1
|
Sardar S, Jyotisha, Amin SA, Khatun S, Qureshi IA, Patil UK, Jha T, Gayen S. Identification of structural fingerprints among natural inhibitors of HDAC1 to accelerate nature-inspired drug discovery in cancer epigenetics. J Biomol Struct Dyn 2024; 42:5642-5656. [PMID: 38870352 DOI: 10.1080/07391102.2023.2227710] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/15/2023] [Indexed: 06/15/2024]
Abstract
Histone deacetylase 1 (HDAC1), a class I HDAC enzyme, is crucial for histone modification. Currently, it is emerged as one of the important biological targets for designing small molecule drugs through cancer epigenetics. Along with synthetic inhibitors different natural inhibitors are showing potential HDAC1 inhibitions. In order to gain insights into the relationship between the molecular structures of the natural inhibitors and HDAC1, different molecular modelling techniques (Bayesian classification, recursive partitioning, molecular docking and molecular dynamics simulations) have been applied on a dataset of 155 HDAC1 nature-inspired inhibitors with diverse scaffolds. The Bayesian study showed acceptable ROC values for both the training set and test sets. The Recursive partitioning study produced decision tree 1 with 6 leaves. Further, molecular docking study was processed for generating the protein ligand complex which identified some potential amino acid residues such as F205, H28, L271, P29, F150, Y204 for the binding interactions in case of natural inhibitors. Stability of these HDAC1-natutal inhibitors complexes has been also evaluated by molecular dynamics simulation study. The current modelling study is an attempt to get a deep insight into the different important structural fingerprints among different natural compounds modulating HDAC1 inhibition.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sourav Sardar
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Jyotisha
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Sk Abdul Amin
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Samima Khatun
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Umesh Kumar Patil
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| |
Collapse
|
2
|
Nunes FM, Apolónio JD, Mota-Pinto A, Leão R. Epigenetic alterations in urothelial bladder cancer associated with disease outcomes. Int J Urol 2024; 31:220-229. [PMID: 37961796 DOI: 10.1111/iju.15335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023]
Abstract
OBJECTIVES Bladder cancer (BLCA) is a molecular heterogeneous disease with known genetic distinctive signatures. However, DNA methylation is highly prevalent across a wide range of tumors, suggesting its potential in oncogenesis. Here, we aimed to interrogate the role of nine epigenetic alterations as diagnostic and prognostic markers in BLCA. METHODS DNA methylation, gene expression, and clinicopathological information were retrieved from The Cancer Genome Atlas data portal. Methylation values and gene expression were assessed to determine their association with normal and malignant tissue. Additionally, we studied the association between methylation values and clinicopathological variables. For the prognostic model, Kaplan-Meier Survival curves were generated. Lastly, univariate and multivariate analysis were performed to evaluate the simultaneous impact of methylation and clinicopathological variables on the risk of tumor progression and survival. RESULTS Nine CpG sites' methylation β -values involved in our study demonstrated different methylation signatures between normal and malignant urothelium. Hypermethylated CpGs were overrepresented in tumor tissue (p < 0.0001). Opposingly, 4 CpG sites showed lower methylation values in tumor samples (p < 0.0001). Cg12743248high and cg17192862low are risk factors for progression-free survival, whereas cg12374721high (HR:3.003 (1.283-7.030)) also demonstrated to be the most valuable independent risk factor for disease progression and a risk factor for overall survival. CONCLUSIONS We have identified that methylated cg12374721 shows promise as a diagnostic and independent prognostic marker in BLCA progression.
Collapse
Affiliation(s)
| | - Joana Dias Apolónio
- Algarve Biomedical Center Research Institute (ABC-RI), University of Algarve, Faro, Portugal
- Algarve Biomedical Center, Faro, Portugal
| | | | - Ricardo Leão
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| |
Collapse
|
3
|
Gupta MK, Kushwah AS, Singh R, Srivastava K, Banerjee M. Genetic and epigenetic alterations in MGMT gene and correlation with concomitant chemoradiotherapy (CRT) in cervical cancer. J Cancer Res Clin Oncol 2023; 149:15159-15170. [PMID: 37634205 DOI: 10.1007/s00432-023-05305-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/16/2023] [Indexed: 08/29/2023]
Abstract
PURPOSE The MGMT (O6-methylguanine-DNA methyltransferase) gene plays a crucial role in repairing DNA damage caused by alkylating agents, including those used in chemotherapy. Genetic and epigenetic alterations can influence the regulation of MGMT gene, which in turn may impact the response to concomitant chemoradiotherapy (CRT) in cervical cancer. The present study was undertaken to evaluate the correlation of such variations in MGMT gene with the treatment outcome of concomitant chemoradiotherapy (CRT) in cervical cancer. METHODS A total of 460 study subjects (240 controls and 220 patients) were subjected to genotypic analysis of MGMT gene variants rs12917(T/C) and rs2308327(A/G) by Amplification Refractory Mutation System-Polymerase Chain Reaction (ARMS-PCR). Out of them, 48 each of controls and patients were analyzed for promoter methylation and expression by methylation-specific PCR and real-time PCR, respectively. Patients (n = 48) were followed up and evaluated for treatment (CRT) outcome. Statistical analyses were done using GraphPad (9.0) and SPSS version 18.0. RESULTS Individuals with GG genotype, G allele of rs2308327, and haplotype 'TA' of both variants showed a significant increase in the development of cervical cancer (P ≤ 0.05). In epigenetic regulation, there was a significant hypermethylation of MGMT gene and down-regulation of their expression in patients compared to control individuals. In treatment outcome of CRT, GG genotype of rs2308327(A/G) gene variant showed better response and GG + AG was significantly associated with vital status (alive). Unmethylated MGMT gene showed better median overall survival up to 25 months significant in comparison to methylated MGMT promoter. CONCLUSION Gene variant rs2308327(A/G) and promoter hypermethylation regulated MGMT gene can be a good prognostic for treatment response in cervical cancer patients.
Collapse
Affiliation(s)
- Maneesh Kumar Gupta
- Molecular and Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow, 226007, India
| | - Atar Singh Kushwah
- Molecular and Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow, 226007, India
- Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | - Renu Singh
- Department of Obstetrics and Gynecology, King George's Medical University, Lucknow, 226003, India
| | - Kirti Srivastava
- Department of Radiotherapy, King George's Medical University, Lucknow, 226003, India
| | - Monisha Banerjee
- Molecular and Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow, 226007, India.
| |
Collapse
|
4
|
Labat-de-Hoz L, Rubio-Ramos A, Correas I, Alonso MA. The MAL Family of Proteins: Normal Function, Expression in Cancer, and Potential Use as Cancer Biomarkers. Cancers (Basel) 2023; 15:2801. [PMID: 37345137 DOI: 10.3390/cancers15102801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/06/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023] Open
Abstract
The MAL family of integral membrane proteins consists of MAL, MAL2, MALL, PLLP, CMTM8, MYADM, and MYADML2. The best characterized members are elements of the machinery that controls specialized pathways of membrane traffic and cell signaling. This review aims to help answer the following questions about the MAL-family genes: (i) is their expression regulated in cancer and, if so, how? (ii) What role do they play in cancer? (iii) Might they have biomedical applications? Analysis of large-scale gene expression datasets indicated altered levels of MAL-family transcripts in specific cancer types. A comprehensive literature search provides evidence of MAL-family gene dysregulation and protein function repurposing in cancer. For MAL, and probably for other genes of the family, dysregulation is primarily a consequence of gene methylation, although copy number alterations also contribute to varying degrees. The scrutiny of the two sources of information, datasets and published studies, reveals potential prognostic applications of MAL-family members as cancer biomarkers-for instance, MAL2 in breast cancer, MAL2 and MALL in pancreatic cancer, and MAL and MYADM in lung cancer-and other biomedical uses. The availability of validated antibodies to some MAL-family proteins sanctions their use as cancer biomarkers in routine clinical practice.
Collapse
Affiliation(s)
- Leticia Labat-de-Hoz
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Armando Rubio-Ramos
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Isabel Correas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Miguel A Alonso
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| |
Collapse
|
5
|
Albitar M, Zhang H, Charifa A, Ip A, Ma W, McCloskey J, Donato M, Siegel D, Waintraub S, Gutierrez M, Pecora A, Goy A. Combining cell-free RNA with cell-free DNA in liquid biopsy for hematologic and solid tumors. Heliyon 2023; 9:e16261. [PMID: 37251903 PMCID: PMC10208940 DOI: 10.1016/j.heliyon.2023.e16261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 05/31/2023] Open
Abstract
Current use of liquid biopsy is based on cell-free DNA (cfDNA) and the evaluation of mutations or methylation pattern. However, expressed RNA can capture mutations, changes in expression levels due to methylation, and provide information on cell of origin, growth, and proliferation status. We developed an approach to isolate cell-free total nucleic acid (cfDNA) and used targeted next generation sequencing to sequence cell-free RNA (cfRNA) and cfDNA as new approach in liquid biopsy. We demonstrate that cfRNA is overall more sensitive than cfDNA in detecting mutations. We show that cfRNA is reliable in detecting fusion genes and cfDNA is reliable in detecting chromosomal gains and losses. cfRNA levels of various solid tumor biomarkers were significantly higher (P < 0.0001) in samples from solid tumors as compared with normal control. Similarly, cfRNA lymphoid markers and cfRNA myeloid markers were all higher in lymphoid and myeloid neoplasms, respectively as compared with control (P < 0.0001). Using machine learning we demonstrate cfRNA was highly predictive of diagnosis (AUC >0.98) of solid tumors, B-cell lymphoid neoplasms, T-cell lymphoid neoplasms, and myeloid neoplasms. In evaluating the host immune system, cfRNA CD4:CD8B and CD3D:CD19 ratios in normal controls were as expected (median: 5.92 and 6.87, respectively) and were significantly lower in solid tumors (P < 0.0002). This data suggests that liquid biopsy combining analysis of cfRNA with cfDNA is practical and may provide helpful information in predicting genomic abnormalities, diagnosis of neoplasms and evaluating both the tumor biology and the host response.
Collapse
Affiliation(s)
- Maher Albitar
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - Hong Zhang
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - Ahmad Charifa
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - Andrew Ip
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Wanlong Ma
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - James McCloskey
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Michele Donato
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - David Siegel
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Stanley Waintraub
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Martin Gutierrez
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Andrew Pecora
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Andre Goy
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| |
Collapse
|
6
|
Pramio DT, Vieceli FM, Varella-Branco E, Goes CP, Kobayashi GS, da Silva Pelegrina DV, de Moraes BC, El Allam A, De Kumar B, Jara G, Farfel JM, Bennett DA, Kundu S, Viapiano MS, Reis EM, de Oliveira PSL, Dos Santos E Passos-Bueno MR, Rothlin CV, Ghosh S, Schechtman D. DNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain-specific PKMζ. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194909. [PMID: 36682583 PMCID: PMC10037092 DOI: 10.1016/j.bbagrm.2023.194909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 01/05/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023]
Abstract
Protein kinase M zeta, PKMζ, is a brain enriched kinase with a well characterized role in Long-Term Potentiation (LTP), the activity-dependent strengthening of synapses involved in long-term memory formation. However, little is known about the molecular mechanisms that maintain the tissue specificity of this kinase. Here, we characterized the epigenetic factors, mainly DNA methylation, regulating PKMζ expression in the human brain. The PRKCZ gene has an upstream promoter regulating Protein kinase C ζ (PKCζ), and an internal promoter driving PKMζ expression. A demethylated region, including a canonical CREB binding site, situated at the internal promoter was only observed in human CNS tissues. The induction of site-specific hypermethylation of this region resulted in decreased CREB1 binding and downregulation of PKMζ expression. Noteworthy, CREB binding sites were absent in the upstream promoter of PRKCZ locus, suggesting a specific mechanism for regulating PKMζ expression. These observations were validated using a system of human neuronal differentiation from induced pluripotent stem cells (iPSCs). CREB1 binding at the internal promoter was detected only in differentiated neurons, where PKMζ is expressed. The same epigenetic mechanism in the context of CREB binding site was identified in other genes involved in neuronal differentiation and LTP. Additionally, aberrant DNA hypermethylation at the internal promoter was observed in cases of Alzheimer's disease, correlating with decreased expression of PKMζ in patient brains. Altogether, we present a conserved epigenetic mechanism regulating PKMζ expression and other genes enhanced in the CNS with possible implications in neuronal differentiation and Alzheimer's disease.
