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Hong L, Chen M, Huang M, Chen W, Abudukeremu X, She F, Chen Y. FOXA2 suppresses gallbladder carcinoma cell migration, invasion, and epithelial-mesenchymal transition by targeting SERPINB5. ENVIRONMENTAL TOXICOLOGY 2024; 39:708-722. [PMID: 37665156 DOI: 10.1002/tox.23953] [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: 06/13/2023] [Revised: 08/11/2023] [Accepted: 08/20/2023] [Indexed: 09/05/2023]
Abstract
BACKGROUND Gallbladder cancer (GBC), a highly malignant gastrointestinal tumor, lacks effective therapies. Foxhead box A2 (FOXA2) is a tumor suppressor that is poorly expressed in various human malignancies. This study aimed to ascertain FOXA2 expression in GBC and its relevance to tumor metastasis, and to elucidate its regulatory mechanism with epithelial-mesenchymal transition (EMT) as an entry point, in the hope of providing a potential therapeutic target for GBC. METHODS FOXA2 expression in GBC tissues was first detected using immunohistochemistry (IHC), followed by correlation analysis with clinicopathological characteristics and survival prognosis. Subsequently, the effects of FOXA2 on GBC cell migration and invasion, as well as EMT induction, were evaluated by scratch, Transwell, RT-PCR, and Western blot assays, together with animal experimentation. Ultimately, mRNA sequencing was carried out to identify the key downstream target genes of FOXA2 in controlling the EMT process in GBC cells, and dual-luciferase reporter and chromatin immunoprecipitation assays were used to determine its regulatory mechanism. RESULTS FOXA2 was underexpressed in GBC tissues and inversely correlated with tumor node metastasis stage, lymph node metastasis, and poor patient prognosis. FOXA2 exerts suppressive effects on EMT and metastasis of GBC in vivo and in vitro. FOXA2 can impede GBC cell migratory and invasive functions and EMT by positively mediating serine protein kinase inhibitor B5 (SERPINB5) expression. CONCLUSION FOXA2 directly binds to the SERPINB5 promoter region to stimulate its transcription, thereby modulating the migration and invasion behaviors of GBC cells as well as the EMT process, which might be an effective therapeutic target against GBC.
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Affiliation(s)
- Lingju Hong
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fujian Medical University, Fuzhou, China
- Fujian Medical University Cancer Center, Fujian Medical University, Fuzhou, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
| | - Mingyuan Chen
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fujian Medical University, Fuzhou, China
- Fujian Medical University Cancer Center, Fujian Medical University, Fuzhou, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
| | - Maotuan Huang
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fujian Medical University, Fuzhou, China
- Fujian Medical University Cancer Center, Fujian Medical University, Fuzhou, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
| | - Weihong Chen
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fujian Medical University, Fuzhou, China
- Fujian Medical University Cancer Center, Fujian Medical University, Fuzhou, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
| | - Xiahenazi Abudukeremu
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fujian Medical University, Fuzhou, China
- Fujian Medical University Cancer Center, Fujian Medical University, Fuzhou, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
| | - Feifei She
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
| | - Yanling Chen
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fujian Medical University, Fuzhou, China
- Fujian Medical University Cancer Center, Fujian Medical University, Fuzhou, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
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2
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Anwar M, Haseeb M, Choi S, Kim KP. P176S Mutation Rewires Electrostatic Interactions That Alter Maspin Functionality. ACS OMEGA 2023; 8:28258-28267. [PMID: 37576651 PMCID: PMC10413834 DOI: 10.1021/acsomega.3c01850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 06/21/2023] [Indexed: 08/15/2023]
Abstract
Maspin is known to regress tumors by inhibiting angiogenesis; however, its roles have been reported to be context- and sequence-dependent. Various proteins and cofactors bind to maspin, possibly explaining its conflicting roles. Moreover, polymorphic forms of maspin have also been linked to tumor regression and survival; for instance, maspin with Ser at 176 (maspin-S176) promotes tumors, while maspin with Pro at 176 (maspin-P176) has opposing roles in cancer pathogenesis. With the help of long molecular dynamics simulations, a possible link between polymorphic forms and tumor progression has been established. First, maspin is dynamically stable with either amino acid at the 176 position. Second, differential contacts have been observed among various regions; third, these contacts have significantly altered the electrostatic energetics of various residues; finally, these altered electrostatics of maspin-S176 and maspin-P176 rewire the polar contacts that abolished the allosteric control of the protein. By combining these factors, the altered electrostatics substantially affect the localization and preference of maspin-binding partners, thus culminating in a different maspin-protein(cofactor)-interaction landscape that may have been manifested in previous conflicting reports. Here, the underlying reason has been highlighted and discussed, which may be helpful for better therapeutic manipulation.
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Affiliation(s)
- Muhammad
Ayaz Anwar
- Department
of Applied Chemistry, Institute of Natural Science, Global Center
for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin 17104, Republic
of Korea
| | - Muhammad Haseeb
- Department
of Molecular Science and Technology, Ajou
University, Suwon 16499, Republic
of Korea
| | - Sangdun Choi
- Department
of Molecular Science and Technology, Ajou
University, Suwon 16499, Republic
of Korea
| | - Kwang Pyo Kim
- Department
of Applied Chemistry, Institute of Natural Science, Global Center
for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin 17104, Republic
of Korea
- Department
of Biomedical Science and Technology, Kyung
Hee Medical Science Research Institute, Kyung Hee University, Seoul 02447, Republic of Korea
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3
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Sgro A, Cursons J, Waryah C, Woodward EA, Foroutan M, Lyu R, Yeoh GCT, Leedman PJ, Blancafort P. Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma. Clin Epigenetics 2023; 15:73. [PMID: 37120619 PMCID: PMC10149030 DOI: 10.1186/s13148-023-01482-0] [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: 11/22/2022] [Accepted: 04/09/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Epigenetic silencing of tumor suppressor genes (TSGs) is a key feature of oncogenesis in hepatocellular carcinoma (HCC). Liver-targeted delivery of CRISPR-activation (CRISPRa) systems makes it possible to exploit chromatin plasticity, by reprogramming transcriptional dysregulation. RESULTS Using The Cancer Genome Atlas HCC data, we identify 12 putative TSGs with negative associations between promoter DNA methylation and transcript abundance, with limited genetic alterations. All HCC samples harbor at least one silenced TSG, suggesting that combining a specific panel of genomic targets could maximize efficacy, and potentially improve outcomes as a personalized treatment strategy for HCC patients. Unlike epigenetic modifying drugs lacking locus selectivity, CRISPRa systems enable potent and precise reactivation of at least 4 TSGs tailored to representative HCC lines. Concerted reactivation of HHIP, MT1M, PZP, and TTC36 in Hep3B cells inhibits multiple facets of HCC pathogenesis, such as cell viability, proliferation, and migration. CONCLUSIONS By combining multiple effector domains, we demonstrate the utility of a CRISPRa toolbox of epigenetic effectors and gRNAs for patient-specific treatment of aggressive HCC.
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Affiliation(s)
- Agustin Sgro
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
- School of Human Sciences, The University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Joseph Cursons
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Charlene Waryah
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Eleanor A Woodward
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Momeneh Foroutan
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Ruqian Lyu
- Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, Fitzroy, Melbourne, VIC, 3065, Australia
- Melbourne Integrative Genomics/School of Mathematics and Statistics, Faculty of Science, The University of Melbourne, Royal Parade, Parkville, VIC, 3010, Australia
| | - George C T Yeoh
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
- School of Molecular Sciences, University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Peter J Leedman
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, Perth, WA, 6009, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia.
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.
- School of Human Sciences, The University of Western Australia, Crawley, Perth, WA, 6009, Australia.
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4
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Sapozhnikov DM, Szyf M. Unraveling the functional role of DNA demethylation at specific promoters by targeted steric blockage of DNA methyltransferase with CRISPR/dCas9. Nat Commun 2021; 12:5711. [PMID: 34588447 PMCID: PMC8481236 DOI: 10.1038/s41467-021-25991-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/07/2021] [Indexed: 01/10/2023] Open
Abstract
Despite four decades of research to support the association between DNA methylation and gene expression, the causality of this relationship remains unresolved. Here, we reaffirm that experimental confounds preclude resolution of this question with existing strategies, including recently developed CRISPR/dCas9 and TET-based epigenetic editors. Instead, we demonstrate a highly effective method using only nuclease-dead Cas9 and guide RNA to physically block DNA methylation at specific targets in the absence of a confounding flexibly-tethered enzyme, thereby enabling the examination of the role of DNA demethylation per se in living cells, with no evidence of off-target activity. Using this method, we probe a small number of inducible promoters and find the effect of DNA demethylation to be small, while demethylation of CpG-rich FMR1 produces larger changes in gene expression. This method could be used to reveal the extent and nature of the contribution of DNA methylation to gene regulation.
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Affiliation(s)
- Daniel M Sapozhnikov
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, Canada.
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5
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Pacheco MB, Camilo V, Henrique R, Jerónimo C. Epigenetic Editing in Prostate Cancer: Challenges and Opportunities. Epigenetics 2021; 17:564-588. [PMID: 34130596 DOI: 10.1080/15592294.2021.1939477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Epigenome editing consists of fusing a predesigned DNA recognition unit to the catalytic domain of a chromatin modifying enzyme leading to the introduction or removal of an epigenetic mark at a specific locus. These platforms enabled the study of the mechanisms and roles of epigenetic changes in several research domains such as those addressing pathogenesis and progression of cancer. Despite the continued efforts required to overcome some limitations, which include specificity, off-target effects, efficacy, and longevity, these tools have been rapidly progressing and improving.Since prostate cancer is characterized by multiple genetic and epigenetic alterations that affect different signalling pathways, epigenetic editing constitutes a promising strategy to hamper cancer progression. Therefore, by modulating chromatin structure through epigenome editing, its conformation might be better understood and events that drive prostate carcinogenesis might be further unveiled.This review describes the different epigenome engineering tools, their mechanisms concerning gene's expression and regulation, highlighting the challenges and opportunities concerning prostate cancer research.
