1
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Li Y, Jaiswal SK, Kaur R, Alsaadi D, Liang X, Drews F, DeLoia JA, Krivak T, Petrykowska HM, Gotea V, Welch L, Elnitski L. Differential gene expression identifies a transcriptional regulatory network involving ER-alpha and PITX1 in invasive epithelial ovarian cancer. BMC Cancer 2021; 21:768. [PMID: 34215221 PMCID: PMC8254236 DOI: 10.1186/s12885-021-08276-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/23/2021] [Indexed: 12/16/2022] Open
Abstract
Background The heterogeneous subtypes and stages of epithelial ovarian cancer (EOC) differ in their biological features, invasiveness, and response to chemotherapy, but the transcriptional regulators causing their differences remain nebulous. Methods In this study, we compared high-grade serous ovarian cancers (HGSOCs) to low malignant potential or serous borderline tumors (SBTs). Our aim was to discover new regulatory factors causing distinct biological properties of HGSOCs and SBTs. Results In a discovery dataset, we identified 11 differentially expressed genes (DEGs) between SBTs and HGSOCs. Their expression correctly classified 95% of 267 validation samples. Two of the DEGs, TMEM30B and TSPAN1, were significantly associated with worse overall survival in patients with HGSOC. We also identified 17 DEGs that distinguished stage II vs. III HGSOC. In these two DEG promoter sets, we identified significant enrichment of predicted transcription factor binding sites, including those of RARA, FOXF1, BHLHE41, and PITX1. Using published ChIP-seq data acquired from multiple non-ovarian cell types, we showed additional regulatory factors, including AP2-gamma/TFAP2C, FOXA1, and BHLHE40, bound at the majority of DEG promoters. Several of the factors are known to cooperate with and predict the presence of nuclear hormone receptor estrogen receptor alpha (ER-alpha). We experimentally confirmed ER-alpha and PITX1 presence at the DEGs by performing ChIP-seq analysis using the ovarian cancer cell line PEO4. Finally, RNA-seq analysis identified recurrent gene fusion events in our EOC tumor set. Some of these fusions were significantly associated with survival in HGSOC patients; however, the fusion genes are not regulated by the transcription factors identified for the DEGs. Conclusions These data implicate an estrogen-responsive regulatory network in the differential gene expression between ovarian cancer subtypes and stages, which includes PITX1. Importantly, the transcription factors associated with our DEG promoters are known to form the MegaTrans complex in breast cancer. This is the first study to implicate the MegaTrans complex in contributing to the distinct biological trajectories of malignant and indolent ovarian cancer subtypes. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08276-8.
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Affiliation(s)
- Yichao Li
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, USA
| | - Sushil K Jaiswal
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rupleen Kaur
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Dana Alsaadi
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xiaoyu Liang
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, USA
| | - Frank Drews
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, USA
| | - Julie A DeLoia
- Present address: Dignity Health Global Education, Roanoke, Virginia, USA
| | - Thomas Krivak
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh Medical School, Pittsburgh, PA, USA.,Present address: The Western Pennsylvania Hospital, Pittsburgh, PA, USA
| | - Hanna M Petrykowska
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Valer Gotea
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lonnie Welch
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, USA
| | - Laura Elnitski
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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2
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Brägelmann J, Barahona Ponce C, Marcelain K, Roessler S, Goeppert B, Gallegos I, Colombo A, Sanhueza V, Morales E, Rivera MT, de Toro G, Ortega A, Müller B, Gabler F, Scherer D, Waldenberger M, Reischl E, Boekstegers F, Garate-Calderon V, Umu SU, Rounge TB, Popanda O, Lorenzo Bermejo J. Epigenome-Wide Analysis of Methylation Changes in the Sequence of Gallstone Disease, Dysplasia, and Gallbladder Cancer. Hepatology 2021; 73:2293-2310. [PMID: 33020926 DOI: 10.1002/hep.31585] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Gallbladder cancer (GBC) is a highly aggressive malignancy of the biliary tract. Most cases of GBC are diagnosed in low-income and middle-income countries, and research into this disease has long been