Collapse
Affiliation(s)
| | | | | | - Carolina Purcell Goes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil; Laboratory of Neuromodulation of Experimental Pain, Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo, SP, Brazil
| | | | | | | | - Aicha El Allam
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | | | - Gabriel Jara
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian National Biosciences Laboratory (LNBio) Campinas, SP, Brazil
| | - José Marcelo Farfel
- Traumatology and Orthopedy Department, Faculdade de Medicina, Universidade de São Paulo, SP, Brazil; Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Health Sciences Program, Instituto de Assistência Medica ao Servidor Público do Estado (IAMSPE), SP, Brazil
| | - David Alan Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Somanath Kundu
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Mariano S Viapiano
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Eduardo Moraes Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil
| | - Paulo Sergio Lopes de Oliveira
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian National Biosciences Laboratory (LNBio) Campinas, SP, Brazil
| | | | - Carla V Rothlin
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA; Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Sourav Ghosh
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - Deborah Schechtman
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil.
| |
Collapse
|
7
|
Wang C, Yuan A, Cope L, Qin J. A semiparametric isotonic regression model for skewed distributions with application to DNA-RNA-protein analysis. Biometrics 2022; 78:1464-1474. [PMID: 34492116 DOI: 10.1111/biom.13528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 12/30/2022]
Abstract
In this paper, we propose a semiparametric regression model that is built upon an isotonic regression model with the assumption that the random error follows a skewed distribution. We develop an expectation-maximization algorithm for obtaining the maximum likelihood estimates of the model parameters, examine the asymptotic properties of the estimators, conduct simulation studies to explore the performance of the proposed model, and apply the method to evaluate the DNA-RNA-protein relationship and identify genes that are key factors in tumor progression.
Collapse
Affiliation(s)
- Chenguang Wang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ao Yuan
- Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University, Washington D.C., USA
| | - Leslie Cope
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jing Qin
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| |
Collapse
|
8
|
HOPX: A Unique Homeodomain Protein in Development and Tumor Suppression. Cancers (Basel) 2022; 14:cancers14112764. [PMID: 35681746 PMCID: PMC9179269 DOI: 10.3390/cancers14112764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/05/2022] Open
Abstract
Simple Summary Homeobox (HOX) genes encode homeodomain proteins that regulate a wide range of molecular pathways. The homeodomain is highly conserved and binds to DNA. One exception is homeodomain-only protein (HOPX) that lacks DNA-binding capacity. HOPX plays a crucial role in development and its functional impairment is associated with a variety of diseases, including cancer. Loss of HOPX function occurs in a wide range of cancer types, where it functions as a tumor suppressor gene. Understanding the molecular mechanisms by which HOPX regulates carcinogenesis will likely lead to the development of new therapeutic approaches. Abstract Homeobox genes are master regulators of morphogenesis and differentiation by acting at the top of genetic hierarchies and their deregulation is associated with a variety of human diseases. They usually contain a highly conserved sequence that codes for the homeodomain of the protein, a specialized motif with three α helices and an N-terminal arm that aids in DNA binding. However, one homeodomain protein, HOPX, is unique among its family members in that it lacks the capacity to bind DNA and instead functions by interacting with transcriptional regulators. HOPX plays crucial roles in organogenesis and is expressed in both embryonic and adult stem cells. Loss of HOPX expression is common in cancer, where it functions primarily as a tumor suppressor gene. In this review, we describe the function of HOPX in development and discuss its role in carcinogenesis.
Collapse
|
9
|
Hamad SH, Montgomery SA, Simon JM, Bowman BM, Spainhower KB, Murphy RM, Knudsen ES, Fenton SE, Randell SH, Holt JR, Hayes DN, Witkiewicz AK, Oliver TG, Major MB, Weissman BE. TP53, CDKN2A/P16, and NFE2L2/NRF2 regulate the incidence of pure- and combined-small cell lung cancer in mice. Oncogene 2022; 41:3423-3432. [PMID: 35577980 PMCID: PMC10039451 DOI: 10.1038/s41388-022-02348-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 12/11/2022]
Abstract
Studies have shown that Nrf2E79Q/+ is one of the most common mutations found in human tumors. To elucidate how this genetic change contributes to lung cancer, we compared lung tumor development in a genetically-engineered mouse model (GEMM) with dual Trp53/p16 loss, the most common mutations found in human lung tumors, in the presence or absence of Nrf2E79Q/+. Trp53/p16-deficient mice developed combined-small cell lung cancer (C-SCLC), a mixture of pure-SCLC (P-SCLC) and large cell neuroendocrine carcinoma. Mice possessing the LSL-Nrf2E79Q mutation showed no difference in the incidence or latency of C-SCLC compared with Nrf2+/+ mice. However, these tumors did not express NRF2 despite Cre-induced recombination of the LSL-Nrf2E79Q allele. Trp53/p16-deficient mice also developed P-SCLC, where activation of the NRF2E79Q mutation associated with a higher incidence of this tumor type. All C-SCLCs and P-SCLCs were positive for NE-markers, NKX1-2 (a lung cancer marker) and negative for P63 (a squamous cell marker), while only P-SCLC expressed NRF2 by immunohistochemistry. Analysis of a consensus NRF2 pathway signature in human NE+-lung tumors showed variable activation of NRF2 signaling. Our study characterizes the first GEMM that develops C-SCLC, a poorly-studied human cancer and implicates a role for NRF2 activation in SCLC development.
Collapse
Affiliation(s)
- Samera H Hamad
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephanie A Montgomery
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jeremy M Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Brittany M Bowman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Kyle B Spainhower
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Ryan M Murphy
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Erik S Knudsen
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Suzanne E Fenton
- Division of National Toxicology Program, NIEHS/NIH, Research Triangle Park, NC, USA
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jeremiah R Holt
- University of Tennessee Health Science Center for Cancer Research, Department of Medicine, Division of Hematology and Oncology, University of Tennessee, Memphis, TN, USA
| | - D Neil Hayes
- University of Tennessee Health Science Center for Cancer Research, Department of Medicine, Division of Hematology and Oncology, University of Tennessee, Memphis, TN, USA
| | | | - Trudy G Oliver
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - M Ben Major
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| | - Bernard E Weissman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| |
Collapse
|
10
|
Cancer: More than a geneticist’s Pandora’s box. J Biosci 2022. [DOI: 10.1007/s12038-022-00254-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
11
|
Histone Deacetylase (HDAC) Inhibitors: A Promising Weapon to Tackle Therapy Resistance in Melanoma. Int J Mol Sci 2022; 23:ijms23073660. [PMID: 35409020 PMCID: PMC8998190 DOI: 10.3390/ijms23073660] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
Abstract
Melanoma is an aggressive malignant tumor, arising more commonly on the skin, while it can also occur on mucosal surfaces and the uveal tract of the eye. In the context of the unresectable and metastatic cases that account for the vast majority of melanoma-related deaths, the currently available therapeutic options are of limited value. The exponentially increasing knowledge in the field of molecular biology has identified epigenetic reprogramming and more specifically histone deacetylation (HDAC), as a crucial regulator of melanoma progression and as a key driver in the emergence of drug resistance. A variety of HDAC inhibitors (HDACi) have been developed and evaluated in multiple solid and hematologic malignancies, showing promising results. In melanoma, various experimental models have elucidated a critical role of histone deacetylases in disease pathogenesis. They could, therefore, represent a promising novel therapeutic approach for advanced disease. A number of clinical trials assessing the efficacy of HDACi have already been completed, while a few more are in progress. Despite some early promising signs, a lot of work is required in the field of clinical studies, and larger patient cohorts are needed in order for more valid conclusions to be extracted, regarding the potential of HDACi as mainstream treatment options for melanoma.
Collapse
|
12
|
Sox2 induces glioblastoma cell stemness and tumor propagation by repressing TET2 and deregulating 5hmC and 5mC DNA modifications. Signal Transduct Target Ther 2022; 7:37. [PMID: 35136034 PMCID: PMC8826438 DOI: 10.1038/s41392-021-00857-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 12/01/2021] [Accepted: 12/05/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is a reversible process catalyzed by the ten–eleven translocation (TET) family of enzymes (TET1, TET2, TET3) that convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Altered patterns of 5hmC and 5mC are widely reported in human cancers and loss of 5hmC correlates with poor prognosis. Understanding the mechanisms leading to 5hmC loss and its role in oncogenesis will advance the development of epigenetic-based therapeutics. We show that TET2 loss associates with glioblastoma (GBM) stem cells and correlates with poor survival of GBM patients. We further identify a SOX2:miR-10b-5p:TET2 axis that represses TET2 expression, represses 5hmC, increases 5mC levels, and induces GBM cell stemness and tumor-propagating potential. In vivo delivery of a miR-10b-5p inhibitor that normalizes TET2 expression and 5hmC levels inhibits tumor growth and prolongs survival of animals bearing pre-established orthotopic GBM xenografts. These findings highlight the importance of TET2 and 5hmC loss in Sox2-driven oncogenesis and their potential for therapeutic targeting.
Collapse
|
13
|
Ji H, Li K, Jiang W, Li J, Zhang JA, Zhu X. MRVI1 and NTRK3 Are Potential Tumor Suppressor Genes Commonly Inactivated by DNA Methylation in Cervical Cancer. Front Oncol 2022; 11:802068. [PMID: 35141152 PMCID: PMC8818726 DOI: 10.3389/fonc.2021.802068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
The abnormally methylated tumor suppressor genes (TSGs) associated with cervical cancer are unclear. DNA methylation data, RNA-seq expression profiles, and overall survival data were downloaded from TCGA CESC database. DMGs and DEGs were obtained through CHAMP and DESeq packages, respectively. TSGs were downloaded from TSGene 2.0. Candidate hypermethylated/down-regulated TSGs were further evaluated and pyrosequencing was used to confirm their difference in methylation levels of selected TSGs in cervical cancer patients. A total of 25946 differentially methylated CpGs corresponding to 2686 hypermethylated genes and 4898 hypomethylated genes between cervical cancer and adjacent normal cervical tissues were found in this study. Besides, 693 DEGs (109 up-regulated and 584 down-regulated) were discovered in cervical cancer tissues. Then, 192 hypermethylated/down-regulated genes were obtained in cervical cancer compared to adjacent tissues. Interestingly, 26 TSGs were found in hypermethylated/down-regulated genes. Among these genes, low expression of MRVI1 and NTRK3 was associated with poor overall survival in cervical cancer. Moreover, GEO data showed that MRVI1 and NTRK3 were significantly decreased in cervical cancer tissues. The expression levels of MRVI1 and NTRK3 were negatively correlated with the methylation levels of their promoter CpG sites. Additionally, elevated methylation levels of MRVI1 and NTRK3 promoter were further verified in cervical cancer tissues by pyrosequencing experiments. Finally, the ROC results showed that the promoter methylation levels of MRVI1 and NTRK3 had the ability to discriminate cervical cancer from healthy samples. The study contributes to our understanding of the roles of MRVI1 and NTRK3 in cervical cancer.
Collapse
Affiliation(s)
- Huihui Ji
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kehan Li
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wenxiao Jiang
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jingwei Li
- Department of Obstetrics and Gynecology, Taizhou Woman and Children’s Hospital of Wenzhou Medical University, Taizhou, China
| | - Jian-an Zhang
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xueqiong Zhu
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Obstetrics and Gynecology, Taizhou Woman and Children’s Hospital of Wenzhou Medical University, Taizhou, China
- *Correspondence: Xueqiong Zhu,
| |
Collapse
|
14
|
Woods ML, Weiss A, Sokol AM, Graumann J, Boettger T, Richter AM, Schermuly RT, Dammann RH. Epigenetically silenced apoptosis-associated tyrosine kinase (AATK) facilitates a decreased expression of Cyclin D1 and WEE1, phosphorylates TP53 and reduces cell proliferation in a kinase-dependent manner. Cancer Gene Ther 2022; 29:1975-1987. [PMID: 35902728 PMCID: PMC9750878 DOI: 10.1038/s41417-022-00513-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 06/28/2022] [Accepted: 07/13/2022] [Indexed: 01/25/2023]
Abstract
Silencing of the Apoptosis associated Tyrosine Kinase gene (AATK) has been described in cancer. In our study, we specifically investigated the epigenetic inactivation of AATK in pancreatic adenocarcinoma, lower grade glioma, lung, breast, head, and neck cancer. The resulting loss of AATK correlates with impaired patient survival. Inhibition of DNA methyltransferases (DNMTs) reactivated AATK in glioblastoma and pancreatic cancer. In contrast, epigenetic targeting via the CRISPR/dCas9 system with either EZH2 or DNMT3A inhibited the expression of AATK. Via large-scale kinomic profiling and kinase assays, we demonstrate that AATK acts a Ser/Thr kinase that phosphorylates TP53 at Ser366. Furthermore, whole transcriptome analyses and mass spectrometry associate AATK expression with the GO term 'regulation of cell proliferation'. The kinase activity of AATK in comparison to the kinase-dead mutant mediates a decreased expression of the key cell cycle regulators Cyclin D1 and WEE1. Moreover, growth suppression through AATK relies on its kinase activity. In conclusion, the Ser/Thr kinase AATK represses growth and phosphorylates TP53. Furthermore, expression of AATK was correlated with a better patient survival for different cancer entities. This data suggests that AATK acts as an epigenetically inactivated tumor suppressor gene.
