1
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Xiao X, Chen H, Yang L, Xie G, Shimuzu R, Murai A. Concise review: Cancer cell reprogramming and therapeutic implications. Transl Oncol 2022; 24:101503. [PMID: 35933935 PMCID: PMC9364012 DOI: 10.1016/j.tranon.2022.101503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/22/2022] [Accepted: 07/28/2022] [Indexed: 11/18/2022] Open
Abstract
The cancer stem cell (CSC) act as tumor initiating cells. Reprogramming technology can convert cells into CSCs. Metabolic reprogramming is critical for CSCs. MiRNA can mediate cancer cell reprogramming as emerging alternatives.
The cancer stem cell (CSC) hypothesis postulates that cancer originates from the malignant transformation of stem cells and is considered to apply to a variety of cancers. Additionally, cancer cells alter metabolic processes to sustain their characteristic uncontrolled growth and proliferation. Further, microRNAs (miRNAs) are found to be involved in acquisition of stem cell-like properties, regulation and reprogramming of cancer cells during cancer progression through its post-transcriptional-regulatory activity. In this concise review, we aim to integrate the current knowledge and recent advances to elucidate the mechanisms involved in the regulation of cell reprogramming and highlights the potential therapeutic implications for the future.
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Affiliation(s)
- Xue Xiao
- Laboratory Department of xingouqiao Street Community Health Service Center, Qingshan District, Wuhan City, Hubei Province, China
| | - Hua Chen
- Laboratory Department of community health service station, Wuhan Engineering University, Wuhan City, Hubei Province, China
| | - Lili Yang
- Laboratory Department of xingouqiao Street Community Health Service Center, Qingshan District, Wuhan City, Hubei Province, China
| | - Guoping Xie
- Laboratory of the second staff hospital of Wuhan Iron and steel (Group) Company, Wuhan City, Hubei Province, China
| | - Risa Shimuzu
- Department of medicine and molecular science, Gunma University, Maebeshi, Japan
| | - Akiko Murai
- Department of Gynecology Oncology, University of Chicago, , 5841 South Maryland Ave, Chicago, IL 60637, USA.
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2
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Mahmoodi N, Ai J, Hassannejad Z, Ebrahimi-Barough S, Hasanzadeh E, Nekounam H, Vaccaro AR, Rahimi-Movaghar V. Improving motor neuron-like cell differentiation of hEnSCs by the combination of epothilone B loaded PCL microspheres in optimized 3D collagen hydrogel. Sci Rep 2021; 11:21722. [PMID: 34741076 PMCID: PMC8571364 DOI: 10.1038/s41598-021-01071-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/22/2021] [Indexed: 12/28/2022] Open
Abstract
Spinal cord regeneration is limited due to various obstacles and complex pathophysiological events after injury. Combination therapy is one approach that recently garnered attention for spinal cord injury (SCI) recovery. A composite of three-dimensional (3D) collagen hydrogel containing epothilone B (EpoB)-loaded polycaprolactone (PCL) microspheres (2.5 ng/mg, 10 ng/mg, and 40 ng/mg EpoB/PCL) were fabricated and optimized to improve motor neuron (MN) differentiation efficacy of human endometrial stem cells (hEnSCs). The microspheres were characterized using liquid chromatography-mass/mass spectrometry (LC-mas/mas) to assess the drug release and scanning electron microscope (SEM) for morphological assessment. hEnSCs were isolated, then characterized by flow cytometry, and seeded on the optimized 3D composite. Based on cell morphology and proliferation, cross-linked collagen hydrogels with and without 2.5 ng/mg EpoB loaded PCL microspheres were selected as the optimized formulations to compare the effect of EpoB release on MN differentiation. After differentiation, the expression of MN markers was estimated by real-time PCR and immunofluorescence (IF). The collagen hydrogel containing the EpoB group had the highest HB9 and ISL-1 expression and the longest neurite elongation. Providing a 3D permissive environment with EpoB, significantly improves MN-like cell differentiation and maturation of hEnSCs and is a promising approach to replace lost neurons after SCI.
