
- The 2nd Medical College of Binzhou Medical University, Yantai, China
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Wenting Wang
- Department of Central Laboratory, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Huiying Tao
- The 2nd Medical College of Binzhou Medical University, Yantai, China
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Ning Liang
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
- School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Shuang Wu
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Tianxi Yu
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
- School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Xin Cui
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
- School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Yaqi Xie
- The 2nd Medical College of Binzhou Medical University, Yantai, China
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Hongwei Zuo
- The 2nd Medical College of Binzhou Medical University, Yantai, China
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Chunhua Lin
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Fuyi Xu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, China
| |
Collapse
|
2
|
Allione A, Viberti C, Cotellessa I, Catalano C, Casalone E, Cugliari G, Russo A, Guarrera S, Mirabelli D, Sacerdote C, Gentile M, Eichelmann F, Schulze MB, Harlid S, Eriksen AK, Tjønneland A, Andersson M, Dollé MET, Van Puyvelde H, Weiderpass E, Rodriguez-Barranco M, Agudo A, Heath AK, Chirlaque MD, Truong T, Dragic D, Severi G, Sieri S, Sandanger TM, Ardanaz E, Vineis P, Matullo G. Blood cell DNA methylation biomarkers in preclinical malignant pleural mesothelioma: The EPIC prospective cohort. Int J Cancer 2023; 152:725-737. [PMID: 36305648 DOI: 10.1002/ijc.34339] [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: 02/03/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 02/01/2023]
Abstract
Malignant pleural mesothelioma (MPM) is a rare and aggressive cancer mainly caused by asbestos exposure. Specific and sensitive noninvasive biomarkers may facilitate and enhance screening programs for the early detection of cancer. We investigated DNA methylation (DNAm) profiles in MPM prediagnostic blood samples in a case-control study nested in the European Prospective Investigation into Cancer and nutrition (EPIC) cohort, aiming to characterise DNAm biomarkers associated with MPM. From the EPIC cohort, we included samples from 135 participants who developed MPM during 20 years of follow-up and from 135 matched, cancer-free, controls. For the discovery phase we selected EPIC participants who developed MPM within 5 years from enrolment (n = 36) with matched controls. We identified nine differentially methylated CpGs, selected by 10-fold cross-validation and correlation analyses: cg25755428 (MRI1), cg20389709 (KLF11), cg23870316, cg13862711 (LHX6), cg06417478 (HOOK2), cg00667948, cg01879420 (AMD1), cg25317025 (RPL17) and cg06205333 (RAP1A). Receiver operating characteristic (ROC) analysis showed that the model including baseline characteristics (age, sex and PC1wbc) along with the nine MPM-related CpGs has a better predictive value for MPM occurrence than the baseline model alone, maintaining some performance also at more than 5 years before diagnosis (area under the curve [AUC] < 5 years = 0.89; AUC 5-10 years = 0.80; AUC >10 years = 0.75; baseline AUC range = 0.63-0.67). DNAm changes as noninvasive biomarkers in prediagnostic blood samples of MPM cases were investigated for the first time. Their application can improve the identification of asbestos-exposed individuals at higher MPM risk to possibly adopt more intensive monitoring for early disease identification.
Collapse
Affiliation(s)
| | - Clara Viberti
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Chiara Catalano
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | | | - Alessia Russo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Simonetta Guarrera
- IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Dario Mirabelli
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
- Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates "G. Scansetti", University of Turin, Turin, Italy
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, Città Della Salute e Della Scienza University-Hospital and Center for Cancer Prevention (CPO), Turin, Italy
| | | | - Fabian Eichelmann
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- University of Potsdam, Institute of Nutritional Science, Nuthetal, Germany
| | - Sophia Harlid
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
| | - Anne Kirstine Eriksen
- Danish Cancer Society Research Center, Diet, Genes and Environment, Copenhagen, Denmark
| | - Anne Tjønneland
- Danish Cancer Society Research Center, Diet, Genes and Environment, Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Martin Andersson
- Department of Public Health and Clinical Medicine, Sustainable Health, Umeå University, Umeå, Sweden
| | - Martijn E T Dollé
- Centre for Health Protection National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Heleen Van Puyvelde
- International Agency for Research on Cancer, World Health Organisation, Lyon, France
| | - Elisabete Weiderpass
- International Agency for Research on Cancer, World Health Organisation, Lyon, France
| | - Miguel Rodriguez-Barranco
- Escuela Andaluza de Salud Pública (EASP), Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Antonio Agudo
- Unit of Nutrition and Cancer, Catalan Institute of Oncology-ICO, L'Hospitalet de Llobregat, Barcelona, Spain
- Nutrition and Cancer Group, Epidemiology, Public Health, Cancer Prevention and Palliative Care Program, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Alicia K Heath
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - María-Dolores Chirlaque
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Epidemiology, Regional Health Council, IMIB-Arrixaca, Murcia University, Murcia, Spain
| | - Thérèse Truong
- Université Paris-Saclay, UVSQ, Inserm, CESP U1018, "Exposome, Heredity, Cancer and Health" Team, Paris, France
| | - Dzevka Dragic
- Université Paris-Saclay, UVSQ, Inserm, CESP U1018, "Exposome, Heredity, Cancer and Health" Team, Paris, France
- Centre de Recherche sur le Cancer de l'Université Laval, Département de Médecine Sociale et Préventive, Faculté de Médecine, Québec, Canada
- Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, Canada
| | - Gianluca Severi
- Université Paris-Saclay, UVSQ, Inserm, CESP U1018, "Exposome, Heredity, Cancer and Health" Team, Paris, France
- Department of Statistics, Computer Science and Applications "G. Parenti" (DISIA), University of Florence, Florence, Italy
| | - Sabina Sieri
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano Via Venezian, Milan, Italy
| | - Torkjel M Sandanger
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Eva Ardanaz
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Navarra Public Health Institute, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Paolo Vineis
- MRC Centre for Environment and Health, Imperial College London, London, UK
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
- Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates "G. Scansetti", University of Turin, Turin, Italy
- Medical Genetics Unit, AOU Città della Salute e Della Scienza, Turin, Italy
| |
Collapse
|
3
|
LHX6 promoter hypermethylation in oncological pediatric patients conceived by IVF. J Dev Orig Health Dis 2023; 14:140-145. [PMID: 36154949 DOI: 10.1017/s2040174422000526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The multifactorial etiology of pediatric cancer is poorly understood. Environmental factors occurring during embryogenesis can disrupt epigenetic signaling, resulting in several diseases after birth, including cancer. Associations between assisted reproductive technologies (ART), such as in vitro fertilization (IVF), and birth defects, imprinting disorders and other perinatal adverse events have been reported. IVF can result in methylation changes in the offspring, and a link with pediatric cancer has been suggested. In this study, we investigated the peripheral blood methylomes of 11 patients conceived by IVF who developed cancer in childhood. Methylation data of patients and paired sex/aged controls were obtained using the Infinium MethylationEPIC Kit (Illumina). We identified 25 differentially methylated regions (DMRs), 17 of them hypermethylated, and 8 hypomethylated in patients. The most significant DMR was a hypermethylated genomic segment located in the promoter region of LHX6, a transcription factor involved in the forebrain development and interneuron migration during embryogenesis. An additional control group was included to verify the LHX6 methylation status in children with similar cancers who were not conceived by ART. The higher LHX6 methylation levels in IVF patients compared to both control groups (healthy children and children conceived naturally who developed similar pediatric cancers), suggested that hypermethylation at the LHX6 promoter could be due to the IVF process and not secondary to the cancer itself. Further studies are required to evaluate this association and the potential role of LHX6 promoter hypermethylation for tumorigenesis.
Collapse
|
4
|
Wang L, Zhou Y, Cao C, Lin S, Zhi W, Zhang D, Li J, Wei R, Jiang G, Xu H, Wang X, Xi L, Wu P. The exon 12-containing LHX6 isoforms promote cervical cancer cell proliferation by regulating the MAPK signaling pathway. Cancer Med 2022; 11:3657-3673. [PMID: 35384355 PMCID: PMC9554449 DOI: 10.1002/cam4.4734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 01/31/2022] [Accepted: 03/18/2022] [Indexed: 12/24/2022] Open
Abstract
LIM homeobox 6 (LHX6) has been reported to be downregulated and inhibits cell proliferation in various cancers. Alternative splicing of LHX6 leads to six annotated isoforms, which can be found in the NCBI database. However, the expression patterns and potential roles of these isoforms remain poorly characterized in cervical cancer. Here, we demonstrated that the LHX6 isoforms containing exon 12 (LHX6EX(+12) group) and isoforms lacking exon 12 (LHX6EX(-12) group) were differentially expressed in cervical tissue by qRT-PCR. The mRNA expression level of LHX6EX(+12) group was higher than that of LHX6EX(-12) group in cervical cancer tissue. Knockdown of LHX6EX(+12) group and all LHX6 isoforms (LHX6All group) inhibited cell growth, increased cell apoptosis, and induced cell cycle arrest from G0/G1 phase to S phase in vitro. Consistently, overexpression of the LHX6EX(+12) group promoted cervical cancer cell proliferation in vitro. In contrast, no significant differences in cell proliferation were found between LHX6EX(-12) isoform knockdown group and its control. RNA-sequencing suggested that the LHX6EX(+12) isoform group might exert its cancer-promoting effects in cervical cancer via regulating MAPK signaling pathway. Downregulation of the LHX6EX(+12) group significantly suppressed the phosphorylation of MRK, ERK, JNK, and P38 at the protein level. We also identified some unique biological processes and signaling pathways in which each isoform group might be involved. In summary, our results indicated that LHX6EX(+12) isoform group was the dominant oncogenic type of LHX6 in cervical cancer, which may be a new biomarker and a potential precise therapeutic target for cervical cancer in the future.