Collapse
Affiliation(s)
- Michelle L. Woods
- grid.8664.c0000 0001 2165 8627Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Astrid Weiss
- grid.8664.c0000 0001 2165 8627Department of Internal Medicine, Justus-Liebig-University Giessen, 35392 Giessen, Germany ,grid.452624.3German Center for Lung Research (DZL), Giessen, Germany
| | - Anna M. Sokol
- grid.418032.c0000 0004 0491 220XScientific Service Group Biomolecular Mass Spectrometry, Max-Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Johannes Graumann
- grid.418032.c0000 0004 0491 220XScientific Service Group Biomolecular Mass Spectrometry, Max-Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany ,grid.10253.350000 0004 1936 9756Present Address: Institute for Translational Proteomics, Department of Medicine, Philipps-University, 35037 Marburg, Germany
| | - Thomas Boettger
- grid.418032.c0000 0004 0491 220XMax-Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Antje M. Richter
- grid.8664.c0000 0001 2165 8627Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Ralph T. Schermuly
- grid.8664.c0000 0001 2165 8627Department of Internal Medicine, Justus-Liebig-University Giessen, 35392 Giessen, Germany ,grid.452624.3German Center for Lung Research (DZL), Giessen, Germany
| | - Reinhard H. Dammann
- grid.8664.c0000 0001 2165 8627Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany ,grid.440517.3German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center, 35392 Giessen, Germany
| |
Collapse
|
15
|
Amin R, Shukla A, Zhu JJ, Kim S, Wang P, Tian SZ, Tran AD, Paul D, Cappell SD, Burkett S, Liu H, Lee MP, Kruhlak MJ, Dwyer JE, Simpson RM, Hager GL, Ruan Y, Hunter KW. Nuclear pore protein NUP210 depletion suppresses metastasis through heterochromatin-mediated disruption of tumor cell mechanical response. Nat Commun 2021; 12:7216. [PMID: 34903738 PMCID: PMC8669001 DOI: 10.1038/s41467-021-27451-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/16/2021] [Indexed: 12/26/2022] Open
Abstract
Mechanical signals from the extracellular microenvironment have been implicated in tumor and metastatic progression. Here, we identify nucleoporin NUP210 as a metastasis susceptibility gene for human estrogen receptor positive (ER+) breast cancer and a cellular mechanosensor. Nup210 depletion suppresses lung metastasis in mouse models of breast cancer. Mechanistically, NUP210 interacts with LINC complex protein SUN2 which connects the nucleus to the cytoskeleton. In addition, the NUP210/SUN2 complex interacts with chromatin via the short isoform of BRD4 and histone H3.1/H3.2 at the nuclear periphery. In Nup210 knockout cells, mechanosensitive genes accumulate H3K27me3 heterochromatin modification, mediated by the polycomb repressive complex 2 and differentially reposition within the nucleus. Transcriptional repression in Nup210 knockout cells results in defective mechanotransduction and focal adhesion necessary for their metastatic capacity. Our study provides an important role of nuclear pore protein in cellular mechanosensation and metastasis. The involvement of nuclear pore proteins in cellular mechanosensing and metastasis is unclear. Here the authors identify that nuclear pore protein NUP210 promotes metastasis through the interaction with mechanotransducer LINC complex protein and chromatin to regulate mechanosensitive genes.
Collapse
Affiliation(s)
- Ruhul Amin
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.
| | - Anjali Shukla
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Sohyoung Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Andy D Tran
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,Confocal Microscopy Core Facility, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Debasish Paul
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Steven D Cappell
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sandra Burkett
- Molecular Cytogenetics Core Facility, National Cancer Institute, NIH, Frederick, MD, USA
| | - Huaitian Liu
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,High-Dimension Data Analysis Group, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Maxwell P Lee
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,High-Dimension Data Analysis Group, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael J Kruhlak
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,Confocal Microscopy Core Facility, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Jennifer E Dwyer
- Molecular Pathology Unit, Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - R Mark Simpson
- Molecular Pathology Unit, Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kent W Hunter
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.
| |
Collapse
|
16
|
Firmal P, Shah VK, Pant R, Chattopadhyay S. RING finger protein TOPORS modulates the expression of tumor suppressor SMAR1 in colorectal cancer via the TLR4-TRIF pathway. Mol Oncol 2021; 16:1523-1540. [PMID: 34689394 PMCID: PMC8978522 DOI: 10.1002/1878-0261.13126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
TOP1‐binding arginine/serine‐rich protein (TOPORS), a really interesting new gene finger protein, has the ability to bind to a palindromic consensus DNA sequence that enables it to function as a potential transcriptional regulator. However, its role in regulating the transcription of cancer‐associated genes is yet to be explored. As Toll‐like receptor 4 (TLR4) agonists are known to regress solid tumors, we observed that lipopolysaccharide (LPS) induces TOPORS via a TLR4‐TIR domain‐containing adapter‐inducing interferon‐β‐dependent pathway, which in turn modulates the transcription of tumor suppressor scaffold/matrix attachment region‐binding protein 1 (SMAR1, also known as BANP). ChIP analysis showed that TOPORS binds on the SMAR1 promoter and its occupancy increases upon LPS treatment. A previous study from our laboratory revealed that SMAR1 acts as a repressor of signal transducer and activator of transcription 3 (STAT3) transcription. Tumor growth, as well as tumor‐associated macrophage polarization, depends on the status of the STAT1:STAT3 ratio. LPS‐induced SMAR1 expression decreases STAT3 expression and also skews the macrophage polarization toward M1 phenotype. In contrast, LPS failed to polarize tumor‐associated macrophages to M1 phenotype in a SMAR1‐silenced condition, which shows the involvement of SMAR1 in dictating the fate of colorectal cancer progression. Identification of the molecular mechanism behind LPS‐mediated tumor regression would be crucial for designing cancer treatment strategies involving bacterial components.
Collapse
Affiliation(s)
- Priyanka Firmal
- National Centre for Cell Science, S.P. Pune University Campus, Ganeshkhind, Pune, 411007
| | - Vibhuti Kumar Shah
- National Centre for Cell Science, S.P. Pune University Campus, Ganeshkhind, Pune, 411007
| | - Richa Pant
- National Centre for Cell Science, S.P. Pune University Campus, Ganeshkhind, Pune, 411007
| | - Samit Chattopadhyay
- National Centre for Cell Science, S.P. Pune University Campus, Ganeshkhind, Pune, 411007.,Department of Biological Sciences, BITS Pilani, K. K. Birla Goa Campus, NH 17B, Zuarinagar, Goa, 403726.,Indian Institute of Chemical Biology, Raja S C Mullick Road, Jadavpur, Kolkata, 700032
| |
Collapse
|
17
|
Kafita D, Nkhoma P, Zulu M, Sinkala M. Proteogenomic analysis of pancreatic cancer subtypes. PLoS One 2021; 16:e0257084. [PMID: 34506537 PMCID: PMC8432812 DOI: 10.1371/journal.pone.0257084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 08/23/2021] [Indexed: 12/26/2022] Open
Abstract
Pancreatic cancer remains a significant public health problem with an ever-rising incidence of disease. Cancers of the pancreas are characterised by various molecular aberrations, including changes in the proteomics and genomics landscape of the tumour cells. Therefore, there is a need to identify the proteomic landscape of pancreatic cancer and the specific genomic and molecular alterations associated with disease subtypes. Here, we carry out an integrative bioinformatics analysis of The Cancer Genome Atlas dataset, including proteomics and whole-exome sequencing data collected from pancreatic cancer patients. We apply unsupervised clustering on the proteomics dataset to reveal the two distinct subtypes of pancreatic cancer. Using functional and pathway analysis based on the proteomics data, we demonstrate the different molecular processes and signalling aberrations of the pancreatic cancer subtypes. In addition, we explore the clinical characteristics of these subtypes to show differences in disease outcome. Using datasets of mutations and copy number alterations, we show that various signalling pathways previously associated with pancreatic cancer are altered among both subtypes of pancreatic tumours, including the Wnt pathway, Notch pathway and PI3K-mTOR pathways. Altogether, we reveal the proteogenomic landscape of pancreatic cancer subtypes and the altered molecular processes that can be leveraged to devise more effective treatments.
Collapse
Affiliation(s)
- Doris Kafita
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Panji Nkhoma
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Mildred Zulu
- Department of Pathology and Microbiology, School of Medicine, University of Zambia, Lusaka, Zambia
| | - Musalula Sinkala
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
- * E-mail:
| |
Collapse
|
18
|
Guardia T, Eason M, Kontrogianni-Konstantopoulos A. Obscurin: A multitasking giant in the fight against cancer. Biochim Biophys Acta Rev Cancer 2021; 1876:188567. [PMID: 34015411 PMCID: PMC8349851 DOI: 10.1016/j.bbcan.2021.188567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/03/2021] [Accepted: 05/11/2021] [Indexed: 12/19/2022]
Abstract
Giant obscurins (720-870 kDa), encoded by OBSCN, were originally discovered in striated muscles as cytoskeletal proteins with scaffolding and regulatory roles. Recently though, they have risen to the spotlight as key players in cancer development and progression. Herein, we provide a timely prudent synopsis of the expanse of OBSCN mutations across 16 cancer types. Given the extensive work on OBSCN's role in breast epithelium, we summarize functional studies implicating obscurins as potent tumor suppressors in breast cancer and delve into an in silico analysis of its mutational profile and epigenetic (de)regulation using different dataset platforms and sophisticated computational tools. Lastly, we formally describe the OBSCN-Antisense-RNA-1 gene, which belongs to the long non-coding RNA family and discuss its potential role in modulating OBSCN expression in breast cancer. Collectively, we highlight the escalating involvement of obscurins in cancer biology and outline novel potential mechanisms of OBSCN (de)regulation that warrant further investigation.
Collapse
Affiliation(s)
- Talia Guardia
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Matthew Eason
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Aikaterini Kontrogianni-Konstantopoulos
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, USA.
| |
Collapse
|
19
|
Di Fiore R, Suleiman S, Drago-Ferrante R, Felix A, O’Toole SA, O’Leary JJ, Ward MP, Beirne J, Yordanov A, Vasileva-Slaveva M, Subbannayya Y, Pentimalli F, Giordano A, Calleja-Agius J. LncRNA MORT (ZNF667-AS1) in Cancer-Is There a Possible Role in Gynecological Malignancies? Int J Mol Sci 2021; 22:ijms22157829. [PMID: 34360598 PMCID: PMC8346052 DOI: 10.3390/ijms22157829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/09/2021] [Accepted: 07/17/2021] [Indexed: 01/21/2023] Open
Abstract
Gynecological cancers (GCs) are currently among the major threats to female health. Moreover, there are different histologic subtypes of these cancers, which are defined as ‘rare’ due to an annual incidence of <6 per 100,000 women. The majority of these tend to be associated with a poor prognosis. Long non-coding RNAs (lncRNAs) play a critical role in the normal development of organisms as well as in tumorigenesis. LncRNAs can be classified into tumor suppressor genes or oncogenes, depending on their function within the cellular context and the signaling pathways in which they are involved. These regulatory RNAs are potential therapeutic targets for cancer due to their tissue and tumor specificity. However, there still needs to be a deeper understanding of the mechanisms by which lncRNAs are involved in the regulation of numerous biological functions in humans, both in normal health and disease. The lncRNA Mortal Obligate RNA Transcript (MORT; alias ZNF667-AS1) has been identified as a tumor-related lncRNA. ZNF667-AS1 gene, located in the human chromosome region 19q13.43, has been shown to be silenced by DNA hypermethylation in several cancers. In this review, we report on the biological functions of ZNF667-AS1 from recent studies and describe the regulatory functions of ZNF667-AS1 in human disease, including cancer. Furthermore, we discuss the emerging insights into the potential role of ZNF667-AS1 as a biomarker and novel therapeutic target in cancer, including GCs (ovarian, cervical, and endometrial cancers).
