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Abstract
Thymocyte selection-associated high mobility group box protein (TOX) is expressed differently at all T lymphocytes development stages. Owing to more advanced scientific and technological means, including single-cell sequencing technology, heterogeneity of T lymphocytes and TOX has gradually been revealed. Further exploration of such heterogeneity will help us comprehend the developmental stage and functional characteristics of T lymphocytes in greater detail. Emerging evidence supports its regulation not only in exhausting, but also in activating T lymphocytes, thereby verifying TOX heterogeneity. TOX can be used not only as a latent intervention target for tumor diseases and chronic infections, and a therapeutic strategy for autoimmune diseases, but also as a critical factor predicting the drug response and overall survival of patients with malignant tumors.
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Tu CL, Chang W, Sosa JA, Koh J. Digital spatial profiling of human parathyroid tumors reveals cellular and molecular alterations linked to vitamin D deficiency. PNAS Nexus 2023; 2:pgad073. [PMID: 36992820 PMCID: PMC10042281 DOI: 10.1093/pnasnexus/pgad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/12/2023]
Abstract
Primary hyperparathyroidism (PHPT) is a common endocrine neoplastic disorder characterized by disrupted calcium homeostasis secondary to inappropriately elevated parathyroid hormone (PTH) secretion. Low levels of serum 25-hydroxyvitamin D (25OHD) are significantly more prevalent in PHPT patients than in the general population (1-3), but the basis for this association remains unclear. We employed a spatially defined in situ whole-transcriptomics and selective proteomics profiling approach to compare gene expression patterns and cellular composition in parathyroid adenomas from vitamin D-deficient or vitamin D-replete PHPT patients. A cross-sectional panel of eucalcemic cadaveric donor parathyroid glands was examined in parallel as normal tissue controls. Here, we report that parathyroid tumors from vitamin D-deficient PHPT patients (Def-Ts) are intrinsically different from those of vitamin D-replete patients (Rep-Ts) of similar age and preoperative clinical presentation. The parathyroid oxyphil cell content is markedly higher in Def-Ts (47.8%) relative to Rep-Ts (17.8%) and normal donor glands (7.7%). Vitamin D deficiency is associated with increased expression of electron transport chain and oxidative phosphorylation pathway components. Parathyroid oxyphil cells, while morphologically distinct, are comparable to chief cells at the transcriptional level, and vitamin D deficiency affects the transcriptional profiles of both cell types in a similar manner. These data suggest that oxyphil cells are derived from chief cells and imply that their increased abundance may be induced by low vitamin D status. Gene set enrichment analysis reveals that pathways altered in Def-Ts are distinct from Rep-Ts, suggesting alternative tumor etiologies in these groups. Increased oxyphil content may thus be a morphological indicator of tumor-predisposing cellular stress.
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Affiliation(s)
- Chia-Ling Tu
- Endocrine Research Unit, Department of Medicine, San Francisco Department of Veterans Affairs Medical Center, University of California San Francisco, San Francisco, CA 94158
| | - Wenhan Chang
- Endocrine Research Unit, Department of Medicine, San Francisco Department of Veterans Affairs Medical Center, University of California San Francisco, San Francisco, CA 94158
| | - Julie A Sosa
- Endocrine Neoplasia Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA 94143
| | - James Koh
- Endocrine Neoplasia Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA 94143
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3
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Zapata-García JA, Riveros-Magaña AR, Ortiz-Lazareno PC, Hernández-Flores G, Jave-Suárez LF, Aguilar-Lemarroy A. Comparative Genomic Hybridization and Transcriptome Sequencing Reveal Genes with Gain in Acute Lymphoblastic Leukemia: JUP Expression Emerges as a Survival-Related Gene. Diagnostics (Basel) 2022; 12:diagnostics12112788. [PMID: 36428851 PMCID: PMC9689318 DOI: 10.3390/diagnostics12112788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) in children or adults is characterized by structural and numeric aberrations in chromosomes; these anomalies strongly correlate with prognosis and clinical outcome. Therefore, this work aimed to identify the genes present in chromosomal gain regions found more frequently in patients with acute lymphoblastic leukemia (ALL) and ALL-derived cell lines using comparative genomic hybridization (CGH). In addition, validation of the genes found in these regions was performed utilizing RNAseq from JURKAT, CEM, and SUP-B15 cell lines, as well as expression microarrays derived from a MILE study. Chromosomes with common gain zones that were maintained in six or more samples were 14, 17, and 22, in which a total of 22 genes were identified. From them, NT5C3B, CNP, ACLY, and GNB1L maintained overexpression at the mRNA level in the cell lines and in patients with ALL. It is noteworthy that SALL2 showed very high expression in T-ALL, while JUP was highly expressed in B-ALL lineages. Interestingly, the latter correlated with worse survival in patients. This provided evidence that the measurement of these genes has high potential for clinical utility; however, their expressions should first be evaluated with a sensitive test in a more significant number of patients.
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Affiliation(s)
- Jessica Alejandra Zapata-García
- Programa de Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara C.P. 44340, Mexico
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Alma Rocío Riveros-Magaña
- Centro Universitario del Sur, Universidad de Guadalajara, Ciudad Guzmán C.P. 49000, Mexico
- Hospital General Zona 9, Ciudad Guzmán C.P. 49000, Mexico
| | - Pablo Cesar Ortiz-Lazareno
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Georgina Hernández-Flores
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Luis Felipe Jave-Suárez
- Programa de Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara C.P. 44340, Mexico
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Adriana Aguilar-Lemarroy
- Programa de Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara C.P. 44340, Mexico
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
- Correspondence: ; Tel.: +52-331-520-7625
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Han J, Wan M, Ma Z, He P. The TOX subfamily: all-round players in the immune system. Clin Exp Immunol 2022; 208:268-280. [PMID: 35485425 PMCID: PMC9226143 DOI: 10.1093/cei/uxac037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/29/2022] [Accepted: 04/26/2022] [Indexed: 12/14/2022] Open
Abstract
The thymocyte selection-related HMG box protein (TOX) subfamily comprises evolutionarily conserved DNA-binding proteins, and is expressed in certain immune cell subsets and plays key roles in the development of CD4+ T cells, innate lymphoid cells (ILCs), T follicular helper (Tfh) cells, and in CD8+ T-cell exhaustion. Although its roles in CD4+ T and natural killer (NK) cells have been extensively studied, recent findings have demonstrated previously unknown roles for TOX in the development of ILCs, Tfh cells, as well as CD8+ T-cell exhaustion; however, the molecular mechanism underlying TOX regulation of these immune cells remains to be elucidated. In this review, we discuss recent studies on the influence of TOX on the development of various immune cells and CD8+ T-cell exhaustion and the roles of specific TOX family members in the immune system. Moreover, this review suggests candidate regulatory targets for cell therapy and immunotherapies.
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Affiliation(s)
- Jiawen Han
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Minjie Wan
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China.,Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhanchuan Ma
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Ping He
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, Jilin, China
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Joshi S, Garlapati C, Aneja R. Epigenetic Determinants of Racial Disparity in Breast Cancer: Looking beyond Genetic Alterations. Cancers (Basel) 2022; 14:cancers14081903. [PMID: 35454810 PMCID: PMC9025441 DOI: 10.3390/cancers14081903] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary A substantial disparity in breast cancer incidence and mortality exists between African American (AA) and European American (EA) women. However, the basis for these disparities is poorly understood. In this article, we describe that gene–environment interactions mediated through epigenetic modifications may play a significant role in racial disparities in BC incidence and outcomes. Our in silico analyses and an in-depth literature survey suggest that there exists a significant difference in epigenetic patterns between AA and EA women with breast cancer. Herein, we describe the environmental factors that contribute to these epigenetic changes, which may underlie the disparate racial burden in patients with breast cancer. We suggest that AA women with higher basal epigenetic changes, may have higher pre-disposition to cancer onset, and an aggressive disease course. Pre-existing racial differences in epigenetic profiles of breast tissues raises the possibility of examining these profiles for early diagnosis. Abstract Breast cancer (BC) is the most commonly diagnosed cancer in women. Despite advancements in BC screening, prevention, and treatment, BC incidence and mortality remain high among African American (AA) women. Compared with European American (EA) women, AA women tend to be diagnosed with more advanced and aggressive tumors and exhibit worse survival outcomes. Most studies investigating the determinants of racial disparities in BC have focused on genetic factors associated with African ancestry. However, various environmental and social stressors over an individual’s life course can also shape racial stratification in BC. These social and environmental exposures result in long-term changes in gene expression mediated by epigenetic mechanisms. Epigenetics is often portrayed as an intersection of socially patterned stress and genetic expression. The enduring nature of epigenetic changes makes them suitable for studying the effects of different environmental exposures over an individual’s life course on gene expression. The role of differential social and environmental exposures in racial disparities in BC suggests varied epigenetic profiles or signatures associated with specific BC subtypes in AA and EA women. These epigenetic profiles in EA and AA women could be used as biomarkers for early BC diagnosis and disease prognosis and may prove valuable for the development of targeted therapies for BC. This review article discusses the current state of knowledge regarding epigenetic differences between AA and EA women with BC. We also discuss the role of socio-environmental factors, including psychosocial stress, environmental toxicants, and dietary factors, in delineating the different epigenetic profiles in AA and EA patients with BC.
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Affiliation(s)
- Shriya Joshi
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (S.J.); (C.G.)
| | | | - Ritu Aneja
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (S.J.); (C.G.)
- Department of Clinical and Diagnostics Sciences, School of Health Professions, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Correspondence: or
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Yang W, Wu W, Liang H, Chen J, Dong X. TOX3 regulates the proliferation and apoptosis of colorectal cancer by downregulating RhoB via the activation of MAPK pathway. Cell Biol Int 2022; 46:1074-1088. [PMID: 35347804 DOI: 10.1002/cbin.11802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/30/2022] [Accepted: 02/12/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Wei Yang
- Department of General Surgery, The first affiliated hospital of Soochow UniversitySuzhou215006P.R.China
| | - Wei Wu
- Department of General Surgery, The affiliated hospital of Yangzhou UniversityYangzhou225000P.R.China
| | - Hailiang Liang
- Department of General Surgery, The affiliated hospital of Yangzhou UniversityYangzhou225000P.R.China
| | - Jiejing Chen
- Department of General Surgery, The affiliated hospital of Yangzhou UniversityYangzhou225000P.R.China
| | - Xiaoqiang Dong
- Department of General Surgery, The first affiliated hospital of Soochow UniversitySuzhou215006P.R.China
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Avella Patino DM, Radhakrishnan V, Suvilesh KN, Manjunath Y, Li G, Kimchi ET, Staveley-O'Carroll KF, Warren WC, Kaifi JT, Mitchem JB. Epigenetic Regulation of Cancer Immune Cells. Semin Cancer Biol 2021:S1044-579X(21)00192-9. [PMID: 34182142 DOI: 10.1016/j.semcancer.2021.06.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 05/06/2021] [Accepted: 06/23/2021] [Indexed: 12/17/2022]
Abstract
The epigenetic regulation of immune response involves reversible and heritable changes that do not alter the DNA sequence. Though there have been extensive studies accomplished relating to epigenetic changes in cancer cells, recent focus has been shifted on epigenetic-mediated changes in the immune cells including T cells, Macrophages, Natural Killer cells and anti-tumor immune responses. This review compiles the most relevant and recent literature related to the role of epigenetic mechanisms including DNA methylation and histone modifications in immune cells of wide range of cancers. We also include recent research with respect to role of the most relevant transcription factors that epigenetically control the anti-tumor immune response. Finally, a statement of future direction that promises to look forward for strategies to improve immunotherapy in cancer.
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Ghafarpour V, Khansari M, Banaei-Moghaddam AM, Najafi A, Masoudi-Nejad A. DNA methylation association with stage progression of head and neck squamous cell carcinoma. Comput Biol Med 2021; 134:104473. [PMID: 34034219 DOI: 10.1016/j.compbiomed.2021.104473] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/27/2021] [Accepted: 05/02/2021] [Indexed: 01/13/2023]
Abstract
Head and Neck Squamous Cell Carcinoma (HNSCC) is the sixth most common cancer worldwide, which accounts for approximately 6% of all cases and is responsible for an estimated 2% of all cancer deaths. Despite progress in the treatment of squamous cell carcinomas, survival rates remain low. It is a fact that epigenetic modifications have numerous associations with biological processes and complex diseases such as cancer. Hence, a more systematic approach is needed to provide potential screening targets and have an effective therapy method. This study developed a workflow to analyze HM450 methylation arrays with mRNA expression profiles that identified novel signatures of epigenetic regulators for tumor progression. We identified differentially expressed genes and differentially methylated regions and the correlation between associated genes to identify epigenetic modifications underlying regulation roles. We have taken the differentiation direction of expressions into account during the integration of gene expression and DNA methylation modification to detect epigenetic regulators of core genes of tumor-stage progression. Enrichment analysis of selected key genes provides better insight into their functionality. Thus, we have investigated gene copy number alteration and mutations to filter differentially expressed genes, including some members of the fibroblast growth factor family and cyclin-dependent kinase inhibitor family with other potential known regulators. Our analysis has revealed the list of 61 commercial methylation probes positively correlated with 31 differentially expressed genes, which can be associated with HNSC metastasis stages. Most of these genes have already reported potential epigenetic regulators, and their role in cancer progression was studied. We suggest these selected probes of DNA methylation as potential targets of the epigenetic regulators in revealed genes that have displayed significant genetic and epigenetic modification behavior during cancer stage progression and tumor metastasis.