Collapse
Affiliation(s)
- Ling Wang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ying Zhou
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Canhui Cao
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Shitong Lin
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wenhua Zhi
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Danya Zhang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jie Li
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Rui Wei
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guiying Jiang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hanjie Xu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xueqian Wang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ling Xi
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Peng Wu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| |
Collapse
|
5
|
Flausino CS, Daniel FI, Modolo F. DNA methylation in oral squamous cell carcinoma: from its role in carcinogenesis to potential inhibitor drugs. Crit Rev Oncol Hematol 2021; 164:103399. [PMID: 34147646 DOI: 10.1016/j.critrevonc.2021.103399] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is one of epigenetic changes most frequently studied nowadays, together with its relationship with oral carcinogenesis. A group of enzymes is responsible for methylation process, known as DNA methyltransferases (DNMT). Although essential during embryogenesis, DNA methylation pattern alterations, including global hypomethylation or gene promoter hypermethylation, can be respectively associated with chromosomal instability and tumor suppressor gene silencing. Higher expression of DNA methyltransferases is a common finding in oral cancer and may contribute to inactivation of important tumor suppressor genes, influencing development, progression, metastasis, and prognosis of the tumor. To control these alterations, inhibitor drugs have been developed as a way to regulate DNMT overexpression, and they are intended to be associated with ongoing chemo- and radiotherapy in oral cancer treatments. In this article, we aimed to highlight the current knowledge about DNA methylation in oral cancer, including main hyper/hypomethylated genes, DNMT expression and its inhibitor treatments.
Collapse
Affiliation(s)
| | - Filipe Ivan Daniel
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil.
| | - Filipe Modolo
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| |
Collapse
|
6
|
Wang Q, Liao J, He Z, Su Y, Lin D, Xu L, Xu H, Lin J. LHX6 Affects Erlotinib Resistance and Migration of EGFR-Mutant Non-Small-Cell Lung Cancer HCC827 Cells Through Suppressing Wnt/β-Catenin Signaling. Onco Targets Ther 2020; 13:10983-10994. [PMID: 33149613 PMCID: PMC7605383 DOI: 10.2147/ott.s258896] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 10/08/2020] [Indexed: 12/24/2022] Open
Abstract
Background miR-214 has been reported to contribute to erlotinib resistance in non-small-cell lung cancer (NSCLC) through targeting LHX6; however, the molecular mechanisms underlying the involvement of LHX6 in mediating the resistance to EGFR-TKIs in erlotinib-resistant NSCLC HCC827 (HCC827/ER) cells remain unknown. This study aimed to investigate the mechanisms responsible for the contribution of LHX6 to EGFR-TKIs resistance in HCC827/ER cells. Materials and Methods HCC827/ER cells were generated by erlotinib treatment at a dose-escalation scheme. LHX6 knockout or overexpression was modeled in HCC827 and HCC827/ER cells, and then erlotinib IC50 values were measured. The cell migration ability was evaluated using a transwell migration assay, and the TCF/LEF luciferase activity was assessed with a TCF/LEF reporter luciferase assay. LHX6, β-catenin and Cyclin D1 expression was quantified using qPCR and Western blotting assays. In addition, the LHX6 expression was detected in lung cancer and peri-cancer specimens using immunohistochemical staining, and the associations of LHX expression with the clinicopathological characteristics of lung cancer were evaluated. Results Lower LHX6 expression was detected in HCC827/ER cells than in HCC827 cells (P < 0.0001), while higher β-catenin expression was seen in HCC827/ER cells than in HCC827 cells (P < 0.001). LHX6 knockout increased erlotinib resistance and cell migration ability in HCC827 cells, and LHX6 overexpression inhibited erlotinib resistance and cell migration ability in HCC827/ER cells. In addition, LHX6 mediated erlotinib resistance and cell migration ability in HCC827/ER cells via the Wnt/β-catenin pathway. Immunohistochemical staining showed lower LHX6 expression in lung cancer specimens relative to peri-cancer specimens, and there were no associations of LHX6 expression with pathologic stage, gender, age or tumor size in lung cancer patients (P > 0.05). Conclusion LHX6 down-regulation may induce EGFR-TKIs resistance and increase the migration ability of HCC827/ER cells via activation of the Wnt/β-catenin pathway.
Collapse
Affiliation(s)
- Qiang Wang
- Department of Thoracic Medical Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou 350014, People's Republic of China
| | - Jinrong Liao
- Department of Radiobiology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou 350014, People's Republic of China
| | - Zhiyong He
- Department of Thoracic Medical Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou 350014, People's Republic of China.,Fujian Provincial Key Laboratory of Translation Cancer Medicine, Fuzhou 350014, People's Republic of China
| | - Ying Su
- Department of Radiobiology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou 350014, People's Republic of China
| | - Dong Lin
- Department of Thoracic Medical Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou 350014, People's Republic of China
| | - Ling Xu
- Department of Thoracic Medical Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou 350014, People's Republic of China
| | - Haipeng Xu
- Department of Thoracic Medical Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou 350014, People's Republic of China
| | - Jinghui Lin
- Department of Thoracic Medical Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou 350014, People's Republic of China
| |
Collapse
|
7
|
Abudurexiti Y, Gu Z, Chakma K, Hata T, Motoi F, Unno M, Horii A, Fukushige S. Methylation-mediated silencing of the LIM homeobox 6 (LHX6) gene promotes cell proliferation in human pancreatic cancer. Biochem Biophys Res Commun 2020; 526:626-632. [PMID: 32248980 DOI: 10.1016/j.bbrc.2020.03.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 03/20/2020] [Indexed: 12/17/2022]
Abstract
Epigenetic gene silencing by aberrant DNA methylation leads to loss of key cellular pathways in tumorigenesis. DNA methylation-mediated silenced genes in pancreatic cancer were searched for using the methyl-CpG targeted transcriptional activation (MeTA) method, and LHX6 (LIM homeobox 6), a transcription factor involved in embryogenesis and head development, was selected as a strong candidate gene. LHX6 was downregulated in most of the pancreatic cancer cell lines (83%, 10/12), mainly through promoter hypermethylation and histone deacetylation. Furthermore, LHX6 was methylated in primary pancreatic cancer specimens (57%, 16/28) in a tumor-specific manner. Re-expression of LHX6 inhibited colony formation and proliferation in LHX6 low-expressing pancreatic cancer cell lines, PK-1 and PK-9. In contrast, knockdown of LHX6 accelerated cell proliferation in LHX6 high-expressing pancreatic cancer cell lines, PCI-35 and MIA PaCa-2. In order to analyze LHX6 downstream genes, we performed microarray analyses using LHX6 inducible PK-1 and PK-9 and found that LHX6 induction upregulated several genes that had tumor suppressive functions. Among these, we focused on TFPI2 (Tissue factor pathway inhibitor-2) and found that TFPI2 was greatly downregulated in all twelve pancreatic cancer cell lines. Our present results suggest that epigenetic inactivation of LHX6 plays an important role in pancreatic tumorigenesis by promoting cell proliferation through aberrant transcriptional regulation of several cancer-related genes.
Collapse
Affiliation(s)
| | - Zhaodi Gu
- Division of Pathology, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Kanchan Chakma
- Division of Pathology, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Tatsuo Hata
- Department of Gastroenterological Surgery, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Fuyuhiko Motoi
- Department of Gastroenterological Surgery, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Michiaki Unno
- Department of Gastroenterological Surgery, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Akira Horii
- Division of Pathology, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Shinichi Fukushige
- Division of Pathology, Tohoku University School of Medicine, Sendai, Miyagi, Japan; Center for Regulatory Epigenome and Diseases, Tohoku University School of Medicine, Sendai, Miyagi, Japan.
| |
Collapse
|
8
|
Huang B, Tian ZF, Li LF, Fan Y, Yin HY, Li Y, Mao Q, You ZL. LHX3 is an advanced-stage prognostic biomarker and metastatic oncogene in hepatocellular carcinoma. Cancer Biomark 2020; 26:31-39. [PMID: 31306102 DOI: 10.3233/cbm-182257] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a common cancer and exhibits high morbidity and mortality in the world. We recently identified LHX3 as a preferentially expressed gene with a possible involvement in HCC. OBJECTIVE To determine the expression, clinical relevance, prognostic significance and functions of LHX3 in HCC. MATERIALS AND METHODS LHX3 expression was assessed in 190 cancerous and 40 adjacent non-cancerous tissues by PCR, western blot and immunohistochemistry. Associations between LHX3 expression and clinicopathological characteristics of patients were investigated. Correlations between LHX3 expression and overall survival of patients were analyzed by Kaplan-Meier and Cox-regression methods. Functional roles of LHX3 were evaluated by transwell assays. RESULTS LHX3 expression is significantly increased in carcinoma tissues, and associated with clinical stage and metastasis of patients. LHX3 expression is much higher in the advanced-stage patients than the early-stage patients, and is sharply increased in metastasic patients. High LHX3 expression is associated with unfavorable overall survival, and is an independent prognostic factor of patients. Moreover, LHX3 is an unfavorable and independent prognostic factor unique to advanced-stage patients. Knockdown expression of LHX3 obviously inhibits tumor cell migration and invasion. CONCLUSION LHX3 is an advanced-stage prognostic biomarker, and acts as a new potential metastatic oncogene in HCC.
Collapse
Affiliation(s)
- Bo Huang
- The People's Hospital of Shapingba District in Chongqing, Chongqing, China.,The People's Hospital of Shapingba District in Chongqing, Chongqing, China
| | - Zhan-Fei Tian
- Institute of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing, China.,Department of Infectious Diseases, Chinese PLA Central Theater General Hospital, Wuhan, Hubei, China.,The People's Hospital of Shapingba District in Chongqing, Chongqing, China
| | - Lu-Feng Li
- Institute of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yi Fan
- Institute of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing, China
| | - Hao-Yang Yin
- Institute of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yan Li
- Chongqing University Cancer Hospital, Chongqing, China
| | - Qing Mao
- Institute of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing, China
| | - Zhong-Lan You
- The People's Hospital of Shapingba District in Chongqing, Chongqing, China.,Institute of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing, China
| |
Collapse
|
9
|
Angara K, Pai ELL, Bilinovich SM, Stafford AM, Nguyen JT, Li KX, Paul A, Rubenstein JL, Vogt D. Nf1 deletion results in depletion of the Lhx6 transcription factor and a specific loss of parvalbumin + cortical interneurons. Proc Natl Acad Sci U S A 2020; 117:6189-6195. [PMID: 32123116 PMCID: PMC7084085 DOI: 10.1073/pnas.1915458117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Neurofibromatosis 1 (NF1) is caused by mutations in the NF1 gene, which encodes the protein, neurofibromin, an inhibitor of Ras activity. Cortical GABAergic interneurons (CINs) are implicated in NF1 pathology, but the cellular and molecular changes to CINs are unknown. We deleted mouse Nf1 from the medial ganglionic eminence, which gives rise to both oligodendrocytes and CINs that express somatostatin and parvalbumin. Nf1 loss led to a persistence of immature oligodendrocytes that prevented later-generated oligodendrocytes from occupying the cortex. Moreover, molecular and cellular properties of parvalbumin (PV)-positive CINs were altered by the loss of Nf1, without changes in somatostatin (SST)-positive CINs. We discovered that loss of Nf1 results in a dose-dependent decrease in Lhx6 expression, the transcription factor necessary to establish SST+ and PV+ CINs, which was rescued by the MEK inhibitor SL327, revealing a mechanism whereby a neurofibromin/Ras/MEK pathway regulates a critical CIN developmental milestone.