Collapse
Affiliation(s)
- Riccardo Di Fiore
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta;
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
- Correspondence: (R.D.F.); (J.C.-A.)
| | - Sherif Suleiman
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta;
| | | | - Ana Felix
- Department of Pathology, Instituto Portugues de Oncologia de Lisboa, NOVA Medical School, University NOVA of Lisbon, Campo dos Mártires da Pátria, 130, 1169-056 Lisbon, Portugal;
| | - Sharon A. O’Toole
- Departments of Obstetrics and Gynaecology, Trinity St James’s Cancer Institute, Trinity College Dublin, D08 HD53 Dublin, Ireland;
| | - John J. O’Leary
- Department of Histopathology, Trinity St James’s Cancer Institute, Emer Casey Molecular Pathology Laboratory, Trinity College Dublin and Coombe Women’s and Infants University Hospital, D08 RX0X Dublin, Ireland; (J.J.O.); (M.P.W.)
| | - Mark P. Ward
- Department of Histopathology, Trinity St James’s Cancer Institute, Emer Casey Molecular Pathology Laboratory, Trinity College Dublin and Coombe Women’s and Infants University Hospital, D08 RX0X Dublin, Ireland; (J.J.O.); (M.P.W.)
| | - James Beirne
- Department of Gynaecological Oncology, Trinity St James’s Cancer Institute, St James Hospital, Trinity College Dublin, D08 X4RX Dublin, Ireland;
| | - Angel Yordanov
- Department of Gynecologic Oncology, Medical University Pleven, 5800 Pleven, Bulgaria;
| | | | - Yashwanth Subbannayya
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway;
| | - Francesca Pentimalli
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Napoli, Italy;
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Jean Calleja-Agius
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta;
- Correspondence: (R.D.F.); (J.C.-A.)
| |
Collapse
|
20
|
Siraj AK, Poyil PK, Parvathareddy SK, Alobaisi K, Ahmed SO, Al-Sobhi SS, Al-Dayel F, Al-Kuraya KS. Loss of ZNF677 Expression Is an Independent Predictor for Distant Metastasis in Middle Eastern Papillary Thyroid Carcinoma Patients. Int J Mol Sci 2021; 22:ijms22157833. [PMID: 34360599 PMCID: PMC8346014 DOI: 10.3390/ijms22157833] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 01/08/2023] Open
Abstract
Thyroid cancer incidence has increased in recent decades. Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Approximately 30% of PTC patients develop recurrence or distant metastasis and tend to have poor prognosis. Therefore, the identification of targetable biomarkers in this subset of patients is of great importance. Accumulating evidence indicates that zinc finger protein 677 (ZNF677), which belongs to the zinc finger protein family, is an important effector during the progression of multiple malignancies. However, its role in Middle Eastern PTC patients has not been fully illustrated. Here, we uncovered the molecular mechanism and the clinical impact of ZNF677 expression in a large cohort of more than 1200 Middle Eastern PTC and 15 metastatic tissues. We demonstrated that ZNF677 is frequently downregulated in primary PTC (13.6%, 168/1235) and showed that complete loss of expression of ZNF677 is significantly associated with aggressive clinico-pathological markers such as extrathyroidal extension (p = 0.0008) and distant metastases (p < 0.0001). We also found a significantly higher incidence of ZNF677 loss in primary tumors with distant metastases (33.3%; p < 0.0001) as well as in distant metastatic tissues (46.7%; p = 0.0002) compared to the overall cohort (13.6%). More importantly, PTC with loss of ZNF677 expression showed significantly lower metastasis-free survival (p = 0.0090). Interestingly, on multivariate logistic regression analysis, ZNF677 loss was an independent predictor of distant metastasis in PTC (Odds ratio = 2.60, 95% Confidence interval = 1.20–5.62, p = 0.0155). In addition, we found a significant association between ZNF677 loss and phospho-AKT expression (p < 0.0001). Our functional molecular results suggest that ZNF677 acts as a tumor suppressor, mediating its effect by inhibiting AKT phosphorylation. Taken together, our results highlight the pivotal role played by ZNF677 during carcinogenesis and metastasis formation in Middle Eastern PTC patients.
Collapse
Affiliation(s)
- Abdul K. Siraj
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (A.K.S.); (P.K.P.); (S.K.P.); (K.A.); (S.O.A.)
| | - Pratheesh Kumar Poyil
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (A.K.S.); (P.K.P.); (S.K.P.); (K.A.); (S.O.A.)
| | - Sandeep Kumar Parvathareddy
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (A.K.S.); (P.K.P.); (S.K.P.); (K.A.); (S.O.A.)
| | - Khadija Alobaisi
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (A.K.S.); (P.K.P.); (S.K.P.); (K.A.); (S.O.A.)
| | - Saeeda O. Ahmed
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (A.K.S.); (P.K.P.); (S.K.P.); (K.A.); (S.O.A.)
| | - Saif S. Al-Sobhi
- Department of Surgery, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia;
| | - Fouad Al-Dayel
- Department of Pathology, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia;
| | - Khawla S. Al-Kuraya
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (A.K.S.); (P.K.P.); (S.K.P.); (K.A.); (S.O.A.)
- Correspondence: ; Tel.: +966-11-205-5167
| |
Collapse
|
21
|
Bosire C, Vidal AC, Smith JS, Jima D, Huang Z, Skaar D, Valea F, Bentley R, Gradison M, Yarnall KSH, Ford A, Overcash F, Murphy SK, Hoyo C. Association between PEG3 DNA methylation and high-grade cervical intraepithelial neoplasia. Infect Agent Cancer 2021; 16:42. [PMID: 34120615 PMCID: PMC8201933 DOI: 10.1186/s13027-021-00382-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 06/02/2021] [Indexed: 02/03/2023] Open
Abstract
Background Epigenetic mechanisms are hypothesized to contribute substantially to the progression of cervical intraepithelial neoplasia (CIN) to cervical cancer, although empirical data are limited. Methods Women (n = 419) were enrolled at colposcopic evaluation at Duke Medical Center in Durham, North Carolina. Human papillomavirus (HPV) was genotyped by HPV linear array and CIN grade was ascertained by biopsy pathologic review. DNA methylation was measured at differentially methylated regions (DMRs) regulating genomic imprinting of the IGF2/H19, IGF2AS, MESTIT1/MEST, MEG3, PLAGL1/HYMAI, KvDMR and PEG10, PEG3 imprinted domains, using Sequenom-EpiTYPER assays. Logistic regression models were used to evaluate the associations between HPV infection, DMR methylation and CIN risk overall and by race. Results Of the 419 participants, 20 had CIN3+, 52 had CIN2, and 347 had ≤ CIN1 (CIN1 and negative histology). The median participant age was 28.6 (IQR:11.6) and 40% were African American. Overall, we found no statistically significant association between altered methylation in selected DMRs and CIN2+ compared to ≤CIN1. Similarly, there was no significant association between DMR methylation and CIN3+ compared to ≤CIN2. Restricting the outcome to CIN2+ cases that were HR-HPV positive and p16 staining positive, we found a significant association with PEG3 DMR methylation (OR: 1.56 95% CI: 1.03–2.36). Conclusions While the small number of high-grade CIN cases limit inferences, our findings suggest an association between altered DNA methylation at regulatory regions of PEG3 and high grade CIN in high-risk HPV positive cases. Supplementary Information The online version contains supplementary material available at 10.1186/s13027-021-00382-3.
Collapse
Affiliation(s)
- Claire Bosire
- Department of Health Behavior, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.
| | - Adriana C Vidal
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jennifer S Smith
- Department of Epidemiology, Gillings School of Global Public Health and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Dereje Jima
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology, Division of Reproductive Sciences, Duke University School of Medicine, Durham, NC, USA
| | - David Skaar
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Fidel Valea
- Department of Obstetrics and Gynecology, Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | - Rex Bentley
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Margaret Gradison
- Department of Family Medicine and Community Health, Duke University School of Medicine, Durham, NC, USA
| | - Kimberly S H Yarnall
- Department of Family Medicine and Community Health, Duke University School of Medicine, Durham, NC, USA
| | - Anne Ford
- Department of Obstetrics and Gynecology, Division of Reproductive Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Francine Overcash
- Department of Family Medicine and Community Health, Duke University School of Medicine, Durham, NC, USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Division of Reproductive Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| |
Collapse
|
22
|
Leite JA, Ghirotto B, Targhetta VP, de Lima J, Câmara NOS. Sirtuins as pharmacological targets in neurodegenerative and neuropsychiatric disorders. Br J Pharmacol 2021; 179:1496-1511. [PMID: 34029375 DOI: 10.1111/bph.15570] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022] Open
Abstract
Histone deacetylases (HDACs) are enzymes that regulate several processes, such as transcription, cell proliferation, differentiation and development. HDACs are classified as either Zn2+ -dependent or NAD+ -dependent enzymes. Over the years, experimental and clinical evidence has demonstrated that HDAC modulation is a critical process in neurodegenerative and psychiatric disorders. Nevertheless, most of the studies have focused on the role of Zn2+ -dependent HDACs in the development of these diseases, although there is growing evidence showing that the NAD+ -dependent HDACs, known as sirtuins, are also very promising targets. This possibility has been strengthened by reports of decreased levels of NAD+ in CNS disorders, which can lead to alterations in sirtuin activation and therefore result in increased pathology. In this review, we discuss the role of sirtuins in neurodegenerative and neuropsychiatric disorders as well the possible rationale for them to be considered as pharmacological targets in future therapeutic interventions.
Collapse
Affiliation(s)
- Jefferson A Leite
- Department of Biochemistry and Immunology, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.,Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Bruno Ghirotto
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Vitor P Targhetta
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jean de Lima
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Niels O S Câmara
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Division of Nephrology, School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| |
Collapse
|
23
|
Rubio-Ramos A, Labat-de-Hoz L, Correas I, Alonso MA. The MAL Protein, an Integral Component of Specialized Membranes, in Normal Cells and Cancer. Cells 2021; 10:1065. [PMID: 33946345 PMCID: PMC8145151 DOI: 10.3390/cells10051065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
The MAL gene encodes a 17-kDa protein containing four putative transmembrane segments whose expression is restricted to human T cells, polarized epithelial cells and myelin-forming cells. The MAL protein has two unusual biochemical features. First, it has lipid-like properties that qualify it as a member of the group of proteolipid proteins. Second, it partitions selectively into detergent-insoluble membranes, which are known to be enriched in condensed cell membranes, consistent with MAL being distributed in highly ordered membranes in the cell. Since its original description more than thirty years ago, a large body of evidence has accumulated supporting a role of MAL in specialized membranes in all the cell types in which it is expressed. Here, we review the structure, expression and biochemical characteristics of MAL, and discuss the association of MAL with raft membranes and the function of MAL in polarized epithelial cells, T lymphocytes, and myelin-forming cells. The evidence that MAL is a putative receptor of the epsilon toxin of Clostridium perfringens, the expression of MAL in lymphomas, the hypermethylation of the MAL gene and subsequent loss of MAL expression in carcinomas are also presented. We propose a model of MAL as the organizer of specialized condensed membranes to make them functional, discuss the role of MAL as a tumor suppressor in carcinomas, consider its potential use as a cancer biomarker, and summarize the directions for future research.
Collapse
Affiliation(s)
- Armando Rubio-Ramos
- Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.R.-R.); (L.L.-d.-H.); (I.C.)
| | - Leticia Labat-de-Hoz
- Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.R.-R.); (L.L.-d.-H.); (I.C.)
| | - Isabel Correas
- Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.R.-R.); (L.L.-d.-H.); (I.C.)
- Department of Molecular Biology, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Miguel A. Alonso
- Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.R.-R.); (L.L.-d.-H.); (I.C.)
| |
Collapse
|
24
|
Mastoraki A, Schizas D, Charalampakis N, Naar L, Ioannidi M, Tsilimigras D, Sotiropoulou M, Moris D, Vassiliu P, Felekouras E. Contribution of Histone Deacetylases in Prognosis and Therapeutic Management of Cholangiocarcinoma. Mol Diagn Ther 2021; 24:175-184. [PMID: 32125662 DOI: 10.1007/s40291-020-00454-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cholangiocarcinoma (CCA), a malignant tumor that occurs in the epithelium of the biliary tract, has a very poor prognosis because affected patients are frequently diagnosed at an advanced stage and recurrence after resection is common. Over the last two decades, our understanding of the molecular biology of this malignancy has expanded, and various studies have explored targeted therapy for CCA in order to improve patient survival. The histone acetylation/deacetylation equilibrium is affected in carcinogenesis, leading to altered chromatin structure and therefore changes in gene expression. Understanding the molecular identity of histone deacetylases (HDACs), their cellular interactions and potential role as anticancer agents will help us develop new therapeutic strategies for CCA-affected patients. Furthermore, HDAC inhibitors act on cellular stress response pathways and decrease cancer angiogenesis. Downregulation of pro-angiogenic genes such as vascular endothelial growth factor (VEGF), hypoxia inducible factor-1 (HIF-1), and endothelial nitric oxide synthase (eNOS) inhibit formation of new vessels and can negatively affect the metastatic process. Finally, recent clinical trials prove that administration of both HDAC inhibitors and DNA-targeting chemotherapeutic agents, such as topoisomerase inhibitors, DNA intercalating agents, inhibitors of DNA synthesis, covalently modifying DNA agents, and ionizing radiation, maximizes the anticancer effect by increasing the cytotoxic efficiency of a variety of DNA-damaging anticancer drugs. Therefore, combination therapy of classic chemotherapeutic drugs with HDAC inhibitors can act synergistically for the patients' benefit.