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Affiliation(s)
- Vahid Ghafarpour
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mohammad Khansari
- Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Ali M Banaei-Moghaddam
- Laboratory of Genomics and Epigenomics (LGE), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. http://lbb.ut.ac.ir/
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9
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Mijnheer G, Lutter L, Mokry M, van der Wal M, Scholman R, Fleskens V, Pandit A, Tao W, Wekking M, Vervoort S, Roberts C, Petrelli A, Peeters JGC, Knijff M, de Roock S, Vastert S, Taams LS, van Loosdregt J, van Wijk F. Conserved human effector Treg cell transcriptomic and epigenetic signature in arthritic joint inflammation. Nat Commun 2021; 12:2710. [PMID: 33976194 PMCID: PMC8113485 DOI: 10.1038/s41467-021-22975-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 04/08/2021] [Indexed: 02/07/2023] Open
Abstract
Treg cells are critical regulators of immune homeostasis, and environment-driven Treg cell differentiation into effector (e)Treg cells is crucial for optimal functioning. However, human Treg cell programming in inflammation is unclear. Here, we combine transcriptional and epigenetic profiling to identify a human eTreg cell signature. Inflammation-derived functional Treg cells have a transcriptional profile characterized by upregulation of both a core Treg cell (FOXP3, CTLA4, TIGIT) and effector program (GITR, BLIMP-1, BATF). We identify a specific human eTreg cell signature that includes the vitamin D receptor (VDR) as a predicted regulator in eTreg cell differentiation. H3K27ac/H3K4me1 occupancy indicates an altered (super-)enhancer landscape, including enrichment of the VDR and BATF binding motifs. The Treg cell profile has striking overlap with tumor-infiltrating Treg cells. Our data demonstrate that human inflammation-derived Treg cells acquire a conserved and specific eTreg cell profile guided by epigenetic changes, and fine-tuned by environment-specific adaptations.
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MESH Headings
- Adolescent
- Arthritis, Juvenile/genetics
- Arthritis, Juvenile/immunology
- Arthritis, Juvenile/pathology
- Base Sequence
- Basic-Leucine Zipper Transcription Factors/genetics
- Basic-Leucine Zipper Transcription Factors/immunology
- CTLA-4 Antigen/genetics
- CTLA-4 Antigen/immunology
- Case-Control Studies
- Cell Differentiation
- Child
- Child, Preschool
- Epigenesis, Genetic
- Female
- Forkhead Transcription Factors/genetics
- Forkhead Transcription Factors/immunology
- Gene Expression Profiling
- Gene Regulatory Networks
- Glucocorticoid-Induced TNFR-Related Protein/genetics
- Glucocorticoid-Induced TNFR-Related Protein/immunology
- Histones/genetics
- Histones/immunology
- Humans
- Joints/immunology
- Joints/pathology
- Male
- Metabolic Networks and Pathways/genetics
- Metabolic Networks and Pathways/immunology
- Positive Regulatory Domain I-Binding Factor 1/genetics
- Positive Regulatory Domain I-Binding Factor 1/immunology
- Primary Cell Culture
- Receptors, Calcitriol/genetics
- Receptors, Calcitriol/immunology
- Receptors, Immunologic/genetics
- Receptors, Immunologic/immunology
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/pathology
- Transcriptome
- Young Adult
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Affiliation(s)
- Gerdien Mijnheer
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Lisanne Lutter
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Michal Mokry
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, Department of Pediatrics, University Medical Center Utrecht, Utrecht, The Netherlands
- Epigenomics facility, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marlot van der Wal
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Rianne Scholman
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Veerle Fleskens
- Centre for Inflammation Biology and Cancer Immunology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Aridaman Pandit
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Weiyang Tao
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Mark Wekking
- Epigenomics facility, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stephin Vervoort
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ceri Roberts
- Centre for Inflammation Biology and Cancer Immunology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Alessandra Petrelli
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Janneke G C Peeters
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marthe Knijff
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Sytze de Roock
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Sebastiaan Vastert
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Leonie S Taams
- Centre for Inflammation Biology and Cancer Immunology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jorg van Loosdregt
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Femke van Wijk
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
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10
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Yang M, Huang Q, Li C, Jiang Z, Sun J, Wang Z, Liang R, Li D, Li B, Zhao H. TOX Acts as a Tumor Suppressor by Inhibiting mTOR Signaling in Colorectal Cancer. Front Immunol 2021; 12:647540. [PMID: 33897695 PMCID: PMC8062716 DOI: 10.3389/fimmu.2021.647540] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/23/2021] [Indexed: 01/05/2023] Open
Abstract
The treatment and prognosis of advanced colorectal cancer (CRC) remain a challenging clinical research focus. Here, we describe a new CRC tumor suppressor and potential therapeutic target: thymocyte selection associated high mobility group box (TOX) protein. The expression of TOX was lower in CRC than para-CRC. With the increase of tumor stage, TOX expression decreased, indicating the presence of TOX relates to better overall survival (OS). TOX suppressed the mechanistic target of rapamycin kinase (mTOR) signaling to inhibit cell proliferation, migration, invasion, and change the epithelial-mesenchymal transition (EMT) process. In addition, TOX promoted apoptosis. As tumor mutation burden and tumor microenvironment play vital roles in the occurrence and development of tumors, we analyzed the TOX expression in the immune microenvironment of CRC. The high TOX expression was negatively correlated with TumorPurity. Moreover, it was positively related to ImmuneScore, StromalScore, microsatellite instability (MSI) status, and Consensus Molecular Subtypes (CMS) 3 typing. Based on gene set enrichment analysis (GSEA), the reduced expression of TOX activated mTOR. We found rapamycin, a mTOR inhibitor, partly inhibited cell proliferation, invasion, and migration in shTOX HCT116 cells. Lastly, TOX suppressed tumorigenesis and lung metastasis of CRC in vivo. Rapamycin alone or combined with PD1 inhibitor is more effective than PD1 inhibitor alone in a tumor model. Taken together, these findings highlight the tumor-suppressive role of TOX in CRC, especially in MSI CRC, and provide valuable information that rapamycin alone or combined with PD1 inhibitor has therapeutic potential in CRC.
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Affiliation(s)
- Mengdi Yang
- Department of Internal Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qianru Huang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Changcan Li
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyuan Jiang
- Department of Internal Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Sun
- Department of Internal Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Zhiyu Wang
- Department of Internal Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Rui Liang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dan Li
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bin Li
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Henan Key Laboratory of Digestive Organ Transplantation, Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan, China.,Institute of Arthritis Research, Guanghua Integrative Medicine Hospital, Shanghai, China
| | - Hui Zhao
- Department of Internal Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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11
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Zhang H, Fan F, Yu Y, Wang Z, Liu F, Dai Z, Zhang L, Liu Z, Cheng Q. Clinical characterization, genetic profiling, and immune infiltration of TOX in diffuse gliomas. J Transl Med 2020; 18:305. [PMID: 32762688 PMCID: PMC7409670 DOI: 10.1186/s12967-020-02460-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 07/26/2020] [Indexed: 01/19/2023] Open
Abstract
Background Immunotherapies targeting glioblastoma (GBM) have led to significant improvements in patient outcomes. TOX is closely associated with the immune environment surrounding tumors, but its role in gliomas is not fully understood. Methods Using data from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA), we analyzed the transcriptomes of 1691 WHO grade I-IV human glioma samples. The R language was used to perform most of the statistical analyses. Somatic mutations and somatic copy number variation (CNV) were analyzed using GISTIC 2.0. Results TOX was down-regulated in malignant gliomas compared to low grade gliomas, and upregulated in the proneural and IDH mutant subtypes of GBM. TOXlow tumours are associated with the loss of PTEN and amplification of EGFR, while TOXhigh tumours harbor frequent mutations in IDH1 (91%). TOX was highly expressed in leading edge regions of tumours. Gene ontology and pathway analyses demonstrated that TOX was enriched in multiple immune related processes including lymphocyte migration in GBM. Finally, TOX had a negative association with the infiltration of several immune cell types in the tumour microenvironment. Conclusion TOX has the potential to be a new prognostic marker for GBM.
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Affiliation(s)
- Hao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fan Fan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,Center for Medical Genetics and Hunan Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuanqiang Yu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fangkun Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Liyang Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Department of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA. .,Clinical Diagnosis and Therapeutic Center of Glioma, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, People's Republic of China.
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China. .,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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12
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Arora M, Kumari S, Singh J, Chopra A, Chauhan SS. Expression pattern, regulation, and clinical significance of TOX in breast cancer. Cancer Immunol Immunother 2021; 70:349-63. [PMID: 32757053 DOI: 10.1007/s00262-020-02689-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/30/2020] [Indexed: 12/11/2022]
Abstract
Thymocyte selection-associated high mobility group box protein (TOX) is a transcription factor implicated in the regulation of T cell exhaustion during chronic infection and cancer. While TOX is being targeted for cancer immunotherapy, limited information is available about its significance in breast cancer and other solid tumors. We performed a comprehensive analysis of TOX gene expression, its epigenetic regulation, protein localization, relation to tumor infiltrating immune cell composition, and prognostic significance in breast cancer using publicly available datasets. Our results suggest an inverse correlation between TOX expression and DNA methylation in tumor cells. However, its expression is elevated in tumor infiltrating immune cells (TIICs), which may compensates for the total TOX levels in the tumor as a whole. Furthermore, higher TOX levels in tumors are associated with T cell exhaustion signatures along with presence of active inflammatory response, including elevated levels of T cell effector cytokines. Survival analysis also confirmed that higher expression of TOX is associated with better prognosis in breast cancer. Therefore, expression of TOX may serve as a novel prognostic marker for this malignancy.
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13
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Tessema M, Tassew DD, Yingling CM, Do K, Picchi MA, Wu G, Petersen H, Randell S, Lin Y, Belinsky SA, Tesfaigzi Y. Identification of novel epigenetic abnormalities as sputum biomarkers for lung cancer risk among smokers and COPD patients. Lung Cancer 2020; 146:189-196. [PMID: 32559455 DOI: 10.1016/j.lungcan.2020.05.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/09/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Smoking is a common risk factor for chronic obstructive pulmonary disease (COPD) and lung cancer. Although COPD patients have higher risk of lung cancer compared to non-COPD smokers, the molecular links between these diseases are not well-defined. This study aims to identify genes that are downregulated by cigarette smoke and commonly repressed in COPD and lung cancer. MATERIALS AND METHODS Primary human airway epithelial cells (HAEC) were exposed to cigarette-smoke-extract (CSE) for 10-weeks and significantly suppressed genes were identified by transcriptome array. Epigenetic abnormalities of these genes in lung adenocarcinoma (LUAD) from patients with or without COPD were determined using genome-wide and gene-specific assays and by in vitro treatment of cell lines with trichostatin-A or 5-aza-2-deoxycytidine. RESULTS The ten most commonly downregulated genes following chronic CSE exposure of HAEC and show promoter hypermethylation in LUAD were selected. Among these, expression of CCNA1, SNCA, and ZNF549 was significantly reduced in lung tissues from COPD compared with non-COPD cases while expression of CCNA1 and SNCA was further downregulated in tumors with COPD. The promoter regions of all three genes were hypermethylated in LUAD but not normal or COPD lungs. The reduced expression and aberrant promoter hypermethylation of these genes in LUAD were independently validated using data from the Cancer Genome Atlas project. Importantly, SNCA and ZNF549 methylation detected in sputum DNA from LUAD (52% and 38%) cases were more prevalent compared to cancer-free smokers (26% and 15%), respectively (p < 0.02). CONCLUSIONS Our data show that suppression of CCNA1, SNCA, and ZNF549 in lung cancer and COPD occurs with or without promoter hypermethylation, respectively. Detecting methylation of these and previously identified genes in sputum of cancer-free smokers may serve as non-invasive biomarkers for early detection of lung cancer among high risk smokers including COPD patients.
