1
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Feng Y, Wang Y. Comparison of the classifiers based on mRNA, microRNA and lncRNA expression and DNA methylation profiles for the tumor origin detection. Front Genet 2024; 15:1383852. [PMID: 38933920 PMCID: PMC11199677 DOI: 10.3389/fgene.2024.1383852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024] Open
Abstract
Background Tumor tissue origin detection is of great importance in determining the appropriate course of treatment for cancer patients. Classifiers based on gene expression and DNA methylation profiles have been confirmed to be feasible and reliable to predict the tumor primary. However, few works have been performed to compare the performance of these classifiers based on different profiles. Methods Using gene expression and DNA methylation profiles from The Cancer Genome Atlas (TCGA) project, eight machine learning methods were employed for the tumor tissue origin detection. We then evaluated the predictive performance using DNA methylation, mRNA, microRNA (miRNA) and long non-coding RNA (lncRNA) expression profiles in a comparative manner. A statistical method was introduced to select the most informative CpG sites. Results We found that LASSO is the most predictive models based on various profiles. Further analyses indicated that the results derived from DNA methylation (overall accuracy: 97.77%) are better than those derived from mRNA expression (overall accuracy: 88.01%), microRNA expression (overall accuracy: 91.03%) and lncRNA expression (overall accuracy: 95.7%). It has been suggested that we can achieve an overall accuracy >90% using only 1,000 methylated CpG sites for prediction. Conclusion In this work, we comprehensively evaluated the performance of classifiers based on different profiles for the tumor origin detection. Our findings demonstrated the effectiveness of DNA methylation as biomarker for tracing tumor tissue origin using LASSO and neural network.
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Affiliation(s)
| | - Yilin Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
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2
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Zhang X, Wang H, Zhang Y, Wang X. Advances in epigenetic alterations of chronic lymphocytic leukemia: from pathogenesis to treatment. Clin Exp Med 2024; 24:54. [PMID: 38492089 PMCID: PMC10944427 DOI: 10.1007/s10238-023-01268-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 12/01/2023] [Indexed: 03/18/2024]
Abstract
Chronic lymphocytic leukemia (CLL) is a heterogeneous disease with alterations in genetic expression and epigenetic modifications. In recent years, the new insight into epigenetics in the pathogenesis of CLL has been developed considerably, including DNA methylation, histone modification, RNA methylation, non-coding RNAs as well as chromatin remodeling. Epigenetic modification regulates various processes such as stem cell biology, cell growth, and tumorigenesis without altering gene sequence. Growing evidence indicates that the disturbance of gene expression profiles which were regulated by epigenetic modifications exerts vital roles in the development and progress in CLL, which provides novel perspectives to explore the etiology of CLL. In addition, the integration with epigenetic therapeutic targets and the in-depth understanding of epigenetic therapy contribute to develop new therapeutic strategies for CLL. Herein, the present review discusses the advances of epigenetic alterations in the pathogenesis, diagnosis, and prognostic assessment of CLL patients and also highlights existing and emerging agents targeting epigenetic regulators.
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Affiliation(s)
- Xin Zhang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Hua Wang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Ya Zhang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China.
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.
- Taishan Scholars Program of Shandong Province, Jinan, 250021, Shandong, China.
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China.
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.
- Taishan Scholars Program of Shandong Province, Jinan, 250021, Shandong, China.
- Branch of National Clinical Research Center for Hematologic Diseases, Jinan, 250021, Shandong, China.
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China.
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3
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Chatzidavid S, Kontandreopoulou CN, Giannakopoulou N, Diamantopoulos PT, Stafylidis C, Kyrtsonis MC, Dimou M, Panayiotidis P, Viniou NA. The Role of Methylation in Chronic Lymphocytic Leukemia and Its Prognostic and Therapeutic Impacts in the Disease: A Systematic Review. Adv Hematol 2024; 2024:1370364. [PMID: 38435839 PMCID: PMC10907108 DOI: 10.1155/2024/1370364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 03/05/2024] Open
Abstract
Epigenetic regulation has been thoroughly investigated in recent years and has emerged as an important aspect of chronic lymphocytic leukemia (CLL) biology. Characteristic aberrant features such as methylation patterns and global DNA hypomethylation were the early findings of the research during the last decades. The investigation in this field led to the identification of a large number of genes where methylation features correlated with important clinical and laboratory parameters. Gene-specific analyses investigated methylation in the gene body enhancer regions as well as promoter regions. The findings included genes and proteins involved in key pathways that play central roles in the pathophysiology of the disease. Τhe application of these findings beyond the theoretical understanding can not only lead to the creation of prognostic and predictive models and scores but also to the design of novel therapeutic agents. The following is a review focusing on the present knowledge about single gene/gene promoter methylation or mRNA expression in CLL cases as well as records of older data that have been published in past papers.
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Affiliation(s)
- Sevastianos Chatzidavid
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
- Thalassemia and Sickle Cell Disease Center, Laikon General Hospital, Athens, Greece
| | - Christina-Nefeli Kontandreopoulou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Panagiotis T. Diamantopoulos
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos Stafylidis
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Marie-Christine Kyrtsonis
- Hematology Section of the First Department of Propaedeutic Internal Medicine, Laikon University Hospital, Athens, Greece
| | - Maria Dimou
- Hematology Section of the First Department of Propaedeutic Internal Medicine, Laikon University Hospital, Athens, Greece
| | - Panayiotis Panayiotidis
- Department of Hematology and Bone Marrow Transplantation Unit, National and Kapodistrian University of Athens, School of Medicine, Laikon General Hospital, Athens, Greece
| | - Nora-Athina Viniou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
- Hematology Department, Iatriko Kentro Palaiou Falirou, Athens, Greece
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4
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Piroeva KV, McDonald C, Xanthopoulos C, Fox C, Clarkson CT, Mallm JP, Vainshtein Y, Ruje L, Klett LC, Stilgenbauer S, Mertens D, Kostareli E, Rippe K, Teif VB. Nucleosome repositioning in chronic lymphocytic leukemia. Genome Res 2023; 33:1649-1661. [PMID: 37699659 PMCID: PMC10691546 DOI: 10.1101/gr.277298.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/07/2023] [Indexed: 09/14/2023]
Abstract
The location of nucleosomes in the human genome determines the primary chromatin structure and regulates access to regulatory regions. However, genome-wide information on deregulated nucleosome occupancy and its implications in primary cancer cells is scarce. Here, we conducted a genome-wide comparison of high-resolution nucleosome maps in peripheral blood B cells from patients with chronic lymphocytic leukemia (CLL) and healthy individuals at single-base-pair resolution. Our investigation uncovered significant changes of nucleosome positioning in CLL. Globally, the spacing between nucleosomes-the nucleosome repeat length (NRL)-is shortened in CLL. This effect is stronger in the more aggressive IGHV-unmutated CLL subtype than in the IGHV-mutated CLL subtype. Changes in nucleosome occupancy at specific sites are linked to active chromatin remodeling and reduced DNA methylation. Nucleosomes lost or gained in CLL marks differential binding of 3D chromatin organizers such as CTCF as well as immune response-related transcription factors and delineated mechanisms of epigenetic deregulation. The principal component analysis of nucleosome occupancy in cancer-specific regions allowed the classification of samples between cancer subtypes and normal controls. Furthermore, patients could be better assigned to CLL subtypes according to differential nucleosome occupancy than based on DNA methylation or gene expression. Thus, nucleosome positioning constitutes a novel readout to dissect molecular mechanisms of disease progression and to stratify patients. Furthermore, we anticipate that the global nucleosome repositioning detected in our study, such as changes in the NRL, can be exploited for liquid biopsy applications based on cell-free DNA to stratify patients and monitor disease progression.