Collapse
Affiliation(s)
- Kartik Angara
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503
| | - Emily Ling-Lin Pai
- Department of Psychiatry, University of California, San Francisco, CA 94158
- Neuroscience Program, University of California, San Francisco, CA 94158
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158
| | - Stephanie M Bilinovich
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503
| | - April M Stafford
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503
| | - Julie T Nguyen
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503
| | - Katie X Li
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503
| | - Anirban Paul
- Department of Neural and Behavioral Sciences, PennState University, Hershey, PA 17033
| | - John L Rubenstein
- Department of Psychiatry, University of California, San Francisco, CA 94158
- Neuroscience Program, University of California, San Francisco, CA 94158
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158
| | - Daniel Vogt
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503;
- Neuroscience Program, Michigan State University, Grand Rapids, MI 49503
| |
Collapse
|
10
|
Chen HQ, Zhao J, Li Y, Huang YJ, Chen DJ, He LX, Wang LQ, Zheng CF, Wang J, Cao J, Shu WQ, Liu JY, Liu WB. Epigenetic inactivation of LHX6 mediated microcystin-LR induced hepatocarcinogenesis via the Wnt/β-catenin and P53 signaling pathways. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:216-226. [PMID: 31151060 DOI: 10.1016/j.envpol.2019.05.049] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 04/14/2019] [Accepted: 05/10/2019] [Indexed: 06/09/2023]
Abstract
Microcystins (MCs) have been shown to be carcinogenic by animal and cellular experiments and found to be associated with the development of human hepatocellular carcinoma (HCC) through epidemiological studies. However, the molecular mechanism of microcystin-LR (MC-LR) induced HCC is still unclear. This study is determined to clarify the role and mechanism of LHX6 in MC-LR-induced hepatocarcinogenesis. Using the previously established MC-LR-induced malignant transformation model in L02 cells, we screened out LHX6, homeobox gene that was significantly changed. We found that LHX6 was significantly down-regulated in MC-LR treated L02 cells and the liver tissue of rats treated for 35 weeks with 10 μg/kg body weight of MC-LR. Expression of LHX6 in human tumor tissue was significantly down-regulated in high MC-LR-exposure group. LHX6 was hypermethylated in MC-LR treated L02 cells and up-regulated after treatment with 10 μM of 5-aza-2'-deoxycytidine. Furthermore, overexpression of LHX6 inhibited proliferation, invasion and migration of malignantly transformed L02 cells in vitro and in vivo, while knockdown of LHX6 resulted in an opposite phenotype. In addition, we found that up-regulation of P53 and Bax resulted in apoptosis, and that down-regulation of CTNNB1 and MMP7 led to migration of MC-LR treated L02 cells. Blockade of P53 and CTNNB1 by its inhibitor significantly diminished the effect of LHX6. These genes were working together during the process of MC-LR-induced hepatocarcinogenesis. Our study demonstrated for the first time that LHX6 gene expression is regulated by DNA methylation and can inhibit the proliferation, invasion and migration through Wnt/β-catenin and P53 signaling pathways during the MC-LR-induced hepatocarcinogenesis. This result may suggest that LHX6 gene can be used as a potential target gene and a biomarker for liver cancer treatment.
Collapse
Affiliation(s)
- Hong-Qiang Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Ji Zhao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; College of Public Health and Management, Ningxia Medical University, Yinchuan, 750004, PR China
| | - Yan Li
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; The Calmette International Hospital, Kunming, 650224, PR China
| | - Yu-Jing Huang
- Department of Environmental Hygiene, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Dong-Jiao Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; College of Public Health and Management, Ningxia Medical University, Yinchuan, 750004, PR China
| | - Li-Xiong He
- Department of Environmental Hygiene, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Ling-Qiao Wang
- Department of Environmental Hygiene, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Chuan-Fen Zheng
- Department of Environmental Hygiene, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Jia Wang
- Department of Environmental Hygiene, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Wei-Qun Shu
- Department of Environmental Hygiene, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Jin-Yi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China.
| | - Wen-Bin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China.
| |
Collapse
|
11
|
Lim WJ, Kim KH, Kim JY, Kim HJ, Kim M, Park JL, Yoon S, Oh JH, Cho JW, Kim YS, Kim N. Investigation of Gene Expression and DNA Methylation From Seven Different Brain Regions of a Crab-Eating Monkey as Determined by RNA-Seq and Whole-Genome Bisulfite Sequencing. Front Genet 2019; 10:694. [PMID: 31428131 PMCID: PMC6690020 DOI: 10.3389/fgene.2019.00694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/02/2019] [Indexed: 01/04/2023] Open
Abstract
The crab-eating monkey is widely used in biomedical research for pharmacological experiments. Epigenetic regulation in the brain regions of primates involves complex patterns of DNA methylation. Previous studies of methylated CpG-binding domains using microarray technology or peak identification of sequence reads mostly focused on developmental stages or disease, rather than normal brains. To identify correlations between gene expression and DNA methylation levels that may be related to transcriptional regulation, we generated RNA-seq and whole-genome bisulfite sequencing data from seven different brain regions from a single crab-eating monkey. We identified 92 genes whose expression levels were significantly correlated, positively or negatively, with DNA methylation levels. Among them, 11 genes exhibited brain region-specific characteristics, and their expression patterns were strongly correlated with DNA methylation level. Nine genes (SLC2A5, MCM5, DRAM1, TTC12, DHX40, COR01A, LRAT, FLVCR2, and PTER) had effects on brain and eye function and development, and two (LHX6 and MEST) were previously identified as genes in which DNA methylation levels change significantly in the promoter region and are therefore considered brain epigenetic markers. Furthermore, we characterized DNA methylation of repetitive elements at the whole genome through repeat annotation at single-base resolution. Our results reveal the diverse roles of DNA methylation at single-base resolution throughout the genome and reflect the epigenetic variations in adult brain tissues.
Collapse
Affiliation(s)
- Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Hee-Jin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Mirang Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Jong-Lyul Park
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Seokjoo Yoon
- Predictive Toxicity Department, Korea Institute of Toxicology (KIT), Daejeon, South Korea
| | - Jung-Hwa Oh
- Predictive Toxicity Department, Korea Institute of Toxicology (KIT), Daejeon, South Korea
| | - Jae-Woo Cho
- Predictive Toxicity Department, Korea Institute of Toxicology (KIT), Daejeon, South Korea
| | - Yong Sung Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| |
Collapse
|
12
|
Liu C, Fennell LJ, Bettington ML, Walker NI, Dwine J, Leggett BA, Whitehall VLJ. DNA methylation changes that precede onset of dysplasia in advanced sessile serrated adenomas. Clin Epigenetics 2019; 11:90. [PMID: 31200767 PMCID: PMC6570920 DOI: 10.1186/s13148-019-0691-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/04/2019] [Indexed: 12/31/2022] Open
Abstract
Background Sessile serrated adenomas (SSAs) are common polyps which give rise to 20–30% of colorectal cancer (CRC). SSAs display clinicopathologic features which present challenges in surveillance, including overrepresentation in young patients, proclivity for the proximal colon and rarity of histologic dysplasia (referred to then as SSAs with dysplasia, SSADs). Once dysplasia develops, there is rapid progression to CRC, even at a small size. There is therefore a clinical need to separate the “advanced” SSAs at high risk of progression to SSAD and cancer from ordinary SSAs. Since SSAs are known to accumulate methylation over time prior to the development of dysplasia, SSAD backgrounds (the remnant SSA present within an SSAD) likely harbour additional methylation events compared with ordinary SSAs. We therefore performed MethyLight and comprehensive methylation array (Illumina MethylationEPIC) on 40 SSAD backgrounds and 40 matched ordinary SSAs, and compared the methylation results with CRC methylation, CRC expression and immunohistochemical data. Results SSAD backgrounds demonstrated significant hypermethylation of CpG islands compared with ordinary SSAs, and the proportion of hypermethylated probes decreased progressively in the shore, shelf and open sea regions. Hypomethylation occurred in concert with hypermethylation, which showed a reverse pattern, increasing progressively away from the island regions. These methylation changes were also identified in BRAF-mutant hypermethylated CRCs. When compared with CRC expression data, SV2B, MLH1/EPM2AIP1, C16orf62, RCOR3, BAIAP3, OGDHL, HDHD3 and ATP1B2 demonstrated both promoter hypermethylation and decreased expression. Although SSAD backgrounds were histologically indistinguishable from ordinary SSAs, MLH1 methylation was detectable via MethyLight in 62.9% of SSAD backgrounds, and focal immunohistochemical MLH1 loss was seen in 52.5% of SSAD backgrounds. Conclusions Significant hyper- and hypomethylation events occur during SSA progression well before the development of histologically identifiable changes. Methylation is a heterogeneous process within individual SSAs, as typified by MLH1, where both MLH1 methylation and focal immunohistochemical MLH1 loss can be seen in the absence of dysplasia. This heterogeneity is likely a generalised phenomenon and should be taken into account in future methylation-based studies and the development of clinical methylation panels. Electronic supplementary material The online version of this article (10.1186/s13148-019-0691-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Cheng Liu
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia. .,Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia. .,Envoi Specialist Pathologists, Brisbane, QLD, Australia.