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Affiliation(s)
- Mathewos Tessema
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA.
| | - Dereje D Tassew
- COPD Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA; Currently, Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Christin M Yingling
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Kieu Do
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Guodong Wu
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Hans Petersen
- COPD Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Scott Randell
- Department of Cell and Molecular Physiology, The University of North Carolina, Chapel Hill, NC, USA
| | - Yong Lin
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Yohannes Tesfaigzi
- COPD Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA; Currently, Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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14
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Maestre L, García-García JF, Jiménez S, Reyes-García AI, García-González Á, Montes-Moreno S, Arribas AJ, González-García P, Caleiras E, Banham AH, Piris MÁ, Roncador G. High-mobility group box (TOX) antibody a useful tool for the identification of B and T cell subpopulations. PLoS One 2020; 15:e0229743. [PMID: 32106280 PMCID: PMC7046285 DOI: 10.1371/journal.pone.0229743] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/13/2020] [Indexed: 11/19/2022] Open
Abstract
Thymocyte selection-associated high-mobility group box (TOX) is a DNA-binding factor that is able to regulate transcription by modifying local chromatin structure and modulating the formation of multi-protein complexes. TOX has multiple roles in the development of the adaptive immune system including development of CD4 T cells, NK cells and lymph node organogenesis. However very few antibodies recognizing this molecule have been reported and no extensive study of the expression of TOX in reactive and neoplastic lymphoid tissue has been performed to date. In the present study, we have investigated TOX expression in normal and neoplastic lymphoid tissues using a novel rat monoclonal antibody that recognizes its target molecule in paraffin-embedded tissue sections. A large series of normal tissues and B- and T-cell lymphomas was studied, using whole sections and tissue microarrays. We found that the majority of precursor B/T lymphoblastic, follicular and diffuse large B-cell lymphomas, nodular lymphocyte-predominant Hodgkin lymphomas and angioimmunoblastic T-cell lymphomas strongly expressed the TOX protein. Burkitt and mantle cell lymphomas showed TOX expression in a small percentage of cases. TOX was not found in the majority of chronic lymphocytic leukemia, myelomas, marginal zone lymphomas and classical Hodgkin lymphomas. In conclusion, we describe for the first time the expression of TOX in normal and neoplastic lymphoid tissues. The co-expression of TOX and PD-1 identified in normal and neoplastic T cells is consistent with recent studies identifying TOX as a critical regulator of T-cell exhaustion and a potential immunotherapy target. Its differential expression may be of diagnostic relevance in the differential diagnosis of follicular lymphoma, the identification of the phenotype of diffuse large B-cell lymphoma and the recognition of peripheral T-cell lymphoma with a follicular helper T phenotype.
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MESH Headings
- Animals
- Antibodies, Monoclonal, Murine-Derived/immunology
- Antibody Specificity
- B-Lymphocyte Subsets/immunology
- B-Lymphocyte Subsets/metabolism
- B-Lymphocyte Subsets/pathology
- Cell Line, Tumor
- Female
- Gene Expression
- High Mobility Group Proteins/genetics
- High Mobility Group Proteins/immunology
- High Mobility Group Proteins/metabolism
- Humans
- Lymphoid Tissue/immunology
- Lymphoid Tissue/metabolism
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/metabolism
- Lymphoma, B-Cell/pathology
- Lymphoma, T-Cell/immunology
- Lymphoma, T-Cell/metabolism
- Lymphoma, T-Cell/pathology
- Male
- Mice
- Mice, Inbred C57BL
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Rats
- Rats, Wistar
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- T-Lymphocyte Subsets/pathology
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Affiliation(s)
| | | | | | | | | | | | - Alberto J. Arribas
- Università della Svizzera Italiana, Institute of Oncology Research, Bellinzona, Switzerland
| | | | | | - Alison H. Banham
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Miguel Ángel Piris
- Department of Pathology, Fundación Jiménez Díaz, CIBERONC, Madrid, Spain
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15
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Fan HN, Chen W, Peng SQ, Chen XY, Zhang R, Liang R, Liu H, Zhu JS, Zhang J. Sanguinarine inhibits the tumorigenesis of gastric cancer by regulating the TOX/DNA-PKcs/ KU70/80 pathway. Pathol Res Pract 2019; 215:152677. [DOI: 10.1016/j.prp.2019.152677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/17/2019] [Accepted: 09/27/2019] [Indexed: 02/08/2023]
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16
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Vanheer L, Song J, De Geest N, Janiszewski A, Talon I, Provenzano C, Oh T, Chappell J, Pasque V. Tox4 modulates cell fate reprogramming. J Cell Sci 2019; 132:jcs.232223. [PMID: 31519808 PMCID: PMC6826012 DOI: 10.1242/jcs.232223] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 09/06/2019] [Indexed: 01/05/2023] Open
Abstract
Reprogramming to induced pluripotency induces the switch of somatic cell identity to induced pluripotent stem cells (iPSCs). However, the mediators and mechanisms of reprogramming remain largely unclear. To elucidate the mediators and mechanisms of reprogramming, we used a siRNA-mediated knockdown approach for selected candidate genes during the conversion of somatic cells into iPSCs. We identified Tox4 as a novel factor that modulates cell fate through an assay that determined the efficiency of iPSC reprogramming. We found that Tox4 is needed early in reprogramming to efficiently generate early reprogramming intermediates, irrespective of the reprogramming conditions used. Tox4 enables proper exogenous reprogramming factor expression, and the closing and opening of putative somatic and pluripotency enhancers early during reprogramming, respectively. We show that the TOX4 protein assembles into a high molecular form. Moreover, Tox4 is also required for the efficient conversion of fibroblasts towards the neuronal fate, suggesting a broader role of Tox4 in modulating cell fate. Our study reveals Tox4 as a novel transcriptional modulator of cell fate that mediates reprogramming from the somatic state to the pluripotent and neuronal fate.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Lotte Vanheer
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Juan Song
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Natalie De Geest
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Adrian Janiszewski
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Irene Talon
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Caterina Provenzano
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Taeho Oh
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Joel Chappell
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Vincent Pasque
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
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17
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Suzuki H, Kumar SA, Shuai S, Diaz-Navarro A, Gutierrez-Fernandez A, De Antonellis P, Cavalli FMG, Juraschka K, Farooq H, Shibahara I, Vladoiu MC, Zhang J, Abeysundara N, Przelicki D, Skowron P, Gauer N, Luu B, Daniels C, Wu X, Forget A, Momin A, Wang J, Dong W, Kim SK, Grajkowska WA, Jouvet A, Fèvre-Montange M, Garrè ML, Nageswara Rao AA, Giannini C, Kros JM, French PJ, Jabado N, Ng HK, Poon WS, Eberhart CG, Pollack IF, Olson JM, Weiss WA, Kumabe T, López-Aguilar E, Lach B, Massimino M, Van Meir EG, Rubin JB, Vibhakar R, Chambless LB, Kijima N, Klekner A, Bognár L, Chan JA, Faria CC, Ragoussis J, Pfister SM, Goldenberg A, Wechsler-Reya RJ, Bailey SD, Garzia L, Morrissy AS, Marra MA, Huang X, Malkin D, Ayrault O, Ramaswamy V, Puente XS, Calarco JA, Stein L, Taylor MD. Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma. Nature 2019; 574:707-711. [PMID: 31664194 PMCID: PMC7141958 DOI: 10.1038/s41586-019-1650-0] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/03/2019] [Indexed: 11/30/2022]
Abstract
Recurrent somatic single nucleotide variants (SNVs) in cancer are largely confined to protein coding genes, and are rare in most pediatric cancers1–3. We report highly recurrent hotspot mutations of U1 spliceosomal small nuclear RNAs (snRNAs) in ~50% of Sonic Hedgehog medulloblastomas (Shh-MB), which were not present across other medulloblastoma subgroups. This U1-snRNA hotspot mutation (r.3a>g), was identified in <0.1% of 2,442 cancers across 36 other tumor types. Largely absent from infant Shh-MB, the mutation occurs in 97% of adults (Shhδ), and 25% of adolescents (Shhα). The U1-snRNA mutation occurs in the 5′ splice site binding region, and snRNA mutant tumors have significantly disrupted RNA splicing with an excess of 5′ cryptic splicing events. Mutant U1-snRNA mediated alternative splicing inactivates tumor suppressor genes (PTCH1), and activates oncogenes (GLI2, CCND2), represents a novel target for therapy, and constitutes a highly recurrent and tissue-specific mutation of a non-protein coding gene in cancer.
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Affiliation(s)
- Hiromichi Suzuki
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sachin A Kumar
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shimin Shuai
- Informatics and Biocomputing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ander Diaz-Navarro
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Ana Gutierrez-Fernandez
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Pasqualino De Antonellis
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Florence M G Cavalli
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kyle Juraschka
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Hamza Farooq
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ichiyo Shibahara
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maria C Vladoiu
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jiao Zhang
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Namal Abeysundara
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - David Przelicki
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Patryk Skowron
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Nicole Gauer
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Betty Luu
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Craig Daniels
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xiaochong Wu
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Antoine Forget
- CNRS UMR, INSERM, Institut Curie, PSL Research University, Orsay, France.,CNRS UMR 3347, INSERM U1021, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Ali Momin
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jun Wang
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Weifan Dong
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Seung-Ki Kim
- Department of Neurosurgery, Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, South Korea
| | | | - Anne Jouvet
- Centre de Pathologie EST, Groupement Hospitalier EST, Université de Lyon, Bron, France
| | - Michelle Fèvre-Montange
- CNRS UMR5292, INSERM U1028, Centre de Recherche en Neurosciences, Université de Lyon, Lyon, France
| | | | | | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Johan M Kros
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Pim J French
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nada Jabado
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Sang Poon
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Charles G Eberhart
- Department of Pathology, John Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Opthalmology, John Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, John Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ian F Pollack
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - William A Weiss
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.,Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Toshihiro Kumabe
- Department of Neurosurgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Enrique López-Aguilar
- Division of Pediatric Hematology/Oncology, Hospital Pediatría Centro Médico Nacional Century XXI, Mexico City, Mexico
| | - Boleslaw Lach
- Department of Pathology and Molecular Medicine, Division of Anatomical Pathology, McMaster University, Hamilton, Ontario, Canada.,Department of Pathology and Laboratory Medicine, Hamilton General Hospital, Hamilton, Ontario, Canada
| | | | - Erwin G Van Meir
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.,Laboratory of Molecular Neuro-Oncology, Department of Neurosurgery, School of Medicine, Emory University, Atlanta, GA, USA.,Department of Hematology and Medical Oncology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Joshua B Rubin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA.,Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Rajeev Vibhakar
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lola B Chambless
- Department of Neurological Surgery, Vanderbilt Medical Center, Nashville, TN, USA
| | - Noriyuki Kijima
- Department of Neurosurgery, Osaka National Hospital, Osaka, Japan
| | - Almos Klekner
- Department of Neurosurgery, Medical and Health Science Centre, University of Debrecen, Debrecen, Hungary
| | - László Bognár
- Department of Neurosurgery, Medical and Health Science Centre, University of Debrecen, Debrecen, Hungary
| | - Jennifer A Chan
- Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Claudia C Faria
- Division of Neurosurgery, Centro Hospitalar Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Jiannis Ragoussis
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, Montreal, Canada.,Department of Bioengineering, McGill University, Montreal, Canada
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Anna Goldenberg
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Swneke D Bailey
- Department of Surgery, Division of Thoracic and Upper Gastrointestinal Surgery, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Livia Garzia
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,Department of Surgery, Division of Orthopedic Surgery, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - A Sorana Morrissy
- Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada.,Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xi Huang
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - David Malkin
- Division of Haematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Olivier Ayrault
- CNRS UMR, INSERM, Institut Curie, PSL Research University, Orsay, France.,CNRS UMR 3347, INSERM U1021, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Vijay Ramaswamy
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Haematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xose S Puente
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - John A Calarco
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Lincoln Stein
- Informatics and Biocomputing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada. .,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada. .,Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada.
