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Behrouzian Fard G, Ahmadi MH, Gholamin M, Amirfakhrian R, Saberi Teimourian E, Karimi MA, Hosseini Bafghi M. CRISPR-Cas9 technology: As an efficient genome modification tool in the cancer diagnosis and treatment. Biotechnol Bioeng 2024; 121:472-488. [PMID: 37986642 DOI: 10.1002/bit.28603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/30/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023]
Abstract
Cancer is the second most common cause of death globally and is a major public health concern. Managing this disease is difficult due to its multiple stages and numerous genetic and epigenetic changes. Traditional cancer diagnosis and treatment methods have limitations, making it crucial to develop new modalities to combat the increasing burden of cancer. The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system has transformed genetic engineering due to its simplicity, specificity, low cytotoxicity, and cost-effectiveness. It has been proposed as an effective technology to enhance cancer diagnosis and treatment strategies. This article presents the most recent discoveries regarding the structure, mechanism, and delivery methods of the highly powerful genome editing tool, CRISPR-Cas9. In terms of diagnosis, the article examines the role of CRISPR-Cas9 in detecting microRNAs and DNA methylation, and discusses two popular gene detection techniques that utilize the CRISPR-Cas system: DNA endonuclease-targeted CRISPR trans reporter and specific high sensitivity enzymatic reporter unlocking. Regarding treatment, the article explores several genes that have been identified and modified by CRISPR-Cas9 for effective tumorigenesis of common cancers such as breast, lung, and colorectal cancer. The present review also addresses the challenges and ethical issues associated with using CRISPR-Cas9 as a diagnostic and therapeutic tool. Despite some limitations, CRISPR-Cas9-based cancer diagnosis has the potential to become the next generation of cancer diagnostic tools, and the continuous progress of CRISPR-Cas9 can greatly aid in cancer treatment.
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Affiliation(s)
- Ghazaleh Behrouzian Fard
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Hossein Ahmadi
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehran Gholamin
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Razieh Amirfakhrian
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elahe Saberi Teimourian
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ali Karimi
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahdi Hosseini Bafghi
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
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2
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Lei K, Sun R, Chen LH, Diplas BH, Moure CJ, Wang W, Hansen LJ, Tao Y, Chen X, Chen CPJ, Greer PK, Zhao F, Yan H, Bigner DD, Huang J, He Y. Mutant allele quantification reveals a genetic basis for TP53 mutation-driven castration resistance in prostate cancer cells. Sci Rep 2018; 8:12507. [PMID: 30131529 PMCID: PMC6104024 DOI: 10.1038/s41598-018-30062-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 07/23/2018] [Indexed: 12/02/2022] Open
Abstract
The concept that human cancer is in essence a genetic disease driven by gene mutations has been well established, yet its utilization in functional studies of cancer genes has not been fully explored. Here, we describe a simple genetics-based approach that can quickly and sensitively reveal the effect of the alteration of a gene of interest on the fate of its host cells within a heterogeneous population, essentially monitoring the genetic selection that is associated with and powers the tumorigenesis. Using this approach, we discovered that loss-of-function of TP53 can promote the development of resistance of castration in prostate cancer cells via both transiently potentiating androgen-independent cell growth and facilitating the occurrence of genome instability. The study thus reveals a novel genetic basis underlying the development of castration resistance in prostate cancer cells and provides a facile genetic approach for studying a cancer gene of interest in versatile experimental conditions.
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Affiliation(s)
- Kefeng Lei
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA.,General Surgery, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang, 310014, China
| | - Ran Sun
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA.,Scientific Research Center, China-Japan Union Hospital, Jilin University, Jilin, 130033, China
| | - Lee H Chen
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Bill H Diplas
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Casey J Moure
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Wenzhe Wang
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA.,Center for Molecular Medicine, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, 310012, China
| | - Landon J Hansen
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Yulei Tao
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Xufeng Chen
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Chin-Pu Jason Chen
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Paula K Greer
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | | | - Hai Yan
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Darell D Bigner
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Jiaoti Huang
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Yiping He
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA. .,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA.
