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De Beck L, Awad RM, Basso V, Casares N, De Ridder K, De Vlaeminck Y, Gnata A, Goyvaerts C, Lecocq Q, San José-Enériz E, Verhulst S, Maes K, Vanderkerken K, Agirre X, Prosper F, Lasarte JJ, Mondino A, Breckpot K. Inhibiting Histone and DNA Methylation Improves Cancer Vaccination in an Experimental Model of Melanoma. Front Immunol 2022; 13:799636. [PMID: 35634329 PMCID: PMC9134079 DOI: 10.3389/fimmu.2022.799636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Immunotherapy has improved the treatment of malignant skin cancer of the melanoma type, yet overall clinical response rates remain low. Combination therapies could be key to meet this cogent medical need. Because epigenetic hallmarks represent promising combination therapy targets, we studied the immunogenic potential of a dual inhibitor of histone methyltransferase G9a and DNA methyltransferases (DNMTs) in the preclinical B16-OVA melanoma model. Making use of tumor transcriptomic and functional analyses, methylation-targeted epigenetic reprogramming was shown to induce tumor cell cycle arrest and apoptosis in vitro coinciding with transient tumor growth delay and an IFN-I response in immune-competent mice. In consideration of a potential impact on immune cells, the drug was shown not to interfere with dendritic cell maturation or T-cell activation in vitro. Notably, the drug promoted dendritic cell and, to a lesser extent, T-cell infiltration in vivo, yet failed to sensitize tumor cells to programmed cell death-1 inhibition. Instead, it increased therapeutic efficacy of TCR-redirected T cell and dendritic cell vaccination, jointly increasing overall survival of B16-OVA tumor-bearing mice. The reported data confirm the prospect of methylation-targeted epigenetic reprogramming in melanoma and sustain dual G9a and DNMT inhibition as a strategy to tip the cancer-immune set-point towards responsiveness to active and adoptive vaccination against melanoma.
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Affiliation(s)
- Lien De Beck
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Laboratory of Hematology and Immunology, Department of Biomedical Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Robin Maximilian Awad
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Veronica Basso
- Lymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Noelia Casares
- Immunology and Immunotherapy Program, Centro de Investigación Médica Aplicada (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Universidad de Navarra, Pamplona, Spain
| | - Kirsten De Ridder
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Yannick De Vlaeminck
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Alessandra Gnata
- Lymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Cleo Goyvaerts
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Quentin Lecocq
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Edurne San José-Enériz
- Hemato-Oncology Program, Centro de Investigación Médica Aplicada (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Universidad de Navarra, Pamplona, Spain
| | - Stefaan Verhulst
- Liver Cell Biology Research Group, Department of Biomedical Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Ken Maes
- Laboratory of Hematology and Immunology, Department of Biomedical Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Center for Medical Genetics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Karin Vanderkerken
- Laboratory of Hematology and Immunology, Department of Biomedical Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Xabier Agirre
- Hemato-Oncology Program, Centro de Investigación Médica Aplicada (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Universidad de Navarra, Pamplona, Spain
- Laboratory of Cancer Epigenetics, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Felipe Prosper
- Hemato-Oncology Program, Centro de Investigación Médica Aplicada (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Universidad de Navarra, Pamplona, Spain
- Laboratory of Cancer Epigenetics, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology and Cell Therapy Department, Clínica Universidad de Navarra, Universidad de Navarra, Pamplona, Spain
| | - Juan José Lasarte
- Immunology and Immunotherapy Program, Centro de Investigación Médica Aplicada (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Universidad de Navarra, Pamplona, Spain