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Affiliation(s)
- Mariana Brütt Pacheco
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal
| | - Vânia Camilo
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. DR. António Bernardino De Almeida, Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, Porto, Portugal
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6
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Alves E, Taifour S, Dolcetti R, Chee J, Nowak AK, Gaudieri S, Blancafort P. Reprogramming the anti-tumor immune response via CRISPR genetic and epigenetic editing. Mol Ther Methods Clin Dev 2021; 21:592-606. [PMID: 34095343 PMCID: PMC8142043 DOI: 10.1016/j.omtm.2021.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Precise clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genetic and epigenetic manipulation of the immune response has become a promising immunotherapeutic approach toward combating tumorigenesis and tumor progression. CRISPR-based immunologic reprograming in cancer therapy comprises the locus-specific enhancement of host immunity, the improvement of tumor immunogenicity, and the suppression of tumor immunoevasion. To date, the ex vivo re-engineering of immune cells directed to inhibit the expression of immune checkpoints or to express synthetic immune receptors (chimeric antigen receptor therapy) has shown success in some settings, such as in the treatment of melanoma, lymphoma, liver, and lung cancer. However, advancements in nuclease-deactivated CRISPR-associated nuclease-9 (dCas9)-mediated transcriptional activation or repression and Cas13-directed gene suppression present novel avenues for the development of tumor immunotherapies. In this review, the basis for development, mechanism of action, and outcomes from recently published Cas9-based clinical trial (genetic editing) and dCas9/Cas13-based pre-clinical (epigenetic editing) data are discussed. Lastly, we review cancer immunotherapy-specific considerations and barriers surrounding use of these approaches in the clinic.
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Affiliation(s)
- Eric Alves
- School of Human Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Shahama Taifour
- School of Human Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Riccardo Dolcetti
- Diamantina Institute, The University of Queensland, Brisbane, QLD 4102, Australia
- Sir Peter MacCallum Centre for Cancer Immunotherapy, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Jonathan Chee
- National Centre for Asbestos Related Diseases, Institute of Respiratory Health, The University of Western Australia, Perth, WA 6009, Australia
- School of Biomedical Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Anna K. Nowak
- National Centre for Asbestos Related Diseases, Institute of Respiratory Health, The University of Western Australia, Perth, WA 6009, Australia
- School of Medicine, The University of Western Australia, Perth, WA 6009, Australia
| | - Silvana Gaudieri
- School of Human Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Pilar Blancafort
- School of Human Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
- The Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
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7
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Sgro A, Blancafort P. Epigenome engineering: new technologies for precision medicine. Nucleic Acids Res 2021; 48:12453-12482. [PMID: 33196851 PMCID: PMC7736826 DOI: 10.1093/nar/gkaa1000] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/10/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Chromatin adopts different configurations that are regulated by reversible covalent modifications, referred to as epigenetic marks. Epigenetic inhibitors have been approved for clinical use to restore epigenetic aberrations that result in silencing of tumor-suppressor genes, oncogene addictions, and enhancement of immune responses. However, these drugs suffer from major limitations, such as a lack of locus selectivity and potential toxicities. Technological advances have opened a new era of precision molecular medicine to reprogram cellular physiology. The locus-specificity of CRISPR/dCas9/12a to manipulate the epigenome is rapidly becoming a highly promising strategy for personalized medicine. This review focuses on new state-of-the-art epigenome editing approaches to modify the epigenome of neoplasms and other disease models towards a more 'normal-like state', having characteristics of normal tissue counterparts. We highlight biomolecular engineering methodologies to assemble, regulate, and deliver multiple epigenetic effectors that maximize the longevity of the therapeutic effect, and we discuss limitations of the platforms such as targeting efficiency and intracellular delivery for future clinical applications.
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Affiliation(s)
- Agustin Sgro
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, Perth, Western Australia 6009, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, Perth, Western Australia 6009, Australia.,The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
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8
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Functional Comparison between VP64-dCas9-VP64 and dCas9-VP192 CRISPR Activators in Human Embryonic Kidney Cells. Int J Mol Sci 2021; 22:ijms22010397. [PMID: 33401508 PMCID: PMC7795359 DOI: 10.3390/ijms22010397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Reversal in the transcriptional status of desired genes has been exploited for multiple research, therapeutic, and biotechnological purposes. CRISPR/dCas9-based activators can activate transcriptionally silenced genes after being guided by gene-specific gRNA(s). Here, we performed a functional comparison between two such activators, VP64-dCas9-VP64 and dCas9-VP192, in human embryonic kidney cells by the concomitant targeting of POU5F1 and SOX2. We found 22- and 6-fold upregulations in the mRNA level of POU5F1 by dCas9-VP192 and VP64-dCas9-VP64, respectively. Likewise, SOX2 was up-regulated 4- and 2-fold using dCas9-VP192 and VP64dCas9VP64, respectively. For the POU5F1 protein level, we observed 3.7- and 2.2-fold increases with dCas9-VP192 and VP64-dCas9-VP64, respectively. Similarly, the SOX2 expression was 2.4- and 2-fold higher with dCas9-VP192 and VP64-dCas9-VP64, respectively. We also confirmed that activation only happened upon co-transfecting an activator plasmid with multiplex gRNA plasmid with a high specificity to the reference genes. Our data revealed that dCas9-VP192 is more efficient than VP64-dCas9-VP64 for activating reference genes.
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9
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Dai X, Blancafort P, Wang P, Sgro A, Thompson EW, Ostrikov K(K. Innovative Precision Gene-Editing Tools in Personalized Cancer Medicine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1902552. [PMID: 32596104 PMCID: PMC7312441 DOI: 10.1002/advs.201902552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/08/2020] [Indexed: 05/07/2023]
Abstract
The development of clustered regularly interspaced short palindromic repeats (CRISPR) has spurred a successive wave of genome-engineering following zinc finger nucleases and transcription activator-like effector nucleases, and made gene-editing a promising strategy in the prevention and treatment of genetic diseases. However, gene-editing is not widely adopted in clinics due to some technical issues that challenge its safety and efficacy, and the lack of appropriate clinical regulations allowing them to advance toward improved human health without impinging on human ethics. By systematically examining the oncological applications of gene-editing tools and critical factors challenging their medical translation, genome-editing has substantial contributions to cancer driver gene discovery, tumor cell epigenome normalization, targeted delivery, cancer animal model establishment, and cancer immunotherapy and prevention in clinics. Gene-editing tools, epitomized by CRISPR, are predicted to represent a promising strategy toward the precise control of cancer initiation and development. However, some technical problems and ethical concerns are serious issues that need to be appropriately addressed before CRISPR can be incorporated into the next generation of molecular precision medicine. In this light, new technical developments to limit off-target effects are discussed herein, and the use of gene-editing approaches for treating otherwise incurable cancers is brought into focus.
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Affiliation(s)
- Xiaofeng Dai
- Wuxi School of MedicineJiangnan UniversityWuxi214122China
| | - Pilar Blancafort
- The Harry Perkins Institute of Medical ResearchNedlandsWestern Australia6009Australia
- School of Human SciencesThe University of Western AustraliaNedlandsWestern Australia6009Australia
- The Greehey Children's Cancer Research InstituteThe University of Texas Health Science Center at San AntonioSan AntonioTX78229USA
| | - Peiyu Wang
- Institute of Health and Biomedical InnovationQueensland University of TechnologyBrisbaneQueensland4059Australia
- School of Biomedical SciencesQueensland University of TechnologyBrisbaneQueensland4059Australia
- Translational Research InstituteWoolloongabbaQueensland4102Australia
| | - Agustin Sgro
- The Harry Perkins Institute of Medical ResearchNedlandsWestern Australia6009Australia
- School of Human SciencesThe University of Western AustraliaNedlandsWestern Australia6009Australia
| | - Erik W. Thompson
- Institute of Health and Biomedical InnovationQueensland University of TechnologyBrisbaneQueensland4059Australia
- School of Biomedical SciencesQueensland University of TechnologyBrisbaneQueensland4059Australia
- Translational Research InstituteWoolloongabbaQueensland4102Australia
| | - Kostya (Ken) Ostrikov
- Translational Research InstituteWoolloongabbaQueensland4102Australia
- School of Chemistry and PhysicsQueensland University of TechnologyBrisbaneQueensland4000Australia
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10
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Olney KC, Nyer DB, Vargas DA, Wilson Sayres MA, Haynes KA. The synthetic histone-binding regulator protein PcTF activates interferon genes in breast cancer cells. BMC SYSTEMS BIOLOGY 2018; 12:83. [PMID: 30253781 PMCID: PMC6156859 DOI: 10.1186/s12918-018-0608-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/12/2018] [Indexed: 02/06/2023]
Abstract
Background Mounting evidence from genome-wide studies of cancer shows that chromatin-mediated epigenetic silencing at large cohorts of genes is strongly linked to a poor prognosis. This mechanism is thought to prevent cell differentiation and enable evasion of the immune system. Drugging the cancer epigenome with small molecule inhibitors to release silenced genes from the repressed state has emerged as a powerful approach for cancer research and drug development. Targets of these inhibitors include chromatin-modifying enzymes that can acquire drug-resistant mutations. In order to directly target a generally conserved feature, elevated trimethyl-lysine 27 on histone H3 (H3K27me3), we developed the Polycomb-based Transcription Factor (PcTF), a fusion activator that targets methyl-histone marks via its N-terminal H3K27me3-binding motif, and co-regulates sets of silenced genes. Results Here, we report transcriptome profiling analyses of PcTF-treated breast cancer model cell lines. We identified a set of 19 PcTF-upregulated genes, or PUGs, that were consistent across three distinct breast cancer cell lines. These genes are associated with the interferon response pathway. Conclusions Our results demonstrate for the first time a chromatin-mediated interferon-related transcriptional response driven by an engineered fusion protein that physically links repressive histone marks with active transcription. Electronic supplementary material The online version of this article (10.1186/s12918-018-0608-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kimberly C Olney
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, 85287-4501, AZ, USA
| | - David B Nyer
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Tempe, AZ, 85287-9709, USA
| | - Daniel A Vargas
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Tempe, AZ, 85287-9709, USA
| | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, 85287-4501, AZ, USA.,Center for Evolution and Medicine, Arizona State University, 427 E Tyler Mall, Tempe, 85287-1701, AZ, USA
| | - Karmella A Haynes
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Tempe, AZ, 85287-9709, USA.
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11
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Moses C, Garcia-Bloj B, Harvey AR, Blancafort P. Hallmarks of cancer: The CRISPR generation. Eur J Cancer 2018; 93:10-18. [PMID: 29433054 DOI: 10.1016/j.ejca.2018.01.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/03/2018] [Indexed: 02/08/2023]
Abstract
The hallmarks of cancer were proposed as a logical framework to guide research efforts that aim to understand the molecular mechanisms and derive treatments for this highly complex disease. Recent technological advances, including comprehensive sequencing of different cancer subtypes, have illuminated how genetic and epigenetic alterations are associated with specific hallmarks of cancer. However, as these associations are purely descriptive, one particularly exciting development is the emergence of genome editing technologies, which enable rapid generation of precise genetic and epigenetic modifications to assess the consequences of these perturbations on the cancer phenotype. The most recently developed of these tools, the system of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), consists of an RNA-guided endonuclease that can be repurposed to edit both genome and epigenome with high specificity, and facilitates the functional interrogation of multiple loci in parallel. This system has the potential to dramatically accelerate progress in cancer research, whether by modelling the genesis and progression of cancer in vitro and in vivo, screening for novel therapeutic targets, conducting functional genomics/epigenomics, or generating targeted cancer therapies. Here, we discuss CRISPR research on each of the ten hallmarks of cancer, outline potential barriers for its clinical implementation and speculate on the advances it may allow in cancer research in the near future.