| | - Lochlan J Fennell
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia.,Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Mark L Bettington
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.,Envoi Specialist Pathologists, Brisbane, QLD, Australia
| | - Neal I Walker
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.,Envoi Specialist Pathologists, Brisbane, QLD, Australia
| | - Joel Dwine
- Envoi Specialist Pathologists, Brisbane, QLD, Australia
| | - Barbara A Leggett
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia.,Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.,The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Vicki L J Whitehall
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia.,Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.,Department of Chemical Pathology, Pathology Queensland, Brisbane, QLD, Australia
| |
Collapse
|
13
|
Kogan V, Millstein J, London SJ, Ober C, White SR, Naureckas ET, Gauderman WJ, Jackson DJ, Barraza-Villarreal A, Romieu I, Raby BA, Breton CV. Genetic-Epigenetic Interactions in Asthma Revealed by a Genome-Wide Gene-Centric Search. Hum Hered 2019; 83:130-152. [PMID: 30669148 PMCID: PMC7365350 DOI: 10.1159/000489765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES There is evidence to suggest that asthma pathogenesis is affected by both genetic and epigenetic variation independently, and there is some evidence to suggest that genetic-epigenetic interactions affect risk of asthma. However, little research has been done to identify such interactions on a genome-wide scale. The aim of this studies was to identify genes with genetic-epigenetic interactions associated with asthma. METHODS Using asthma case-control data, we applied a novel nonparametric gene-centric approach to test for interactions between multiple SNPs and CpG sites simultaneously in the vicinities of 18,178 genes across the genome. RESULTS Twelve genes, PF4, ATF3, TPRA1, HOPX, SCARNA18, STC1, OR10K1, UPK1B, LOC101928523, LHX6, CHMP4B, and LANCL1, exhibited statistically significant SNP-CpG interactions (false discovery rate = 0.05). Of these, three have previously been implicated in asthma risk (PF4, ATF3, and TPRA1). Follow-up analysis revealed statistically significant pairwise SNP-CpG interactions for several of these genes, including SCARNA18, LHX6, and LOC101928523 (p = 1.33E-04, 8.21E-04, 1.11E-03, respectively). CONCLUSIONS Joint effects of genetic and epigenetic variation may play an important role in asthma pathogenesis. Statistical methods that simultaneously account for multiple variations across chromosomal regions may be needed to detect these types of effects on a genome-wide scale.
Collapse
Affiliation(s)
- Vladimir Kogan
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Joshua Millstein
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA,
| | - Stephanie J London
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, RTP, Research Triangle Park, North Carolina, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Steven R White
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - W James Gauderman
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Daniel J Jackson
- University of Wisconsin School of Medicine and Public Health, Madison, Illinois, USA
| | - Albino Barraza-Villarreal
- Department of Environmental Health, Population Health Center, National Institute of Public Health of Mexico, Cuernavaca, Mexico
| | - Isabelle Romieu
- International Agency for Research on Cancer, Section of Nutrition and Metabolism, Lyon, France
| | - Benjamin A Raby
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Carrie V Breton
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| |
Collapse
|
14
|
Downregulation of tumor-suppressor gene LHX6 in cancer: a systematic review. ROMANIAN JOURNAL OF INTERNAL MEDICINE 2018. [DOI: 10.2478/rjim-2018-0008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Abstract
Introduction. LIM Homeobox 6 (LHX6) encodes a LIM homeodomain transcription factor, contributes to tissue development and morphogenesis, and is mostly expressed in medial ganglionic eminence and odontogenic mesenchyme. However, it has been reported to play a role in cancer progression. This narrative review summarizes literatures that emphasize the molecular regulation of LHX6 in tumorigenesis.
Methods. In our systematic review, the PubMed database was used for the literature search using the combination of words that included “LHX6” and “cancer”. Relevant studies, including in vitro, in vivo experiments, and clinical studies, were analyzed in this review.
Results. We found evidences that LHX6 might be important in the inhibition of tumor cell proliferation, growth, invasion, and metastasis through the suppression of Wnt/β-catenin signaling pathway. Moreover, LHX6 is observed to be downregulated in certain types of cancer due to hypermethylation, thus hindering its tumor suppressing ability. In addition, hypermethylation can also be used to determine the stage of cancer development.
Conclusion. The downregulation of LHX6 expression might be responsible in promoting cancer progression. Future studies are necessary to investigate the potential of LHX6 as a novel cancer biomarker as well as its therapeutic implications towards certain types of cancer.
Collapse
|
15
|
Yang J, Han F, Liu W, Zhang M, Huang Y, Hao X, Jiang X, Yin L, Chen H, Cao J, Zhang H, Liu J. LHX6, An Independent Prognostic Factor, Inhibits Lung Adenocarcinoma Progression through Transcriptional Silencing of β-catenin. J Cancer 2017; 8:2561-2574. [PMID: 28900494 PMCID: PMC5595086 DOI: 10.7150/jca.19972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/10/2017] [Indexed: 12/27/2022] Open
Abstract
Introduction: Our previous study identified LIM homeobox domain 6 (LHX6) as a frequently epigenetically silenced tumor-suppressor gene in lung cancer. However, its clinical value has never been evaluated, and the in-depth anti-tumor mechanism remains unclear. Methods: Public database was used for lung cancer, lung adenocarcinoma and lung squamous carcinoma patients and tissue microarray data was used for lung adenocarcinoma patients to study prognostic outcome of LHX6 expression by Kaplan-Meier and Cox-regression analysis. In vitro proliferation, metastasis and in vivo nude mice model were used to evaluate the anti-tumor effect of LHX6 on lung adenocarcinoma cell lines. The mechanisms were explored using western blot, TOP/FOP flash assays and luciferase reporter assays. LHX6 expression and clinical stages data were collected from The Cancer Genome Atlas database (TCGA). Results: Expression of LHX6 was found to be a favorable independent prognostic factor for overall survival (OS) of total lung adenocarcinoma patients (P=0.014) and patients with negative lymph nodes status (P=0.014) but not related the prognostic outcome of lung squamous cell carcinoma patients. The expression status of LHX6 significantly correlated to histological grade (P<0.01), tumor size (P=0.026), lymph node status (P=0.039) and clinical stages (P<0.01) of lung adenocarcinoma patients. Functionally, LHX6 inhibited the proliferation and metastasis of lung adenocarcinoma cells in vitro and in vivo. Furthermore, LHX6 suppressed the Wnt/β-catenin pathway through transcriptionally silencing the expression of β-catenin, and the promoter region (-1161 bp to +27 bp) was crucial for its inhibitory activity. Conclusions: Our data indicate that the expression of LHX6 may serve as a favorable prognostic biomarker for lung adenocarcinoma patients and provide a novel mechanism of LHX6 involving in the tumorigenesis of lung adenocarcinoma.
Collapse
Affiliation(s)
- Juntang Yang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Wenbin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Mingqian Zhang
- Department of emergency, Yan'an Hospital, Kunming Medical University, Kunming 650500, PR China
| | - Yongsheng Huang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Xianglin Hao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Xiao Jiang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Li Yin
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Hongqiang Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Huidong Zhang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Jinyi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| |
Collapse
|
16
|
Lin X, Li Y, Wang J, Han F, Lu S, Wang Y, Luo W, Zhang M. LHX3 is an early stage and radiosensitivity prognostic biomarker in lung adenocarcinoma. Oncol Rep 2017; 38:1482-1490. [PMID: 28731174 PMCID: PMC5549242 DOI: 10.3892/or.2017.5833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 07/03/2017] [Indexed: 12/19/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is the most common type of lung cancer. We previously identified LHX3 as a new preferentially expressed gene in NSCLC. In the present study, we sought to determine its expression, the clinical relevance and the functional roles in NSCLC. LHX3 expression is sharply increased in carcinoma tissues compared to non-carcinoma tissues. Relational analysis reveals a significant association between LHX3 expression and clinical stage (n=172, P=0.032) or radiotherapy (n=167, P=0.022) of patients. LHX3 expression is much higher in the patients at advanced stages (stage III–IV) than in the patients at early stages (stage I–II, P=0.0304), and LHX3 expression is remarkably increased in the patients with radiotherapy treatment (P=0.0002). Survival analyses indicate that LHX3 is associated with unfavorable survival (n=180, P=0.002) and represents an independent prognostic factor [hazard ratio (HR)=1.834, P=0.004] of the NSCLC patients. Furthermore, LHX3 is associated with unfavorable overall survival (n=866, P=0.004) and represents an independent prognostic factor (HR=2.36, P=0.000) in lung adenocarcinoma (ADC) patients, but is not associated with overall survival of squamous cell carcinoma (SCC) patients (n=524, P=0.27). Further analyses found that LHX3 is an early-stage (n=94, P=0.003) and radiosensitivity (n=45, P=0.002) prognostic factor in ADC patients. The patients without radiotherapy have a significantly prolonged survival compared to those with radiotherapy (P=0.0069). Further functional studies show that forced expression of LHX3 in lung cancer cells obviously promotes cell proliferation and invasion, whereas inhibits cell apoptosis. In summary, LHX3 is an early-stage and radiosensitivity prognostic biomarker, and a novel potential oncogene in ADC.
