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Pandey P, Vavilala SL. From Gene Editing to Biofilm Busting: CRISPR-CAS9 Against Antibiotic Resistance-A Review. Cell Biochem Biophys 2024:10.1007/s12013-024-01276-y. [PMID: 38702575 DOI: 10.1007/s12013-024-01276-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2024] [Indexed: 05/06/2024]
Abstract
In recent decades, the development of novel antimicrobials has significantly slowed due to the emergence of antimicrobial resistance (AMR), intensifying the global struggle against infectious diseases. Microbial populations worldwide rapidly develop resistance due to the widespread use of antibiotics, primarily targeting drug-resistant germs. A prominent manifestation of this resistance is the formation of biofilms, where bacteria create protective layers using signaling pathways such as quorum sensing. In response to this challenge, the CRISPR-Cas9 method has emerged as a ground-breaking strategy to counter biofilms. Initially identified as the "adaptive immune system" of bacteria, CRISPR-Cas9 has evolved into a state-of-the-art genetic engineering tool. Its exceptional precision in altering specific genes across diverse microorganisms positions it as a promising alternative for addressing antibiotic resistance by selectively modifying genes in diverse microorganisms. This comprehensive review concentrates on the historical background, discovery, developmental stages, and distinct components of CRISPR Cas9 technology. Emphasizing its role as a widely used genome engineering tool, the review explores how CRISPR Cas9 can significantly contribute to the targeted disruption of genes responsible for biofilm formation, highlighting its pivotal role in reshaping strategies to combat antibiotic resistance and mitigate the challenges posed by biofilm-associated infectious diseases.
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Affiliation(s)
- Pooja Pandey
- School of Biological Sciences, UM DAE Centre for Excellence in Basic Sciences, Mumbai, 400098, India
| | - Sirisha L Vavilala
- School of Biological Sciences, UM DAE Centre for Excellence in Basic Sciences, Mumbai, 400098, India.
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2
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Yin W, Chen Z, Huang J, Ye H, Lu T, Lu M, Rao Y. [Application of CRISPR-Cas9 gene editing technology in crop breeding]. Sheng Wu Gong Cheng Xue Bao 2023; 39:399-424. [PMID: 36847080 DOI: 10.13345/j.cjb.220664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The CRISPR-Cas9 system is composed of a clustered regularly interspaced short palindromic repeat (CRISPR) and its associated proteins, which are widely present in bacteria and archaea, serving as a specific immune protection against viral and phage secondary infections. CRISPR-Cas9 technology is the third generation of targeted genome editing technologies following zinc finger nucleases (ZFNs) and transcription activator like effector nucleases (TALENs). The CRISPR-Cas9 technology is now widely used in various fields. Firstly, this article introduces the generation, working mechanism and advantages of CRISPR-Cas9 technology; secondly, it reviews the applications of CRISPR-Cas9 technology in gene knockout, gene knock-in, gene regulation and genome in breeding and domestication of important food crops such as rice, wheat, maize, soybean and potato. Finally, the article summarizes the current problems and challenges encountered by CRISPR-Cas9 technology and prospects future development and application of CRISPR-Cas9 technology.
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Affiliation(s)
- Wenjing Yin
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Zhengai Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Jiahui Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Hanfei Ye
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Tao Lu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Mei Lu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Yuchun Rao
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
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3
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Li L, Yi H, Liu Z, Long P, Pan T, Huang Y, Li Y, Li Q, Ma Y. Genetic correction of concurrent α- and β-thalassemia patient-derived pluripotent stem cells by the CRISPR-Cas9 technology. Stem Cell Res Ther 2022; 13:102. [PMID: 35255977 PMCID: PMC8900422 DOI: 10.1186/s13287-022-02768-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Thalassemia is a genetic blood disorder characterized by decreased hemoglobin production. Severe anemia can damage organs and severe threat to life safety. Allogeneic transplantation of bone marrow-derived hematopoietic stem cell (HSCs) at present represents a promising therapeutic approach for thalassemia. However, immune rejection and lack of HLA-matched donors limited its clinical application. In recent years, human-induced pluripotent stem cells (hiPSCs) technology offers prospects for autologous cell-based therapy since it could avoid the immunological problems mentioned above. METHODS In the present study, we established a new hiPSCs line derived from amniotic cells of a fetus with a homozygous β41-42 (TCTT) deletion mutation in the HBB gene and a heterozygous Westmead mutation (C > G) in the HBA2 gene. We designed a CRISPR-Cas9 to target these casual mutations and corrected them. Gene-corrected off-target analysis was performed by whole-exome capture sequencing. The corrected hiPSCs were analyzed by teratoma formation and erythroblasts differentiation assays. RESULTS These mutations were corrected with linearized donor DNA through CRISPR/Cas9-mediated homology-directed repair. Corrections of hiPSCs were validated by sequences. The corrected hiPSCs retain normal pluripotency. Moreover, they could be differentiated into hematopoietic progenitors, which proves that they maintain the multilineage differentiation potential. CONCLUSIONS We designed sgRNAs and demonstrated that these sgRNAs facilitating the CRISPR-Cas9 genomic editing system could be applied to correct concurrent α- and β-thalassemia in patient-derived hiPSCs. In the future, these corrected hiPSCs can be applied for autologous transplantation in patients with concurrent α- and β-thalassemia.