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Affiliation(s)
- Kristan V Piroeva
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Charlotte McDonald
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, United Kingdom
| | - Charalampos Xanthopoulos
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, United Kingdom
| | - Chelsea Fox
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Christopher T Clarkson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Jan-Philipp Mallm
- German Cancer Research Center (DKFZ) Heidelberg, Single Cell Open Lab, 69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, 69120 Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, 69120 Heidelberg, Germany
| | - Yevhen Vainshtein
- Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik IGB, 70569 Stuttgart, Germany
| | - Luminita Ruje
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Lara C Klett
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, 69120 Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, 69120 Heidelberg, Germany
| | - Stephan Stilgenbauer
- Division of CLL, University Hospital Ulm, Department of Internal Medicine III, 89081 Ulm, Germany
| | - Daniel Mertens
- Division of CLL, University Hospital Ulm, Department of Internal Medicine III, 89081 Ulm, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Cooperation Unit Mechanisms of Leukemogenesis, 69120 Heidelberg, Germany
| | - Efterpi Kostareli
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, United Kingdom;
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, 69120 Heidelberg, Germany;
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, 69120 Heidelberg, Germany
| | - Vladimir B Teif
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom;
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5
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Zhang Q, Gao Y, Lin S, Goldin LR, Wang Y, Stevenson H, Edelman DC, Killian K, Marti G, Meltzer PS, Xiang S, Caporaso NE. Genome-wide DNA methylation profiling in chronic lymphocytic leukaemia. Front Genet 2023; 13:1056043. [PMID: 36712882 PMCID: PMC9873975 DOI: 10.3389/fgene.2022.1056043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/14/2022] [Indexed: 01/12/2023] Open
Abstract
Background: DNA methylation aberrations are widespread among the malignant B lymphocytes of patients with chronic lymphocytic leukaemia (CLL), suggesting that DNA methylation might contribute to the pathogenesis of CLL. Aim: We aimed to explore the differentially methylated positions (DMPs) associated with CLL and screen the differentially methylated and expressed genes (DMEGs) by combining public databases. We aimed to observe the direction of each DMEG in CLL based on the DMPs in the promoter and the body region respectively to narrow down DMEGs. We also aimed to explore the methylation heterogeneity of CLL subgroups and the effect of B cells maturation on CLL. Methods: In this population-based case control study, we reported a genome-wide DNA methylation association study using the Infinium HumanMethylation450 BeadChip, profiling the DNA methylation of CD19+ B Cells from 48 CLL cases and 28 healthy controls. By integrating methylation data and expression data from public databases, gene sets were jointly screened, and then the relationship between methylation sites in promoter and body region and expression of each gene was explored. In addition, support vector machine (SVM) classification algorithm was used to identify subgroups of CLL cases based on methylation pattern, and the effect of B-cell differentiation related methylation sites on CLL-related sites was observed. Results: We identified 34,797 DMPs related to CLL across the genome, most of which were hypomethylated; the majority were located in gene body regions. By combining these DMPs with published DNA methylation and RNA sequencing data, we detected 26,244 replicated DMPs associated with 1,130 genes whose expression were significantly different in CLL cases. Among these DMEGs, nine low expressed DMEGs were selected with hypermethylated in promoter and hypomethylated in body region, and 83 high expressed DMEGs were selected with both hypomethylated in promoter and body region. The 48 CLL cases were divided into 3 subgroups based on methylation site by SVM algorithm. Over 92% of CpGs associated with B cell subtypes were found in CLL-related DMPs. Conclusion: The DNA methylation pattern was altered across the genome in CLL patients. The methylation of ZAP70, FMOD, and ADAMTS17 was significantly different between CLL cases and controls. Further studies are warranted to confirm our findings and identify the underlying mechanisms through which these methylation markers are associated with CLL.
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Affiliation(s)
- Qiuyi Zhang
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ying Gao
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China,Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States,*Correspondence: Ying Gao,
| | - Shuchun Lin
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lynn R. Goldin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Yonghong Wang
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Holly Stevenson
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Daniel C. Edelman
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Keith Killian
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Gerald Marti
- Lymphoid Malignancies Section, Hematology Branch, NHLBI, National Institutes of Health, Bethesda, MD, United States
| | - Paul S. Meltzer
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Song Xiang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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6
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Targeting DNA Methylation in Leukemia, Myelodysplastic Syndrome, and Lymphoma: A Potential Diagnostic, Prognostic, and Therapeutic Tool. Int J Mol Sci 2022; 24:ijms24010633. [PMID: 36614080 PMCID: PMC9820560 DOI: 10.3390/ijms24010633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022] Open
Abstract
DNA methylation represents a crucial mechanism of epigenetic regulation in hematologic malignancies. The methylation process is controlled by specific DNA methyl transferases and other regulators, which are often affected by genetic alterations. Global hypomethylation and hypermethylation of tumor suppressor genes are associated with hematologic cancer development and progression. Several epi-drugs have been successfully implicated in the treatment of hematologic malignancies, including the hypomethylating agents (HMAs) decitabine and azacytidine. However, combinations with other treatment modalities and the discovery of new molecules are still the subject of research to increase sensitivity to anti-cancer therapies and improve patient outcomes. In this review, we summarized the main functions of DNA methylation regulators and genetic events leading to changes in methylation landscapes. We provide current knowledge about target genes with aberrant methylation levels in leukemias, myelodysplastic syndromes, and malignant lymphomas. Moreover, we provide an overview of the clinical trials, focused mainly on the combined therapy of HMAs with other treatments and its impact on adverse events, treatment efficacy, and survival rates among hematologic cancer patients. In the era of precision medicine, a transition from genes to their regulation opens up the possibility of an epigenetic-based approach as a diagnostic, prognostic, and therapeutic tool.
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7
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Panda D, Das N, Thakral D, Gupta R. Genomic landscape of mature B-cell non-Hodgkin lymphomas - an appraisal from lymphomagenesis to drug resistance. J Egypt Natl Canc Inst 2022; 34:52. [PMID: 36504392 DOI: 10.1186/s43046-022-00154-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 09/27/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Mature B-cell non-Hodgkin lymphomas are one of the most common hematological malignancies with a divergent clinical presentation, phenotype, and course of disease regulated by underlying genetic mechanism. MAIN BODY Genetic and molecular alterations are not only critical for lymphomagenesis but also largely responsible for differing therapeutic response in these neoplasms. In recent years, advanced molecular tools have provided a deeper understanding regarding these oncogenic drives for predicting progression as well as refractory behavior in these diseases. The prognostic models based on gene expression profiling have also been proved effective in various clinical scenarios. However, considerable overlap does exist between the genotypes of individual lymphomas and at the same time where additional molecular lesions may be associated with each entity apart from the key genetic event. Therefore, genomics is one of the cornerstones in the multimodality approach essential for classification and risk stratification of B-cell non-Hodgkin lymphomas. CONCLUSION We hereby in this review discuss the wide range of genetic aberrancies associated with tumorigenesis, immune escape, and chemoresistance in major B-cell non-Hodgkin lymphomas.
