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Li Y, Li C, Yan J, Liao Y, Qin C, Wang L, Huang Y, Yang C, Wang J, Ding X, Yang YY, Yuan P. Polymeric micellar nanoparticles for effective CRISPR/Cas9 genome editing in cancer. Biomaterials 2024; 309:122573. [PMID: 38677222 DOI: 10.1016/j.biomaterials.2024.122573] [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: 11/12/2023] [Revised: 03/21/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 9 (Cas9) gene editing has attracted extensive attentions in various fields, however, its clinical application is hindered by the lack of effective and safe delivery system. Herein, we reported a cationic micelle nanoparticle composed of cholesterol-modified branched small molecular PEI (PEI-CHO) and biodegradable PEG-b-polycarbonate block copolymer (PEG-PC), denoted as PEG-PC/PEI-CHO/pCas9, for the CRISPR/Cas9 delivery to realize genomic editing in cancer. Specifically, PEI-CHO condensed pCas9 into nanocomplexes, which were further encapsulated into PEG-PC nanoparticles (PEG-PC/PEI-CHO/pCas9). PEG-PC/PEI-CHO/pCas9 had a PEG shell, protecting DNA from degradation by nucleases. Enhanced cellular uptake of PEG-PC/PEI-CHO/pCas9 nanoparticles was observed as compared to that mediated by Lipo2k/pCas9 nanoparticles, thus leading to significantly elevated transfection efficiency after escaping from endosomes via the proton sponge effect of PEI. In addition, the presence of PEG shell greatly improved biocompatibility, and significantly enhanced the in vivo tumor retention of pCas9 compared to PEI-CHO/pCas9. Notably, apparent downregulation of GFP expression could be achieved both in vitro and in vivo by using PEG-PC/PEI-CHO/pCas9-sgGFP nanoparticles. Furthermore, PEG-PC/PEI-CHO/pCas9-sgMcl1 induced effective apoptosis and tumor suppression in a HeLa tumor xenograft mouse model by downregulating Mcl1 expression. This work may provide an alternative paradigm for the efficient and safe genome editing in cancer.
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Affiliation(s)
- Yuzhen Li
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chun Li
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Jiachang Yan
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Ying Liao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Chengyuan Qin
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Lingyin Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Yi Huang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chuan Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Republic of Singapore
| | - Jianwei Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
| | - Xin Ding
- School of Medicine, Sun Yat-sen University, Shenzhen, 518107, China.
| | - Yi Yan Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Republic of Singapore.
| | - Peiyan Yuan
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China.
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2
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Miao P, Sun Y, Zheng G, Wang B, Wang W, Zhang J, Yan M, Lv Y. Near-infrared light-induced homogeneous photoelectrochemical biosensor based on 3D walking nanomotor-assisted CRISPR/Cas12a for ultrasensitive microRNA-155 detection. J Colloid Interface Sci 2024; 667:82-90. [PMID: 38621334 DOI: 10.1016/j.jcis.2024.04.012] [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: 01/22/2024] [Revised: 03/30/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024]
Abstract
The dysregulation of microRNA (miRNA) expression levels is intricately linked to a myriad of human diseases, and the precise and delicate detection thereof holds paramount significance in the realm of clinical diagnosis and therapy. Herein, a near-infrared (NIR) light-mediated homogeneous photoelectrochemical (PEC) biosensor was constructed for miRNA-155 detection based on NaYF4: Yb, Tm@ZnIn2S4 (NYF@ ZIS) coupled with a three-dimensional (3D) walking nanomotor-assisted CRISPR/Cas12a strategy. The upconverted light emitted by the NYF in the visible and UV region upon NIR light excitation could be utilized to excite ZIS to produce a photocurrent response. The presence of target miRNA-155 initiated an amplification reaction within the 3D walking nanomotor, resulting in the production of multiple nucleic acid fragments. These fragments could activate the collateral cleavage capability of CRISPR/Cas12a, leading to the indiscriminate cleavage of single-stranded DNA (ssDNA) on ALP-ssDNA-modified magnetic beads and the subsequent liberation of alkaline phosphatase (ALP). The released ALP facilitated the catalysis of ascorbic acid 2-phosphate to generate ascorbic acid as the electron donor to capture the photogenerated holes on the NYF@ZIS surface, resulting in a positively correlated alteration in the photocurrent response. Under optimal conditions, the NIR light-initiated homogeneous PEC biosensor had the merits of good linear range (0.1 fM to 100 pM), an acceptable limit of detection (65.77 aM) for miRNA-155 detection. Considering the pronounced sensitivity, light stability, and low photodamage, this strategy presents a promising platform for detecting various other miRNA biomarkers in molecular diagnostic practice.
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Affiliation(s)
- Pei Miao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Yan Sun
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Gengxiu Zheng
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Bin Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Wenshou Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Jing Zhang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China.
| | - Mei Yan
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China.
| | - Yanfeng Lv
- Department of Colorectal & Anal Surgery, The Second Hospital of Shandong University, Jinan 250033, PR China.
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3
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Niu Z, Du H, Ma L, Zhou J, Yuan Z, Sun R, Liu G, Zhang F, Zeng Y. Wavelength Division Multiplexing-Based High-Sensitivity Surface Plasmon Resonance Imaging Biosensor for High-Throughput Real-Time Molecular Interaction Analysis. Molecules 2024; 29:2811. [PMID: 38930876 PMCID: PMC11206673 DOI: 10.3390/molecules29122811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
In this study, we report the successful development of a novel high-sensitivity intensity-based Surface Plasmon Resonance imaging (SPRi) biosensor and its application for detecting molecular interactions. By optimizing the excitation wavelength and employing a wavelength division multiplexing (WDM) algorithm, the system can determine the optimal excitation wavelength based on the initial refractive index of the sample without adjusting the incidence angle. The experimental results demonstrate that the refractive index resolution of the system reaches 1.77×10-6 RIU. Moreover, it can obtain the optimal excitation wavelength for samples with an initial refractive index in the range of 1.333 to 1.370 RIU and accurately monitor variations within the range of 0.0037 RIU without adjusting the incidence angle. Additionally, our new SPRi technique realized real-time detection of high-throughput biomolecular binding processes, enabling analysis of kinetic parameters. This research is expected to advance the development of more accurate SPRi technologies for molecular interaction analysis.
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Affiliation(s)
- Zhenxiao Niu
- School of Physics and Optoelectronic Engineering, Guangdong University of Technology, Guangzhou 510006, China; (Z.N.); (H.D.); (L.M.); (G.L.); (F.Z.)
- Guangdong Provincial Key Laboratory of Sensing Physics and System Integration Applications, Guangdong University of Technology, Guangzhou 510006, China
| | - Hao Du
- School of Physics and Optoelectronic Engineering, Guangdong University of Technology, Guangzhou 510006, China; (Z.N.); (H.D.); (L.M.); (G.L.); (F.Z.)
- Guangdong Provincial Key Laboratory of Sensing Physics and System Integration Applications, Guangdong University of Technology, Guangzhou 510006, China
| | - Lin Ma
- School of Physics and Optoelectronic Engineering, Guangdong University of Technology, Guangzhou 510006, China; (Z.N.); (H.D.); (L.M.); (G.L.); (F.Z.)
- Guangdong Provincial Key Laboratory of Sensing Physics and System Integration Applications, Guangdong University of Technology, Guangzhou 510006, China
| | - Jie Zhou
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, China;
- Hubei Shizhen Laboratory, Wuhan 430065, China
| | - Zhengqiang Yuan
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China; (Z.Y.); (R.S.)
| | - Ronghui Sun
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China; (Z.Y.); (R.S.)
| | - Guanyu Liu
- School of Physics and Optoelectronic Engineering, Guangdong University of Technology, Guangzhou 510006, China; (Z.N.); (H.D.); (L.M.); (G.L.); (F.Z.)
- Guangdong Provincial Key Laboratory of Sensing Physics and System Integration Applications, Guangdong University of Technology, Guangzhou 510006, China
| | - Fangteng Zhang
- School of Physics and Optoelectronic Engineering, Guangdong University of Technology, Guangzhou 510006, China; (Z.N.); (H.D.); (L.M.); (G.L.); (F.Z.)
- Guangdong Provincial Key Laboratory of Sensing Physics and System Integration Applications, Guangdong University of Technology, Guangzhou 510006, China
| | - Youjun Zeng
- School of Physics and Optoelectronic Engineering, Guangdong University of Technology, Guangzhou 510006, China; (Z.N.); (H.D.); (L.M.); (G.L.); (F.Z.)