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Affiliation(s)
- Colette Moses
- Cancer Epigenetics Laboratory, Harry Perkins Institute of Medical Research, Perth, Australia; School of Human Sciences, The University of Western Australia, Perth, Australia
| | - Benjamin Garcia-Bloj
- Cancer Epigenetics Laboratory, Harry Perkins Institute of Medical Research, Perth, Australia; School of Medicine, P. Universidad Catolica de Chile, Santiago, Chile
| | - Alan R Harvey
- School of Human Sciences, The University of Western Australia, Perth, Australia; Perron Institute for Neurological and Translational Science, Perth, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Laboratory, Harry Perkins Institute of Medical Research, Perth, Australia; School of Human Sciences, The University of Western Australia, Perth, Australia.
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Waking up dormant tumor suppressor genes with zinc fingers, TALEs and the CRISPR/dCas9 system. Oncotarget 2018; 7:60535-60554. [PMID: 27528034 PMCID: PMC5312401 DOI: 10.18632/oncotarget.11142] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/19/2016] [Indexed: 12/24/2022] Open
Abstract
The aberrant epigenetic silencing of tumor suppressor genes (TSGs) plays a major role during carcinogenesis and regaining these dormant functions by engineering of sequence-specific epigenome editing tools offers a unique opportunity for targeted therapies. However, effectively normalizing the expression and regaining tumor suppressive functions of silenced TSGs by artificial transcription factors (ATFs) still remains a major challenge. Herein we describe novel combinatorial strategies for the potent reactivation of two class II TSGs, MASPIN and REPRIMO, in cell lines with varying epigenetic states, using the CRISPR/dCas9 associated system linked to a panel of effector domains (VP64, p300, VPR and SAM complex), as well as with protein-based ATFs, Zinc Fingers and TALEs. We found that co-delivery of multiple effector domains using a combination of CRISPR/dCas9 and TALEs or SAM complex maximized activation in highly methylated promoters. In particular, CRISPR/dCas9 VPR with SAM upregulated MASPIN mRNA (22,145-fold change) in H157 lung cancer cells, with accompanying re-expression of MASPIN protein, which led to a concomitant inhibition of cell proliferation and induction of apoptotic cell death. Consistently, CRISPR/dCas9 VP64 with SAM upregulated REPRIMO (680-fold change), which led to phenotypic reprogramming in AGS gastric cancer cells. Altogether, our results outlined novel sequence-specific, combinatorial epigenome editing approaches to reactivate highly methylated TSGs as a promising therapy for cancer and other diseases.
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Waryah CB, Moses C, Arooj M, Blancafort P. Zinc Fingers, TALEs, and CRISPR Systems: A Comparison of Tools for Epigenome Editing. Methods Mol Biol 2018. [PMID: 29524128 DOI: 10.1007/978-1-4939-7774-1_2] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The completion of genome, epigenome, and transcriptome mapping in multiple cell types has created a demand for precision biomolecular tools that allow researchers to functionally manipulate DNA, reconfigure chromatin structure, and ultimately reshape gene expression patterns. Epigenetic editing tools provide the ability to interrogate the relationship between epigenetic modifications and gene expression. Importantly, this information can be exploited to reprogram cell fate for both basic research and therapeutic applications. Three different molecular platforms for epigenetic editing have been developed: zinc finger proteins (ZFs), transcription activator-like effectors (TALEs), and the system of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins. These platforms serve as custom DNA-binding domains (DBDs), which are fused to epigenetic modifying domains to manipulate epigenetic marks at specific sites in the genome. The addition and/or removal of epigenetic modifications reconfigures local chromatin structure, with the potential to provoke long-lasting changes in gene transcription. Here we summarize the molecular structure and mechanism of action of ZF, TALE, and CRISPR platforms and describe their applications for the locus-specific manipulation of the epigenome. The advantages and disadvantages of each platform will be discussed with regard to genomic specificity, potency in regulating gene expression, and reprogramming cell phenotypes, as well as ease of design, construction, and delivery. Finally, we outline potential applications for these tools in molecular biology and biomedicine and identify possible barriers to their future clinical implementation.
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Affiliation(s)
- Charlene Babra Waryah
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
| | - Colette Moses
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Mahira Arooj
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia.
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia.
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Chakravarthi BVSK, Nepal S, Varambally S. Genomic and Epigenomic Alterations in Cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 186:1724-35. [PMID: 27338107 DOI: 10.1016/j.ajpath.2016.02.023] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 01/27/2016] [Accepted: 02/23/2016] [Indexed: 12/20/2022]
Abstract
Multiple genetic and epigenetic events characterize tumor progression and define the identity of the tumors. Advances in high-throughput technologies, like gene expression profiling, next-generation sequencing, proteomics, and metabolomics, have enabled detailed molecular characterization of various tumors. The integration and analyses of these high-throughput data have unraveled many novel molecular aberrations and network alterations in tumors. These molecular alterations include multiple cancer-driving mutations, gene fusions, amplification, deletion, and post-translational modifications, among others. Many of these genomic events are being used in cancer diagnosis, whereas others are therapeutically targeted with small-molecule inhibitors. Multiple genes/enzymes that play a role in DNA and histone modifications are also altered in various cancers, changing the epigenomic landscape during cancer initiation and progression. Apart from protein-coding genes, studies are uncovering the critical regulatory roles played by noncoding RNAs and noncoding regions of the genome during cancer progression. Many of these genomic and epigenetic events function in tandem to drive tumor development and metastasis. Concurrent advances in genome-modulating technologies, like gene silencing and genome editing, are providing ability to understand in detail the process of cancer initiation, progression, and signaling as well as opening up avenues for therapeutic targeting. In this review, we discuss some of the recent advances in cancer genomic and epigenomic research.
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Affiliation(s)
| | - Saroj Nepal
- Department of Pathology and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Sooryanarayana Varambally
- Department of Pathology and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama.
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Wongnoppavich A, Dukaew N, Choonate S, Chairatvit K. Upregulation of maspin expression in human cervical carcinoma cells by transforming growth factor β1 through the convergence of Smad and non-Smad signaling pathways. Oncol Lett 2017; 13:3646-3652. [PMID: 28521467 PMCID: PMC5431325 DOI: 10.3892/ol.2017.5939] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 01/31/2017] [Indexed: 01/08/2023] Open
Abstract
Mammary serine protease inhibitor (maspin), encoded by the serpin family B member 5 gene, serves as a tumor suppressor through the inhibition of cancer cell invasion and metastasis. Paradoxically, maspin levels are upregulated in a number of types of malignant cells. Therefore, the regulation of maspin expression may depend on the genetic or epigenetic background and the specific microenvironment of carcinoma cells. In the present study, it was demonstrated that transforming growth factor β1 (TGF-β1) induced maspin expression at the transcript and protein levels in the human cervical carcinoma HeLa and human oral squamous carcinoma HSC4 cell lines. The inhibition of the mothers against decapentaplegic homolog (Smad)-dependent pathway by a Smad3-specific inhibitor suppressed maspin induction by TGF-β1 in HeLa cells. Inhibition of the non-Smad pathway by pretreatment with the mitogen-activated protein kinase kinase 1/2 (MEK1/2) inhibitor U0126, or the p38 mitogen-activated protein kinase (p38 MAPK) inhibitor SB202190, attenuated the effect of TGF-β1 on maspin upregulation, whereas pretreatment with pyrrolidine dithiocarbamate (a nuclear factor κB inhibitor), wortmannin (a phosphoinositide 3-kinase inhibitor) or SP600125 (a c-Jun N-terminal kinase inhibitor) did not. Notably, none of these inhibitors eliminated the TGF-β1-induced phosphorylation of Smad2. In addition, mutations at p53-binding sites in the maspin promoter suppressed TGF-β1-induced maspin expression, indicating the necessity of intact p53-binding sites on the maspin promoter. In summary, the induction of maspin expression in HeLa cells requires the convergence of TGF-β1-induced Smad and non-Smad signaling pathways, in which the latter acts via the intermediate signaling molecules MEK1/2 and p38 MAPK.
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Affiliation(s)
- Ariyaphong Wongnoppavich
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nahathai Dukaew
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sirinthip Choonate
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok 10400, Thailand
| | - Kongthawat Chairatvit
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok 10400, Thailand
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Goubert D, Beckman WF, Verschure PJ, Rots MG. Epigenetic editing: towards realization of the curable genome concept. CONVERGENT SCIENCE PHYSICAL ONCOLOGY 2017. [DOI: 10.1088/2057-1739/aa5cc0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Kikutake C, Yahara K. Identification of Epigenetic Biomarkers of Lung Adenocarcinoma through Multi-Omics Data Analysis. PLoS One 2016; 11:e0152918. [PMID: 27042856 PMCID: PMC4820141 DOI: 10.1371/journal.pone.0152918] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/21/2016] [Indexed: 12/28/2022] Open
Abstract
Epigenetic mechanisms such as DNA methylation or histone modifications are essential for the regulation of gene expression and development of tissues. Alteration of epigenetic modifications can be used as an epigenetic biomarker for diagnosis and as promising targets for epigenetic therapy. A recent study explored cancer-cell specific epigenetic biomarkers by examining different types of epigenetic modifications simultaneously. However, it was based on microarrays and reported biomarkers that were also present in normal cells at a low frequency. Here, we first analyzed multi-omics data (including ChIP-Seq data of six types of histone modifications: H3K27ac, H3K4me1, H3K9me3, H3K36me3, H3K27me3, and H3K4me3) obtained from 26 lung adenocarcinoma cell lines and a normal cell line. We identified six genes with both H3K27ac and H3K4me3 histone modifications in their promoter regions, which were not present in the normal cell line, but present in ≥85% (22 out of 26) and ≤96% (25 out of 26) of the lung adenocarcinoma cell lines. Of these genes, NUP210 (encoding a main component of the nuclear pore complex) was the only gene in which the two modifications were not detected in another normal cell line. RNA-Seq analysis revealed that NUP210 was aberrantly overexpressed among the 26 lung adenocarcinoma cell lines, although the frequency of NUP210 overexpression was lower (19.3%) in 57 lung adenocarcinoma tissue samples studied and stored in another database. This study provides a basis to discover epigenetic biomarkers highly specific to a certain cancer, based on multi-omics data at the cell population level.