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18
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Zeng D, Lin H, Cui J, Liang W. TOX3 is a favorable prognostic indicator and potential immunomodulatory factor in lung adenocarcinoma. Oncol Lett 2019; 18:4144-4152. [PMID: 31516613 PMCID: PMC6732997 DOI: 10.3892/ol.2019.10748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 01/14/2019] [Indexed: 02/06/2023] Open
Abstract
Thymocyte selection-associated high mobility group box (TOX) genes represent a novel family of genes. Deregulated expression of TOXs has been reported in a variety of cancer types, including lung cancer. It has also been reported that TOXs are crucial regulators of the immune system. The present study systematically evaluated the prognostic values of TOX family members using a set of publicly accessible databases, including Oncomine, Kaplan-Meier plotter and cBioPortal. It was revealed that TOX expression profiles differed between lung cancer and normal tissues, and high expression of TOX mRNAs generally predicted improved survival outcomes. Notably, TOX3 expression was significantly increased in lung adenocarcinoma, compared with other pathological subtypes of lung cancer. Survival analysis demonstrated that elevated TOX3 expression was significantly associated with improved progression-free and overall survival in patients with lung adenocarcinoma. Furthermore, correlation analysis indicated that TOX3 expression was negatively correlated with the expression of programmed death-1 receptor (PD-1), PD-ligand 1 and Hepatitis A virus cellular receptor 2 in lung adenocarcinoma. These results indicated that TOX3 is a prognostic indicator and promising immunomodulatory factor in lung adenocarcinoma. Future studies investigating the role of TOX3 in lung cancer immunity are warranted.
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Affiliation(s)
- De Zeng
- Department of Medical Oncology, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong 515000, P.R. China
- Correspondence to: Dr De Zeng, Department of Medical Oncology, Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, Guangdong 515000, P.R. China, E-mail:
| | - Haoyu Lin
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515000, P.R. China
| | - Jianxiong Cui
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515000, P.R. China
| | - Weiquan Liang
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515000, P.R. China
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19
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Santucci-Pereira J, Zeleniuch-Jacquotte A, Afanasyeva Y, Zhong H, Slifker M, Peri S, Ross EA, López de Cicco R, Zhai Y, Nguyen T, Sheriff F, Russo IH, Su Y, Arslan AA, Bordas P, Lenner P, Åhman J, Landström Eriksson AS, Johansson R, Hallmans G, Toniolo P, Russo J. Genomic signature of parity in the breast of premenopausal women. Breast Cancer Res 2019; 21:46. [PMID: 30922380 PMCID: PMC6438043 DOI: 10.1186/s13058-019-1128-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 03/14/2019] [Indexed: 12/17/2022] Open
Abstract
Background Full-term pregnancy (FTP) at an early age confers long-term protection against breast cancer. Previously, we reported that a FTP imprints a specific gene expression profile in the breast of postmenopausal women. Herein, we evaluated gene expression changes induced by parity in the breast of premenopausal women. Methods Gene expression profiling of normal breast tissue from 30 nulliparous (NP) and 79 parous (P) premenopausal volunteers was performed using Affymetrix microarrays. In addition to a discovery/validation analysis, we conducted an analysis of gene expression differences in P vs. NP women as a function of time since last FTP. Finally, a laser capture microdissection substudy was performed to compare the gene expression profile in the whole breast biopsy with that in the epithelial and stromal tissues. Results Discovery/validation analysis identified 43 differentially expressed genes in P vs. NP breast. Analysis of expression as a function of time since FTP revealed 286 differentially expressed genes (238 up- and 48 downregulated) comparing all P vs. all NP, and/or P women whose last FTP was less than 5 years before biopsy vs. all NP women. The upregulated genes showed three expression patterns: (1) transient: genes upregulated after FTP but whose expression levels returned to NP levels. These genes were mainly related to immune response, specifically activation of T cells. (2) Long-term changing: genes upregulated following FTP, whose expression levels decreased with increasing time since FTP but did not return to NP levels. These were related to immune response and development. (3) Long-term constant: genes that remained upregulated in parous compared to nulliparous breast, independently of time since FTP. These were mainly involved in development/cell differentiation processes, and also chromatin remodeling. Lastly, we found that the gene expression in whole tissue was a weighted average of the expression in epithelial and stromal tissues. Conclusions Genes transiently activated by FTP may have a role in protecting the mammary gland against neoplastically transformed cells through activation of T cells. Furthermore, chromatin remodeling and cell differentiation, represented by the genes that are maintained upregulated long after the FTP, may be responsible for the lasting preventive effect against breast cancer. Electronic supplementary material The online version of this article (10.1186/s13058-019-1128-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julia Santucci-Pereira
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center - Temple University Health System, 333 Cottman Ave, P2051, Philadelphia, PA, 19111, USA.
| | - Anne Zeleniuch-Jacquotte
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, 10016, USA.,New York University Perlmutter Cancer Center, New York, NY, 10016, USA
| | - Yelena Afanasyeva
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, 10016, USA
| | - Hua Zhong
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, 10016, USA
| | - Michael Slifker
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center - Temple University Health System, Philadelphia, PA, 19111, USA
| | - Suraj Peri
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center - Temple University Health System, Philadelphia, PA, 19111, USA
| | - Eric A Ross
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center - Temple University Health System, Philadelphia, PA, 19111, USA
| | - Ricardo López de Cicco
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center - Temple University Health System, 333 Cottman Ave, P2051, Philadelphia, PA, 19111, USA
| | - Yubo Zhai
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center - Temple University Health System, 333 Cottman Ave, P2051, Philadelphia, PA, 19111, USA
| | - Theresa Nguyen
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center - Temple University Health System, 333 Cottman Ave, P2051, Philadelphia, PA, 19111, USA
| | - Fathima Sheriff
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center - Temple University Health System, 333 Cottman Ave, P2051, Philadelphia, PA, 19111, USA
| | - Irma H Russo
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center - Temple University Health System, 333 Cottman Ave, P2051, Philadelphia, PA, 19111, USA
| | - Yanrong Su
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center - Temple University Health System, 333 Cottman Ave, P2051, Philadelphia, PA, 19111, USA
| | - Alan A Arslan
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, 10016, USA.,Department of Obstetrics and Gynecology, New York University School of Medicine, New York, NY, 10016, USA
| | - Pal Bordas
- Sunderby Hospital, Luleå and the Norrbotten Mammography Screening Program, Luleå, Sweden.,Departments of Radiation Sciences and Oncology, Umeå University, Umeå, Sweden
| | - Per Lenner
- Departments of Radiation Sciences and Oncology, Umeå University, Umeå, Sweden
| | - Janet Åhman
- Sunderby Hospital, Luleå and the Norrbotten Mammography Screening Program, Luleå, Sweden
| | | | | | - Göran Hallmans
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Paolo Toniolo
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, NY, 10016, USA
| | - Jose Russo
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center - Temple University Health System, 333 Cottman Ave, P2051, Philadelphia, PA, 19111, USA
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20
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Jiang B, Chen W, Qin H, Diao W, Li B, Cao W, Zhang Z, Qi W, Gao J, Chen M, Zhao X, Guo H. TOX3 inhibits cancer cell migration and invasion via transcriptional regulation of SNAI1 and SNAI2 in clear cell renal cell carcinoma. Cancer Lett 2019; 449:76-86. [PMID: 30772441 DOI: 10.1016/j.canlet.2019.02.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/07/2019] [Accepted: 02/10/2019] [Indexed: 12/13/2022]
Abstract
Studies on the mechanism of clear cell renal cell carcinoma (ccRCC) progression are lacking. In this study, TOX3 was identified as a novel cancer suppressor gene in ccRCC. Hypermethylation of CpG probes in the promoter region was associated with the functional loss of TOX3 in ccRCC cancer tissues. Downregulation of TOX3 mRNA was strongly associated with poor clinical outcomes in ccRCC. Immunohistochemistry confirmed TOX3 was downregulated in primary tumors without metastasis (n = 126) and further downregulated in primary metastatic tumors (n = 23) compared with adjacent noncancerous tissues (n = 92). In vitro, overexpression of TOX3 inhibited RCC cell growth, migration and invasion. Mechanistic investigations showed that TOX3 deficiency facilitates the epithelial-mesenchymal transition due to impairment of transcriptional repression of SNAIL members SNAI1 and SNAI2 and promotes cancer cell migration and invasion. In vivo, restoring TOX3 expression reduced lung metastatic lesions and prolonged survival of mice. TOX3 combined with SNAI1 or SNAI2 predicted overall survival in ccRCC patients. Blockage of this pathway could be a promising therapeutic target for advanced ccRCC.
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21
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Tanikawa C, Kamatani Y, Takahashi A, Momozawa Y, Leveque K, Nagayama S, Mimori K, Mori M, Ishii H, Inazawa J, Yasuda J, Tsuboi A, Shimizu A, Sasaki M, Yamaji T, Sawada N, Iwasaki M, Tsugane S, Naito M, Wakai K, Koyama T, Takezaki T, Yuji K, Murakami Y, Nakamura Y, Kubo M, Matsuda K. GWAS identifies two novel colorectal cancer loci at 16q24.1 and 20q13.12. Carcinogenesis 2019; 39:652-660. [PMID: 29471430 DOI: 10.1093/carcin/bgy026] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 02/13/2018] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancer (CRC) is the fourth leading cause of cancer mortality worldwide. Genome-wide association studies (GWAS) identified more than 50 CRC loci. However, most of the previous studies were conducted in European population, and host genetic factors among Japanese population are largely remained to be identified. To identify novel loci in the Japanese population, here, we performed a large-scale GWAS using 6692 cases and 27 178 controls followed by a replication analysis using more than 11 000 case-control samples. We found the significant association of 10 loci (P < 5 × 10-8), including 2 novel loci on 16q24.1 (IRF8-FOXF1, rs847208, P = 3.15 × 10-9 and odds ratio = 1.107 with 95% confidence interval (CI) of 1.071-1.145) and 20q13.12 (TOX2, rs6065668, P = 4.47 × 10-11 and odds ratio = 0.897 with 95% CI of 0.868-0.926). Moreover, 35 previously reported single nucleotide polymorphisms (SNPs) in 24 regions were validated in the Japanese population (P < 0.05) with the same risk allele as in the previous studies. SNP rs6065668 was significantly associated with TOX2 expression in the sigmoid colon. In addition, nucleotide substitutions in the regulatory region of TOX2 were predicted to alter the binding of several transcription factors, including KLF5. Our findings elucidate the important role of genetic variations in the development of CRC in the Japanese population.
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Affiliation(s)
- Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan.,Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Karine Leveque
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.,Oncology Master Progam, University Claude Bernard, Lyon I, Lyon, France
| | - Satoshi Nagayama
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Koshi Mimori
- Department of Surgery and Molecular Oncology, Medical Institute of Bioregulation, Kyushu University, Oita, Japan
| | - Masaki Mori
- Department of Gastroenterological Surgery and Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hideshi Ishii
- Department of Medical Data Science, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Akito Tsuboi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Taiki Yamaji
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Norie Sawada
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Shoichiro Tsugane
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Mariko Naito
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Teruhide Koyama
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Toshiro Takezaki
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Koichiro Yuji
- Project Division of International Advanced Medical Research, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yusuke Nakamura
- Department of Medicine, The University of Chicago, IL, USA.,Department of Surgery, The University of Chicago, IL, USA.,Center for Personalized Therapeutics, The University of Chicago, IL, USA
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Koichi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
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22
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Zeng X, Vonk JM, van der Plaat DA, Faiz A, Paré PD, Joubert P, Nickle D, Brandsma CA, Kromhout H, Vermeulen R, Xu X, Huo X, de Jong K, Boezen HM. Genome-wide interaction study of gene-by-occupational exposures on respiratory symptoms. Environ Int 2019; 122:263-269. [PMID: 30449631 DOI: 10.1016/j.envint.2018.11.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/05/2018] [Accepted: 11/08/2018] [Indexed: 02/05/2023]
Abstract
Respiratory symptoms are important indicators of respiratory diseases. Both genetic and environmental factors contribute to respiratory symptoms development but less is known about gene-environment interactions. We aimed to assess interactions between single nucleotide polymorphisms (SNPs) and occupational exposures on respiratory symptoms cough, dyspnea and phlegm. As identification cohort LifeLines I (n = 7976 subjects) was used. Job-specific exposure was estimated using the ALOHA + job exposure matrix. SNP-by-occupational exposure interactions on respiratory symptoms were tested using logistic regression adjusted for gender, age, and current smoking. SNP-by-exposure interactions with a p-value <10-4 were tested for replication in two independent cohorts: LifeLines II (n = 5260) and the Vlagtwedde-Vlaardingen cohort (n = 1529). The interaction estimates of the replication cohorts were meta-analyzed using PLINK. Replication was achieved when the meta-analysis p-value was <0.05 and the interaction effect had the same direction as in the identification cohort. Additionally, we assessed whether replicated SNPs associated with gene expression by analyzing if they were cis-acting expression quantitative trait loci (eQTL) in lung tissue. In the replication meta-analysis, sixteen out of 477 identified SNP-by-occupational exposure interactions had a p-value <0.05 and 9 of these interactions had the same direction as in the identification cohort. Several identified loci were plausible candidates for respiratory symptoms, such as TMPRSS9, SERPINH1, TOX3, and ARHGAP18. Three replicated SNPs were cis-eQTLs for FCER1A, CHN1, and TIMM13 in lung tissue. Taken together, this genome-wide SNP-by-occupational exposure interaction study in relation to cough, dyspnea, and phlegm identified several suggestive susceptibility genes. Further research should determine if these genes are true susceptibility loci for respiratory symptoms in relation to occupational exposures.
