1
|
Miller KJ, Henry I, Maylin Z, Smith C, Arunachalam E, Pandha H, Asim M. A compendium of Androgen Receptor Variant 7 target genes and their role in Castration Resistant Prostate Cancer. Front Oncol 2023; 13:1129140. [PMID: 36937454 PMCID: PMC10014620 DOI: 10.3389/fonc.2023.1129140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
Persistent androgen receptor (AR) signalling is the main driver of prostate cancer (PCa). Truncated isoforms of the AR called androgen receptor variants (AR-Vs) lacking the ligand binding domain often emerge during treatment resistance against AR pathway inhibitors such as Enzalutamide. This review discusses how AR-Vs drive a more aggressive form of PCa through the regulation of some of their target genes involved in oncogenic pathways, enabling disease progression. There is a pressing need for the development of a new generation of AR inhibitors which can repress the activity of both the full-length AR and AR-Vs, for which the knowledge of differentially expressed target genes will allow evaluation of inhibition efficacy. This review provides a detailed account of the most common variant, AR-V7, the AR-V7 regulated genes which have been experimentally validated, endeavours to understand their relevance in aggressive AR-V driven PCa and discusses the utility of the downstream protein products as potential drug targets for PCa treatment.
Collapse
Affiliation(s)
| | | | - Zoe Maylin
- *Correspondence: Zoe Maylin, ; Mohammad Asim,
| | | | | | | | | |
Collapse
|
2
|
Li C, Zhou Z, Ren C, Deng Y, Peng F, Wang Q, Zhang H, Jiang Y. Triplex-forming oligonucleotides as an anti-gene technique for cancer therapy. Front Pharmacol 2022; 13:1007723. [PMID: 36618947 PMCID: PMC9811266 DOI: 10.3389/fphar.2022.1007723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Triplex-forming oligonucleotides (TFOs) can bind to the major groove of double-stranded DNA with high specificity and affinity and inhibit gene expression. Triplex-forming oligonucleotides have gained prominence because of their potential applications in antigene therapy. In particular, the target specificity of triplex-forming oligonucleotides combined with their ability to suppress oncogene expression has driven their development as anti-cancer agents. So far, triplex-forming oligonucleotides have not been used for clinical treatment and seem to be gradually snubbed in recent years. But triplex-forming oligonucleotides still represent an approach to down-regulate the expression of the target gene and a carrier of active substances. Therefore, in the present review, we will introduce the characteristics of triplex-forming oligonucleotides and their anti-cancer research progress. Then, we will discuss the challenges in their application.
Collapse
Affiliation(s)
- Chun Li
- Department of Rehabilitation Medicine, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Zunzhen Zhou
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Chao Ren
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Yi Deng
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Feng Peng
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Qiongfen Wang
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Hong Zhang
- Department of Rehabilitation Medicine, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China,*Correspondence: Hong Zhang, ; Yuan Jiang,
| | - Yuan Jiang
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China,*Correspondence: Hong Zhang, ; Yuan Jiang,
| |
Collapse
|
3
|
Hussein MK, Papež M, Dhiman H, Baumann M, Galosy S, Borth N. In silico design of CMV promoter binding oligonucleotides and their impact on inhibition of gene expression in Chinese hamster ovary cells. J Biotechnol 2022; 359:185-193. [DOI: 10.1016/j.jbiotec.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 10/31/2022]
|
4
|
Noé V, Aubets E, Félix AJ, Ciudad CJ. Nucleic acids therapeutics using PolyPurine Reverse Hoogsteen hairpins. Biochem Pharmacol 2020; 189:114371. [PMID: 33338475 DOI: 10.1016/j.bcp.2020.114371] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 02/08/2023]
Abstract
PolyPurine Reverse Hoogsteen hairpins (PPRHs) are DNA hairpins formed by intramolecular reverse Hoogsteen bonds which can bind to polypyrimidine stretches in dsDNA by Watson:Crick bonds, thus forming a triplex and displacing the fourth strand of the DNA complex. PPRHs were first described as a gene silencing tool in vitro for DHFR, telomerase and survivin genes. Then, the effect of PPRHs directed against the survivin gene was also determined in vivo using a xenograft model of prostate cancer cells (PC3). Since then, the ability of PPRHs to inhibit gene expression has been explored in other genes involved in cancer (BCL-2, mTOR, topoisomerase, C-MYC and MDM2), in immunotherapy (SIRPα/CD47 and PD-1/PD-L1 tandem) or in replication stress (WEE1 and CHK1). Furthermore, PPRHs have the ability to target the complementary strand of a G-quadruplex motif as a regulatory element of the TYMS gene. PPRHs have also the potential to correct point mutations in the DNA as shown in two collections of CHO cell lines bearing mutations in either the dhfr or aprt loci. Finally, based on the capability of PPRHs to form triplexes, they have been incorporated as probes in biosensors for the determination of the DNA methylation status of PAX-5 in cancer and the detection of mtLSU rRNA for the diagnosis of Pneumocystis jirovecii. Of note, PPRHs have high stability and do not present immunogenicity, hepatotoxicity or nephrotoxicity in vitro. Overall, PPRHs constitute a new economical biotechnological tool with multiple biomedical applications.
Collapse
Affiliation(s)
- Véronique Noé
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, & IN2UB, University of Barcelona, 08028 Barcelona, Spain
| | - Eva Aubets
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, & IN2UB, University of Barcelona, 08028 Barcelona, Spain
| | - Alex J Félix
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, & IN2UB, University of Barcelona, 08028 Barcelona, Spain
| | - Carlos J Ciudad
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, & IN2UB, University of Barcelona, 08028 Barcelona, Spain.
| |
Collapse
|
5
|
Xu H, Yang X, Huang W, Ma Y, Ke H, Zou L, Yang Q, Jiao B. Single-cell profiling of long noncoding RNAs and their cell lineage commitment roles via RNA-DNA-DNA triplex formation in mammary epithelium. Stem Cells 2020; 38:1594-1611. [PMID: 32930441 DOI: 10.1002/stem.3274] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/21/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Long noncoding RNAs (lncRNAs), which are crucial for organ development, exhibit cell-specific expression. Thus, transcriptomic analysis based on total tissue (bulk-seq) cannot accurately reflect the expression pattern of lncRNAs. Here, we used high-throughput single-cell RNA-seq data to investigate the role of lncRNAs using the hierarchical model of mammary epithelium. With our comprehensive annotation of the mammary epithelium, lncRNAs showed much greater cell-lineage specific expression than coding genes. The lineage-specific lncRNAs were functionally correlated with lineage commitment through the coding genes via the cis- and trans-effects of lncRNAs. For the working mechanism, lncRNAs formed a triplex structure with the DNA helix to regulate downstream lineage-specific marker genes. We used lncRNA-Carmn as an example to validate the above findings. Carmn, which is specifically expressed in mammary gland stem cells (MaSCs) and basal cells, positively regulated the Wnt signaling ligand Wnt10a through formation of a lncRNA-DNA-DNA triplex, and thus controlled the stemness of MaSCs. Our study suggests that lncRNAs play essential roles in cell-lineage commitment and provides an approach to decipher lncRNA functions based on single-cell RNA-seq data.
Collapse
Affiliation(s)
- Haibo Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, People's Republic of China
- International Cancer Center, Shenzhen University School of Medicine, Shenzhen, People's Republic of China
| | - Xing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China
- Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, People's Republic of China
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, Yunnan, People's Republic of China
| | - Weiren Huang
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, People's Republic of China
- International Cancer Center, Shenzhen University School of Medicine, Shenzhen, People's Republic of China
| | - Yujie Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China
| | - Hao Ke
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China
| | - Li Zou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China
| | - Qin Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China
| | - Baowei Jiao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China
| |
Collapse
|
6
|
Comparing the effects of physiologically-based metal oxide nanoparticles on ribonucleic acid and RAS/RBD-targeted triplex and aptamer interactions. Biochem Biophys Res Commun 2019; 517:43-48. [PMID: 31307783 DOI: 10.1016/j.bbrc.2019.06.164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 06/30/2019] [Indexed: 12/11/2022]
Abstract
Physiological metals such as zinc, magnesium, and nickel facilitate nucleic acid and protein interactions and stability. In the nanoscale, the impact these have on nucleic acid structure-function is very poorly understood and was investigated here. Nanoparticles' (NP) RNA precipitation efficiency was in the order; NiO > MgO > ZnO > CaO > CaCO3>Cu. Gel mobility shift was observed for MgO and especially ZnO NP. Loss of staining intensity was shown for Cu suggesting this NP may denature RNA supported by the UV- and CD-spectroscopy patterns, change in area-under-the-curve (AUC) and abs260 nm measurements. Aptamer and triplex-forming oligomer (TFO) sequences were designed targeting RAS/Ras binding domain (RBD) and the impact of the NP on target interaction investigated. MgO NP promotes aptamer:RBD interaction and preserves triplex formation whereas NiO NP effects duplex migration and intensifies staining of the triplex suggesting a novel mechanism of interaction and conformation. These data strongly support the role of MgO, ZnO and NiO NP for nucleic acid nanobio interaction and suggest potential biomedical application for such novel interfaces.