- Guangdong Provincial Key Laboratory of Sensing Physics and System Integration Applications, Guangdong University of Technology, Guangzhou 510006, China
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Esposito F, Dell'Aquila F, Rhiel M, Auricchio S, Chmielewski KO, Andrieux G, Ferla R, Horrach PS, Padmanabhan A, Di Cunto R, Notaro S, Santeularia ML, Boerries M, Dell'Anno M, Nusco E, Padula A, Nutarelli S, Cornu TI, Sorrentino NC, Piccolo P, Trapani I, Cathomen T, Auricchio A. Safe and effective liver-directed AAV-mediated homology-independent targeted integration in mouse models of inherited diseases. Cell Rep Med 2024:101619. [PMID: 38897206 DOI: 10.1016/j.xcrm.2024.101619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/13/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024]
Abstract
Liver-directed adeno-associated viral (AAV) vector-mediated homology-independent targeted integration (AAV-HITI) by CRISPR-Cas9 at the highly transcribed albumin locus is under investigation to provide sustained transgene expression following neonatal treatment. We show that targeting the 3' end of the albumin locus results in productive integration in about 15% of mouse hepatocytes achieving therapeutic levels of systemic proteins in two mouse models of inherited diseases. We demonstrate that full-length HITI donor DNA is preferentially integrated upon nuclease cleavage and that, despite partial AAV genome integrations in the target locus, no gross chromosomal rearrangements or insertions/deletions at off-target sites are found. In line with this, no evidence of hepatocellular carcinoma is observed within the 1-year follow-up. Finally, AAV-HITI is effective at vector doses considered safe if directly translated to humans providing therapeutic efficacy in the adult liver in addition to newborn. Overall, our data support the development of this liver-directed AAV-based knockin strategy.
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Affiliation(s)
- Federica Esposito
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Fabio Dell'Aquila
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Medical Genetics, Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | - Manuel Rhiel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
| | - Stefano Auricchio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Kay Ole Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany; PhD Program, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Rita Ferla
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Arjun Padmanabhan
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Roberto Di Cunto
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Simone Notaro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK), Partner site Freiburg, a partnership between DKFZ and Medical Center - University of Freiburg, Freiburg, Germany
| | | | - Edoardo Nusco
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Agnese Padula
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Sofia Nutarelli
- Department of Life Science and Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - Tatjana I Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nicolina Cristina Sorrentino
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Pasquale Piccolo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Ivana Trapani
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Medical Genetics, Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK), Partner site Freiburg, a partnership between DKFZ and Medical Center - University of Freiburg, Freiburg, Germany
| | - Alberto Auricchio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Gene Therapy Joint lab, Dept. of Advanced Biomedical Sciences and Dept. of Translational Medicine, University of Naples "Federico II", Naples, Italy.
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5
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Fang T, Chen G. Non-viral vector-based genome editing for cancer immunotherapy. Biomater Sci 2024; 12:3068-3085. [PMID: 38716572 DOI: 10.1039/d4bm00286e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Despite the exciting promise of cancer immunotherapy in the clinic, immune checkpoint blockade therapy and T cell-based therapies are often associated with low response rates, intrinsic and adaptive immune resistance, and systemic side effects. CRISPR-Cas-based genome editing appears to be an effective strategy to overcome these unmet clinical needs. As a safer delivery platform for the CRISPR-Cas system, non-viral nanoformulations have been recently explored to target tumor cells and immune cells, aiming to improve cancer immunotherapy on a gene level. In this review, we summarized the efforts of non-viral vector-based CRISPR-Cas-mediated genome editing in tumor cells and immune cells for cancer immunotherapy. Their design rationale and specific applications were highlighted.
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Affiliation(s)
- Tianxu Fang
- Department of Biomedical Engineering, McGill University, Montreal, QC, H3G 0B1, Canada.
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Guojun Chen
- Department of Biomedical Engineering, McGill University, Montreal, QC, H3G 0B1, Canada.
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3G 0B1, Canada
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Nasri M, Ritter MU, Mir P, Dannenmann B, Kaufmann MM, Arreba-Tutusaus P, Xu Y, Borbaran-Bravo N, Klimiankou M, Lengerke C, Zeidler C, Cathomen T, Welte K, Skokowa J. CRISPR-Cas9n-mediated ELANE promoter editing for gene therapy of severe congenital neutropenia. Mol Ther 2024; 32:1628-1642. [PMID: 38556793 PMCID: PMC11184331 DOI: 10.1016/j.ymthe.2024.03.037] [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: 06/29/2023] [Revised: 12/07/2023] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
Severe congenital neutropenia (CN) is an inherited pre-leukemia bone marrow failure syndrome commonly caused by autosomal-dominant ELANE mutations (ELANE-CN). ELANE-CN patients are treated with daily injections of recombinant human granulocyte colony-stimulating factor (rhG-CSF). However, some patients do not respond to rhG-CSF, and approximately 15% of ELANE-CN patients develop myelodysplasia or acute myeloid leukemia. Here, we report the development of a curative therapy for ELANE-CN through inhibition of ELANE mRNA expression by introducing two single-strand DNA breaks at the opposing DNA strands of the ELANE promoter TATA box using CRISPR-Cas9D10A nickases-termed MILESTONE. This editing effectively restored defective neutrophil differentiation of ELANE-CN CD34+ hematopoietic stem and progenitor cells (HSPCs) in vitro and in vivo, without affecting the functions of the edited neutrophils. CRISPResso analysis of the edited ELANE-CN CD34+ HSPCs revealed on-target efficiencies of over 90%. Simultaneously, GUIDE-seq, CAST-Seq, and rhAmpSeq indicated a safe off-target profile with no off-target sites or chromosomal translocations. Taken together, ex vivo gene editing of ELANE-CN HSPCs using MILESTONE in the setting of autologous stem cell transplantation could be a universal, safe, and efficient gene therapy approach for ELANE-CN patients.
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Affiliation(s)
- Masoud Nasri
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany.
| | - Malte U Ritter
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany.
| | - Perihan Mir
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Benjamin Dannenmann
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Masako M Kaufmann
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; Spemann Graduate School of Biology and Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Patricia Arreba-Tutusaus
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Yun Xu
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Natalia Borbaran-Bravo
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Maksim Klimiankou
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Claudia Lengerke
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Cornelia Zeidler
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Karl Welte
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; Department of Pediatric Hematology, Oncology and Bone Marrow Transplantation, Children`s Hospital, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Julia Skokowa
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; Gene and RNA Therapy Center (GRTC), University Hospital Tübingen, 72076 Tübingen, Germany
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7
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Li T, Wang J, Fang J, Chen F, Wu X, Wang L, Gao M, Zhang L, Li S. A universal nucleic acid detection platform combing CRISPR/Cas12a and strand displacement amplification with multiple signal readout. Talanta 2024; 273:125922. [PMID: 38503121 DOI: 10.1016/j.talanta.2024.125922] [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: 08/07/2023] [Revised: 02/08/2024] [Accepted: 03/13/2024] [Indexed: 03/21/2024]
Abstract
Rapid and sensitive detection of nucleic acids has become crucial in various fields. However, most current nucleic acid detection methods can only be used in specific scenarios, such as RT-qPCR, which relies on fluorometer for signal readout, limiting its application at home or in the field due to its high price. In this paper, a universal nucleic acid detection platform combing CRISPR/Cas12a and strand displacement amplification (CRISPR-SDA) with multiple signal readout was established to adapt to different application scenarios. Nucleocapsid protein gene of SARS-CoV-2 (N gene) and hepatitis B virus (HBV) DNA were selected as model targets. The proposed strategy achieved the sensitivity of 53.1 fM, 0.15 pM, and 1 pM for N gene in fluorescence mode, personal glucose meter (PGM) mode and lateral flow assay (LFA) mode, respectively. It possessed the ability to differentiate single-base mismatch and the presence of salmon sperm DNA with a mass up to 105-fold of the targets did not significantly interfere with the assay signal. The general and modular design idea made CRISPR-SDA as simple as building blocks to construct nucleic acid sensing methods to meet different requirements by simply changing the SDA template and selecting suitable signal report probes, which was expected to find a breadth of applications in nucleic acids detection.
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Affiliation(s)
- Tian Li
- College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, 471023, China.
| | - Jinjin Wang
- College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, 471023, China
| | - Jiaoyuan Fang
- College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, 471023, China
| | - Fei Chen
- College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xinru Wu
- College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, 471023, China
| | - Lan Wang
- College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, 471023, China
| | - Meng Gao
- College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, 471023, China
| | - Liping Zhang
- College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, 471023, China.
| | - Sanqiang Li
- College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, 471023, China.
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8
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Lazar NH, Celik S, Chen L, Fay MM, Irish JC, Jensen J, Tillinghast CA, Urbanik J, Bone WP, Gibson CC, Haque IS. High-resolution genome-wide mapping of chromosome-arm-scale truncations induced by CRISPR-Cas9 editing. Nat Genet 2024:10.1038/s41588-024-01758-y. [PMID: 38811841 DOI: 10.1038/s41588-024-01758-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 04/18/2024] [Indexed: 05/31/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) is a powerful tool for introducing targeted mutations in DNA, but recent studies have shown that it can have unintended effects such as structural changes. However, these studies have not yet looked genome wide or across data types. Here we performed a phenotypic CRISPR-Cas9 scan targeting 17,065 genes in primary human cells, revealing a 'proximity bias' in which CRISPR knockouts show unexpected similarities to unrelated genes on the same chromosome arm. This bias was found to be consistent across cell types, laboratories, Cas9 delivery methods and assay modalities, and the data suggest that it is caused by telomeric truncations of chromosome arms, with cell cycle and apoptotic pathways playing a mediating role. Additionally, a simple correction is demonstrated to mitigate this pervasive bias while preserving biological relationships. This previously uncharacterized effect has implications for functional genomic studies using CRISPR-Cas9, with applications in discovery biology, drug-target identification, cell therapies and genetic therapeutics.