Collapse
Affiliation(s)
- Aikaterini Mastoraki
- Fourth Department of Surgery, Attikon University Hospital, National and Kapodistrian University of Athens, 1 Rimini Str, 12462, Athens, Greece.
| | - Dimitrios Schizas
- First Department of Surgery, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Leon Naar
- Fourth Department of Surgery, Attikon University Hospital, National and Kapodistrian University of Athens, 1 Rimini Str, 12462, Athens, Greece
| | - Maria Ioannidi
- Fourth Department of Surgery, Attikon University Hospital, National and Kapodistrian University of Athens, 1 Rimini Str, 12462, Athens, Greece
| | - Diamantis Tsilimigras
- Division of Surgical Oncology, Department of Surgery, James Cancer Hospital, Solove Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | | | - Dimitrios Moris
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Pantelis Vassiliu
- Fourth Department of Surgery, Attikon University Hospital, National and Kapodistrian University of Athens, 1 Rimini Str, 12462, Athens, Greece
| | - Evangelos Felekouras
- First Department of Surgery, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| |
Collapse
|
25
|
Tang L, Zhu S, Peng W, Yin X, Tan C, Yang Y. Epigenetic identification of mitogen-activated protein kinase 10 as a functional tumor suppressor and clinical significance for hepatocellular carcinoma. PeerJ 2021; 9:e10810. [PMID: 33604188 PMCID: PMC7863782 DOI: 10.7717/peerj.10810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022] Open
Abstract
Background Mitogen-activated protein kinase 10 (Mapk10) is a member of the c-jun N-terminal kinases (jnk) subgroup in the MAPK superfamily, and was proposed as a tumor suppressor inactivated epigenetically. Its role in hepatocellular carcinoma (HCC) has not yet been illustrated. We aimed to investigate the expression and epigenetic regulation of mapk10 as well as its clinical significance in HCC. Results Mapk10 was expressed in almost all the normal tissues including liver, while we found that the protein expression of MAPK10 was significantly downregulated in clinical samples of HCC patients compared with these levels in adjacent normal tissues (29/46, P < 0.0001). Clinical significance of MAPK10 expression was then assessed in a cohort of 59 HCC cases, which indicated its negative expression was significantly correlated with advanced tumor stage (P = 0.001), more microsatellite nodules (P = 0.025), higher serum AFP (P = 0.001) and shorter overall survival time of HCC patients. Methylation was further detected in 58% of the HCC cell lines we tested and in 66% of primary HCC tissues by methylation-specific PCR (MSP), which was proved to be correlated with the silenced or downregulated expression of mapk10. To get the mechanisms more clear, the transcriptional silencing of mapk10 was reversed by pharmacological demethylation, and ectopic expression of mapk10 in silenced HCC cell lines significantly inhibited the colony formation ability, induced apoptosis, or enhanced the chemosensitivity of HCC cells to 5-fluorouracil. Conclusion Mapk10 appears to be a functional tumor suppressor gene frequently methylated in HCC, which could be a valuable biomarker or a new diagnosis and therapy target in a clinical setting.
Collapse
Affiliation(s)
- Liping Tang
- Department of Gastroenterology, the First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Shasha Zhu
- The Center for Clinical Molecular Medical Detection, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Weiyan Peng
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, the First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Xuedong Yin
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, the First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Cui Tan
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, the First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Yaying Yang
- Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| |
Collapse
|
26
|
Aftab A, Afzal S, Idrees M, Shahid AA. p53 and rb promoter methylation in hepatitis C virus-related chronic hepatitis and hepatocellular carcinoma. Future Virol 2021. [DOI: 10.2217/fvl-2020-0154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To identify methylation in p53 and rb during hepatitis C virus (HCV) infection in individuals in Pakistan. Materials & methods: Methylation-specific PCR was used on liver biopsies from hepatocellular carcinoma and chronic hepatitis C patients and on blood samples from healthy individuals. Real-time PCR was used to assess changes in the expression of p53 and rb in Huh-7 cells transfected with HCV-3a. Results: The p53 and rb promoters were methylated in hepatocellular carcinoma patients. The presence of HCV-3a- Core (p = 0.03), HCV-3a- NS-3 (p = 0.01) and HCV-3a- NS-5a (p = 0.02) downregulated p53 expression. Exposure to HCV-3a- Core (p = 0.04) downregulated rb expression. Conclusion: It can be hypothesized that HCV-induced epigenetic modifications may lead to the development of hepatic cancer that in turn inactivates p53 and rb.
Collapse
Affiliation(s)
- Ayma Aftab
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Samia Afzal
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Idrees
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ahmad Ali Shahid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| |
Collapse
|
27
|
PH-responsive strontium nanoparticles for targeted gene therapy against mammary carcinoma cells. Asian J Pharm Sci 2020; 16:236-252. [PMID: 33995617 PMCID: PMC8105532 DOI: 10.1016/j.ajps.2020.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/27/2020] [Accepted: 11/06/2020] [Indexed: 01/09/2023] Open
Abstract
Genetic intervention via the delivery of functional genes such as plasmid DNA (pDNA) and short-interfering RNA (siRNA) offers a great way to treat many single or multiple genetic defects effectively, including mammary carcinoma. Delivery of naked therapeutic genes or siRNAs is, however, short-lived due to biological clearance by scavenging nucleases and circulating monocytes. Low cellular internalization of negatively-charged nucleic acids further causes low transfection or silencing activity. Development of safe and effectual gene vectors is therefore undeniably crucial to the success of nucleic acid delivery. Inorganic nanoparticles have attracted considerable attention in the recent years due to their high loading capacity and encapsulation activity. Here we introduce strontium salt-based nanoparticles, namely, strontium sulfate, strontium sulfite and strontium fluoride as new inorganic nanocarriers. Generated strontium salt particles were found to be nanosized with high affinity towards negatively-charged pDNA and siRNA. Degradation of the particles was seen with a drop in pH, suggesting their capacity to respond to pH change and undergo dissolution at endosomal pH to release the genetic materials. While the particles are relatively nontoxic towards the cells, siRNA-loaded SrF2 and SrSO3 particles exerted superior transgene expression and knockdown activity of MAPK and AKT, leading to inhibition of their phosphorylation to a distinctive extent in both MCF-7 and 4T1 cells. Strontium salt nanoparticles have thus emerged as a promising tool for applications in cancer gene therapy.
Collapse
|
28
|
Zhang P, Zhang M. Epigenetic alterations and advancement of treatment in peripheral T-cell lymphoma. Clin Epigenetics 2020; 12:169. [PMID: 33160401 PMCID: PMC7648940 DOI: 10.1186/s13148-020-00962-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/28/2020] [Indexed: 02/08/2023] Open
Abstract
Peripheral T-cell lymphoma (PTCL) is a rare and heterogeneous group of clinically aggressive diseases associated with poor prognosis. Except for ALK + anaplastic large-cell lymphoma (ALCL), most peripheral T-cell lymphomas are highly malignant and have an aggressive disease course and poor clinical outcomes, with a poor remission rate and frequent relapse after first-line treatment. Aberrant epigenetic alterations play an important role in the pathogenesis and development of specific types of peripheral T-cell lymphoma, including the regulation of the expression of genes and signal transduction. The most common epigenetic alterations are DNA methylation and histone modification. Histone modification alters the level of gene expression by regulating the acetylation status of lysine residues on the promoter surrounding histones, often leading to the silencing of tumour suppressor genes or the overexpression of proto-oncogenes in lymphoma. DNA methylation refers to CpG islands, generally leading to tumour suppressor gene transcriptional silencing. Genetic studies have also shown that some recurrent mutations in genes involved in the epigenetic machinery, including TET2, IDH2-R172, DNMT3A, RHOA, CD28, IDH2, TET2, MLL2, KMT2A, KDM6A, CREBBP, and EP300, have been observed in cases of PTCL. The aberrant expression of miRNAs has also gradually become a diagnostic biomarker. These provide a reasonable molecular mechanism for epigenetic modifying drugs in the treatment of PTCL. As epigenetic drugs implicated in lymphoma have been continually reported in recent years, many new ideas for the diagnosis, treatment, and prognosis of PTCL originate from epigenetics in recent years. Novel epigenetic-targeted drugs have shown good tolerance and therapeutic effects in the treatment of peripheral T-cell lymphoma as monotherapy or combination therapy. NCCN Clinical Practice Guidelines also recommended epigenetic drugs for PTCL subtypes as second-line therapy. Epigenetic mechanisms provide new directions and therapeutic strategies for the research and treatment of peripheral T-cell lymphoma. Therefore, this paper mainly reviews the epigenetic changes in the pathogenesis of peripheral T-cell lymphoma and the advancement of epigenetic-targeted drugs in the treatment of peripheral T-cell lymphoma (PTCL).
Collapse
Affiliation(s)
- Ping Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou City, 450052, Henan Province, China.,Academy of Medical Sciences of Zhengzhou University, Zhengzhou City, 450052, Henan Province, China
| | - Mingzhi Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou City, 450052, Henan Province, China. .,Academy of Medical Sciences of Zhengzhou University, Zhengzhou City, 450052, Henan Province, China.
| |
Collapse
|
29
|
Reynolds BA, Oli MW, Oli MK. Eco-oncology: Applying ecological principles to understand and manage cancer. Ecol Evol 2020; 10:8538-8553. [PMID: 32884638 PMCID: PMC7452771 DOI: 10.1002/ece3.6590] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 12/25/2022] Open
Abstract
Cancer is a disease of single cells that expresses itself at the population level. The striking similarities between initiation and growth of tumors and dynamics of biological populations, and between metastasis and ecological invasion and community dynamics suggest that oncology can benefit from an ecological perspective to improve our understanding of cancer biology. Tumors can be viewed as complex, adaptive, and evolving systems as they are spatially and temporally heterogeneous, continually interacting with each other and with the microenvironment and evolving to increase the fitness of the cancer cells. We argue that an eco-evolutionary perspective is essential to understand cancer biology better. Furthermore, we suggest that ecologically informed therapeutic approaches that combine standard of care treatments with strategies aimed at decreasing the evolutionary potential and fitness of neoplastic cells, such as disrupting cell-to-cell communication and cooperation, and preventing successful colonization of distant organs by migrating cancer cells, may be effective in managing cancer as a chronic condition.
Collapse
Affiliation(s)
- Brent A. Reynolds
- Department of NeurosurgeryCollege of MedicineUniversity of FloridaGainesvilleFLUSA
| | - Monika W. Oli
- Department of Microbiology and Cell ScienceInstitute of Food and Agricultural SciencesUniversity of FloridaGainesvilleFLUSA
| | - Madan K. Oli
- Department of Wildlife Ecology and ConservationInstitute of Food and Agricultural SciencesUniversity of FloridaGainesvilleFLUSA
| |
Collapse
|
30
|
Alwithenani AI, Althubiti MA. Systematic Analysis of Spleen Tyrosine Kinase Expression and its Clinical Outcomes in Various Cancers. SAUDI JOURNAL OF MEDICINE & MEDICAL SCIENCES 2020; 8:95-104. [PMID: 32587490 PMCID: PMC7305679 DOI: 10.4103/sjmms.sjmms_300_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/28/2019] [Accepted: 02/06/2020] [Indexed: 12/04/2022]
Abstract
Background: Spleen tyrosine kinase (SYK) is an important enzyme in the proliferation and differentiation of all hematopoietic tissues. Its role as a cancer driver is well documented in liquid tumors; however, cumulative evidence has suggested an opposite role in other tumor types. Objectives: To systematically assess the expression of SYK, its prognostic value and epigenetic status in different cancers using bioinformatics tools. Methods: In this bioinformatics study, Oncomine database and cBioPortal were used to study the SYK gene expression, Kaplan–Meier plotter to study its prognostic value and MethHC to assess the SYK gene methylation in various cancers. Results: From 542 unique analyses of the SYK gene, it was found to be overexpressed in bladder, breast and colon cancers but downregulated in leukemia, lymphoma and myeloma. Compared with normal tissues, breast and brain tumors showed an overexpression of the SYK gene, whereas lymphoma and leukemia had lower expression. The Kaplan–Meier survival analysis revealed that SYK expression in pancreatic, gastric, liver and lung patients were correlated with better overall survival. Using cBioPortal, prostate cancer was found to have the highest SYK gene mutation frequency, and the mean expression was highest in diffuse large B-cell lymphoma, acute myeloid leukemia and thymoma. Using the MethHC database, SYK promoter hypermethylation was found to be significantly higher in breast, renal, liver, lung, pancreatic, prostatic, skin and stomach cancers compared with the normal tissue (P < 0.005). Conclusion: The results of this study indicate the potential use of SYK as a diagnostic and therapeutic target for different type of cancers. However, further experimental data are required to validate these results before use of SYK in clinical settings.
Collapse
Affiliation(s)
- Akram I Alwithenani
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mohammad A Althubiti
- Department of Biochemistry, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| |
Collapse
|
31
|
Quagliano A, Gopalakrishnapillai A, Barwe SP. Understanding the Mechanisms by Which Epigenetic Modifiers Avert Therapy Resistance in Cancer. Front Oncol 2020; 10:992. [PMID: 32670880 PMCID: PMC7326773 DOI: 10.3389/fonc.2020.00992] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/19/2020] [Indexed: 12/19/2022] Open
Abstract
The development of resistance to anti-cancer therapeutics remains one of the core issues preventing the improvement of survival rates in cancer. Therapy resistance can arise in a multitude of ways, including the accumulation of epigenetic alterations in cancer cells. By remodeling DNA methylation patterns or modifying histone proteins during oncogenesis, cancer cells reorient their epigenomic landscapes in order to aggressively resist anti-cancer therapy. To combat these chemoresistant effects, epigenetic modifiers such as DNA hypomethylating agents, histone deacetylase inhibitors, histone demethylase inhibitors, along with others have been used. While these modifiers have achieved moderate success when used either alone or in combination with one another, the most positive outcomes were achieved when they were used in conjunction with conventional anti-cancer therapies. Epigenome modifying drugs have succeeded in sensitizing cancer cells to anti-cancer therapy via a variety of mechanisms: disrupting pro-survival/anti-apoptotic signaling, restoring cell cycle control and preventing DNA damage repair, suppressing immune system evasion, regulating altered metabolism, disengaging pro-survival microenvironmental interactions and increasing protein expression for targeted therapies. In this review, we explore different mechanisms by which epigenetic modifiers induce sensitivity to anti-cancer therapies and encourage the further identification of the specific genes involved with sensitization to facilitate development of clinical trials.