Collapse
|
7
|
LncRNA MIR100HG promotes cell proliferation in triple-negative breast cancer through triplex formation with p27 loci. Cell Death Dis 2018; 9:805. [PMID: 30042378 PMCID: PMC6057987 DOI: 10.1038/s41419-018-0869-2] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 06/10/2018] [Accepted: 07/09/2018] [Indexed: 12/13/2022]
Abstract
Triple-negative breast cancer (TNBC) exhibits poor prognosis, with high metastasis and low survival. Long non-coding RNAs (lncRNAs) play critical roles in tumor progression. Here, we identified lncRNA MIR100HG as a pro-oncogene for TNBC progression. Knockdown of MIR100HG decreased cell proliferation and induced cell arrest in the G1 phase, whereas overexpression of MIR100HG significantly increased cell proliferation. Furthermore, MIR100HG regulated the p27 gene to control the cell cycle, and subsequently impacted the progression of TNBC. In analyzing its underlying mechanism, bioinformatics prediction and experimental data demonstrated that MIR100HG participated in the formation of RNA–DNA triplex structures. MIR100HG in The Cancer Genome Atlas (TCGA) and breast cancer cell lines showed higher expression in TNBC than in other tumor types with poor prognosis. In conclusion, our data indicated a novel working pattern of lncRNA in TNBC progression, which may be a potential therapeutic target in such cancers.
Collapse
|
8
|
Zhang W, Le TD, Liu L, Zhou ZH, Li J. Mining heterogeneous causal effects for personalized cancer treatment. Bioinformatics 2018; 33:2372-2378. [PMID: 28369195 DOI: 10.1093/bioinformatics/btx174] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/20/2017] [Indexed: 01/03/2023] Open
Abstract
Motivation Cancer is not a single disease and involves different subtypes characterized by different sets of molecules. Patients with different subtypes of cancer often react heterogeneously towards the same treatment. Currently, clinical diagnoses rather than molecular profiles are used to determine the most suitable treatment. A molecular level approach will allow a more precise and informed way for making treatment decisions, leading to a better survival chance and less suffering of patients. Although many computational methods have been proposed to identify cancer subtypes at molecular level, to the best of our knowledge none of them are designed to discover subtypes with heterogeneous treatment responses. Results In this article we propose the Survival Causal Tree (SCT) method. SCT is designed to discover patient subgroups with heterogeneous treatment effects from censored observational data. Results on TCGA breast invasive carcinoma and glioma datasets have shown that for each subtype identified by SCT, the patients treated with radiotherapy exhibit significantly different relapse free survival pattern when compared to patients without the treatment. With the capability to identify cancer subtypes with heterogeneous treatment responses, SCT is useful in helping to choose the most suitable treatment for individual patients. Availability and Implementation Data and code are available at https://github.com/WeijiaZhang24/SurvivalCausalTree . Contact weijia.zhang@mymail.uinsa.edu.au. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Weijia Zhang
- School of Information Technology and Mathematical Sciences
| | - Thuc Duy Le
- School of Information Technology and Mathematical Sciences.,Centre for Cancer Biology, University of South Australia, Adelaide 5000, Australia
| | - Lin Liu
- School of Information Technology and Mathematical Sciences
| | - Zhi-Hua Zhou
- National Key Laboratory for Novel Software Technology, Nanjing University, Nanjing 210023, China
| | - Jiuyong Li
- School of Information Technology and Mathematical Sciences
| |
Collapse
|
9
|
Archer LK, Frame FM, Maitland NJ. Stem cells and the role of ETS transcription factors in the differentiation hierarchy of normal and malignant prostate epithelium. J Steroid Biochem Mol Biol 2017; 166:68-83. [PMID: 27185499 DOI: 10.1016/j.jsbmb.2016.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/25/2016] [Accepted: 05/07/2016] [Indexed: 12/18/2022]
Abstract
Prostate cancer is the most common cancer of men in the UK and accounts for a quarter of all new cases. Although treatment of localised cancer can be successful, there is no cure for patients presenting with invasive prostate cancer and there are less treatment options. They are generally treated with androgen-ablation therapies but eventually the tumours become hormone resistant and patients develop castration-resistant prostate cancer (CRPC) for which there are no further successful or curative treatments. This highlights the need for new treatment strategies. In order to prevent prostate cancer recurrence and treatment resistance, all the cell populations in a heterogeneous prostate tumour must be targeted, including the rare cancer stem cell (CSC) population. The ETS transcription factor family members are now recognised as a common feature in multiple cancers including prostate cancer; with aberrant expression, loss of tumour suppressor function, inactivating mutations and the formation of fusion genes observed. Most notably, the TMPRSS2-ERG gene fusion is present in approximately 50% of prostate cancers and in prostate CSCs. However, the role of other ETS transcription factors in prostate cancer is less well understood. This review will describe the prostate epithelial cell hierarchy and discuss the evidence behind prostate CSCs and their inherent resistance to conventional cancer therapies. The known and proposed roles of the ETS family of transcription factors in prostate epithelial cell differentiation and regulation of the CSC phenotype will be discussed, as well as how they might be targeted for therapy.
Collapse
Affiliation(s)
- Leanne K Archer
- Cancer Research Unit, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Fiona M Frame
- Cancer Research Unit, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Norman J Maitland
- Cancer Research Unit, Department of Biology, University of York, York, YO10 5DD, United Kingdom.
| |
Collapse
|
10
|
Chen Z, Zhang H, Ma X, Lin Z, Zhang L, Chen G. A novel fluorescent reagent for recognition of triplex DNA with high specificity and selectivity. Analyst 2016; 140:7742-7. [PMID: 26456316 DOI: 10.1039/c5an01852h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A fluorescent agent (DMT) was screened for recognizing triplex DNA with a specific and selective characteristic, which was embedded into the triplex DNA structure. The triplex DNA was firstly formed by a complementary target sequence through two distinct and sequential events. The conditions including pH and hybridization time, fluorescent agent concentration and embedding time were optimized in the experiment. Under the optimum conditions, the fluorescence signal was enhanced up to 9-fold in comparison with the DMT embedding into the ssDNA, dsDNA and G-quadruplexes. Under the same fluorescence conditions, the changes of the fluorescence signal were also investigated by several kinds of base mismatched DNAs in the experiment. The results showed that our biosensor provided excellent discrimination efficiency toward the perfectly mismatched target DNA with no formation of triplex DNA. We preliminarily deduced the mechanism of the fluorescent reagent for recognizing triplex DNA with high specificity and selectivity.
Collapse
Affiliation(s)
- Zongbao Chen
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China. and Key Laboratory of Applied Organic Chemistry, College of Jiangxi Province Department of Chemistry, Shangrao Normal University, 334001, Jiangxi, China
| | - Huimi Zhang
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China.
| | - Xiaoming Ma
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China.
| | - Zhenyu Lin
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China.
| | - Lan Zhang
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China.
| | - Guonan Chen
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China.
| |
Collapse
|
11
|
Evans K, Bhamra I, Wheelhouse RT, Arnold JRP, Cosstick R, Fisher J. Stabilization of a Bimolecular Triplex by 3'-S-Phosphorothiolate Modifications: An NMR and UV Thermal Melting Investigation. Chemistry 2015; 21:7278-84. [PMID: 25802084 DOI: 10.1002/chem.201500369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 11/08/2022]
Abstract
Triplexes formed from oligonucleic acids are key to a number of biological processes. They have attracted attention as molecular biology tools and as a result of their relevance in novel therapeutic strategies. The recognition properties of single-stranded nucleic acids are also relevant in third-strand binding. Thus, there has been considerable activity in generating such moieties, referred to as triplex forming oligonucleotides (TFOs). Triplexes, composed of Watson-Crick (W-C) base-paired DNA duplexes and a Hoogsteen base-paired RNA strand, are reported to be more thermodynamically stable than those in which the third strand is DNA. Consequently, synthetic efforts have been focused on developing TFOs with RNA-like structural properties. Here, the structural and stability studies of such a TFO, composed of deoxynucleic acids, but with 3'-S-phosphorothiolate (3'-SP) linkages at two sites is described. The modification results in an increase in triplex melting temperature as determined by UV absorption measurements. (1) H NMR analysis and structure generation for the (hairpin) duplex component and the native and modified triplexes revealed that the double helix is not significantly altered by the major groove binding of either TFO. However, the triplex involving the 3'-SP modifications is more compact. The 3'-SP modification was previously shown to stabilise G-quadruplex and i-motif structures and therefore is now proposed as a generic solution to stabilising multi-stranded DNA structures.