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Affiliation(s)
| | | | - Lu Chen
- Recursion, Salt Lake City, UT, USA
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9
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Zhang R, Chai N, Liu T, Zheng Z, Lin Q, Xie X, Wen J, Yang Z, Liu YG, Zhu Q. The type V effectors for CRISPR/Cas-mediated genome engineering in plants. Biotechnol Adv 2024; 74:108382. [PMID: 38801866 DOI: 10.1016/j.biotechadv.2024.108382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/07/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
A plethora of CRISPR effectors, such as Cas3, Cas9, and Cas12a, are commonly employed as gene editing tools. Among these, Cas12 effectors developed based on Class II type V proteins exhibit distinct characteristics compared to Class II type VI and type II effectors, such as their ability to generate non-allelic DNA double-strand breaks, their compact structures, and the presence of a single RuvC-like nuclease domain. Capitalizing on these advantages, Cas12 family proteins have been increasingly explored and utilized in recent years. However, the characteristics and applications of different subfamilies within the type V protein family have not been systematically summarized. In this review, we focus on the characteristics of type V effector (CRISPR/Cas12) proteins and the current methods used to discover new effector proteins. We also summarize recent modifications based on engineering of type V effectors. In addition, we introduce the applications of type V effectors for gene editing in animals and plants, including the development of base editors, tools for regulating gene expression, methods for gene targeting, and biosensors. We emphasize the prospects for development and application of CRISPR/Cas12 effectors with the goal of better utilizing toolkits based on this protein family for crop improvement and enhanced agricultural production.
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Affiliation(s)
- Ruixiang Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Nan Chai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Taoli Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhiye Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qiupeng Lin
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jun Wen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zi Yang
- College of Natural & Agricultural Sciences, University of California, Riverside, 900 University Ave, Riverside, CA 92507, USA
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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10
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Guo Y, Chen X, Gan Y, Li Y, Wang R. Targeted i 6A-RNA degradation through sequential Fluorination-Azidation and Click reaction with imidazole-based probes. Bioorg Med Chem Lett 2024; 108:129815. [PMID: 38795737 DOI: 10.1016/j.bmcl.2024.129815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/07/2024] [Accepted: 05/22/2024] [Indexed: 05/28/2024]
Abstract
We report the use of trimethylsilyl azide and Selectfluor to implement a standard protocol targeted at the prenylated nucleic acid known as i6A-RNA. After optimizing the conditions, we applied this method to regulate a wide range of i6A-RNA species using synthetic imidazole-based probes (I-IV). We observed that prenylated nucleic acid plays a crucial role in the cell hemostasis in A549 cell lines.
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Affiliation(s)
- Yuyang Guo
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Xiaoqian Chen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Youfang Gan
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yuanyuan Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Rui Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong 518063, China.
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11
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Zhou Y, Tao L, Qiu J, Xu J, Yang X, Zhang Y, Tian X, Guan X, Cen X, Zhao Y. Tumor biomarkers for diagnosis, prognosis and targeted therapy. Signal Transduct Target Ther 2024; 9:132. [PMID: 38763973 PMCID: PMC11102923 DOI: 10.1038/s41392-024-01823-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 03/07/2024] [Accepted: 04/02/2024] [Indexed: 05/21/2024] Open
Abstract
Tumor biomarkers, the substances which are produced by tumors or the body's responses to tumors during tumorigenesis and progression, have been demonstrated to possess critical and encouraging value in screening and early diagnosis, prognosis prediction, recurrence detection, and therapeutic efficacy monitoring of cancers. Over the past decades, continuous progress has been made in exploring and discovering novel, sensitive, specific, and accurate tumor biomarkers, which has significantly promoted personalized medicine and improved the outcomes of cancer patients, especially advances in molecular biology technologies developed for the detection of tumor biomarkers. Herein, we summarize the discovery and development of tumor biomarkers, including the history of tumor biomarkers, the conventional and innovative technologies used for biomarker discovery and detection, the classification of tumor biomarkers based on tissue origins, and the application of tumor biomarkers in clinical cancer management. In particular, we highlight the recent advancements in biomarker-based anticancer-targeted therapies which are emerging as breakthroughs and promising cancer therapeutic strategies. We also discuss limitations and challenges that need to be addressed and provide insights and perspectives to turn challenges into opportunities in this field. Collectively, the discovery and application of multiple tumor biomarkers emphasized in this review may provide guidance on improved precision medicine, broaden horizons in future research directions, and expedite the clinical classification of cancer patients according to their molecular biomarkers rather than organs of origin.
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Affiliation(s)
- Yue Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lei Tao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jiahao Qiu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jing Xu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinyu Yang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yu Zhang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
- School of Medicine, Tibet University, Lhasa, 850000, China
| | - Xinyu Tian
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinqi Guan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaobo Cen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yinglan Zhao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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12
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Ottonelli I, Adani E, Bighinati A, Cuoghi S, Tosi G, Vandelli MA, Ruozi B, Marigo V, Duskey JT. Strategies for Improved pDNA Loading and Protection Using Cationic and Neutral LNPs with Industrial Scalability Potential Using Microfluidic Technology. Int J Nanomedicine 2024; 19:4235-4251. [PMID: 38766661 PMCID: PMC11102183 DOI: 10.2147/ijn.s457302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024] Open
Abstract
Purpose In recent years, microfluidic technologies have become mainstream in producing gene therapy nanomedicines (NMeds) following the Covid-19 vaccine; however, extensive optimizations are needed for each NMed type and genetic material. This article strives to improve LNPs for pDNA loading, protection, and delivery, while minimizing toxicity. Methods The microfluidic technique was optimized to form cationic or neutral LNPs to load pDNA. Classical "post-formulation" DNA addition vs "pre" addition in the aqueous phase were compared. All formulations were characterized (size, homogeneity, zeta potential, morphology, weight yield, and stability), then tested for loading efficiency, nuclease protection, toxicity, and cell uptake. Results Optimized LNPs formulated with DPPC: Chol:DOTAP 1:1:0.1 molar ratio and 10 µg of DOPE-Rhod, had a size of 160 nm and good homogeneity. The chemico-physical characteristics of cationic LNPs worsened when adding 15 µg/mL of pDNA with the "post" method, while maintaining their characteristics up to 100 µg/mL of pDNA with the "pre" addition remaining stable for 30 days. Interestingly, neutral LNPs formulated with the same method loaded up to 50% of the DNA. Both particles could protect the DNA from nucleases even after one month of storage, and low cell toxicity was found up to 40 µg/mL LNPs. Cell uptake occurred within 2 hours for both formulations with the DNA intact in the cytoplasm, outside of the lysosomes. Conclusion In this study, the upcoming microfluidic technique was applied to two strategies to generate pDNA-LNPs. Cationic LNPs could load 10x the amount of DNA as the classical approach, while neutral LNPs, which also loaded and protected DNA, showed lower toxicity and good DNA protection. This is a big step forward at minimizing doses and toxicity of LNP-based gene therapy.
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Affiliation(s)
- Ilaria Ottonelli
- Nanotech Lab, Te.Far.T.I., Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Elisa Adani
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea Bighinati
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Sabrina Cuoghi
- Nanotech Lab, Te.Far.T.I., Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Giovanni Tosi
- Nanotech Lab, Te.Far.T.I., Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Center for Neuroscience and Neurotechnology, Modena, Italy
| | - Maria Angela Vandelli
- Nanotech Lab, Te.Far.T.I., Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Barbara Ruozi
- Nanotech Lab, Te.Far.T.I., Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Valeria Marigo
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Center for Neuroscience and Neurotechnology, Modena, Italy
| | - Jason Thomas Duskey
- Nanotech Lab, Te.Far.T.I., Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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13
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Wu Y, Jin R, Chang Y, Liu M. A high-fidelity DNAzyme-assisted CRISPR/Cas13a system with single-nucleotide resolved specificity. Chem Sci 2024; 15:6934-6942. [PMID: 38725495 PMCID: PMC11077575 DOI: 10.1039/d4sc01501k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/01/2024] [Indexed: 05/12/2024] Open
Abstract
A CRISPR/Cas system represents an innovative tool for developing a new-generation biosensing and diagnostic strategy. However, the off-target issue (i.e., mistaken cleavage of nucleic acid targets and reporters) remains a great challenge for its practical applications. We hypothesize that this issue can be overcome by taking advantage of the site-specific cleavage ability of RNA-cleaving DNAzymes. To test this idea, we propose a DNAzyme Operation Enhances the Specificity of CRISPR/Cas13a strategy (termed DOES-CRISPR) to overcome the problem of relatively poor specificity that is typical of the traditional CRISPR/Cas13a system. The key to the design is that the partial hybridization of the CRISPR RNA (crRNA) with the cleavage fragment of off-target RNA was not able to activate the collateral cleavage activity of Cas13a. We showed that DOES-CRISPR can significantly improve the specificity of traditional CRISPR/Cas13a-based molecular detection by up to ∼43-fold. The broad utility of the strategy is illustrated through engineering three different systems for the detection of microRNAs (miR-17 and let-7e), CYP2C19*17 gene, SARS-Cov-2 variants (Gamma, Delta, and Omicron) and Omicron subtypes (BQ.1 and XBB.1) with single-nucleotide resolved specificity. Finally, clinical evaluation of this assay using 10 patient blood samples demonstrated a clinical sensitivity of 100% and specificity of 100% for genotyping CYP2C19*17, and analyzing 20 throat swab samples provided a diagnostic sensitivity of 95% and specificity of 100% for Omicron detection, and a clinical sensitivity of 92% and specificity of 100% for XBB.1 detection.
