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Li Z, Lu T, Chen Z, Yu X, Wang L, Shen G, Huang H, Li Z, Ren Y, Guo W, Hu Y. HOXA11 promotes lymphatic metastasis of gastric cancer via transcriptional activation of TGFβ1. iScience 2023; 26:107346. [PMID: 37539033 PMCID: PMC10393827 DOI: 10.1016/j.isci.2023.107346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/09/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
Most gastric cancer (GC) patients with early stage often have no lymph node (LN) metastases, while LN metastases appear in the advanced stage. However, there are some patients who present with early stage LN metastases and no LN metastases in the advanced stage. To explore the deeper molecular mechanisms involved, we collected clinical samples from early and advanced stage GC with and without LN metastases, as well as metastatic lymph nodes. Herein, we identified a key target, HOXA11, that was upregulated in GC tissues and closely associated with lymphatic metastases. HOXA11 transcriptionally regulates TGFβ1 expression and activates the TGFβ1/Smad2 pathway, which not only promotes EMT development but also induces VEGF-C secretion and lymphangiogenesis. These findings provide a plausible mechanism for HOXA11-modulated tumor in lymphatic metastasis and suggest that HOXA11 may represent a potential therapeutic target for clinical intervention in LN-metastatic gastric cancer.
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Affiliation(s)
- Zhenyuan Li
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Tailiang Lu
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Zhian Chen
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Xiang Yu
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Lingzhi Wang
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Guodong Shen
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Huilin Huang
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Zhenhao Li
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Yingxin Ren
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Weihong Guo
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Yanfeng Hu
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
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Ignatavicius P, Dauksa A, Zilinskas J, Kazokaite M, Riauka R, Barauskas G. DNA Methylation of HOXA11 Gene as Prognostic Molecular Marker in Human Gastric Adenocarcinoma. Diagnostics (Basel) 2022; 12:diagnostics12071686. [PMID: 35885590 PMCID: PMC9317388 DOI: 10.3390/diagnostics12071686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 12/24/2022] Open
Abstract
Hypermethylation of tumor suppressor genes and hypomethylation of oncogenes might be identified as possible biomarkers in gastric cancer (GC). We aimed to assess the DNA methylation status of selected genes in GC tissue samples and evaluate these genes’ prognostic importance on patient survival. Patients (99) diagnosed with GC and who underwent gastrectomy were included. We selected a group of genes (RAD51B, GFRA3, AKR7A3, HOXA11, TUSC3, FLI1, SEZ6L, GLDC, NDRG) which may be considered as potential tumor suppressor genes and oncogenes. Methylation of the HOXA11 gene promoter was significantly more frequent in GC tumor tissue (p = 0.006) than in healthy gastric mucosa. The probability of surviving longer (71.2 months (95% CI 57–85.3) vs. 44.3 months (95% CI 34.8–53.9)) was observed with unmethylated HOXA11 promoter in cancer tissues. Survival in patients with a methylation of HOXA11 promoter either in healthy gastric mucosa or gastric cancer tissue was twice as high as in patients with a methylation of HOXA11 promoter in both healthy gastric mucosa and cancer tissue (61.2 months (95% CI 50.9–71.4) vs. 28.5 months (95% CI 20.8–36.2)). Multivariate Cox analysis revealed the HOXA11 methylation as significantly associated with patients’ survival (HR = 2.4, 95% CI 1.19–4.86). Our results suggest that the HOXA11 gene might be a potential prognostic molecular marker in patients with gastric adenocarcinoma.
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Affiliation(s)
- Povilas Ignatavicius
- Department of Surgery, Medical Academy, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania; (A.D.); (J.Z.); (R.R.); (G.B.)
- Correspondence: ; Tel.: +370-37-326751
| | - Albertas Dauksa
- Department of Surgery, Medical Academy, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania; (A.D.); (J.Z.); (R.R.); (G.B.)
- Institute of Digestive Research, Medical Academy, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania
| | - Justas Zilinskas
- Department of Surgery, Medical Academy, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania; (A.D.); (J.Z.); (R.R.); (G.B.)
| | - Mintaute Kazokaite
- Institute of Endocrinology, Medical Academy, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania;
| | - Romualdas Riauka
- Department of Surgery, Medical Academy, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania; (A.D.); (J.Z.); (R.R.); (G.B.)
| | - Giedrius Barauskas
- Department of Surgery, Medical Academy, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania; (A.D.); (J.Z.); (R.R.); (G.B.)
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3
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Carvalho Â, Guimarães-Teixeira C, Constâncio V, Fernandes M, Macedo-Silva C, Henrique R, Monteiro FJ, Jerónimo C. One sample fits all: a microfluidic-assisted methodology for label-free isolation of CTCs with downstream methylation analysis of cfDNA in lung cancer. Biomater Sci 2022; 10:3296-3308. [PMID: 35583893 DOI: 10.1039/d2bm00044j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lung cancer (LC) is a major cause of mortality. Late diagnosis, associated with limitations in tissue biopsies for adequate tumor characterization contribute to limited survival of lung cancer patients. Liquid biopsies have been introduced to improve tumor characetrization through the analysis of biomarkers, including circulating tumour cells (CTCs) and cell-free DNA (cfDNA). Considering their availability in blood, several enrichment strategies have been developed to augment circulating biomarkers for improving diagnostic, prognostic and treament efficacy assessment; often, however, only one biomarker is tested. In this work we developed and implemented a microfluidic chip for label-free enrichment of CTCs with a methodology for subsequent cfDNA analysis from the same cryopreserved sample. CTCs were successfully isolated in 38 of 42 LC patients with the microfluidic chip. CTCs frequency was significantly higher in LC patients with advanced disease. A cut-off of 1 CTC per mL was established for diagnosis (sensitivity = 76.19%, specificity = 100%) and in patients with late stage lung cancer, the presence of ≥5 CTCs per mL was significantly associated with shorter overall survival. MIR129-2me and ADCY4me panel of cfDNA methylation performed well for LC detection, whereas MIR129-2me combined with HOXA11me allowed for patient risk stratification. Analysis of combinations of biomarkers enabled the definition of panels for LC diagnosis and prognosis. Overall, this study demonstrates that multimodal analysis of tumour biomarkers via microfluidic devices may significantly improve LC characterization in cryopreserved samples, constituting a reliable source for continuous disease monitoring.