Collapse
Affiliation(s)
- Kathryn Evans
- School of Chemistry, University of Leeds, Leeds, LS2 9JT (UK)
| | | | | | | | | | | |
Collapse
|
12
|
Kulyté A, Belarbi Y, Lorente-Cebrián S, Bambace C, Arner E, Daub CO, Hedén P, Rydén M, Mejhert N, Arner P. Additive effects of microRNAs and transcription factors on CCL2 production in human white adipose tissue. Diabetes 2014; 63:1248-58. [PMID: 24379347 DOI: 10.2337/db13-0702] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Adipose tissue inflammation is present in insulin-resistant conditions. We recently proposed a network of microRNAs (miRNAs) and transcription factors (TFs) regulating the production of the proinflammatory chemokine (C-C motif) ligand-2 (CCL2) in adipose tissue. We presently extended and further validated this network and investigated if the circuits controlling CCL2 can interact in human adipocytes and macrophages. The updated subnetwork predicted that miR-126/-193b/-92a control CCL2 production by several TFs, including v-ets erythroblastosis virus E26 oncogene homolog 1 (avian) (ETS1), MYC-associated factor X (MAX), and specificity protein 12 (SP1). This was confirmed in human adipocytes by the observation that gene silencing of ETS1, MAX, or SP1 attenuated CCL2 production. Combined gene silencing of ETS1 and MAX resulted in an additive reduction in CCL2 production. Moreover, overexpression of miR-126/-193b/-92a in different pairwise combinations reduced CCL2 secretion more efficiently than either miRNA alone. However, although effects on CCL2 secretion by co-overexpression of miR-92a/-193b and miR-92a/-126 were additive in adipocytes, the combination of miR-126/-193b was primarily additive in macrophages. Signals for miR-92a and -193b converged on the nuclear factor-κB pathway. In conclusion, TF and miRNA-mediated regulation of CCL2 production is additive and partly relayed by cell-specific networks in human adipose tissue that may be important for the development of insulin resistance/type 2 diabetes.
Collapse
Affiliation(s)
- Agné Kulyté
- Department of Medicine, Huddinge, Lipid Laboratory, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Findlay VJ, LaRue AC, Turner DP, Watson PM, Watson DK. Understanding the role of ETS-mediated gene regulation in complex biological processes. Adv Cancer Res 2014; 119:1-61. [PMID: 23870508 DOI: 10.1016/b978-0-12-407190-2.00001-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ets factors are members of one of the largest families of evolutionarily conserved transcription factors, regulating critical functions in normal cell homeostasis, which when perturbed contribute to tumor progression. The well-documented alterations in ETS factor expression and function during cancer progression result in pleiotropic effects manifested by the downstream effect on their target genes. Multiple ETS factors bind to the same regulatory sites present on target genes, suggesting redundant or competitive functions. The anti- and prometastatic signatures obtained by examining specific ETS regulatory networks will significantly improve our ability to accurately predict tumor progression and advance our understanding of gene regulation in cancer. Coordination of multiple ETS gene functions also mediates interactions between tumor and stromal cells and thus contributes to the cancer phenotype. As such, these new insights may provide a novel view of the ETS gene family as well as a focal point for studying the complex biological control involved in tumor progression. One of the goals of molecular biology is to elucidate the mechanisms that contribute to the development and progression of cancer. Such an understanding of the molecular basis of cancer will provide new possibilities for: (1) earlier detection, as well as better diagnosis and staging of disease; (2) detection of minimal residual disease recurrences and evaluation of response to therapy; (3) prevention; and (4) novel treatment strategies. Increased understanding of ETS-regulated biological pathways will directly impact these areas.
Collapse
Affiliation(s)
- Victoria J Findlay
- Department of Pathology and Laboratory Medicine, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA
| | | | | | | | | |
Collapse
|
14
|
Bhowmik D, Buzzetti F, Fiorillo G, Lombardi P, Suresh Kumar G. Spectroscopic studies on the binding interaction of novel 13-phenylalkyl analogs of the natural alkaloid berberine to nucleic acid triplexes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 120:257-264. [PMID: 24184628 DOI: 10.1016/j.saa.2013.09.081] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/13/2013] [Accepted: 09/25/2013] [Indexed: 06/02/2023]
Abstract
In this study we have characterized the capability of six 13-phenylalkyl analogs of berberine to stabilize nucleic acid triplex structures, poly(rA)⋅2poly(rU) and poly(dA)⋅2poly(dT). Berberine analogs bind to the RNA and DNA triplexes non-cooperatively. As the chain length of the substitution increased beyond CH2, the affinity enhanced up to critical length of (CH2)4, there after which the binding affinity decreased for both the triplexes. A remarkably stronger intercalative binding of the analogs compared to berberine to the triplexes was confirmed from ferrocyanide fluorescence quenching, fluorescence polarization and viscosity results. Circular dichroism results had indicated strong conformational changes in the triplexes on binding of the analogs. The analogs enhanced the stability of the Hoogsteen base paired third strand of both the triplexes while no significant change in the high-temperature duplex-to-single strand transitions was observed. Energetics of the interaction revealed that as the alkyl chain length increased, the binding was more entropy driven. This study demonstrates that phenylalkyl substitution at the 13-position of berberine increased the triplex binding affinity of berberine but a threshold length of the side chain is critical for the strong intercalative binding to occur.
Collapse
Affiliation(s)
- Debipreeta Bhowmik
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR - Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Franco Buzzetti
- Naxopharma srl, Via G. Di Vittorio, 70, 20026 Novate Milanese (MI), Italy
| | - Gaetano Fiorillo
- Naxopharma srl, Via G. Di Vittorio, 70, 20026 Novate Milanese (MI), Italy
| | - Paolo Lombardi
- Naxopharma srl, Via G. Di Vittorio, 70, 20026 Novate Milanese (MI), Italy
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR - Indian Institute of Chemical Biology, Kolkata 700 032, India.
| |
Collapse
|
15
|
Bhowmik D, Kumar GS. Interaction of 9-O-(ω-amino) alkyl ether berberine analogs with poly(dT)·poly(dA)*poly(dT) triplex and poly(dA)·poly(dT) duplex: a comparative study. Mol Biol Rep 2013; 40:5439-50. [PMID: 23666107 DOI: 10.1007/s11033-013-2642-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 05/03/2013] [Indexed: 10/26/2022]
Abstract
Isoquinoline alkaloids and their analogs represent an important class of molecules for their broad range of clinical and pharmacological utility. These compounds are of current interest owing to their low toxicity and excellent chemo preventive properties. These alkaloids can play important role in stabilising the nucleic acid triple helices. The present study has focused on the interaction of five 9-O-(ω-amino) alkyl ether berberine analogs with the DNA triplex poly(dT)·poly(dA)*poly(dT) and the parent duplex poly(dA)·poly(dT) studied using various biophysical techniques. Scatchard analysis of the spectral data indicated that the analogs bind both to the duplex and triplex in a non-cooperative manner in contrast to the cooperative binding of berberine to the DNA triplex. Strong intercalative binding to the DNA triplex structure was revealed from ferrocyanide quenching, fluorescence polarization and viscosity results. Thermal melting studies demonstrated higher stabilization of the Hoogsteen base paired third strand of the DNA triplex compared to the Watson-Crick strand. Circular dichroism studies suggested a stronger perturbation of the DNA triplex conformation by the alkaloid analogs compared to the duplex. The binding was entropy-driven in each case and the entropy contribution to free energy increased as the length of the alkyl side chain increased. The analogs exhibited stronger binding affinity to the triple helical structure compared to the parent double helical structure.
Collapse
Affiliation(s)
- Debipreeta Bhowmik
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700 032, India
| | | |
Collapse
|
16
|
Biomaterial-Based Vectors for Targeted Delivery of Nucleic Acids to the Nervous System. DRUG DELIVERY SYSTEMS: ADVANCED TECHNOLOGIES POTENTIALLY APPLICABLE IN PERSONALISED TREATMENT 2013. [DOI: 10.1007/978-94-007-6010-3_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
17
|
Papadakis G, Gizeli E. In silico search of DNA drugs targeting oncogenes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012; 9:1826-1830. [PMID: 23221090 DOI: 10.1109/tcbb.2012.127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Triplex forming oligonucleotides (TFOs) represent a class of drug candidates for antigene therapy. Based on strict criteria, we investigated the potential of 25 known oncogenes to be regulated by TFOs in the mRNA synthesis level and we report specific target sequences found in seven of these genes.
Collapse
Affiliation(s)
- George Papadakis
- Department of Biology, University of Crete and Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology Hellas (FORTH), 100 Nikolaou Plastira str, Heraklion 70013, Greece.
| | | |
Collapse
|
18
|
Govan JM, Uprety R, Hemphill J, Lively MO, Deiters A. Regulation of transcription through light-activation and light-deactivation of triplex-forming oligonucleotides in mammalian cells. ACS Chem Biol 2012; 7:1247-56. [PMID: 22540192 DOI: 10.1021/cb300161r] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Triplex-forming oligonucleotides (TFOs) are efficient tools to regulate gene expression through the inhibition of transcription. Here, nucleobase-caging technology was applied to the temporal regulation of transcription through light-activated TFOs. Through site-specific incorporation of caged thymidine nucleotides, the TFO:DNA triplex formation is blocked, rendering the TFO inactive. However, after a brief UV irradiation, the caging groups are removed, activating the TFO and leading to the inhibition of transcription. Furthermore, the synthesis and site-specific incorporation of caged deoxycytidine nucleotides within TFO inhibitor sequences was developed, allowing for the light-deactivation of TFO function and thus photochemical activation of gene expression. After UV-induced removal of the caging groups, the TFO forms a DNA dumbbell structure, rendering it inactive, releasing it from the DNA, and activating transcription. These are the first examples of light-regulated TFOs and their application in the photochemical activation and deactivation of gene expression. In addition, hairpin loop structures were found to significantly increase the efficacy of phosphodiester DNA-based TFOs in tissue culture.