limited. In this study we therefore investigate the epigenetic changes along the model of GBC carcinogenesis represented by the sequence gallstone disease → dysplasia → GBC in Chile, the country with the highest incidence of GBC worldwide. APPROACH AND RESULTS To perform epigenome-wide methylation profiling, genomic DNA extracted from sections of formalin-fixed, paraffin-embedded gallbladder tissue was analyzed using Illumina Infinium MethylationEPIC BeadChips. Preprocessed, quality-controlled data from 82 samples (gallstones n = 32, low-grade dysplasia n = 13, high-grade dysplasia n = 9, GBC n = 28) were available to identify differentially methylated markers, regions, and pathways as well as changes in copy number variations (CNVs). The number and magnitude of epigenetic changes increased with disease development and predominantly involved the hypermethylation of cytosine-guanine dinucleotide islands and gene promoter regions. The methylation of genes implicated in Wnt signaling, Hedgehog signaling, and tumor suppression increased with tumor grade. CNVs also increased with GBC development and affected cyclin-dependent kinase inhibitor 2A, MDM2 proto-oncogene, tumor protein P53, and cyclin D1 genes. Gains in the targetable Erb-B2 receptor tyrosine kinase 2 gene were detected in 14% of GBC samples. CONCLUSIONS Our results indicate that GBC carcinogenesis comprises three main methylation stages: early (gallstone disease and low-grade dysplasia), intermediate (high-grade dysplasia), and late (GBC). The identified gradual changes in methylation and CNVs may help to enhance our understanding of the mechanisms underlying this aggressive disease and eventually lead to improved treatment and early diagnosis of GBC.
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Affiliation(s)
- Johannes Brägelmann
- Statistical Genetics Research Group, Institute of Medical Biometry and Informatic, University of Heidelberg, Heidelberg, Germany.,Molecular Pathology, Institute of Pathology & Department of Translational Genomics, University Hospital of Cologne, Cologne, Germany.,Mildred Scheel School of Oncology, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Carol Barahona Ponce
- Statistical Genetics Research Group, Institute of Medical Biometry and Informatic, University of Heidelberg, Heidelberg, Germany.,Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago, Chile
| | - Katherine Marcelain
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago, Chile
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Benjamin Goeppert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ivan Gallegos
- Servicio de Anatomía Patológica, Hospital Clínico de la Universidad de Chile, Santiago, Chile
| | - Alicia Colombo
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago, Chile.,Servicio de Anatomía Patológica, Hospital Clínico de la Universidad de Chile, Santiago, Chile
| | - Verónica Sanhueza
- Servicio de Anatomía Patológica, Hospital Padre Hurtado, Santiago, Chile
| | - Erik Morales
- Facultad de Medicina, Universidad Catolica del Maule & Unidad de Anatomia Patologica del Hospital Regional de Talca, Talca, Chile
| | | | - Gonzalo de Toro
- Escuela de Tecnologia Medica, Universidad Austral de Chile sede Puerto Montt & Servicio de Anatomía Patológica, Hospital de Puerto Montt, Puerto Montt, Chile
| | - Alejandro Ortega
- Servicio de Anatomía Patológica, Hospital Regional, Arica, Chile
| | - Bettina Müller
- Servicio de Oncología Médica, Instituto Nacional del Cáncer, Santiago, Chile
| | - Fernando Gabler
- Unidad de Anatomia Patologica, Hospital San Borja Arriaran, Santiago, Chile
| | - Dominique Scherer
- Statistical Genetics Research Group, Institute of Medical Biometry and Informatic, University of Heidelberg, Heidelberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology and Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Eva Reischl
- Research Unit of Molecular Epidemiology and Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Felix Boekstegers
- Statistical Genetics Research Group, Institute of Medical Biometry and Informatic, University of Heidelberg, Heidelberg, Germany
| | - Valentina Garate-Calderon
- Statistical Genetics Research Group, Institute of Medical Biometry and Informatic, University of Heidelberg, Heidelberg, Germany.,Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago, Chile
| | - Sinan U Umu
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway
| | - Odilia Popanda
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
| | - Justo Lorenzo Bermejo
- Statistical Genetics Research Group, Institute of Medical Biometry and Informatic, University of Heidelberg, Heidelberg, Germany
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3