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Affiliation(s)
- Yunping Wu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
| | - Ruigang Jin
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
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14
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Lemmens M, Dorsheimer L, Zeller A, Dietz-Baum Y. Non-clinical safety assessment of novel drug modalities: Genome safety perspectives on viral-, nuclease- and nucleotide-based gene therapies. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2024; 896:503767. [PMID: 38821669 DOI: 10.1016/j.mrgentox.2024.503767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/08/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024]
Abstract
Gene therapies have emerged as promising treatments for various conditions including inherited diseases as well as cancer. Ensuring their safe clinical application requires the development of appropriate safety testing strategies. Several guidelines have been provided by health authorities to address these concerns. These guidelines state that non-clinical testing should be carried out on a case-by-case basis depending on the modality. This review focuses on the genome safety assessment of frequently used gene therapy modalities, namely Adeno Associated Viruses (AAVs), Lentiviruses, designer nucleases and mRNAs. Important safety considerations for these modalities, amongst others, are vector integrations into the patient genome (insertional mutagenesis) and off-target editing. Taking into account the constraints of in vivo studies, health authorities endorse the development of novel approach methodologies (NAMs), which are innovative in vitro strategies for genotoxicity testing. This review provides an overview of NAMs applied to viral and CRISPR/Cas9 safety, including next generation sequencing-based methods for integration site analysis and off-target editing. Additionally, NAMs to evaluate the oncogenicity risk arising from unwanted genomic modifications are discussed. Thus, a range of promising techniques are available to support the safe development of gene therapies. Thorough validation, comparisons and correlations with clinical outcomes are essential to identify the most reliable safety testing strategies. By providing a comprehensive overview of these NAMs, this review aims to contribute to a better understanding of the genome safety perspectives of gene therapies.
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Affiliation(s)
| | - Lena Dorsheimer
- Research and Development, Preclinical Safety, Sanofi, Industriepark Hoechst, Frankfurt am Main 65926, Germany.
| | - Andreas Zeller
- Pharmaceutical Sciences, pRED Innovation Center Basel, Hoffmann-La Roche Ltd, Basel 4070, Switzerland
| | - Yasmin Dietz-Baum
- Research and Development, Preclinical Safety, Sanofi, Industriepark Hoechst, Frankfurt am Main 65926, Germany
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15
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Locatelli F, Cavazzana M, Frangoul H, Fuente JDL, Algeri M, Meisel R. Autologous gene therapy for hemoglobinopathies: From bench to patient's bedside. Mol Ther 2024; 32:1202-1218. [PMID: 38454604 PMCID: PMC11081872 DOI: 10.1016/j.ymthe.2024.03.005] [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: 05/05/2023] [Revised: 01/31/2024] [Accepted: 03/05/2024] [Indexed: 03/09/2024] Open
Abstract
In recent years, a growing number of clinical trials have been initiated to evaluate gene therapy approaches for the treatment of patients with transfusion-dependent β-thalassemia and sickle cell disease (SCD). Therapeutic modalities being assessed in these trials utilize different molecular techniques, including lentiviral vectors to add functional copies of the gene encoding the hemoglobin β subunit in defective cells and CRISPR-Cas9, transcription activator-like effector protein nuclease, and zinc finger nuclease gene editing strategies to either directly address the underlying genetic cause of disease or induce fetal hemoglobin production by gene disruption. Here, we review the mechanisms of action of these various gene addition and gene editing approaches and describe the status of clinical trials designed to evaluate the potentially for these approaches to provide one-time functional cures to patients with transfusion-dependent β-thalassemia and SCD.
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Affiliation(s)
- Franco Locatelli
- Department of Pediatric Haematology/Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, 00165 Rome, Italy; Catholic University of the Sacred Heart, 00168 Rome, Italy.
| | - Marina Cavazzana
- Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), University of Paris, 75006 Paris, France
| | - Haydar Frangoul
- Sarah Cannon Center for Blood Cancer at The Children's Hospital at TriStar Centennial, Nashville, TN 37203, USA
| | - Josu de la Fuente
- Imperial College Healthcare NHS Trust, St Mary's Hospital, London W21NY, UK
| | - Mattia Algeri
- Department of Pediatric Haematology/Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, 00165 Rome, Italy; Department of Health Sciences, Magna Graecia University, 88100 Catanzaro, Italy
| | - Roland Meisel
- Division of Pediatric Stem Cell Therapy, Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Duesseldorf, Germany
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16
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Eghbalsaied S, Lawler C, Petersen B, Hajiyev RA, Bischoff SR, Frankenberg S. CRISPR/Cas9-mediated base editors and their prospects for mitochondrial genome engineering. Gene Ther 2024; 31:209-223. [PMID: 38177342 DOI: 10.1038/s41434-023-00434-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024]
Abstract
Base editors are a type of double-stranded break (DSB)-free gene editing technology that has opened up new possibilities for precise manipulation of mitochondrial DNA (mtDNA). This includes cytosine and adenosine base editors and more recently guanosine base editors. Because of having low off-target and indel rates, there is a growing interest in developing and evolving this research field. Here, we provide a detailed update on DNA base editors. While base editing has widely been used for nuclear genome engineering, the growing interest in applying this technology to mitochondrial DNA has been faced with several challenges. While Cas9 protein has been shown to enter mitochondria, use of smaller Cas proteins, such as Cas12a, has higher import efficiency. However, sgRNA transfer into mitochondria is the most challenging step. sgRNA structure and ratio of Cas protein to sgRNA are both important factors for efficient sgRNA entry into mitochondria. In conclusion, while there are still several challenges to be addressed, ongoing research in this field holds the potential for new treatments and therapies for mitochondrial disorders.
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Affiliation(s)
- Shahin Eghbalsaied
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia.
- Department of Animal Science, Isfahan Branch, Islamic Azad University (IAU), Isfahan, Iran.
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Göttingen, Germany.
| | - Clancy Lawler
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Björn Petersen
- Department of Biotechnology, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institute (FLI), Mariensee, Germany
- eGenesis, 2706 HWY E, 53572, Mount Horeb, WI, USA
| | - Raul A Hajiyev
- Department of Genome Engineering, NovoHelix, Miami, FL, USA
- Department of Computer Science, Kent State University, Kent, OH, USA
| | - Steve R Bischoff
- Department of Genome Engineering, NovoHelix, Miami, FL, USA
- Foundry for Genome Engineering & Reproductive Medicine (FGERM), Miami, FL, USA
| | - Stephen Frankenberg
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia.
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17
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Zaman QU, Raza A, Lozano-Juste J, Chao L, Jones MGK, Wang HF, Varshney RK. Engineering plants using diverse CRISPR-associated proteins and deregulation of genome-edited crops. Trends Biotechnol 2024; 42:560-574. [PMID: 37993299 DOI: 10.1016/j.tibtech.2023.10.007] [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: 08/20/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/24/2023]
Abstract
The CRISPR/Cas system comprises RNA-guided nucleases, the target specificity of which is directed by Watson-Crick base pairing of target loci with single guide (sg)RNA to induce the desired edits. CRISPR-associated proteins and other engineered nucleases are opening new avenues of research in crops to induce heritable mutations. Here, we review the diversity of CRISPR-associated proteins and strategies to deregulate genome-edited (GEd) crops by considering them to be close to natural processes. This technology ensures yield without penalties, advances plant breeding, and guarantees manipulation of the genome for desirable traits. DNA-free and off-target-free GEd crops with defined characteristics can help to achieve sustainable global food security under a changing climate, but need alignment of international regulations to operate in existing supply chains.
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Affiliation(s)
- Qamar U Zaman
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Yazhou-Bay Seed Laboratory, Hainan University, Sanya, 572025, China; Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou 570228, China; Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan 430062, China
| | - Ali Raza
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Valencia 46022, Spain
| | - Li Chao
- Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan 430062, China
| | - Michael G K Jones
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, WA 6150, Australia
| | - Hua-Feng Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Yazhou-Bay Seed Laboratory, Hainan University, Sanya, 572025, China; Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou 570228, China.
| | - Rajeev K Varshney
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, WA 6150, Australia.