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Affiliation(s)
- Lingli Li
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, 3 Longhua Road, Haikou, 570102, Hainan, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan, China.,Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
| | - Hongyan Yi
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, 3 Longhua Road, Haikou, 570102, Hainan, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan, China.,Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
| | - Zheng Liu
- College of Medical Laboratory Science, Guilin Medical University, Guilin, Guangxi, China
| | - Ping Long
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, 3 Longhua Road, Haikou, 570102, Hainan, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan, China.,Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
| | - Tao Pan
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan, China.,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, 571199, China
| | - Yuanhua Huang
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, 3 Longhua Road, Haikou, 570102, Hainan, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan, China.,Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
| | - Yongsheng Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan, China. .,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, 571199, China.
| | - Qi Li
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, 3 Longhua Road, Haikou, 570102, Hainan, China. .,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan, China. .,Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China.
| | - Yanlin Ma
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, 3 Longhua Road, Haikou, 570102, Hainan, China. .,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan, China. .,Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China.
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4
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Huang Z, Loewer A. Generating Somatic Knockout Cell Lines with CRISPR-Cas9 Technology to Investigate SMAD Signaling. Methods Mol Biol 2022; 2488:81-97. [PMID: 35347684 DOI: 10.1007/978-1-0716-2277-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Genome engineering provides a powerful tool to explore TGF-β/SMAD signaling by enabling the deletion and modification of critical components of the pathway. Over the past years, CRISPR-Cas9 technology has matured and can now be used to routinely generate knockout cell lines. Here, we describe a method to design and generate deletions of genes from the SMAD pathway in somatic human cell lines based on homologous recombination.
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Affiliation(s)
- Zixin Huang
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Alexander Loewer
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany.
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5
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Sledzinski P, Dabrowska M, Nowaczyk M, Olejniczak M. Paving the way towards precise and safe CRISPR genome editing. Biotechnol Adv 2021; 49:107737. [PMID: 33785374 DOI: 10.1016/j.biotechadv.2021.107737] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 03/11/2021] [Accepted: 03/19/2021] [Indexed: 12/13/2022]
Abstract
As the possibilities of CRISPR-Cas9 technology have been revealed, we have entered a new era of research aimed at increasing its specificity and safety. This stage of technology development is necessary not only for its wider application in the clinic but also in basic research to better control the process of genome editing. Research during the past eight years has identified some factors influencing editing outcomes and led to the development of highly specific endonucleases, modified guide RNAs and computational tools supporting experiments. More recently, large-scale experiments revealed a previously overlooked feature: Cas9 can generate reproducible mutation patterns. As a result, it has become apparent that Cas9-induced double-strand break (DSB) repair is nonrandom and can be predicted to some extent. Here, we review the present state of knowledge regarding the specificity and safety of CRISPR-Cas9 technology to define gRNA, protein and target-related problems and solutions. These issues include sequence-specific off-target effects, immune responses, genetic variation and chromatin accessibility. We present new insights into the role of DNA repair in genome editing and define factors influencing editing outcomes. In addition, we propose practical guidelines for increasing the specificity of editing and discuss novel perspectives in improvement of this technology.
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Affiliation(s)
- Pawel Sledzinski
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland
| | - Magdalena Dabrowska
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland
| | - Mateusz Nowaczyk
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland
| | - Marta Olejniczak
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland.