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Affiliation(s)
- Ângela Carvalho
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal. .,INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal.,Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Catarina Guimarães-Teixeira
- Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.,Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Vera Constâncio
- Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.,Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Mariana Fernandes
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal. .,INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Catarina Macedo-Silva
- Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.,Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Rui Henrique
- Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.,Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Fernando Jorge Monteiro
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal. .,INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal.,Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.,Faculdade de Engenharia, Departamento de Engenharia Metalúrgica e Materiais, Universidade do Porto, Rua Dr Roberto Frias, s/n, 4200-465 Porto, Portugal
| | - Carmen Jerónimo
- Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.,Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
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Chakravarthi S, Karikalan B. Molecular Biomarkers for Lung Adenocarcinoma: A Short Review. CURRENT CANCER THERAPY REVIEWS 2021. [DOI: 10.2174/1573394716666200724164654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Lung cancer is a disease with higher death rates and is responsible for around 2 million
deaths per year worldwide. Recently, several breakthroughs have been made in the field of lung
cancer that has led to a revolution in the management of lung cancer patients. Identification of
molecular markers and the implication of respective targeted therapies has been a great success in
the treatment of lung adenocarcinoma patients. Despite the fact that targeted therapy of lung adenocarcinomas
represents one of the significant milestones in the treatment of lung cancer that resulted
in increased survival rates even in advanced stages, the mortality rates of lung cancer still remain
to be significantly high. This warrants further research for gaining better insights into molecular alterations
that can lead to newer innovations in targeted drug therapy towards lung adenocarcinoma.
In this review, we briefly summarized the literature on molecular markers that are already in use.
We also consolidated newer molecular markers that are under study with the potential for being targeted
for therapies in future.
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5
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Fu JF, Shih LY, Yen TH. HOXA11 plays critical roles in disease progression and response to cytarabine in AML. Oncol Rep 2021; 46:150. [PMID: 34080665 PMCID: PMC8185505 DOI: 10.3892/or.2021.8101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/05/2021] [Indexed: 12/15/2022] Open
Abstract
Lysine methyltransferase 2A (KMT2A, also known as MLL) translocations (MLL-t) are frequently associated with mutations in RAS pathway genes in acute myeloid leukemia (AML). Previous findings with a mouse model showed that cooperation of MLL/AF10 with tyrosine-protein phosphatase non-receptor type 11 (PTPN11)G503A accelerated leukemia development, but increased cytarabine (Ara-C) sensitivity of leukemia cells. To identify the genes responsible for reduced survival and Ara-C resistance, transcriptomic profiling between six pairs of mouse MLL/AF10(OM-LZ) leukemia cells harboring activating and wild-type KRAS or PTPN11 was compared. A total of 23 differentially expressed genes (DEGs) with >1.5-fold-change between the paired cell lines were identified. The Gene Ontology (GO) terms overrepresented in these 23 DEGs included ‘immune system process’, ‘actin filament binding’, ‘cellular response to interferon-alpha’ and ‘sequence-specific DNA’. Among the four genes (Hoxa11, PR domain zinc finger protein 5, Iroquois-class homeodomain protein IRX-5 and homeobox protein PKNOX2) mapped to the GO term ‘sequence-specific DNA’, HOXA11 upregulation was associated with AML harboring MLL-t and RAS signaling mutations based on a meta-analysis using data deposited in Oncomine™ and analysis of the clinical samples in the present study. Microarray data revealed that only Hoxa11 was upregulated in those cells harboring activating PTPN11. Functional studies of Hoxa11 knockdown or overexpression in MLL/AF10(OM-LZ) cells revealed that Hoxa11 expression levels were associated with survival in vivo and Ara-C sensitivity/apoptosis in vitro. In addition, Hoxa11 regulated the expression of the apoptosis-related genes, NF-κB inhibitor α, transcription factor p65 and transformation-related protein p53. Furthermore, the results of a meta-analysis using Heuser's AML dataset supported the finding that chemotherapy responders have higher expression levels of HOXA11. These results indicated that the expression of HOXA11 increased cell apoptosis and predicted an improved response to Ara-C in AML.
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Affiliation(s)
- Jen-Fen Fu
- Department of Medical Research, Chang Gung Memorial Hospital, Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan 333, Taiwan, R.O.C
| | - Lee-Yung Shih
- Department of Internal Medicine, Division of Hematology‑Oncology, Chang Gung Memorial Hospital, Taipei 105, Taiwan, R.O.C
| | - Tzung-Hai Yen
- Department of Nephrology, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 333, Taiwan, R.O.C
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Ding S, Zhang H, Zhao X, Dang J, Li G. UNC5A, an epigenetically silenced gene, functions as a tumor suppressor in non-small cell lung cancer. Saudi J Biol Sci 2020; 27:3009-3017. [PMID: 33100860 PMCID: PMC7569136 DOI: 10.1016/j.sjbs.2020.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 11/01/2022] Open
Abstract
UNC5A has been reported to be related with human cancers. However, the function and mechanism in non-small cell lung carcinoma (NSCLC) remains unknown. We analyzed two NSCLC cell lines (A549 and H157), one normal human bronchial epithelial cell line (BEAS-2B) and the tissues of NSCLC. We used quantitative real-time PCR (qRT-PCR), western blot and immunohistochemical (IHC) staining to examine the expression of UNC5A. Methylation status of the UNC5A promoter was analyzed using methylation-specific PCR (MSP) and bisulfite sequencing PCR (BSP). We used western blot to analyzed protein levels of PI3K/Akt pathway. We found that the mRNA expression of UNCA5 was significantly downregulated in NSCLC cells and tissues. The promoter of UNC5A was hypermethylated in NSCLC cells compared to normal control cells. The expression of UNC5A could be reversed by demethylation agent in NSCLC cells. The expression of UNC5A was decreased in NSCLC samples and significantly associated with the advanced types of NSCLC. Functionally, knockdown of UNC5A promoted cell proliferation, migration, invasion and induced apoptosis in NSCLC, overexpression of UNC5A yielded the opposite result. Moreover, we found that UNC5A negatively regulated PI3K/Akt signaling pathway in NSCLC. UNC5A is a novel epigenetically silenced gene in NSCLC and consequent under-expression of UNC5A may contribute to NSCLC tumorigenesis through regulating PI3K/Akt pathway.
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Affiliation(s)
- Silu Ding
- Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang 110000, China
| | - Hongwei Zhang
- Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang 110000, China
| | - Xinyu Zhao
- Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang 110000, China
| | - Jun Dang
- Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang 110000, China
| | - Guang Li
- Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang 110000, China
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Paço A, de Bessa Garcia SA, Freitas R. Methylation in HOX Clusters and Its Applications in Cancer Therapy. Cells 2020; 9:cells9071613. [PMID: 32635388 PMCID: PMC7408435 DOI: 10.3390/cells9071613] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 02/08/2023] Open
Abstract
HOX genes are commonly known for their role in embryonic development, defining the positional identity of most structures along the anterior–posterior axis. In postembryonic life, HOX gene aberrant expression can affect several processes involved in tumorigenesis such as proliferation, apoptosis, migration and invasion. Epigenetic modifications are implicated in gene expression deregulation, and it is accepted that methylation events affecting HOX gene expression play crucial roles in tumorigenesis. In fact, specific methylation profiles in the HOX gene sequence or in HOX-associated histones are recognized as potential biomarkers in several cancers, helping in the prediction of disease outcomes and adding information for decisions regarding the patient’s treatment. The methylation of some HOX genes can be associated with chemotherapy resistance, and its identification may suggest the use of other treatment options. The use of epigenetic drugs affecting generalized or specific DNA methylation profiles, an approach that now deserves much attention, seems likely to be a promising weapon in cancer therapy in the near future. In this review, we summarize these topics, focusing particularly on how the regulation of epigenetic processes may be used in cancer therapy.