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Affiliation(s)
- Xiang Zeng
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands; Shantou University Medical College, Laboratory of Environmental Medicine and Developmental Toxicology, Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, China; Xinxiang Medical University, School of Public Health, Department of Epidemiology and Health Statistics, Xinxiang, China
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Diana A van der Plaat
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Alen Faiz
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
| | - Peter D Paré
- University of British Columbia, Department of Medicine, Center for Heart Lung Innovation and Institute for Heart and Lung Health, St. Paul's Hospital, Vancouver, BC, Canada
| | - Philippe Joubert
- Institut universitaire de cardiologie et de pneumologie de Québec, Laval University, Québec, QC, Canada
| | | | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
| | - Hans Kromhout
- University of Utrecht, Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht, the Netherlands
| | - Roel Vermeulen
- University of Utrecht, Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht, the Netherlands
| | - Xijin Xu
- Shantou University Medical College, Laboratory of Environmental Medicine and Developmental Toxicology, Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, China
| | - Xia Huo
- Jinan University, School of Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Guangzhou Key Laboratory of Environmental Exposure and Health, Guangzhou, China
| | - Kim de Jong
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - H Marike Boezen
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands.
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23
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Tessema M, Rossi MR, Picchi MA, Yingling CM, Lin Y, Ramalingam SS, Belinsky SA. Common cancer-driver mutations and their association with abnormally methylated genes in lung adenocarcinoma from never-smokers. Lung Cancer 2018; 123:99-106. [PMID: 30089603 PMCID: PMC6331003 DOI: 10.1016/j.lungcan.2018.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/28/2018] [Accepted: 07/10/2018] [Indexed: 12/30/2022]
Abstract
OBJECTIVES Lung adenocarcinoma in never-smokers accounts for 15-20% of all lung cancer. Although targetable mutations are more prevalent in these tumors, the biological and clinical importance of coexisting and/or mutually exclusive abnormalities is just emerging. This study evaluates the relationships between common genetic and epigenetic aberrations in these tumors. MATERIALS AND METHODS Next-generation sequencing was employed to screen 20 commonly mutated cancer-driver genes in 112 lung adenocarcinomas from never-smokers. The relationship of these mutations with cancer-related methylation of 59 genes, and geographical/ethnic differences in the prevalence for mutations compared to multiple East Asian never-smoker lung adenocarcinoma cohorts was studied. RESULTS The most common driver mutation detected in 40% (45/112) of the tumors was EGFR, followed by TP53 (18%), SETD2 (11%), and SMARCA4 (11%). Over 72% (81/112) of the cases have mutation of at least one driver gene. While 30% (34/112) of the tumors have co-mutations of two or more genes, 42% (47/112) have only one driver gene mutation. Differences in the prevalence for some of these mutations were seen between adenocarcinomas in East Asian versus US (mainly Caucasian) never-smokers including a significantly lower rate of EGFR mutation among the US patients. Interestingly, aberrant methylation of multiple cancer-related genes was significantly associated with EGFR wildtype tumors. Among 15 differentially methylated genes by EGFR mutation, 14 were more commonly methylated in EGFR wildtype compared to mutant tumors. These findings were independently validated using publicly available data. CONCLUSION Most lung adenocarcinomas from never-smokers harbor targetable mutation/co-mutations. In the absence of EGFR mutation that drives 40% of these tumors, EGFR wildtype tumors appear to develop by acquiring aberrant promoter methylation that silences tumor-suppressor genes.
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Affiliation(s)
- Mathewos Tessema
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA.
| | - Michael R Rossi
- Departments of Pathology and Laboratory Medicine, Radiation Oncology, USA
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Christin M Yingling
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Yong Lin
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Suresh S Ramalingam
- Hematology and Oncology, Emory University School of Medicine, Winship Cancer Institute, Atlanta, GA, USA
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA.
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24
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Chen T, Li Q, Zhang X, Long R, Wu Y, Wu J, Fu X. TOX expression decreases with progression of colorectal cancers and is associated with CD4 T-cell density and Fusobacterium nucleatum infection. Hum Pathol 2018; 79:93-101. [PMID: 29792893 DOI: 10.1016/j.humpath.2018.05.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/01/2018] [Accepted: 05/11/2018] [Indexed: 12/22/2022]
Abstract
Fusobacterium nucleatum in the tumor microenvironment plays an important role in the development of colorectal cancer. The underlying mechanism of action, however, remains to be elucidated. We evaluated the relation of F nucleatum amount to thymocyte selection-associated high-mobility group box (TOX) protein expression and CD4+ T-cell density in 138 human colorectal tissues. TOX expression and CD4+ T-cell density in Fnucleatum-negative tissues were significantly higher compared to those in Fnucleatum-positive tissues (P < .001 and P = .002, respectively). We found a negative correlation between F nucleatum abundance and TOX expression (P < .001) and CD4+ T-cell density (P < .001). TOX expression in normal mucosa, hyperplastic polyps, and adenomas was significantly higher than in sessile serrated adenomas and different stages of carcinomas (P < .05). Moreover, CD4+ T-cell density in high-TOX expression tissues was significantly higher than in low-TOX expression tissues (P = .003). A positive correlation was found between TOX expression and CD4+ T-cell density in colorectal tissues (Spearman correlation coefficient: 0.362, 95% confidence interval: 0.051-0.641, P = .022). Our findings suggest that F nucleatum may suppress antitumor immune responses by decreasing CD4+ T-cell density and TOX expression in the progression of colorectal cancer.
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Affiliation(s)
- Ting Chen
- Department of Gastroenterology, the Affiliated Hospital of Southwest Medical University, Sichuan, China 646000
| | - Qing Li
- Department of Gastroenterology, the Affiliated Hospital of Southwest Medical University, Sichuan, China 646000
| | - Xiaoyan Zhang
- Department of Dermatology, the Affiliated Hospital of Southwest Medical University, Sichuan, China 646000
| | - Ran Long
- Department of Medical Imaging, the Affiliated Hospital of Southwest Medical University, Sichuan, China 646000
| | - Yaxin Wu
- Department of Gastroenterology, the Affiliated Hospital of Southwest Medical University, Sichuan, China 646000
| | - Jiao Wu
- Department of Gastroenterology, the Affiliated Hospital of Southwest Medical University, Sichuan, China 646000
| | - Xiangsheng Fu
- Department of Gastroenterology, the Affiliated Hospital of Southwest Medical University, Sichuan, China 646000; Department of Gastroenterology, the Affiliated Hospital of North Sichuan Medical College, Sichuan, China 637000.
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25
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Um SW, Kim Y, Lee BB, Kim D, Lee KJ, Kim HK, Han J, Kim H, Shim YM, Kim DH. Genome-wide analysis of DNA methylation in bronchial washings. Clin Epigenetics 2018; 10:65. [PMID: 29796116 PMCID: PMC5960087 DOI: 10.1186/s13148-018-0498-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/09/2018] [Indexed: 12/03/2022] Open
Abstract
Background The objective of this study was to discover DNA methylation biomarkers for detecting non-small lung cancer (NSCLC) in bronchial washings and understanding the association between DNA methylation and smoking cessation. Methods DNA methylation was analyzed in bronchial washing samples from 70 NSCLCs and 53 hospital-based controls using Illumina HumanMethylation450K BeadChip. Methylation levels in these bronchial washings were compared to those in 897 primary lung tissues of The Cancer Genome Atlas (TCGA) data. Results Twenty-four CpGs (p < 1.03E−07) were significantly methylated in bronchial washings from 70 NSCLC patients compared to those from 53 controls. The CpGs also had significant methylation in the TCGA cohort. The 123 participants were divided into a training set (N = 82) and a test set (N = 41) to build a classification model. Logistic regression model showed the best performance for classification of lung cancer in bronchial washing samples: the sensitivity and specificity of a marker panel consisting of seven CpGs in TFAP2A, TBX15, PHF11, TOX2, PRR15, PDGFRA, and HOXA11 genes were 87.0 and 83.3% in the test set, respectively. The area under the curve (AUC) was equal to 0.87 (95% confidence interval = 0.73–0.96, p < 0.001). Methylation levels of two CpGs in RUNX3 and MIR196A1 genes were inversely associated with duration of smoking cessation in the controls, but not in NSCLCs, after adjusting for pack-years of smoking. Conclusions The present study suggests that NSCLC may be detected by analyzing methylation changes of seven CpGs in bronchial washings. Furthermore, smoking cessation may lead to decreased DNA methylation in nonmalignant bronchial epithelial cells in a gene-specific manner. Electronic supplementary material The online version of this article (10.1186/s13148-018-0498-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sang-Won Um
- 1Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Yujin Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746 South Korea
| | - Bo Bin Lee
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746 South Korea
| | - Dongho Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746 South Korea
| | - Kyung-Jong Lee
- 1Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Hong Kwan Kim
- 3Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Joungho Han
- 4Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Hojoong Kim
- 1Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Young Mog Shim
- 3Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746 South Korea.,Samsung Medical Center, Research Institute for Future Medicine, #50 Ilwon-dong, Kangnam-gu, Professor Rm #5, Seoul, 135-710 South Korea
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26
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Sun H, Wang Y, Chen Y, Li Y, Wang S. pETM: a penalized Exponential Tilt Model for analysis of correlated high-dimensional DNA methylation data. Bioinformatics 2018; 33:1765-1772. [PMID: 28165116 DOI: 10.1093/bioinformatics/btx064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/31/2017] [Indexed: 12/31/2022] Open
Abstract
Motivation DNA methylation plays an important role in many biological processes and cancer progression. Recent studies have found that there are also differences in methylation variations in different groups other than differences in methylation means. Several methods have been developed that consider both mean and variance signals in order to improve statistical power of detecting differentially methylated loci. Moreover, as methylation levels of neighboring CpG sites are known to be strongly correlated, methods that incorporate correlations have also been developed. We previously developed a network-based penalized logistic regression for correlated methylation data, but only focusing on mean signals. We have also developed a generalized exponential tilt model that captures both mean and variance signals but only examining one CpG site at a time. Results In this article, we proposed a penalized Exponential Tilt Model (pETM) using network-based regularization that captures both mean and variance signals in DNA methylation data and takes into account the correlations among nearby CpG sites. By combining the strength of the two models we previously developed, we demonstrated the superior power and better performance of the pETM method through simulations and the applications to the 450K DNA methylation array data of the four breast invasive carcinoma cancer subtypes from The Cancer Genome Atlas (TCGA) project. The developed pETM method identifies many cancer-related methylation loci that were missed by our previously developed method that considers correlations among nearby methylation loci but not variance signals. Availability and Implementation The R package 'pETM' is publicly available through CRAN: http://cran.r-project.org . Contact sw2206@columbia.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hokeun Sun
- Department of Statistics, Pusan National University, Busan, Korea
| | - Ya Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Yong Chen
- Division of Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.,Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
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27
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Castillo-Rodríguez RA, Dávila-Borja VM, Juárez-Méndez S. Data mining of pediatric medulloblastoma microarray expression reveals a novel potential subdivision of the Group 4 molecular subgroup. Oncol Lett 2018; 15:6241-6250. [PMID: 29616106 PMCID: PMC5876455 DOI: 10.3892/ol.2018.8094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 01/11/2018] [Indexed: 11/09/2022] Open
Abstract
Medulloblastoma is the most common type of solid brain tumor in children. This type of embryonic tumor is highly heterogeneous and has been classified into 4 molecular subgroups based on their gene expression profiles: WNT, SHH, Group 3 (G3) and Group 4 (G4). WNT and SHH tumors exhibit the specific dysregulation of genes and pathways, whereas G3 and G4 tumors, two of the more frequent subtypes, are the least characterized. Thus, novel markers to aid in the diagnosis, prognosis and management of medulloblastoma are required. In the present study, microarray gene expression data was downloaded from the Gene Expression Omnibus database, including data from the 4 subgroups of medulloblastoma and healthy cerebellum tissue (CT). The data was utilized in an in silico analysis to characterize each subgroup at a transcriptomic level. Using Partek Genomics Suite software, the data were visualized via hierarchical clustering and principal component analysis. The differentially expressed genes were uploaded to the MetaCore portal to perform enrichment analysis using CT gene expression as baseline, with fold change thresholds of <-5 and >5 for differential expression. The data mining analysis of microarray gene expression data enabled the identification of a range of dysregulated molecules associated with each subgroup of medulloblastoma. G4 is the most heterogeneous subgroup, as no definitive pathway defines its pathogenesis; analysis of the gene expression profiles were associated with the G4α and G4β subcategories. TOX high mobility group box family member 3, synuclein α interacting protein and, potassium voltage-gated channel interacting protein 4 were identified as three novel potential markers for distinguishing the α and β subcategories of G4. These genes may be associated with medulloblastoma pathogenesis, and thus may provide a basis for researching novel targeted treatment strategies for G4 medulloblastoma.