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Affiliation(s)
- Narges Mahmoodi
- Sina Trauma and Surgery Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Jafar Ai
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Hassannejad
- Pediatric Urology and Regenerative Medicine Research Center, Tissue, Cell and Gene Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Ebrahimi-Barough
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Elham Hasanzadeh
- Immunogenetics Research Center, Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Houra Nekounam
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Alexander R Vaccaro
- Department of Orthopedic Surgery, Rothman Institute, Thomas Jefferson University, Philadelphia, PA, USA
| | - Vafa Rahimi-Movaghar
- Sina Trauma and Surgery Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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3
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Redirection of the Transcription Factor SP1 to AT Rich Binding Sites by a Synthetic Adaptor Molecule. Helv Chim Acta 2021. [DOI: 10.1002/hlca.202100095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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4
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Kumar D, Anand T, Talluri TR, Kues WA. Potential of transposon-mediated cellular reprogramming towards cell-based therapies. World J Stem Cells 2020; 12:527-544. [PMID: 32843912 PMCID: PMC7415244 DOI: 10.4252/wjsc.v12.i7.527] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/09/2020] [Accepted: 05/28/2020] [Indexed: 02/07/2023] Open
Abstract
Induced pluripotent stem (iPS) cells present a seminal discovery in cell biology and promise to support innovative treatments of so far incurable diseases. To translate iPS technology into clinical trials, the safety and stability of these reprogrammed cells needs to be shown. In recent years, different non-viral transposon systems have been developed for the induction of cellular pluripotency, and for the directed differentiation into desired cell types. In this review, we summarize the current state of the art of different transposon systems in iPS-based cell therapies.
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Affiliation(s)
- Dharmendra Kumar
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar 125001, India
| | - Taruna Anand
- NCVTC, ICAR-National Research Centre on Equines, Hisar 125001, India
| | - Thirumala R Talluri
- Equine Production Campus, ICAR-National Research Centre on Equines, Bikaner 334001, India
| | - Wilfried A Kues
- Friedrich-Loeffler-Institut, Institute of Farm Animal Genetics, Department of Biotechnology, Mariensee 31535, Germany
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5
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Gong L, Yan Q, Zhang Y, Fang X, Liu B, Guan X. Cancer cell reprogramming: a promising therapy converting malignancy to benignity. Cancer Commun (Lond) 2019; 39:48. [PMID: 31464654 PMCID: PMC6716904 DOI: 10.1186/s40880-019-0393-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023] Open
Abstract
In the past decade, remarkable progress has been made in reprogramming terminally differentiated somatic cells and cancer cells into induced pluripotent cells and cancer cells with benign phenotypes. Recent studies have explored various approaches to induce reprogramming from one cell type to another, including lineage-specific transcription factors-, combinatorial small molecules-, microRNAs- and embryonic microenvironment-derived exosome-mediated reprogramming. These reprogramming approaches have been proven to be technically feasible and versatile to enable re-activation of sequestered epigenetic regions, thus driving fate decisions of differentiated cells. One of the significant utilities of cancer cell reprogramming is the therapeutic potential of retrieving normal cell functions from various malignancies. However, there are several major obstacles to overcome in cancer cell reprogramming before clinical translation, including characterization of reprogramming mechanisms, improvement of reprogramming efficiency and safety, and development of delivery methods. Recently, several insights in reprogramming mechanism have been proposed, and determining progress has been achieved to promote reprogramming efficiency and feasibility, allowing it to emerge as a promising therapy against cancer in the near future. This review aims to discuss recent applications in cancer cell reprogramming, with a focus on the clinical significance and limitations of different reprogramming approaches, while summarizing vital roles played by transcription factors, small molecules, microRNAs and exosomes during the reprogramming process.
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Affiliation(s)
- Lanqi Gong
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, 999077, P.R. China.,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, 999077, P.R. China
| | - Qian Yan
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, 999077, P.R. China.,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, 999077, P.R. China
| | - Yu Zhang
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, 999077, P.R. China.,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, 999077, P.R. China
| | - Xiaona Fang
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, 999077, P.R. China.,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, 999077, P.R. China
| | - Beilei Liu
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, 999077, P.R. China.,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, 999077, P.R. China
| | - Xinyuan Guan
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, 999077, P.R. China. .,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, 999077, P.R. China.
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6
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Roy K, Mazumder A, Ghosh P, Naiya G, Ghosh B, Roy S. A peptide-based synthetic transcription factor selectively activates transcription in a mammalian cell. Chem Commun (Camb) 2018; 54:1611-1614. [PMID: 29369310 DOI: 10.1039/c7cc09279b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A peptide-based cell permeable synthetic transcription factor is reported, which binds to its target site with high affinity and specificity. When linked to a HAT-binding peptide, it causes significant upregulation of gene expression in a mammalian cell. Such molecules may be developed for selectively activating repressed genes in mammalian cells.