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Affiliation(s)
- Ana Paço
- Centre Bio: Bioindustries, Biorefineries and Bioproducts, BLC3 Association—Technology and Innovation Campus, 3405-169 Oliveira do Hospital, Portugal;
| | | | - Renata Freitas
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal;
- ICBAS—Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- Correspondence:
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Wang C, Shi M, Ji J, Cai Q, Jiang J, Zhang H, Zhu Z, Zhang J. A self-enforcing HOXA11/Stat3 feedback loop promotes stemness properties and peritoneal metastasis in gastric cancer cells. Am J Cancer Res 2019; 9:7628-7647. [PMID: 31695791 PMCID: PMC6831465 DOI: 10.7150/thno.36277] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/05/2019] [Indexed: 12/13/2022] Open
Abstract
Rationale: Peritoneal metastasis is one of the most common and life-threatening metastases in gastric cancer patients. The disseminated gastric cancer cells forming peritoneal metastasis exhibit a variety of characteristics that contrast with those of adjacent epithelial cell of gastric mucosa and even primary gastric cancer cells. We hypothesized that the gene expression profiles of peritoneal foci could reveal the identities of genes that might function as metastatic activator. Methods: In this study, we show, using in vitro, in vivo, in silico and gastric cancer tissues studies in humans and mice, that Homoebox A11 (HOXA11) potently promote peritoneal metastasis of gastric cancer cells. Results: Its mechanism of action involves alternation of cancer stemness and subsequently enhancement of the adhesion, migration and invasion and anti-apoptosis. This is achieved, mainly, through formation of a positive feedback loop between HOXA11 and Stat3, which is involved in the stimulation of Stat3 signaling pathway. Conclusions: These observations uncover a novel peritoneal metastatic activator and demonstrate the association between HOXA11, Stat3 and cancer stemness of gastric cancer cells, thereby revealing a previously undescribed mechanism of peritoneal metastasis.
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Chen J, Huang L, Zhu Q, Wang Z, Tang Z. MTSS1 hypermethylation is associated with prostate cancer progression. J Cell Physiol 2019; 235:2687-2697. [PMID: 31541465 DOI: 10.1002/jcp.29172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 08/23/2019] [Indexed: 01/08/2023]
Abstract
This study was conducted to evaluate the influence of DNA methylation of metastasis suppressor 1 (MTSS1) on prostate cancer (PCa) progression. Forty-nine paired PCa tissue samples and normal tissue samples from The Cancer Genome Atlas were analyzed. Methylome analysis, CpG island arrays and Hierarchical clustering were used to analyze methylation profiles of PCa tissues. MTSS1 methylation level was detected by methylation-specific PCR. Relative messenger RNA and the expression level of MTSS1 protein were identified by quantitative real-time PCR (qRT-PCR) and western blot analysis. The migration, invasion, proliferation, and cell cycle were detected separately by wound-healing assay, transwell chamber assay, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay and flow cytometry. The roles of MTSS1 in PCa progression were demonstrated in vivo by tumor formation assays in nude mice. MTSS1 expression was decreased in PCa tissues in comparison with paired adjacent normal prostate tissues. Compared to the methylation of MTSS1 in normal prostate tissues based on the MethHC website, the MTSS1 in PCa tissues was hypermethylated. The expression of MTSS1 detected by qRT-PCR and western blot analysis was found to be downregulated in PCa cells and tissues. The reduced expression of MTSS1 by small interfering RNA-MTSS1 was recovered by 5-aza-2'-deoxycytidine treatment. Besides, MTSS1 demethylation inhibited migration, invasion, and proliferation of PCa cells, and induced cell cycle to be arrested at G0/G1 phase. Furthermore, it was shown by tumor xenograft assay that MTSS1 inhibited the growth of tumor in vivo. Hypermethylated MTSS1 promoted PCa cells migration, invasion, and proliferation, and suppressed cell cycle arrest at the G0/G1 phase.
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Affiliation(s)
- Junjie Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Liang Huang
- Department of Urology, Hunan Provincial People's Hospital, Changsha, Hunan, China
| | - Quan Zhu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhao Wang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhengyan Tang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Engineering Laboratory for Diagnosis and Treatment Technology of Urogenital Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China
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10
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Cai L, Bai H, Duan J, Wang Z, Gao S, Wang D, Wang S, Jiang J, Han J, Tian Y, Zhang X, Ye H, Li M, Huang B, He J, Wang J. Epigenetic alterations are associated with tumor mutation burden in non-small cell lung cancer. J Immunother Cancer 2019; 7:198. [PMID: 31349879 PMCID: PMC6660715 DOI: 10.1186/s40425-019-0660-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/28/2019] [Indexed: 12/16/2022] Open
Abstract
Background To profile genomic and epigenomic of a naïve Chinese non-small cell lung cancer (NSCLC) cohort and investigate the association between tumor mutation burden (TMB) and DNA methylation (DNAm) to explore potential alternative/complimentary biomarkers for NSCLC immunotherapies. Methods A total of 89 tumor tissues with matched normal tissues from Chinese NSCLC patients were collected and subjected to whole exome sequencing (WES). From comparison, each patient was evaluated for the TMB value and divided into high, medium and low TMB based on TMB tertile distribution and then relatively high and low TMB samples were selected and subjected to DNAm profiling. Results Patients in the low (n = 30), medium (n = 29), and high (n = 30) TMB tertiles had 1.1–2.5, 2.5–4.1, and 4.2–13.9 mutations/Mb, respectively. A statistical directly association between differential methylation probes (DMPs) and TMB level was observed in our cohort (r = 0.63, P value =0.0003) and this was confirmed by using TCGA NSCLC dataset (r = 0.43, P value =0.006). Relatively high TMB group (n = 16, 7.5–13.9 mutations/Mb) harbors more differential DMPs while less in relatively low TMB group (n = 13, 1.1–2.4 mutations/Mb). Eight hundred fifty-eight differential methylation regions (DMRs) were found in relatively high TMB group. In addition, 437 genes show DNAm aberrance status in high TMB patient group and 99 have been reported as its association with lung cancer. Conclusion To our knowledge, this is the first report for direct link between the methylome alterations and TMB in NSCLCs. High TMB NSCLCs had more DNAm aberrance and copy number variations (CNVs). In addition, the TMB distribution of Chinese NSCLCs population is lower than that of TCGA. Electronic supplementary material The online version of this article (10.1186/s40425-019-0660-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liangliang Cai
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hua Bai
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianchun Duan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhijie Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugeng Gao
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Di Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuhang Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jun Jiang
- Department of Oncology, Affiliated Hospital of Qinghai University, Xining, China
| | - Jiefei Han
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanhua Tian
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xue Zhang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Ye
- Sinotech Genomics Ltd, Shanghai, China
| | | | | | - Jie He
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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11
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Zhang Y, Yuan Y, Li Y, Zhang P, Chen P, Sun S. An inverse interaction between HOXA11 and HOXA11-AS is associated with cisplatin resistance in lung adenocarcinoma. Epigenetics 2019; 14:949-960. [PMID: 31144606 DOI: 10.1080/15592294.2019.1625673] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
HOXA11, which is a member of the homeobox (HOX) gene family, and its natural antisense transcript (NAT) HOXA11-AS have been reported to be closely related to the development of lung cancer. We aimed to investigate their specific roles in cisplatin (DDP) resistance in lung adenocarcinoma (LUAD). First, we found that HOXA11 is hypermethylated and significantly downregulated in a DDP-resistant A549 cell line (A549/DDP) and LUAD tissues, while the HOXA11-AS expression level is elevated. Although HOXA11 and HOXA11-AS mRNA overlap in the 5'-untranslated region (5' UTR) and share two CpG islands, DNA methylation only regulates the expression of HOXA11. Then, we found that HOXA11 and HOXA11-AS have an inverse interaction by transfecting their siRNAs and overexpression vectors into A549 and A549/DDP cells. A dual-luciferase reporter assay further confirmed that the overlapping 5'UTR is essential for the bidirectional regulation between HOXA11 and HOXA11-AS. Functional analysis showed that knockdown of HOXA11 expression in A549 cells induced DDP resistance and activated Akt/β-catenin signaling, while overexpression of HOXA11 in A549/DDP cells increased DDP sensitivity and inhibited Akt/β-catenin signaling. Moreover, HOXA11-AS knockdown in A549 cells increased DDP sensitivity and inhibited Akt/β-catenin signaling, while the overexpression of HOXA11-AS in A549/DDP cells induced DDP resistance and activated Akt/β-catenin signaling. In conclusion, our study demonstrates that the inverse interaction between HOXA11 and HOXA11-AS promotes DDP resistance in LUAD.