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Affiliation(s)
- Devasis Panda
- Department of Laboratory Oncology, Dr. BRAIRCH, AIIMS, New Delhi, 110029, India
| | - Nupur Das
- Department of Laboratory Oncology, Dr. BRAIRCH, AIIMS, New Delhi, 110029, India
| | - Deepshi Thakral
- Department of Laboratory Oncology, Dr. BRAIRCH, AIIMS, New Delhi, 110029, India
| | - Ritu Gupta
- Department of Laboratory Oncology, Dr. BRAIRCH, AIIMS, New Delhi, 110029, India.
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8
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Chen X, Li Y, Paiboonrungruang C, Li Y, Peters H, Kist R, Xiong Z. PAX9 in Cancer Development. Int J Mol Sci 2022; 23:5589. [PMID: 35628401 PMCID: PMC9147292 DOI: 10.3390/ijms23105589] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/12/2022] [Accepted: 05/14/2022] [Indexed: 02/05/2023] Open
Abstract
Paired box 9 (PAX9) is a transcription factor of the PAX family functioning as both a transcriptional activator and repressor. Its functional roles in the embryonic development of various tissues and organs have been well studied. However, its roles and molecular mechanisms in cancer development are largely unknown. Here, we review the current understanding of PAX9 expression, upstream regulation of PAX9, and PAX9 downstream events in cancer development. Promoter hypermethylation, promoter SNP, microRNA, and inhibition of upstream pathways (e.g., NOTCH) result in PAX9 silencing or downregulation, whereas gene amplification and an epigenetic axis upregulate PAX9 expression. PAX9 may contribute to carcinogenesis through dysregulation of its transcriptional targets and related molecular pathways. In summary, extensive studies on PAX9 in its cellular and tissue contexts are warranted in various cancers, in particular, HNSCC, ESCC, lung cancer, and cervical SCC.
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Affiliation(s)
- Xiaoxin Chen
- Cancer Research Program, Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, 700 George Street, Durham, NC 27707, USA; (X.C.); (Y.L.); (C.P.); (Y.L.)
| | - Yahui Li
- Cancer Research Program, Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, 700 George Street, Durham, NC 27707, USA; (X.C.); (Y.L.); (C.P.); (Y.L.)
| | - Chorlada Paiboonrungruang
- Cancer Research Program, Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, 700 George Street, Durham, NC 27707, USA; (X.C.); (Y.L.); (C.P.); (Y.L.)
| | - Yong Li
- Cancer Research Program, Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, 700 George Street, Durham, NC 27707, USA; (X.C.); (Y.L.); (C.P.); (Y.L.)
- Department of Thoracic Surgery, National Cancer Center, Cancer Hospital of Chinese Academy of Medical Sciences, 17 Panjiayuan Nanli Road, Beijing 100021, China
| | - Heiko Peters
- Newcastle University Biosciences Institute, Newcastle upon Tyne NE2 4BW, UK;
| | - Ralf Kist
- Newcastle University Biosciences Institute, Newcastle upon Tyne NE2 4BW, UK;
- School of Dental Sciences, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4BW, UK
| | - Zhaohui Xiong
- Cancer Research Program, Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, 700 George Street, Durham, NC 27707, USA; (X.C.); (Y.L.); (C.P.); (Y.L.)
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9
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Bhol CS, Mishra SR, Patil S, Sahu SK, Kirtana R, Manna S, Shanmugam MK, Sethi G, Patra SK, Bhutia SK. PAX9 reactivation by inhibiting DNA methyltransferase triggers antitumor effect in oral squamous cell carcinoma. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166428. [PMID: 35533906 DOI: 10.1016/j.bbadis.2022.166428] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/11/2022] [Accepted: 04/29/2022] [Indexed: 01/07/2023]
Abstract
Aberrant DNA hypermethylation is associated with oral carcinogenesis. Procaine, a local anesthetic, is a DNA methyltransferase (DNMT) inhibitor that activates anticancer mechanisms. However, its effect on silenced tumor suppressor gene (TSG) activation and its biological role in oral squamous cell carcinoma (OSCC) remain unknown. Here, we report procaine inhibited DNA methylation by suppressing DNMT activity and increased the expression of PAX9, a differentiation gene in OSCC cells. Interestingly, the reactivation of PAX9 by procaine found to inhibit cell growth and trigger apoptosis in OSCC in vitro and in vivo. Likely, the enhanced PAX9 expression after exposure to procaine controls stemness and differentiation through the autophagy-dependent pathway in OSCC cells. PAX9 inhibition abrogated procaine-induced apoptosis, autophagy, and inhibition of stemness. In OSCC cells, procaine improved anticancer drug sensitivity through PAX9, and its deficiency significantly blunted the anticancer drug sensitivity mediated by procaine. Additionally, NRF2 activation by procaine facilitated the antitumor response of PAX9, and pharmacological inhibition of NRF2 by ML385 reduced death and prevented the decrease in the orosphere-forming potential of OSCC cells. Furthermore, procaine promoted antitumor activity in FaDu xenografts in athymic nude mice, and immunohistochemistry data showed that PAX9 expression was significantly enhanced in the procaine group compared to the vehicle control. In conclusion, PAX9 reactivation in response to DNMT inhibition could trigger a potent antitumor mechanism to provide a new therapeutic strategy for OSCC.
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Affiliation(s)
- Chandra Sekhar Bhol
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Sundergarh 769008, Odisha, India
| | - Soumya Ranjan Mishra
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Sundergarh 769008, Odisha, India
| | - Shankargouda Patil
- Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | - Sunil Kumar Sahu
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Sundergarh 769008, Odisha, India
| | - R Kirtana
- Epigenetics and Cancer Research Laboratory, Department of Life Science, National Institute of Technology Rourkela, Sundergarh 769008, Odisha, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Department of Life Science, National Institute of Technology Rourkela, Sundergarh 769008, Odisha, India
| | - Muthu Kumaraswamy Shanmugam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Department of Life Science, National Institute of Technology Rourkela, Sundergarh 769008, Odisha, India
| | - Sujit Kumar Bhutia
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Sundergarh 769008, Odisha, India.