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Affiliation(s)
- Chie Kikutake
- Division of Biostatistics, Kurume University School of Medicine, Fukuoka, Japan
| | - Koji Yahara
- Biostatistics Center, Kurume University, Kurume, Fukuoka, Japan
- Institute of Life Science, College of Medicine, Swansea University, Swansea, United Kingdom
- * E-mail:
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Chen J, Wang L, Tang Y, Gong G, Liu L, Chen M, Chen Z, Cui Y, Li C, Cheng X, Qi L, Zu X. Maspin enhances cisplatin chemosensitivity in bladder cancer T24 and 5637 cells and correlates with prognosis of muscle-invasive bladder cancer patients receiving cisplatin based neoadjuvant chemotherapy. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2016; 35:2. [PMID: 26733306 PMCID: PMC4702361 DOI: 10.1186/s13046-015-0282-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 12/30/2015] [Indexed: 12/12/2022]
Abstract
Background Maspin, a non-inhibitory member of the serine protease inhibitor superfamily, has been characterized as a tumor suppressor gene in multiple cancer types. Chemotherapeutic insensitivity is one of major obstacles to effectively treating muscle invasive bladder cancer (MIBC). This study was conducted to investigate the role and probable mechanism of Maspin enhancing cisplatin chemosensitivity of bladder cancer in vitro and MIBC patients. Methods Maspin expression was quantified by qRT-PCR in two MIBC cell lines (T24 and 5637). After successful established Maspin overexpression model by lipidosome transfection, MTT and cell apoptosis assay were used to assess the MIBC’s cisplatin sensitivity. Western blot method was used to test PI3K/ AKT/mTOR signal passway and apoptosis related molecules Caspase3 and Bcl-2. Additionally, we evaluated Maspin expression and prognosis in 62 MIBC cases who underwent cisplatin based neoadjuvant chemotherapy (NACT) using immunohistochemistry. Result Upregulate Maspin expression could enhance the chemosensitivity induced by cisplatin in T24 and 5637 cell lines. The cell viability, cloning ability and IC50 were reduced while apoptosis rate was upregulated when cells were transfected Maspin. Phospho(p)-AKT, PI3K, mTOR, and Bcl-2 expression were significantly decreased, whereas Caspase3 was greatly increased in the Maspin group. In the clinic study, there was significant correlation between Maspin expression and overall survival (OS) and progression-free survival (PFS) rate in MIBC patients who received cisplatin based NACT. Conclusion Maspin could enhance cisplatin chemosensitivity in T24 and 5637 cell lines. Its expression correlated with prognosis of MIBC patients who received cisplatin based neoadjuvant chemotherapy.
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Affiliation(s)
- Jinbo Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Long Wang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Yunhua Tang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Guanghui Gong
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Longfei Liu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Minfeng Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Zhi Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Yu Cui
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Chao Li
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Xu Cheng
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Lin Qi
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Xiongbing Zu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
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Rewriting DNA Methylation Signatures at Will: The Curable Genome Within Reach? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:475-490. [DOI: 10.1007/978-3-319-43624-1_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Marioni G, Martini A, Favaretto N, Franchella S, Cappellesso R, Marino F, Blandamura S, Mazzoni A, Zanoletti E. Temporal bone carcinoma: a first glance beyond the conventional clinical and pathological prognostic factors. Eur Arch Otorhinolaryngol 2015; 273:2903-10. [PMID: 26518208 DOI: 10.1007/s00405-015-3811-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 10/20/2015] [Indexed: 11/29/2022]
Abstract
Temporal bone squamous cell carcinoma (TBSCC) is an uncommon, aggressive malignancy with a poor prognosis in advanced cases. The dismal outcome is partially related to: the lack of reliable clinical or pathological prognostic factors and the largely unstandardized surgical and integrated treatments adopted. There is an undeniable need for novel diagnostic/therapeutic strategies to improve the prognosis. The purpose of this critical review was to explore the level of available knowledge concerning the molecular markers involved in the biology of TBSCC that have a prognostic potential. The Pub-Med and Scopus electronic databases were searched without publication date limits for studies investigating molecular markers in cohorts of patients with primary TBSCC. The search terms used were: "temporal bone cancer", "temporal bone carcinoma", "temporal bone malignancy", "ear cancer", "ear carcinoma", and "ear malignancy". We decided preliminarily not to consider series with less than five cases. Nine retrospective case series of TBSCC were found in which different analytical techniques had been used to study the role of several biomarkers (HPV, vimentin, transforming growth factor β, CD105, RECK, matrix metalloproteinase-9, MASPIN, EBV, p16, TP53 mutation, pSTAT3, relaxin-2). CD105 expression (in tumor vessel endothelial cells) and MASPIN cytoplasmic expression (in carcinoma cells) were, respectively, found directly and inversely related with the neoplasm's recurrence rate. CD105 expression was also inversely related with disease-free survival in TBSCC. A future goal of such analyses should be to ascertain the radio- and chemo-sensitivity profiles of individual TBSCCs, enabling truly personalized therapies. A further, more ambitious goal will be to find targets for therapeutic agents that might prove crucial in improving the disease-specific survival for patients with advanced TBSCC.
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Affiliation(s)
- Gino Marioni
- Otolaryngology Section, Department of Neurosciences DNS, Padova University, Via Giustiniani 2, 35128, Padova, Italy.
| | - Alessandro Martini
- Otolaryngology Section, Department of Neurosciences DNS, Padova University, Via Giustiniani 2, 35128, Padova, Italy
| | - Niccolò Favaretto
- Otolaryngology Section, Department of Neurosciences DNS, Padova University, Via Giustiniani 2, 35128, Padova, Italy
| | - Sebastiano Franchella
- Otolaryngology Section, Department of Neurosciences DNS, Padova University, Via Giustiniani 2, 35128, Padova, Italy
| | | | - Filippo Marino
- Department of Medicine DIMED, Padova University, Padova, Italy
| | | | - Antonio Mazzoni
- Otolaryngology Section, Department of Neurosciences DNS, Padova University, Via Giustiniani 2, 35128, Padova, Italy
| | - Elisabetta Zanoletti
- Otolaryngology Section, Department of Neurosciences DNS, Padova University, Via Giustiniani 2, 35128, Padova, Italy
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A Higher Angiogenin Expression is Associated With a Nonnuclear Maspin Location in Laryngeal Carcinoma. Clin Exp Otorhinolaryngol 2015; 8:268-74. [PMID: 26330923 PMCID: PMC4553359 DOI: 10.3342/ceo.2015.8.3.268] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/14/2014] [Accepted: 03/23/2014] [Indexed: 12/13/2022] Open
Abstract
Objectives In numerous malignancies, angiogenin (ANG) and Maspin are important proangiogenic and antiangiogenic regulators, respectively. The aim of this study was to identify potential relationships between the biological roles of these two proteins in laryngeal squamous cell carcinoma (LSCC). Methods Immunohistochemical staining for ANG and Maspin was performed on specimens from 76 consecutive LSCC patients treated with surgery alone, considering the subcellular pattern of Maspin expression. Univariate and multivariate statistical models were used for prognostic purposes. Results On univariate analysis, a different level of ANG expression was seen for patients stratified by subcellular Maspin expression pattern: the mean ANG expression was higher in cases with a nonnuclear MASPIN expression than in those with a nuclear pattern (P=0.002). Disease-free survival (DFS; in months) differed significantly when patients were stratified by N stage (P=0.01). Patients whose Maspin expression was nonnuclear (i.e., it was cytoplasmic or there was none) had a significantly higher recurrence rate (P<0.001), and shorter DFS (P=0.01) than those with a nuclear Maspin pattern. The mean ANG expression was significantly higher in cases with loco-regional recurrent disease (P=0.007); and patients with an ANG expression ≥5.0% had a significantly shorter DFS than those with an ANG expression <5.0% (P=0.007). On multivariate analysis, ANG expression ≥5.0% was a significant, independent, negative prognostic factor in terms of DFS (P=0.041). Conclusion Our results support the hypothesis that a higher ANG expression is associated with a nonnuclear Maspin expression pattern in patients with LSCC. Further studies are needed to clarify the relationship between the ANG and Maspin pathways, and their potential diagnostic and therapeutic role in LSCC.
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Falahi F, Sgro A, Blancafort P. Epigenome engineering in cancer: fairytale or a realistic path to the clinic? Front Oncol 2015; 5:22. [PMID: 25705610 PMCID: PMC4319383 DOI: 10.3389/fonc.2015.00022] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/19/2015] [Indexed: 01/15/2023] Open
Abstract
Epigenetic modifications such as histone post-transcriptional modifications, DNA methylation, and non-protein-coding RNAs organize the DNA in the nucleus of eukaryotic cells and are critical for the spatio-temporal regulation of gene expression. These epigenetic modifications are reversible and precisely regulated by epigenetic enzymes. In addition to genetic mutations, epigenetic modifications are highly disrupted in cancer relative to normal tissues. Many epigenetic alterations (epi-mutations) are associated with aberrations in the expression and/or activity of epigenetic enzymes. Thus, epigenetic regulators have emerged as prime targets for cancer therapy. Currently, several inhibitors of epigenetic enzymes (epi-drugs) have been approved for use in the clinic to treat cancer patients with hematological malignancies. However, one potential disadvantage of epi-drugs is their lack of locus-selective specificity, which may result in the over-expression of undesirable parts of the genome. The emerging and rapidly growing field of epigenome engineering has opened new grounds for improving epigenetic therapy in view of reducing the genome-wide “off-target” effects of the treatment. In the current review, we will first describe the language of epigenetic modifications and their involvement in cancer. Next, we will overview the current strategies for engineering of artificial DNA-binding domains in order to manipulate and ultimately normalize the aberrant landscape of the cancer epigenome (epigenome engineering). Lastly, the potential clinical applications of these emerging genome-engineering approaches will be discussed.
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Affiliation(s)
- Fahimeh Falahi
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, School of Anatomy, Physiology and Human Biology, The University of Western Australia , Perth, WA , Australia
| | - Agustin Sgro
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, School of Anatomy, Physiology and Human Biology, The University of Western Australia , Perth, WA , Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, School of Anatomy, Physiology and Human Biology, The University of Western Australia , Perth, WA , Australia
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Wang X, Wang Y, Li S, Dong B, Zheng Q, Yan S, Ma Y, Zhang J, Fang J, Wu N, Wu H, Yang Y. Decreased maspin combined with elevated vascular endothelial growth factor C is associated with poor prognosis in non-small cell lung cancer. Thorac Cancer 2014; 5:383-90. [PMID: 26767029 DOI: 10.1111/1759-7714.12104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 02/24/2014] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND This study aimed to investigate the clinical significance of the combination of maspin and vascular endothelial growth factor (VEGF)-C expression in the prognosis of non-small cell lung cancer (NSCLC). METHODS Immunohistochemistry was performed to assay the expression of maspin and VEGF-C in primary tumor tissues, metastatic, and non-metastatic lymph nodes in 98 NSCLC patients. Survival analysis was determined by Kaplan-Meier curves. RESULTS The positive expression rate of maspin was 26.5% (26/98) in NSCLC primary tumor tissues, significantly associated with histological type (P = 0.005) and the absence of nodal metastasis (P < 0.001). The expression of maspin in primary tumor tissues was stronger than metastatic lymph nodes of the N1 group (P = 0.048), while the metastatic lymph nodes of the N1 group had a stronger maspin expression than the N2 group (P = 0.008). In survival analysis, a positive expression of maspin of the N1 lymph node was also found to be an independent positive prognostic factor in overall survival (P = 0.003). We also found that decreased maspin combined with elevated VEGF-C is associated with a poor prognosis for disease-free survival (P = 0.019). CONCLUSION Our results suggest that positive expression of maspin might significantly inhibit nodal metastasis in NSCLC. Decreased maspin combined with elevated VEGF-C might be associated with a poor prognosis in NSCLC.