Collapse
Affiliation(s)
- Anthony Quagliano
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Anilkumar Gopalakrishnapillai
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Sonali P. Barwe
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| |
Collapse
|
32
|
Association between mercury in cord serum and sex-specific DNA methylation in cord tissues. J Dev Orig Health Dis 2020; 12:124-131. [PMID: 32241331 DOI: 10.1017/s2040174420000161] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Prenatal exposure to mercury in utero causes abnormal foetal growth and adverse outcomes. DNA methylation is currently considered a possible mechanism through which this occurs. However, few studies have investigated the association between prenatal exposure to mercury and DNA methylation in detail. This study aimed to clarify the relationship between prenatal exposure to total mercury (Hg) and DNA methylation and its associations with sex-specific characteristics in male and female offspring. In a birth cohort study known as the Chiba study of Mother and Child Health, the DNA methylation status in cord tissue and Hg concentrations in cord serum were examined. A total of 67 participants (27 males and 40 females) were analysed based on Spearman's correlations, adjusted by a false discovery rate of the sex of each offspring. Only one methylated locus was positively correlated with Hg concentrations in cord serum in male offspring, but not in female offspring, and was annotated to the haloacid dehalogenase-like hydrolase domain-containing protein 1 (HDHD1) gene on chromosome X. This locus was located in the intron of the HDHD1 gene body and is a binding site for the zinc finger protein CCCTC-binding factor. One of the other loci, located in HDHD1, was highly methylated in the group with higher mercury concentrations, and this locus was in the gene body of HDHD1. Our results suggest that prenatal exposure to Hg might affect the epigenetic status of male foetuses.
Collapse
|
33
|
Barros TMB, Lima APB, Almeida TC, da Silva GN. Inhibition of urinary bladder cancer cell proliferation by silibinin. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:445-455. [PMID: 32078183 DOI: 10.1002/em.22363] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/16/2020] [Indexed: 05/27/2023]
Abstract
Silibinin, a natural compound extracted from milk thistle, has demonstrated antitumor properties in urinary bladder cancer cells; however, the role of TP53 gene in these effects is unclear. In order to better understand the molecular and antiproliferative mechanisms of this compound, urinary bladder cancer cells with different TP53 gene status, RT4 (low-grade tumor, wild TP53 gene), 5637 (high-grade tumor, Grade 2, mutated TP53 gene), and T24 (high-grade tumor, Grade 3, mutated TP53 gene) were treated with several concentrations of silibinin (1, 5, 10, 50, 100, and 150 μM). Cytotoxicity, prooxidant effect, morphological changes, cell migration, cell cycle progression, global methylation profile, and relative expression of HOXB3, c-MYC, PLK1, SMAD4, SRC, HAT, HDAC, and RASSF1A genes were evaluated. The silibinin presented cytotoxic and prooxidant effects in the three cell lines. In mutated TP53 cells, significant interference in cell migration and cell cycle arrest at the G2/M phase was observed. Additionally, silibinin induced global DNA hypomethylation in the highest grade tumor cells. For wild-type TP53 cells, a sub-G1 apoptotic population was present. Furthermore, there was modulation of gene expression responsible for cell growth (SMAD and c-MYC), migration (SRC), cell cycle kinetics (PLK1), angiogenesis (HOXB3), and of genes associated with epigenetic events such as DNA acetylation (HAT) and deacetylation (HDAC). In conclusion, the silibinin inhibited the urinary bladder tumor cell proliferation independently of TP53 status; however, cell cycle effects, gene expression changes, and alteration of cell migration are dependent on TP53 status. © 2020 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Tatiane M B Barros
- Programa de Pós-graduação em Ciências Farmacêuticas (CIPHARMA), Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Ana P B Lima
- Programa de Pós-graduação em Ciências Farmacêuticas (CIPHARMA), Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Tamires C Almeida
- Programa de Pós-graduação em Ciências Farmacêuticas (CIPHARMA), Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Glenda N da Silva
- Programa de Pós-graduação em Ciências Farmacêuticas (CIPHARMA), Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
- Departamento de Análises Clínicas (DEACL), Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
- Programa de Pós-graduação em Ciência Biológicas (CBIOL), Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| |
Collapse
|
34
|
John Mary DJS, Sikarwar G, Kumar A, Limaye AM. Interplay of ERα binding and DNA methylation in the intron-2 determines the expression and estrogen regulation of cystatin A in breast cancer cells. Mol Cell Endocrinol 2020; 504:110701. [PMID: 31926189 DOI: 10.1016/j.mce.2020.110701] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/05/2020] [Accepted: 01/05/2020] [Indexed: 12/11/2022]
Abstract
Despite advances in early detection and treatment, invasion and metastasis of breast tumors remains a major hurdle. Cystatin A (CSTA, also called stefin A), an estrogen-regulated gene in breast cancer cells, is an inhibitor of cysteine cathepsins, and a purported tumor suppressor. Loss of CSTA expression in breast tumors evidently shifts the balance in favor of cysteine cathepsins, thereby promoting extracellular matrix remodeling, tumor invasion and metastasis. However, the underlying mechanism behind the loss of CSTA expression in breast tumors is not known. Here, we have analyzed CSTA expression, and methylation of upstream and intron-2 CpG sites within the CSTA locus in human breast cancer cell lines and breast tumors of the TCGA cohort. Results showed an inverse relationship between expression and methylation. Sequence analysis revealed a potential estrogen response element (ERE) in the intron-2. Analysis of ChIP-seq data (ERP000380) and our own ChIP experiments showed that 17β-estradiol (E2) enhanced ERα binding to this ERE in MCF-7 cells. This ERE was located amidst the differentially methylated intron-2 CpG sites, which provoked us to examine the possible conflict between estrogen-regulation of CSTA and DNA methylation in the intron-2. We analyzed the expression of CSTA and its regulation by E2 in MDA-MB-231 and T47D cells subjected to global demethylation by 5-azacytidine (5-aza). 5-aza significantly demethylated intron-2 CpGs, and enhanced estrogen-induced ERα occupancy at the intron-2 ERE, leading to restoration of estrogen-regulation. Taken together, our results indicate that DNA methylation-dependent silencing could play a significant role in the loss of CSTA expression in breast tumors. The potential of DNA methylation as an indicator of CSTA expression or as a marker of tumor progression can be explored in future investigations. Furthermore, our results indicate the convergence of ERα-mediated estrogen regulation and DNA methylation in the intron-2, thereby offering a novel context to understand the role of estrogen-ERα signaling axis in breast tumor invasion and metastasis.
Collapse
Affiliation(s)
- Dixcy Jaba Sheeba John Mary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Girija Sikarwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Ajay Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Anil Mukund Limaye
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
| |
Collapse
|
35
|
Mahdi MR, Georges RB, Ali DM, Bedeer RF, Eltahry HM, Gabr AEHZ, Berger MR. Modulation of the Endothelin System in Colorectal Cancer Liver Metastasis: Influence of Epigenetic Mechanisms? Front Pharmacol 2020; 11:180. [PMID: 32194414 PMCID: PMC7063057 DOI: 10.3389/fphar.2020.00180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 02/10/2020] [Indexed: 12/13/2022] Open
Abstract
Targeting of endothelin system genes is a promising strategy in cancer therapy. The modulation of these genes was explored in a model of colorectal cancer (CRC) liver metastasis and in a panel of CRC tumor cell lines that were exposed to the demethylating agent decitabine. The CC531 rat model mimicking CRC liver metastasis was used for tumor cell re-isolation and analysis of the endothelin system genes and DNA methyltransferases (DNMTs) by microarray. To mimic the effects caused by methylation changes, a panel of seven CRC cell lines was treated with the demethylating agent decitabine. Three genes of the endothelin system were potently modulated at messenger RNA (mRNA) level in rat CC531 cells during liver colonization. The concomitant decrease of two DNMTs suggested an influence from altered methylation. Changes in gene expression were also accomplished by exposure of CRC cells to the demethylating agent decitabine, when using daily low concentrations for 3 days, with minimal cytotoxic effects. Sensitive human SW480 cells showed an almost 100fold upregulation of endothelin-1 mRNA compared to untreated cells. This, however, was different in LS174T cells, which showed no significant increase in gene expression although the methylation levels were significantly decreased at a variety of corresponding loci. We suggest that the mechanism induced by methylation on gene expression in metastatic CRC cells can be compromised. The results question the overall success of treating metastatic CRC by methylation inhibitors.
Collapse
Affiliation(s)
- Mohamed R. Mahdi
- Toxicology and Chemotherapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Human Anatomy & Embryology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Rania B. Georges
- Toxicology and Chemotherapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Doaa M. Ali
- Toxicology and Chemotherapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raouf F. Bedeer
- Department of Human Anatomy & Embryology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Huda M. Eltahry
- Department of Human Anatomy & Embryology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Abd-El Hakiem Z. Gabr
- Department of Human Anatomy & Embryology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Martin R. Berger
- Toxicology and Chemotherapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
36
|
Ahmed AA, Adam Essa ME. Epigenetic alterations in female urogenital organs cancer: Premise, properties, and perspectives. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
37
|
Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development. Nat Genet 2020; 52:264-272. [PMID: 32094912 PMCID: PMC7869692 DOI: 10.1038/s41588-020-0581-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/15/2020] [Indexed: 12/30/2022]
Abstract
In metazoan development, lineage specific gene expression is modulated by the delicate balance between transcription activation and repression. Despite much of our knowledge in the enhancer-centered transcription activation, silencers and their roles in normal development are poorly understood. Here, we performed chromatin interaction analyses of Polycomb repressive complex 2 (PRC2), a key regulator inducing transcriptional gene silencing, to uncover silencers, their molecular identity and associated chromatin connectivity. Systematic analysis of the cis-regulatory silencer elements reveals their chromatin features and gene targeting specificity. Deletion of these PRC2-bound silencers in mice results in transcriptional derepression of their interacting genes and pleiotropic developmental phenotypes, including embryonic lethality. While functioning as PRC2-bound silencers in pluripotent cells, they can transition into active tissue-specific enhancers during development, suggesting their regulatory versatility. Our study characterizes the molecular nature of silencers, their associated chromatin architectures, and offers the exciting possibility of targeted re-activation of epigenetically silenced genes.
Collapse
|
38
|
Machine Learning and Network Analyses Reveal Disease Subtypes of Pancreatic Cancer and their Molecular Characteristics. Sci Rep 2020; 10:1212. [PMID: 31988390 PMCID: PMC6985164 DOI: 10.1038/s41598-020-58290-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/09/2020] [Indexed: 12/12/2022] Open
Abstract
Given that the biological processes governing the oncogenesis of pancreatic cancers could present useful therapeutic targets, there is a pressing need to molecularly distinguish between different clinically relevant pancreatic cancer subtypes. To address this challenge, we used targeted proteomics and other molecular data compiled by The Cancer Genome Atlas to reveal that pancreatic tumours can be broadly segregated into two distinct subtypes. Besides being associated with substantially different clinical outcomes, tumours belonging to each of these subtypes also display notable differences in diverse signalling pathways and biological processes. At the proteome level, we show that tumours belonging to the less severe subtype are characterised by aberrant mTOR signalling, whereas those belonging to the more severe subtype are characterised by disruptions in SMAD and cell cycle-related processes. We use machine learning algorithms to define sets of proteins, mRNAs, miRNAs and DNA methylation patterns that could serve as biomarkers to accurately differentiate between the two pancreatic cancer subtypes. Lastly, we confirm the biological relevance of the identified biomarkers by showing that these can be used together with pattern-recognition algorithms to accurately infer the drug sensitivity of pancreatic cancer cell lines. Our study shows that integrative profiling of multiple data types enables a biological and clinical representation of pancreatic cancer that is comprehensive enough to provide a foundation for future therapeutic strategies.
Collapse
|
39
|
Moena D, Nardocci G, Acevedo E, Lian J, Stein G, Stein J, Montecino M. Ezh2-dependent H3K27me3 modification dynamically regulates vitamin D3-dependent epigenetic control of CYP24A1 gene expression in osteoblastic cells. J Cell Physiol 2020; 235:5404-5412. [PMID: 31907922 DOI: 10.1002/jcp.29428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 01/22/2023]
Abstract
Epigenetic control is critical for the regulation of gene transcription in mammalian cells. Among the most important epigenetic mechanisms are those associated with posttranslational modifications of chromosomal histone proteins, which modulate chromatin structure and increased accessibility of promoter regulatory elements for competency to support transcription. A critical histone mark is trimethylation of histone H3 at lysine residue 27 (H3K27me3), which is mediated by Ezh2, the catalytic subunit of the polycomb group complex PRC2 to repress transcription. Treatment of cells with the active vitamin D metabolite 1,25(OH)2 D3 , results in transcriptional activation of the CYP24A1 gene, which encodes a 24-hydroxylase enzyme, that is, essential for physiological control of vitamin D3 levels. We report that the Ezh2-mediated deposition of H3K27me3 at the CYP24A1 gene promoter is a requisite regulatory component during transcriptional silencing of this gene in osteoblastic cells in the absence of 1,25(OH)2 D3 . 1,25(OH)2 D3 dependent transcriptional activation of the CYP24A1 gene is accompanied by a rapid release of Ezh2 from the promoter, together with the binding of the H3K27me3-specific demethylase Utx/Kdm6a and thereby subsequent erasing of the H3K27me3 mark. Importantly, we find that these changes in H3K27me3 enrichment at the CYP24A1 gene promoter are highly dynamic, as this modification is rapidly reacquired following the withdrawal of 1,25(OH)2 D3 .