Collapse
Affiliation(s)
- Jeane M. Govan
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
| | - Rajendra Uprety
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
| | - James Hemphill
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
| | - Mark O. Lively
- Center
for Structural Biology, Wake Forest University School of Medicine, Winston-Salem,
North Carolina 27157, United States
| | - Alexander Deiters
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
| |
Collapse
|
19
|
Buske FA, Mattick JS, Bailey TL. Potential in vivo roles of nucleic acid triple-helices. RNA Biol 2011; 8:427-39. [PMID: 21525785 DOI: 10.4161/rna.8.3.14999] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The ability of double-stranded DNA to form a triple-helical structure by hydrogen bonding with a third strand is well established, but the biological functions of these structures remain largely unknown. There is considerable albeit circumstantial evidence for the existence of nucleic triplexes in vivo and their potential participation in a variety of biological processes including chromatin organization, DNA repair, transcriptional regulation, and RNA processing has been investigated in a number of studies to date. There is also a range of possible mechanisms to regulate triplex formation through differential expression of triplex-forming RNAs, alteration of chromatin accessibility, sequence unwinding and nucleotide modifications. With the advent of next generation sequencing technology combined with targeted approaches to isolate triplexes, it is now possible to survey triplex formation with respect to their genomic context, abundance and dynamical changes during differentiation and development, which may open up new vistas in understanding genome biology and gene regulation.
Collapse
Affiliation(s)
- Fabian A Buske
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD Australia
| | | | | |
Collapse
|
20
|
Triplex-forming MicroRNAs form stable complexes with HIV-1 provirus and inhibit its replication. Appl Immunohistochem Mol Morphol 2011; 18:532-45. [PMID: 20502318 DOI: 10.1097/pai.0b013e3181e1ef6a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND One of the most fascinating discoveries in biology in recent years is unquestionably the identification of the family of small, noncoding RNAs known as microRNAs (miRNAs). Each miRNA targets multiple mRNA species through recognition of complementary sequences, typically located at multiple sites within the 3 untranslated region. In animals, single-stranded miRNA binds specific messenger RNA (mRNA) by a mechanism that is yet to be fully characterized. The bound mRNA remains untranslated resulting in reduced levels of the corresponding protein; however, if the sequence match between the miRNA and its target is precise, the bound mRNA can be degraded resulting in reduced levels of the corresponding transcript. Eukaryotic genes are also regulated by triplex formation between double helix and a third small RNA or DNA molecule. Thousands of triplex-forming (TF) islands in human genomes are mapped. However, the role of TF miRNAs within the hairpin structures of miRNA and the target mRNA has not been reported. We have explored TF complexes between human miRNAs (hsa-miR) that are complementary to human immunodeficiency virus (HIV)-1 and their antiviral potential as therapeutic agents. METHODS We downloaded mature miRNA sequences from the human miRBase Sequence Database (http://microrna.sanger.ac.uk/sequences/), and computationally analyzed miRNAs that have significant homologies to HIV-1 genome (pNL 4-3 Accession #AF324493). We developed an algorithm to look for triplex-binding motifs (C+CG and T AT) and selected 4 miRNAs with 3 negative controls. TF stability was tested by using fluorophore-labeled duplexes connected by a single hexaethylene glycol moiety, representing HIV-1 proviral motifs, and black-hole quencher-1 labeled oligonucleotides, representing miRNA. RESULTS Fifty miRNAs were discovered that showed greater than 80% homology to HIV-1, of which 4 hsa-miR that exhibited an ability to form stable triplex with double stranded-HIV-1 sequences were selected. Three negative controls were used. The TF stability of the 4 hsa-miRs and the negative controls were confirmed and measured. Stably transfected Hela-CD4+ cell lines expressing each of the hsa-miR were developed. All 4 miRNAs exhibited a significant inhibition of HIV-1 as measured by HIV-1 p24 enzyme-linked immunosorbent assay (>90%; P>0.001) when compared with the 3 negative controls. By using immunohistochemical staining with triplex binding monoclonal antibodies, significant expression of TF miRNAs was detected in the cell lines, but not in the negative controls (P<0.001). CONCLUSIONS In this study, we demonstrated for the first time that besides the well-established post-transcriptional silencing based on mRNA degradation, miRNAs may be responsible for long-term latency of HIV-1 by TF, a different mechanism. We provide a possible molecular mechanism by which HIV-1 homologous miRNAs may impart resistance to HIV-1 and suggest a new miRNA-based therapeutic strategy for HIV-1.
Collapse
|
21
|
Malnuit V, Duca M, Benhida R. Targeting DNA base pair mismatch with artificial nucleobases. Advances and perspectives in triple helix strategy. Org Biomol Chem 2010; 9:326-36. [PMID: 21046036 DOI: 10.1039/c0ob00418a] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This review, divided into three sections, describes the contribution of the chemists' community to the development and application of triple helix strategy by using artificial nucleic acids, particularly for the recognition of DNA sequences incorporating base pair inversions. Firstly, the development of nucleobases that recognise CG inversion is surveyed followed secondly by specific recognition of TA inverted base pair. Finally, we point out in the last section recent perspectives and applications, driven from knowledge in nucleic acids interactions, in the growing field of nanotechnology and supramolecular chemistry at the border area of physics, chemistry and molecular biology.
Collapse
Affiliation(s)
- Vincent Malnuit
- Laboratoire de Chimie des Molécules Bioactives et des Arômes, LCMBA, UMR 6001, Institut de Chimie de Nice, Université de Nice Sophia Antipolis, Parc Valrose, 06108 Nice Cedex 2, France
| | | | | |
Collapse
|
22
|
Srisawat C, Engelke DR. Selection of RNA aptamers that bind HIV-1 LTR DNA duplexes: strand invaders. Nucleic Acids Res 2010; 38:8306-15. [PMID: 20693539 PMCID: PMC3001068 DOI: 10.1093/nar/gkq696] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
RNA that can specifically bind to double-stranded DNA is of interest because it might be used as a means to regulate transcription of the target genes. To explore possible interactions between RNA and duplex DNA, we selected for RNA aptamers that can bind to the long terminal repeats (LTRs) of human immunodeficiency virus type 1 DNA. The selected aptamers were classified into four major groups based on the consensus sequences, which were found to locate in the non-stem regions of the predicted RNA secondary structures, consistent with roles in target binding. Analysis of the aptamer consensus sequences suggested that the conserved segments could form duplexes via Watson–Crick base-pairing with preferred sequences in one strand of the DNA, assuming the aptamer invaded the duplex. The aptamer binding sites on the LTR were experimentally determined to be located preferentially at these sites near the termini of double-stranded target DNA, despite selection schemes that were designed to minimize preferences for termini. The results presented here show that aptamer RNAs can be selected in vitro that strand-invade at preferred DNA duplex sequences to form stable complexes.
Collapse
Affiliation(s)
- Chatchawan Srisawat
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok 10700, Thailand
| | | |
Collapse
|
23
|
Kunderfranco P, Mello-Grand M, Cangemi R, Pellini S, Mensah A, Albertini V, Malek A, Chiorino G, Catapano CV, Carbone GM. ETS transcription factors control transcription of EZH2 and epigenetic silencing of the tumor suppressor gene Nkx3.1 in prostate cancer. PLoS One 2010; 5:e10547. [PMID: 20479932 PMCID: PMC2866657 DOI: 10.1371/journal.pone.0010547] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 04/12/2010] [Indexed: 12/18/2022] Open
Abstract
Background ETS transcription factors regulate important signaling pathways involved in cell differentiation and development in many tissues and have emerged as important players in prostate cancer. However, the biological impact of ETS factors in prostate tumorigenesis is still debated. Methodology/Principal Findings We performed an analysis of the ETS gene family using microarray data and real-time PCR in normal and tumor tissues along with functional studies in normal and cancer cell lines to understand the impact in prostate tumorigenesis and identify key targets of these transcription factors. We found frequent dysregulation of ETS genes with oncogenic (i.e., ERG and ESE1) and tumor suppressor (i.e., ESE3) properties in prostate tumors compared to normal prostate. Tumor subgroups (i.e., ERGhigh, ESE1high, ESE3low and NoETS tumors) were identified on the basis of their ETS expression status and showed distinct transcriptional and biological features. ERGhigh and ESE3low tumors had the most robust gene signatures with both distinct and overlapping features. Integrating genomic data with functional studies in multiple cell lines, we demonstrated that ERG and ESE3 controlled in opposite direction transcription of the Polycomb Group protein EZH2, a key gene in development, differentiation, stem cell biology and tumorigenesis. We further demonstrated that the prostate-specific tumor suppressor gene Nkx3.1 was controlled by ERG and ESE3 both directly and through induction of EZH2. Conclusions/Significance These findings provide new insights into the role of the ETS transcriptional network in prostate tumorigenesis and uncover previously unrecognized links between aberrant expression of ETS factors, deregulation of epigenetic effectors and silencing of tumor suppressor genes. The link between aberrant ETS activity and epigenetic gene silencing may be relevant for the clinical management of prostate cancer and design of new therapeutic strategies.