Collapse
Affiliation(s)
- Xin Lin
- Department of Emergency, Yan'an Hospital, Kunming Medical University, Kunming, Yunnan, P.R. China
| | - Yan Li
- Department of Emergency, Yan'an Hospital, Kunming Medical University, Kunming, Yunnan, P.R. China
| | - Jin Wang
- Department of Emergency, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, P.R. China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P.R. China
| | - Shuang Lu
- Department of Emergency, Yan'an Hospital, Kunming Medical University, Kunming, Yunnan, P.R. China
| | - Yu Wang
- Department of Gerontology, Yan'an Hospital, Kunming Medical University, Kunming, Yunnan, P.R. China
| | - Wenjian Luo
- Department of Gerontology, Yan'an Hospital, Kunming Medical University, Kunming, Yunnan, P.R. China
| | - Mingqian Zhang
- Department of Emergency, Yan'an Hospital, Kunming Medical University, Kunming, Yunnan, P.R. China
| |
Collapse
|
17
|
|
18
|
Zhou C, Yang G, Chen M, He L, Xiang L, Ricupero C, Mao JJ, Ling J. Lhx6 and Lhx8: cell fate regulators and beyond. FASEB J 2015; 29:4083-91. [PMID: 26148970 PMCID: PMC4566936 DOI: 10.1096/fj.14-267500] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 06/22/2015] [Indexed: 12/11/2022]
Abstract
As transcription factors of the lines (LIN)-11/Islet (Isl)-1/mitosis entry checkpoint (MEC)-3 (LIM)-homeobox subfamily, LIM homeobox (Lhx)6 and -8 are remarkably conserved and involved in the morphogenesis of multiple organ systems. Lhx6 and -8 play overlapping and distinctive roles, but in general act as cell fate mediators and in turn are regulated by several transcriptional factors, such as sonic hedgehog, fibroblast growth factors, and wingless-int (Wnt)/β-catenin. In this review, we first summarize Lhx6 and -8 distributions in development and then explore how Lhx6 and -8 act as transcription factors and coregulators of cell lineage specification. Known Lhx6 and -8 functions and targets are outlined in neurogenesis, craniofacial development, and germ cell differentiation. The underlying mechanisms of Lhx6 and -8 in regulating cell fate remain elusive. Whether Lhx6 and -8 affect functions in tissues and organs other than neural, craniofacial, oocytes, and germ cells is largely unexplored. Taken together, Lhx6 and -8 are important regulators of cell lineage specification and may act as one of the pivotal mediators of stem cell fate. Undoubtedly, future investigations of Lhx6 and -8 biology will continue to yield fascinating insights into tissue development and homeostasis, in addition to their putative roles in tissue regeneration and ageing.
Collapse
Affiliation(s)
- Chen Zhou
- *Center for Craniofacial Regeneration, Columbia University Medical Center, New York, New York, USA; Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Guodong Yang
- *Center for Craniofacial Regeneration, Columbia University Medical Center, New York, New York, USA; Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Mo Chen
- *Center for Craniofacial Regeneration, Columbia University Medical Center, New York, New York, USA; Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Ling He
- *Center for Craniofacial Regeneration, Columbia University Medical Center, New York, New York, USA; Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Lusai Xiang
- *Center for Craniofacial Regeneration, Columbia University Medical Center, New York, New York, USA; Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Christopher Ricupero
- *Center for Craniofacial Regeneration, Columbia University Medical Center, New York, New York, USA; Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Jeremy J Mao
- *Center for Craniofacial Regeneration, Columbia University Medical Center, New York, New York, USA; Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Junqi Ling
- *Center for Craniofacial Regeneration, Columbia University Medical Center, New York, New York, USA; Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
19
|
Hu Z, Xie L. LHX6 inhibits breast cancer cell proliferation and invasion via repression of the Wnt/β-catenin signaling pathway. Mol Med Rep 2015; 12:4634-4639. [PMID: 26129710 DOI: 10.3892/mmr.2015.3997] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 06/11/2015] [Indexed: 11/05/2022] Open
Abstract
LIM homeobox domain 6 (LHX6), a member of the LHX family of proteins, has been implicated in cancer development. However, the involvement of LHX6 in the development of breast cancer remains unclear. In the present study, the epigenetic regulation, biological function and associated molecular mechanisms of LHX6 in breast cancer were analyzed. The expression levels of LHX6 were demonstrated to be markedly decreased in breast cancer tissues and cell lines. In addition, it was found that increased LHX6 expression in breast cancer cell lines inhibited cell proliferation and invasion. Furthermore, increased LHX6 expression significantly decreased the expression of β‑catenin in MDA‑MB‑231 breast cancer cells, and small interfering RNA‑β‑catenin enhanced LHX6‑induced inhibition of cell proliferation and invasion in MDA‑MB‑231 breast cancer cells. These results indicate that LHX6 inhibits breast cancer cell growth and invasion through suppression of the Wnt/β‑catenin signaling pathway. Thus, the present study provides a novel insight into the underlying mechanism of tumorigenesis in breast cancer, indicating the therapeutic potential of LHX6 in the treatment of breast cancer.
Collapse
Affiliation(s)
- Zhuang Hu
- Department of Breast and Thyroid Surgery, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Lingling Xie
- Operation Room, Zhangqiu City Hospital of Traditional Chinese Medicine, Zhangqiu, Shandong 250200, P.R. China
| |
Collapse
|
20
|
Estécio MRH, Maddipoti S, Bueso-Ramos C, DiNardo CD, Yang H, Wei Y, Kondo K, Fang Z, Stevenson W, Chang KS, Pierce SA, Bohannan Z, Borthakur G, Kantarjian H, Garcia-Manero G. RUNX3 promoter hypermethylation is frequent in leukaemia cell lines and associated with acute myeloid leukaemia inv(16) subtype. Br J Haematol 2015; 169:344-51. [PMID: 25612675 DOI: 10.1111/bjh.13299] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 12/08/2014] [Indexed: 01/15/2023]
Abstract
Correlative and functional studies support the involvement of the RUNX gene family in haematological malignancies. To elucidate the role of epigenetics in RUNX inactivation, we evaluated promoter DNA methylation of RUNX1, 2, and 3 in 23 leukaemia cell lines and samples from acute myeloid leukaemia (AML), acute lymphocytic leukaemia (ALL) and myelodysplatic syndromes (MDS) patients. RUNX1 and RUNX2 gene promoters were mostly unmethylated in cell lines and clinical samples. Hypermethylation of RUNX3 was frequent among cell lines (74%) and highly variable among patient samples, with clear association to cytogenetic status. High frequency of RUNX3 hypermethylation (85% of the 20 studied cases) was found in AML patients with inv(16)(p13.1q22) compared to other AML subtypes (31% of the other 49 cases). RUNX3 hypermethylation was also frequent in ALL (100% of the six cases) but low in MDS (21%). In support of a functional role, hypermethylation of RUNX3 was correlated with low levels of protein, and treatment of cell lines with the DNA demethylating agent, decitabine, resulted in mRNA re-expression. Furthermore, relapse-free survival of non-inv(16)(p13.1q22) AML patients without RUNX3 methylation was significantly better (P = 0·016) than that of methylated cases. These results suggest that RUNX3 silencing is an important event in inv(16)(p13.1q22) leukaemias.
Collapse
Affiliation(s)
- Marcos R H Estécio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
WANG XI, HE CHAO, HU XIAOTONG. LIM homeobox transcription factors, a novel subfamily which plays an important role in cancer (Review). Oncol Rep 2014; 31:1975-85. [DOI: 10.3892/or.2014.3112] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 03/13/2014] [Indexed: 11/06/2022] Open
|
22
|
Kabekkodu SP, Bhat S, Radhakrishnan R, Aithal A, Mascarenhas R, Pandey D, Rai L, Kushtagi P, Mundyat GP, Satyamoorthy K. DNA promoter methylation-dependent transcription of the double C2-like domain β (DOC2B) gene regulates tumor growth in human cervical cancer. J Biol Chem 2014; 289:10637-10649. [PMID: 24570007 DOI: 10.1074/jbc.m113.491506] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Double C2-like domain β (DOC2B) gene encodes for a calcium-binding protein, which is involved in neurotransmitter release, sorting, and exocytosis. We have identified the promoter region of the DOC2B gene as hypermethylated in pre-malignant, malignant cervical tissues, and cervical cancer cell lines by methylation-sensitive dimethyl sulfoxide-polymerase chain reaction and bisulfite genome sequencing; whereas, it was unmethylated in normal cervical tissues (p < 0.05). The promoter hypermethylation was inversely associated with mRNA expression in SiHa, CaSki, and HeLa cells and treatment with demethylating agent 5-aza-2-deoxycytidine restored DOC2B expression. The region -630 to +25 bp of the DOC2B gene showed robust promoter activity by a luciferase reporter assay and was inhibited by in vitro artificial methylation with Sss1 methylase prior to transient transfections. Overexpression of the DOC2B gene in SiHa cells when compared with controls showed significantly reduced colony formation, cell proliferation, induced cell cycle arrest, and repressed cell migration and invasion (p < 0.05). Ectopic expression of DOC2B resulted in anoikis-mediated cell death and repressed tumor growth in a nude mice xenograft model (p < 0.05). DOC2B expressing cells showed a significant increase in intracellular calcium level (p < 0.05), impaired AKT1 and ERK1/2 signaling, and induced actin cytoskeleton remodeling. Our results show that promoter hypermethylation and silencing of the DOC2B gene is an early and frequent event during cervical carcinogenesis and whose reduced expression due to DNA promoter methylation may lead to selective cervical tumor growth.