| | - Anna Mondino
- Lymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Karine Breckpot
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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Pan Z, Zhong B, Ling X, Zhang H, Tan Q, Huang D, Chen J, Zhang H, Zheng D, Li H, Chen X, Liu L. The DNMT1-associated lncRNA UCA1 was upregulated in TK6 cells transformed by long-term exposure to hydroquinone and benzene-exposed workers via DNA hypomethylation. J Biochem Mol Toxicol 2021; 35:e22920. [PMID: 34612549 DOI: 10.1002/jbt.22920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 08/09/2021] [Accepted: 09/20/2021] [Indexed: 11/09/2022]
Abstract
Exposure to benzene or its metabolite hydroquinone (HQ) is a risk factor for a series of myeloid malignancies, and long noncoding RNAs play an important role in the process of pathogenesis. Urothelial cancer-associated 1 (UCA1) functions as an oncogene in the development of acute myeloid leukemia. However, the association between DNMT1 and UCA1 with benzene or HQ exposure has not been explored. We characterized UCA1 expression in cells briefly exposed to HQ (HQ-ST cells) and HQ-induced malignantly transformed (TK6-HT cells) treated with 5-aza-2'-deoxycytidine (5-AzaC) or trichostatin A (TSA). Compared to that in control cells, UCA1 expression was increased, whereas DNMT1 was decreased in HQ-ST cells and TK6-HT cells treated with 5-AzaC or TSA. Moreover, UCA1 expression was also upregulated and positively correlated with benzene exposure time in benzene-exposed workers. Furthermore, the expression of UCA1 was negatively associated with the DNA methylation level of its promoter in benzene-exposed workers. DNMT1 rather than DNMT3b knockout in TK6-HT cells activated the expression of UCA1 by inducing its promoter hypomethylation. These results suggest that benzene or HQ exposure leads to UCA1 upregulation via DNA hypomethylation in the UCA1 promoter, which is mediated by DNMT1.
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Affiliation(s)
- Zhijie Pan
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China.,Department of Preventive Medicine, Guangdong Medical University, Dongguan, China
| | - Bohuan Zhong
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China.,Department of Preventive Medicine, Guangdong Medical University, Dongguan, China
| | - Xiaoxuan Ling
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China.,Department of Preventive Medicine, Guangdong Medical University, Dongguan, China
| | - Haiqiao Zhang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China.,Department of Preventive Medicine, Guangdong Medical University, Dongguan, China.,Department of Hospital Infection Management, Dongguan Maternal and Child Health Care Hospital, Dongguan, China
| | - Qiang Tan
- Integrated Services Division, Foshan Institute of Occupational Disease Prevention and Control, Foshan, China
| | - Dongsheng Huang
- Department of Respiratory and Critical Care Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Jialong Chen
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China.,Department of Preventive Medicine, Guangdong Medical University, Dongguan, China
| | - He Zhang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China.,Department of Preventive Medicine, Guangdong Medical University, Dongguan, China
| | - Dongyan Zheng
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China.,Department of Preventive Medicine, Guangdong Medical University, Dongguan, China
| | - Huifang Li
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China.,Department of Preventive Medicine, Guangdong Medical University, Dongguan, China
| | - Xiaobing Chen
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China.,Department of Preventive Medicine, Guangdong Medical University, Dongguan, China
| | - Linhua Liu
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China.,Department of Preventive Medicine, Guangdong Medical University, Dongguan, China