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Yin X, Kong L, Liu P. Identification of prognosis-related molecular subgroups based on DNA methylation in pancreatic cancer. Clin Epigenetics 2021; 13:109. [PMID: 33980289 PMCID: PMC8117591 DOI: 10.1186/s13148-021-01090-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/22/2021] [Indexed: 12/24/2022] Open
Abstract
Background Pancreatic cancer (PC) is one of the most lethal and aggressive cancer malignancies. The lethality of PC is associated with delayed diagnosis, presence of distant metastasis, and its easy relapse. It is known that clinical treatment decisions are still mainly based on the clinical stage and pathological grade, which are insufficient to determine an appropriate treatment. Considering the significant heterogeneity of PC biological characteristics, the current clinical classificatory pattern relying solely on classical clinicopathological features identification needs to be urgently improved. In this study, we conducted in-depth analyses to establish prognosis-related molecular subgroups based on DNA methylation signature. Results DNA methylation, RNA sequencing, somatic mutation, copy number variation, and clinicopathological data of PC patients were obtained from The Cancer Genome Atlas (TCGA) dataset. A total of 178 PC samples were used to develop distinct molecular subgroups based on the 4227 prognosis-related CpG sites. By using consensus clustering analysis, four prognosis-related molecular subgroups were identified based on DNA methylation. The molecular characteristics and clinical features analyses based on the subgroups offered novel insights into the development of PC. Furthermore, we built a risk score model based on the expression data of five CpG sites to predict the prognosis of PC patients by using Lasso regression. Finally, the risk score model and other independent prognostic clinicopathological information were integrative utilised to construct a nomogram model. Conclusion Novel prognosis-related molecular subgroups based on the DNA methylation signature were established. The specific five CpG sites model for PC prognostic prediction and the derived nomogram model are effective and intuitive tools. Moreover, the construction of molecular subgroups based on the DNA methylation data is an innovative complement to the traditional classification of PC and may contribute to precision medicine development, therapeutic efficacy prediction, and clinical decision guidance. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01090-w.
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Affiliation(s)
- Xiaoli Yin
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Lingming Kong
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Peng Liu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
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4
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Wong CH, Lou UK, Li Y, Chan SL, Tong JH, To KF, Chen Y. CircFOXK2 Promotes Growth and Metastasis of Pancreatic Ductal Adenocarcinoma by Complexing with RNA-Binding Proteins and Sponging MiR-942. Cancer Res 2020; 80:2138-2149. [PMID: 32217695 DOI: 10.1158/0008-5472.can-19-3268] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 02/04/2020] [Accepted: 03/18/2020] [Indexed: 11/16/2022]
Abstract
The detailed biological functions of circular RNA (circRNA) are largely unexplored. Using circRNA sequencing, we identified 169 differentially expressed circRNA in pancreatic ductal adenocarcinoma (PDAC) cells compared with nontumor human pancreatic ductal epithelial cells. Among them, circFOXK2 was validated with significant upregulation in PDAC cells and 63% of primary tumors (53 of 84). circFOXK2 promoted cell growth, migration, and invasion and was involved in cell-cycle progression and apoptosis. circFOXK2 contained multiple miRNA binding sites, functioning as a sponge for miR-942, which in turn promoted expression of ANK1, GDNF, and PAX6. A novel and highly specific circRNA-pulldown followed by mass spectrometry analysis identified 94 circFOXK2-interacting proteins, which were involved in cell adhesion, mRNA splicing, and structural molecule activity. Of these, circFOKX2 interactions with YBX1 and hnRNPK enhanced expression of oncogenes NUF2 and PDXK. Knockdown of circFOXK2 reduced binding of YBX1 and hnRNPK to NUF2 and PDXK, in turn decreasing their expression. Collectively, our findings demonstrate that circFOXK2 in complex with YBX1 and hnRNPK promotes expression of oncogenic proteins that contribute to PDAC progression. SIGNIFICANCE: This study reveals a prominent role for the circRNA circFOXK2 in PDAC progression, suggesting that circFOXK2 might be a novel diagnostic marker for PDAC.