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6
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Tiruneh G/Medhin M, Chekol Abebe E, Sisay T, Berhane N, Bekele T, Asmamaw Dejenie T. Current Applications and Future Perspectives of CRISPR-Cas9 for the Treatment of Lung Cancer. Biologics 2021; 15:199-204. [PMID: 34103894 PMCID: PMC8178582 DOI: 10.2147/btt.s310312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/21/2021] [Indexed: 12/21/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins are referred to as CRISPR-Cas9. Bacteria and archaea have an adaptive (acquired) immune system. As a result, developing the best single regulated RNA and Cas9 endonuclease proteins and implementing the method in clinical practice would aid in the treatment of diseases of various origins, including lung cancers. This seminar aims to provide an overview of CRISPR-Cas9 technology, as well as current and potential applications and perspectives for the method, as well as its mechanism of action in lung cancer therapy. This technology can be used to treat lung cancer in two different ways. The first approach involves creating single directed RNA and Cas9 proteins and then distributing them to cancer cells using suitable methods. Single directed RNA looks directly at the lung's mutated epidermal growth factor receptor and makes a complementary match, which is then cleaved with Cas9 protein, slowing cancer progression. The second method is to manipulate the expression of ligand-receptors on immune lymphocytic cells. For example, if the CRISPR-Cas9 system disables the expression of cancer receptors on lymphocytes, it decreases the contact between the tumor cell and its ligand-receptor, thus slowing cancer progression.
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Affiliation(s)
- Markeshaw Tiruneh G/Medhin
- Department of Biochemistry, School of Medicine, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Endeshaw Chekol Abebe
- Department of Biochemistry, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Tekeba Sisay
- Institute of Biotechnology, College of Natural Science, University of Gondar, Gondar, Ethiopia
| | - Nega Berhane
- Institute of Biotechnology, College of Natural Science, University of Gondar, Gondar, Ethiopia
| | - Tesfahun Bekele
- Department of Biochemistry, School of Medicine, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Tadesse Asmamaw Dejenie
- Department of Biochemistry, School of Medicine, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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7
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Singh HD, Ma JX, Takahashi Y. Distinct roles of LRP5 and LRP6 in Wnt signaling regulation in the retina. Biochem Biophys Res Commun 2021; 545:8-13. [PMID: 33545636 DOI: 10.1016/j.bbrc.2021.01.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Dysregulation of Wnt signaling is implicated in multiple ocular disorders. The roles of Wnt co-receptors LRP5 and LRP6 in Wnt signaling regulation remain elusive, as most retinal cells express both of the co-receptors. To address this question, LRP5 and LRP6 were individually knocked-out in a human retinal pigment epithelium cell line using the CRISPR-Cas9 technology. Wnt signaling activity induced by various Wnt ligands was measured using wild-type and the KO cell lines. The results identified three groups of Wnt ligands based on their co-receptor specificity: 1) activation of Wnt signaling only through LRP6, 2) through both LRP5 and LRP6 and 3) predominantly through LRP5. These results indicate that LRP5 and LRP6 have differential roles in Wnt signaling regulation.
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Affiliation(s)
- Harminder D Singh
- Department of Physiology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jian-Xing Ma
- Department of Physiology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Harold Hamm Diabetes Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Yusuke Takahashi
- Department of Physiology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Harold Hamm Diabetes Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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8
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Abstract
Until recently, our understanding of chromosome organization in higher eukaryotic cells has been based on analyses of large-scale, low-resolution changes in chromosomes structure. More recently, CRISPR-Cas9 technologies have allowed us to "zoom in" and visualize specific chromosome regions in live cells so that we can begin to examine in detail the dynamics of chromosome organization in individual cells. In this review, we discuss traditional methods of chromosome locus visualization and look at how CRISPR-Cas9 gene-targeting methodologies have helped improve their application. We also describe recent developments of the CRISPR-Cas9 technology that enable visualization of specific chromosome regions without the requirement for complex genetic manipulation.
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Affiliation(s)
- John K Eykelenboom
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK
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9
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Abstract
Genome editing technologies have led to fundamental changes in genetic science. Among them, CRISPR-Cas9 technology particularly stands out due to its advantages such as easy handling, high accuracy, and low cost. It has made a quick introduction in fields related to humans, animals, and the environment, while raising difficult questions, applications, concerns, and bioethical issues to be discussed. Most concerns stem from the use of CRISPR-Cas9 to genetically alter human germline cells and embryos (called germline genome editing). Germline genome editing leads to serial bioethical issues, such as the occurrence of undesirable changes in the genome, from whom and how informed consent is obtained, and the breeding of the human species (eugenics). However, the bioethical issues that CRISPR-Cas9 technology could cause in the environment, agriculture and livestock should also not be forgotten. In order for CRISPR-Cas9 to be used safely in all areas and to solve potential issues, worldwide legislation should be prepared, taking into account the opinions of both life and social scientists, policy makers, and all other stakeholders of the sectors, and CRISPR-Cas9 applications should be implemented according to such legislations. However, these controls should not restrict scientific freedom. Here, various applications of CRISPR-Cas9 technology, especially in medicine and agriculture, are described and ethical issues related to genome editing using CRISPR-Cas9 technology are discussed. The social and bioethical concerns in relation to human beings, other organisms, and the environment are addressed.