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Acetylated DNMT1 Downregulation and Related Regulatory Factors Influence Metastatic Melanoma Patients Survival. Cancers (Basel) 2021; 13:cancers13184691. [PMID: 34572918 PMCID: PMC8471314 DOI: 10.3390/cancers13184691] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary DNA methyltransferase-1 (DNMT1) is a key epigenetic regulatory protein of gene expression in cutaneous melanoma. DNMT1 is acetylated by TIP60 promoting its degradation. This study demonstrated that DNMT1 and ac-DNMT1 protein levels were inversely correlated in stage III (n = 17) and stage IV (n = 164) metastatic melanoma tumors, and both influenced melanoma progression. Reduced TIP60 and USP7 protein expression levels were correlated with decreased ac-DNMT1 levels. Of clinical translational relevance, patients with high ac-DNMT1 protein levels, or high-acDNMT1 with concurrent low DNMT1, high TIP60, or high USP7 protein levels showed significantly better prognosis for 4-year melanoma-specific survival. These results suggested that ac-DNMT1 is a significant post-translational modification influencing advanced melanoma patient disease outcomes. Abstract The role of post-translational modifications (PTM) of the key epigenetic factor DNMT1 protein has not been well explored in cutaneous metastatic melanoma progression. The acetylated DNMT1 (ac-DNMT1) protein level was assessed using an anti-acetylated lysine antibody in a clinically annotated melanoma patient tumor specimen cohort. In this study, we showed that surgically resected tumors have significantly higher DNMT1 protein expression in metastatic melanoma (stage III metastasis n = 17, p = 0.0009; stage IV metastasis n = 164, p = 0.003) compared to normal organ tissues (n = 19). Additionally, reduced ac-DNMT1 protein levels were associated with melanoma progression. There was a significant inverse correlation between ac-DNMT1 and DNMT1 protein levels in stage IV metastatic melanoma (r = −0.18, p = 0.02, n = 164). Additionally, ac-DNMT1 protein levels were also significantly positively correlated with TIP60 (r = 0.6, p < 0.0001) and USP7 (r = 0.74, p < 0.0001) protein levels in stage IV metastatic melanoma (n = 164). Protein analysis in metastatic melanoma tumor tissues showed that with high ac-DNMT1 (p = 0.006, n = 59), or concurrent high ac-DNMT1 with low DNMT1 (p = 0.05, n = 27), or high TIP60 (p = 0.007, n = 41), or high USP7 (p = 0.01, n = 48) consistently showed better 4-year melanoma-specific survival (MSS). Multivariate Cox proportional hazard analysis showed that ac-DNMT1 level is a significant independent factor associated with MSS (HR, 0.994; 95% confidential interval (CI), 0.990–0.998; p = 0.002). These results demonstrated that low ac-DNMT1 levels may represent an important regulatory factor in controlling metastatic melanoma progression and a promising factor for stratifying aggressive stage IV metastasis.
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Transcriptional overlap links DNA hypomethylation with DNA hypermethylation at adjacent promoters in cancer. Sci Rep 2021; 11:17346. [PMID: 34462486 PMCID: PMC8405634 DOI: 10.1038/s41598-021-96844-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
Tumor development involves alterations in DNA methylation patterns, which include both gains (hypermethylation) and losses (hypomethylation) in different genomic regions. The mechanisms underlying these two opposite, yet co-existing, alterations in tumors remain unclear. While studying the human MAGEA6/GABRA3 gene locus, we observed that DNA hypomethylation in tumor cells can lead to the activation of a long transcript (CT-GABRA3) that overlaps downstream promoters (GABRQ and GABRA3) and triggers their hypermethylation. Overlapped promoters displayed increases in H3K36me3, a histone mark deposited during transcriptional elongation and known to stimulate de novo DNA methylation. Consistent with such a processive mechanism, increases in H3K36me3 and DNA methylation were observed over the entire region covered by the CT-GABRA3 overlapping transcript. Importantly, experimental induction of CT-GABRA3 by depletion of DNMT1 DNA methyltransferase, resulted in a similar pattern of regional DNA hypermethylation. Bioinformatics analyses in lung cancer datasets identified other genomic loci displaying this process of coupled DNA hypo/hypermethylation, and some of these included tumor suppressor genes, e.g. RERG and PTPRO. Together, our work reveals that focal DNA hypomethylation in tumors can indirectly contribute to hypermethylation of nearby promoters through activation of overlapping transcription, and establishes therefore an unsuspected connection between these two opposite epigenetic alterations.