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Affiliation(s)
- Chi Hin Wong
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin NT, Hong Kong
| | - Ut Kei Lou
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin NT, Hong Kong
| | - Youjia Li
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin NT, Hong Kong
| | - Stephen L Chan
- Department of Clinical Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Joanna Hm Tong
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yangchao Chen
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin NT, Hong Kong. .,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
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5
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Chou ST, Peng HY, Mo KC, Hsu YM, Wu GH, Hsiao JR, Lin SF, Wang HD, Shiah SG. MicroRNA-486-3p functions as a tumor suppressor in oral cancer by targeting DDR1. J Exp Clin Cancer Res 2019; 38:281. [PMID: 31253192 PMCID: PMC6599238 DOI: 10.1186/s13046-019-1283-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 06/17/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Discoidin domain receptor-1 (DDR1) tyrosine kinase is highly expressed in a variety of human cancers and involved in various steps of tumorigenesis. However, the precise mechanisms underlying the abnormal expression of DDR1 in oral squamous cell carcinoma (OSCC) has not been well investigated. METHODS The expression of DDR1 on OSCC patients was determine by quantitative real-time PCR (qRT-PCR) and immunohistochemistry. Specific targeting by miRNAs was determined by software prediction, luciferase reporter assay, and correlation with target protein expression. The functions of miR-486-3p and DDR1 were accessed by MTT and Annexin V analyses using gain- and loss-of-function approaches. Chromatin immunoprecipitation (ChIP) and methylation specific PCR (MSP) were performed to explore the molecular mechanisms by arecoline treatment. RESULTS Here, we reported that DDR1 was significantly upregulated in OSCC tissues and its levels were inversely correlated with miR-486-3p expression. The experimental results in vitro confirmed that miR-486-3p decreased DDR1 expression by targeting the 3'-UTR of DDR1 mRNA. Overexpression of miR-486-3p led to growth inhibition and apoptosis induction with a similar function by knockdown of DDR1. Aberrant methylation of ANK1 promoter was a highly prevalent in OSCC and contributes to oral carcinogenesis by epigenetic silencing of ANK1 and miR-486-3p. We found that miR-486-3p can be transcriptionally co-regulated with its host gene ANK1 through epigenetic repression. DNA methylation inhibitor treatment re-expressed ANK1 and miR-486-3p. Importantly, arecoline, a major betel nut alkaloid, recruited DNMT3B binding to ANK1 promoter for DNA methylation and then attenuated the expression of miR-486-3p in OSCC. CONCLUSION This study was the first to demonstrate that betel nut alkaloid may recruit DNMT3B to regulate miR-486-3p/DDR1 axis in oral cancer andmiR-486-3p and DDR1 may serve as potential therapeutic targets of oral cancer.