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Affiliation(s)
- Koushik Roy
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C.Mullick Road, Kolkata 700032, India
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7
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Kim MS, Gernapudi R, Choi EY, Lapidus RG, Passaniti A. Characterization of CADD522, a small molecule that inhibits RUNX2-DNA binding and exhibits antitumor activity. Oncotarget 2017; 8:70916-70940. [PMID: 29050333 PMCID: PMC5642608 DOI: 10.18632/oncotarget.20200] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 07/12/2017] [Indexed: 12/29/2022] Open
Abstract
The RUNX2 transcription factor promotes breast cancer growth and metastasis through interactions with a variety of cofactors that activate or repress target genes. Using a direct drug discovery approach we identified CADD522 as a small molecule that inhibits the DNA binding of the runt box domain protein, RUNX2. The current study defines the effect of CADD522 on breast cancer growth and metastasis, and addresses the mechanisms by which it exerts its anti-tumor activity. CADD522 treatment resulted in significant growth inhibition, clonogenic survival, tumorsphere formation, and invasion of breast cancer cells. CADD522 negatively regulated transcription of RUNX2 target genes such as matrix metalloproteinase-13, vascular endothelial growth factor and glucose transporter-1, but upregulated RUNX2 expression by increasing RUNX2 stability. CADD522 reduced RUNX2-mediated increases in glucose uptake and decreased the level of CBF-β and RUNX2 phosphorylation at the S451 residue. These results suggest several potential mechanisms by which CADD522 exerts an inhibitory function on RUNX2-DNA binding; interference with RUNX2 for the DNA binding pocket, inhibition of glucose uptake leading to cell cycle arrest, down-regulation of CBF-β, and reduction of S451-RUNX2 phosphorylation. The administration of CADD522 into MMTV-PyMT mice resulted in significant delay in tumor incidence and reduction in tumor burden. A significant decrease of tumor volume was also observed in a CADD522-treated human triple-negative breast cancer-patient derived xenograft model. CADD522 impaired the lung retention and outgrowth of breast cancer cells in vivo with no apparent toxicity to the mice. Therefore, by inhibiting RUNX2-DNA binding, CADD522 may represent a potential antitumor drug.
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Affiliation(s)
- Myoung Sook Kim
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA.,The Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.,The Veteran's Health Administration Research & Development Service, Baltimore, MD, USA
| | - Ramkishore Gernapudi
- Department of Biochemistry & Molecular Biology and Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.,The Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Eun Yong Choi
- The Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Rena G Lapidus
- The Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Antonino Passaniti
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Biochemistry & Molecular Biology and Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.,The Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.,The Veteran's Health Administration Research & Development Service, Baltimore, MD, USA
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8
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Erkina TY, Erkine AM. Nucleosome distortion as a possible mechanism of transcription activation domain function. Epigenetics Chromatin 2016; 9:40. [PMID: 27679670 PMCID: PMC5029090 DOI: 10.1186/s13072-016-0092-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/09/2016] [Indexed: 11/24/2022] Open
Abstract
After more than three decades since the discovery of transcription activation domains (ADs) in gene-specific activators, the mechanism of their function remains enigmatic. The widely accepted model of direct recruitment by ADs of co-activators and basal transcriptional machinery components, however, is not always compatible with the short size yet very high degree of sequence randomness and intrinsic structural disorder of natural and synthetic ADs. In this review, we formulate the basis for an alternative and complementary model, whereby sequence randomness and intrinsic structural disorder of ADs are necessary for transient distorting interactions with promoter nucleosomes, triggering promoter nucleosome translocation and subsequently gene activation.