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Wong KK. DNMT1: A key drug target in triple-negative breast cancer. Semin Cancer Biol 2020; 72:198-213. [PMID: 32461152 DOI: 10.1016/j.semcancer.2020.05.010] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/04/2020] [Accepted: 05/18/2020] [Indexed: 02/06/2023]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer. Altered epigenetics regulation including DNA hypermethylation by DNA methyltransferase 1 (DNMT1) has been implicated as one of the causes of TNBC tumorigenesis. In this review, the oncogenic functions rendered by DNMT1 in TNBCs, and DNMT1 inhibitors targeting TNBC cells are presented and discussed. In summary, DNMT1 expression is associated with poor breast cancer survival, and it is overexpressed in TNBC subtype. The oncogenic roles of DNMT1 in TNBCs include: (1) Repression of estrogen receptor (ER) expression; (2) Promotion of epithelial-mesenchymal transition (EMT) required for metastasis; (3) Induces cellular autophagy and; (4) Promotes the growth of cancer stem cells in TNBCs. DNMT1 confers these phenotypes by hypermethylating the promoter regions of ER, multiple tumor suppressor genes, microRNAs and epithelial markers involved in suppressing EMT. DNMT1 inhibitors exert anti-tumorigenic effects against TNBC cells. This includes the hypomethylating agents azacitidine, decitabine and guadecitabine that might sensitize TNBC patients to immune checkpoint blockade therapy. DNMT1 represents an epigenetic target for TNBC cells destruction as well as to derail their metastatic and aggressive phenotypes.
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Affiliation(s)
- Kah Keng Wong
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
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Maric H, Supic G, Kandolf-Sekulovic L, Maric V, Mijuskovic Z, Radevic T, Rajovic M, Magic Z. DNMT1 and DNMT3B genetic polymorphisms affect the clinical course and outcome of melanoma patients. Melanoma Res 2019; 29:596-602. [PMID: 30950914 DOI: 10.1097/cmr.0000000000000612] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The aberrant DNA methylation plays a critical role in a number of different malignancies, including melanoma. DNA methylation is catalyzed by DNA methyltransferases (DNMTs), involved in methylation maintenance (DNMT1) and de novo DNA methylation (DNMT3A and DNMT3B). The current study investigated the association of genetic variants in the DNMT1 and DNMT3B with the clinicopathologic features and the clinical course of melanoma patients. In the present study, DNMT1 (rs2228612, rs2228611, and rs2114724) and DNMT3B (rs406193 and rs2424932) polymorphisms were examined in 123 melanoma patients. Single nucleotide polymorphisms were assessed using TaqMan SNPs Genotyping Assays according to the manufacturer's protocols. The carriers of the variant genotype of DNMT1 rs2228612 had poorer overall survival and recurrence-free survival, (P = 0.000 and 0.000, respectively), and an increased risk for adverse outcome [hazard ratio (HR) = 6.620, 95% confidence interval (CI): 2.214-19.791, P = 0.001]. DNMT1 rs2228612 was also associated with ulceration (P = 0.045), nodal status (P = 0.030), progression (P = 0. 007), and stage of disease (P = 0.003). Univariate analysis indicated that tumor-infiltrating lymphocytes could be a marker of good prognosis in melanoma patients (HR = 0.323, 95% CI: 0.127-0.855, P = 0.025), whereas the genotype distribution of the DNMT3B rs406193 polymorphism correlated significantly with the presence of tumor-infiltrating lymphocytes (P = 0.012). The multivariate analysis showed that the DNMT1 rs2228612 polymorphism (HR = 12.126, 95% CI: 2.345-62.715, P = 0.003) is an independent predictor of poor overall survival in melanoma patients. As expected, disease progression was also found to be an independent prognostic factor in melanoma patients (HR = 37.888, 95% CI: 3.615-397.062, P = 0.002). DNMT1 rs2228612 was found to be an independent predictor of poor overall survival in melanoma patients. DNMTs polymorphisms could serve as a potential target for novel therapeutic approaches.