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Affiliation(s)
- Xing Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery, Peking University Cancer Hospital & Institute Beijing, China
| | - Yang Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Respiratory Medicine, Peking University Cancer Hospital & Institute Beijing, China
| | - Shaolei Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery, Peking University Cancer Hospital & Institute Beijing, China
| | - Bin Dong
- Department of Pathology, Peking University Cancer Hospital & Institute Beijing, China
| | - Qingfeng Zheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery, Peking University Cancer Hospital & Institute Beijing, China
| | - Shi Yan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery, Peking University Cancer Hospital & Institute Beijing, China
| | - Yuanyuan Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery, Peking University Cancer Hospital & Institute Beijing, China
| | - Jianzhi Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery, Peking University Cancer Hospital & Institute Beijing, China
| | - Jian Fang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Respiratory Medicine, Peking University Cancer Hospital & Institute Beijing, China
| | - Nan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery, Peking University Cancer Hospital & Institute Beijing, China
| | - Huijuan Wu
- Beijing Center for Physical and Chemical Analysis Beijing, China
| | - Yue Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery, Peking University Cancer Hospital & Institute Beijing, China
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Grimmer MR, Stolzenburg S, Ford E, Lister R, Blancafort P, Farnham PJ. Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation. Nucleic Acids Res 2014; 42:10856-68. [PMID: 25122745 PMCID: PMC4176344 DOI: 10.1093/nar/gku708] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Artificial transcription factors (ATFs) and genomic nucleases based on a DNA binding platform consisting of multiple zinc finger domains are currently being developed for clinical applications. However, no genome-wide investigations into their binding specificity have been performed. We have created six-finger ATFs to target two different 18 nt regions of the human SOX2 promoter; each ATF is constructed such that it contains or lacks a super KRAB domain (SKD) that interacts with a complex containing repressive histone methyltransferases. ChIP-seq analysis of the effector-free ATFs in MCF7 breast cancer cells identified thousands of binding sites, mostly in promoter regions; the addition of an SKD domain increased the number of binding sites ∼5-fold, with a majority of the new sites located outside of promoters. De novo motif analyses suggest that the lack of binding specificity is due to subsets of the finger domains being used for genomic interactions. Although the ATFs display widespread binding, few genes showed expression differences; genes repressed by the ATF-SKD have stronger binding sites and are more enriched for a 12 nt motif. Interestingly, epigenetic analyses indicate that the transcriptional repression caused by the ATF-SKD is not due to changes in active histone modifications.
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Affiliation(s)
- Matthew R Grimmer
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA Integrated Genetics and Genomics, University of California-Davis, Davis, CA 95616, USA
| | - Sabine Stolzenburg
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA School of Anatomy, Physiology and Human Biology, M309, The University of Western Australia, Crawley, WA 6009, Australia
| | - Ethan Ford
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia
| | - Pilar Blancafort
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA School of Anatomy, Physiology and Human Biology, M309, The University of Western Australia, Crawley, WA 6009, Australia Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, Nedlands, WA 6008, Australia
| | - Peggy J Farnham
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
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Kabadi AM, Gersbach CA. Engineering synthetic TALE and CRISPR/Cas9 transcription factors for regulating gene expression. Methods 2014; 69:188-97. [PMID: 25010559 DOI: 10.1016/j.ymeth.2014.06.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 06/26/2014] [Accepted: 06/27/2014] [Indexed: 12/22/2022] Open
Abstract
Engineered DNA-binding proteins that can be targeted to specific sites in the genome to manipulate gene expression have enabled many advances in biomedical research. This includes generating tools to study fundamental aspects of gene regulation and the development of a new class of gene therapies that alter the expression of endogenous genes. Designed transcription factors have entered clinical trials for the treatment of human diseases and others are in preclinical development. High-throughput and user-friendly platforms for designing synthetic DNA-binding proteins present innovative methods for deciphering cell biology and designing custom synthetic gene circuits. We review two platforms for designing synthetic transcription factors for manipulating gene expression: Transcription activator-like effectors (TALEs) and the RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system. We present an overview of each technology and a guide for designing and assembling custom TALE- and CRISPR/Cas9-based transcription factors. We also discuss characteristics of each platform that are best suited for different applications.
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Affiliation(s)
- Ami M Kabadi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, United States
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, United States; Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, United States; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC 27710, United States.
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Gersbach CA, Perez-Pinera P. Activating human genes with zinc finger proteins, transcription activator-like effectors and CRISPR/Cas9 for gene therapy and regenerative medicine. Expert Opin Ther Targets 2014; 18:835-9. [PMID: 24917359 DOI: 10.1517/14728222.2014.913572] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
New technologies have recently been developed to control the expression of human genes in their native genomic context by engineering synthetic transcription factors that can be targeted to any DNA sequence. The ability to precisely regulate any gene as it occurs naturally in the genome provides a means to address a variety of diseases and disorders. This approach also circumvents some of the traditional challenges of gene therapy. In this editorial, we review the technologies that have enabled targeted human gene activation, including the engineering of transcription factors based on zinc finger proteins, transcription activator-like effectors and the CRISPR/Cas9 system. Additionally, we highlight examples in which these methods have been developed for therapeutic applications and discuss challenges and opportunities.
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Affiliation(s)
- Charles A Gersbach
- Duke University, Department of Biomedical Engineering , Room 136 Hudson Hall, Box 90281, Durham, NC 27708-0281 , USA +1 919 613 2147 ; +1 919 668 0795 ;
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Liao XH, Li YQ, Wang N, Zheng L, Xing WJ, Zhao DW, Yan TB, Wang Y, Liu LY, Sun XG, Hu P, Zhou H, Zhang TC. Re-expression and epigenetic modification of maspin induced apoptosis in MCF-7 cells mediated by myocardin. Cell Signal 2014; 26:1335-46. [PMID: 24607789 DOI: 10.1016/j.cellsig.2014.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 03/02/2014] [Indexed: 02/06/2023]
Abstract
Breast cancer is the leading cause of cancer death in women worldwide. It is well known that oncogene activation and anti-oncogene inactivation affect the development and progression of breast cancer, but the role of oncogene activation and anti-oncogene inactivation in breast cancer is still not fully understood. We now report that maspin acts as a tumor suppressor gene to induce MCF-7 cell apoptosis. In addition, maspin promoter hypermethylation and histone hypoacetylation lead to silencing of maspin gene expression in MCF-7 cells. Moreover, DNA methyltransferase (DNMT) inhibitor 5-aza-2'-deoxycytidine (5-aza-dc) and/or the histone deacetylase (HDAC) inhibitor Trichostatin A (TSA) strongly up-regulated the expression of maspin in MCF-7 cells. Notably, myocardin can promote the re-expression of maspin in MCF-7 cells. Luciferase assay shows that myocardin activates the transcription of maspin promoter by CArG box. More importantly, 5-aza-dc/TSA and myocardin synergetically enhance re-expression of maspin and augment maspin-mediated apoptosis in MCF-7 cells. Thus, these data reveal the new insight that myocardin meditates apoptosis in breast cancer through affecting maspin re-expression and epigenetic modification to regulate the development of breast cancer, thereby raising the possibility of its use in breast cancer therapy.
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Affiliation(s)
- Xing-Hua Liao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology, Tianjin University of Science and Technology, 300457, PR China; Institute of Biology and Medicine, Wuhan University of Science and Technology, 430000, PR China
| | - Yan-Qi Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology, Tianjin University of Science and Technology, 300457, PR China
| | - Nan Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology, Tianjin University of Science and Technology, 300457, PR China.
| | - Li Zheng
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology, Tianjin University of Science and Technology, 300457, PR China
| | - Wen-Jing Xing
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology, Tianjin University of Science and Technology, 300457, PR China
| | - Dong-Wei Zhao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology, Tianjin University of Science and Technology, 300457, PR China
| | - Ting-Bao Yan
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology, Tianjin University of Science and Technology, 300457, PR China
| | - Yue Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology, Tianjin University of Science and Technology, 300457, PR China
| | - Long-Yue Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology, Tianjin University of Science and Technology, 300457, PR China
| | - Xue-Guang Sun
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology, Tianjin University of Science and Technology, 300457, PR China
| | - Peng Hu
- Institute of Biology and Medicine, Wuhan University of Science and Technology, 430000, PR China
| | - Hao Zhou
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology, Tianjin University of Science and Technology, 300457, PR China
| | - Tong-Cun Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology, Tianjin University of Science and Technology, 300457, PR China; Institute of Biology and Medicine, Wuhan University of Science and Technology, 430000, PR China.
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Zhang B, Xiang S, Yin Y, Gu L, Deng D. C-terminal in Sp1-like artificial zinc-finger proteins plays crucial roles in determining their DNA binding affinity. BMC Biotechnol 2013; 13:106. [PMID: 24289163 PMCID: PMC4219604 DOI: 10.1186/1472-6750-13-106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 11/25/2013] [Indexed: 11/17/2022] Open
Abstract
Background It is well known that the C-terminal zinc-finger-3 in transcription factor Sp1 contributes more than the N-terminal zinc-finger-1 in determining Sp1’s DNA binding capacity. Sp1-like artificial poly-zinc-finger proteins (ZFPs) are powerful biotechnological tools for gene-specific recognization and manipulation. It is important to understand whether the C-terminal fingers in the Sp1-like artificial ZFPs remain crucial for their DNA binding ability. Recently, a set of p16 promoter-specific seven-ZFPs (7ZFPs) has been constructed to reactivate the expression of methylation-silenced p16. These 7ZFPs contain one N-terminal three-zinc-finger domain of Sp1 (3ZF), two Sp1-like two-zinc-finger domains derived from the Sp1 finger-2 and finger-3 (2ZF) in the middle and C-terminal regions. Results In the present study, sets of variants for several representative 7ZFPs with the p16-binding affinity were further constructed. This was accomplished through finger replacements and key amino acid mutations in the N-terminal fingers, C-terminal fingers, and linker peptide, respectively. Their p16-binding activity was analysed using gel mobility shift assays. Results showed that the motif replacement or a key amino acid mutation (S > R) at position +2 of the α-helix in the C-terminal 2ZF domain completely abolished their p16-binding affinity. Deletion of three amino acids in a consensus linker (TGEKP > TG) between finger-7 and the 6 × Histidine-tag in the C-terminal also dramatically abolished their binding affinity. In contrast, the replacement of the finger-3 in the N-terminal 3ZF domain did not affect their binding affinity, but decreased their binding stability. Conclusions Altogether, the present study show that the C-terminal region may play crucial roles in determining the DNA binding affinity of Sp1-like artificial ZFPs.