Collapse
Affiliation(s)
- Paolo Kunderfranco
- Laboratory of Experimental Oncology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Xi H, Kumar S, Dosen-Micovic L, Arya DP. Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices. Biochimie 2010; 92:514-29. [PMID: 20167243 PMCID: PMC3977217 DOI: 10.1016/j.biochi.2010.02.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2009] [Accepted: 02/08/2010] [Indexed: 11/21/2022]
Abstract
Calorimetric and fluorescence techniques were used to characterize the binding of aminoglycosides-neomycin, paromomycin, and ribostamycin, with 5'-dA(12)-x-dT(12)-x-dT(12)-3' intramolecular DNA triplex (x = hexaethylene glycol) and poly(dA).2poly(dT) triplex. Our results demonstrate the following features: (1) UV thermal analysis reveals that the T(m) for triplex decreases with increasing pH value in the presence of neomycin, while the T(m) for the duplex remains unchanged. (2) The binding affinity of neomycin decreases with increased pH, although there is an increase in observed binding enthalpy. (3) ITC studies conducted in two buffers (sodium cacodylate and MOPS) yield the number of protonated drug amino groups (Deltan) as 0.29 and 0.40 for neomycin and paromomycin interaction with 5'-dA(12)-x-dT(12)-x-dT(12)-3', respectively. (4) The specific heat capacity change (DeltaC(p)) determined by ITC studies is negative, with more negative values at lower salt concentrations. From 100 mM to 250 mM KCl, the DeltaC(p) ranges from -402 to -60 cal/(mol K) for neomycin. At pH 5.5, a more positive DeltaC(p) is observed, with a value of -98 cal/(mol K) at 100 mM KCl. DeltaC(p) is not significantly affected by ionic strength. (5) Salt dependence studies reveal that there are at least three amino groups of neomycin participating in the electrostatic interactions with the triplex. (6) FID studies using thiazole orange were used to derive the AC(50) (aminoglycoside concentration needed to displace 50% of the dye from the triplex) values. Neomycin shows a seven fold higher affinity than paromomycin and eleven fold higher affinity than ribostamycin at pH 6.8. (7) Modeling studies, consistent with UV and ITC results, show the importance of an additional positive charge in triplex recognition by neomycin. The modeling and thermodynamic studies indicate that neomycin binding to the DNA triplex depends upon significant contributions from charge as well as shape complementarity of the drug to the DNA triplex Watson-Hoogsteen groove.
Collapse
Affiliation(s)
- Hongjuan Xi
- Contribution from the Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
| | - Sunil Kumar
- Contribution from the Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
| | - Ljiljana Dosen-Micovic
- Contribution from the Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
| | - Dev P. Arya
- Contribution from the Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
| |
Collapse
|
25
|
Zhu X, Liu Y, Yang J, Liang Z, Li G. Gold nanoparticle-based colorimetric assay of single-nucleotide polymorphism of triplex DNA. Biosens Bioelectron 2010; 25:2135-9. [PMID: 20233656 DOI: 10.1016/j.bios.2010.02.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 02/04/2010] [Accepted: 02/18/2010] [Indexed: 11/26/2022]
Abstract
Triplex DNA technology has been considered as an attractive antigen strategy for the treatment of genetic-based diseases. Assay of the formation of triplex is an important part in the development of triplex technology. In this paper, we present a novel method to assay triplex DNA. The strategy is based on the unspecific interaction between single-stranded triplex-forming oligonucleotide (TFO) and negatively charged gold nanoparticles (AuNPs). While triplex is formed, gold nanoparticles will aggregate without the protection of triplex-forming oligonucleotide under a certain concentration of salt. Consequently, the color of the gold nanoparticles will change from red to blue. The formation of triplex DNA and the discrimination of triplex-forming oligonucleotide candidates are thereby easily monitored by the color changes of gold nanoparticles. Also by precisely controlling the working salt concentration, we are allowed to assay single-nucleotide polymorphism of triplex-forming oligonucleotides. Mismatched variants and length variants of triplex-forming oligonucleotides with single-nucleotide or double-nucleotides differences can be well discriminated. This method presented here is simple, fast, and with considerable selectivity, so we expect it will be a promising candidate for the assay of triplex DNA and the screening of appropriate triplex-forming oligonucleotide.
Collapse
Affiliation(s)
- Xiaoli Zhu
- Laboratory of Biosensing Technology, School of Life Science, Shanghai University, Shanghai 200444, PR China
| | | | | | | | | |
Collapse
|
26
|
Duca M, Vekhoff P, Oussedik K, Halby L, Arimondo PB. The triple helix: 50 years later, the outcome. Nucleic Acids Res 2008; 36:5123-38. [PMID: 18676453 PMCID: PMC2532714 DOI: 10.1093/nar/gkn493] [Citation(s) in RCA: 265] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Triplex-forming oligonucleotides constitute an interesting DNA sequence-specific tool that can be used to target cleaving or cross-linking agents, transcription factors or nucleases to a chosen site on the DNA. They are not only used as biotechnological tools but also to induce modifications on DNA with the aim to control gene expression, such as by site-directed mutagenesis or DNA recombination. Here, we report the state of art of the triplex-based anti-gene strategy 50 years after the discovery of such a structure, and we show the importance of the actual applications and the main challenges that we still have ahead of us.
Collapse
Affiliation(s)
- Maria Duca
- LCMBA CNRS UMR6001, University of Nice-Sophia Antipolis, Parc Valrose, 06108 NICE Cedex 2, France
| | | | | | | | | |
Collapse
|
27
|
Paramasivam M, Cogoi S, Filichev VV, Bomholt N, Pedersen EB, Xodo LE. Purine twisted-intercalating nucleic acids: a new class of anti-gene molecules resistant to potassium-induced aggregation. Nucleic Acids Res 2008; 36:3494-507. [PMID: 18456705 PMCID: PMC2425464 DOI: 10.1093/nar/gkn242] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Sequence-specific targeting of genomic DNA by triplex-forming oligonucleotides (TFOs) is a promising strategy to modulate in vivo gene expression. Triplex formation involving G-rich oligonucleotides as third strand is, however, strongly inhibited by potassium-induced TFO self-association into G-quartet structures. We report here that G-rich TFOs with bulge insertions of (R)-1-O-[4-(1-pyrenylethynyl)-phenylmethyl] glycerol (called twisted intercalating nucleic acids, TINA) show a much lower tendency to aggregate in potassium than wild-type analogues do. We designed purine-motif TINA–TFOs for binding to a regulatory polypurine-polypyrimidine (pur/pyr) motif present in the promoter of the KRAS proto-oncogene. The binding of TINA–TFOs to the KRAS target has been analysed by electrophoresis mobility shift assays and DNase I footprinting experiments. We discovered that in the presence of potassium the wild-type TFOs did not bind to the KRAS target, differently from the TINA analogues, whose binding was observed up to 140 mM KCl. The designed TINA–TFOs were found to abrogate the formation of a DNA–protein complex at the pur/pyr site and to down-regulate the transcription of CAT driven by the murine KRAS promoter. Molecular modelling of the DNA/TINA–TFO triplexes are also reported. This study provides a new and promising approach to create TFOs to target in vivo the genome.
Collapse
|
28
|
Jain A, Wang G, Vasquez KM. DNA triple helices: biological consequences and therapeutic potential. Biochimie 2008; 90:1117-30. [PMID: 18331847 DOI: 10.1016/j.biochi.2008.02.011] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Accepted: 02/08/2008] [Indexed: 01/25/2023]
Abstract
DNA structure is a critical element in determining its function. The DNA molecule is capable of adopting a variety of non-canonical structures, including three-stranded (i.e. triplex) structures, which will be the focus of this review. The ability to selectively modulate the activity of genes is a long-standing goal in molecular medicine. DNA triplex structures, either intermolecular triplexes formed by binding of an exogenously applied oligonucleotide to a target duplex sequence, or naturally occurring intramolecular triplexes (H-DNA) formed at endogenous mirror repeat sequences, present exploitable features that permit site-specific alteration of the genome. These structures can induce transcriptional repression and site-specific mutagenesis or recombination. Triplex-forming oligonucleotides (TFOs) can bind to duplex DNA in a sequence-specific fashion with high affinity, and can be used to direct DNA-modifying agents to selected sequences. H-DNA plays important roles in vivo and is inherently mutagenic and recombinogenic, such that elements of the H-DNA structure may be pharmacologically exploitable. In this review we discuss the biological consequences and therapeutic potential of triple helical DNA structures. We anticipate that the information provided will stimulate further investigations aimed toward improving DNA triplex-related gene targeting strategies for biotechnological and potential clinical applications.