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Affiliation(s)
- Helena Maric
- Second Surgery Clinic, University Hospital of Foca, Foca
| | | | | | - Veljko Maric
- Department of Surgery, Faculty of Medicine Foca, University of East Sarajevo, Lukavica, Serbia
| | | | | | - Milica Rajovic
- Clinic for Plastic and Reconstructive Surgery, Military Medical Academy, University of Defense, Belgrade
| | - Zvonko Magic
- Faculty of Medicine
- Institute for Medical Research
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Li B, Wang Y, Xu Y, Liu H, Bloomer W, Zhu D, Amos CI, Fang S, Lee JE, Li X, Han J, Wei Q. Genetic variants in RORA and DNMT1 associated with cutaneous melanoma survival. Int J Cancer 2018; 142:2303-2312. [PMID: 29313974 PMCID: PMC5893376 DOI: 10.1002/ijc.31243] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 02/06/2023]
Abstract
Cutaneous melanoma (CM) is considered as a steroid hormone-related malignancy. However, few studies have evaluated the roles of genetic variants encoding steroid hormone receptor genes and their related regulators (SHR-related genes) in CM-specific survival (CMSS). Here, we performed a pathway-based analysis to evaluate genetic variants of 191 SHR-related genes in 858 CMSS patients using a dataset from a genome-wide association study (GWAS) from The University of Texas MD Anderson Cancer Center (MDACC), and then validated the results in an additional dataset of 409 patients from the Harvard GWAS. Using multivariate Cox proportional hazards regression analysis, we identified three-independent SNPs (RORA rs782917 G > A, RORA rs17204952 C > T and DNMT1 rs7253062 G > A) as predictors of CMSS, with a variant-allele attributed hazards ratio (HR) and 95% confidence interval of 1.62 (1.25-2.09), 1.60 (1.20-2.13) and 1.52 (1.20-1.94), respectively. Combined analysis of risk genotypes of these three SNPs revealed a decreased CMSS in a dose-response manner as the number of risk genotypes increased (ptrend < 0.001); however, no improvement in the prediction model was observed (area under the curve [AUC] = 79.6-80.8%, p = 0.656), when these risk genotypes were added to the model containing clinical variables. Our findings suggest that genetic variants of RORA and DNMT1 may be promising biomarkers for CMSS, but these results needed to be validated in future larger studies.
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Affiliation(s)
- Bo Li
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, PR China
| | - Yanru Wang
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yinghui Xu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, PR China
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wendy Bloomer
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dakai Zhu
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Christopher I. Amos
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Shenying Fang
- Department of Surgical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey E. Lee
- Department of Surgical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Xin Li
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Jiali Han
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC 27710, USA
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Padua MB, Bhat-Nakshatri P, Anjanappa M, Prasad MS, Hao Y, Rao X, Liu S, Wan J, Liu Y, McElyea K, Jacobsen M, Sandusky G, Althouse S, Perkins S, Nakshatri H. Dependence receptor UNC5A restricts luminal to basal breast cancer plasticity and metastasis. Breast Cancer Res 2018; 20:35. [PMID: 29720215 PMCID: PMC5932758 DOI: 10.1186/s13058-018-0963-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 03/23/2018] [Indexed: 12/18/2022] Open
Abstract
Background The majority of estrogen receptor-positive (ERα+) breast cancers respond to endocrine therapies. However, resistance to endocrine therapies is common in 30% of cases, which may be due to altered ERα signaling and/or enhanced plasticity of cancer cells leading to breast cancer subtype conversion. The mechanisms leading to enhanced plasticity of ERα-positive cancer cells are unknown. Methods We used short hairpin (sh)RNA and/or the CRISPR/Cas9 system to knockdown the expression of the dependence receptor UNC5A in ERα+ MCF7 and T-47D cell lines. RNA-seq, quantitative reverse transcription polymerase chain reaction, chromatin immunoprecipitation, and Western blotting were used to measure the effect of UNC5A knockdown on basal and estradiol (E2)-regulated gene expression. Mammosphere assay, flow cytometry, and immunofluorescence were used to determine the role of UNC5A in restricting plasticity. Xenograft models were used to measure the effect of UNC5A knockdown on tumor growth and metastasis. Tissue microarray and immunohistochemistry were utilized to determine the prognostic value of UNC5A in breast cancer. Log-rank test, one-way, and two-way analysis of variance (ANOVA) were used for statistical analyses. Results Knockdown of the E2-inducible UNC5A resulted in altered basal gene expression affecting plasma membrane integrity and ERα signaling, as evident from ligand-independent activity of ERα, altered turnover of phosphorylated