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Predisposition to atrioventricular septal defects may be caused by SOX7 variants that impair interaction with GATA4. Mol Genet Genomics 2022; 297:671-687. [PMID: 35260939 DOI: 10.1007/s00438-022-01859-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 01/12/2022] [Indexed: 10/18/2022]
Abstract
Atrioventricular septal defects (AVSD) are a complicated subtype of congenital heart defects for which the genetic basis is poorly understood. Many studies have demonstrated that the transcription factor SOX7 plays a pivotal role in cardiovascular development. However, whether SOX7 single nucleotide variants are involved in AVSD pathogenesis is unclear. To explore the potential pathogenic role of SOX7 variants, we recruited a total of 100 sporadic non-syndromic AVSD Chinese Han patients and screened SOX7 variants in the patient cohort by targeted sequencing. Functional assays were performed to evaluate pathogenicity of nonsynonymous variants of SOX7. We identified three rare SOX7 variants, c.40C > G, c.542G > A, and c.743C > T, in the patient cohort, all of which were found to be highly conserved in mammals. Compared to the wild type, these SOX7 variants had increased mRNA expression and decreased protein expression. In developing hearts, SOX7 and GATA4 were highly expressed in the region of atrioventricular cushions. Moreover, SOX7 overexpression promoted the expression of GATA4 in human umbilical vein endothelial cells. A chromatin immunoprecipitation assay revealed that SOX7 could directly bind to the GATA4 promoter and luciferase assays demonstrated that SOX7 activated the GATA4 promoter. The SOX7 variants had impaired transcriptional activity relative to wild-type SOX7. Furthermore, the SOX7 variants altered the ability of GATA4 to regulate its target genes. In conclusion, our findings showed that deleterious SOX7 variants potentially contribute to human AVSD by impairing its interaction with GATA4. This study provides novel insights into the etiology of AVSD and contributes new strategies to the prenatal diagnosis of AVSD.
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11
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Tsagiopoulou M, Pechlivanis N, Maniou M, Psomopoulos F. InterTADs: integration of multi-omics data on topologically associated domains, application to chronic lymphocytic leukemia. NAR Genom Bioinform 2022; 4:lqab121. [PMID: 35047813 PMCID: PMC8759567 DOI: 10.1093/nargab/lqab121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/21/2021] [Accepted: 12/13/2021] [Indexed: 11/25/2022] Open
Abstract
The integration of multi-omics data can greatly facilitate the advancement of research in Life Sciences by highlighting new interactions. However, there is currently no widespread procedure for meaningful multi-omics data integration. Here, we present a robust framework, called InterTADs, for integrating multi-omics data derived from the same sample, and considering the chromatin configuration of the genome, i.e. the topologically associating domains (TADs). Following the integration process, statistical analysis highlights the differences between the groups of interest (normal versus cancer cells) relating to (i) independent and (ii) integrated events through TADs. Finally, enrichment analysis using KEGG database, Gene Ontology and transcription factor binding sites and visualization approaches are available. We applied InterTADs to multi-omics datasets from 135 patients with chronic lymphocytic leukemia (CLL) and found that the integration through TADs resulted in a dramatic reduction of heterogeneity compared to individual events. Significant differences for individual events and on TADs level were identified between patients differing in the somatic hypermutation status of the clonotypic immunoglobulin genes, the core biological stratifier in CLL, attesting to the biomedical relevance of InterTADs. In conclusion, our approach suggests a new perspective towards analyzing multi-omics data, by offering reasonable execution time, biological benchmarking and potentially contributing to pattern discovery through TADs.
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12
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Nicolò A, Linder AT, Jumaa H, Maity PC. The Determinants of B Cell Receptor Signaling as Prototype Molecular Biomarkers of Leukemia. Front Oncol 2022; 11:771669. [PMID: 34993136 PMCID: PMC8724047 DOI: 10.3389/fonc.2021.771669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/02/2021] [Indexed: 12/20/2022] Open
Abstract
Advanced genome-wide association studies (GWAS) identified several transforming mutations in susceptible loci which are recognized as valuable prognostic markers in chronic lymphocytic leukemia (CLL) and B cell lymphoma (BCL). Alongside, robust genetic manipulations facilitated the generation of preclinical mouse models to validate mutations associated with poor prognosis and refractory B cell malignancies. Taken together, these studies identified new prognostic markers that could achieve characteristics of precision biomarkers for molecular diagnosis. On the contrary, the idea of augmented B cell antigen receptor (BCR) signaling as a transforming cue has somewhat receded despite the efficacy of Btk and Syk inhibitors. Recent studies from several research groups pointed out that acquired mutations in BCR components serve as faithful biomarkers, which become important for precision diagnostics and therapy, due to their relevant role in augmented BCR signaling and CLL pathogenesis. For example, we showed that expression of a single point mutated immunoglobulin light chain (LC) recombined through the variable gene segment IGLV3-21, named IGLV3-21R110, marks severe CLL cases. In this perspective, we summarize the molecular mechanisms fine-tuning B cell transformation, focusing on immunoglobulin point mutations and recurrent mutations in tumor suppressors. We present a stochastic model for gain-of-autonomous BCR signaling and subsequent neoplastic transformation. Of note, additional mutational analyses on immunoglobulin heavy chain (HC) derived from non-subset #2 CLL IGLV3-21R110 cases endorses our perspective. Altogether, we propose a model of malignant transformation in which the augmented BCR signaling creates a conducive platform for the appearance of transforming mutations.
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Affiliation(s)
| | | | - Hassan Jumaa
- Institute of Immunology, Ulm University, Ulm, Germany
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13
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Liu J, Wang YQ, Niu HB, Zhang CX. PAX9 functions as a tumor suppressor gene for cervical cancer via modulating cell proliferation and apoptosis. Kaohsiung J Med Sci 2021; 38:357-366. [PMID: 34931758 DOI: 10.1002/kjm2.12489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/27/2021] [Accepted: 11/16/2021] [Indexed: 01/16/2023] Open
Abstract
To investigate the effect of PAX9 on the progression of cervical cancer (CC). PAX9 expression was quantified in CC tissues and adjacent normal tissues, as well as human CC cell lines and human cervical epithelial cells (HCerEpiC). PAX9-overexpression lentiviral vectors were transfected into CC cell lines, followed by the measurement of proliferation and apoptosis and the quantification of apoptosis-related proteins. In vivo, mice were subcutaneously injected with CaSki cells transfected with PAX9-overexpression lentiviral vectors and control vectors. Then, the volume and weight of tumors were measured followed by hematoxylin and eosin (HE) staining, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining, and immunohistochemistry. PAX9 expression in the CC tissues was lower than that in the adjacent normal tissues, which was correlated with the FIGO stage, tumor size, infiltration depth, parametrium invasion, lympho-vascular space invasion tumor-positive lymph nodes, and prognosis. Furthermore, PAX9 in CC cell lines was also lower than in HCerEpiC. PAX9 inhibits the CC cell proliferation and promotes the apoptosis, with the up-regulations of caspase-3, poly(ADP-ribose) polymerase (PARP), and Bax and the down-regulation of Bcl-2. In vivo experiments demonstrated that in the PAX9 group, the tumor weight and volume were lower than those in the vector group accompanying the decreased Ki-67, cleaved-caspase-3, and Bax expressions and the increased TUNEL and Bcl-2 expression. PAX9 was lowly expressed in the CC tissues and associated with the clinicopathological characteristics and prognosis. PAX9 could inhibit proliferation of CC cell lines and promote the apoptosis, thus suppressing the tumor growth in vivo, indicating its potential therapeutic role for CC treatment.