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Affiliation(s)
- Youwei Zhang
- a Department of Medical Oncology, Affiliated Xuzhou Central Hospital, Southeast University , Xuzhou , China
| | - Yuan Yuan
- a Department of Medical Oncology, Affiliated Xuzhou Central Hospital, Southeast University , Xuzhou , China
| | - Yang Li
- b Department of Molecular Laboratory, Affiliated Xuzhou Central Hospital, Southeast University , Xuzhou , China
| | - Peiying Zhang
- a Department of Medical Oncology, Affiliated Xuzhou Central Hospital, Southeast University , Xuzhou , China
| | - Pingsheng Chen
- c Department of Pathology, School of Basic Medical Sciences, Southeast University , Nanjing , China
| | - Sanyuan Sun
- a Department of Medical Oncology, Affiliated Xuzhou Central Hospital, Southeast University , Xuzhou , China
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12
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Yang X, Deng Y, He RQ, Li XJ, Ma J, Chen G, Hu XH. Upregulation of HOXA11 during the progression of lung adenocarcinoma detected via multiple approaches. Int J Mol Med 2018; 42:2650-2664. [PMID: 30106131 PMCID: PMC6192730 DOI: 10.3892/ijmm.2018.3826] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/10/2018] [Indexed: 12/22/2022] Open
Abstract
The altered expression of homeobox (HOX)A11 has been observed in various malignant tumor types, but it has remained to be determined in human lung adenocarcinoma (LUAD). In the present study, the expression of HOXA11 in LUAD and the potential associated mechanisms were assessed. Data from The Cancer Genome Atlas and Oncomine microarrays were gathered and in‑house polymerase chain reaction data were produced to investigate the altered expression of HOXA11 in LUAD and its association with various clinicopathological characteristics. Genes co‑expressed with HOXA11 were also identified by searching the cBioPortal and Multi Experiment Matrix databases, and performing a bioinformatics analysis, through which the potential molecular mechanisms of HOXA11 in LUAD were explored. The data analyses indicated that HOXA11 was overexpressed in the LUAD samples, and together with its co‑expressed genes, it was indicated to participate in various key signaling pathways, including the focal adhesion, extracellular matrix‑receptor interaction, axon guidance and small cell lung cancer signaling pathways. Furthermore, collagen type III α 1 chain (COL3A1), ephrin B2 (EFNB2), integrin subunit α 8 (ITGA8) and syndecan 2 (SDC2) were confirmed to be differentially expressed in LUAD vs. normal controls at the mRNA and protein level. Of note, LUAD patients with low expression of HOXA11 and ITGB1 had better overall survival rates. The present study indicated that HOXA11 may function as an oncogene in LUAD, and HOXA11 protein probably combines with ITGB1, COL3A1, EFNB2, ITGA8 and SDC2 to have a role in the focal adhesion pathway.
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Affiliation(s)
- Xia Yang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Yun Deng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Rong-Quan He
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xiao-Jiao Li
- Department of Positron Emission Tomography‑Computed Tomography, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Jie Ma
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xiao-Hua Hu
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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13
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Zhang R, Zhang TT, Zhai GQ, Guo XY, Qin Y, Gan TQ, Zhang Y, Chen G, Mo WJ, Feng ZB. Evaluation of the HOXA11 level in patients with lung squamous cancer and insights into potential molecular pathways via bioinformatics analysis. World J Surg Oncol 2018; 16:109. [PMID: 29914539 PMCID: PMC6006563 DOI: 10.1186/s12957-018-1375-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 03/26/2018] [Indexed: 01/11/2023] Open
Abstract
Background This study was carried out to discover the underlying role that HOXA11 plays in lung squamous cancer (LUSC) and uncover the potential corresponding molecular mechanisms and functions of HOXA11-related genes. Methods Twenty-three clinical paired LUSC and non-LUSC samples were utilized to examine the level of HOXA11 using quantitative real-time polymerase chain reaction (qRT-PCR). The clinical significance of HOXA11 was systematically analyzed based on 475 LUSC and 18 non-cancerous adjacent tissues from The Cancer Genome Atlas (TCGA) database. A total of 102 LUSC tissues and 121 non-cancerous tissues were available from Oncomine to explore the expressing profiles of HOXA11 in LUSC. A meta-analysis was carried out to further assess the differential expression of HOXA11 in LUSC, including in-house qRT-PCR data, expressing data extracted from TCGA and Oncomine databases. Moreover, the enrichment analysis and potential pathway annotations of HOXA11 in LUSC were accomplished via Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The expression of hub genes and according correlations with HOXA11 were assessed to further explore the biological role of HOXA11 in LUSC. Results HOXA11 expression in LUSC had a tendency to be upregulated in comparison to adjacent non-cancerous tissues by qRT-PCR. TCGA data displayed that HOXA11 was remarkably over-expressed in LUSC compared with that in non-LUSC samples, and the area under curves (AUC) was 0.955 (P < 0.001). A total of 1523 co-expressed genes were sifted for further analysis. The most significant term enriched in the KEGG pathway was focal adhesion. Among the six hub genes of HOXA11, including PARVA, ILK, COL4A1, COL4A2, ITGB1, and ITGA5, five (with the exception of COL4A1) were significantly decreased compared with the normal lung tissues. Moreover, the expression of ILK was negatively related to HOXA11 (r = − 0.141, P = 0.002). Conclusion High HOXA11 expression may lead to carcinogenesis and the development of LUSC. Furthermore, co-expressed genes might affect the prognosis of LUSC.