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18
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Johnston M, Urban N, Dincer C. Cas13d-mediated gene knockdown in CAR T cells: towards off-the-shelf cancer treatment. Signal Transduct Target Ther 2024; 9:113. [PMID: 38670950 PMCID: PMC11053049 DOI: 10.1038/s41392-024-01830-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/02/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Affiliation(s)
- Midori Johnston
- FIT Freiburg Centre for Interactive Materials and Bioinspired Technology, University of Freiburg, Freiburg, Germany
- IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Nadine Urban
- FIT Freiburg Centre for Interactive Materials and Bioinspired Technology, University of Freiburg, Freiburg, Germany
- IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Can Dincer
- FIT Freiburg Centre for Interactive Materials and Bioinspired Technology, University of Freiburg, Freiburg, Germany.
- IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany.
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19
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De Castro V, Galaine J, Loyon R, Godet Y. CRISPR-Cas gene knockouts to optimize engineered T cells for cancer immunotherapy. Cancer Gene Ther 2024:10.1038/s41417-024-00771-x. [PMID: 38609574 DOI: 10.1038/s41417-024-00771-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
While CAR-T and tgTCR-T therapies have exhibited noteworthy and promising outcomes in hematologic and solid tumors respectively, a set of distinct challenges remains. Consequently, the quest for novel strategies has become imperative to safeguard and more effectively release the full functions of engineered T cells. These factors are intricately linked to the success of adoptive cell therapy. Recently, CRISPR-based technologies have emerged as a major breakthrough for maintaining T cell functions. These technologies have allowed the discovery of T cells' negative regulators such as specific cell-surface receptors, cell-signaling proteins, and transcription factors that are involved in the development or maintenance of T cell dysfunction. By employing a CRISPR-genic invalidation approach to target these negative regulators, it has become possible to prevent the emergence of hypofunctional T cells. This review revisits the establishment of the dysfunctional profile of T cells before delving into a comprehensive summary of recent CRISPR-gene invalidations, with each invalidation contributing to the enhancement of engineered T cells' antitumor capacities. The narrative unfolds as we explore how these advancements were discovered and identified, marking a significant advancement in the pursuit of superior adoptive cell therapy.
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Affiliation(s)
- Valentine De Castro
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT, F-25000, Besançon, France
| | - Jeanne Galaine
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT, F-25000, Besançon, France
| | - Romain Loyon
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT, F-25000, Besançon, France
| | - Yann Godet
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT, F-25000, Besançon, France.
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20
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Miskalis A, Shirguppe S, Winter J, Elias G, Swami D, Nambiar A, Stilger M, Woods WS, Gosstola N, Gapinske M, Zeballos A, Moore H, Maslov S, Gaj T, Perez-Pinera P. SPLICER: A Highly Efficient Base Editing Toolbox That Enables In Vivo Therapeutic Exon Skipping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587650. [PMID: 38883727 PMCID: PMC11178003 DOI: 10.1101/2024.04.01.587650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Exon skipping technologies enable exclusion of targeted exons from mature mRNA transcripts, which has broad applications in molecular biology, medicine, and biotechnology. Existing exon skipping techniques include antisense oligonucleotides, targetable nucleases, and base editors, which, while effective for specific applications at some target exons, remain hindered by shortcomings, including transient effects for oligonucleotides, genotoxicity for nucleases and inconsistent exon skipping for base editors. To overcome these limitations, we created SPLICER, a toolbox of next-generation base editors consisting of near-PAMless Cas9 nickase variants fused to adenosine or cytosine deaminases for the simultaneous editing of splice acceptor (SA) and splice donor (SD) sequences. Synchronized SA and SD editing with SPLICER improves exon skipping, reduces aberrant outcomes, including cryptic splicing and intron retention, and enables skipping of exons refractory to single splice-site editing. To demonstrate the therapeutic potential of SPLICER, we targeted APP exon 17, which encodes the amino acid residues that are cleaved to form the Aβ plaques in Alzheimer's disease. SPLICER reduced the formation of Aβ42 peptides in vitro and enabled efficient exon skipping in a mouse model of Alzheimer's disease. Overall, SPLICER is a widely applicable and efficient toolbox for exon skipping with broad therapeutic applications.
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21
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Kovalev MA, Davletshin AI, Karpov DS. Engineering Cas9: next generation of genomic editors. Appl Microbiol Biotechnol 2024; 108:209. [PMID: 38353732 PMCID: PMC10866799 DOI: 10.1007/s00253-024-13056-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
The Cas9 endonuclease of the CRISPR/Cas type IIA system from Streptococcus pyogenes is the heart of genome editing technology that can be used to treat human genetic and viral diseases. Despite its large size and other drawbacks, S. pyogenes Cas9 remains the most widely used genome editor. A vast amount of research is aimed at improving Cas9 as a promising genetic therapy. Strategies include directed evolution of the Cas9 protein, rational design, and domain swapping. The first generation of Cas9 editors comes directly from the wild-type protein. The next generation is obtained by combining mutations from the first-generation variants, adding new mutations to them, or refining mutations. This review summarizes and discusses recent advances and ways in the creation of next-generation genomic editors derived from S. pyogenes Cas9. KEY POINTS: • The next-generation Cas9-based editors are more active than in the first one. • PAM-relaxed variants of Cas9 are improved by increased specificity and activity. • Less mutagenic and immunogenic variants of Cas9 are created.
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Affiliation(s)
- Maxim A Kovalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991, Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Artem I Davletshin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991, Moscow, Russia
| | - Dmitry S Karpov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991, Moscow, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991, Moscow, Russia.
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22
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Huang CH, Chiu SY, Chou YC, Wu KJ. A refined Uni-vector prime editing system improves genome editing outcomes in mammalian cells. Biotechnol J 2024; 19:e2300353. [PMID: 38403398 DOI: 10.1002/biot.202300353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/27/2024]
Abstract
Prime editing is an advanced technology in CRISPR/Cas research with increasing numbers of improved methodologies. The original multi-vector method hampers the efficiency and precision of prime editing and also has inherent difficulty in generating homozygous mutations in mammalian cells. To overcome these technical issues, we developed a Uni-vector prime editing system, wherein the major components for prime editing were constructed in all-in-one plasmids, pPE3-pPuro and pePEmax-pPuro. The Uni-vector prime editing plasmids enhance the editing efficiency of prime editing and improved the generation of homozygous mutated mammalian cell lines. The editing efficiency is dependent of the transfection efficiency. Remarkably, the Uni-vector ePE5max system achieved an impressive editing rate approximately 79% in average, even in cell lines that are traditionally difficult to transfect, such as FaDu cell line. Furthermore, it resulted in a high frequency of homozygous knocked-in cells, with a rate of 99% in HeLa and 85% in FaDu cells. Together, our Uni-vector approach simplifies the delivery of editing components and improves the editing efficiency, especially in cells with low transfection efficiency. This approach presents an advancement in the field of prime editing.
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Affiliation(s)
- Ching-Hui Huang
- Cancer Genome Research Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Szu-Ying Chiu
- Cancer Genome Research Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Yu-Chi Chou
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Kou-Juey Wu
- Cancer Genome Research Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
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23
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Bonnycastle LL, Swift AJ, Mansell EC, Lee A, Winnicki E, Li ES, Robertson CC, Parsons VA, Huynh T, Krilow C, Mohlke KL, Erdos MR, Narisu N, Collins FS. Generation of Human Isogenic Induced Pluripotent Stem Cell Lines with CRISPR Prime Editing. CRISPR J 2024; 7:53-67. [PMID: 38353623 PMCID: PMC10880268 DOI: 10.1089/crispr.2023.0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024] Open
Abstract
We developed an efficient CRISPR prime editing protocol and generated isogenic-induced pluripotent stem cell (iPSC) lines carrying heterozygous or homozygous alleles for putatively causal single nucleotide variants at six type 2 diabetes loci (ABCC8, MTNR1B, TCF7L2, HNF4A, CAMK1D, and GCK). Our two-step sequence-based approach to first identify transfected cell pools with the highest fraction of edited cells significantly reduced the downstream efforts to isolate single clones of edited cells. We found that prime editing can make targeted genetic changes in iPSC and optimization of system components and guide RNA designs that were critical to achieve acceptable efficiency. Systems utilizing PEmax, epegRNA modifications, and MLH1dn provided significant benefit, producing editing efficiencies of 36-73%. Editing success and pegRNA design optimization required for each variant differed depending on the sequence at the target site. With attention to design, prime editing is a promising approach to generate isogenic iPSC lines, enabling the study of specific genetic changes in a common genetic background.