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Affiliation(s)
- Sung-Tau Chou
- National Institute of Cancer Research, National Health Research Institutes, No. 35 Keyan Road, Zhunan Town, Miaoli County 35053 Taiwan
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Hsuan-Yu Peng
- National Institute of Cancer Research, National Health Research Institutes, No. 35 Keyan Road, Zhunan Town, Miaoli County 35053 Taiwan
| | - Kuan-Chi Mo
- National Institute of Cancer Research, National Health Research Institutes, No. 35 Keyan Road, Zhunan Town, Miaoli County 35053 Taiwan
| | - Yuan-Ming Hsu
- National Institute of Cancer Research, National Health Research Institutes, No. 35 Keyan Road, Zhunan Town, Miaoli County 35053 Taiwan
| | - Guan-Hsun Wu
- National Institute of Cancer Research, National Health Research Institutes, No. 35 Keyan Road, Zhunan Town, Miaoli County 35053 Taiwan
| | - Jenn-Ren Hsiao
- Department of Otolaryngology, Head and Neck Collaborative Oncology Group, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Su-Fang Lin
- National Institute of Cancer Research, National Health Research Institutes, No. 35 Keyan Road, Zhunan Town, Miaoli County 35053 Taiwan
| | - Horng-Dar Wang
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Shine-Gwo Shiah
- National Institute of Cancer Research, National Health Research Institutes, No. 35 Keyan Road, Zhunan Town, Miaoli County 35053 Taiwan
- Program in Environmental and Occupational Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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6
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Hu G, Cheng Z, Wu Z, Wang H. Identification of potential key genes associated with osteosarcoma based on integrated bioinformatics analyses. J Cell Biochem 2019; 120:13554-13561. [PMID: 30920023 DOI: 10.1002/jcb.28630] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/09/2019] [Accepted: 01/14/2019] [Indexed: 12/14/2022]
Abstract
Due to high rates of metastasis and poor clinical outcomes for patients, it is important to study the pathomechanisms of osteosarcoma. However, due to the fact that osteosarcoma shows significant interindividual variation and high heterogeneity, the identification of differentially expressed genes (DEGs) at the population level cannot answer many important questions related to osteosarcoma tumorigenesis. Therefore, a new strategy to identify dysregulated genes in osteosarcoma samples is required. The aim of this study was to improve our understanding of osteosarcoma pathogenesis by identifying genes with universal aberrant expression in osteosarcoma samples. Because the relative expression ordering of genes is stable in normal bone tissues but is disrupted in osteosarcoma tissues, we used the RankComp algorithm to identify DEGs in normal and osteosarcoma tissue samples. We then calculated the dysregulation frequency for each gene. Genes with deregulation frequencies above 80% were deemed to be universal DEGs. Next, coexpression, pathway enrichment, and protein-protein interaction network analyses were performed to characterize the functions of these genes. From 188 samples of osteosarcoma obtained from four datasets measured on different platforms, 51 universal DEGs were identified, including 4 universally upregulated genes and 47 universally downregulated genes. Genes that were differentially coexpressed with these universal DEGs were found to be enriched in 46 cancer-related pathways. In addition, functional and network analyses showed that genes with high dysregulation frequencies were involved in cancer-related functions. Thus, the commonly aberrant genes identified in osteosarcoma tissues may be important targets for osteosarcoma diagnosis and therapy.
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Affiliation(s)
- Guangbing Hu
- Department of Orthopedics, Nanchang Hongdu Hospital of Traditional Chinese Medicine, Nanchang, Jiangxi, China
| | - Zhian Cheng
- Department of Orthopedics, Guangdong Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.,The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zizhuo Wu
- Department of Orthopedics, Guangdong Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.,The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Hanyu Wang
- Department of Orthopedics, Guangdong Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.,The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
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7
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Sarne V, Braunmueller S, Rakob L, Seeboeck R. The Relevance of Gender in Tumor-Influencing Epigenetic Traits. EPIGENOMES 2019; 3:epigenomes3010006. [PMID: 34991275 PMCID: PMC8594720 DOI: 10.3390/epigenomes3010006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/20/2019] [Accepted: 01/24/2019] [Indexed: 12/22/2022] Open
Abstract
Tumorigenesis as well as the molecular orchestration of cancer progression are very complex mechanisms that comprise numerous elements of influence and regulation. Today, many of the major concepts are well described and a basic understanding of a tumor's fine-tuning is given. Throughout the last decade epigenetics has been featured in cancer research and it is now clear that the underlying mechanisms, especially DNA and histone modifications, are important regulators of carcinogenesis and tumor progression. Another key regulator, which is well known but has been neglected in scientific approaches as well as molecular diagnostics and, consequently, treatment conceptualization for a long time, is the subtle influence patient gender has on molecular processes. Naturally, this is greatly based on hormonal differences, but from an epigenetic point of view, the diverse susceptibility to stress and environmental influences is of prime interest. In this review we present the current view on which and how epigenetic modifications, emphasizing DNA methylation, regulate various tumor diseases. It is our aim to elucidate gender and epigenetics and their interconnectedness, which will contribute to understanding of the prospect molecular orchestration of cancer in individual tumors.