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Affiliation(s)
- Rosa Angélica Castillo-Rodríguez
- Laboratory of Experimental Oncology, National Institute of Pediatrics, Mexico City 04530, Mexico.,CONACyT, National Institute of Pediatrics, Mexico City 04530, Mexico
| | | | - Sergio Juárez-Méndez
- Laboratory of Experimental Oncology, National Institute of Pediatrics, Mexico City 04530, Mexico
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28
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Antonelli M, Fadda A, Loi E, Moi L, Zavattari C, Sulas P, Gentilini D, Cameli C, Bacchelli E, Badiali M, Arcella A, Morra I, Giangaspero F, Zavattari P. Integrated DNA methylation analysis identifies topographical and tumoral biomarkers in pilocytic astrocytomas. Oncotarget 2018; 9:13807-13821. [PMID: 29568396 PMCID: PMC5862617 DOI: 10.18632/oncotarget.24480] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/31/2018] [Indexed: 12/20/2022] Open
Abstract
Pilocytic astrocytoma (PA) is the most common glioma in pediatric patients and occurs in different locations. Chromosomal alterations are mostly located at chromosome 7q34 comprising the BRAF oncogene with consequent activation of the mitogen-activated protein kinase pathway. Although genetic and epigenetic alterations characterizing PA from different localizations have been reported, the role of epigenetic alterations in PA development is still not clear. The aim of this study was to investigate whether distinctive methylation patterns may define biologically relevant groups of PAs. Integrated DNA methylation analysis was performed on 20 PAs and 4 normal brain samples by Illumina Infinium HumanMethylation27 BeadChips. We identified distinct methylation profiles characterizing PAs from different locations (infratentorial vs supratentorial) and tumors with onset before and after 3 years of age. These results suggest that PA may be related to the specific brain site where the tumor arises from region-specific cells of origin. We identified and validated in silico the methylation alterations of some CpG islands. Furthermore, we evaluated the expression levels of selected differentially methylated genes and identified two biomarkers, one, IRX2, related to the tumor localization and the other, TOX2, as tumoral biomarker.
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Affiliation(s)
- Manila Antonelli
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, University Sapienza of Rome, Rome, Italy
| | - Antonio Fadda
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Eleonora Loi
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Loredana Moi
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy.,Bone Marrow Transplantation Unit, Microcitemico Children's Hospital, Cagliari, Italy
| | | | - Pia Sulas
- Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy.,Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | - Cinzia Cameli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Manuela Badiali
- Bone Marrow Transplantation Unit, Microcitemico Children's Hospital, Cagliari, Italy
| | | | - Isabella Morra
- Department of Pathology OIRM-S, Anna Hospital, A.O.U. City of Health and Science, Turin, Italy
| | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, University Sapienza of Rome, Rome, Italy.,IRCCS Neuromed, Pozzilli, Italy
| | - Patrizia Zavattari
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
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29
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Sadhu A, Bhattacharyya B. Common Subcluster Mining in Microarray Data for Molecular Biomarker Discovery. Interdiscip Sci 2019; 11:348-59. [PMID: 29022249 DOI: 10.1007/s12539-017-0262-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 08/07/2017] [Accepted: 09/12/2017] [Indexed: 12/11/2022]
Abstract
Molecular biomarkers can be potential facilitators for detection of cancer at early stage which is otherwise difficult through conventional biomarkers. Gene expression data from microarray experiments on both normal and diseased cell samples provide enormous scope to explore genetic relations of disease using computational techniques. Varied patterns of expressions of thousands of genes at different cell conditions along with inherent experimental error make the task of isolating disease related genes challenging. In this paper, we present a data mining method, common subcluster mining (CSM), to discover highly perturbed genes under diseased condition from differential expression patterns. The method builds heap through superposing near centroid clusters from gene expression data of normal samples and extracts its core part. It, thus, isolates genes exhibiting the most stable state across normal samples and constitute a reference set for each centroid. It performs the same operation on datasets from corresponding diseased samples and isolates the genes showing drastic changes in their expression patterns. The method thus finds the disease-sensitive genesets when applied to datasets of lung cancer, prostrate cancer, pancreatic cancer, breast cancer, leukemia and pulmonary arterial hypertension. In majority of the cases, few new genes are found over and above some previously reported ones. Genes with distinct deviations in diseased samples are prospective candidates for molecular biomarkers of the respective disease.
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30
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Lobbardi R, Pinder J, Martinez-Pastor B, Theodorou M, Blackburn JS, Abraham BJ, Namiki Y, Mansour M, Abdelfattah NS, Molodtsov A, Alexe G, Toiber D, de Waard M, Jain E, Boukhali M, Lion M, Bhere D, Shah K, Gutierrez A, Stegmaier K, Silverman LB, Sadreyev RI, Asara JM, Oettinger MA, Haas W, Look AT, Young RA, Mostoslavsky R, Dellaire G, Langenau DM. TOX Regulates Growth, DNA Repair, and Genomic Instability in T-cell Acute Lymphoblastic Leukemia. Cancer Discov 2017; 7:1336-1353. [PMID: 28974511 DOI: 10.1158/2159-8290.cd-17-0267] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/07/2017] [Accepted: 09/07/2017] [Indexed: 01/03/2023]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy of thymocytes. Using a transgenic screen in zebrafish, thymocyte selection-associated high mobility group box protein (TOX) was uncovered as a collaborating oncogenic driver that accelerated T-ALL onset by expanding the initiating pool of transformed clones and elevating genomic instability. TOX is highly expressed in a majority of human T-ALL and is required for proliferation and continued xenograft growth in mice. Using a wide array of functional analyses, we uncovered that TOX binds directly to KU70/80 and suppresses recruitment of this complex to DNA breaks to inhibit nonhomologous end joining (NHEJ) repair. Impaired NHEJ is well known to cause genomic instability, including development of T-cell malignancies in KU70- and KU80-deficient mice. Collectively, our work has uncovered important roles for TOX in regulating NHEJ by elevating genomic instability during leukemia initiation and sustaining leukemic cell proliferation following transformation.Significance: TOX is an HMG box-containing protein that has important roles in T-ALL initiation and maintenance. TOX inhibits the recruitment of KU70/KU80 to DNA breaks, thereby inhibiting NHEJ repair. Thus, TOX is likely a dominant oncogenic driver in a large fraction of human T-ALL and enhances genomic instability. Cancer Discov; 7(11); 1336-53. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 1201.
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Affiliation(s)
- Riadh Lobbardi
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.,Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - Jordan Pinder
- Departments of Pathology and Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, Canada
| | | | - Marina Theodorou
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.,Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Harvard Stem Cell Institute, Cambridge, Massachusetts
| | | | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
| | - Yuka Namiki
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Marc Mansour
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Haematology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Nouran S Abdelfattah
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.,Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Aleksey Molodtsov
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.,Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Debra Toiber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Manon de Waard
- Institute of Biology Leiden, University of Leiden, Leiden, the Netherlands
| | - Esha Jain
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Myriam Boukhali
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Mattia Lion
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Deepak Bhere
- Center for Stem Cell Therapeutics and Imaging, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Khalid Shah
- Center for Stem Cell Therapeutics and Imaging, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Alejandro Gutierrez
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Ruslan I Sadreyev
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Marjorie A Oettinger
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
| | - Raul Mostoslavsky
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Graham Dellaire
- Departments of Pathology and Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, Canada
| | - David M Langenau
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts. .,Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Harvard Stem Cell Institute, Cambridge, Massachusetts.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
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31
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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 DOI: 10.1016/j.canlet.2017.09.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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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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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32
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Hsu YL, Hung JY, Lee YL, Chen FW, Chang KF, Chang WA, Tsai YM, Chong IW, Kuo PL. Identification of novel gene expression signature in lung adenocarcinoma by using next-generation sequencing data and bioinformatics analysis. Oncotarget 2017; 8:104831-104854. [PMID: 29285217 PMCID: PMC5739604 DOI: 10.18632/oncotarget.21022] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/28/2017] [Indexed: 12/22/2022] Open
Abstract
Lung adenocarcinoma is one of the leading causes of cancer-related death worldwide. We showed transcriptomic profiles in three pairs of tumors and adjacent non-tumor lung tissues using next-generation sequencing (NGS) to screen protein-coding RNAs and microRNAs. Combined with meta-analysis from the Oncomine and Gene Expression Omnibus (GEO) databases, we identified a representative genetic expression signature in lung adenocarcinoma. There were 9 upregulated genes, and 8 downregulated genes in lung adenocarcinoma. The analysis of the effects from each gene expression on survival outcome indicated that 6 genes (AGR2, SPDEF, CDKN2A, CLDN3, SFN, and PHLDA2) play oncogenic roles, and 7 genes (PDK4, FMO2, CPED1, GNG11, IL33, BTNL9, and FABP4) act as tumor suppressors in lung adenocarcinoma. In addition, we also identified putative genetic interactions, in which there were 5 upregulated microRNAs with specific targets - hsa-miR-183-5p-BTNL9, hsa-miR-33b-5p-CPED1, hsa-miR-429-CPED1, hsa-miR-182-5p-FMO2, and hsa-miR-130b-5p-IL33. These 5 microRNAs have been shown to be associated with tumorigenesis in lung cancer. Our findings suggest that these genetic interactions play important roles in the progression of lung adenocarcinoma. We propose that this molecular change of genetic expression may represent a novel signature in lung adenocarcinoma, which may be developed for diagnostic and therapeutic strategies in the future.
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Affiliation(s)
- Ya-Ling Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jen-Yu Hung
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yen-Lung Lee
- Division of Thoracic surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Feng-Wei Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | | | - Wei-An Chang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ying-Ming Tsai
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Inn-Wen Chong
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Respiratory Therapy, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Po-Lin Kuo
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung, Taiwan.,Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung, Taiwan
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Crujeiras AB, Diaz-Lagares A, Stefansson OA, Macias-Gonzalez M, Sandoval J, Cueva J, Lopez-Lopez R, Moran S, Jonasson JG, Tryggvadottir L, Olafsdottir E, Tinahones FJ, Carreira MC, Casanueva FF, Esteller M. Obesity and menopause modify the epigenomic profile of breast cancer. Endocr Relat Cancer 2017; 24:351-363. [PMID: 28442560 DOI: 10.1530/erc-16-0565] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 04/25/2017] [Indexed: 12/20/2022]
Abstract
Obesity is a high risk factor for breast cancer. This relationship could be marked by a specific methylome. The current work was aimed to explore the impact of obesity and menopausal status on variation in breast cancer methylomes. Data from Infinium 450K array-based methylomes of 64 breast tumors were coupled with information on BMI and menopausal status. Additionally, DNA methylation results were validated in 18 non-tumor and 81 tumor breast samples. Breast tumors arising in either pre- or postmenopausal women stratified by BMI or menopausal status alone were not associated with a specific DNA methylation pattern. Intriguingly, the DNA methylation pattern identified in association with the high-risk group (postmenopausal women with high BMI (>25) and premenopausal women with normal or low BMI < 25) exclusively characterized by hypermethylation of 1287 CpG sites as compared with the low-risk group. These CpG sites included the promoter region of fourteen protein-coding genes of which CpG methylation over the ZNF577 promoter region represents the top scoring associated event. In an independent cohort, the ZNF577 promoter methylation remained statistically significant in association with the high-risk group. Additionally, the impact of ZNF577 promoter methylation on mRNA expression levels was demonstrated in breast cancer cell lines after treatment with a demethylating agent (5-azacytidine). In conclusion, the epigenome of breast tumors is affected by a complex interaction between BMI and menopausal status. The ZNF577 methylation quantification is clearly relevant for the development of novel biomarkers of precision therapy in breast cancer.