Collapse
Affiliation(s)
- Shama Prasada Kabekkodu
- Division of Biotechnology, Manipal Life Sciences Centre, Manipal University, Manipal 576104, India
| | - Samatha Bhat
- Division of Biotechnology, Manipal Life Sciences Centre, Manipal University, Manipal 576104, India
| | - Raghu Radhakrishnan
- Division of Biotechnology, Manipal Life Sciences Centre, Manipal University, Manipal 576104, India
| | - Abhijit Aithal
- Division of Biotechnology, Manipal Life Sciences Centre, Manipal University, Manipal 576104, India
| | - Roshan Mascarenhas
- Division of Biotechnology, Manipal Life Sciences Centre, Manipal University, Manipal 576104, India
| | - Deeksha Pandey
- Department of OBGYN, Kasturba Medical College, Manipal University, Manipal 576104, India
| | - Lavanya Rai
- Department of OBGYN, Kasturba Medical College, Manipal University, Manipal 576104, India
| | - Pralhad Kushtagi
- Department of OBGYN, Kasturba Medical College, Manipal University, Mangalore 575001, India
| | - Gopinath Puthiya Mundyat
- Division of Biotechnology, Manipal Life Sciences Centre, Manipal University, Manipal 576104, India
| | - Kapaettu Satyamoorthy
- Division of Biotechnology, Manipal Life Sciences Centre, Manipal University, Manipal 576104, India.
| |
Collapse
|
23
|
Demokan S, Chuang AY, Pattani KM, Sidransky D, Koch W, Califano JA. Validation of nucleolar protein 4 as a novel methylated tumor suppressor gene in head and neck cancer. Oncol Rep 2013; 31:1014-20. [PMID: 24337411 PMCID: PMC3896520 DOI: 10.3892/or.2013.2927] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 11/27/2013] [Indexed: 11/10/2022] Open
Abstract
Methylation of CpG islands in the promoter region of genes acts as a significant mechanism of epigenetic gene silencing in head and neck cancer. In the present study, we assessed the association of epigenetic alterations of a panel of 12 genes [nucleolar protein 4 (NOL4), iroquois homeobox 1 (IRX1), SLC5A8, LRRC3B, FUSSEL18, EBF3, GBX2, HMX2, SEPT9, ALX3, SOCS3 and LHX6] with head and neck squamous cell carcinoma (HNSCC) via a candidate gene approach. After the initial screening of methylated CpG islands on the promoter regions by bisulfite sequencing using salivary rinse samples, only two genes had methylated CpG dinucleotides on their promoter regions in tumor samples and absence of methylated CpGs were found in normal salivary rinse samples after bisulfite modification and bisulfite sequencing. We then performed real-time quantitative methylation-specific PCR (QMSP) on 16 salivary rinse and 14 normal mucosal samples from healthy subjects and 33 HNSCC tumor samples for the two genes selected. After validation with QMSP, one gene, NOL4, was highly methylated (91%) in tumor samples and unmethylated in normal salivary rinses and minimally methylated in normal mucosal samples demonstrating cancer-specific methylation in HNSCC tissues. Although the IRX1 gene was observed as methylated in normal mucosal and salivary rinse samples, the methylation values of these normal samples were very low (<10%). In conclusion, we identified NOL4 as a highly specific promoter methylated gene associated with HNSCC. IRX1 may have potential as a biomarker for HNSCC and should be assessed in a larger cohort.
Collapse
Affiliation(s)
- Semra Demokan
- Department of Basic Oncology, Oncology Institute, Istanbul University, Capa, Istanbul 34093, Turkey
| | - Alice Y Chuang
- Department of Dermatology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Kavita M Pattani
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Wayne Koch
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Joseph A Califano
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| |
Collapse
|
24
|
Liu WB, Han F, Jiang X, Yin L, Chen HQ, Li YH, Liu Y, Cao J, Liu JY. Epigenetic regulation of ANKRD18B in lung cancer. Mol Carcinog 2013; 54:312-21. [PMID: 24249358 DOI: 10.1002/mc.22101] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/23/2013] [Accepted: 10/11/2013] [Indexed: 12/25/2022]
Abstract
The identification of the key genetic and epigenetic changes underlying lung carcinogenesis would aid effective early diagnosis and targeted therapies for lung cancer. In this study, we screened a novel hypermethylated gene ankyrin repeat domain 18B (ANKRD18B), to determine whether it is regulated by DNA methylation and clarify its biological and clinical implications in lung cancer. Methylation status and expression level were analyzed by methylation-specific PCR, bisulfite genomic sequencing, and quantitative reverse transcription-polymerase chain reaction (qRT-PCR). We detected ANKRD18B hypermethylation in 52 of 98 (53.1%) primary lung cancer tissues and in nine of 10 (90%) cell lines, whereas no methylation was seen in 10 normal lung tissue samples. ANKRD18B methylation was more frequently observed in patients with poor differentiation (P < 0.05). Notably, 62 pairs of samples from patients whose tumor tissue showed hypermethylation of ANKRD18B exhibited the same aberrant methylation in 72.7% and 69.7% of their corresponding plasma and sputum samples, respectively; whereas no hypermethylation of ANKRD18B was detected in the sputum and plasma from patients whose tumor sample lacked this alteration. In addition, ANKRD18B mRNA expression was significantly decreased or silenced in lung cancer tissues and cell lines associated with hypermethylation of the ANKRD18B region. Demethylation agent 5-aza-2'-deoxycytidine significantly increased ANKRD18B mRNA expression in lung cancer cell lines. Furthermore, overexpression of ANKRD18B suppressed lung cancer cell growth. These results suggest that the expression of ANKRD18B is regulated by CpG island hypermethylation in lung cancer. Our findings confirm the importance of the identification of new markers of epigenetic dysregulation in cancer.
Collapse
Affiliation(s)
- Wen-Bin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Liu WB, Jiang X, Han F, Li YH, Chen HQ, Liu Y, Cao J, Liu JY. LHX6 acts as a novel potential tumour suppressor with epigenetic inactivation in lung cancer. Cell Death Dis 2013; 4:e882. [PMID: 24157876 PMCID: PMC3824675 DOI: 10.1038/cddis.2013.366] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 08/07/2013] [Accepted: 08/07/2013] [Indexed: 12/23/2022]
Abstract
LIM homeobox domain 6 (LHX6) is a putative transcriptional regulator that controls the differentiation and development of neural and lymphoid cells. However, the function of LHX6 in cancer development remains largely unclear. Recently, we found that LHX6 is hypermethylated in lung cancer. In this study, we analysed its epigenetic regulation, biological functions, and related molecular mechanisms in lung cancer. Methylation status was evaluated by methylation-specific PCR and bisulfite genomic sequencing. LHX6 mRNA levels were measured in relation to the methylation status. The effects of LHX6 expression on tumourigenesis were studied in vitro and in vivo. LHX6 was readily expressed in normal lung tissues without methylation, but was downregulated or silenced in lung cancer cell lines and tissues with hypermethylation status. Treatment of lung cancer cells with the demethylating agent 5-aza-2′-deoxycytidine restored LHX6 expression. Moreover, LHX6 hypermethylation was detected in 56% (52/93) of primary lung cancers compared with none (0/20) of the tested normal lung tissues. In lung cancer cell lines 95D and H358, forced expression of LHX6 suppressed cell viability, colony formation, and migration, induced apoptosis and G1/S arrest, and inhibited their tumorigenicity in nude mice. On the other hand, knockdown of LHX6 expression by RNA interference increased cell proliferation and inhibited apoptosis and cell cycle arrest. These effects were associated with upregulation of p21 and p53, and downregulation of Bcl-2, cyclinD1, c-myc, CD44, and MMP7. In conclusion, our results suggest that LHX6 is a putative tumour suppressor gene with epigenetic silencing in lung cancer.
Collapse
Affiliation(s)
- W-b Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Bao ZS, Zhang CB, Wang HJ, Yan W, Liu YW, Li MY, Zhang W. Whole-genome mRNA expression profiling identifies functional and prognostic signatures in patients with mesenchymal glioblastoma multiforme. CNS Neurosci Ther 2013; 19:714-20. [PMID: 23663361 DOI: 10.1111/cns.12118] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/01/2013] [Accepted: 04/01/2013] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The Cancer Genome Atlas (TCGA) has divided patients with glioblastoma multiforme (GBM) into four subtypes based on mRNA expression microarray. The mesenchymal subtype, with a larger proportion, is considered a more lethal one. Clinical outcome prediction is required to better guide more personalized treatment for these patients. AIMS The objective of this study was to identify a mRNA expression signature to improve outcome prediction for patients with mesenchymal GBM. RESULTS For signature identification and validation, we downloaded mRNA expression microarray data from TCGA as training set and data from Rembrandt and GSE16011 as validation set. Cox regression and risk-score analysis were used to develop the 4 signatures, which were function and prognosis associated as revealed by Gene Ontology (GO) analysis and Gene Set Variation Analysis (GSVA). Patients who had high-risk scores according to the signatures had poor overall survival compared with patients who had low-risk scores. CONCLUSIONS The signatures were identified as risk predictors that patients who had a high-risk score tended to have unfavorable outcome, demonstrating their potential for personalizing cancer management.
Collapse
Affiliation(s)
- Zhao-Shi Bao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | | | | | | | | | | | | |
Collapse
|
27
|
Wong TS, Gao W, Li ZH, Chan JYW, Ho WK. Epigenetic dysregulation in laryngeal squamous cell carcinoma. JOURNAL OF ONCOLOGY 2012; 2012:739461. [PMID: 22645613 PMCID: PMC3356733 DOI: 10.1155/2012/739461] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/16/2012] [Accepted: 02/16/2012] [Indexed: 12/17/2022]
Abstract
Laryngeal carcinoma is a common head and neck cancer with poor prognosis. Patients with laryngeal carcinoma usually present late leading to the reduced treatment efficacy and high rate of recurrence. Despite the advance in the use of molecular markers for monitoring human cancers in the past decades, there are still no reliable markers for use to screen laryngeal carcinoma and follow the patients after treatment. Epigenetics emerged as an important field in understanding the biology of the human malignancies. Epigenetic alterations refer to the dysregulation of gene, which do not involve the alterations of the DNA sequence. Major epigenetic changes including methylation imbalance, histone modification, and small RNA dysregulation could play a role in the development of human malignancies. Global epigenetic change is now regarded as a molecular signature of cancer. The characteristics and behavior of a cancer could be predicted based on the specific epigenetic pattern. We here provide a review on the understanding of epigenetic dysregulation in laryngeal carcinoma. Further knowledge on the initiation and progression of laryngeal carcinoma at epigenetic level could promote the translation of the knowledge to clinical use.