Collapse
Affiliation(s)
- Daniel Moena
- Institute of Biomedical Sciences and FONDAP Center for Genome Regulation, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,Department of Biological Sciences, Faculty of Life Sciences, Universidad Andres Bello, Concepcion, Chile
| | - Gino Nardocci
- Institute of Biomedical Sciences and FONDAP Center for Genome Regulation, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Elvis Acevedo
- Institute of Biomedical Sciences and FONDAP Center for Genome Regulation, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Jane Lian
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont
| | - Gary Stein
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont
| | - Janet Stein
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont
| | - Martin Montecino
- Institute of Biomedical Sciences and FONDAP Center for Genome Regulation, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| |
Collapse
|
40
|
A Ras-LSD1 axis activates PI3K signaling through PIK3IP1 suppression. Oncogenesis 2020; 9:2. [PMID: 31900384 PMCID: PMC6949251 DOI: 10.1038/s41389-019-0185-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023] Open
Abstract
PI3K Interacting Protein 1 (PIK3IP1) is a suppressor of the PI3K/Akt/mTOR pathway. We previously reported that activated Ras suppresses PIK3IP1 expression to positively regulate the PI3K pathway in cancer cells. Using doxycycline-inducible PIK3IP1, here we confirm that reversing the effect of Ras by inducing expression of PIK3IP1 suppresses Ras-induced anchorage-independent growth, supporting the central role of PIK3IP1 in transformation. However, the molecular mechanisms by which Ras-activation that causes loss of PIK3IP1 expression are unknown. We find that Ras activity represses PIK3IP1 expression via the recruitment of lysine-specific demethylase 1 (LSD1) to the PIK3IP1 gene promoter and enhancer, resulting in erasure of active histone marks. These studies demonstrate cross-activation of Ras/Raf/MEK/ERK and PI3K/AKT/mTOR pathways, where Ras decommissions PIK3IP1 gene expression by enhancing LSD1 and its corepressor activities to suppress PIK3IP1 transcription.
Collapse
|
41
|
Bagger FO, Probst V. Single Cell Sequencing in Cancer Diagnostics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:175-193. [PMID: 32949400 DOI: 10.1007/978-981-15-4494-1_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Personalized medicine has been driven by improvements in genomic sequencing and analysis. For several diseases, in particular cancers, it has for nearly a decade been standard clinical practice to analyze the genome and expression of the genes of patients. The results are reflected directly in the treatment plan for the patient, in targeted medical inventions. This specialized mode of diagnostics has been restricted to account for averaged trends in the tumor. The approach sharply contrasts our knowledge on heterogeneity within tumors. Several studies further describe how treatment against one tumor subclone in some cases merely serves to provide space and support for uncontrolled growth of more aggressive subclones. In this chapter, we describe current possibilities for implementation of single cell sequencing of malignomas in clinic, as well as discuss hands-on practical advice for single cell routine diagnostics that allows for full delineation of tumor clonality.
Collapse
Affiliation(s)
- Frederik Otzen Bagger
- Department of Genomic Medicine, Rigshospitalet, Centre of Diagnostics, Section 4113, Copenhagen, Denmark.
| | - Victoria Probst
- Department of Genomic Medicine, Rigshospitalet, Centre of Diagnostics, Section 4113, Copenhagen, Denmark
| |
Collapse
|
42
|
Li X. Epigenetics and cell cycle regulation in cystogenesis. Cell Signal 2019; 68:109509. [PMID: 31874209 DOI: 10.1016/j.cellsig.2019.109509] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 12/16/2022]
Abstract
The role of genetic mutations in the development of polycystic kidney disease (PKD), such as alterations in PKD1 and PKD2 genes in autosomal dominant PKD (ADPKD), is well understood. However, the significance of epigenetic mechanisms in the progression of PKD remains unclear and is increasingly being investigated. The term of epigenetics describes a range of mechanisms in genome function that do not solely result from the DNA sequence itself. Epigenetic information can be inherited during mammalian cell division to sustain phenotype specifically and physiologically responsive gene expression in the progeny cells. A multitude of functional studies of epigenetic modifiers and systematic genome-wide mapping of epigenetic marks reveal the importance of epigenomic mechanisms, including DNA methylation, histone/chromatin modifications and non-coding RNAs, in PKD pathologies. Deregulated proliferation is a characteristic feature of cystic renal epithelial cells. Moreover, defects in many of the molecules that regulate the cell cycle have been implicated in cyst formation and progression. Recent evidence suggests that alterations of DNA methylation and histone modifications on specific genes and the whole genome involved in cell cycle regulation and contribute to the pathogenesis of PKD. This review summarizes the recent advances of epigenetic mechanisms in PKD, which helps us to define the term of "PKD epigenetics" and group PKD epigenetic changes in three categories. In particularly, this review focuses on the interplay of epigenetic mechanisms with cell cycle regulation during normal cell cycle progression and cystic cell proliferation, and discusses the potential to detect and quantify DNA methylation from body fluids as diagnostic/prognostic biomarkers. Collectively, this review provides concepts and examples of epigenetics in cell cycle regulation to reveal a broad view of different aspects of epigenetics in biology and PKD, which may facilitate to identify possible novel therapeutic intervention points and to explore epigenetic biomarkers in PKD.
Collapse
Affiliation(s)
- Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, United States of America; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, United States of America.
| |
Collapse
|
43
|
Zhang Y, Wu X, Kai Y, Lee CH, Cheng F, Li Y, Zhuang Y, Ghaemmaghami J, Chuang KH, Liu Z, Meng Y, Keswani M, Gough NR, Wu X, Zhu W, Tzatsos A, Peng W, Seto E, Sotomayor EM, Zheng X. Secretome profiling identifies neuron-derived neurotrophic factor as a tumor-suppressive factor in lung cancer. JCI Insight 2019; 4:129344. [PMID: 31852841 DOI: 10.1172/jci.insight.129344] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 11/13/2019] [Indexed: 12/12/2022] Open
Abstract
Clinical and preclinical studies show tissue-specific differences in tumorigenesis. Tissue specificity is controlled by differential gene expression. We prioritized genes that encode secreted proteins according to their preferential expression in normal lungs to identify candidates associated with lung cancer. Indeed, most of the lung-enriched genes identified in our analysis have known or suspected roles in lung cancer. We focused on the gene encoding neuron-derived neurotrophic factor (NDNF), which had not yet been associated with lung cancer. We determined that NDNF was preferentially expressed in the normal adult lung and that its expression was decreased in human lung adenocarcinoma and a mouse model of this cancer. Higher expression of NDNF was associated with better clinical outcome of patients with lung adenocarcinoma. Purified NDNF inhibited proliferation of lung cancer cells, whereas silencing NDNF promoted tumor cell growth in culture and in xenograft models. We determined that NDNF is downregulated through DNA hypermethylation near CpG island shores in human lung adenocarcinoma. Furthermore, the lung cancer-related DNA hypermethylation sites corresponded to the methylation sites that occurred in tissues with low NDNF expression. Thus, by analyzing the tissue-specific secretome, we identified a tumor-suppressive factor, NDNF, which is associated with patient outcomes in lung adenocarcinoma.
Collapse
Affiliation(s)
- Ya Zhang
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Xuefeng Wu
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Yan Kai
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Department of Physics, George Washington University Columbian College of Arts and Sciences, Washington, DC, USA
| | - Chia-Han Lee
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Department of Biochemistry and Molecular Medicine
| | - Fengdong Cheng
- GW Cancer Center and.,Division of Hematology and Oncology, Department of Medicine, and
| | - Yixuan Li
- GW Cancer Center and.,Department of Biochemistry and Molecular Medicine
| | - Yongbao Zhuang
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Javid Ghaemmaghami
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Kun-Han Chuang
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Zhuo Liu
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Yunxiao Meng
- GW Cancer Center and.,Department of Biochemistry and Molecular Medicine
| | - Meghana Keswani
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Nancy R Gough
- Center for Translational Medicine, Department of Surgery, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Xiaojun Wu
- Department of Pathology, Johns Hopkins Sibley Memorial Hospital, Washington, DC, USA.,Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Wenge Zhu
- GW Cancer Center and.,Department of Biochemistry and Molecular Medicine
| | - Alexandros Tzatsos
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Weiqun Peng
- GW Cancer Center and.,Department of Physics, George Washington University Columbian College of Arts and Sciences, Washington, DC, USA
| | - Edward Seto
- GW Cancer Center and.,Department of Biochemistry and Molecular Medicine
| | - Eduardo M Sotomayor
- GW Cancer Center and.,Division of Hematology and Oncology, Department of Medicine, and
| | - Xiaoyan Zheng
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| |
Collapse
|
44
|
Gokulnath P, de Cristofaro T, Manipur I, Di Palma T, Soriano AA, Guarracino MR, Zannini M. Long Non-Coding RNA MAGI2-AS3 is a New Player with a Tumor Suppressive Role in High Grade Serous Ovarian Carcinoma. Cancers (Basel) 2019; 11:cancers11122008. [PMID: 31842477 PMCID: PMC6966615 DOI: 10.3390/cancers11122008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/03/2019] [Accepted: 12/06/2019] [Indexed: 12/24/2022] Open
Abstract
High-Grade Serous Ovarian Carcinoma (HGSC) is the most incidental and lethal subtype of epithelial ovarian cancer (EOC) with a high mortality rate of nearly 65%. Recent findings aimed at understanding the pathogenesis of HGSC have attributed its principal source as the Fallopian Tube (FT). To further comprehend the exact mechanism of carcinogenesis, which is still less known, we performed a transcriptome analysis comparing FT and HGSC. Our study aims at exploring new players involved in the development of HGSC from FT, along with their signaling network, and we chose to focus on non-coding RNAs. Non-coding RNAs (ncRNAs) are increasingly observed to be the major regulators of several cellular processes and could have key functions as biological markers, as well as even a therapeutic approach. The most physiologically relevant and significantly dysregulated non-coding RNAs were identified bioinformatically. After analyzing the trend in HGSC and other cancers, MAGI2-AS3 was observed to be an important player in EOC. We assessed its tumor-suppressive role in EOC by means of various assays. Further, we mapped its signaling pathway using its role as a miRNA sponge to predict the miRNAs binding to MAGI2AS3 and showed it experimentally. We conclude that MAGI2-AS3 acts as a tumor suppressor in EOC, specifically in HGSC by sponging miR-15-5p, miR-374a-5p and miR-374b-5p, and altering downstream signaling of certain mRNAs through a ceRNA network.
Collapse
Affiliation(s)
- Priyanka Gokulnath
- IEOS - Institute of Experimental Endocrinology and Oncology ‘G. Salvatore’, National Research Council, via S. Pansini 5, 80131 Napoli, Italy; (P.G.)
- Dpt. Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Tiziana de Cristofaro
- IEOS - Institute of Experimental Endocrinology and Oncology ‘G. Salvatore’, National Research Council, via S. Pansini 5, 80131 Napoli, Italy; (P.G.)
| | - Ichcha Manipur
- High Performance Computing and Networking Institute, National Research Council, via P. Castellino 111, 80131 Napoli, Italy
| | - Tina Di Palma
- IEOS - Institute of Experimental Endocrinology and Oncology ‘G. Salvatore’, National Research Council, via S. Pansini 5, 80131 Napoli, Italy; (P.G.)
| | - Amata Amy Soriano
- IEOS - Institute of Experimental Endocrinology and Oncology ‘G. Salvatore’, National Research Council, via S. Pansini 5, 80131 Napoli, Italy; (P.G.)
- Present affiliation: IRCCS Casa Sollievo della Sofferenza, Cancer Stem Cells Unit, ISReMIT, 71013 San Giovanni Rotondo FG, Italy
| | - Mario Rosario Guarracino
- Dpt. Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Mariastella Zannini
- IEOS - Institute of Experimental Endocrinology and Oncology ‘G. Salvatore’, National Research Council, via S. Pansini 5, 80131 Napoli, Italy; (P.G.)
- Correspondence:
| |
Collapse
|
45
|
Grant AD, Vail P, Padi M, Witkiewicz AK, Knudsen ES. Interrogating Mutant Allele Expression via Customized Reference Genomes to Define Influential Cancer Mutations. Sci Rep 2019; 9:12766. [PMID: 31484939 PMCID: PMC6726654 DOI: 10.1038/s41598-019-48967-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 08/12/2019] [Indexed: 11/16/2022] Open
Abstract
Genetic alterations are essential for cancer initiation and progression. However, differentiating mutations that drive the tumor phenotype from mutations that do not affect tumor fitness remains a fundamental challenge in cancer biology. To better understand the impact of a given mutation within cancer, RNA-sequencing data was used to categorize mutations based on their allelic expression. For this purpose, we developed the MAXX (Mutation Allelic Expression Extractor) software, which is highly effective at delineating the allelic expression of both single nucleotide variants and small insertions and deletions. Results from MAXX demonstrated that mutations can be separated into three groups based on their expression of the mutant allele, lack of expression from both alleles, or expression of only the wild-type allele. By taking into consideration the allelic expression patterns of genes that are mutated in PDAC, it was possible to increase the sensitivity of widely used driver mutation detection methods, as well as identify subtypes that have prognostic significance and are associated with sensitivity to select classes of therapeutic agents in cell culture. Thus, differentiating mutations based on their mutant allele expression via MAXX represents a means to parse somatic variants in tumor genomes, helping to elucidate a gene’s respective role in cancer.