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Affiliation(s)
- Ana B Crujeiras
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Laboratory of Molecular and Cellular EndocrinologyInstituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela University (USC), Santiago de Compostela, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Translational Medical Oncology Group (Oncomet)Instituto de Investigación Sanitaria (IDIS); Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and CIBER de Cancer (CIBERONC), Santiago de Compostela, Spain
| | - Olafur A Stefansson
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Cancer Research LaboratoryFaculty of Medicine, University of Iceland, Reykjavic, Iceland
| | - Manuel Macias-Gonzalez
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
- Unidad de Gestión Clínica de Endocrinología y NutriciónInstituto de Investigación Biomédica de Málaga (IBIMA), Complejo Hospitalario de Málaga (Virgen de la Victoria), Universidad de Málaga, Málaga, Spain
| | - Juan Sandoval
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Juan Cueva
- Translational Medical Oncology Group (Oncomet)Instituto de Investigación Sanitaria (IDIS); Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and CIBER de Cancer (CIBERONC), Santiago de Compostela, Spain
| | - Rafael Lopez-Lopez
- Translational Medical Oncology Group (Oncomet)Instituto de Investigación Sanitaria (IDIS); Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and CIBER de Cancer (CIBERONC), Santiago de Compostela, Spain
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Jon G Jonasson
- Department of Pathology and the Icelandic Cancer RegistryIcelandic Cancer society and Landspitali University Hospital, Reykjavik, Iceland
| | - Laufey Tryggvadottir
- Department of Pathology and the Icelandic Cancer RegistryIcelandic Cancer society and Landspitali University Hospital, Reykjavik, Iceland
| | - Elinborg Olafsdottir
- Department of Pathology and the Icelandic Cancer RegistryIcelandic Cancer society and Landspitali University Hospital, Reykjavik, Iceland
| | - Francisco J Tinahones
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
- Unidad de Gestión Clínica de Endocrinología y NutriciónInstituto de Investigación Biomédica de Málaga (IBIMA), Complejo Hospitalario de Málaga (Virgen de la Victoria), Universidad de Málaga, Málaga, Spain
| | - Marcos C Carreira
- Laboratory of Molecular and Cellular EndocrinologyInstituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela University (USC), Santiago de Compostela, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
| | - Felipe F Casanueva
- Laboratory of Molecular and Cellular EndocrinologyInstituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela University (USC), Santiago de Compostela, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Department of Physiological Sciences IISchool of Medicine, University of Barcelona and Instituto Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
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Tessema M, Yingling CM, Picchi MA, Wu G, Liu Y, Weissfeld JL, Siegfried JM, Tesfaigzi Y, Belinsky SA. Epigenetic Repression of CCDC37 and MAP1B Links Chronic Obstructive Pulmonary Disease to Lung Cancer. J Thorac Oncol 2015; 10:1181-8. [PMID: 26200272 DOI: 10.1097/JTO.0000000000000592] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Lung cancer and chronic obstructive pulmonary disease (COPD) share environmental risk factors. COPD also increases the risk of lung cancer; however, the molecular mechanisms are unclear. METHODS An epigenome-wide association study of lung tumors and cancer-free lung tissue (CFLT) pairs from non-small-cell lung cancer cases with (n = 18) or without (n = 17) COPD was conducted using the HumanMethylation450 beadchip (HM450K). COPD-associated methylation of top-ranked genes was confirmed in a larger sample set, independently validated, and their potential as sputum-based biomarkers was investigated. RESULTS Methylation of CCDC37 and MAP1B was more prevalent in lung tumors from COPD than non-COPD cases [54 of 71 (76%) versus 20 of 46 (43%), p = 0.0013] and [48 of 71 (68%) versus 17 of 46 (37%), p = 0.0035], respectively, after adjustment for age, sex, smoking status, and tumor histology. HM450K probes across CCDC37 and MAP1B promoters showed higher methylation in tumors than CFLT with the highest methylation seen in tumors from COPD cases (p < 0.05). These results were independently validated using The Cancer Genome Atlas data. CCDC37 methylation was more prevalent in sputum from COPD than non-COPD smokers (p < 0.005) from two cohorts. CCDC37 and MAP1B expression was dramatically repressed in tumors and CFLT from COPD than non-COPD cases, p less than 0.02. CONCLUSIONS The reduced expression of CCDC37 and MAP1B associated with COPD likely predisposes these genes to methylation that in turn, may contribute to lung cancer.
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Han CC, Yue LL, Yang Y, Jian BY, Ma LW, Liu JC. TOX3 protein expression is correlated with pathological characteristics in breast cancer. Oncol Lett 2016; 11:1762-1768. [PMID: 26998074 PMCID: PMC4774471 DOI: 10.3892/ol.2016.4117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 12/23/2015] [Indexed: 01/20/2023] Open
Abstract
TOX3 is a newly identified gene that has been observed to correlate with breast cancer by genome-wide association studies (GWAS) in recent years. In addition, it has been noted that single-nucleotide polymorphisms (SNPs) in the TOX3 gene have a strong correlation with estrogen receptor (ER)-positive tumors. However, the role of TOX3 in breast carcinoma development is still unclear. There are limited studies on the subject of TOX3 mRNA expression in breast tumors and little information on the variation of TOX3 protein expression in relation to the clinical pathological features in breast cancer and healthy tissues. In this study, we characterize the protein expression of TOX3 in breast tumors with respect to various clinical and pathological characteristics and explore the correlation between TOX3 protein expression and ER-positive tumors. A breast cancer tissue microarray containing 267 human breast tumors and 25 healthy controls, breast cancer cell lines (ZR-75-1, MDA-MB-231, MCF-7 and Bcap-37) with positive or negative ER expression, tumor tissues and matched controls were used to analyze the protein expression levels of TOX3 by immunohistochemistry, western blot analysis and quantitative polymerase chain reaction. Among the 267 breast tumor specimens, ER expression was detected in 66 tumor tissues. The expression levels of TOX3 increased in breast carcinoma tissue compared with controls, and were higher in advanced carcinoma (T3 and T4), lymph node metastases tissues (N2) and stage III tissues. Furthermore, TOX3 protein expression was more intense in ER-positive tumors, but did not demonstrate a statistical significance. However, it was significantly increased in ER-positive breast cancer cell lines (ZR-75-1, MCF-7 and Bcap-37) compared with the MDA-MB-231 cell line, which had ER-negative expression. Our findings provide support to the hypothesis that TOX3 has a strong correlation with the development of breast cancer. The current study is likely to assist in investigating the mechanisms involved in breast cancer development.
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Affiliation(s)
- Cui-Cui Han
- Institute of Medicine, Qiqihar Medical University, Qiqihar, Heilongjiang 161042, P.R. China
| | - Li-Ling Yue
- Institute of Medicine, Qiqihar Medical University, Qiqihar, Heilongjiang 161042, P.R. China
| | - Ying Yang
- Institute of Medicine, Qiqihar Medical University, Qiqihar, Heilongjiang 161042, P.R. China
| | - Bai-Yu Jian
- Institute of Medicine, Qiqihar Medical University, Qiqihar, Heilongjiang 161042, P.R. China
| | - Li-Wei Ma
- Institute of Medicine, Qiqihar Medical University, Qiqihar, Heilongjiang 161042, P.R. China
| | - Ji-Cheng Liu
- Institute of Medicine, Qiqihar Medical University, Qiqihar, Heilongjiang 161042, P.R. China
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36
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Yu X, Li Z. TOX gene: a novel target for human cancer gene therapy. Am J Cancer Res 2015; 5:3516-3524. [PMID: 26885442 PMCID: PMC4731627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 06/26/2015] [Indexed: 06/05/2023] Open
Abstract
Thymocyte selection-associated high mobility group box factor (TOX) is a member of an evolutionarily conserved DNA-binding protein family and is expressed in several immune-relevant cell subsets. TOX encodes a nuclear protein of the high-mobility group box superfamily. It contains a DNA-binding domain, which allows it to regulate transcription by modifying local chromatin structure and modulating the formation of multi-protein complexes. Previous studies have shown that TOX play important roles in immune system. More recently, several studies have described TOX expression is frequently upregulated in diverse types of human tumors and the overregulation often associates with tumor progression. Moreover, TOXis involved in the control of cell apoptosis, growth, metastasis, DNA repair and so on. In this review, we provide an overview of current knowledge concerning the role of TOX in tumor development and progression biology function. To our knowledge, this is the first review about the role of thisnew oncogene in tumor development and progression.
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Affiliation(s)
- Xin Yu
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100042, China
| | - Zheng Li
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
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37
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Seehus CR, Kaye J. The Role of TOX in the Development of Innate Lymphoid Cells. Mediators Inflamm 2015; 2015:243868. [PMID: 26556952 DOI: 10.1155/2015/243868] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/27/2015] [Indexed: 11/18/2022] Open
Abstract
TOX, an evolutionarily conserved member of the HMG-box family of proteins, is essential for the development of various cells of both the innate and adaptive immune system. TOX is required for the development of CD4(+) T lineage cells in the thymus, including natural killer T and T regulatory cells, as well as development of natural killer cells and fetal lymphoid tissue inducer cells, the latter required for lymph node organogenesis. Recently, we have identified a broader role for TOX in the innate immune system, demonstrating that this nuclear protein is required for generation of bone marrow progenitors that have potential to give rise to all innate lymphoid cells. Innate lymphoid cells, classified according to transcription factor expression and cytokine secretion profiles, derive from common lymphoid progenitors in the bone marrow and require Notch signals for their development. We discuss here the role of TOX in specifying CLP toward an innate lymphoid cell fate and hypothesize a possible role for TOX in regulating Notch gene targets during innate lymphoid cell development.
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38
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Bawa P, Zackaria S, Verma M, Gupta S, Srivatsan R, Chaudhary B, Srinivasan S. Integrative Analysis of Normal Long Intergenic Non-Coding RNAs in Prostate Cancer. PLoS One 2015; 10:e0122143. [PMID: 25933431 PMCID: PMC4416928 DOI: 10.1371/journal.pone.0122143] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/10/2015] [Indexed: 02/03/2023] Open
Abstract
Recently, large numbers of normal human tissues have been profiled for non-coding RNAs and more than fourteen thousand long intergenic non-coding RNAs (lincRNAs) are found expressed in normal human tissues. The functional roles of these normal lincRNAs (nlincRNAs) in the regulation of protein coding genes in normal and disease biology are yet to be established. Here, we have profiled two RNA-seq datasets including cancer and matched non-neoplastic tissues from 12 individuals from diverse demography for both coding genes and nlincRNAs. We find 130 nlincRNAs significantly regulated in cancer, with 127 regulated in the same direction in the two datasets. Interestingly, according to Illumina Body Map, significant numbers of these nlincRNAs display baseline null expression in normal prostate tissues but are specific to other tissues such as thyroid, kidney, liver and testis. A number of the regulated nlincRNAs share loci with coding genes, which are either co-regulated or oppositely regulated in all cancer samples studied here. For example, in all cancer samples i) the nlincRNA, TCONS_00029157, and a neighboring tumor suppressor factor, SIK1, are both down regulated; ii) several thyroid-specific nlincRNAs in the neighborhood of the thyroid-specific gene TPO, are both up-regulated; and iii) the TCONS_00010581, an isoform of HEIH, is down-regulated while the neighboring EZH2 gene is up-regulated in cancer. Several nlincRNAs from a prostate cancer associated chromosomal locus, 8q24, are up-regulated in cancer along with other known prostate cancer associated genes including PCAT-1, PVT1, and PCAT-92. We observe that there is significant bias towards up-regulation of nlincRNAs with as high as 118 out of 127 up-regulated in cancer, even though regulation of coding genes is skewed towards down-regulation. Considering that all reported cancer associated lincRNAs (clincRNAs) are biased towards up-regulation, we conclude that this bias may be functionally relevant.
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Affiliation(s)
- Pushpinder Bawa
- IBAB, Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
- Manipal University, Manipal, Karnataka, India
| | - Sajna Zackaria
- IBAB, Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
| | - Mohit Verma
- IBAB, Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
| | - Saurabh Gupta
- IBAB, Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
| | - R Srivatsan
- IBAB, Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
| | - Bibha Chaudhary
- IBAB, Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
| | - Subhashini Srinivasan
- IBAB, Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
- * E-mail:
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Carrió E, Díez-Villanueva A, Lois S, Mallona I, Cases I, Forn M, Peinado MA, Suelves M. Deconstruction of DNA methylation patterns during myogenesis reveals specific epigenetic events in the establishment of the skeletal muscle lineage. Stem Cells 2015; 33:2025-36. [PMID: 25801824 DOI: 10.1002/stem.1998] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/06/2015] [Indexed: 12/17/2022]
Abstract
The progressive restriction of differentiation potential from pluripotent embryonic stem cells (ESCs) to tissue-specific stem cells involves widespread epigenetic reprogramming, including modulation of DNA methylation patterns. Skeletal muscle stem cells are required for the growth, maintenance, and regeneration of skeletal muscle. To investigate the contribution of DNA methylation to the establishment of the myogenic program, we analyzed ESCs, skeletal muscle stem cells in proliferating (myoblasts) and differentiating conditions (myotubes), and mature myofibers. About 1.000 differentially methylated regions were identified during muscle-lineage determination and terminal differentiation, mainly located in gene bodies and intergenic regions. As a whole, myogenic stem cells showed a gain of DNA methylation, while muscle differentiation was accompanied by loss of DNA methylation in CpG-poor regions. Notably, the hypomethylated regions in myogenic stem cells were neighbored by enhancer-type chromatin, suggesting the involvement of DNA methylation in the regulation of cell-type specific enhancers. Interestingly, we demonstrated the hypomethylation of the muscle cell-identity Myf5 super-enhancer only in muscle cells. Furthermore, we observed that upstream stimulatory factor 1 binding to Myf5 super-enhancer occurs upon DNA demethylation in myogenic stem cells. Taken altogether, we characterized the unique DNA methylation signature of skeletal muscle stem cells and highlighted the importance of DNA methylation-mediated regulation of cell identity Myf5 super-enhancer during cellular differentiation.