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Affiliation(s)
| | | | | | | | - Dajun Deng
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China.
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29
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Perez-Pinera P, Kocak DD, Vockley CM, Adler AF, Kabadi AM, Polstein LR, Thakore PI, Glass KA, Ousterout DG, Leong KW, Guilak F, Crawford GE, Reddy TE, Gersbach CA. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods 2013; 10:973-6. [PMID: 23892895 PMCID: PMC3911785 DOI: 10.1038/nmeth.2600] [Citation(s) in RCA: 933] [Impact Index Per Article: 84.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/18/2013] [Indexed: 02/06/2023]
Abstract
Technologies for engineering synthetic transcription factors have enabled many advances in medical and scientific research. In contrast to existing methods based on engineering of DNA-binding proteins, we created a Cas9-based transactivator that is targeted to DNA sequences by guide RNA molecules. Coexpression of this transactivator and combinations of guide RNAs in human cells induced specific expression of endogenous target genes, demonstrating a simple and versatile approach for RNA-guided gene activation.
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Affiliation(s)
- Pablo Perez-Pinera
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
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30
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Chapdelaine P, Coulombe Z, Chikh A, Gérard C, Tremblay JP. A Potential New Therapeutic Approach for Friedreich Ataxia: Induction of Frataxin Expression With TALE Proteins. MOLECULAR THERAPY. NUCLEIC ACIDS 2013; 2:e119. [PMID: 24002729 PMCID: PMC4028015 DOI: 10.1038/mtna.2013.41] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 06/04/2013] [Indexed: 12/31/2022]
Abstract
TALEs targeting a promoter sequence and fused with a transcription activation domain (TAD) may be used to specifically induce the expression of a gene as a potential treatment for haploinsufficiency. This potential therapeutic approach was applied to increase the expression of frataxin in fibroblasts of Friedreich ataxia (FRDA) patients. FRDA fibroblast cells were nucleofected with a pCR3.1 expression vector coding for TALEFrat#8 fused with VP64. A twofold increase of the frataxin mRNA (detected by quantitative reverse transcription-PCR (qRT-PCR)) associated with a similar increase of the mature form of the frataxin protein was observed. The frataxin mRNA and protein were also increased by this TALE in the fibroblasts of the YG8R mouse model. The addition of 5-aza-2′-deoxycytidine (5-Aza-dC) or of valproic acid (VPA) to the TALE treatment did not produce significant improvement. Other TADs (i.e., p65, TFAP2α, SRF, SP1, and MyoD) fused with the TALEFrat#8 gene did not produce a significant increase in the frataxin protein. Thus the TALEFrat#8-VP64 recombinant protein targeting the frataxin promoter could eventually be used to increase the frataxin expression and alleviate the FRDA symptoms.
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Affiliation(s)
- Pierre Chapdelaine
- 1] Centre de Recherche du Centre Hospitalier Universitaire de Québec, Québec, Québec, Canada [2] Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec, Québec, Canada
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31
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Bodenstine TM, Seftor REB, Khalkhali-Ellis Z, Seftor EA, Pemberton PA, Hendrix MJC. Maspin: molecular mechanisms and therapeutic implications. Cancer Metastasis Rev 2013; 31:529-51. [PMID: 22752408 DOI: 10.1007/s10555-012-9361-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Maspin, a non-inhibitory member of the serine protease inhibitor superfamily, has been characterized as a tumor suppressor gene in multiple cancer types. Among the established anti-tumor effects of Maspin are the inhibition of cancer cell invasion, attachment to extracellular matrices, increased sensitivity to apoptosis, and inhibition of angiogenesis. However, while significant experimental data support the role of Maspin as a tumor suppressor, clinical data regarding the prognostic implications of Maspin expression have led to conflicting results. This highlights the need for a better understanding of the context dependencies of Maspin in normal biology and how these are perturbed in the context of cancer. In this review, we outline the regulation and roles of Maspin in normal and developmental biology while discussing novel evidence and emerging theories related to its functions in cancer. We provide insight into the immense therapeutic potential of Maspin and the challenges related to its successful clinical translation.
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Affiliation(s)
- Thomas M Bodenstine
- Children's Hospital of Chicago Research Center, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 225 E. Chicago Avenue, Box 222, Chicago, IL 60611, USA
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Marioni G, Zanoletti E, Stritoni P, Lionello M, Giacomelli L, Gianatti A, Cattaneo L, Blandamura S, Mazzoni A, Martini A. Expression of the tumour-suppressor maspin in temporal bone carcinoma. Histopathology 2013; 63:242-9. [PMID: 23730906 DOI: 10.1111/his.12151] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 03/26/2013] [Indexed: 02/06/2023]
Abstract
AIMS Although it accounts for fewer than 0.2% of all head and neck tumours, temporal bone squamous cell carcinoma (SCC) is an aggressive malignancy with a poor prognosis in advanced cases. Novel therapeutic strategies should be developed focusing on specific targeted therapies. Maspin is a serpin showing tumour-suppressing activity which has therapeutic potential. The present study is the first to investigate maspin expression in temporal bone SCCs, using a series of 29 cases. METHODS AND RESULTS Cytoplasmic maspin expression was significantly higher in the group of patients whose SCC did not recur than in the group experiencing recurrences (P = 0.029), and in G1-G2 SCCs than in G3 cases (P = 0.001). cT correlated with recurrence rate (P = 0.05), disease-free survival (DFS) (P = 0.008) and disease-specific survival (DSS) (P = 0.0043), and pT and pathological regional lymph node status correlated with recurrence rate (P = 0.008 and P = 0.03, respectively), DFS (P = 0.017 and P = 0.0049, respectively) and DSS (P = 0.008 and P = 0.0009, respectively). CONCLUSIONS Although further studies using larger series are required, our preliminary findings suggest that cytoplasmic maspin expression has promise as a prognostic indicator of disease recurrence in temporal bone SCC, and that reactivating maspin functions in association with apoptosis-inducing or anti-angiogenic chemotherapeutic agents might be an important goal in the treatment of temporal bone SCC.
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Affiliation(s)
- Gino Marioni
- Otolaryngology Section, Department of Neurosciences, Padova University, Padova, Italy.
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Abstract
Maspin (mammary serine protease inhibitor), is a member of the serine protease inhibitor/non-inhibitor superfamily. Its expression is down-regulated in breast, prostate, gastric and melanoma cancers but over-expressed in pancreatic, gallbladder, colorectal, and thyroid cancers suggesting that maspin may play different activities in different cell types. However, maspin expression seems to be correlated with better prognosis in prostate, bladder, lung, gastric, colorectal, head and neck, thyroid and melanoma cancer. In breast and ovarian cancer maspin significance is associated with its subcellular localization: nucleus maspin expression correlates with a good prognosis, whilst in pancreatic cancer it predicts a poor prognosis. Since tumor metastasis requires the detachment and invasion of tumor cells through the basement membrane and stroma, a selectively increased adhesion by the presence of maspin may contribute to the inhibition of tumor metastasis. Furthermore the different position of maspin inside the cell or its epigenetic modifications may explain the different behavior of the expression of maspin between tumors. The expression of maspin might be useful as a prognostic and possibly predictive factor for patients with particular types of cancer and data can guide physicians in selecting therapy. Its expression in circulating tumor cells especially in breast cancer, could be also useful in clinical practice along with other factors, such as age, comorbidities, blood examinations in order to select the best therapy to be carried out. Focusing on the malignancies in which maspin showed a positive prognostic value, therapeutic approaches studied so far aimed to re-activate a dormant tumor suppressor gene by designed transcription factors, to hit the system that inhibits the expression of maspin, to identify natural substances that can determine the activation and the expression of maspin or possible “molecules binds” to introduce maspin in cancer cell and gene therapy capable of up-regulating the maspin in an attempt to reduce primarily the risk of metastasis. Further studies in these directions are necessary to better define the therapeutic implication of maspin.
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Huisman C, Wisman GBA, Kazemier HG, van Vugt MATM, van der Zee AGJ, Schuuring E, Rots MG. Functional validation of putative tumor suppressor gene C13ORF18 in cervical cancer by Artificial Transcription Factors. Mol Oncol 2013; 7:669-79. [PMID: 23522960 DOI: 10.1016/j.molonc.2013.02.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 02/03/2013] [Accepted: 02/21/2013] [Indexed: 01/04/2023] Open
Abstract
C13ORF18 is frequently hypermethylated in cervical cancer but not in normal cervix and might serve as a biomarker for the early detection of cervical cancer in scrapings. As hypermethylation is often observed for silenced tumor suppressor genes (TSGs), hypermethylated biomarker genes might exhibit tumor suppressive activities upon re-expression. Epigenetic drugs are successfully exploited to reverse TSG silencing, but act genome-wide. Artificial Transcription Factors (ATFs) provide a gene-specific approach for re-expression of silenced genes. Here, we investigated the potential tumor suppressive role of C13ORF18 in cervical cancer by ATF-induced re-expression. Five zinc finger proteins were engineered to bind the C13ORF18 promoter and fused to a strong transcriptional activator. C13ORF18 expression could be induced in cervical cell lines: ranging from >40-fold in positive (C13ORF18-unmethylated) cells to >110-fold in negative (C13ORF18-methylated) cells. Re-activation of C13ORF18 resulted in significant cell growth inhibition and/or induction of apoptosis. Co-treatment of cell lines with ATFs and epigenetic drugs further enhanced the ATF-induced effects. Interestingly, re-activation of C13ORF18 led to partial demethylation of the C13ORF18 promoter and decreased repressive histone methylation. These data demonstrate the potency of ATFs to re-express and potentially demethylate hypermethylated silenced genes. Concluding, we show that C13ORF18 has a TSG function in cervical cancer and may serve as a therapeutic anti-cancer target. As the amount of epimutations in cancer exceeds the number of gene mutations, ATFs provide promising tools to validate hypermethylated marker genes as therapeutic targets.
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Affiliation(s)
- Christian Huisman
- Dept. of Pathology and Medical Biology, University Medical Centre Groningen (UMCG), University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands.