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Affiliation(s)
- Tamara Y Erkina
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Butler University, Indianapolis, IN 46208 USA
| | - Alexandre M Erkine
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Butler University, Indianapolis, IN 46208 USA
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9
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Vistain LF, Yamamoto N, Rathore R, Cha P, Meade TJ. Targeted Inhibition of Snail Activity in Breast Cancer Cells by Using a Co(III) -Ebox Conjugate. Chembiochem 2015; 16:2065-72. [PMID: 26305708 DOI: 10.1002/cbic.201500289] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Indexed: 12/29/2022]
Abstract
The transition from a non-invasive to an invasive phenotype is an essential step in tumor metastasis. The Snail family of transcription factors (TFs) is known to play a significant role in this transition. These TFs are zinc fingers that bind to the CAGGTG Ebox consensus sequence. Co(III) -Ebox is a cobalt(III) complex attached to an Ebox oligonucleotide that confers specificity towards Snail TFs. Co(III) -Ebox has been shown to inhibit Snail-mediated embryonic neural crest development in Xenopus laevis, but its efficacy in inhibiting Snail-induced cancer cell invasiveness has not been explored. Here, we describe the efficacy of Co(III) -Ebox in inhibiting the invasive aspects of heregulin-β1(HRG)-treated breast cancer cells. Co(III) -Ebox was found to inhibit the capacity of Snail to repress target genes after HRG induction. Snail inhibition by Co(III) -Ebox reduced the invasive propensity of cells in 2D and 3D, thereby demonstrating promise in inhibiting metastasis.
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Affiliation(s)
- Luke F Vistain
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3113, USA
| | - Natsuho Yamamoto
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3113, USA
| | - Richa Rathore
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3113, USA
| | - Peter Cha
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3113, USA
| | - Thomas J Meade
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3113, USA.
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10
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Controlling gene networks and cell fate with precision-targeted DNA-binding proteins and small-molecule-based genome readers. Biochem J 2014; 462:397-413. [PMID: 25145439 DOI: 10.1042/bj20140400] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Transcription factors control the fate of a cell by regulating the expression of genes and regulatory networks. Recent successes in inducing pluripotency in terminally differentiated cells as well as directing differentiation with natural transcription factors has lent credence to the efforts that aim to direct cell fate with rationally designed transcription factors. Because DNA-binding factors are modular in design, they can be engineered to target specific genomic sequences and perform pre-programmed regulatory functions upon binding. Such precision-tailored factors can serve as molecular tools to reprogramme or differentiate cells in a targeted manner. Using different types of engineered DNA binders, both regulatory transcriptional controls of gene networks, as well as permanent alteration of genomic content, can be implemented to study cell fate decisions. In the present review, we describe the current state of the art in artificial transcription factor design and the exciting prospect of employing artificial DNA-binding factors to manipulate the transcriptional networks as well as epigenetic landscapes that govern cell fate.
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11
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Cellular reprogramming by transcription factor engineering. Curr Opin Genet Dev 2014; 28:1-9. [DOI: 10.1016/j.gde.2014.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 07/03/2014] [Indexed: 12/20/2022]
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12
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Patel S, Jung D, Yin PT, Carlton P, Yamamoto M, Bando T, Sugiyama H, Lee KB. NanoScript: a nanoparticle-based artificial transcription factor for effective gene regulation. ACS NANO 2014; 8:8959-67. [PMID: 25133310 PMCID: PMC4174092 DOI: 10.1021/nn501589f] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 08/18/2014] [Indexed: 05/22/2023]
Abstract
Transcription factor (TF) proteins are master regulators of transcriptional activity and gene expression. TF-based gene regulation is a promising approach for many biological applications; however, several limitations hinder the full potential of TFs. Herein, we developed an artificial, nanoparticle-based transcription factor, termed NanoScript, which is designed to mimic the structure and function of TFs. NanoScript was constructed by tethering functional peptides and small molecules called synthetic transcription factors, which mimic the individual TF domains, onto gold nanoparticles. We demonstrate that NanoScript localizes within the nucleus and initiates transcription of a reporter plasmid by over 15-fold. Moreover, NanoScript can effectively transcribe targeted genes on endogenous DNA in a nonviral manner. Because NanoScript is a functional replica of TF proteins and a tunable gene-regulating platform, it has great potential for various stem cell applications.