ERα, unique E2-dependent expression of genes effecting histone demethylase activity, enhanced upregulation of E2-inducible genes such as BCL2, and E2-independent tumorigenesis accompanied by multiorgan metastases. UNC5A depletion led to the appearance of a luminal/basal hybrid phenotype supported by elevated expression of basal/stem cell-enriched ∆Np63, CD44, CD49f, epidermal growth factor receptor (EGFR), and the lymphatic vessel permeability factor NTN4, but lower expression of luminal/alveolar differentiation-associated ELF5 while maintaining functional ERα. In addition, UNC5A-depleted cells acquired bipotent luminal progenitor characteristics based on KRT14+/KRT19+ and CD49f+/EpCAM+ phenotype. Consistent with in vitro results, UNC5A expression negatively correlated with EGFR expression in breast tumors, and lower expression of UNC5A, particularly in ERα+/PR+/HER2− tumors, was associated with poor outcome. Conclusion These studies reveal an unexpected role of the axon guidance receptor UNC5A in fine-tuning ERα and EGFR signaling and the luminal progenitor status of hormone-sensitive breast cancers. Furthermore, UNC5A knockdown cells provide an ideal model system to investigate metastasis of ERα+ breast cancers. Electronic supplementary material The online version of this article (10.1186/s13058-018-0963-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria B Padua
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Present Address: Department of Pediatrics and Herman B. Wells Center for Pediatrics Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Manjushree Anjanappa
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Mayuri S Prasad
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yangyang Hao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Xi Rao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kyle McElyea
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Max Jacobsen
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - George Sandusky
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sandra Althouse
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Susan Perkins
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,VA Roudebush Medical Center, C218C, 980 West Walnut St, Indianapolis, IN, 46202, USA.
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Chadaeva IV, Ponomarenko PM, Rasskazov DA, Sharypova EB, Kashina EV, Zhechev DA, Drachkova IA, Arkova OV, Savinkova LK, Ponomarenko MP, Kolchanov NA, Osadchuk LV, Osadchuk AV. Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters. BMC Genomics 2018; 19:0. [PMID: 29504899 PMCID: PMC5836831 DOI: 10.1186/s12864-018-4478-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The progress of medicine, science, technology, education, and culture improves, year by year, quality of life and life expectancy of the populace. The modern human has a chance to further improve the quality and duration of his/her life and the lives of his/her loved ones by bringing their lifestyle in line with their sequenced individual genomes. With this in mind, one of genome-based developments at the junction of personalized medicine and bioinformatics will be considered in this work, where we used two Web services: (i) SNP_TATA_Comparator to search for alleles with a single nucleotide polymorphism (SNP) that alters the affinity of TATA-binding protein (TBP) for the TATA boxes of human gene promoters and (ii) PubMed to look for retrospective clinical reviews on changes in physiological indicators of reproductive potential in carriers of these alleles. RESULTS A total of 126 SNP markers of female reproductive potential, capable of altering the affinity of TBP for gene promoters, were found using the two above-mentioned Web services. For example, 10 candidate SNP markers of thrombosis (e.g., rs563763767) can cause overproduction of coagulation inducers. In pregnant women, Hughes syndrome provokes thrombosis with a fatal outcome although this syndrome can be diagnosed and eliminated even at the earliest stages of its development. Thus, in women carrying any of the above SNPs, preventive treatment of this syndrome before a planned pregnancy can reduce the risk of death. Similarly, seven SNP markers predicted here (e.g., rs774688955) can elevate the risk of myocardial infarction. In line with Bowles' lifespan theory, women carrying any of these SNPs may modify their lifestyle to improve their longevity if they can take under advisement that risks of myocardial infarction increase with age of the mother, total number of pregnancies, in multiple pregnancies, pregnancies under the age of 20, hypertension, preeclampsia, menstrual cycle irregularity, and in women smokers. CONCLUSIONS According to Bowles' lifespan theory-which links reproductive potential, quality of life, and life expectancy-the above information was compiled for those who would like to reduce risks of diseases corresponding to alleles in own sequenced genomes. Candidate SNP markers can focus the clinical analysis of unannotated SNPs, after which they may become useful for people who would like to bring their lifestyle in line with their sequenced individual genomes.