Collapse
Affiliation(s)
- Thian-Sze Wong
- Department of Surgery, Queen Mary Hospital, The University of Hong Kong, 102 Pokfulam Road, Hong Kong
| | - Wei Gao
- Department of Surgery, Queen Mary Hospital, The University of Hong Kong, 102 Pokfulam Road, Hong Kong
| | - Zeng-Hong Li
- Department of Surgery, Queen Mary Hospital, The University of Hong Kong, 102 Pokfulam Road, Hong Kong
| | - Jimmy Yu-Wai Chan
- Department of Surgery, Queen Mary Hospital, The University of Hong Kong, 102 Pokfulam Road, Hong Kong
| | - Wai-Kuen Ho
- Department of Surgery, Queen Mary Hospital, The University of Hong Kong, 102 Pokfulam Road, Hong Kong
| |
Collapse
|
28
|
Differential differences in methylation status of putative imprinted genes among cloned swine genomes. PLoS One 2012; 7:e32812. [PMID: 22393450 PMCID: PMC3290620 DOI: 10.1371/journal.pone.0032812] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 02/06/2012] [Indexed: 11/30/2022] Open
Abstract
DNA methylation is a major epigenetic modification in the mammalian genome that regulates crucial aspects of gene function. Mammalian cloning by somatic cell nuclear transfer (SCNT) often results in gestational or neonatal failure with only a small proportion of manipulated embryos producing live births. Many of the embryos that survive to term later succumb to a variety of abnormalities that are likely due to inappropriate epigenetic reprogramming. Aberrant methylation patterns of imprinted genes in cloned cattle and mice have been elucidated, but few reports have analyzed the cloned pig genome. Four surviving cloned sows that were created by ear fibroblast nuclear transfer, each with a different life span and multiple organ defects, such as heart defects and bone growth delay, were used as epigenetic study materials. First, we identified four putative differential methylation regions (DMR) of imprinted genes in the wild-type pig genome, including two maternally imprinted loci (INS and IGF2) and two paternally imprinted loci (H19 and IGF2R). Aberrant DNA methylation, either hypermethylation or hypomethylation, commonly appeared in H19 (45% of imprinted loci hypermethylated vs. 30% hypomethylated), IGF2 (40% vs. 0%), INS (50% vs. 5%), and IGF2R (15% vs. 45%) in multiple tissues from these four cloned sows compared with wild-type pigs. Our data suggest that aberrant epigenetic modifications occur frequently in the genome of cloned swine. Even with successful production of cloned swine that avoid prenatal or postnatal death, the perturbation of methylation in imprinted genes still exists, which may be one of reason for their adult pathologies and short life. Understanding the aberrant pattern of gene imprinting would permit improvements in future cloning techniques.
Collapse
|
29
|
Epigenetic screen of human DNA repair genes identifies aberrant promoter methylation of NEIL1 in head and neck squamous cell carcinoma. Oncogene 2012; 31:5108-16. [DOI: 10.1038/onc.2011.660] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
30
|
Yang CH, Cheng YH, Chuang LY, Chang HW. A combined bisulfite restriction analysis bioinformatics tool: methyl-typing. Methods Mol Biol 2011; 791:73-88. [PMID: 21913072 DOI: 10.1007/978-1-61779-316-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
In this chapter, we introduce our developed freeware tool Methyl-Typing. It provides methylation-related bioinformatics with a special focus on combined bisulfite restriction analysis (COBRA). We give an overview of the implementation and program modules for Methyl-Typing. Various databases and methylation-related functions are integrated into Methyl-Typing and a helpful example is illustrated in detail. Several input protocols and their outputs for COBRA-related information are demonstrated, such as the inputs of multiple gene names in official gene symbols, multiple accession numbers for nucleotide sequence retrieval, multiple template sequences in a free format, primer sequences, and file uploads. The program goal of Methyl-Typing is to provide computation and visualization of the essential information for COBRA assay so that methylation can easily be analyzed by COBRA. It is a fast and efficient tool for providing all possible methylation sites of restriction enzymes.
Collapse
Affiliation(s)
- Cheng-Hong Yang
- Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan
| | | | | | | |
Collapse
|
31
|
Role of DNA methylation in head and neck cancer. Clin Epigenetics 2011; 2:123-50. [PMID: 22704334 PMCID: PMC3365391 DOI: 10.1007/s13148-011-0045-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 06/14/2011] [Indexed: 02/07/2023] Open
Abstract
Head and neck cancer (HNC) is a heterogenous and complex entity including diverse anatomical sites and a variety of tumor types displaying unique characteristics and different etilogies. Both environmental and genetic factors play a role in the development of the disease, but the underlying mechanism is still far from clear. Previous studies suggest that alterations in the genes acting in cellular signal pathways may contribute to head and neck carcinogenesis. In cancer, DNA methylation patterns display specific aberrations even in the early and precancerous stages and may confer susceptibility to further genetic or epigenetic changes. Silencing of the genes by hypermethylation or induction of oncogenes by promoter hypomethylation are frequent mechanisms in different types of cancer and achieve increasing diagnostic and therapeutic importance since the changes are reversible. Therefore, methylation analysis may provide promising clinical applications, including the development of new biomarkers and prediction of the therapeutic response or prognosis. In this review, we aimed to analyze the available information indicating a role for the epigenetic changes in HNC.
Collapse
|
32
|
Estécio MR, Gallegos J, Vallot C, Castoro RJ, Chung W, Maegawa S, Oki Y, Kondo Y, Jelinek J, Shen L, Hartung H, Aplan PD, Czerniak BA, Liang S, Issa JPJ. Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer. Genome Res 2010; 20:1369-82. [DOI: 10.1101/gr.107318.110] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Epigenetic silencing plays an important role in cancer development. An attractive hypothesis is that local DNA features may participate in differential predisposition to gene hypermethylation. We found that, compared with methylation-resistant genes, methylation-prone genes have a lower frequency of SINE and LINE retrotransposons near their transcription start site. In several large testing sets, this distribution was highly predictive of promoter methylation. Genome-wide analysis showed that 22% of human genes were predicted to be methylation-prone in cancer; these tended to be genes that are down-regulated in cancer and that function in developmental processes. Moreover, retrotransposon distribution marks a larger fraction of methylation-prone genes compared to Polycomb group protein (PcG) marking in embryonic stem cells; indeed, PcG marking and our predictive model based on retrotransposon frequency appear to be correlated but also complementary. In summary, our data indicate that retrotransposon elements, which are widespread in our genome, are strongly associated with gene promoter DNA methylation in cancer and may in fact play a role in influencing epigenetic regulation in normal and abnormal physiological states.
Collapse
|
33
|
Samuelsson JK, Alonso S, Yamamoto F, Perucho M. DNA fingerprinting techniques for the analysis of genetic and epigenetic alterations in colorectal cancer. Mutat Res 2010; 693:61-76. [PMID: 20851135 DOI: 10.1016/j.mrfmmm.2010.08.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 08/07/2010] [Accepted: 08/24/2010] [Indexed: 01/03/2023]
Abstract
Genetic somatic alterations are fundamental hallmarks of cancer. In addition to point and other small mutations targeting cancer genes, solid tumors often exhibit aneuploidy as well as multiple chromosomal rearrangements of large fragments of the genome. Whether somatic chromosomal alterations and aneuploidy are a driving force or a mere consequence of tumorigenesis remains controversial. Recently it became apparent that not only genetic but also epigenetic alterations play a major role in carcinogenesis. Epigenetic regulation mechanisms underlie the maintenance of cell identity crucial for development and differentiation. These epigenetic regulatory mechanisms have been found substantially altered during cancer development and progression. In this review, we discuss approaches designed to analyze genetic and epigenetic alterations in colorectal cancer, especially DNA fingerprinting approaches to detect changes in DNA copy number and methylation. DNA fingerprinting techniques, despite their modest throughput, played a pivotal role in significant discoveries in the molecular basis of colorectal cancer. The aim of this review is to revisit the fingerprinting technologies employed and the oncogenic processes that they unveiled.
Collapse
Affiliation(s)
- Johanna K Samuelsson
- Sanford-Burnham Medical Research Institute (SBMRI), 10901N. Torrey Pines Rd, La Jolla, CA 92037, United States
| | | | | | | |
Collapse
|
34
|
Singh KP, Kumari R, Dumond JW. Simulated microgravity-induced epigenetic changes in human lymphocytes. J Cell Biochem 2010; 111:123-9. [PMID: 20506542 DOI: 10.1002/jcb.22674] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Real space flight and modeled microgravity conditions result in changes in the expression of genes that control important cellular functions. However, the mechanisms for microgravity-induced gene expression changes are not clear. The epigenetic changes of DNA methylation and chromatin histones modifications are known to regulate gene expression. The objectives of this study were to investigate whether simulated microgravity alters (a) the DNA methylation and histone acetylation, and (b) the expression of DNMT1, DNMT3a, DNMT3b, and HDAC1 genes that regulate epigenetic events. To achieve these objectives, human T-lymphocyte cells were grown in a rotary cell culture system (RCCS) that simulates microgravity, and in parallel under normal gravitational conditions as control. The microgravity-induced DNA methylation changes were detected by methylation sensitive-random amplified polymorphic DNA (MS-RAPD) analysis of genomic DNA. The gene expression was measured by Quantitative Real-time PCR. The expression of DNMT1, DNMT3a, and DNMT3b was found to be increased at 72 h, and decreased at 7 days in microgravity exposed cells. The MS-RAPD analysis revealed that simulated microgravity exposure results in DNA hypomethylation and mutational changes. Gene expression analysis revealed microgravity exposure time-dependent decreased expression of HDAC1. Decreased expression of HDAC1 should result in increased level of acetylated histone H3, however a decreased level of acetylated H3 was observed in microgravity condition, indicating thereby that other HDACs may be involved in regulation of H3 deacetylation. The findings of this study suggest that epigenetic events could be one of the mechanistic bases for microgravity-induced gene expression changes and associated adverse health effects.
Collapse
Affiliation(s)
- Kamaleshwar P Singh
- Department of Environmental Toxicology, The Institute of Environmental and Human Health, Texas Tech University, Lubbock, Texas 79409, USA.
| | | | | |
Collapse
|
35
|
Mydlarz WK, Hennessey PT, Califano JA. Advances and Perspectives in the Molecular Diagnosis of Head and Neck Cancer. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2010; 4:53-65. [PMID: 20161611 PMCID: PMC2811380 DOI: 10.1517/17530050903338068] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) is a debilitating and lethal disease. Despite significant advances in radiotherapy and surgical management, the 5-year survival rate for head and neck cancer has remained a dismal 50%. Advances in early detection have been made, but to improve patient outcomes better biomarkers and targeted therapeutic agents are needed. Novel biomarkers can improve early detection and provide data to optimize therapeutic strategy and patient survival, and could lead to potentially effective targeted therapies. OBJECTIVE: Report the advances in the discovery of novel biomarkers for HNSCC, and review the potential utility of biomarkers in the molecular diagnosis of HNSCC. METHODS: A review of the English literature (PubMed) from 1980 to 2009. RESULTS/CONCLUSION: Currently the most widely accepted biomarker for HNSCC is high risk HPV status. EGFR is another promising biomarker, however, further research is necessary to determine its prognostic benefit. A large number of promising biomarker candidates are currently being evaluated including epigenetic, expression, and genomic based markers. Studies to validate the sensitivity and specificity of these biomarkers in clinical samples from adequately powered prospective cohorts are needed for successful translation of these findings into potential molecular diagnostic, prognostic, and therapeutic biomarkers for HNSCC.