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8
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Zhou D, Alver BM, Li S, Hlady RA, Thompson JJ, Schroeder MA, Lee JH, Qiu J, Schwartz PH, Sarkaria JN, Robertson KD. Distinctive epigenomes characterize glioma stem cells and their response to differentiation cues. Genome Biol 2018; 19:43. [PMID: 29587824 PMCID: PMC5872397 DOI: 10.1186/s13059-018-1420-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/12/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Glioma stem cells (GSCs) are a subpopulation of stem-like cells that contribute to glioblastoma (GBM) aggressiveness, recurrence, and resistance to radiation and chemotherapy. Therapeutically targeting the GSC population may improve patient survival, but unique vulnerabilities need to be identified. RESULTS We isolate GSCs from well-characterized GBM patient-derived xenografts (PDX), characterize their stemness properties using immunofluorescence staining, profile their epigenome including 5mC, 5hmC, 5fC/5caC, and two enhancer marks, and define their transcriptome. Fetal brain-derived neural stem/progenitor cells are used as a comparison to define potential unique and common molecular features between these different brain-derived cells with stem properties. Our integrative study reveals that abnormal expression of ten-eleven-translocation (TET) family members correlates with global levels of 5mC and 5fC/5caC and may be responsible for the distinct levels of these marks between glioma and neural stem cells. Heterogenous transcriptome and epigenome signatures among GSCs converge on several genes and pathways, including DNA damage response and cell proliferation, which are highly correlated with TET expression. Distinct enhancer landscapes are also strongly associated with differential gene regulation between glioma and neural stem cells; they exhibit unique co-localization patterns with DNA epigenetic mark switching events. Upon differentiation, glioma and neural stem cells exhibit distinct responses with regard to TET expression and DNA mark changes in the genome and GSCs fail to properly remodel their epigenome. CONCLUSIONS Our integrative epigenomic and transcriptomic characterization reveals fundamentally distinct yet potentially targetable biologic features of GSCs that result from their distinct epigenomic landscapes.
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Affiliation(s)
- Dan Zhou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Bonnie M Alver
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Shuang Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Joyce J Thompson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Mark A Schroeder
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN, USA
| | - Jeong-Heon Lee
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.,Epigenomics Translational Program, Mayo Clinic, Rochester, MN, USA
| | - Jingxin Qiu
- Department of Pathology and Laboratory Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Philip H Schwartz
- National Human Neural Stem Cell Resource, Children's Hospital of Orange County Research Institute, Orange, CA, USA
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN, USA
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA. .,Epigenomics Translational Program, Mayo Clinic, Rochester, MN, USA. .,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA. .,Mayo Clinic Cancer Center, Mayo Clinic, Rochester, MN, USA.