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Poluri RTK, Audet-Walsh É. Genomic Deletion at 10q23 in Prostate Cancer: More Than PTEN Loss? Front Oncol 2018; 8:246. [PMID: 30009155 PMCID: PMC6033966 DOI: 10.3389/fonc.2018.00246] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/18/2018] [Indexed: 12/19/2022] Open
Abstract
The PTEN gene encodes for the phosphatase and tensin homolog; it is a tumor suppressor gene that is among the most frequently inactivated genes throughout the human cancer spectrum. The most recent sequencing approaches have allowed the identification of PTEN genomic alterations, including deletion, mutation, or rearrangement in about 50% of prostate cancer (PCa) cases. It appears that mechanisms leading to PTEN inactivation are cancer-specific, comprising gene mutations, small insertions/deletions, copy number alterations (CNAs), promoter hypermethylation, and RNA interference. The examination of publicly available results from deep-sequencing studies of various cancers showed that PCa appears to be the only cancer in which PTEN is lost mostly through CNA. Instead of inactivating mutations, which are seen in other cancers, deletion of the 10q23 locus is the most common form of PTEN inactivation in PCa. By investigating the minimal deleted region at 10q23, several other genes appear to be lost simultaneously with PTEN. Expression data indicate that, like PTEN, these genes are also downregulated upon loss of 10q23. These analyses raise the possibility that 10q23 is lost upon selective pressure not only to inactivate PTEN but also to impair the expression of surrounding genes. As such, several genes from this deleted region, which represents about 500 kb, may also act as tumor suppressors in PCa, requiring further studies on their respective functions in that context.
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Affiliation(s)
- Raghavendra Tejo Karthik Poluri
- Department of Molecular Medicine, Axe Endocrinologie – Néphrologie du Centre de recherche du CHU de Québec, Université Laval, Québec, QC, Canada
| | - Étienne Audet-Walsh
- Department of Molecular Medicine, Axe Endocrinologie – Néphrologie du Centre de recherche du CHU de Québec, Université Laval, Québec, QC, Canada
- Centre de recherche sur le cancer de l’Université Laval, Québec, QC, Canada
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Abstract
CRISPR-based genome editing technologies are poised to enable countless new therapies to prevent, treat, or cure diseases with a genetic basis. However, the safe and effective delivery of genome editing enzymes represents a substantial challenge that must be tackled to enable the next generation of genetic therapies. In this Review, we summarize recent progress in developing enzymatic tools to combat genetic disease and examine current efforts to deliver these enzymes to the cells in need of correction. Viral vectors already in use for traditional gene therapy are being applied to enable in vivo CRISPR-based therapeutics, as are emerging technologies such as nanoparticle-based delivery of CRISPR components and direct delivery of preassembled RNA-protein complexes. Success in these areas will allow CRISPR-based genome editing therapeutics to reach their full potential.
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Affiliation(s)
- Ross C Wilson
- Innovative Genomics Institute, University of California , Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States
| | - Luke A Gilbert
- Innovative Genomics Institute, University of California , Berkeley, California 94720, United States
- Helen Diller Family Comprehensive Cancer Center, University of California , San Francisco, California 94158, United States
- Department of Urology, University of California , San Francisco, California 94158, United States
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Modulating signaling networks by CRISPR/Cas9-mediated transposable element insertion. Curr Genet 2017; 64:405-412. [DOI: 10.1007/s00294-017-0765-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 10/01/2017] [Accepted: 10/09/2017] [Indexed: 12/11/2022]
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Quirin KA, Kwon JJ, Alioufi A, Factora T, Temm CJ, Jacobsen M, Sandusky GE, Shontz K, Chicoine LG, Clark KR, Mendell JT, Korc M, Kota J. Safety and Efficacy of AAV Retrograde Pancreatic Ductal Gene Delivery in Normal and Pancreatic Cancer Mice. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2017; 8:8-20. [PMID: 29349096 PMCID: PMC5675991 DOI: 10.1016/j.omtm.2017.09.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/27/2017] [Indexed: 02/07/2023]
Abstract
Recombinant adeno-associated virus (rAAV)-mediated gene delivery shows promise to transduce the pancreas, but safety/efficacy in a neoplastic context is not well established. To identify an ideal AAV serotype, route, and vector dose and assess safety, we have investigated the use of three AAV serotypes (6, 8, and 9) expressing GFP in a self-complementary (sc) AAV vector under an EF1α promoter (scAAV.GFP) following systemic or retrograde pancreatic intraductal delivery. Systemic delivery of scAAV9.GFP transduced the pancreas with high efficiency, but gene expression did not exceed >45% with the highest dose, 5 × 1012 viral genomes (vg). Intraductal delivery of 1 × 1011 vg scAAV6.GFP transduced acini, ductal cells, and islet cells with >50%, ∼48%, and >80% efficiency, respectively, and >80% pancreatic transduction was achieved with 5 × 1011 vg. In a KrasG12D-driven pancreatic cancer mouse model, intraductal delivery of scAAV6.GFP targeted acini, epithelial, and stromal cells and exhibited persistent gene expression 5 months post-delivery. In normal mice, intraductal delivery induced a transient increase in serum amylase/lipase that resolved within a day of infusion with no sustained pancreatic inflammation or fibrosis. Similarly, in PDAC mice, intraductal delivery did not increase pancreatic intraepithelial neoplasia progression/fibrosis. Our study demonstrates that scAAV6 targets the pancreas/neoplasm efficiently and safely via retrograde pancreatic intraductal delivery.