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Affiliation(s)
- Jie Liu
- Department of Gynecology, Yantaishan Hospital, Yantai, China
| | - Ya-Qi Wang
- Department of Gynecology, Yantaishan Hospital, Yantai, China
| | - Hai-Bo Niu
- Department of Gynecology, Yantaishan Hospital, Yantai, China
| | - Chun-Xiao Zhang
- Department of Gynecology, Yantaishan Hospital, Yantai, China
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14
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Zhao Z, Szczepanski AP, Tsuboyama N, Abdala-Valencia H, Goo YA, Singer BD, Bartom ET, Yue F, Wang L. PAX9 Determines Epigenetic State Transition and Cell Fate in Cancer. Cancer Res 2021; 81:4696-4708. [PMID: 34341073 PMCID: PMC8448979 DOI: 10.1158/0008-5472.can-21-1114] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/01/2021] [Accepted: 07/28/2021] [Indexed: 01/07/2023]
Abstract
Abnormalities in genetic and epigenetic modifications can lead to drastic changes in gene expression profiles that are associated with various cancer types. Small cell lung cancer (SCLC) is an aggressive and deadly form of lung cancer with limited effective therapies currently available. By utilizing a genome-wide CRISPR-Cas9 dropout screen in SCLC cells, we identified paired box protein 9 (PAX9) as an essential factor that is overexpressed in human malignant SCLC tumor samples and is transcriptionally driven by the BAP1/ASXL3/BRD4 epigenetic axis. Genome-wide studies revealed that PAX9 occupies distal enhancer elements and represses gene expression by restricting enhancer activity. In multiple SCLC cell lines, genetic depletion of PAX9 led to significant induction of a primed-active enhancer transition, resulting in increased expression of a large number of neural differentiation and tumor-suppressive genes. Mechanistically, PAX9 interacted and cofunctioned with the nucleosome remodeling and deacetylase (NuRD) complex at enhancers to repress nearby gene expression, which was reversed by pharmacologic HDAC inhibition. Overall, this study provides mechanistic insight into the oncogenic function of the PAX9/NuRD complex epigenetic axis in human SCLC and suggests that reactivation of primed enhancers may have potential therapeutic efficacy in treating SCLC expressing high levels of PAX9. SIGNIFICANCE: A genome-wide screen in small cell lung cancer reveals PAX9/NuRD-mediated epigenetic enhancer silencing and tumor progression, supporting the development of novel personalized therapeutic approaches targeting the PAX9-regulated network.
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Affiliation(s)
- Zibo Zhao
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Aileen P. Szczepanski
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Natsumi Tsuboyama
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Young Ah Goo
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
| | - Benjamin D. Singer
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Elizabeth T. Bartom
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Lu Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Corresponding Author: Lu Wang, Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611. E-mail:
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15
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Hassan SS, Maqsood N, Wang Q, Tao S, Sadaf S. A panel of epigenetically dysregulated Wnt signaling pathway genes for non-invasive diagnosis of pediatric acute lymphoblastic leukemia. Cancer Biomark 2021; 32:459-470. [PMID: 34334378 DOI: 10.3233/cbm-200814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Genetic and epigenetic dysregulation of Wnt signaling pathway is widely linked up with abnormal proliferation and/or epithelial-to-mesenchymal transition, in different cancer cell types. OBJECTIVE In the present research, we have tested whether promoter DNA methylation of a set of Wnt/non-Wnt genes such as [cadherin-2 (CDH2)], "present in circulation", could serve as "bone-marrow biopsy surrogate" and help in diagnosing the status, sub-type or treatment outcome in pediatric acute lymphoblastic leukemia (ALL) patients. METHODS Promoter DNA methylation was quantified in the bisulfite modified blood from the pediatric ALL patients (n= 86) in comparison with age-matched cancer-free subjects (n= 28), using real-time methylation specific PCR followed by rigorous statistical validations. RESULTS The observed methylation index, sensitivity and specificity of selected molecular markers (viz., SALL1, WNT5α, LRP1b, CDH2) in patients' liquid-biopsies was clinically significant showing high positive correlation in the pre-B ALL cases (p-value < 0.001). A substantial drop in promoter methylation signal of the follow-up/post-treatment patients was also noted (p-value < 0.001), which suggested an impending role of minimally invasive liquid-biopsy approach in the diagnosis and/or therapeutic monitoring of pediatric leukemia. CONCLUSIONS Whilst the reported metadata provides useful insight into the plausible involvement of epigenetic glitches in leukemogensis, our findings strengthen the remarkable functional consequences of dysregulated Wnt signaling genes in the hematological malignancies besides offering a novel panel of epigenetic marks.
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Affiliation(s)
- Syeda Saliha Hassan
- Biopharmaceuticals and Biomarkers Discovery Lab., Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Neha Maqsood
- Biopharmaceuticals and Biomarkers Discovery Lab., Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Qingbing Wang
- Department of Interventional Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sun Tao
- Key Laboratory of Smart Drug Delivery (Ministry of Education), State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Pharmaceutics, School of Pharmacy, Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Saima Sadaf
- Biopharmaceuticals and Biomarkers Discovery Lab., Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
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16
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Bhol CS, Patil S, Sahu BB, Patra SK, Bhutia SK. The clinical significance and correlative signaling pathways of paired box gene 9 in development and carcinogenesis. Biochim Biophys Acta Rev Cancer 2021; 1876:188561. [PMID: 33965511 DOI: 10.1016/j.bbcan.2021.188561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/29/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022]
Abstract
Paired box 9 (PAX9) gene belongs to the PAX family, which encodes a family of metazoan transcription factors documented by a conserved DNA binding paired domain 128-amino-acids, critically essential for physiology and development. It is primarily expressed in embryonic tissues, such as the pharyngeal pouch endoderm, somites, neural crest-derived mesenchyme, and distal limb buds. PAX9 plays a vital role in craniofacial development by maintaining the odontogenic potential, mutations, and polymorphisms associated with the risk of tooth agenesis, hypodontia, and crown size in dentition. The loss-of-function of PAX9 in the murine model resulted in a short life span due to the arrest of cleft palate formation and skeletal abnormalities. According to recent studies, the PAX9 gene has a significant role in maintaining squamous cell differentiation, odontoblast differentiation of pluripotent stem cells, deregulation of which is associated with tumor initiation, and malignant transformation. Moreover, PAX9 contributes to promoter hypermethylation and alcohol- induced oro-esophageal squamous cell carcinoma mediated by downregulation of differentiation and apoptosis. Likewise, PAX9 activation is also reported to be associated with drug sensitivity. In summary, this current review aims to understand PAX9 function in the regulation of development, differentiation, and carcinogenesis, along with the underlying signaling pathways for possible cancer therapeutics.
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Affiliation(s)
- Chandra Sekhar Bhol
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela, 769008, Odisha, India
| | - Shankargouda Patil
- Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | - Binod Bihari Sahu
- Plant Immunity Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela, 769008, Odisha, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela, 769008, Odisha, India
| | - Sujit Kumar Bhutia
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela, 769008, Odisha, India.