Collapse
Affiliation(s)
- Aklank Jain
- Department of Carcinogenesis, University of Texas, M.D. Anderson Cancer Center, Science Park--Research Division, 1808 Park Road 1-C, P.O. Box 389, Smithville, TX 78957, USA
| | | | | |
Collapse
|
29
|
Turner DP, Watson DK. ETS transcription factors: oncogenes and tumor suppressor genes as therapeutic targets for prostate cancer. Expert Rev Anticancer Ther 2008; 8:33-42. [PMID: 18095881 DOI: 10.1586/14737140.8.1.33] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
ETS factors represent one of the largest families of transcriptional regulators and have known functional roles in many biological processes. Significantly, ETS factors have oncogenic and suppressive activity and their aberrant expression is associated with many of the processes that lead to prostate cancer progression. The targeting of transcription for therapeutic gain has met with some success. Therefore, better understanding the mechanisms that regulate ETS factor activity during both normal and aberrant transcription provides a novel means to identify processes that may be targeted in order to re-establish the normal ETS regulatory networks that are perturbed in cancer. Specific examples of altered ETS factor expression are highlighted, and therapeutic technologies that may be used to target ETS factors and their cofactors and downstream target genes in prostate cancer are discussed.
Collapse
Affiliation(s)
- David P Turner
- Department of Pathology & Laboratory Medicine, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA.
| | | |
Collapse
|
30
|
Rossetti L, D'Isa G, Mauriello C, Varra M, De Santis P, Mayol L, Savino M. A model for triple helix formation on human telomerase reverse transcriptase (hTERT) promoter and stabilization by specific interactions with the water soluble perylene derivative, DAPER. Biophys Chem 2007; 129:70-81. [PMID: 17560709 DOI: 10.1016/j.bpc.2007.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 05/14/2007] [Accepted: 05/14/2007] [Indexed: 01/07/2023]
Abstract
The promoter of human telomerase reverse transcriptase (hTERT) gene, in the region from -1000 to +1, contains two homopurine-homopyrimidine sequences (-835/-814 and -108/-90), that can be considered as potential targets to triple helix forming oligonucleotides (TFOs) for applying antigene strategy. We have chosen the sequence (-108/-90) on the basis of its unfavorable chromatin organization, evaluated by theoretical nucleosome positioning and nuclease hypersensitive sites mapping. On this sequence, anti-parallel triplex with satisfactory thermodynamic stability is formed by two TFOs, having different lengths. Triplex stability is significantly increased by specific interactions with the perylene derivative N,N'-bis[3,3'-(dimethylamino) propylamine]-3,4,9,10-perylenetetracarboxylic diimide (DAPER). Since DAPER is a symmetric molecule, the induced Circular Dichroism (CD) spectra in the range 400-600 nm allows us to obtain information on drug binding to triplex and duplex DNA. The drug-induced ellipticity is significantly higher in the case of triplex with respect to duplex and, surprisingly, it increases at decreasing of DNA. A model is proposed where self-stacked DAPER binds to triplex or to duplex narrow grooves.
Collapse
Affiliation(s)
- Luigi Rossetti
- Dipartimento di Genetica e Biologia Molecolare, Università di Roma La Sapienza, Piazzale Aldo Moro, 5, c.a.p. 00185, Roma, Italy
| | | | | | | | | | | | | |
Collapse
|
31
|
Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 2007; 445:666-70. [PMID: 17237763 DOI: 10.1038/nature05519] [Citation(s) in RCA: 579] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Accepted: 12/08/2006] [Indexed: 12/15/2022]
Abstract
Alternative promoters within the same gene are a general phenomenon in gene expression. Mechanisms of their selective regulation vary from one gene to another and are still poorly understood. Here we show that in quiescent cells the mechanism of transcriptional repression of the major promoter of the gene encoding dihydrofolate reductase depends on a non-coding transcript initiated from the upstream minor promoter and involves both the direct interaction of the RNA and promoter-specific interference. The specificity and efficiency of repression is ensured by the formation of a stable complex between non-coding RNA and the major promoter, direct interaction of the non-coding RNA with the general transcription factor IIB and dissociation of the preinitiation complex from the major promoter. By using in vivo and in vitro assays such as inducible and reconstituted transcription, RNA bandshifts, RNA interference, chromatin immunoprecipitation and RNA immunoprecipitation, we show that the regulatory transcript produced from the minor promoter has a critical function in an epigenetic mechanism of promoter-specific transcriptional repression.
Collapse
Affiliation(s)
- Igor Martianov
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | | | | | | | | |
Collapse
|
32
|
Daunomycin-TFO Conjugates for Downregulation of Gene Expression. Top Curr Chem (Cham) 2007; 283:45-71. [DOI: 10.1007/128_2007_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
33
|
Yoshimoto M, Ludkovski O, Bayani J, Graham C, Zielenska M, Squire JA. Microdeletion and concurrent translocation associated with a complexTMPRSS2:ERG prostate cancer gene fusion. Genes Chromosomes Cancer 2007; 46:861-3. [PMID: 17584912 DOI: 10.1002/gcc.20470] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
|
34
|
Albertini V, Jain A, Vignati S, Napoli S, Rinaldi A, Kwee I, Nur-e-Alam M, Bergant J, Bertoni F, Carbone GM, Rohr J, Catapano CV. Novel GC-rich DNA-binding compound produced by a genetically engineered mutant of the mithramycin producer Streptomyces argillaceus exhibits improved transcriptional repressor activity: implications for cancer therapy. Nucleic Acids Res 2006; 34:1721-34. [PMID: 16571899 PMCID: PMC1420802 DOI: 10.1093/nar/gkl063] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The aureolic acid antibiotic mithramycin (MTM) binds selectively to GC-rich DNA sequences and blocks preferentially binding of proteins, like Sp1 transcription factors, to GC-rich elements in gene promoters. Genetic approaches can be applied to alter the MTM biosynthetic pathway in the producing microorganism and obtain new products with improved pharmacological properties. Here, we report on a new analog, MTM SDK, obtained by targeted gene inactivation of the ketoreductase MtmW catalyzing the last step in MTM biosynthesis. SDK exhibited greater activity as transcriptional inhibitor compared to MTM. SDK was a potent inhibitor of Sp1-dependent reporter activity and interfered minimally with reporters of other transcription factors, indicating that it retained a high degree of selectivity toward GC-rich DNA-binding transcription factors. RT-PCR and microarray analysis showed that SDK repressed transcription of multiple genes implicated in critical aspects of cancer development and progression, including cell cycle, apoptosis, migration, invasion and angiogenesis, consistent with the pleiotropic role of Sp1 family transcription factors. SDK inhibited proliferation and was a potent inducer of apoptosis in ovarian cancer cells while it had minimal effects on viability of normal cells. The new MTM derivative SDK could be an effective agent for treatment of cancer and other diseases with abnormal expression or activity of GC-rich DNA-binding transcription factors.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Mohammad Nur-e-Alam
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky725 Rose Street, Lexington, KY 40536-0082, USA
| | - Julia Bergant
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky725 Rose Street, Lexington, KY 40536-0082, USA
| | | | | | - Jürgen Rohr
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky725 Rose Street, Lexington, KY 40536-0082, USA
- To whom correspondence should be addressed. Tel: +41 91 820 0365; Fax: +41 91 820 0397;
| | - Carlo V. Catapano
- To whom correspondence should be addressed. Tel: +41 91 820 0365; Fax: +41 91 820 0397;
| |
Collapse
|
35
|
Napoli S, Carbone GM, Catapano CV, Shaw N, Arya DP. Neomycin improves cationic lipid-mediated transfection of DNA in human cells. Bioorg Med Chem Lett 2005; 15:3467-9. [PMID: 15950473 DOI: 10.1016/j.bmcl.2005.04.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2005] [Revised: 04/20/2005] [Accepted: 04/21/2005] [Indexed: 11/18/2022]
Abstract
Delivery of oligonucleotides has been a major impediment in the development of nucleic acid based drugs. In this report, we show that neomycin, an aminoglycoside antibiotic, when combined with a cationic lipid preparation such as DOTAP, enhances transfection efficiency of both reporter plasmids and oligonucleotides and results in a significant increase in transgene expression. The results described here open a new lead in ongoing efforts for oligonucleotide delivery.
Collapse
Affiliation(s)
- Sara Napoli
- Laboratory of Experimental Oncology, Oncology Institute of Southern Switzerland (IOSI) Via Vela 6, 6500 Bellinzona, Switzerland
| | | | | | | | | |
Collapse
|
36
|
DiPaolo JA, Alvarez-Salas LM. Advances in the development of therapeutic nucleic acids against cervical cancer. Expert Opin Biol Ther 2005; 4:1251-64. [PMID: 15268660 DOI: 10.1517/14712598.4.8.1251] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cervical cancer is the second most common neoplastic disease affecting women worldwide. Basic, clinical and epidemiological analyses indicate that expression of high-risk human papillomaviruses (HPVs) E6/E7 genes is the primary cause of cervical cancer and represent ideal targets for the application of therapeutic nucleic acids (TNAs). Antisense oligodeoxyribonucleotides (AS-ODNs) and ribozymes (RZs) are the most effective TNAs able to inhibit in vivo tumour growth by eliminating HPV-16 and HPV-18 E6/E7 transcripts. Expression of multiple RZs directed against alternative target sites by triplex expression systems may result in the abrogation of highly variable HPVs. More recently, RNA interference (RNAi) gene knockdown phenomenon, induced by small interfering RNA (siRNA), has demonstrated its potential value as an effective TNA for cervical cancer. siRNA and aptamers as TNAs will have a place in the armament for cervical cancer. TNAs against cervical cancer is in a dynamic state, and clinical trials will define the TNAs in preventive and therapeutic roles to control tumour growth, debulk tumour mass, prevent metastasis and facilitate immune interaction.