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Affiliation(s)
- Lori L. Bonnycastle
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Amy J. Swift
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Erin C. Mansell
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Angela Lee
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Elizabeth Winnicki
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Elizabeth S. Li
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Catherine C. Robertson
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Victoria A. Parsons
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Trung Huynh
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Chad Krilow
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Michael R. Erdos
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Narisu Narisu
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Francis S. Collins
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
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24
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Begagić E, Bečulić H, Đuzić N, Džidić-Krivić A, Pugonja R, Muharemović A, Jaganjac B, Salković N, Sefo H, Pojskić M. CRISPR/Cas9-Mediated Gene Therapy for Glioblastoma: A Scoping Review. Biomedicines 2024; 12:238. [PMID: 38275409 PMCID: PMC10813360 DOI: 10.3390/biomedicines12010238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 01/27/2024] Open
Abstract
This scoping review examines the use of CRISPR/Cas9 gene editing in glioblastoma (GBM), a predominant and aggressive brain tumor. Categorizing gene targets into distinct groups, this review explores their roles in cell cycle regulation, microenvironmental dynamics, interphase processes, and therapy resistance reduction. The complexity of CRISPR-Cas9 applications in GBM research is highlighted, providing unique insights into apoptosis, cell proliferation, and immune responses within the tumor microenvironment. The studies challenge conventional perspectives on specific genes, emphasizing the potential therapeutic implications of manipulating key molecular players in cell cycle dynamics. Exploring CRISPR/Cas9 gene therapy in GBMs yields significant insights into the regulation of cellular processes, spanning cell interphase, renewal, and migration. Researchers, by precisely targeting specific genes, uncover the molecular orchestration governing cell proliferation, growth, and differentiation during critical phases of the cell cycle. The findings underscore the potential of CRISPR/Cas9 technology in unraveling the complex dynamics of the GBM microenvironment, offering promising avenues for targeted therapies to curb GBM growth. This review also outlines studies addressing therapy resistance in GBM, employing CRISPR/Cas9 to target genes associated with chemotherapy resistance, showcasing its transformative potential in effective GBM treatments.
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Affiliation(s)
- Emir Begagić
- Department of General Medicine, School of Medicine, University of Zenica, Travnička 1, 72000 Zenica, Bosnia and Herzegovina
| | - Hakija Bečulić
- Department of Neurosurgery, Cantonal Hospital Zenica, Crkvice 67, 72000 Zenica, Bosnia and Herzegovina
- Department of Anatomy, School of Medicine, University of Zenica, Travnička 1, 72000 Zenica, Bosnia and Herzegovina
| | - Nermin Đuzić
- Department of Genetics and Bioengineering, International Burch University Sarajevo, Francuske revolucije BB, 71000 Sarajevo, Bosnia and Herzegovina
| | - Amina Džidić-Krivić
- Department of Neurology, Cantonal Hospital Zenica, Crkvice 67, 72000 Zenica, Bosnia and Herzegovina
| | - Ragib Pugonja
- Department of Neurosurgery, Cantonal Hospital Zenica, Crkvice 67, 72000 Zenica, Bosnia and Herzegovina
| | - Asja Muharemović
- Department of Genetics and Bioengineering, International Burch University Sarajevo, Francuske revolucije BB, 71000 Sarajevo, Bosnia and Herzegovina
| | - Belma Jaganjac
- Department of Histology, School of Medicine, University of Zenica, Travnička 1, 72000 Zenica, Bosnia and Herzegovina
| | - Naida Salković
- Department of General Medicine, School of Medicine, University of Tuzla, Univerzitetska 1, 75000 Tuzla, Bosnia and Herzegovina;
| | - Haso Sefo
- Clinic of Neurosurgery, University Clinical Center Sarajevo, Bolnička 25, 71000 Sarajevo, Bosnia and Herzegovina
| | - Mirza Pojskić
- Department of Neurosurgery, University Hospital Marburg, Baldingerstr., 35033 Marburg, Germany;
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25
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Chehelgerdi M, Chehelgerdi M, Khorramian-Ghahfarokhi M, Shafieizadeh M, Mahmoudi E, Eskandari F, Rashidi M, Arshi A, Mokhtari-Farsani A. Comprehensive review of CRISPR-based gene editing: mechanisms, challenges, and applications in cancer therapy. Mol Cancer 2024; 23:9. [PMID: 38195537 PMCID: PMC10775503 DOI: 10.1186/s12943-023-01925-5] [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: 09/08/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024] Open
Abstract
The CRISPR system is a revolutionary genome editing tool that has the potential to revolutionize the field of cancer research and therapy. The ability to precisely target and edit specific genetic mutations that drive the growth and spread of tumors has opened up new possibilities for the development of more effective and personalized cancer treatments. In this review, we will discuss the different CRISPR-based strategies that have been proposed for cancer therapy, including inactivating genes that drive tumor growth, enhancing the immune response to cancer cells, repairing genetic mutations that cause cancer, and delivering cancer-killing molecules directly to tumor cells. We will also summarize the current state of preclinical studies and clinical trials of CRISPR-based cancer therapy, highlighting the most promising results and the challenges that still need to be overcome. Safety and delivery are also important challenges for CRISPR-based cancer therapy to become a viable clinical option. We will discuss the challenges and limitations that need to be overcome, such as off-target effects, safety, and delivery to the tumor site. Finally, we will provide an overview of the current challenges and opportunities in the field of CRISPR-based cancer therapy and discuss future directions for research and development. The CRISPR system has the potential to change the landscape of cancer research, and this review aims to provide an overview of the current state of the field and the challenges that need to be overcome to realize this potential.
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Affiliation(s)
- Mohammad Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran.
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Matin Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Milad Khorramian-Ghahfarokhi
- Division of Biotechnology, Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | | | - Esmaeil Mahmoudi
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Fatemeh Eskandari
- Faculty of Molecular and Cellular Biology -Genetics, Islamic Azad University of Falavarjan, Isfahan, Iran
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Asghar Arshi
- Young Researchers and Elite Club, Najafabad Branch, Islamic Azad University, Najafabad, Iran
| | - Abbas Mokhtari-Farsani
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Department of Biology, Nourdanesh Institute of Higher Education, Meymeh, Isfahan, Iran
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26
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Badon IW, Oh Y, Kim HJ, Lee SH. Recent application of CRISPR-Cas12 and OMEGA system for genome editing. Mol Ther 2024; 32:32-43. [PMID: 37952084 PMCID: PMC10787141 DOI: 10.1016/j.ymthe.2023.11.013] [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: 09/11/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
In 2012, it was discovered that precise gene editing could be induced in target DNA using the reprogrammable characteristics of the CRISPR system. Since then, several studies have investigated the potential of the CRISPR system to edit various biological organisms. For the typical CRISPR system obtained from bacteria and archaea, many application studies have been conducted and have spread to various fields. To date, orthologs with various characteristics other than CRISPR-Cas9 have been discovered and are being intensively studied in the field of gene editing. CRISPR-Cas12 and its varied orthologs are representative examples of genome editing tools and have superior properties in terms of in vivo target gene editing compared with Cas9. Recently, TnpB and Fanzor of the OMEGA (obligate mobile element guided activity) system were identified to be the ancestor of CRISPR-Cas12 on the basis of phylogenetic analysis. Notably, the compact sizes of Cas12 and OMEGA endonucleases allow adeno-associated virus (AAV) delivery; hence, they are set to challenge Cas9 for in vivo gene therapy. This review is focused on these RNA-guided reprogrammable endonucleases: their structure, biochemistry, off-target effects, and applications in therapeutic gene editing.
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Affiliation(s)
- Isabel Wen Badon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yeounsun Oh
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ho-Joong Kim
- Department of Chemistry, Chosun University, Gwangju 61452, Republic of Korea.
| | - Seung Hwan Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
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27
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Baik R, Cromer MK, Glenn SE, Vakulskas CA, Chmielewski KO, Dudek AM, Feist WN, Klermund J, Shipp S, Cathomen T, Dever DP, Porteus MH. Transient inhibition of 53BP1 increases the frequency of targeted integration in human hematopoietic stem and progenitor cells. Nat Commun 2024; 15:111. [PMID: 38169468 PMCID: PMC10762240 DOI: 10.1038/s41467-023-43413-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024] Open
Abstract
Genome editing by homology directed repair (HDR) is leveraged to precisely modify the genome of therapeutically relevant hematopoietic stem and progenitor cells (HSPCs). Here, we present a new approach to increasing the frequency of HDR in human HSPCs by the delivery of an inhibitor of 53BP1 (named "i53") as a recombinant peptide. We show that the use of i53 peptide effectively increases the frequency of HDR-mediated genome editing at a variety of therapeutically relevant loci in HSPCs as well as other primary human cell types. We show that incorporating the use of i53 recombinant protein allows high frequencies of HDR while lowering the amounts of AAV6 needed by 8-fold. HDR edited HSPCs were capable of long-term and bi-lineage hematopoietic reconstitution in NSG mice, suggesting that i53 recombinant protein might be safely integrated into the standard CRISPR/AAV6-mediated genome editing protocol to gain greater numbers of edited cells for transplantation of clinically meaningful cell populations.