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Affiliation(s)
- Fatma Betül Ayanoğlu
- Tissue Engineering, Biomaterials and Nanobiotechnology Laboratory, Ankara University Faculty of Science,Ankara University Biotechnology Institute, Ankara University Stem Cell Institute, Ankara Turkey
| | - Ayşe Eser Elçin
- Tissue Engineering, Biomaterials and Nanobiotechnology Laboratory, Ankara University Faculty of Science,Ankara University Biotechnology Institute, Ankara University Stem Cell Institute, Ankara Turkey
| | - Yaşar Murat Elçin
- Tissue Engineering, Biomaterials and Nanobiotechnology Laboratory, Ankara University Faculty of Science,Ankara University Biotechnology Institute, Ankara University Stem Cell Institute, Ankara Turkey.,Biovalda Health Technologies, Inc., Ankara Turkey
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10
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Filice F, Schwaller B, Michel TM, Grünblatt E. Profiling parvalbumin interneurons using iPSC: challenges and perspectives for Autism Spectrum Disorder (ASD). Mol Autism 2020; 11:10. [PMID: 32000856 PMCID: PMC6990584 DOI: 10.1186/s13229-020-0314-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/02/2020] [Indexed: 02/07/2023] Open
Abstract
Autism spectrum disorders (ASD) are persistent conditions resulting from disrupted/altered neurodevelopment. ASD multifactorial etiology-and its numerous comorbid conditions-heightens the difficulty in identifying its underlying causes, thus obstructing the development of effective therapies. Increasing evidence from both animal and human studies suggests an altered functioning of the parvalbumin (PV)-expressing inhibitory interneurons as a common and possibly unifying pathway for some forms of ASD. PV-expressing interneurons (short: PVALB neurons) are critically implicated in the regulation of cortical networks' activity. Their particular connectivity patterns, i.e., their preferential targeting of perisomatic regions and axon initial segments of pyramidal cells, as well as their reciprocal connections, enable PVALB neurons to exert a fine-tuned control of, e.g., spike timing, resulting in the generation and modulation of rhythms in the gamma range, which are important for sensory perception and attention.New methodologies such as induced pluripotent stem cells (iPSC) and genome-editing techniques (CRISPR/Cas9) have proven to be valuable tools to get mechanistic insight in neurodevelopmental and/or neurodegenerative and neuropsychiatric diseases. Such technological advances have enabled the generation of PVALB neurons from iPSC. Tagging of these neurons would allow following their fate during the development, from precursor cells to differentiated (and functional) PVALB neurons. Also, it would enable a better understanding of PVALB neuron function, using either iPSC from healthy donors or ASD patients with known mutations in ASD risk genes. In this concept paper, the strategies hopefully leading to a better understanding of PVALB neuron function(s) are briefly discussed. We envision that such an iPSC-based approach combined with emerging (genetic) technologies may offer the opportunity to investigate in detail the role of PVALB neurons and PV during "neurodevelopment ex vivo."
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Affiliation(s)
- Federica Filice
- Department of Neuroscience & Movements Science, Section of Medicine, University of Fribourg, Fribourg, Switzerland.