Collapse
MESH Headings
- Female
- Gene Expression Regulation, Neoplastic
- Gene Expression Regulation, Viral
- Gene Targeting
- Genetic Therapy
- Humans
- Nucleic Acid Conformation
- Nucleic Acids/administration & dosage
- Nucleic Acids/genetics
- Nucleic Acids/therapeutic use
- Oligodeoxyribonucleotides, Antisense/administration & dosage
- Oligodeoxyribonucleotides, Antisense/genetics
- Oligodeoxyribonucleotides, Antisense/therapeutic use
- Oncogene Proteins, Viral/antagonists & inhibitors
- Oncogene Proteins, Viral/genetics
- Oncogene Proteins, Viral/physiology
- Papillomaviridae/genetics
- Papillomaviridae/pathogenicity
- Papillomavirus Infections/genetics
- Papillomavirus Infections/therapy
- RNA Interference
- RNA, Catalytic/administration & dosage
- RNA, Catalytic/genetics
- RNA, Catalytic/therapeutic use
- RNA, Small Interfering/administration & dosage
- RNA, Small Interfering/genetics
- RNA, Small Interfering/therapeutic use
- Uterine Cervical Neoplasms/genetics
- Uterine Cervical Neoplasms/therapy
- Uterine Cervical Neoplasms/virology
Collapse
Affiliation(s)
- Joseph A DiPaolo
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20894, USA.
| | | |
Collapse
|
37
|
Ziemba AJ, Zhilina ZV, Krotova-Khan Y, Stankova L, Ebbinghaus SW. Targeting and regulation of the HER-2/neu oncogene promoter with bis-peptide nucleic acids. Oligonucleotides 2005; 15:36-50. [PMID: 15788899 DOI: 10.1089/oli.2005.15.36] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Antigene oligonucleotides have the potential to regulate gene expression through site-specific DNA binding. However, in vivo applications have been hindered by inefficient cellular uptake, degradation, and strand displacement. Peptide nucleic acids (PNAs) address several of these problems, as they are resistant to degradation and bind DNA with high affinity. We designed two cationic pyrimidine bis-PNAs (cpy-PNAs) to target the polypurine tract of the HER-2/neu promoter and compared them to an unmodified phosphodiester triplex-forming oligonucleotide (TFO1) and a TFO-nitrogen mustard conjugate (TFO2). PNA1 contains a + 2 charge and bound two adjacent 9-bp target sequences with high affinity and specificity, but only at low pH. PNA2 contains a +5 charge and bound one 11-bp target with high affinity up to pH 7.4, but with lower specificity. The PNA:DNA:PNA triplex formed by these cpy-bis-PNAs presented a stable barrier to DNA polymerase extension. The cpy-bis-PNAs and the TFO-alkylator conjugate prevented HER-2/neu transcription in a reporter gene assay (TFO2 = PNA1 > PNA2 >> TFO1). Both PNAs and TFOs were effective at binding the target sequence in naked genomic DNA, but only the TFO-alkylator (TFO2) and the more cationic PNA (PNA2) were detected at the endogenous HER-2/neu promoter in permeabilized cells. This work demonstrates the potential for preventing HER-2/neu gene expression with cpy-bis-PNAs in tumor cells.
Collapse
|
38
|
Thenmalarchelvi R, Yathindra N. New insights into DNA triplexes: residual twist and radial difference as measures of base triplet non-isomorphism and their implication to sequence-dependent non-uniform DNA triplex. Nucleic Acids Res 2005; 33:43-55. [PMID: 15657986 PMCID: PMC546132 DOI: 10.1093/nar/gki143] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2004] [Revised: 11/19/2004] [Accepted: 12/02/2004] [Indexed: 11/29/2022] Open
Abstract
DNA triplexes are formed by both isomorphic (structurally alike) and non-isomorphic (structurally dissimilar) base triplets. It is espoused here that (i) the base triplet non-isomorphism may be articulated in structural terms by a residual twist (Delta(t) degrees), the angle formed by line joining the C1'...C1' atoms of the adjacent Hoogsteen or reverse Hoogsteen (RH) base pairs and the difference in base triplet radius (Delta(r) A), and (ii) their influence on DNA triplex is largely mechanistic, leading to the prediction of a high (t + Delta(t))degrees and low (t - Deltat)degrees twist at the successive steps of Hoogsteen or RH duplex of a parallel or antiparallel triplex. Efficacy of this concept is corroborated by molecular dynamics (MD) simulation of an antiparallel DNA triplex comprising alternating non-isomorphic G*GC and T*AT triplets. Conformational changes necessitated by base triplet non-isomorphism are found to induce an alternating (i) high anti and anti glycosyl and (ii) BII and an unusual BIII conformation resulting in a zigzag backbone for the RH strand. Thus, base triplet non-isomorphism causes DNA triplexes into exhibiting sequence-dependent non-uniform conformation. Such structural variations may be relevant in deciphering the specificity of interaction with DNA triplex binding proteins. Seemingly then, residual twist (Delta(t) degrees) and radial difference (Deltar A) suffice as indices to define and monitor the effect of base triplet non-isomorphism in nucleic acid triplexes.
Collapse
Affiliation(s)
- R. Thenmalarchelvi
- Department of Crystallography and Biophysics, University of MadrasGuindy Campus, Chennai 600 025, India
| | - N. Yathindra
- Department of Crystallography and Biophysics, University of MadrasGuindy Campus, Chennai 600 025, India
| |
Collapse
|
39
|
Nagatsugi F, Sasaki S. Chemical tools for targeted mutagenesis of DNA based on triple helix formation. Biol Pharm Bull 2004; 27:463-7. [PMID: 15056848 DOI: 10.1248/bpb.27.463] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The development of methods for targeted mutagenesis shows promise as an alternative form of gene therapy. Triple helix-forming oligonucleotides (TFOs) provide an attractive strategy for inducing mutations. Especially, alkylation of nucleobases with functionalized TFOs would have potential for site-directed mutation. Several studies have demonstrated that treatment of mammalian cells with TFOs can be exploited to introduce desired sequence changes and point mutations. This review summarizes targeted mutagenesis using reactive TFOs, including studies with photo reactive psolaren derivatives as well as a new reactive derivative recently developed by our group.
Collapse
Affiliation(s)
- Fumi Nagatsugi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | | |
Collapse
|
40
|
Bello-Roufaï M, Roulon T, Escudé C. Ligand-mediated transcription elongation control using triplex-based padlock oligonucleotides. ACTA ACUST UNITED AC 2004; 11:509-16. [PMID: 15123245 DOI: 10.1016/j.chembiol.2004.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2003] [Revised: 01/08/2004] [Accepted: 01/14/2004] [Indexed: 11/16/2022]
Abstract
Triplex-forming oligonucleotides (TFOs) provide useful tools for the artificial regulation of gene expression at the transcriptional level. They can become topologically linked to their DNA target upon circularization, thereby forming very stable triple helical structures. These "padlock oligonucleotides" are able to interfere with transcription elongation when their target site is located in the transcribed region of a gene. In vitro transcription experiments showed that a bacterial RNA polymerase was stopped at the site of triple-helix formation, whereas expression of a reporter gene was inhibited in live cells. In both cases, the padlock oligonucleotide was more efficient at inhibiting transcription elongation than a linear TFO, and the inhibition was observed only in the presence of a triplex stabilizing agent. These results provide new insights into the ligand-modulated locking of padlock oligonucleotides around their DNA target.
Collapse
Affiliation(s)
- Mahajoub Bello-Roufaï
- Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, INSERM U565, CNRS UMR5153, 43 rue Cuvier, 75231 Paris Cedex 05, France
| | | | | |
Collapse
|
41
|
Carbone GM, Napoli S, Valentini A, Cavalli F, Watson DK, Catapano CV. Triplex DNA-mediated downregulation of Ets2 expression results in growth inhibition and apoptosis in human prostate cancer cells. Nucleic Acids Res 2004; 32:4358-67. [PMID: 15314206 PMCID: PMC514370 DOI: 10.1093/nar/gkh744] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Ets2 is a member of the Ets family of transcription factors that in humans comprise 25 distinct members. Various Ets-domain transcription factors have been implicated in cancer development. Ets2 is expressed in prostate and breast cancer cells and is thought to have a role in promoting growth and survival in these cell types. However, a definitive role and the mechanisms whereby Ets2 acts in cancer cells are still unclear. Structural and functional similarities as well as overlapping DNA binding specificities complicate the identification of the specific roles of the various Ets factors. In this study, we used a triplex-forming oligonucleotide (TFO) to selectively inhibit Ets2 transcription in prostate cancer cells. We had previously shown that the Ets2-targeting TFO, which was directed to a unique purine-rich sequence critical for Ets2 promoter activity, acted with a high degree of sequence-specificity and target selectivity. TFO-mediated downregulation of Ets2 in prostate cancer cells induced important phenotypic changes, including inhibition of anchorage-dependent and anchorage -independent growth, cell cycle alterations and induction of apoptotic cell death. Expression of Ets2 under the control of a heterologous promoter abolished the anti-proliferative effects of the TFO in both short- and long-term assays, suggesting that these effects were a direct result of downregulation of Ets2 transcription and confirming target selectivity of the TFO. Furthermore, normal human fibroblasts, which expressed low levels of Ets2, were not affected by the Ets2-targeting TFO. Downregulation of Ets2 in prostate cancer cells was associated with reduced levels of the anti-apoptotic protein bcl-x(L) and growth regulatory factors cyclin D1 and c-myc. These data revealed a specific role of this transcription factor in promoting growth and survival of prostate cancer cells. Furthermore, the activity and selectivity of the Ets2-targeting TFO suggest that it might represent a valid approach to prostate cancer therapy.