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Affiliation(s)
- Elvira Carrió
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC).,Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Anna Díez-Villanueva
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC).,Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Sergi Lois
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC)
| | - Izaskun Mallona
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC).,Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Ildefonso Cases
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC)
| | - Marta Forn
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC)
| | - Miguel A Peinado
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC).,Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Mònica Suelves
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC).,Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
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Abstract
Mycosis fungoides (MF) is a low-grade lymphoma characterized by clonal expansion of atypical CD4+ skin-homing T lymphocytes. Herein, we examined the role of thymocytes selection associated HMG-box (TOX), a gene previously found to be unregulated in MF skin biopsies, in MF pathogenesis. TOX encodes a high-mobility group family (HMG) domain DNA binding nuclear protein, which regulates the differentiation of developing T-cells. First, we confirmed that TOX expression levels in MF were increased compared with those in benign inflammatory dermatitis (BID) and normal skin. In addition, TOX level increased with the progression MF from patch stage to tumor stage. Overexpression of TOX accelerated the proliferation and migration of MF cell lines in vitro, which were blocked by AKT inhibitors. In conclusion, our study confirmed that TOX was highly expressed in MF lesions and accelerates the proliferation and migration of MF. TOX is a diagnostic marker for MF and may play a pathogenic role in disease progression.
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Affiliation(s)
- Xin Yu
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Yixin Luo
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Jie Liu
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Yuehua Liu
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Qiuning Sun
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
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Tessema M, Yingling CM, Snider AM, Do K, Juri DE, Picchi MA, Zhang X, Liu Y, Leng S, Tellez CS, Belinsky SA. GATA2 is epigenetically repressed in human and mouse lung tumors and is not requisite for survival of KRAS mutant lung cancer. J Thorac Oncol 2014; 9:784-93. [PMID: 24807155 DOI: 10.1097/JTO.0000000000000165] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION GATA2 was recently described as a critical survival factor and therapeutic target for KRAS mutant non-small-cell lung cancer (NSCLC). However, whether this role is affected by epigenetic repression of GATA2 in lung cancer is unclear. METHODS GATA2 expression and promoter CpG island methylation were evaluated using human and mouse NSCLC cell lines and tumor-normal pairs. In vitro assays were used to study GATA2 repression on cell survival and during tobacco carcinogen-induced transformation. RESULTS GATA2 expression in KRAS wild-type (n = 15) and mutant (n = 10) NSCLC cell lines and primary lung tumors (n = 24) was significantly lower, 1.3- to 33.6-fold (p = 2.2 × 10(9)), compared with corresponding normal lung. GATA2 promoter was unmethylated in normal lung (0 of 10) but frequently methylated in lung tumors (96%, 159 of 165) and NSCLC cell lines (97%, 30 of 31). This highly prevalent aberrant methylation was independently validated using The Cancer Genome Atlas data for 369 NSCLC tumor-normal pairs. In vitro studies using an established carcinogen-induced premalignancy model revealed that GATA2 expression was initially repressed by chromatin remodeling followed by cytosine methylation during transformation. Similarly, expression of GATA2 in NNK-induced mouse lung tumors (n = 6) and cell lines (n = 5) was fivefold and 100-fold lower, respectively, than normal mouse lung. Finally, siRNA-mediated knockdown of GATA2 in KRAS mutant (human [n = 4] and murine [n = 5]) and wild-type (human [n = 4]) NSCLC cell lines showed that further reduction of expression (up to 95%) does not induce cell death. CONCLUSION GATA2 is epigenetically repressed in human and mouse lung tumors and its further inhibition is not a valid therapeutic strategy for KRAS mutant lung cancer.
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Vong QP, Leung WH, Houston J, Li Y, Rooney B, Holladay M, Oostendorp RA, Leung W. TOX2 regulates human natural killer cell development by controlling T-BET expression. Blood 2014; 124:3905-13. [PMID: 25352127 DOI: 10.1182/blood-2014-06-582965] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thymocyte selection-associated high mobility group box protein family member 2 (TOX2) is a transcription factor belonging to the TOX family that shares a highly conserved high mobility group DNA-binding domain with the other TOX members. Although TOX1 has been shown to be an essential regulator of T-cell and natural killer (NK) cell differentiation in mice, little is known about the roles of the other TOX family members in lymphocyte development, particularly in humans. In this study, we found that TOX2 was preferentially expressed in mature human NK cells (mNK) and was upregulated during in vitro differentiation of NK cells from human umbilical cord blood (UCB)-derived CD34(+) cells. Gene silencing of TOX2 intrinsically hindered the transition between early developmental stages of NK cells, whereas overexpression of TOX2 enhanced the development of mNK cells from UCB CD34(+) cells. We subsequently found that TOX2 was independent of ETS-1 but could directly upregulate the transcription of TBX21 (encoding T-BET). Overexpression of T-BET rescued the TOX2 knockdown phenotypes. Given the essential function of T-BET in NK cell differentiation, TOX2 therefore plays a crucial role in controlling normal NK cell development by acting upstream of TBX21 transcriptional regulation.
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Basson J, Sung YJ, Schwander K, Kume R, Simino J, de las Fuentes L, Rao D. Gene-education interactions identify novel blood pressure loci in the Framingham Heart Study. Am J Hypertens 2014; 27:431-44. [PMID: 24473254 DOI: 10.1093/ajh/hpt283] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Blood pressure (BP) variability has a genetic component, most of which has yet to be attributed to specific variants. One promising strategy for gene discovery is analysis of interactions between single-nucleotide polymorphisms (SNPs) and BP-related factors, including age, sex, and body mass index (BMI). Educational attainment, a marker for socioeconomic status, has effects on both BP and BMI. METHODS We investigated SNP-education interaction effects on BP in genome-wide data on 3,836 subjects in families from the Framingham Heart Study. The ABEL suite was used to adjust for age, sex, BMI, medication use, and kinship and to perform 1 degree-of-freedrom (df) and 2 df SNP-education interaction tests. RESULTS An SNP in PTN was associated with increased systolic BP (5.4mm Hg per minor allele) in those without a bachelor's degree but decreased systolic BP (1.6mm Hg per allele) in those with a bachelor's degree (2 df; P = 2.08 × 10(-8)). An SNP in TOX2 was associated with increased diastolic BP (DBP; 4.1mm Hg per minor allele) in those with no more educational attainment than high school but decreased DBP in those with education past high school (-0.7; 1 df; P = 3.74 × 10(-8)). Three suggestive associations were also found: in MYO16 (pulse pressure: 2 df; P = 2.89 × 10(-7)), in HAS2 (DBP: 1 df; P = 1.41 × 10(-7)), and in DLEU2 (DBP: 2 df; P = 1.93 × 10(-7)). All 5 genes are related to BP, including roles in vasodilation and angiogenesis for PTN and TOX2. CONCLUSIONS PTN and TOX2 are associated with BP. Analyzing SNP-education interactions may detect novel associations. Education may be a surrogate for unmeasured exposures and behaviors modifying SNP effects on BP.
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Affiliation(s)
- Jacob Basson
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, USA
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Tessema M, Yingling CM, Liu Y, Tellez CS, Van Neste L, Baylin SS, Belinsky SA. Genome-wide unmasking of epigenetically silenced genes in lung adenocarcinoma from smokers and never smokers. Carcinogenesis 2014; 35:1248-57. [PMID: 24398667 DOI: 10.1093/carcin/bgt494] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lung cancer in never smokers (NS) shows striking demographic, clinicopathological and molecular distinctions from the disease in smokers (S). Studies on selected genetic and epigenetic alterations in lung cancer identified that the frequency and profile of some abnormalities significantly differ by smoking status. This study compared the transcriptome of lung adenocarcinoma cell lines derived from S (n = 3) and NS (n = 3) each treated with vehicle (control), histone deacetylation inhibitor (trichostatin A) or DNA methylation inhibitor (5-aza-2'-deoxycytidine). Among 122 genes reexpressed following 5-aza-2'-deoxycytidine but not trichostatin A treatment in two or more cell lines (including 32 genes in S-only and 12 NS-only), methylation was validated for 80% (98/122 genes). After methylation analysis of 20 normal tissue samples and 14 additional non-small cell lung cancer cell lines (total 20), 39 genes frequently methylated in normal (>20%, 4/20) and 21 genes rarely methylated in non-small cell lung cancer (≤10%, 2/20) were excluded. The prevalence for methylation of the remaining 38 genes in lung adenocarcinomas from S (n = 97) and NS (n = 75) ranged from 8-89% and significantly differs between S and NS for CPEB1, CST6, EMILIN2, LAYN and MARVELD3 (P < 0.05). Furthermore, methylation of EMILIN2, ROBO3 and IGDCC4 was more prevalent in advanced (Stage II-IV, n = 61) than early (Stage I, n = 110) tumors. Knockdown of MARVELD3, one of the novel epigenetically silenced genes, by small interfering RNA significantly reduced anchorage-independent growth of lung cancer cells (P < 0.001). Collectively, this study has identified multiple, novel, epigenetically silenced genes in lung cancer and provides invaluable resources for the development of diagnostic and prognostic biomarkers.
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Affiliation(s)
- Mathewos Tessema
- Department of Lung Cancer, Lovelace Respiratory Research Institute, Albuquerque, NM 87108, USA, MDxHealth Inc., Irvine, CA 92618, USA, Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD, Maastricht, The Netherlands and Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Christin M Yingling
- Department of Lung Cancer, Lovelace Respiratory Research Institute, Albuquerque, NM 87108, USA, MDxHealth Inc., Irvine, CA 92618, USA, Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD, Maastricht, The Netherlands and Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Yushi Liu
- Department of Lung Cancer, Lovelace Respiratory Research Institute, Albuquerque, NM 87108, USA, MDxHealth Inc., Irvine, CA 92618, USA, Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD, Maastricht, The Netherlands and Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Carmen S Tellez
- Department of Lung Cancer, Lovelace Respiratory Research Institute, Albuquerque, NM 87108, USA, MDxHealth Inc., Irvine, CA 92618, USA, Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD, Maastricht, The Netherlands and Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Leander Van Neste
- MDxHealth Inc., Irvine, CA 92618, USA, Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD, Maastricht, The Netherlands and
| | - Stephen S Baylin
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Steven A Belinsky
- Department of Lung Cancer, Lovelace Respiratory Research Institute, Albuquerque, NM 87108, USA, MDxHealth Inc., Irvine, CA 92618, USA, Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD, Maastricht, The Netherlands and Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
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Akulenko R, Helms V. DNA co-methylation analysis suggests novel functional associations between gene pairs in breast cancer samples. Hum Mol Genet 2013; 22:3016-22. [PMID: 23571108 DOI: 10.1093/hmg/ddt158] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Localized promoter hypermethylation and overall DNA hypomethylation have been associated with the presence of tumor in humans. Yet, despite the large amount of recently produced epigenetic data, there is still a lack of understanding on how several genes behave in tumor cells with respect to their epigenetic alterations such as DNA methylation. Here we performed a novel type of analysis that measures the correlation of DNA methylation levels between two genes across many samples. We linked this so-called co-methylation to the genomic distance of these genes, their functional similarity and their expression levels. Co-methylation analysis of more than 300 breast cancer samples from the TCGA portal yielded 187 pairs of genes showing Pearson correlation coefficients |r| ≥ 0.75. These pairs were formed by 133 genes. Less than half of these pairs are located on the same chromosome. For these, we found that the level of co-methylation is weakly anti-correlated with genomic distance (r = -0.29). Linking co-methylation with the functional similarity of genes showed that genes with r ≥ 0.8 tend to have similar molecular function and to be involved in the same biological process as described in the Gene Ontology project. Clustering of highly co-methylated genes identified four enriched KEGG pathways. Hence we have introduced co-methylation as a new indicator to discover functional associations between gene pairs in breast cancer and furthermore to discover new candidate genes that should be inspected more closely in the context of the studied disease.
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Affiliation(s)
- Ruslan Akulenko
- Center for Bioinformatics, Saarland University, Saarbrücken D-66041, Germany
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