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Affiliation(s)
- Ron Baik
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Kyle Cromer
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Steve E Glenn
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | - Kay O Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
- Ph.D. Program, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Amanda M Dudek
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - William N Feist
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Klermund
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
| | - Suzette Shipp
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
| | - Daniel P Dever
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew H Porteus
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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28
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Becker HJ, Yamazaki S. Understanding genetic heterogeneity in gene-edited hematopoietic stem cell products. Exp Hematol 2024; 129:104133. [PMID: 38036097 DOI: 10.1016/j.exphem.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023]
Abstract
CRISPR/Cas gene editing has transformed genetic research and is poised to drive the next generation of gene therapies targeting hematopoietic stem cells (HSCs). However, the installation of the "desired" edit is most often only achieved in a minor subset of alleles. The array of cellular pathways triggered by gene editing tools produces a broad spectrum of "undesired" editing outcomes, including short insertions and deletions (indels) and chromosome rearrangements, leading to considerable genetic heterogeneity in gene-edited HSC populations. This heterogeneity may undermine the effect of the genetic intervention since only a subset of cells will carry the intended modification. Also, undesired mutations represent a potential safety concern as gene editing advances toward broader clinical use. Here, we will review the different sources of "undesired" edits and will discuss strategies for their mitigation and control.
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Affiliation(s)
- Hans Jiro Becker
- Laboratory for Stem Cell Therapy, Faculty of Medicine, Tsukuba University, Tsukuba, Japan; Division of Cell Regulation, Center of Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Satoshi Yamazaki
- Laboratory for Stem Cell Therapy, Faculty of Medicine, Tsukuba University, Tsukuba, Japan; Division of Cell Regulation, Center of Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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29
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Wang Y, Feng YL, Liu Q, Xiao JJ, Liu SC, Huang ZC, Xie AY. TREX2 enables efficient genome disruption mediated by paired CRISPR-Cas9 nickases that generate 3'-overhanging ends. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102072. [PMID: 38028195 PMCID: PMC10661556 DOI: 10.1016/j.omtn.2023.102072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023]
Abstract
Paired SpCas9 nickases (SpCas9n) are an effective strategy to reduce off-target effect in genome editing. However, this approach is not efficient with 3'-overhanging ends, limiting its applications. In order to expand the utility of paired SpCas9n in genome editing, we tested the effect of the TREX2 3'-5' exonuclease on repair of 3'-overhanging ends. We found ectopic overexpression of Trex2 stimulates the efficiency of paired SpCas9n in genome disruption with 3'-overhanging ends up to 400-fold with little stimulation of off-target editing. TREX2 overexpressed preferentially deletes entire 3' overhangs but has no significant effect on 5' overhangs. Trex2 overexpression also stimulates genome disruption by paired SpCas9n that potentially generate short 3'-overhanging ends at overlapping SpCas9n target sites, suggesting sequential nicking of overlapping target sites by SpCas9n. This approach is further simplified with improved efficiency and safety by fusion of TREX2 and particularly its DNA-binding-deficient mutant to SpCas9n. Junction analysis at overlapping targets revealed the different extent of end resection of 3' single-stranded DNA (ssDNA) by free TREX2 and TREX2 fused to SpCas9n. SpCas9n-TREX2 fusion is more convenient and safer than overexpression of free TREX2 to process 3'-overhanging ends for efficient genome disruption by paired SpCas9n, allowing practical use of this TREX2-based strategy in genome editing.
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Affiliation(s)
- Yue Wang
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, P.R. China
- Hangzhou Qiantang Hospital, Hangzhou, Zhejiang 310018, P.R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang 310029, P.R. China
| | - Yi-Li Feng
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, P.R. China
- Hangzhou Qiantang Hospital, Hangzhou, Zhejiang 310018, P.R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang 310029, P.R. China
| | - Qian Liu
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, P.R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang 310029, P.R. China
| | - Jing-Jing Xiao
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, P.R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang 310029, P.R. China
| | - Si-Cheng Liu
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, P.R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang 310029, P.R. China
| | - Zhi-Cheng Huang
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, P.R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang 310029, P.R. China
| | - An-Yong Xie
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, P.R. China
- Hangzhou Qiantang Hospital, Hangzhou, Zhejiang 310018, P.R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang 310029, P.R. China
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Raynaud CM, Ahmed EI, Jabeen A, Sanchez A, Sherif S, Carneiro-Lobo TC, Awad A, Awartani D, Naik A, Thomas R, Decock J, Zoppoli G, Bedongnetti D, Hendrickx WRL. Modulation of SLFN11 induces changes in DNA Damage response in breast cancer. Cancer Cell Int 2023; 23:291. [PMID: 38001424 PMCID: PMC10668346 DOI: 10.1186/s12935-023-03144-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Lack of Schlafen family member 11 (SLFN11) expression has been recently identified as a dominant genomic determinant of response to DNA damaging agents in numerous cancer types. Thus, several strategies aimed at increasing SLFN11 are explored to restore chemosensitivity of refractory cancers. In this study, we examined various approaches to elevate SLFN11 expression in breast cancer cellular models and confirmed a corresponding increase in chemosensitivity with using the most successful efficient one. As oncogenic transcriptomic downregulation is often driven by methylation of the promotor region, we explore the demethylation effect of 5-aza-2'-deoxycytidine (decitabine), on the SLFN11 gene. Since SLFN11 has been reported as an interferon inducible gene, and interferon is secreted during an active anti-tumor immune response, we investigated the in vitro effect of IFN-γ on SLFN11 expression in breast cancer cell lines. As a secondary approach to pick up cross talk between immune cells and SLFN11 expression we used indirect co-culture of breast cancer cells with activated PBMCs and evaluated if this can drive SLFN11 upregulation. Finally, as a definitive and specific way to modulate SLFN11 expression we implemented SLFN11 dCas9 (dead CRISPR associated protein 9) systems to specifically increase or decrease SLFN11 expression. RESULTS After confirming the previously reported correlation between methylation of SLFN11 promoter and its expression across multiple cell lines, we showed in-vitro that decitabine and IFN-γ could increase moderately the expression of SLFN11 in both BT-549 and T47D cell lines. The use of a CRISPR-dCas9 UNISAM and KRAB system could increase or decrease SLFN11 expression significantly (up to fivefold), stably and specifically in BT-549 and T47D cancer cell lines. We then used the modified cell lines to quantify the alteration in chemo sensitivity of those cells to treatment with DNA Damaging Agents (DDAs) such as Cisplatin and Epirubicin or DNA Damage Response (DDRs) drugs like Olaparib. RNAseq was used to elucidate the mechanisms of action affected by the alteration in SLFN11 expression. In cell lines with robust SLFN11 promoter methylation such as MDA-MB-231, no SLFN11 expression could be induced by any approach. CONCLUSION To our knowledge this is the first report of the stable non-lethal increase of SLFN11 expression in a cancer cell line. Our results show that induction of SLFN11 expression can enhance DDA and DDR sensitivity in breast cancer cells and dCas9 systems may represent a novel approach to increase SLFN11 and achieve higher sensitivity to chemotherapeutic agents, improving outcome or decreasing required drug concentrations. SLFN11-targeting therapies might be explored pre-clinically to develop personalized approaches.
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Affiliation(s)
| | - Eiman I Ahmed
- Tumor Biology and Immunology Lab, Research Branch, Sidra Medicine, Doha, Qatar
- Department of Biomedical Science, College of Health Sciences, Qatar University, Doha, Qatar
| | - Ayesha Jabeen
- Tumor Biology and Immunology Lab, Research Branch, Sidra Medicine, Doha, Qatar
| | - Apryl Sanchez
- Tumor Biology and Immunology Lab, Research Branch, Sidra Medicine, Doha, Qatar
| | - Shimaa Sherif
- Tumor Biology and Immunology Lab, Research Branch, Sidra Medicine, Doha, Qatar
| | | | - Amany Awad
- Tumor Biology and Immunology Lab, Research Branch, Sidra Medicine, Doha, Qatar
| | - Dina Awartani
- Tumor Biology and Immunology Lab, Research Branch, Sidra Medicine, Doha, Qatar
| | - Adviti Naik
- Translational Cancer and Immunity Center, Qatar Biomedical Research Center, Doha, Qatar
| | - Remy Thomas
- Translational Cancer and Immunity Center, Qatar Biomedical Research Center, Doha, Qatar
| | - Julie Decock
- Translational Cancer and Immunity Center, Qatar Biomedical Research Center, Doha, Qatar
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Gabriele Zoppoli
- Department of Internal Medicine (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
- Ospedale Policlinico San Martino IRCCS per l'Oncologia, Genoa, Italy
| | - Davide Bedongnetti
- Tumor Biology and Immunology Lab, Research Branch, Sidra Medicine, Doha, Qatar
- Department of Internal Medicine (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
- Clinical and Experimental Oncology and Hematology, Ospedale Policlinico San Martino, Genoa, Italy
| | - Wouter R L Hendrickx
- Tumor Biology and Immunology Lab, Research Branch, Sidra Medicine, Doha, Qatar.
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, Qatar.