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Affiliation(s)
- Kayla A Quirin
- Department of Medical and Molecular Genetics, Indiana University School of Medicine (IUSM), Indianapolis, IN 46202, USA
| | - Jason J Kwon
- Department of Medical and Molecular Genetics, Indiana University School of Medicine (IUSM), Indianapolis, IN 46202, USA
| | - Arafat Alioufi
- Department of Medical and Molecular Genetics, Indiana University School of Medicine (IUSM), Indianapolis, IN 46202, USA
| | - Tricia Factora
- Department of Medical and Molecular Genetics, Indiana University School of Medicine (IUSM), Indianapolis, IN 46202, USA
| | | | - Max Jacobsen
- Department of Pathology, IUSM, Indianapolis, IN 46202, USA
| | | | - Kim Shontz
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Louis G Chicoine
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - K Reed Clark
- Dimension Therapeutics, Cambridge, MA 02139, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Murray Korc
- The Melvin and Bren Simon Cancer Center, IUSM, Indianapolis, IN 46202, USA.,Pancreatic Cancer Signature Center, Indiana University and Purdue University-Indianapolis (IUPUI), Indianapolis, IN 46202, USA.,Department of Biochemistry and Molecular Biology, IUSM, Indianapolis, IN 43202, USA.,Department of Medicine, IUSM, Indianapolis, IN 43202, USA
| | - Janaiah Kota
- Department of Medical and Molecular Genetics, Indiana University School of Medicine (IUSM), Indianapolis, IN 46202, USA.,The Melvin and Bren Simon Cancer Center, IUSM, Indianapolis, IN 46202, USA.,Pancreatic Cancer Signature Center, Indiana University and Purdue University-Indianapolis (IUPUI), Indianapolis, IN 46202, USA
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7
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Füchtbauer AF, Preus S, Börjesson K, McPhee SA, Lilley DMJ, Wilhelmsson LM. Fluorescent RNA cytosine analogue - an internal probe for detailed structure and dynamics investigations. Sci Rep 2017; 7:2393. [PMID: 28539582 PMCID: PMC5443824 DOI: 10.1038/s41598-017-02453-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/10/2017] [Indexed: 12/22/2022] Open
Abstract
The bright fluorescent cytosine analogue tCO stands out among fluorescent bases due to its virtually unquenched fluorescence emission in duplex DNA. However, like most reported base analogues, it has not been thoroughly characterized in RNA. We here report on the first synthesis and RNA-incorporation of tCO, and characterize its base-mimicking and fluorescence properties in RNA. As in DNA, we find a high quantum yield inside RNA duplexes (<ΦF> = 0.22) that is virtually unaffected by the neighbouring bases (ΦF = 0.20-0.25), resulting in an average brightness of 1900 M-1 cm-1. The average fluorescence lifetime in RNA duplexes is 4.3 ns and generally two lifetimes are required to fit the exponential decays. Fluorescence properties in ssRNA are defined by a small increase in average quantum yield (<ΦF > = 0.24) compared to dsRNA, with a broader distribution (ΦF = 0.17-0.34) and slightly shorter average lifetimes. Using circular dichroism, we find that the tCO-modified RNA duplexes form regular A-form helices and in UV-melting experiments the stability of the duplexes is only slightly higher than that of the corresponding natural RNA (<ΔT m> = + 2.3 °C). These properties make tCO a highly interesting fluorescent RNA base analogue for detailed FRET-based structural measurements, as a bright internal label in microscopy, and for fluorescence anisotropy measurements of RNA dynamics.
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Affiliation(s)
- Anders Foller Füchtbauer
- Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-41296, Sweden
| | - Søren Preus
- Department of Chemistry, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Karl Börjesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, SE-41296, Sweden
| | - Scott A McPhee
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - L Marcus Wilhelmsson
- Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-41296, Sweden.
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Affiliation(s)
- Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1270 Digital Computer Laboratory, MC-278, 1304 West Springfield Avenue, Urbana, IL, 61801, USA. .,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Zheng-Yi Chen
- Department of Otolaryngology, Harvard Medical School and Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, MA, 02114, USA.
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