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9
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PAX3-FOXO1 drives miR-486-5p and represses miR-221 contributing to pathogenesis of alveolar rhabdomyosarcoma. Oncogene 2018; 37:1991-2007. [PMID: 29367756 PMCID: PMC5895609 DOI: 10.1038/s41388-017-0081-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 10/26/2017] [Accepted: 12/01/2017] [Indexed: 01/02/2023]
Abstract
Rhabdomyosarcoma is the most common soft-tissue sarcoma in childhood and histologically resembles developing skeletal muscle. Alveolar rhabdomyosarcoma (ARMS) is an aggressive subtype with a higher rate of metastasis and poorer prognosis. The majority of ARMS tumors (80%) harbor a PAX3-FOXO1 or less commonly a PAX7-FOXO1 fusion gene. The presence of either the PAX3-FOXO1 or PAX7-FOXO1 fusion gene foretells a poorer prognosis resulting in clinical re-classification as either fusion-positive (FP-RMS) or fusion-negative RMS (FN-RMS). The PAX3/7-FOXO1 fusion genes result in the production of a rogue transcription factors that drive FP-RMS pathogenesis and block myogenic differentiation. Despite knowing the molecular driver of FP-RMS, targeted therapies have yet to make an impact for patients, highlighting the need for a greater understanding of the molecular consequences of PAX3-FOXO1 and its target genes including microRNAs. Here we show FP-RMS patient-derived xenografts and cell lines display a distinct microRNA expression pattern. We utilized both loss- and gain-of function approaches in human cell lines with knockdown of PAX3-FOXO1 in FP-RMS cell lines and expression of PAX3-FOXO1 in human myoblasts and identified microRNAs both positively and negatively regulated by the PAX3-FOXO1 fusion protein. We demonstrate PAX3-FOXO1 represses miR-221/222 that functions as a tumor suppressing microRNA through the negative regulation of CCND2, CDK6, and ERBB3. In contrast, miR-486-5p is transcriptionally activated by PAX3-FOXO1 and promotes FP-RMS proliferation, invasion, and clonogenic growth. Inhibition of miR-486-5p in FP-RMS xenografts decreased tumor growth, illustrating a proof of principle for future therapeutic intervention. Therefore, PAX3-FOXO1 regulates key microRNAs that may represent novel therapeutic vulnerabilities in FP-RMS.
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10
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Abstract
DNA methylation is a dynamic epigenetic mark that characterizes different cellular developmental stages, including tissue-specific profiles. This CpG dinucleotide modification cooperates in the regulation of the output of the cellular genetic content, in both healthy and pathological conditions. According to endogenous and exogenous stimuli, DNA methylation is involved in gene transcription, alternative splicing, imprinting, X-chromosome inactivation, and control of transposable elements. When these dinucleotides are organized in dense regions are called CpG islands (CGIs), being commonly known as transcriptional regulatory regions frequently associated with the promoter region of several genes. In cancer, promoter DNA hypermethylation events sustained the mechanistic hypothesis of epigenetic transcriptional silencing of an increasing number of tumor suppressor genes. CGI hypomethylation-mediated reactivation of oncogenes was also documented in several cancer types. In this chapter, we aim to summarize the functional consequences of the differential DNA methylation at CpG dinucleotides in cancer, focused in CGIs. Interestingly, cancer methylome is being recently explored, looking for biomarkers for diagnosis, prognosis, and predictors of drug response.
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Affiliation(s)
- Humberto J Ferreira
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.
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Li Y, Wang M, Huang BW, Ping Y, You J, Gao JQ. Transcriptome-wide elucidation of liposomal formulations for anticancer drug delivery. Int J Nanomedicine 2017; 12:8557-8572. [PMID: 29238192 PMCID: PMC5716676 DOI: 10.2147/ijn.s148975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although widely used in chemotherapy, free doxorubicin (Dox) might enhance cell malignancy undesirably. Liposomal Dox (Doxlipo) has been clinically approved for the treatment of breast cancer due to reduced systematical toxicity and increased tumor targeting, yet the transcriptome-wide elucidation of the Doxlipo formulations remains elusive. To this end, we explored the impact of two Dox liposomal formulations, Doxlipo mainly containing hydrogenated soy phosphatidylcholine or 1,2-dipalmitoyl-sn-glycero-3-phosphocholine, on the transcriptional pattern of MCF-7 cells. The two types of Dox liposomal formulations with different drug release kinetics were investigated to reveal the relationship between the formulation and tumor malignancy. Interestingly, we found that liposomal formulation significantly altered the transcriptional pattern of a wide range of genes. Under equivalent dosage of Dox, free Dox substantially changed the expression of ANK1, ACTA2, GPR87, GDF15, FZD6, and WNT4 in MCF-7 cells. Notably, free Dox induced much higher expression of ABCB1 and significantly enhanced the cell migration behavior in comparison with HSPC Doxlipo under a similar level of cytotoxicity. Finally, siRNA targeting GPR87 was codelivered with cationic Doxlipo to reduce the expression of malignancy-related genes. Our study, for the first time, provides an overview of the influence of formulation on the malignancy at transcriptional level and reveals the relationship between cytotoxicity and cell malignancy from the formulation aspect, offering valuable reference for the future formulation design for anticancer drug delivery.