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Affiliation(s)
- Irina V Chadaeva
- Brain Neurobiology and Neurogenetics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | | | - Dmitry A Rasskazov
- Brain Neurobiology and Neurogenetics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
| | - Ekaterina B Sharypova
- Brain Neurobiology and Neurogenetics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
| | - Elena V Kashina
- Brain Neurobiology and Neurogenetics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
| | - Dmitry A Zhechev
- Brain Neurobiology and Neurogenetics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
| | - Irina A Drachkova
- Brain Neurobiology and Neurogenetics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
| | - Olga V Arkova
- Brain Neurobiology and Neurogenetics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
- Vector-Best Inc., Koltsovo, Novosibirsk Region, 630559, Russia
| | - Ludmila K Savinkova
- Brain Neurobiology and Neurogenetics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
| | - Mikhail P Ponomarenko
- Brain Neurobiology and Neurogenetics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Nikolay A Kolchanov
- Brain Neurobiology and Neurogenetics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Ludmila V Osadchuk
- Brain Neurobiology and Neurogenetics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
- Novosibirsk State Agricultural University, Novosibirsk, 630039, Russia
| | - Alexandr V Osadchuk
- Brain Neurobiology and Neurogenetics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
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10
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Zhou J, Shi J, Fu X, Mao B, Wang W, Li W, Li G, Zhou S. Linc00441 interacts with DNMT1 to regulate RB1 gene methylation and expression in gastric cancer. Oncotarget 2018; 9:37471-37479. [PMID: 30680063 PMCID: PMC6331029 DOI: 10.18632/oncotarget.23928] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 11/03/2017] [Indexed: 01/10/2023] Open
Abstract
Recent studies revealed that several Long noncoding RNAs (LncRNAs) are associated with progression of gastric cancer (GC), while the functional role and molecular mechanism of many GC-associated lncRNAs remain undetermined. The tumor suppressor-gene retinoblastoma gene (RB1) was decreased in several human cancers including gastric cancer (GC). In this study, we investigated whether Linc00441 was involved in the suppression of RB1. Our findings showed that the up-regulated Linc00441 was inversely correlated with RB1 expression in human GC tumor samples. The gain- and loss-of-function investigation revealed that Linc00441 could promote the proliferation of GC cells. Furthermore, RNA pull down and RIP assays demonstrated that Linc00441 could recruit DNMT1 to the RB1 promoter and suppressed RB1 expression in GC cells. In conclusion, our findings revealed that Linc00441 played crucial role in GC progression and suggested that Linc00441 was potentially an effective target for GC therapy in the future.