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Juárez-Moreno K, Erices R, Beltran AS, Stolzenburg S, Cuello-Fredes M, Owen GI, Qian H, Blancafort P. Breaking through an epigenetic wall: re-activation of Oct4 by KRAB-containing designer zinc finger transcription factors. Epigenetics 2013; 8:164-76. [PMID: 23314702 DOI: 10.4161/epi.23503] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The gene Oct4 encodes a transcription factor critical for the maintenance of pluripotency and self-renewal in embryonic stem cells. In addition, improper re-activation of Oct4 contributes to oncogenic processes. Herein, we describe a novel designer zinc finger protein (ZFP) capable of upregulating the endogenous Oct4 promoter in a panel of breast and ovarian cell lines carrying a silenced gene. In some ovarian tumor lines, the ZFP triggered a strong reactivation of Oct4, with levels of expression comparable with exogenous Oct4 cDNA delivery. Surprisingly, the reactivation of Oct4 required a KRAB domain for effective upregulation of the endogenous gene. While KRAB-containing ZFPs are traditionally described as transcriptional repressors, our results suggest that these proteins could, in certain genomic contexts, function as potent activators and, thus, outline an emerging novel function of KRAB-ZFPs. In addition, we document a novel ZFP that could be used for the epigenetic reprograming of cancer cells.
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Affiliation(s)
- Karla Juárez-Moreno
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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36
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Blancafort P, Jin J, Frye S. Writing and rewriting the epigenetic code of cancer cells: from engineered proteins to small molecules. Mol Pharmacol 2012; 83:563-76. [PMID: 23150486 DOI: 10.1124/mol.112.080697] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The epigenomic era has revealed a well-connected network of molecular processes that shape the chromatin landscape. These processes comprise abnormal methylomes, transcriptosomes, genome-wide histone post-transcriptional modifications patterns, histone variants, and noncoding RNAs. The mapping of these processes in large scale by chromatin immunoprecipitation sequencing and other methodologies in both cancer and normal cells reveals novel therapeutic opportunities for anticancer intervention. The goal of this minireview is to summarize pharmacological strategies to modify the epigenetic landscape of cancer cells. These approaches include the use of novel small molecule inhibitors of epigenetic processes specifically deregulated in cancer cells and the design of engineered proteins able to stably reprogram the epigenetic code in cancer cells in a way that is similar to normal cells.
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Affiliation(s)
- Pilar Blancafort
- School of Anatomy, Physiology, and Human Biology, M309, the University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia.
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Yan C, Higgins PJ. Drugging the undruggable: transcription therapy for cancer. Biochim Biophys Acta Rev Cancer 2012; 1835:76-85. [PMID: 23147197 DOI: 10.1016/j.bbcan.2012.11.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 10/30/2012] [Accepted: 11/01/2012] [Indexed: 11/19/2022]
Abstract
Transcriptional regulation is often the convergence point of oncogenic signaling. It is not surprising, therefore, that aberrant gene expression is a hallmark of cancer. Transformed cells often develop a dependency on such a reprogramming highlighting the therapeutic potential of rectifying cancer-associated transcriptional abnormalities in malignant cells. Although transcription is traditionally considered as undruggable, agents have been developed that target various levels of transcriptional regulation including DNA binding by transcription factors, protein-protein interactions, and epigenetic alterations. Some of these agents have been approved for clinical use or entered clinical trials. While artificial transcription factors have been developed that can theoretically modulate expression of any given gene, the emergence of reliable reporter assays greatly facilitates the search for transcription-targeted agents. This review provides a comprehensive overview of these developments, and discusses various strategies applicable for developing transcription-targeted therapeutic agents.
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Affiliation(s)
- Chunhong Yan
- Center for Cell Biology and Cancer Research, Albany Medical College, MC-165, 47 New Scotland Avenue, Albany, NY 12208, USA.
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38
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Zhang B, Xiang S, Zhong Q, Yin Y, Gu L, Deng D. The p16-specific reactivation and inhibition of cell migration through demethylation of CpG islands by engineered transcription factors. Hum Gene Ther 2012; 23:1071-81. [PMID: 22738793 DOI: 10.1089/hum.2012.070] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Methylation of CpG islands inactivates transcription of tumor suppressor genes including p16 (CDKN2A). Inhibitors of DNA methylation and histone deacylation are recognized as useful cancer therapeutic chemicals through reactivation of the expression of methylated genes. However, these inhibitors are not target gene-specific, so that they lead to serious side effects as regular cytotoxic chemotherapy agents. To explore the feasibility of methylated gene-specific reactivation by artificial transcription factors, we engineered a set of Sp1-like seven-finger zinc-finger proteins (7ZFPs) targeted to a 21-bp sequence of the p16 promoter and found that these 7ZFPs could bind specifically to the target p16 promoter probe. Then the p16-specific artificial transcription factors (p16ATFs) were made from these 7ZFPs and the transcription activator VP64. Results showed that transient transfection of some p16ATFs selectively up-regulated the endogenous p16 expression in the p16-active 293T cells. Moreover, the transient transfection of the representative p16ATF-6I specifically reactivated p16 expression in the p16-methylated H1299 and AGS cells pretreated with a nontoxic amount of 5'-aza-deoxycytidine (20 and 80 nM, respectively). In addition, stable transfection of the p16ATF induced demethylation of p16 CpG island and trimethylation of histone H3K4, and inhibited recruitment of DNA methyltransferase 1 and trimethylation of H3K9 and H3K27 in the p16 promoter in H1299 cells without 5'-aza-deoxycytidine pretreatment. Notably, inhibition of cell migration and invasion was observed in these p16-reactivated cells induced by transient and stable p16ATF transfection. These results demonstrate that p16ATF not only specifically reactivates p16 expression through demethylation of CpG islands, but also restores methylated p16 function.
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Affiliation(s)
- Baozhen Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Cancer Aetiology, Peking University Cancer Hospital/Institute, Beijing, 100142, China
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Lara H, Wang Y, Beltran AS, Juárez-Moreno K, Yuan X, Kato S, Leisewitz AV, Cuello Fredes M, Licea AF, Connolly DC, Huang L, Blancafort P. Targeting serous epithelial ovarian cancer with designer zinc finger transcription factors. J Biol Chem 2012; 287:29873-86. [PMID: 22782891 DOI: 10.1074/jbc.m112.360768] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Ovarian cancer is the leading cause of death among gynecological malignancies. It is detected at late stages when the disease is spread through the abdominal cavity in a condition known as peritoneal carcinomatosis. Thus, there is an urgent need to develop novel therapeutic interventions to target advanced stages of ovarian cancer. Mammary serine protease inhibitor (Maspin) represents an important metastasis suppressor initially identified in breast cancer. Herein we have generated a sequence-specific zinc finger artificial transcription factor (ATF) to up-regulate the Maspin promoter in aggressive ovarian cancer cell lines and to interrogate the therapeutic potential of Maspin in ovarian cancer. We found that although Maspin was expressed in some primary ovarian tumors, the promoter was epigenetically silenced in cell lines derived from ascites. Transduction of the ATF in MOVCAR 5009 cells derived from ascitic cultures of a TgMISIIR-TAg mouse model of ovarian cancer resulted in tumor cell growth inhibition, impaired cell invasion, and severe disruption of actin cytoskeleton. Systemic delivery of lipid-protamine-RNA nanoparticles encapsulating a chemically modified ATF mRNA resulted in inhibition of ovarian cancer cell growth in nude mice accompanied with Maspin re-expression in the treated tumors. Gene expression microarrays of ATF-transduced cells revealed an exceptional specificity for the Maspin promoter. These analyses identified novel targets co-regulated with Maspin in human short-term cultures derived from ascites, such as TSPAN12, that could mediate the anti-metastatic phenotype of the ATF. Our work outlined the first targeted, non-viral delivery of ATFs into tumors with potential clinical applications for metastatic ovarian cancers.
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Affiliation(s)
- Haydee Lara
- Department of Pharmacology, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
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Abstract
Epithelial ovarian cancer is the leading cause of death from gynecological cancers, largely owing to the development of recurrent intractable disease. Only a small number of distinct genetic mutations are known to contribute to ovarian carcinogenesis. Furthermore, understanding mechanistic genotype-phenotype links is complicated by frequent aneuploidy. Epigenetic deregulation is even more prominent, and ovarian cancers are replete with such aberrations that repress tumor suppressors and activate proto-oncogenes. Epigenetic therapies are emerging as promising agents for resensitizing platinum-resistant ovarian cancers. These drugs may also have the potential to alter epigenetic programming in cancer progenitor cells and provide a strategy for improving therapy of ovarian cancer.
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Affiliation(s)
- Susan K Murphy
- Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, Duke University Medical Center, PO Box 91012, Durham, NC 27708, USA.
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Stolzenburg S, Rots MG, Beltran AS, Rivenbark AG, Yuan X, Qian H, Strahl BD, Blancafort P. Targeted silencing of the oncogenic transcription factor SOX2 in breast cancer. Nucleic Acids Res 2012; 40:6725-40. [PMID: 22561374 PMCID: PMC3413152 DOI: 10.1093/nar/gks360] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The transcription factor (TF) SOX2 is essential for the maintenance of pluripotency and self-renewal in embryonic stem cells. In addition to its normal stem cell function, SOX2 over-expression is associated with cancer development. The ability to selectively target this and other oncogenic TFs in cells, however, remains a significant challenge due to the ‘undruggable’ characteristics of these molecules. Here, we employ a zinc finger (ZF)-based artificial TF (ATF) approach to selectively suppress SOX2 gene expression in cancer cells. We engineered four different proteins each composed of 6ZF arrays designed to bind 18 bp sites in the SOX2 promoter and enhancer region, which controls SOX2 methylation. The 6ZF domains were linked to the Kruppel Associated Box (SKD) repressor domain. Three engineered proteins were able to bind their endogenous target sites and effectively suppress SOX2 expression (up to 95% repression efficiencies) in breast cancer cells. Targeted down-regulation of SOX2 expression resulted in decreased tumor cell proliferation and colony formation in these cells. Furthermore, induced expression of an ATF in a mouse model inhibited breast cancer cell growth. Collectively, these findings demonstrate the effectiveness and therapeutic potential of engineered ATFs to mediate potent and long-lasting down-regulation of oncogenic TF expression in cancer cells.
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Affiliation(s)
- Sabine Stolzenburg
- Epigenetic Editing, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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Rivenbark AG, Stolzenburg S, Beltran AS, Yuan X, Rots MG, Strahl BD, Blancafort P. Epigenetic reprogramming of cancer cells via targeted DNA methylation. Epigenetics 2012; 7:350-60. [PMID: 22419067 DOI: 10.4161/epi.19507] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
An obstacle in the treatment of human diseases such as cancer is the inability to selectively and effectively target historically undruggable targets such as transcription factors. Here, we employ a novel technology using artificial transcription factors (ATFs) to epigenetically target gene expression in cancer cells. We show that site-specific DNA methylation and long-term stable repression of the tumor suppressor Maspin and the oncogene SOX2 can be achieved in breast cancer cells via zinc-finger ATFs targeting DNA methyltransferase 3a (DNMT3a) to the promoters of these genes. Using this approach, we show Maspin and SOX2 downregulation is more significant as compared with transient knockdown, which is also accompanied by stable phenotypic reprogramming of the cancer cell. These findings indicate that multimodular Zinc Finger Proteins linked to epigenetic editing domains can be used as novel cell resources to selectively and heritably alter gene expression patterns to stably reprogram cell fate.