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17
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Pak B, Schmitt CE, Oh S, Kim JD, Choi W, Han O, Kim M, Kim MJ, Ham HJ, Kim S, Huh TL, Kim JI, Jin SW. Pax9 is essential for granulopoiesis but dispensable for erythropoiesis in zebrafish. Biochem Biophys Res Commun 2020; 534:359-366. [PMID: 33256983 DOI: 10.1016/j.bbrc.2020.11.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/17/2020] [Indexed: 11/26/2022]
Abstract
Paired Box (Pax) gene family, a group of transcription regulators have been implicated in diverse physiological processes. However, their role during hematopoiesis which generate a plethora of blood cells remains largely unknown. Using a previously reported single cell transcriptomics data, we analyzed the expression of individual Pax family members in hematopoietic cells in zebrafish. We have identified that Pax9, which is an essential regulator for odontogenesis and palatogenesis, is selectively localized within a single cluster of the hematopoietic lineage. To further analyze the function of Pax9 in hematopoiesis, we generated two independent pax9 knock-out mutants using the CRISPR-Cas9 technique. We found that Pax9 appears to be an essential regulator for granulopoiesis but dispensable for erythropoiesis during development, as lack of pax9 selectively decreased the number of neutrophils with a concomitant decrease in the expression level of neutrophil markers. In addition, embryos, where pax9 was functionally disrupted by injecting morpholinos, failed to increase the number of neutrophils in response to pathogenic bacteria, suggesting that Pax9 is not only essential for developmental granulopoiesis but also emergency granulopoiesis. Due to the inability to initiate emergency granulopoiesis, innate immune responses were severely compromised in pax9 morpholino-mediated embryos, increasing their susceptibility and mortality. Taken together, our data indicate that Pax9 is essential for granulopoiesis and promotes innate immunity in zebrafish larvae.
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Affiliation(s)
- Boryeong Pak
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Chris E Schmitt
- Yale Cardiovascular Research Center and Section of Cardiovascular Medicine, Dept. of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06511, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Sera Oh
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Jun-Dae Kim
- Yale Cardiovascular Research Center and Section of Cardiovascular Medicine, Dept. of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06511, USA; Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, TX, USA
| | - Woosoung Choi
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Orjin Han
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Minjung Kim
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Myoung-Jin Kim
- School of Life Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Hyung-Jin Ham
- School of Life Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Shanghyeon Kim
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Tae-Lin Huh
- School of Life Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Il Kim
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Suk-Won Jin
- Cell Logistics Research Center and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea; Yale Cardiovascular Research Center and Section of Cardiovascular Medicine, Dept. of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06511, USA.
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18
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Kaur G, Ruhela V, Rani L, Gupta A, Sriram K, Gogia A, Sharma A, Kumar L, Gupta R. RNA-Seq profiling of deregulated miRs in CLL and their impact on clinical outcome. Blood Cancer J 2020; 10:6. [PMID: 31932582 PMCID: PMC6957689 DOI: 10.1038/s41408-019-0272-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/29/2019] [Accepted: 12/03/2019] [Indexed: 12/13/2022] Open
Abstract
Abnormal expression patterns of regulatory small non-coding RNA (sncRNA) molecules such as microRNAs (miRs), piwi-interacting RNAs (piRNAs), and small nucleolar RNAs (snoRNAs) play an important role in the development and progression of cancer. Identification of clinically relevant sncRNA signatures could, therefore, be of tremendous translational value. In the present study, genome-wide small RNA sequencing identified a unique pattern of differential regulation of eight miRs in Chronic Lymphocytic Leukemia (CLL). Among these, three were up-regulated (miR-1295a, miR-155, miR-4524a) and five were down-regulated (miR-30a, miR-423, miR-486*, let-7e, and miR-744) in CLL. Altered expression of all these eight differentially expressed miRs (DEMs) was validated by RQ-PCR. Besides, seven novel sequences identified to have elevated expression levels in CLL turned out to be transfer RNA (tRNA)/piRNAs (piRNA-30799, piRNA-36225)/snoRNA (SNORD43) related. Multivariate analysis showed that miR-4524a (HR: 1.916, 95% CI: 1.080–3.4, p value: 0.026) and miR-744 (HR: 0.415, 95% CI: 0.224–0.769, p value: 0.005) were significantly associated with risk and time to first treatment. Further investigations could help establish the scope of integration of these DEM markers into risk stratification designs and prognostication approaches for CLL.
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Affiliation(s)
- Gurvinder Kaur
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Ruhela
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-D), Delhi, India
| | - Lata Rani
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Anubha Gupta
- SBILab, Department of Electronics and Communication Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-D), Delhi, India.
| | - Krishnamachari Sriram
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-D), Delhi, India
| | - Ajay Gogia
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Atul Sharma
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Lalit Kumar
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences, New Delhi, India.
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19
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Perrard J, Morel A, Meznad K, Paget-Bailly P, Dalstein V, Guenat D, Mourareau C, Clavel C, Fauconnet S, Baguet A, Mougin C, Pretet JL. DNA demethylation agent 5azadC downregulates HPV16 E6 expression in cervical cancer cell lines independently of TBX2 expression. Oncol Lett 2019; 19:1074-1081. [PMID: 31897221 DOI: 10.3892/ol.2019.11158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 09/09/2019] [Indexed: 12/18/2022] Open
Abstract
HPV16 is the most carcinogenic human papillomavirus and causes >50% of cervical cancers, the majority of anal cancers and 30% of oropharyngeal squamous cell carcinomas. HPV carcinogenesis relies on the continuous expression of the two main viral oncoproteins E6 and E7 that target >150 cellular proteins. Among them, epigenetic modifiers, including DNA Methyl Transferases (DNMT), are dysregulated, promoting an aberrant methylation pattern in HPV-positive cancer cells. It has been previously reported that the treatment of HPV-positive cervical cancer cells with DNMT inhibitor 5-aza-2'-deoxycytidine (5azadC) caused the downregulation of E6 expression due to mRNA destabilization that was mediated by miR-375. Recently, the T-box transcription factor 2 (TBX2) has been demonstrated to repress HPV LCR activity. In the current study, the role of TBX2 in E6 repression was investigated in HPV16 cervical cancer cell lines following 5azadC treatment. A decrease of E6 expression was accompanied by p53 and p21 restoration. While TBX2 mRNA was upregulated in 5azadC-treated SiHa and Ca Ski cells, TBX2 protein was not detectable. Furthermore, the overexpression of TBX2 protein in cervical cancer cells did not allow the repression of E6 expression. The TBX2 transcription factor is therefore unlikely to be associated with the repression of E6 following 5azadC treatment of SiHa and Ca Ski cells.