Collapse
Affiliation(s)
- Wojciech K. Mydlarz
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21231 United States
| | - Patrick T. Hennessey
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21231 United States
| | - Joseph A. Califano
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21231 United States
- Milton J Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, MD 21204, United States
| |
Collapse
|
36
|
|
37
|
Aberrant methylation and reduced expression of LHX9 in malignant gliomas of childhood. Neoplasia 2009; 11:700-11. [PMID: 19568415 DOI: 10.1593/neo.09406] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Revised: 04/08/2009] [Accepted: 04/09/2009] [Indexed: 11/18/2022] Open
Abstract
High-grade gliomas (HGGs) of childhood represent approximately 7% of pediatric brain tumors. They are highly invasive tumors and respond poorly to conventional treatments in contrast to pilocytic astrocytomas, which usually are well demarcated and frequently can be cured by surgery. The molecular events for this clinical relevant finding are only partially understood. In the current study, to identify aberrantly methylated genes that may be involved in the tumorigenesis of pediatric HGGs, we performed a microarray-based differential methylation hybridization approach and found frequent hypermethylation of the LHX9 (human Lim-homebox 9) gene encoding a transcription factor involved in brain development. Bisulfite genomic sequencing and combined bisulfite restriction analysis showed that HGGs were frequently methylated at two CpG-rich LHX9 regions in comparison to benign, nondiffuse pilocytic astrocytomas and normal brain tissues. The LHX9 hypermethylation was associated with reduced messenger RNA expression in pediatric HGG samples and corresponding cell lines. This epigenetic modification was reversible by pharmacological inhibition (5-aza-2'-deoxycytidine), and reexpression of LHX9 transcript was induced in pediatric glioma cell lines. Exogenous expression of LHX9 in glioma cell lines did not directly affect cell proliferation and apoptosis but specifically inhibited glioma cell migration and invasion in vitro, suggesting a possible implication of LHX9 in the migratory phenotype of HGGs. Our results demonstrate that the LHX9 gene is frequently silenced in pediatric malignant astrocytomas by hypermethylation and that this epigenetic alteration is involved in glioma cell migration and invasiveness.
Collapse
|
38
|
Applying the molecular biology and epigenetics of head and neck cancer in everyday clinical practice. Oral Oncol 2009; 45:440-6. [DOI: 10.1016/j.oraloncology.2008.05.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
39
|
Abstract
For years, head and neck squamous cell carcinomas (HNSCC) have been among the leading cancers worldwide. Despite considerable efforts, the 5-year survival rate for HNSCC has not changed significantly. To improve this situation, it is necessary to understand the fundamental biological processes leading to the disease and its progression. In addition to known genetic changes in HNSCC, molecular cytogenetic investigations have identified chromosomal regions of gains and losses, but many of the responsible candidate genes have yet to be identified. Furthermore, recent results indicate the importance of epigenetic modifications in HNSCC, such as DNA methylation. Several genes, including the tumor suppressor CDKN2A and other candidates such as DAPK1, MGMT, TIMP3, TCF21, and C/EBPalpha, have been found to harbor hypermethylated regulatory sequences that lead to reduced expression or gene silencing. Hypermethylation in such genes could be used not only as biomarkers for the early detection of HNSCC but also to improve prevention strategies and therapy outcomes.
Collapse
Affiliation(s)
- P Schmezer
- Abteilung Toxikologie und Krebsrisikofaktoren, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg
| | | |
Collapse
|
40
|
SDF-1 and CCR5 genes polymorphism in patients with head and neck cancer. Pathol Oncol Res 2008; 14:45-50. [PMID: 18386165 DOI: 10.1007/s12253-008-9007-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Accepted: 12/14/2007] [Indexed: 12/28/2022]
Abstract
The frequency of SDF1-3'A and CCR5Delta32 in patients with head and neck cancer were determined in this study. The frequencies of alleles and genotypes of SDF-1 and CCR5 were assessed by PCR method in 156 patients with malignant head and neck cancer, 125 (80.1%) cases with squamous cell carcinoma and 31 (19.9%) cases with salivary gland tumors and compared with 262 age-sex matched healthy control individuals. SDF-1 genotypes in patients with SCC of head and neck, but not with salivary gland tumors, showed a statistically significant difference compared to the normal group (P < 0.005 for SCC and P = 0.3 for salivary gland tumors). There were no significant differences in the frequencies of SDF1-3'A allele, CCR5 genotypes and alleles between patients and controls. Based on the present study SDF1-3A may be associated with the susceptibility of patients to SCC of head and neck cancer.
Collapse
|
41
|
Abstract
A cancer develops when a cell acquires specific growth advantages through the stepwise accumulation of heritable changes in gene function. Basically, this process is directed by changes in two different classes of genes: Tumor suppressor genes that inhibit cell growth and survival and oncogenes that promote cell growth and survival. Since several alterations are usually required for a cancer to fully develop, the malignant phenotype is determined by the compound status of tumor suppressor genes and oncogenes. Cancer genes may be changed by several mechanisms, which potentially alter the protein encoding nucleotide template, change the copy number of genes, or lead to increased gene transcription. Epigenetic alterations, which, by definition, comprise mitotically and meiotically heritable changes in gene expression that are not caused by changes in the primary DNA sequence, are increasingly being recognized for their roles in carcinogenesis. These epigenetic alterations may involve covalent modifications of amino acid residues in the histones around which the DNA is wrapped, and changes in the methylation status of cytosine bases (C) in the context of CpG dinucleotides within the DNA itself. Methylation of clusters of CpGs called "CpG-islands" in the promoters of genes has been associated with heritable gene silencing. The present review will focus on how disruption of the epigenome can contribute to cancer. In contrast to genetic alterations, gene silencing by epigenetic modifications is potentially reversible. Treatment by agents that inhibit cytosine methylation and histone deacetylation can initiate chromatin decondensation, demethylation and reestablishment of gene transcription. Accordingly, in the clinical setting, DNA methylation and histone modifications are very attractive targets for the development and implementation of new therapeutic approaches. Many clinical trials are ongoing, and epigenetic therapy has recently been approved by the United States Food and Drug Administration (US FDA) for use in the treatment of myelodysplastic syndrome (MDS) and primary cutaneous T-cell lymphoma (CTCL).
Collapse
|
42
|
Estécio MRH, Yan PS, Ibrahim AEK, Tellez CS, Shen L, Huang THM, Issa JPJ. High-throughput methylation profiling by MCA coupled to CpG island microarray. Genome Res 2007; 17:1529-36. [PMID: 17785535 PMCID: PMC1987348 DOI: 10.1101/gr.6417007] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
An abnormal pattern of DNA methylation occurs at specific genes in almost all neoplasms. The lack of high-throughput methods with high specificity and sensitivity to detect changes in DNA methylation has limited its application for clinical profiling. Here we overcome this limitation and present an improved method to identify methylated genes genome-wide by hybridizing a CpG island microarray with amplicons obtained by the methylated CpG island amplification technique (MCAM). We validated this method in three cancer cell lines and 15 primary colorectal tumors, resulting in the discovery of hundreds of new methylated genes in cancer. The sensitivity and specificity of the method to detect hypermethylated loci were 88% and 96%, respectively, according to validation by bisulfite-PCR. Unsupervised hierarchical clustering segregated the tumors into the expected subgroups based on CpG island methylator phenotype classification. In summary, MCAM is a suitable technique to discover methylated genes and to profile methylation changes in clinical samples in a high-throughput fashion.
Collapse
Affiliation(s)
- Marcos R H Estécio
- Department of Leukemia, UT M.D. Anderson Cancer Center, Houston, Texas 77030, USA.
| | | | | | | | | | | | | |
Collapse
|
43
|
Bennett KL, Hackanson B, Smith LT, Morrison CD, Lang JC, Schuller DE, Weber F, Eng C, Plass C. Tumor suppressor activity of CCAAT/enhancer binding protein alpha is epigenetically down-regulated in head and neck squamous cell carcinoma. Cancer Res 2007; 67:4657-64. [PMID: 17510391 DOI: 10.1158/0008-5472.can-06-4793] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tumor suppressor CCAAT enhancer binding protein alpha (C/EBPalpha) is a transcription factor involved in cell cycle control and cellular differentiation. In a recent study, microarray expression profiling on head and neck squamous cell carcinoma (HNSCC) samples identified significant C/EBPalpha down-regulation, correlating with poor prognosis. However, the mechanisms of C/EBPalpha down-regulation remained elusive. C/EBPalpha has been previously found to provide an antiproliferative role in lung cancer, and our laboratory showed that its down-regulation involves epigenetic mechanisms. This prompted us to investigate the involvement of epigenetics in down-regulating C/EBPalpha in HNSCC. Here, we show that C/EBPalpha is down-regulated in HNSCC by loss of heterozygosity and DNA methylation, but not by gene mutation. We found a consistently methylated upstream regulatory region (-1,399 bp to -1,253 bp in relation to the transcription start site) in 68% of the HNSCC tumor samples, and DNA demethylation using 5-aza-2'-deoxycytidine treatment was able to significantly restore C/EBPalpha mRNA expression in the HNSCC cell lines we tested. In addition, C/EBPalpha overexpression in a HNSCC cell line (SCC22B) revealed its ability to provide tumor suppressor activity in HNSCC in vitro and in vivo. In conclusion, we showed for the first time not only that C/EBPalpha has tumor suppressor activity in HNSCC, but also that it is down-regulated by DNA promoter methylation.
Collapse
Affiliation(s)
- Kristi L Bennett
- Department of Molecular Genetics, The Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, USA
| | | | | | | | | | | | | | | | | |
Collapse
|