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Affiliation(s)
- Rui Zhang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | | | - Gao-Qiang Zhai
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xian-Yu Guo
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yuan Qin
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Ting-Qing Gan
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yu Zhang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Wei-Jia Mo
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
| | - Zhen-Bo Feng
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
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14
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Um SW, Kim Y, Lee BB, Kim D, Lee KJ, Kim HK, Han J, Kim H, Shim YM, Kim DH. Genome-wide analysis of DNA methylation in bronchial washings. Clin Epigenetics 2018; 10:65. [PMID: 29796116 PMCID: PMC5960087 DOI: 10.1186/s13148-018-0498-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/09/2018] [Indexed: 12/03/2022] Open
Abstract
Background The objective of this study was to discover DNA methylation biomarkers for detecting non-small lung cancer (NSCLC) in bronchial washings and understanding the association between DNA methylation and smoking cessation. Methods DNA methylation was analyzed in bronchial washing samples from 70 NSCLCs and 53 hospital-based controls using Illumina HumanMethylation450K BeadChip. Methylation levels in these bronchial washings were compared to those in 897 primary lung tissues of The Cancer Genome Atlas (TCGA) data. Results Twenty-four CpGs (p < 1.03E−07) were significantly methylated in bronchial washings from 70 NSCLC patients compared to those from 53 controls. The CpGs also had significant methylation in the TCGA cohort. The 123 participants were divided into a training set (N = 82) and a test set (N = 41) to build a classification model. Logistic regression model showed the best performance for classification of lung cancer in bronchial washing samples: the sensitivity and specificity of a marker panel consisting of seven CpGs in TFAP2A, TBX15, PHF11, TOX2, PRR15, PDGFRA, and HOXA11 genes were 87.0 and 83.3% in the test set, respectively. The area under the curve (AUC) was equal to 0.87 (95% confidence interval = 0.73–0.96, p < 0.001). Methylation levels of two CpGs in RUNX3 and MIR196A1 genes were inversely associated with duration of smoking cessation in the controls, but not in NSCLCs, after adjusting for pack-years of smoking. Conclusions The present study suggests that NSCLC may be detected by analyzing methylation changes of seven CpGs in bronchial washings. Furthermore, smoking cessation may lead to decreased DNA methylation in nonmalignant bronchial epithelial cells in a gene-specific manner. Electronic supplementary material The online version of this article (10.1186/s13148-018-0498-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sang-Won Um
- 1Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Yujin Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746 South Korea
| | - Bo Bin Lee
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746 South Korea
| | - Dongho Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746 South Korea
| | - Kyung-Jong Lee
- 1Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Hong Kwan Kim
- 3Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Joungho Han
- 4Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Hojoong Kim
- 1Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Young Mog Shim
- 3Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746 South Korea.,Samsung Medical Center, Research Institute for Future Medicine, #50 Ilwon-dong, Kangnam-gu, Professor Rm #5, Seoul, 135-710 South Korea
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15
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Zhu XF, Zhu BS, Wu FM, Hu HB. DNA methylation biomarkers for the occurrence of lung adenocarcinoma from TCGA data mining. J Cell Physiol 2018; 233:6777-6784. [PMID: 29667778 DOI: 10.1002/jcp.26531] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 02/02/2018] [Indexed: 01/11/2023]
Abstract
The development of lung cancer is a combination of multifactor, multistage, and multiple genetic alterations processes. DNA methylation is an important factor. Currently, the study on the genome-scale epigenetic modification for studying the pathogenesis of lung cancer is still lacking. Here, we aimed to identify the epigenetic modifications of lung cancer, thus to provide scientific basis for the personalized medicine, and research of classification screening for lung adenocarcinoma patients. The DNA methylation data, and the corresponding clinical information of lung adenocarcinoma samples were extracted from the Cancer Genome Atlas (TCGA) database. We explored the association of DNA methylation and gene transcription expression of lung adenocarcinoma by identifying the differentially expressed genes, DNA methylated locis, functional gene clusters, and the relevant genes associated with the survival. We identified 17 differentially expressed genes which had differentially methylated locis, 4 functional gene clusters regulated by methylation, and 522 genes, which were relevant to the survival time of patients. Our study suggested that methylation controlled the gene expression in a variety of ways, which had high/low expression and hyper-/hypo-methylation. Genes of different methylation status showed the different survival curve. The genes and methylated locis identified in this study could be potential biomarkers and therapeutic targets for lung adenocarcinoma.
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Affiliation(s)
- Xiao-Feng Zhu
- Department of Cardiothoracic Surgery, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning, China
| | - Bi-Sheng Zhu
- Department of Oncology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning, China
| | - Fei-Ma Wu
- Department of Cardiothoracic Surgery, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning, China
| | - Hai-Bo Hu
- Department of Thoracic Surgery, Huai'an Second People's Hospital, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
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16
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Li Q, Chen C, Ren X, Sun W. DNA methylation profiling identifies the HOXA11 gene as an early diagnostic and prognostic molecular marker in human lung adenocarcinoma. Oncotarget 2018; 8:33100-33109. [PMID: 28380439 PMCID: PMC5464853 DOI: 10.18632/oncotarget.16528] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 03/14/2017] [Indexed: 01/15/2023] Open
Abstract
DNA hypermethylation plays important roles in carcinogenesis by silencing key genes. The goal of our study was to identify pivotal genes using MethyLight and assessed their diagnostic and prognostic values in lung adenocarcinoma (AD). In the present study, we detected DNA methylation at sixteen loci promoter regions in twenty one pairs of primary human lung AD tissues and adjacent non-tumor lung (AdjNL) tissues using the real-time PCR (RT-PCR)-based method MethyLight. By comparing the sixteen analyzed loci in lung AD tissues and AdjNL and non-tumor (NL) tissues, we found that, among the six genes identified with hypermethylation, the HOXA11, CDKN2A-EX2 and EYA4 genes showed highly promising DNA hypermethylation diagnostic markers in the lung AD tissues. Moreover, comparing lung AD tissues (> 2 cm in diameter) to the AdjNL or AD in situ (AIS) tissues by RT-qPCR and immunohistochemistry revealed that HOXA11 expression was significantly increased. A further study showed that HOXA11 expression was controlled by methylation in the promoter region in human lung tumor cell lines. Aberrant hypermethylation and the methylation-induced down-regulation of HOXA11 may promote tumor progression. Our results suggested that HOXA11 might be a diagnostic and prognostic marker in patients with lung AD.