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Affiliation(s)
- Jerome Perrard
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France
| | - Adrien Morel
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 112041, Colombia
| | - Koceila Meznad
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France
| | - Philippe Paget-Bailly
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France
| | - Veronique Dalstein
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche-S 1250 Pathologies Pulmonaires et Plasticité Cellulaire, Université de Reims Champagne-Ardenne, Faculté de Médecine, 51000 Reims, France.,Centre Hospitalier Universitaire Reims, Laboratoire Biopathologie, 51000 Reims, France
| | - David Guenat
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France.,Centre National de Référence Papillomavirus, CHU Besançon, Boulevard Alexandre Fleming, 25000 Besançon, France
| | - Celine Mourareau
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche-S 1250 Pathologies Pulmonaires et Plasticité Cellulaire, Université de Reims Champagne-Ardenne, Faculté de Médecine, 51000 Reims, France.,Centre Hospitalier Universitaire Reims, Laboratoire Biopathologie, 51000 Reims, France
| | - Christine Clavel
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche-S 1250 Pathologies Pulmonaires et Plasticité Cellulaire, Université de Reims Champagne-Ardenne, Faculté de Médecine, 51000 Reims, France.,Centre Hospitalier Universitaire Reims, Laboratoire Biopathologie, 51000 Reims, France
| | - Sylvie Fauconnet
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France
| | - Aurelie Baguet
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France
| | - Christiane Mougin
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France.,Centre National de Référence Papillomavirus, CHU Besançon, Boulevard Alexandre Fleming, 25000 Besançon, France
| | - Jean-Luc Pretet
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France.,Centre National de Référence Papillomavirus, CHU Besançon, Boulevard Alexandre Fleming, 25000 Besançon, France
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20
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Xanthopoulos C, Kostareli E. Advances in Epigenetics and Epigenomics in Chronic Lymphocytic Leukemia. CURRENT GENETIC MEDICINE REPORTS 2019. [DOI: 10.1007/s40142-019-00178-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Abstract
Purpose of Review
The development and progression of chronic lymphocytic leukemia (CLL), a highly heterogenous B cell malignancy, are influenced by both genetic and environmental factors. Environmental factors, including pharmacological interventions, can affect the epigenetic landscape of CLL and thereby determine the CLL phenotype, clonal evolution, and clinical outcome. In this review, we critically present the latest advances in the field of CLL epigenomics/epigenetics in order to provide a systematic overview of to-date achievements and highlight the potential of epigenomics approaches in light of novel treatment therapies.
Recent Findings
Recent technological advances have enabled broad and precise mapping of the CLL epigenome. The identification of CLL-specific DNA methylation patterns has allowed for accurate CLL subtype definition, a better understanding of clonal origin and evolution, and the discovery of reliable biomarkers. More recently, studies have started to unravel the prognostic, predictive, and therapeutic potential of mapping chromatin dynamics and histone modifications in CLL. Finally, analysis of non-coding RNA expression has indicated their contribution to disease pathogenesis and helped to define prognostic subsets in CLL.
Summary
Overall, the potential of CLL epigenomics for predicting treatment response and resistance is mounting, especially with the advent of novel targeted CLL therapies.
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21
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Novel role of sex-determining region Y-box 7 (SOX7) in tumor biology and cardiovascular developmental biology. Semin Cancer Biol 2019; 67:49-56. [PMID: 31473269 DOI: 10.1016/j.semcancer.2019.08.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 08/19/2019] [Accepted: 08/28/2019] [Indexed: 02/06/2023]
Abstract
The sex-determining region Y-box 7 (Sox7) is an important member of the SOX F family, which is characterized by a high-mobility-group DNA-binding domain. Previous studies have demonstrated the role of SOX7 in cardiovascular development. SOX7 expression could be detected in normal adult tissues. Furthermore, the expression levels of SOX7 were different in different tumors. Most studies showed the downregulation of SOX7 in tumors, while some studies reported its upregulation in tumors. In this review, we first summarized the upstream regulators (including transcription factors, microRNAs (miRNAs), long noncoding RNAs (lncRNAs) and some exogenous regulators) and downstream molecules (including factors in the Wnt/β-catenin signaling pathway and some other signaling pathways) of SOX7. Then, the roles of SOX7 in multiple tumors were presented. Finally, the significance of divergent SOX7 expression during cardiovascular development was briefly discussed. The information compiled in this study characterized SOX7 during tumorigenesis and cardiovascular development, which should facilitate the design of future research and promote SOX7 as a therapeutic target.
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22
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Yang Q, Wu F, Wang F, Cai K, Zhang Y, Sun Q, Zhao X, Gui Y, Li Q. Impact of DNA methyltransferase inhibitor 5-azacytidine on cardiac development of zebrafish in vivo and cardiomyocyte proliferation, apoptosis, and the homeostasis of gene expression in vitro. J Cell Biochem 2019; 120:17459-17471. [PMID: 31271227 DOI: 10.1002/jcb.29010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/15/2022]
Abstract
Cardiac development is a peculiar process involving coordinated cellular differentiation, migration, proliferation, and apoptosis. DNA methylation plays a key role in genomic stability, tissue-specific gene expression, cell proliferation, and apoptosis. Hypomethylation in the global genome has been reported in cardiovascular diseases. However, little is known about the impact and specific mechanism of global hypomethylation on cardiomyocytes. In the present study, we explored the impact of DNA methyltransferase inhibitors 5-azacytidine on cardiac development. In vivo experiment showed that hypomethylation of zebrafish embryos with 5-azacytidine exposure significantly reduced survival, induced malformations, and delayed general development process. Furthermore, zebrafish embryos injected with 5-azacytidine developed pericardial edema, ventricular volume reduction, looping deformity, and reduction in heart rate and ventricular shortening fraction. Cardiomyocytes treated with 5-azacytidine in vitro decreased proliferation and induced apoptosis in a concentration-dependent manner. Furthermore, 5-azacytidine treatment in cardiomyocytes resulted in 20 downregulated genes expression and two upregulated genes expression in 45 candidate genes, which indicated that DNA methylation functions as a bidirectional modulator in regulating gene expression. In conclusion, these results show the regulative effects of the epigenetic modifier 5-azacytidine in cardiac development of zebrafish embryos in vivo and cardiomyocyte proliferation and apoptosis and the homeostasis of gene expression in vitro, which offer a novel understanding of aberrant DNA methylation in the etiology of cardiovascular disease.