Collapse
Affiliation(s)
- Adam D Grant
- University of Arizona Cancer Center, Tucson, AZ, 85719, USA
| | - Paris Vail
- University of Arizona Cancer Center, Tucson, AZ, 85719, USA
| | - Megha Padi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85719, USA
| | | | - Erik S Knudsen
- Department of Molecular and Cellular Biology, Roswell Park Cancer Center, Buffalo, NY, 14263, USA.
| |
Collapse
|
46
|
MUC1-C represses the RASSF1A tumor suppressor in human carcinoma cells. Oncogene 2019; 38:7266-7277. [PMID: 31435022 PMCID: PMC6872931 DOI: 10.1038/s41388-019-0940-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/16/2019] [Accepted: 05/21/2019] [Indexed: 01/02/2023]
Abstract
RASSF1A encodes a tumor suppressor that inhibits the RAS→RAF→MEK→ERK pathway and is one of the most frequently inactivated genes in human cancers. MUC1-C is an oncogenic effector of the cancer cell epigenome that is overexpressed in diverse carcinomas. We show here that MUC1-C represses RASSF1A expression in KRAS wild-type and mutant cancer cells. Mechanistically, MUC1-C occupies the RASSF1A promoter in a complex with the ZEB1 transcriptional repressor. In turn, MUC1-C/ZEB1 complexes recruit DNA methyltransferase 3b (DNMT3b) to the CpG island in the RASSF1A promoter. Targeting MUC1-C, ZEB1 and DNMT3b thereby decreases methylation of the CpG island and derepresses RASSF1A transcription. We also show that targeting MUC1-C regulates KRAS signaling, as evidenced by RNA-seq analysis, and decreases MEK/ERK activation, which is of importance for RAS-mediated tumorigenicity. These findings define a previously unrecognized role for MUC1-C in suppression of RASSF1A and support targeting MUC1-C as an approach for inhibiting MEK→ERK signaling.
Collapse
|
47
|
Asghariazar V, Sakhinia E, Mansoori B, Mohammadi A, Baradaran B. Tumor suppressor microRNAs in lung cancer: An insight to signaling pathways and drug resistance. J Cell Biochem 2019; 120:19274-19289. [DOI: 10.1002/jcb.29295] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 06/27/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Vahid Asghariazar
- Department of Medical Genetics, Faculty of Medicine Tabriz University of Medical Sciences Tabriz Iran
- Immunology Research Center Tabriz University of Medical Sciences Tabriz Iran
- Student Research Committee Tabriz University of Medical Sciences Tabriz Iran
| | - Ebrahim Sakhinia
- Department of Medical Genetics, Faculty of Medicine Tabriz University of Medical Sciences Tabriz Iran
| | - Behzad Mansoori
- Immunology Research Center Tabriz University of Medical Sciences Tabriz Iran
- Aging Research Institute, Physical Medicine and Rehabilitation Research Center Tabriz University of Medical Sciences Tabriz Iran
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine University of Southern Denmark Odense Denmark
| | - Ali Mohammadi
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine University of Southern Denmark Odense Denmark
| | - Behzad Baradaran
- Immunology Research Center Tabriz University of Medical Sciences Tabriz Iran
| |
Collapse
|
48
|
Paredes-Céspedes DM, Herrera-Moreno JF, Bernal-Hernández YY, Medina-Díaz IM, Salazar AM, Ostrosky-Wegman P, Barrón-Vivanco BS, Rojas-García AE. Pesticide Exposure Modifies DNA Methylation of Coding Region of WRAP53α, an Antisense Sequence of p53, in a Mexican Population. Chem Res Toxicol 2019; 32:1441-1448. [PMID: 31243981 DOI: 10.1021/acs.chemrestox.9b00153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influence of pesticide exposure in alteration of DNA methylation patterns of specific genes is still limited, specifically in natural antisense transcripts (NAT), such as the WRAP53α gene. The aim of this study was to determine the methylation of the WRAP53α gene in mestizo and indigenous populations as well as its relationship with internal (age, sex, and body mass index) and external factors (pesticide exposure and micronutrient intake). A cross-sectional study was conducted including 91 mestizo individuals without occupational exposure to pesticides, 164 mestizo urban sprayers and 189 indigenous persons without occupational exposure to pesticides. Acute pesticide exposure was evaluated by measurement of urinary dialkylphosphate (DAP) concentration by gas chromatograph coupled to a mass spectrometer. Anthropometric characteristics, unhealthy habits, and chronic pesticide exposure were assessed using a structured questionnaire. The frequency of macro- and micronutrient intake was determined using SNUT software. DNA methylation of the WRAP53α gene was determined by pyrosequencing of bisulfite-modified DNA. The mestizo sprayers group had the higher values of %5mC. In addition, this group had the most DAP urinary concentration with respect to the indigenous and reference groups. Bivariate analysis showed an association between %5mC of the WRAP53α gene with micronutrient intake and pesticide exposure in mestizo sprayers, whereas changes in %5mC of the WRAP53α gene was associated with body mass index in the indigenous group. These data suggest that the %5mC of the WRAP53α gene can be influenced by pesticide exposure and ethnicity in the study population, and changes in the WRAP53α gene might cause an important cell process disturbance.
Collapse
Affiliation(s)
- Diana M Paredes-Céspedes
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado , Universidad Autónoma de Nayarit , 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000 , Tepic , Nayarit , México.,Posgrado en Ciencias Biológico Agropecuarias , Unidad Académica de Agricultura , Km. 9 Carretera Tepic-Compostela, Xalisco , Nayarit , México
| | - José F Herrera-Moreno
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado , Universidad Autónoma de Nayarit , 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000 , Tepic , Nayarit , México.,Posgrado en Ciencias Biológico Agropecuarias , Unidad Académica de Agricultura , Km. 9 Carretera Tepic-Compostela, Xalisco , Nayarit , México
| | - Yael Y Bernal-Hernández
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado , Universidad Autónoma de Nayarit , 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000 , Tepic , Nayarit , México
| | - Irma M Medina-Díaz
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado , Universidad Autónoma de Nayarit , 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000 , Tepic , Nayarit , México
| | - Ana M Salazar
- Instituto de Investigaciones Biomédicas , Universidad Nacional Autónoma de México (UNAM) , P.O. Box 70228, Ciudad Universitaria, México DF 04510 , México
| | - Patricia Ostrosky-Wegman
- Instituto de Investigaciones Biomédicas , Universidad Nacional Autónoma de México (UNAM) , P.O. Box 70228, Ciudad Universitaria, México DF 04510 , México
| | - Briscia S Barrón-Vivanco
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado , Universidad Autónoma de Nayarit , 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000 , Tepic , Nayarit , México
| | - Aurora E Rojas-García
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado , Universidad Autónoma de Nayarit , 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000 , Tepic , Nayarit , México
| |
Collapse
|
49
|
Ryu TY, Kim K, Kim SK, Oh JH, Min JK, Jung CR, Son MY, Kim DS, Cho HS. SETDB1 regulates SMAD7 expression for breast cancer metastasis. BMB Rep 2019. [PMID: 30545440 PMCID: PMC6443319 DOI: 10.5483/bmbrep.2019.52.2.235] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Breast cancer (BRC) is the most invasive cancer in women. Although the survival rate of BRC is gradually increasing due to improved screening systems, development of novel therapeutic targets for inhibition of BRC proliferation, metastasis and recurrence have been constantly needed. Thus, in this study, we identified overexpression of SETDB1 (SET Domain Bifurcated 1), a histone methyltransferase, in RNA-seq data of BRC derived from TCGA portal. In Gene Ontology (GO) analysis, cell migration-related GO terms were enriched, and we confirmed down-regulation of cell migration/invasion and alteration of EMT/MET markers after knockdown of SETDB1. Moreover, gene network analysis showed that SMAD7 expression is regulated by SETDB1 levels, indicating that up-regulation of SMAD7 by SETDB1 knockdown inhibited BRC metastasis. Therefore, development of SETDB1 inhibitors and functional studies may help develop more effective clinical guidelines for BRC treatment.
Collapse
Affiliation(s)
- Tae Young Ryu
- Korea Research Institute of Bioscience and Biotechnology, Korea University of Science and Technology, Daejeon 34141, Korea
| | - Kwangho Kim
- Korea Research Institute of Bioscience and Biotechnology, Korea University of Science and Technology, Daejeon 34141, Korea
| | - Seon-Kyu Kim
- Korea Research Institute of Bioscience and Biotechnology, Korea University of Science and Technology, Daejeon 34141, Korea
| | - Jung-Hwa Oh
- Korea Institute of Toxicology (KIT), Daejeon 34114, Korea
| | - Jeong-Ki Min
- Korea Research Institute of Bioscience and Biotechnology, and Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34141, Korea
| | - Cho-Rok Jung
- Korea Research Institute of Bioscience and Biotechnology, and Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34141, Korea
| | - Mi-Young Son
- Korea Research Institute of Bioscience and Biotechnology, and Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34141, Korea
| | - Dae-Soo Kim
- Korea Research Institute of Bioscience and Biotechnology, and Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34141, Korea
| | - Hyun-Soo Cho
- Korea Research Institute of Bioscience and Biotechnology, and Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34141, Korea
| |
Collapse
|
50
|
Wylie B, Chee J, Forbes CA, Booth M, Stone SR, Buzzai A, Abad A, Foley B, Cruickshank MN, Waithman J. Acquired resistance during adoptive cell therapy by transcriptional silencing of immunogenic antigens. Oncoimmunology 2019; 8:1609874. [PMID: 31413920 PMCID: PMC6682399 DOI: 10.1080/2162402x.2019.1609874] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 12/23/2022] Open
Abstract
Immunotherapies such as adoptive cell therapy (ACT) are promising treatments for solid cancers. However, relapsing disease remains a problem and the molecular mechanisms underlying resistance are poorly defined. We postulated that the deregulated epigenetic landscape in cancer cells could underpin the acquisition of resistance to immunotherapy. To address this question, two preclinical models of ACT were employed to study transcriptional and epigenetic regulatory processes within ACT-treated cancer cells. In these models ACT consistently causes robust tumor regression, but resistance develops and tumors relapse. We identified down-regulated expression of immunogenic antigens at the mRNA level correlated with escape from immune control. To determine whether this down-regulation was under epigenetic control, we treated escaped tumor cells with DNA demethylating agents, azacytidine (AZA) and decitabine (DEC). AZA or DEC treatment restored antigen expression in a proportion of the tumor population. To explore the importance of other epigenetic modifications we isolated tumor cells refractory to DNA demethylation and screened clones against a panel of 19 different epigenetic modifying agents (EMAs). The library of EMAs included inhibitors of a range of chromosomal and transcription regulatory protein complexes, however, when tested as single agents none restored further antigen expression. These findings suggest that tumor cells employ multiple epigenetic and genetic mechanisms to evade immune control, and a combinatorial approach employing several EMAs targeting transcription and genome stability may be required to overcome tumor resistance to immunotherapy.
Collapse
Affiliation(s)
- Ben Wylie
- Phylogica, Harry Perkins Institute for Medical Research, QEII Medical Centre, Nedlands, Australia
| | - Jonathan Chee
- National Centre for Asbestos Related Diseases, School of Biomedical Sciences, University of Western Australia, QEII Medical Centre, Nedlands, Australia
| | - Catherine A Forbes
- Telethon Kids Institute, University of Western Australia, Northern Entrance, Perth Children's Hospital, Nedlands, Australia
| | - Mitchell Booth
- Telethon Kids Institute, University of Western Australia, Northern Entrance, Perth Children's Hospital, Nedlands, Australia
| | - Shane R Stone
- Phylogica, Harry Perkins Institute for Medical Research, QEII Medical Centre, Nedlands, Australia
| | - Anthony Buzzai
- Telethon Kids Institute, University of Western Australia, Northern Entrance, Perth Children's Hospital, Nedlands, Australia
| | - Ana Abad
- Telethon Kids Institute, University of Western Australia, Northern Entrance, Perth Children's Hospital, Nedlands, Australia
| | - Bree Foley
- Telethon Kids Institute, University of Western Australia, Northern Entrance, Perth Children's Hospital, Nedlands, Australia
| | - Mark N Cruickshank
- Telethon Kids Institute, University of Western Australia, Northern Entrance, Perth Children's Hospital, Nedlands, Australia
| | - Jason Waithman
- Telethon Kids Institute, University of Western Australia, Northern Entrance, Perth Children's Hospital, Nedlands, Australia
| |
Collapse
|