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Affiliation(s)
- Ashley G Rivenbark
- Department of Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Huang X, Narayanaswamy R, Fenn K, Szpakowski S, Sasaki C, Costa J, Blancafort P, Lizardi PM. Sequence-specific biosensors report drug-induced changes in epigenetic silencing in living cells. DNA Cell Biol 2012; 31 Suppl 1:S2-10. [PMID: 22313050 DOI: 10.1089/dna.2011.1537] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Treatment with demethylating drugs can induce demethylation and reactivation of abnormally silenced tumor suppressor genes in cancer cells, but it can also induce potentially deleterious loss of methylation of repetitive elements. To enable the observation of unwanted drug effects related to loss of methylation of repetitive DNA, we have developed a novel biosensor capable of reporting changes in DNA accessibility via luminescence, in living cells. The biosensor design comprises two independent modules, each with a polydactyl zinc finger domain fused to a half intein and to a split-luciferase domain that can be joined by conditional protein splicing after binding to adjacent DNA targets. We show that an artificial zinc finger design specifically targeting DNA sequences near the promoter region of the L1PA2 subfamily of Line-1 retroelements is able to generate luminescent signals, reporting loss of epigenetic silencing and increased DNA accessibility of retroelements in human cells treated with the demethylating drugs decitabine or 5-azacytidine.
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Affiliation(s)
- Xudong Huang
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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Goulet B, Chan G, Chambers AF, Lewis JD. An emerging role for the nuclear localization of maspin in the suppression of tumor progression and metastasis. Biochem Cell Biol 2011; 90:22-38. [PMID: 22047058 DOI: 10.1139/o11-053] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Maspin, a member of the serpin family of serine protease inhibitors, was originally identified as a tumor suppressor that is expressed in normal mammary epithelial cells but is reduced or absent in breast carcinomas. Early enthusiasm for maspin as a biomarker for disease progression has been tempered by clinical data that associates maspin with favourable outcomes in some studies and poor prognosis in others. Here, we review all of the published clinical studies for maspin in breast and ovarian cancers and propose that the apparent discordance between clinical reports is a consequence of differential cellular distribution of maspin. Indeed, it was thought that an extracellular pool of maspin possessed tumor suppressor activity, acting by inhibiting migration and increasing cell adhesion. Recent evidence from our group and others indicates, however, that the nuclear localization of maspin in cancer cells is necessary for its tumor suppressor activity. We provide additional data here to demonstrate that nuclear-localized maspin binds to chromatin and is required to effectively prevent cells from metastasizing. Our knowledge of other serpins that localize to the nucleus should help to inform future studies of nuclear maspin. Elucidation of the molecular mechanisms regulating the localization and activities of maspin should pave the way for the development of improved diagnostics and therapies for cancer.
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Affiliation(s)
- Brigitte Goulet
- London Regional Cancer Program, Translational Prostate Cancer Research Group, London, ON N6A 4L6, Canada
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Marioni G, Blandamura S, Lionello M, Giacomelli L, Staffieri C, Fasanaro E, Manzato E, Staffieri A. Nuclear MASPIN expression relates to a better prognosis in elderly patients with laryngeal carcinoma. Acta Otolaryngol 2011; 131:1220-5. [PMID: 21732742 DOI: 10.3109/00016489.2011.599817] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
CONCLUSION MASPIN subcellular location can be considered a prognostic marker that is potentially useful for identifying elderly patients with laryngeal carcinoma at higher risk of early loco-regional recurrence, who may benefit from more aggressive therapy. In a targeted treatment setting, re-activated nuclear MASPIN in combination with anti-angiogenic and/or cytotoxic drugs may be effective in treating laryngeal carcinoma in elderly patients. OBJECTIVES Aging is associated with molecular, cellular, and physiological changes that influence carcinogenesis and cancer growth. MASPIN has multifaceted anti-tumor effects and available evidence supports the hypothesis that its subcellular location influences its functions. The aim of the present study was to firstly assess the potential prognostic role of subcellular MASPIN location in elderly patients (>65 years old) with laryngeal carcinoma. METHODS MASPIN expression and location were immunohistochemically determined in 68 consecutive elderly patients with laryngeal carcinoma. RESULTS Nodal involvement and pathological stage correlated strongly with the prognosis for laryngeal carcinomas in elderly patients, in terms of disease recurrence rate and disease-free survival. The loco-regional recurrence rate was significantly lower (p = 0.041) and the disease-free survival after treatment was significantly longer (p = 0.045) in cases with a nuclear pattern of MASPIN subcellular expression.
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Affiliation(s)
- Gino Marioni
- Department of Medical and Surgical Specialties, Otolaryngology Section, University of Padova, Padova, Italy.
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Suppression of breast tumor growth and metastasis by an engineered transcription factor. PLoS One 2011; 6:e24595. [PMID: 21931769 PMCID: PMC3172243 DOI: 10.1371/journal.pone.0024595] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 08/15/2011] [Indexed: 11/19/2022] Open
Abstract
Maspin is a tumor and metastasis suppressor playing an essential role as gatekeeper of tumor progression. It is highly expressed in epithelial cells but is silenced in the onset of metastatic disease by epigenetic mechanisms. Reprogramming of Maspin epigenetic silencing offers a therapeutic potential to lock metastatic progression. Herein we have investigated the ability of the Artificial Transcription Factor 126 (ATF-126) designed to upregulate the Maspin promoter to inhibit tumor progression in pre-established breast tumors in immunodeficient mice. ATF-126 was transduced in the aggressive, mesenchymal-like and triple negative breast cancer line, MDA-MB-231. Induction of ATF expression in vivo by Doxycycline resulted in 50% reduction in tumor growth and totally abolished tumor cell colonization. Genome-wide transcriptional profiles of ATF-induced cells revealed a gene signature that was found over-represented in estrogen receptor positive (ER+) "Normal-like" intrinsic subtype of breast cancer and in poorly aggressive, ER+ luminal A breast cancer cell lines. The comparison transcriptional profiles of ATF-126 and Maspin cDNA defined an overlapping 19-gene signature, comprising novel targets downstream the Maspin signaling cascade. Our data suggest that Maspin up-regulates downstream tumor and metastasis suppressor genes that are silenced in breast cancers, and are normally expressed in the neural system, including CARNS1, SLC8A2 and DACT3. In addition, ATF-126 and Maspin cDNA induction led to the re-activation of tumor suppressive miRNAs also expressed in neural cells, such as miR-1 and miR-34, and to the down-regulation of potential oncogenic miRNAs, such as miR-10b, miR-124, and miR-363. As expected from its over-representation in ER+ tumors, the ATF-126-gene signature predicted favorable prognosis for breast cancer patients. Our results describe for the first time an ATF able to reduce tumor growth and metastatic colonization by epigenetic reactivation of a dormant, normal-like, and more differentiated gene program.
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Beltran AS, Blancafort P. Reactivation of MASPIN in non-small cell lung carcinoma (NSCLC) cells by artificial transcription factors (ATFs). Epigenetics 2011; 6:224-35. [PMID: 20948306 DOI: 10.4161/epi.6.2.13700] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Tumor suppressor genes have antiproliferative and antimetastatic functions, and thus, they negatively affect tumor progression. Reactivating specific tumor suppressor genes would offer an important therapeutic strategy to block tumor progression. Mammary Serine Protease Inhibitor (MASPIN) is a tumor suppressor gene that is not mutated or rearranged in tumor cells, but is silenced during metastatic progression by transcriptional and epigenetic mechanisms. In this work, we have investigated the ability of Artificial Transcription Factors (ATFs) to reactivate MASPIN expression and to reduce tumor growth and metastatic dissemination in Non-Small Cell Lung Carcinoma (NSCLC) cell lines carrying a hypermethylated MASPIN promoter. We found that the ATFs linked to transactivator domains were able to demethylate the MASPIN promoter. Consistently, we observed that co-treatment of ATF-transduced cells with methyltransferase inhibitors enhanced MASPIN expression as well as induction of tumor cell apoptosis. In addition to tumor suppressive functions, restoration of endogenous MASPIN expression was accompanied by inhibition of metastatic dissemination in nude mice. ATF-mediated reactivation of MASPIN lead to changes in cell motility and to induction of E-CADHERIN. These data suggest that ATFs are able to reprogram aggressive lung tumor cells towards a more epithelial, differentiated phenotype, and thus, represent novel therapeutic agents for metastatic lung cancers.
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Affiliation(s)
- Adriana S Beltran
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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van der Gun BTF, Melchers LJ, Ruiters MHJ, de Leij LFMH, McLaughlin PMJ, Rots MG. EpCAM in carcinogenesis: the good, the bad or the ugly. Carcinogenesis 2010; 31:1913-21. [PMID: 20837599 DOI: 10.1093/carcin/bgq187] [Citation(s) in RCA: 245] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The epithelial cell adhesion molecule (EpCAM) is a membrane glycoprotein that is highly expressed on most carcinomas and therefore of potential use as a diagnostic and prognostic marker for a variety of carcinomas. Interestingly, EpCAM is explored as target in antibody-based therapies. Recently, EpCAM has been identified as an additional marker of cancer-initiating cells. In this review, we describe the controversial biological role of EpCAM with the focus on carcinogenesis: as an adhesion molecule, EpCAM mediates homophilic adhesion interactions, which in turn might prevent metastasis. On the other hand, EpCAM abrogates E-cadherin mediated cell-cell adhesion thereby promoting metastasis. Also, upon cleavage of EpCAM, the intracellular domain functions as a part of a transcriptional complex inducing c-myc and cyclin A and E. In line with these seemingly controversial roles, EpCAM overexpression has been associated with both decreased and increased survival of patients. Similarly, either induction or downregulation of EpCAM expression lowers the oncogenic potential depending on the cell type. As epigenetic dysregulation underlies aberrant EpCAM expression, we propose epigenetic editing as a novel approach to investigate the biological role of EpCAM, expanding the options for EpCAM as a therapeutic target in cancer.
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Affiliation(s)
- Bernardina T F van der Gun
- Epigenetic Editing, Department of Medical Biology, University Medical Centre Groningen, Hanzeplein 1, Groningen, TheNetherlands
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Claes B, Buysschaert I, Lambrechts D. Pharmaco-epigenomics: discovering therapeutic approaches and biomarkers for cancer therapy. Heredity (Edinb) 2010; 105:152-60. [DOI: 10.1038/hdy.2010.42] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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