| | - Beat Schwaller
- Department of Neuroscience & Movements Science, Section of Medicine, University of Fribourg, Fribourg, Switzerland
| | - Tanja M Michel
- Department of Psychiatry, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Psychiatry in the Region of Southern Denmark, Department of Psychiatry, Odense University Hospital Southern Denmark, Odense, Denmark
- Research Unit for Psychiatry Odense, Institute for Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Neumuensterallee 3, 8032, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
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11
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Song X, Xu P, Meng C, Song C, Blackwell TS, Li R, Li H, Zhang J, Lv C. lncITPF Promotes Pulmonary Fibrosis by Targeting hnRNP-L Depending on Its Host Gene ITGBL1. Mol Ther 2018; 27:380-393. [PMID: 30528088 DOI: 10.1016/j.ymthe.2018.08.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/26/2018] [Accepted: 08/31/2018] [Indexed: 01/27/2023] Open
Abstract
The role of long non-coding RNA (lncRNA) in idiopathic pulmonary fibrosis (IPF) is poorly understood. We found a novel lncRNA-ITPF that was upregulated in IPF. Bioinformatics and in vitro translation verified that lncITPF is an actual lncRNA, and its conservation is in evolution. Northern blot and rapid amplification of complementary DNA ends were used to analyze the full-length sequence of lncITPF. RNA fluorescence in situ hybridization and nucleocytoplasmic separation demonstrated that lncITPF was mainly located in the nucleus. RNA sequencing, chromatin immunoprecipitation (ChIP)-qPCR, CRISPR-Cas9 technology, and promoter activity analysis showed that the fibrotic function of lncITPF depends on its host gene integrin β-like 1 (ITGBL1), but they did not share the same promoter and were not co-transcribed. Luciferase activity, pathway inhibitors, and ChIP-qPCR showed that smad2/3 binds to the lncITPF promoter, and TGF-β1-smad2/3 was the upstream inducer of the fibrotic pathway. Furthermore, RNA-protein pull-down, liquid chromatography-mass spectrometry (LC-MS), and protein-RNA immunoprecipitation showed that lncITPF regulated H3 and H4 histone acetylation in the ITGBL1 promoter by targeting heterogeneous nuclear ribonucleoprotein L. Finally, sh-lncITPF was used to evaluate the therapeutic effect of lncITPF. Clinical analysis showed that lncITPF is associated with the clinicopathological features of IPF patients. Our findings provide a therapeutic target or diagnostic biomarker for IPF.
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Affiliation(s)
- Xiaodong Song
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China; Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Pan Xu
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China
| | - Chao Meng
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China
| | - Chenguang Song
- Department of Respiratory Medicine, Zouping Chinese Medicine Hospital, Binzhou 256602, China
| | | | - Rongrong Li
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China
| | - Hongbo Li
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China
| | - Jinjin Zhang
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China; Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China.
| | - Changjun Lv
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China; Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China.
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12
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Wei W, He Y, Wu YM. Identification of genes associated with SiHa cell sensitivity to paclitaxel by CRISPR-Cas9 knockout screening. Int J Clin Exp Pathol 2018; 11:1972-1978. [PMID: 31938303 PMCID: PMC6958192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 02/22/2018] [Indexed: 06/10/2023]
Abstract
Although chemotherapy has significantly improved the prognosis of patients with cervical cancer, many patients exhibit selective responses to chemotherapy. This study aimed to identify genes associated with the sensitivity of cervical cancer cells to paclitaxel. SiHa cells were transfected with lentiCRISPR (genome-scale CRISPR knockout library v.2) and then treated with paclitaxel or vehicle for 14 days. Subsequently, we screened for candidate genes whose loss resulted in sensitivity to paclitaxel. We obtained 374 candidates, some of which were consistent with those reported in previous studies, including ABCC9, IL37, EIF3C, AKT1S1, and several members of the PPP gene family (PPP1R7, PPP2R5B, PPP1R7, and PPP1R11). Importantly, our findings highlighted the newly identified genes that could provide novel insights into the mechanisms of paclitaxel sensitivity in cervical cancer. Cas9 technology provides a reliable method for the exploration of more effective combination chemotherapies for patients at the gene level.
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Affiliation(s)
- Wei Wei
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University Beijing 100006, China
| | - Yue He
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University Beijing 100006, China
| | - Yu-Mei Wu
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University Beijing 100006, China
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Zhan C, Xia X. [Research progress of CRISPR-Cas9 system for gene therapy]. Sheng Wu Gong Cheng Xue Bao 2016; 32:861-869. [PMID: 29019208 DOI: 10.13345/j.cjb.150542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The clustered regulatory interspaced short palindromic repeat-Cas9 (CRISPR-Cas9) system is the part of the prokaryotic immune system, which could recognize and delete the exogenous sequences originated from virus or plasmid. Based on its mechanism, CRISPR-Cas9 system was developed into the new generation of gene editing tool. Compared to the existed technologies such as ES targeting, ZFN or TALEN, CRISPR-Cas9 system is a more efficient, economical and promising approach to manipulate the genome. In this review, we summarize the research progress about CRISPR-Cas9 technology, especially the latest applications in gene therapy studies of human diseases.
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Affiliation(s)
- Changsheng Zhan
- School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Xiaoyu Xia
- School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
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