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Affiliation(s)
- Sahishnu Patel
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Dongju Jung
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
| | - Perry T. Yin
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Peter Carlton
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
| | - Makoto Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Address correspondence to
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13
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Sánchez MI, Mosquera J, Vázquez ME, Mascareñas JL. Reversible Supramolecular Assembly at Specific DNA Sites: Nickel-Promoted Bivalent DNA Binding with Designed Peptide and Bipyridyl-Bis(benzamidine) Components. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405726] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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14
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Sánchez MI, Mosquera J, Vázquez ME, Mascareñas JL. Reversible Supramolecular Assembly at Specific DNA Sites: Nickel-Promoted Bivalent DNA Binding with Designed Peptide and Bipyridyl-Bis(benzamidine) Components. Angew Chem Int Ed Engl 2014; 53:9917-21. [DOI: 10.1002/anie.201405726] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Indexed: 01/20/2023]
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15
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Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG. Fluorescent probes for nucleic Acid visualization in fixed and live cells. Molecules 2013; 18:15357-97. [PMID: 24335616 PMCID: PMC6270009 DOI: 10.3390/molecules181215357] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/20/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022] Open
Abstract
This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
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Affiliation(s)
- Alexandre S. Boutorine
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| | - Olga A. Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
| | - Karine Nozeret
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
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16
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Mazumder A, Maiti A, Roy K, Roy S. A synthetic peptide mimic of λ-Cro shows sequence-specific binding in vitro and in vivo. ACS Chem Biol 2012; 7:1084-94. [PMID: 22480451 DOI: 10.1021/cb200523n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Development of small synthetic transcription factors is important for future cellular engineering and therapeutics. This article describes the chemical synthesis of α-amino-isobutyric acid (Aib) substituted, conformationally constrained, helical peptide mimics of Cro protein from bacteriophage λ that encompasses the DNA recognition elements. The Aib substituted constrained helical peptide monomer shows a moderately reduced dissociation constant compared to the corresponding unsubstituted wild type peptide. A suitably cross-linked dimeric version of the peptide, mimicking the dimeric protein, recapitulates some of the important features of Cro. It binds to the operator site O(R)3, a high affinity Cro binding site in the λ genome, with good affinity and single base-pair discrimination specificity. A dimeric version of an even shorter peptide mimic spanning only the recognition helix of the helix-turn-helix motif of the Cro protein was created following the same design principles. This dimeric peptide binds to O(R)3 with affinity greater than that of the longer version. Chemical shift perturbation experiments show that the binding mode of this peptide dimer to the cognate operator site sequence is similar to the wild type Cro protein. A Green Fluorescent Protein based reporter assay in vivo reveals that the peptide dimer binds the operator site sequences with considerable selectivity and inhibits gene expression. Peptide mimics designed in this way may provide a future framework for creating effective synthetic transcription factors.
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Affiliation(s)
- Abhishek Mazumder
- Divisions of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4, Raja
S.C. Mullick Road, Kolkata 700032, India
| | - Atanu Maiti
- Divisions of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4, Raja
S.C. Mullick Road, Kolkata 700032, India
| | - Koushik Roy
- Divisions of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4, Raja
S.C. Mullick Road, Kolkata 700032, India
| | - Siddhartha Roy
- Divisions of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4, Raja
S.C. Mullick Road, Kolkata 700032, India
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17
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The transcription cycle in eukaryotes: From productive initiation to RNA polymerase II recycling. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:391-400. [DOI: 10.1016/j.bbagrm.2012.01.010] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 01/11/2012] [Accepted: 01/14/2012] [Indexed: 01/03/2023]
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18
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Langlois C, Del Gatto A, Arseneault G, Lafrance-Vanasse J, De Simone M, Morse T, de Paola I, Lussier-Price M, Legault P, Pedone C, Zaccaro L, Omichinski JG. Structure-based design of a potent artificial transactivation domain based on p53. J Am Chem Soc 2012; 134:1715-23. [PMID: 22191432 DOI: 10.1021/ja208999e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Malfunctions in transcriptional regulation are associated with a number of critical human diseases. As a result, there is considerable interest in designing artificial transcription activators (ATAs) that specifically control genes linked to human diseases. Like native transcriptional activator proteins, an ATA must minimally contain a DNA-binding domain (DBD) and a transactivation domain (TAD) and, although there are several reliable methods for designing artificial DBDs, designing artificial TADs has proven difficult. In this manuscript, we present a structure-based strategy for designing short peptides containing natural amino acids that function as artificial TADs. Using a segment of the TAD of p53 as the scaffolding, modifications are introduced to increase the helical propensity of the peptides. The most active artificial TAD, termed E-Cap-(LL), is a 13-mer peptide that contains four key residues from p53, an N-capping motif and a dileucine hydrophobic bridge. In vitro analysis demonstrates that E-Cap-(LL) interacts with several known p53 target proteins, while in vivo studies in a yeast model system show that it is a 20-fold more potent transcriptional activator than the native p53-13 peptide. These results demonstrate that structure-based design represents a promising approach for developing artificial TADs that can be combined with artificial DBDs to create potent and specific ATAs.