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Affiliation(s)
- Qun Li
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200031, China.,The State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Ruijin Hospital, Shanghai Institute of Hypertension, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chang Chen
- Department of Orthodontics, The First Affiliated Hospital of Zhengzhou University, Stomatological College Zhengzhou University, Zhengzhou, 450052, China
| | - Xiaohui Ren
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200031, China
| | - Weihong Sun
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200031, China
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17
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Homeobox A11 hypermethylation indicates unfavorable prognosis in breast cancer. Oncotarget 2018; 8:9794-9805. [PMID: 28038461 PMCID: PMC5354771 DOI: 10.18632/oncotarget.14216] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 12/05/2016] [Indexed: 01/17/2023] Open
Abstract
Homeobox A11 (HOXA11) is one of the hypermethylated genes in breast cancer and its function in breast tumorigenesis remains elusive. In this study, we analyzed the methylation status of HOXA11 in 264 paired breast cancer and normal tissue as well as in matched serum samples by MethyLight assay. Further, the function of HOXA11 in breast tumorigenesis was analyzed by cell proliferation and migration assays. We found that HOXA11 was hypermethylated in cancer tissues (45.08%), especially in invasive ductal carcinomas (P<0.001), patients with a family history of cancer (P=0.033), cases with metastatic lymph nodes (P=0.004) and P53 positive group (P=0.017). Kaplan-Meier survival analysis and Cox regression analysis revealed that HOXA11 hypermethylation is an independent predictor of poor outcomes. The over expression of HOXA11 suppressed cell growth in MDA-MB-231, MCF7, SKBR3 and BT474 cells. In conclusion, the hypermethylation of HOXA11 is an independent prognostic biomarker in breast cancer. Additionally, HOXA11 can be a potential tumor suppressor.
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18
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Shi YX, Wang Y, Li X, Zhang W, Zhou HH, Yin JY, Liu ZQ. Genome-wide DNA methylation profiling reveals novel epigenetic signatures in squamous cell lung cancer. BMC Genomics 2017; 18:901. [PMID: 29169318 PMCID: PMC5701423 DOI: 10.1186/s12864-017-4223-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 10/17/2017] [Indexed: 11/15/2022] Open
Abstract
Background Epigenetic alterations are strongly associated with the development of cancer. The aim of this study was to identify epigenetic pattern in squamous cell lung cancer (LUSC) on a genome-wide scale. Results Here we performed DNA methylation profiling on 24 LUSC and paired non-tumor lung (NTL) tissues by Illumina Human Methylation 450 K BeadArrays, and identified 5214 differentially methylated probes. By integrating DNA methylation and mRNA expression data, 449 aberrantly methylated genes accompanied with altered expression were identified. Ingenuity Pathway analysis highlighted these genes which were closely related to the carcinogenesis of LUSC, such as ERK family, NFKB signaling pathway, Hedgehog signaling pathway, providing new clues for understanding the molecular mechanisms of LUSC pathogenesis. To verify the results of high-throughput screening, we used 56 paired independent tissues for clinical validation by pyrosequencing. Subsequently, another 343 tumor tissues from the Cancer Genome Atlas (TCGA) database were utilized for further validation. Then, we identified a panel of DNA methylation biomarkers (CLDN1, TP63, TBX5, TCF21, ADHFE1 and HNF1B) in LUSC. Furthermore, we performed receiver operating characteristics (ROC) analysis to assess the performance of biomarkers individually, suggesting that they could be suitable as potential diagnostic biomarkers for LUSC. Moreover, hierarchical clustering analysis of the DNA methylation data identified two tumor subgroups, one of which showed increased DNA methylation. Conclusions Collectively, these results suggest that DNA methylation plays critical roles in lung tumorigenesis and may potentially be proposed as a diagnostic biomarker. Trial registration ChiCTR-RCC-12002830 Date of registration: 2012–12-17. Electronic supplementary material The online version of this article (10.1186/s12864-017-4223-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuan-Xiang Shi
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang, 421001, People's Republic of China
| | - Ying Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China
| | - Xi Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang, 421001, People's Republic of China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang, 421001, People's Republic of China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang, 421001, People's Republic of China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China. .,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China. .,Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang, 421001, People's Republic of China.
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China. .,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China. .,Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang, 421001, People's Republic of China.
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19
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Ooki A, Maleki Z, Tsay JCJ, Goparaju C, Brait M, Turaga N, Nam HS, Rom WN, Pass HI, Sidransky D, Guerrero-Preston R, Hoque MO. A Panel of Novel Detection and Prognostic Methylated DNA Markers in Primary Non-Small Cell Lung Cancer and Serum DNA. Clin Cancer Res 2017; 23:7141-7152. [PMID: 28855354 DOI: 10.1158/1078-0432.ccr-17-1222] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/26/2017] [Accepted: 08/23/2017] [Indexed: 11/16/2022]
Abstract
Purpose: To establish a novel panel of cancer-specific methylated genes for cancer detection and prognostic stratification of early-stage non-small cell lung cancer (NSCLC).Experimental Design: Identification of differentially methylated regions (DMR) was performed with bumphunter on "The Cancer Genome Atlas (TCGA)" dataset, and clinical utility was assessed using quantitative methylation-specific PCR assay in multiple sets of primary NSCLC and body fluids that included serum, pleural effusion, and ascites samples.Results: A methylation panel of 6 genes (CDO1, HOXA9, AJAP1, PTGDR, UNCX, and MARCH11) was selected from TCGA dataset. Promoter methylation of the gene panel was detected in 92.2% (83/90) of the training cohort with a specificity of 72.0% (18/25) and in 93.0% (40/43) of an independent cohort of stage IA primary NSCLC. In serum samples from the later 43 stage IA subjects and population-matched 42 control subjects, the gene panel yielded a sensitivity of 72.1% (31/41) and specificity of 71.4% (30/42). Similar diagnostic accuracy was observed in pleural effusion and ascites samples. A prognostic risk category based on the methylation status of CDO1, HOXA9, PTGDR, and AJAP1 refined the risk stratification for outcomes as an independent prognostic factor for an early-stage disease. Moreover, the paralog group for HOXA9, predominantly overexpressed in subjects with HOXA9 methylation, showed poor outcomes.Conclusions: Promoter methylation of a panel of 6 genes has potential for use as a biomarker for early cancer detection and to predict prognosis at the time of diagnosis. Clin Cancer Res; 23(22); 7141-52. ©2017 AACR.