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Affiliation(s)
- Qian Yang
- Shanghai Key Laboratory of Birth Defect, Translational Medical Center for Development and Disease, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Fang Wu
- Shanghai Key Laboratory of Birth Defect, Translational Medical Center for Development and Disease, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Feng Wang
- Shanghai Key Laboratory of Birth Defect, Translational Medical Center for Development and Disease, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Ke Cai
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Yawen Zhang
- Shanghai Key Laboratory of Birth Defect, Translational Medical Center for Development and Disease, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Quanya Sun
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaolong Zhao
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yonghao Gui
- Shanghai Key Laboratory of Birth Defect, Translational Medical Center for Development and Disease, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Qiang Li
- Shanghai Key Laboratory of Birth Defect, Translational Medical Center for Development and Disease, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
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23
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Bai G, Song J, Yuan Y, Chen Z, Tian Y, Yin X, Niu Y, Liu J. Systematic analysis of differentially methylated expressed genes and site-specific methylation as potential prognostic markers in head and neck cancer. J Cell Physiol 2019; 234:22687-22702. [PMID: 31131446 PMCID: PMC6772109 DOI: 10.1002/jcp.28835] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 04/27/2019] [Accepted: 04/30/2019] [Indexed: 12/31/2022]
Abstract
Head and neck cancer (HNC) remains one of the most malignant tumors with a significantly high mortality. DNA methylation exerts a vital role in the prognosis of HNC. In this study, we try to screen abnormal differential methylation genes (DMGs) and pathways in Head-Neck Squamous Cell Carcinoma via integral bioinformatics analysis. Data of gene expression microarrays and gene methylation microarrays were obtained from the Cancer Genome Atlas database. Aberrant DMGs were identified by the R Limma package. We conducted the Cox regression analysis to select the prognostic aberrant DMGs and site-specific methylation. Five aberrant DMGs were recognized that significantly correlated with overall survival. The prognostic model was constructed based on five DMGs (PAX9, STK33, GPR150, INSM1, and EPHX3). The five DMG models acted as prognostic biomarkers for HNC. The area under the curve based on the five DMGs predicting 5-year survival is 0.665. Moreover, the correlation between the DMGs/site-specific methylation and gene expression was also explored. The findings demonstrated that the five DMGs can be used as independent prognostic biomarkers for predicting the prognosis of patients with HNC. Our study might lay the groundwork for further mechanism exploration in HNC and may help identify diagnostic biomarkers for early stage HNC.
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Affiliation(s)
- Guohui Bai
- Zunyi Medical University, Zunyi, Guizhou, China.,Special Key Laboratory of Oral Diseases Research, Stomatological Hospital Affiliated to Zunyi Medical University, Guizhou, China
| | - Jukun Song
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guizhou, China
| | - Yiwen Yuan
- Guizhou Medical Univerisity, Guizhou, China
| | - Zhu Chen
- Guiyang Hospital of Stomatology, Guizhou, China
| | - Yuan Tian
- Stomatology Colledge Affiliated to Zunyi Medical University, Zunyi, Guizhou, China
| | - Xinhai Yin
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guizhou, China
| | - Yuming Niu
- Department of Stomatology and Center for Evidence-Based Medicine and Clinical Research, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jianguo Liu
- Zunyi Medical University, Zunyi, Guizhou, China.,Special Key Laboratory of Oral Diseases Research, Stomatological Hospital Affiliated to Zunyi Medical University, Guizhou, China
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24
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Haider Z, Larsson P, Landfors M, Köhn L, Schmiegelow K, Flaegstad T, Kanerva J, Heyman M, Hultdin M, Degerman S. An integrated transcriptome analysis in T-cell acute lymphoblastic leukemia links DNA methylation subgroups to dysregulated TAL1 and ANTP homeobox gene expression. Cancer Med 2018; 8:311-324. [PMID: 30575306 PMCID: PMC6346238 DOI: 10.1002/cam4.1917] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/12/2018] [Accepted: 11/19/2018] [Indexed: 01/01/2023] Open
Abstract
Classification of pediatric T‐cell acute lymphoblastic leukemia (T‐ALL) patients into CIMP (CpG Island Methylator Phenotype) subgroups has the potential to improve current risk stratification. To investigate the biology behind these CIMP subgroups, diagnostic samples from Nordic pediatric T‐ALL patients were characterized by genome‐wide methylation arrays, followed by targeted exome sequencing, telomere length measurement, and RNA sequencing. The CIMP subgroups did not correlate significantly with variations in epigenetic regulators. However, the CIMP+ subgroup, associated with better prognosis, showed indicators of longer replicative history, including shorter telomere length (P = 0.015) and older epigenetic (P < 0.001) and mitotic age (P < 0.001). Moreover, the CIMP+ subgroup had significantly higher expression of ANTP homeobox oncogenes, namely TLX3, HOXA9, HOXA10, and NKX2‐1, and novel genes in T‐ALL biology including PLCB4, PLXND1, and MYO18B. The CIMP− subgroup, with worse prognosis, was associated with higher expression of TAL1 along with frequent STIL‐TAL1 fusions (2/40 in CIMP+ vs 11/24 in CIMP−), as well as stronger expression of BEX1. Altogether, our findings suggest different routes for leukemogenic transformation in the T‐ALL CIMP subgroups, indicated by different replicative histories and distinct methylomic and transcriptomic profiles. These novel findings can lead to new therapeutic strategies.
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Affiliation(s)
- Zahra Haider
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Pär Larsson
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Mattias Landfors
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Linda Köhn
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Trond Flaegstad
- Department of Pediatrics, University of Tromsø and University Hospital of North Norway, Tromsø, Norway
| | - Jukka Kanerva
- Children's Hospital, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Mats Heyman
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Hultdin
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Sofie Degerman
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
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25
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Wen Y, Li P, Hao J, Duan C, Han J, He A, Du Y, Liu L, Liang X, Zhang F, Guo X. Integrating genome-wide DNA methylation and mRNA expression profiles identified different molecular features between Kashin-Beck disease and primary osteoarthritis. Arthritis Res Ther 2018. [PMID: 29514696 PMCID: PMC5842623 DOI: 10.1186/s13075-018-1531-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background Kashin-Beck disease (KBD) is an endemic osteochondropathy of unknown etiology. Osteoarthritis (OA) is a form of degenerative joint disease sharing similar clinical manifestations and pathological changes to articular cartilage with KBD. Methods A genome-wide DNA methylation profile of articular cartilage from five KBD patients and five OA patients was first performed using the Illumina Infinium HumanMethylation450 BeadChip. Together with a previous gene expression profiling dataset comparing KBD cartilage with OA cartilage, an integrative pathway enrichment analysis of the genome-wide DNA methylation and the mRNA expression profiles conducted in articular cartilage was performed by InCroMAP software. Results We identified 241 common genes altered in both the DNA methylation profile and the mRNA expression profile of articular cartilage of KBD versus OA, including CHST13 (NM_152889, fold-change = 0.5979, Pmethy = 0.0430), TGFBR1 (NM_004612, fold-change = 2.077, Pmethy = 0.0430), TGFBR2 (NM_001024847, fold-change = 1.543, Pmethy = 0.037), TGFBR3 (NM_001276, fold-change = 0.4515, Pmethy = 6.04 × 10−4), and ADAM12 (NM_021641, fold-change = 1.9768, Pmethy = 0.0178). Integrative pathway enrichment analysis identified 19 significant KEGG pathways, including mTOR signaling (P = 0.0301), glycosaminoglycan biosynthesis-chondroitin sulfate/dermatan sulfate (P = 0.0391), glycosaminoglycan biosynthesis-keratan sulfate (P = 0.0278), and PI3K-Akt signaling (P = 0.0243). Conclusion This study identified different molecular features between Kashin-Beck disease and primary osteoarthritis and provided novel clues for clarifying the pathogenetic differences between KBD and OA. Electronic supplementary material The online version of this article (10.1186/s13075-018-1531-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Ping Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Jingcan Hao
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China.,The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Chen Duan
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Jing Han
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Awen He
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Yanan Du
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Xiao Liang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China.
| | - Xiong Guo
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China.
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