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Affiliation(s)
- Jianping Zhou
- Department of General Surgery, Yixing People's Hospital The Affiliated Hospital of Jiangsu University, Yixing 214200, Jiangsu, P.R China
| | - Jun Shi
- Department of General Surgery, Yixing People's Hospital The Affiliated Hospital of Jiangsu University, Yixing 214200, Jiangsu, P.R China
| | - Xingli Fu
- Health Science Center, Jiangsu University, Zhenjiang 212000, Jiangsu, P.R China
| | - Boneng Mao
- Department of Gastroenterology, Yixing People's Hospital The Affiliated Hospital of Jiangsu University, Yixing 214200, Jiangsu, P.R China
| | - Weimin Wang
- Department of Oncology, Yixing People's Hospital The Affiliated Hospital of Jiangsu University, Yixing 214200, Jiangsu, P.R China
| | - Weiling Li
- Yixing People's Hospital The Affiliated Hospital of Jiangsu University, Yixing 214200, Jiangsu, P.R China
| | - Gang Li
- Yixing People's Hospital The Affiliated Hospital of Jiangsu University, Yixing 214200, Jiangsu, P.R China
| | - Sujun Zhou
- Department of General Surgery, Yixing People's Hospital The Affiliated Hospital of Jiangsu University, Yixing 214200, Jiangsu, P.R China
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NSD1 inactivation defines an immune cold, DNA hypomethylated subtype in squamous cell carcinoma. Sci Rep 2017; 7:17064. [PMID: 29213088 PMCID: PMC5719078 DOI: 10.1038/s41598-017-17298-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/22/2017] [Indexed: 12/14/2022] Open
Abstract
Chromatin modifying enzymes are frequently mutated in cancer, resulting in widespread epigenetic deregulation. Recent reports indicate that inactivating mutations in the histone methyltransferase NSD1 define an intrinsic subtype of head and neck squamous cell carcinoma (HNSC) that features pronounced DNA hypomethylation. Here, we describe a similar hypomethylated subtype of lung squamous cell carcinoma (LUSC) that is enriched for both inactivating mutations and deletions in NSD1. The ‘NSD1 subtypes’ of HNSC and LUSC are highly correlated at the DNA methylation and gene expression levels, featuring ectopic expression of developmental transcription factors and genes that are also hypomethylated in Sotos syndrome, a congenital disorder caused by germline NSD1 mutations. Further, the NSD1 subtype of HNSC displays an ‘immune cold’ phenotype characterized by low infiltration of tumor-associated leukocytes, particularly macrophages and CD8+ T cells, as well as low expression of genes encoding the immunotherapy target PD-1 immune checkpoint receptor and its ligands. Using an in vivo model, we demonstrate that NSD1 inactivation results in reduced T cell infiltration into the tumor microenvironment, implicating NSD1 as a tumor cell-intrinsic driver of an immune cold phenotype. NSD1 inactivation therefore causes epigenetic deregulation across cancer sites, and has implications for immunotherapy.
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12
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McLoughlin KC, Kaufman AS, Schrump DS. Targeting the epigenome in malignant pleural mesothelioma. Transl Lung Cancer Res 2017; 6:350-365. [PMID: 28713680 DOI: 10.21037/tlcr.2017.06.06] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Malignant pleural mesotheliomas (MPM) are notoriously refractory to conventional treatment modalities. Recent insights regarding epigenetic alterations in MPM provide the preclinical rationale for the evaluation of novel combinatorial regimens targeting the epigenome in these neoplasms.
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Affiliation(s)
- Kaitlin C McLoughlin
- Thoracic Epigenetics Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Andrew S Kaufman
- Thoracic Epigenetics Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - David S Schrump
- Thoracic Epigenetics Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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Micevic G, Theodosakis N, Bosenberg M. Aberrant DNA methylation in melanoma: biomarker and therapeutic opportunities. Clin Epigenetics 2017; 9:34. [PMID: 28396701 PMCID: PMC5381063 DOI: 10.1186/s13148-017-0332-8] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/24/2017] [Indexed: 12/18/2022] Open
Abstract
Aberrant DNA methylation is an epigenetic hallmark of melanoma, known to play important roles in melanoma formation and progression. Recent advances in genome-wide methylation methods have provided the means to identify differentially methylated genes, methylation signatures, and potential biomarkers. However, despite considerable effort and advances in cataloging methylation changes in melanoma, many questions remain unanswered. The aim of this review is to summarize recent developments, emerging trends, and important unresolved questions in the field of aberrant DNA methylation in melanoma. In addition to reviewing recent developments, we carefully synthesize the findings in an effort to provide a framework for understanding the current state and direction of the field. To facilitate clarity, we divided the review into DNA methylation changes in melanoma, biomarker opportunities, and therapeutic developments. We hope this review contributes to accelerating the utilization of the diagnostic, prognostic, and therapeutic potential of DNA methylation for the benefit of melanoma patients.
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Affiliation(s)
- Goran Micevic
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520 USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Nicholas Theodosakis
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520 USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Marcus Bosenberg
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520 USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT 06520 USA
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