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Affiliation(s)
- Akira Ooki
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Zahra Maleki
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Jun-Chieh J Tsay
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, New York
| | - Chandra Goparaju
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Langone Medical Center, New York University of Medicine, New York, New York
| | - Mariana Brait
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Nitesh Turaga
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Hae-Seong Nam
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Division of Pulmonology, Department of Internal Medicine, Inha University School of Medicine, Incheon, South Korea
| | - William N Rom
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, New York
| | - Harvey I Pass
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Langone Medical Center, New York University of Medicine, New York, New York
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Rafael Guerrero-Preston
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland. .,Department of Oncology, Johns Hopkins University, Baltimore, Maryland.,Department of Obstetrics and Gynecology, University of Puerto Rico, San Juan, Puerto Rico
| | - Mohammad Obaidul Hoque
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland. .,Department of Oncology, Johns Hopkins University, Baltimore, Maryland.,Department of Urology, Johns Hopkins University, Baltimore, Maryland
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20
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Wang L, Cui Y, Sheng J, Yang Y, Kuang G, Fan Y, Jin J, Zhang Q. Epigenetic inactivation of HOXA11, a novel functional tumor suppressor for renal cell carcinoma, is associated with RCC TNM classification. Oncotarget 2017; 8:21861-21870. [PMID: 28423531 PMCID: PMC5400629 DOI: 10.18632/oncotarget.15668] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/16/2017] [Indexed: 11/25/2022] Open
Abstract
Epigenetic inactivation of HOXA11, a putative tumor suppressor, is frequently observed in a number of solid tumors, but has not been described in RCC (renal cell carcinoma). In this study, we investigated the expression, epigenetic changes and the function of HOXA11 in human renal cell carcinoma (RCC). HOXA11 was silenced or down-regulated in RCC cell lines and tissues. Methylation specific PCR (MSP) and bisulfite genomic sequencing (BGS) revealed that the HOXA11 promoter was hypermethylated in 5/6 RCC cell lines. Demethylation treatment resulted in demethylation of the promoter and increased HOXA11 expression in these cell lines. HOXA11 methylation was also detected in 68/95 (70.5%) primary RCC tumors, but only rare adjacent non-malignant renal tissues (13%, 3/23) showed hypermethylation of promoter. We also found that the methylation of HOXA11 was associated with higher TNM classification of RCC (p<0.05). Ectopic expression of HOXA11 led to significant inhibition of proliferation, colony formation, migration and invasion abilities and induced RCC cells apoptosis. Moreover, HOXA11 was found to inhibit Wnt signaling. Thus, our study demonstrated that HOXA11 function as a tumor suppressor in RCC, while it is frequently silenced by promoter methylation in RCC.
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Affiliation(s)
- Lu Wang
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China.,Department of Urology, National Urological Cancer Center, Peking University First Hospital, Beijing 100034, China
| | - Yun Cui
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
| | - Jindong Sheng
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
| | - Yang Yang
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
| | - Guanyu Kuang
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
| | - Yu Fan
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China.,Department of Urology, National Research Center for Genitourinary Oncology, Peking University First Hospital, Beijing 100034, China
| | - Jie Jin
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
| | - Qian Zhang
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
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21
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Genome-wide screen for differentially methylated long noncoding RNAs identifies Esrp2 and lncRNA Esrp2-as regulated by enhancer DNA methylation with prognostic relevance for human breast cancer. Oncogene 2017; 36:6446-6461. [PMID: 28759043 PMCID: PMC5701091 DOI: 10.1038/onc.2017.246] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 06/05/2017] [Accepted: 06/08/2017] [Indexed: 12/14/2022]
Abstract
The majority of long noncoding RNAs (lncRNAs) is still poorly characterized with respect to function, interactions with protein-coding genes, and mechanisms that regulate their expression. As for protein-coding RNAs, epigenetic deregulation of lncRNA expression by alterations in DNA methylation might contribute to carcinogenesis. To provide genome-wide information on lncRNAs aberrantly methylated in breast cancer we profiled tumors of the C3(1) SV40TAg mouse model by MCIp-seq (Methylated CpG Immunoprecipitation followed by sequencing). This approach detected 69 lncRNAs differentially methylated between tumor tissue and normal mammary glands, with 26 located in antisense orientation of a protein-coding gene. One of the hypomethylated lncRNAs, 1810019D21Rik (now called Esrp2-antisense (as)) was identified in proximity to the epithelial splicing regulatory protein 2 (Esrp2) that is significantly elevated in C3(1) tumors. ESRPs were shown previously to have a dual role in carcinogenesis. Both gain and loss have been associated with poor prognosis in human cancers, but the mechanisms regulating expression are not known. In-depth analyses indicate that coordinate overexpression of Esrp2 and Esrp2-as inversely correlates with DNA methylation. Luciferase reporter gene assays support co-expression of Esrp2 and the major short Esrp2-as variant from a bidirectional promoter, and transcriptional regulation by methylation of a proximal enhancer. Ultimately, this enhancer-based regulatory mechanism provides a novel explanation for tissue-specific expression differences and upregulation of Esrp2 during carcinogenesis. Knockdown of Esrp2-as reduced Esrp2 protein levels without affecting mRNA expression and resulted in an altered transcriptional profile associated with extracellular matrix (ECM), cell motility and reduced proliferation, whereas overexpression enhanced proliferation. Our findings not only hold true for the murine tumor model, but led to the identification of an unannotated human homolog of Esrp2-as which is significantly upregulated in human breast cancer and associated with poor prognosis.
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22
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Clinical Significance and Effect of lncRNA HOXA11-AS in NSCLC: A Study Based on Bioinformatics, In Vitro and in Vivo Verification. Sci Rep 2017; 7:5567. [PMID: 28717185 PMCID: PMC5514100 DOI: 10.1038/s41598-017-05856-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 06/05/2017] [Indexed: 02/08/2023] Open
Abstract
HOXA11 antisense RNA (HOXA11-AS) has been shown to be involved in tumorigenesis and development of different cancers. However, the role of HOXA11-AS in non-small cell lung cancer (NSCLC) remains unclear. In this study, we firstly explored and confirmed the expression of HOXA11-AS in NSCLC tissues and cells. Cytometry, CCK-8, cell scratch, migration, Matrigel invasion and flow cytometry assays were performed to determine the biological impact of HOXA11-AS in vitro. Furthermore, a chick embryo chorioallantoic membrane (CAM) model of NSCLC was constructed to explore the effect of HOXA11-AS on tumorigenicity and angiogenesis in vivo. Additionally, bioinformatics analyses were performed to investigate the prospective pathways of HOXA11-AS co-expressed genes. As results, HOXA11-AS was markedly highly expressed in NSCLC tissues and cells. Furthermore, the proliferation, migration, invasion, tumorigenic and angiogenic ability of NSCLC cells were all inhibited and apoptosis was induced after HOXA11-AS knock-down. HOXA11-AS RNAi also led to cell cycle arrest on G0/G1 or G2/M phase. In addition, the non-small cell lung cancer pathway might be involved in regulating the co-expressed genes of HOXA11-AS in NSCLC. These results indicate that HOXA11-AS plays pivotal roles in NSCLC and it can become a novel therapeutic direction for treating NSCLC.
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23
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Se YB, Kim SH, Kim JY, Kim JE, Dho YS, Kim JW, Kim YH, Woo HG, Kim SH, Kang SH, Kim HJ, Kim TM, Lee ST, Choi SH, Park SH, Kim IH, Kim DG, Park CK. Underexpression of HOXA11 Is Associated with Treatment Resistance and Poor Prognosis in Glioblastoma. Cancer Res Treat 2016; 49:387-398. [PMID: 27456940 PMCID: PMC5398402 DOI: 10.4143/crt.2016.106] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/30/2016] [Indexed: 12/16/2022] Open
Abstract
Purpose Homeobox (HOX) genes are essential developmental regulators that should normally be in the silenced state in an adult brain. The aberrant expression of HOX genes has been associated with the prognosis of many cancer types, including glioblastoma (GBM). This study examined the identity and role of HOX genes affecting GBM prognosis and treatment resistance. Materials and Methods The full series of HOX genes of five pairs of initial and recurrent human GBM samples were screened by microarray analysis to determine the most plausible candidate responsible for GBM prognosis. Another 20 newly diagnosed GBM samples were used for prognostic validation. In vitro experiments were performed to confirm the role of HOX in treatment resistance. Mediators involved in HOX gene regulation were searched using differentially expressed gene analysis, gene set enrichment tests, and network analysis. Results The underexpression of HOXA11 was identified as a consistent signature for a poor prognosis among the HOX genes. The overall survival of the GBM patients indicated a significantly favorable prognosis in patients with high HOXA11 expression (31±15.3 months) compared to the prognoses in thosewith low HOXA11 expression (18±7.3 months, p=0.03). When HOXA11 was suppressed in the GBM cell lines, the anticancer effect of radiotherapy and/or temozolomide declined. In addition, five candidate mediators (TGFBR2, CRIM1, TXNIP, DPYSL2, and CRMP1) that may confer an oncologic effect after HOXA11 suppression were identified. Conclusion The treatment resistance induced by the underexpression of HOXA11 can contribute to a poor prognosis in GBM. Further investigation will be needed to confirm the value of HOXA11 as a potential target for overcoming the treatment resistance by developing chemo- or radiosensitizers.