Collapse
Affiliation(s)
- Giuseppina M Carbone
- Laboratory of Experimental Oncology, Oncology Institute of Southern Switzerland, Via Vela 6, 6500 Bellinzona, Switzerland.
| | | | | | | | | | | |
Collapse
|
42
|
Abstract
Prostate cancer is one of the commonest causes of illness and death from cancer. Radical prostatectomy, radiotherapy, and hormonal therapy are the main conventional treatments. However, gene therapy is emerging as a promising adjuvant to conventional strategies, and several clinical trials are in progress. Here, we outline several approaches to gene therapy for prostate cancer that have been investigated. Methods of gene delivery are described, particularly those that have commonly been used in research on prostate cancer. We discuss efforts to achieve tissue-specific gene delivery, focusing on the use of tissue-specific gene promoters. Finally, the present use of gene therapy for prostate cancer is evaluated. The ability to deliver gene-therapy vectors directly to prostate tissue, and to regulate gene expression in a tissue-specific manner, offers promise for the use of gene therapy in prostate cancer.
Collapse
Affiliation(s)
- Ruth Foley
- Department of Haematology and Oncology, Institute of Molecular Medicine, St James' Hospital and Trinity College, Dublin, Ireland
| | | | | |
Collapse
|
43
|
Besch R, Marschall C, Schuh T, Giovannangeli C, Kammerbauer C, Degitz K. Triple helix-mediated inhibition of gene expression is increased by PUVA. J Invest Dermatol 2004; 122:1114-20. [PMID: 15140212 DOI: 10.1111/j.0022-202x.2004.22521.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The combination of psoralens with UVA is used as PUVA therapy for psoriasis and other skin diseases. UVA-induced psoralen/DNA photoadducts act via suppression of DNA replication and cell proliferation, but do not sufficiently repress gene transcription. To explore whether PUVA may also be used for gene repression, psoralen was conjugated to a triplex-forming oligonucleotide (TFO) that targets a gene sequence of ICAM-1, a key molecule in cutaneous inflammation. Triplex formation between TFO and target sequence was detected by non-denaturing gel electrophoresis. UVA-irradiation induced psoralen cross-links at the triplex-duplex junction as verified by denaturing gel electrophoresis. When the target sequence was placed within the transcribed portion of the chloramphenicol acetyltransferase (CAT) gene, TFO inhibited CAT expression in A431 cells. Inhibition was sequence-specific, since a scrambled control oligonucleotide or mismatched or scrambled target sequences failed to inhibit CAT expression. Inhibition was not significant without UVA exposure, but was strongly enhanced by PUVA-mediated cross-links at the TFO target site. These results suggest that TFO may add a new quality to PUVA therapy by transcriptionally repressing pathogenically relevant genes, in addition to antiproliferative PUVA effects. TFO designed to repress only after PUVA activation may allow the development of a cutaneous organ specific strategy for gene repression.
Collapse
Affiliation(s)
- Robert Besch
- Department of Dermatology, Ludwig-Maximilians University, München, Germany
| | | | | | | | | | | |
Collapse
|
44
|
Carbone GM, McGuffie E, Napoli S, Flanagan CE, Dembech C, Negri U, Arcamone F, Capobianco ML, Catapano CV. DNA binding and antigene activity of a daunomycin-conjugated triplex-forming oligonucleotide targeting the P2 promoter of the human c-myc gene. Nucleic Acids Res 2004; 32:2396-410. [PMID: 15121897 PMCID: PMC419437 DOI: 10.1093/nar/gkh527] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Triplex-forming oligonucleotides (TFO) that bind DNA in a sequence-specific manner might be used as selective repressors of gene expression and gene-targeted therapeutics. However, many factors, including instability of triple helical complexes in cells, limit the efficacy of this approach. In the present study, we tested whether covalent linkage of a TFO to daunomycin, which is a potent DNA-intercalating agent and anticancer drug, could increase stability of the triple helix and activity of the oligonucleotide in cells. The 11mer daunomycin-conjugated GT (dauno-GT11) TFO targeted a sequence upstream of the P2 promoter, a site known to be critical for transcription of the c-myc gene. Band-shift assays showed that the dauno-GT11 formed triplex DNA with enhanced stability compared to the unmodified TFO. Band shift and footprinting experiments demonstrated that binding of dauno-GT11 was highly sequence-specific with exclusive binding to the 11 bp target site in the c-myc promoter. The daunomycin-conjugated TFO inhibited transcription in vitro and reduced c-myc promoter activity in prostate and breast cancer cells. The daunomycin-conjugated TFO was taken up by cells with a distinctive intracellular distribution compared to free daunomycin. However, cationic lipid-mediated delivery was required for enhanced cellular uptake, nuclear localization and biological activity of the TFO in cells. Dauno-GT11 reduced transcription of the endogenous c-myc gene in cells, but did not affect expression of non-target genes, such as ets-1 and ets-2, which contained very similar target sequences in their promoters. Daunomycin-conjugated control oligonucleotides unable to form triplex DNA with the target sequence did not have any effect in these assays, indicating that daunomycin was not directly responsible for the activity of daunomycin-conjugated TFO. Thus, attachment of daunomycin resulted in increased triplex stability and biological activity of the 11mer GT-rich TFO without compromising its specificity. These results encourage further testing of this approach to develop novel antigene therapeutics.
Collapse
Affiliation(s)
- Giuseppina M Carbone
- Laboratory of Experimental Oncology, Oncology Institute of Southern Switzerland, Bellinzona, Via Vela 6, 6500 Bellinzona, Switzerland
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Uil TG, Haisma HJ, Rots MG. Therapeutic modulation of endogenous gene function by agents with designed DNA-sequence specificities. Nucleic Acids Res 2003; 31:6064-78. [PMID: 14576293 PMCID: PMC275457 DOI: 10.1093/nar/gkg815] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Designer molecules that can specifically target pre-determined DNA sequences provide a means to modulate endogenous gene function. Different classes of sequence-specific DNA-binding agents have been developed, including triplex-forming molecules, synthetic polyamides and designer zinc finger proteins. These different types of designer molecules with their different principles of engineered sequence specificity are reviewed in this paper. Furthermore, we explore and discuss the potential of these molecules as therapeutic modulators of endogenous gene function, focusing on modulation by stable gene modification and by regulation of gene transcription.
Collapse
Affiliation(s)
- Taco G Uil
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | |
Collapse
|
46
|
Affiliation(s)
- Scot W Ebbinghaus
- Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, AZ 85724, USA
| |
Collapse
|
47
|
Cassidy RA, Puri N, Miller PS. Effect of DNA target sequence on triplex formation by oligo-2'-deoxy- and 2'-O-methylribonucleotides. Nucleic Acids Res 2003; 31:4099-108. [PMID: 12853627 PMCID: PMC165951 DOI: 10.1093/nar/gkg436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The interactions of pyrimidine deoxyribo- or 2'-O-methylribo-psoralen-conjugated, triplex-forming oligonucleotides, psTFOs, with a 17-bp env-DNA whose purine tract is 5'-AGAGAGAAAAAAGAG-3', or an 18-bp gag-DNA whose purine tract is 5'-AGG GGGAAAGAAAAAA-3', were studied over the pH range 6.0-7.5. The stability of the triplex formed by a deoxy-env-psTFO containing 5-methylcytosines and thymines decreased with increasing pH (T(m) = 56 degrees C at pH 6.0; 27 degrees C at pH 7.5). Replacement of 5-methylcytosines with 8-oxo-adenines reduced the pH dependence, but lowered triplex stability. A 2'-O-methyl-env-psTFO containing uracil and cytosine did not form a triplex at pH 7.5. Surprisingly, replacement of the cytosines in this oligomer with 5-methylcytosines dramatically increased triplex stability (T(m) = 25 degrees C at pH 7.5), and even greater stability was achieved by selective replacement of uracils with thymines (T(m) = 37 degrees C at pH 7.5). Substitution of the contiguous 5-methylcytosines of the deoxy-gag-psTFO with 8-oxo-adenines significantly reduced pH dependence and increased triplex stability. In contrast to the behavior of env-specific TFOs, triplexes formed by 2'-O-methyl-gag-psTFOs did not show enhanced stability. Replacement of the 3'-terminal phosphodiester of the TFO with a methylphosphonate group significantly increased the resistance of both deoxy- and 2'-O-methyl-TFOs to degradation by 3'-exonucleases, while maintaining triplex stability.
Collapse
Affiliation(s)
- Rachel A Cassidy
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | | | | |
Collapse
|