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Affiliation(s)
- Chantal Langlois
- Département de Biochimie, Université de Montréal, C.P. 6128 Succursale, Centre-Ville, Montréal, Quebec H3C 3J7, Canada
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19
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Grivas PD, Kiaris H, Papavassiliou AG. Tackling transcription factors: challenges in antitumor therapy. Trends Mol Med 2011; 17:537-8. [DOI: 10.1016/j.molmed.2011.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 06/20/2011] [Indexed: 02/05/2023]
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Karamouzis MV, Papavassiliou AG. Transcription factor networks as targets for therapeutic intervention of cancer: the breast cancer paradigm. Mol Med 2011; 17:1133-6. [PMID: 21912809 DOI: 10.2119/molmed.2011.00315] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 08/25/2011] [Indexed: 11/06/2022] Open
Abstract
It has long been shown that many of the presently used anticancer drugs exert their effects partly through modulating the activity of vital transcription factors. The intricacy of transcriptional regulation still represents the main obstacle for the design of transcription factor-directed agents. Systematic mapping of tumor-specific transcriptional networks and application of new molecular tools have reinforced research interest and efforts in this venue. The case of breast cancer is discussed as a representative example.
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Affiliation(s)
- Michalis V Karamouzis
- Molecular Oncology Unit, Department of Biological Chemistry, University of Athens Medical School, Athens, Greece
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21
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Højfeldt JW, Van Dyke AR, Mapp AK. Transforming ligands into transcriptional regulators: building blocks for bifunctional molecules. Chem Soc Rev 2011; 40:4286-94. [PMID: 21701709 DOI: 10.1039/c1cs15050b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The human body is comprised of several hundred distinct cell types that all share a common genomic template. This diversity arises from regulated expression of individual genes. The first critical step in this process is transcription and is governed by a large number of transcription factors. Small molecules that can alter transcription hold tremendous utility as chemical probes and therapeutics. To fully realize their potential, however, artificial transcription factors must be able to orchestrate protein recruitment at gene promoters just like their natural counterparts. This tutorial review surveys the discovery of small ligands (drug-like molecules and short peptides) that bind transcriptional coregulatory proteins, and thus comprise one of the two essential characteristics of a transcription factor. By joining these ligands to DNA-targeting moieties, one can construct a bifunctional molecule that recruits its protein target to specific genes and controls gene transcription.
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Affiliation(s)
- Jonas W Højfeldt
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Tietjen JR, Donato LJ, Bhimisaria D, Ansari AZ. Sequence-specificity and energy landscapes of DNA-binding molecules. Methods Enzymol 2011; 497:3-30. [PMID: 21601080 DOI: 10.1016/b978-0-12-385075-1.00001-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A central goal of biology is to understand how transcription factors target and regulate specific genes and networks to control cell fate and function. An equally important goal of synthetic biology, chemical biology, and personalized medicine is to devise molecules that can regulate genes and networks in a programmable manner. To achieve these goals, it is necessary to chart the sequence specificity of natural and engineered DNA-binding molecules. Cognate site identification (CSI) is now achieved via unbiased, high-throughput platforms that interrogate an entire sequence space bound by typical DNA-binding molecules. Analysis of these comprehensive specificity profiles is facilitated through the use of sequence-specificity landscapes (SSLs). SSLs reveal new modes of sequence cognition and overcome the limitations of current approaches that yield amalgamated "consensus" motifs. The landscapes also reveal the impact of nonconserved flanking sequences on binding to cognate sites. SSLs also serve as comprehensive binding energy landscapes that provide insights into the energetic thresholds at which natural and engineered molecules function within cells. Furthermore, applying the CSI binding data to genomic sequence (genomescapes) provides a powerful tool for identification of potential in vivo binding sites of a given DNA ligand, and can provide insight into differential regulation of gene networks. These tools can be directly applied to the design and development of synthetic therapeutic molecules and to expand our knowledge of the basic principles of molecular recognition.
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Affiliation(s)
- Joshua R Tietjen
- Department of Biochemistry, The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, USA
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