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Affiliation(s)
- Young-Bem Se
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Seung Hyun Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Korea
| | - Ji Young Kim
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ja Eun Kim
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Yun-Sik Dho
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jin Wook Kim
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Yong Hwy Kim
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun Goo Woo
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea
| | - Se-Hyuk Kim
- Department of Neurosurgery, Ajou University School of Medicine, Suwon, Korea
| | - Shin-Hyuk Kang
- Department of Neurosurgery, Korea University College of Medicine, Seoul, Korea
| | - Hak Jae Kim
- Department of Radiation Oncology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Tae Min Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Soon-Tae Lee
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Seung Hong Choi
- Department of Radiology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Il Han Kim
- Department of Radiation Oncology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Dong Gyu Kim
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Korea
| | - Chul-Kee Park
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Korea
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Abe M, Yamashita S, Mori Y, Abe T, Saijo H, Hoshi K, Ushijima T, Takato T. High-risk oral leukoplakia is associated with aberrant promoter methylation of multiple genes. BMC Cancer 2016; 16:350. [PMID: 27255271 PMCID: PMC4891845 DOI: 10.1186/s12885-016-2371-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 05/19/2016] [Indexed: 01/26/2023] Open
Abstract
Background Early detection of oral squamous cell carcinomas (OSCCs) is urgently needed to improve the prognosis and quality of life (QOL) of patients. Oral leukoplakias (OLs), known as the most common premalignant lesions in the oral cavity, often precede OSCCs. Especially, OLs with dysplasia are known to have a high risk of malignant transformation. Here, we searched for the promoter methylation characteristic of high-risk OLs. Methods To identify methylation-silenced genes, a combined analysis of methylated DNA immunoprecipitation (MeDIP) − CpG island (CGI) microarray analysis and expression microarray analysis after treatment with a demethylating agent was performed in two OSCC cell lines (Ca9–22 and HSC-2). The methylation statuses of each gene were examined by methylation-specific PCR. Results A total of 52 genes were identified as candidates for methylation-silenced genes in Ca9-22 or HSC-2. The promoter regions of 13 genes among the 15 genes randomly selected for further analysis were confirmed to be methylated in one or more of five cell lines. In OSCC tissues (n = 26), 8 of the 13 genes, TSPYL5, EGFLAM, CLDN11, NKX2-3, RBP4, CMTM3, TRPC4, and MAP6, were methylated. In OL tissues (n = 24), seven of the eight genes, except for EGFLAM, were found to be methylated in their promoter regions. There were significantly greater numbers of methylated genes in OLs with dysplasia than in those without dysplasia (p < 0.0001). Conclusions OLs at high risk for malignant transformation were associated with aberrant promoter methylation of multiple genes. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2371-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Masanobu Abe
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan. .,Division for Health Service Promotion, University of Tokyo, Tokyo, Japan.
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoshiyuki Mori
- Department of Dentistry, Oral & Maxillofacial Surgery, Jichi Medical University, Tochigi, Japan
| | - Takahiro Abe
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hideto Saijo
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Kazuto Hoshi
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tsuyoshi Takato
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
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25
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Zhao MY, Yu Y, Xie M, Yang MH, Zhu S, Yang LC, Kang R, Tang DL, Zhao LL, Cao LZ. Digital gene expression profiling analysis of childhood acute lymphoblastic leukemia. Mol Med Rep 2016; 13:4321-8. [PMID: 27053012 DOI: 10.3892/mmr.2016.5089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 03/07/2016] [Indexed: 11/06/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most commonly diagnosed malignancy in children. It is a heterogeneous disease, and is determined by multiple gene alterations and chromosomal rearrangements. To improve current understanding of the underlying molecular mechanisms of ALL, the present study profiled genome‑wide digital gene expression (DGE) in a population of children with ALL in China. Using second‑generation sequencing technology, the profiling revealed that 2,825 genes were upregulated and 1,952 were downregulated in the ALL group. Based on the DGE profiling data, the present study further investigated seven genes (WT1, RPS26, MSX1, CD70, HOXC4, HOXA5 and HOXC6) using reverse transcription‑quantitative polymerase chain reaction analysis. Gene Ontology analysis suggested that the differentially expressed genes were predominantly involved in immune cell differentiation, metabolic processes and programmed cell death. The results of the present study provided novel insights into the gene expression patterns in children with ALL.
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Affiliation(s)
- Ming-Yi Zhao
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yan Yu
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Min Xie
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Ming-Hua Yang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Shan Zhu
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410006, P.R. China
| | - Liang-Chun Yang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Rui Kang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Dao-Lin Tang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Ling-Ling Zhao
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410006, P.R. China
| | - Li-Zhi Cao
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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Cui Y, Gao D, Linghu E, Zhan Q, Chen R, Brock MV, Herman JG, Guo M. Epigenetic changes and functional study of HOXA11 in human gastric cancer. Epigenomics 2015; 7:201-13. [PMID: 25590359 DOI: 10.2217/epi.14.92] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
AIM To examine epigenetic changes and the function of HOXA11 in human gastric cancer (GC). MATERIALS & METHODS Seven GC cell lines, five cases of normal gastric mucosa and 112 cases primary GC samples were used in this study. RESULTS Expression of HOXA11 and lack of promoter region methylation were found in NCI-N87, MKN45, BGC823 and HGC27 cells. Loss of expression and complete methylation were found in AGS gastric cancer cells. Reduced expression and partial methylation were found in MGC803 and SGC7901 cells. Restoration of HOXA11 expression was induced by 5-aza-2'-deoxycytidine. HOXA11 was methylated in 81.25% (91/112) of primary GCs. The presence of methylation was associated with male gender, tumor size, tumor differentiation and lymph node metastasis (all p < 0.05). Restoration of HOXA11 expression reduced cell proliferation, invasion, migration and induced apoptosis and G2/M phase arrest. HOXA11 was found to inhibit Wnt signaling by upregulating NKD1 expression. CONCLUSION Epigenetic silencing of HOXA11 promotes GC proliferation, migration and invasion through activation of Wnt signaling.
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Affiliation(s)
- Yingying Cui
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing, China
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