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Affiliation(s)
- Ying Li
- Institute of Pharmaceutics, College of Pharmaceutical Sciences.,Zhejiang Province Key Laboratory of Anticancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Meng Wang
- Institute of Pharmaceutics, College of Pharmaceutical Sciences.,Zhejiang Province Key Laboratory of Anticancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Bu-Wei Huang
- Institute of Pharmaceutics, College of Pharmaceutical Sciences.,Zhejiang Province Key Laboratory of Anticancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Yuan Ping
- School of Materials Science and Engineering, Nanyang Technological University, Singapore
| | - Jian You
- Institute of Pharmaceutics, College of Pharmaceutical Sciences
| | - Jian-Qing Gao
- Institute of Pharmaceutics, College of Pharmaceutical Sciences.,Zhejiang Province Key Laboratory of Anticancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People's Republic of China
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12
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Tessema M, Yingling CM, Picchi MA, Wu G, Ryba T, Lin Y, Bungum AO, Edell ES, Spira A, Belinsky SA. ANK1 Methylation regulates expression of MicroRNA-486-5p and discriminates lung tumors by histology and smoking status. Cancer Lett 2017; 410:191-200. [PMID: 28965852 PMCID: PMC5675764 DOI: 10.1016/j.canlet.2017.09.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
Abstract
The intragenic tumor-suppressor microRNA miR-486-5p is often down-regulated in non-small cell lung cancer (NSCLC) but the mechanism is unclear. This study investigated epigenetic co-regulation of miR-486-5p and its host gene ANK1. MiR-486-5p expression in lung tumors and cell lines was significantly reduced compared to normal lung (p < 0.001) and is strongly correlated with ANK1 expression. In vitro, siRNA-mediated ANK1 knockdown in NSCLC cells also reduced miR-486-5p while the DNA methylation inhibitor 5-aza-2'-deoxycytidine induced expression of both. ANK1 promoter CpG island was unmethylated in normal lung but methylated in 45% (118/262) lung tumors and 55% (17/31) NSCLC cell lines. After adjustment for tumor histology and smoking, methylation was significantly more prevalent in adenocarcinoma (101/200, 51%) compared to squamous cell carcinoma (17/62, 27%), p < 0.001; HR = 3.513 (CI: 1.818-6.788); and in smokers (73/128, 57%) than never-smokers (28/72, 39%), p = 0.014; HR = 2.086 (CI: 1.157-3.759). These results were independently validated using quantitative methylation data for 809 NSCLC cases from The Cancer Genome Atlas project. Together, our data indicate that aberrant ANK1 methylation is highly prevalent in lung cancer, discriminate tumors by histology and patients' smoking history, and contributes to miR-486-5p repression.
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MESH Headings
- Adenocarcinoma/etiology
- Adenocarcinoma/genetics
- Adenocarcinoma/metabolism
- Adenocarcinoma/pathology
- Adenocarcinoma of Lung
- Ankyrins/genetics
- Ankyrins/metabolism
- Carcinoma, Non-Small-Cell Lung/etiology
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Squamous Cell/etiology
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Line, Tumor
- CpG Islands
- DNA Methylation
- Databases, Genetic
- Down-Regulation
- Epigenesis, Genetic
- Gene Expression Regulation, Neoplastic
- Humans
- Introns
- Lung Neoplasms/etiology
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Promoter Regions, Genetic
- Risk Factors
- Smoking/adverse effects
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Affiliation(s)
- Mathewos Tessema
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA.
| | - Christin M Yingling
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Guodong Wu
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Tyrone Ryba
- Division of Natural Sciences, New College of Florida, Sarasota, FL, USA
| | - Yong Lin
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Aaron O Bungum
- Departments of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Eric S Edell
- Departments of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Avrum Spira
- Department of Medicine, Boston University, Boston, MA, USA
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
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