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Zaman QU, Raza A, Gill RA, Hussain MA, Wang HF, Varshney RK. New possibilities for trait improvement via mobile CRISPR-RNA. Trends Biotechnol 2023; 41:1335-1338. [PMID: 37258389 DOI: 10.1016/j.tibtech.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/17/2023] [Accepted: 05/08/2023] [Indexed: 06/02/2023]
Abstract
CRISPR/Cas9 gene technology is transported as RNA from transgenic roots to distal parts of unmodified grafted scion, where it is translated into proteins to induce heritable mutagenesis at desired loci. This technique has the potential to produce transgene-free and genetically stable plants in difficult-to-propagate and near-extinct species.
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Affiliation(s)
- Qamar U Zaman
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Ali Raza
- College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Rafaqat Ali Gill
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Muhammad Azhar Hussain
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Hua Feng Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia.
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Aquino-Jarquin G. Genome and transcriptome engineering by compact and versatile CRISPR-Cas systems. Drug Discov Today 2023; 28:103793. [PMID: 37797813 DOI: 10.1016/j.drudis.2023.103793] [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: 05/10/2023] [Revised: 09/08/2023] [Accepted: 09/28/2023] [Indexed: 10/07/2023]
Abstract
Comparative genomics has enabled the discovery of tiny clustered regularly interspaced short palindromic repeat (CRISPR) bacterial immune system effectors with enormous potential for manipulating eukaryotic genomes. Recently, smaller Cas proteins, including miniature Cas9, Cas12, and Cas13 proteins, have been identified and validated as efficient genome editing and base editing tools in human cells. The compact size of these novel CRISPR effectors is highly desirable for generating CRISPR-based therapeutic approaches, mainly to overcome in vivo delivery constraints, providing a promising opportunity for editing pathogenic mutations of clinical relevance and knocking down RNAs in human cells without inducing chromosomal insertions or genome alterations. Thus, these tiny CRISPR-Cas systems represent new and highly programmable, specific, and efficient platforms, which expand the CRISPR toolkit for potential therapeutic opportunities.
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Affiliation(s)
- Guillermo Aquino-Jarquin
- RNA Biology and Genome Editing Section. Research on Genomics, Genetics, and Bioinformatics Laboratory. Hemato-Oncology Building, 4th Floor, Section 2. Children's Hospital of Mexico, Federico Gómez, Mexico City, Mexico.
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Volke DC, Orsi E, Nikel PI. Emergent CRISPR-Cas-based technologies for engineering non-model bacteria. Curr Opin Microbiol 2023; 75:102353. [PMID: 37413959 DOI: 10.1016/j.mib.2023.102353] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) technologies brought a transformative change in the way bacterial genomes are edited, and a plethora of studies contributed to developing multiple tools based on these approaches. Prokaryotic biotechnology benefited from the implementation of such genome engineering strategies, with an increasing number of non-model bacterial species becoming genetically tractable. In this review, we summarize the recent trends in engineering non-model microbes using CRISPR-Cas technologies, discussing their potential in supporting cell factory design towards biotechnological applications. These efforts include, among other examples, genome modifications as well as tunable transcriptional regulation (both positive and negative). Moreover, we examine how CRISPR-Cas toolkits for engineering non-model organisms enabled the exploitation of emergent biotechnological processes (e.g. native and synthetic assimilation of one-carbon substrates). Finally, we discuss our slant on the future of bacterial genome engineering for domesticating non-model organisms in light of the most recent advances in the ever-expanding CRISPR-Cas field.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Enrico Orsi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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Shaheen N, Ahmad S, Alghamdi SS, Rehman HM, Javed MA, Tabassum J, Shao G. CRISPR-Cas System, a Possible "Savior" of Rice Threatened by Climate Change: An Updated Review. RICE (NEW YORK, N.Y.) 2023; 16:39. [PMID: 37688677 PMCID: PMC10492775 DOI: 10.1186/s12284-023-00652-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/04/2023] [Indexed: 09/11/2023]
Abstract
Climate change has significantly affected agriculture production, particularly the rice crop that is consumed by almost half of the world's population and contributes significantly to global food security. Rice is vulnerable to several abiotic and biotic stresses such as drought, heat, salinity, heavy metals, rice blast, and bacterial blight that cause huge yield losses in rice, thus threatening food security worldwide. In this regard, several plant breeding and biotechnological techniques have been used to raise such rice varieties that could tackle climate changes. Nowadays, gene editing (GE) technology has revolutionized crop improvement. Among GE technology, CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein) system has emerged as one of the most convenient, robust, cost-effective, and less labor-intensive system due to which it has got more popularity among plant researchers, especially rice breeders and geneticists. Since 2013 (the year of first application of CRISPR/Cas-based GE system in rice), several trait-specific climate-resilient rice lines have been developed using CRISPR/Cas-based GE tools. Earlier, several reports have been published confirming the successful application of GE tools for rice improvement. However, this review particularly aims to provide an updated and well-synthesized brief discussion based on the recent studies (from 2020 to present) on the applications of GE tools, particularly CRISPR-based systems for developing CRISPR rice to tackle the current alarming situation of climate change, worldwide. Moreover, potential limitations and technical bottlenecks in the development of CRISPR rice, and prospects are also discussed.
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Affiliation(s)
- Nabeel Shaheen
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia
| | - Shakeel Ahmad
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia.
| | - Salem S Alghamdi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hafiz Mamoon Rehman
- Centre for Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Javaria Tabassum
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, National Rice Research Institute, 310006, Hangzhou, China.
- Zhejiang Lab, 310006, Hangzhou, China.
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35
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Zheng X, Huang C, Lin Y, Han B, Chen Y, Li C, Li J, Ding Y, Song X, Wang W, Liang W, Wu J, Wu J, Gao J, Wei C, Zhang X, Tu Z, Yan S. Generation of inactivated IL2RG and RAG1 monkeys with severe combined immunodeficiency using base editing. Signal Transduct Target Ther 2023; 8:327. [PMID: 37661226 PMCID: PMC10475462 DOI: 10.1038/s41392-023-01544-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/03/2023] [Accepted: 06/16/2023] [Indexed: 09/05/2023] Open
Abstract
Severe combined immunodeficiency (SCID) encompasses a range of inherited disorders that lead to a profound deterioration of the immune system. Among the pivotal genes associated with SCID, RAG1 and IL2RG play crucial roles. IL2RG is essential for the development, differentiation, and functioning of T, B, and NK cells, while RAG1 critically contributes to adaptive immunity by facilitating V(D)J recombination during the maturation of lymphocytes. Animal models carrying mutations in these genes exhibit notable deficiencies in their immune systems. Non-human primates (NHPs) are exceptionally well-suited models for biomedical research due to their genetic and physiological similarities to humans. Cytosine base editors (CBEs) serve as powerful tools for precisely and effectively modifying single-base mutations in the genome. Their successful implementation has been demonstrated in human cells, mice, and crop species. This study outlines the creation of an immunodeficient monkey model by deactivating both the IL2RG and RAG1 genes using the CBE4max system. The base-edited monkeys exhibited a severely compromised immune system characterized by lymphopenia, atrophy of lymphoid organs, and a deficiency of mature T cells. Furthermore, these base-edited monkeys were capable of hosting and supporting the growth of human breast cancer cells, leading to tumor formation. In summary, we have successfully developed an immunodeficient monkey model with the ability to foster tumor growth using the CBE4max system. These immunodeficiency monkeys show tremendous potential as valuable tools for advancing biomedical and translational research.
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Affiliation(s)
- Xiao Zheng
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China
| | - Chunhui Huang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China
| | - Yingqi Lin
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China
| | - Bofeng Han
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Yizhi Chen
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Caijuan Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China
| | - Jiawei Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China
| | - Yongyan Ding
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Xichen Song
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Wei Wang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Weien Liang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Jianhao Wu
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Jiaxi Wu
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Jiale Gao
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Chengxi Wei
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Xudong Zhang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Zhuchi Tu
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China.
| | - Sen Yan
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China.
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China.
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Duarte F, Vachey G, Caron NS, Sipion M, Rey M, Perrier AL, Hayden MR, Déglon N. Limitations of Dual-Single Guide RNA CRISPR Strategies for the Treatment of Central Nervous System Genetic Disorders. Hum Gene Ther 2023; 34:958-974. [PMID: 37658843 DOI: 10.1089/hum.2023.109] [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] [Indexed: 09/05/2023] Open
Abstract
Huntington's disease (HD) is a fatal neurodegenerative disorder caused by a toxic gain-of-function CAG expansion in the first exon of the huntingtin (HTT) gene. The monogenic nature of HD makes mutant HTT (mHTT) inactivation a promising therapeutic strategy. Single nucleotide polymorphisms frequently associated with CAG expansion have been explored to selectively inactivate mHTT allele using the CRISPR/Cas9 system. One of such allele-selective approaches consists of excising a region flanking the first exon of mHTT by inducing simultaneous double-strand breaks at upstream and downstream positions of the mHTT exon 1. The removal of the first exon of mHTT deletes the CAG expansion and important transcription regulatory sites, leading to mHTT inactivation. However, the frequency of deletion events is yet to be quantified either in vitro or in vivo. Here, we developed accurate quantitative digital polymerase chain reaction-based assays to assess HTT exon 1 deletion in vitro and in fully humanized HU97/18 mice. Our results demonstrate that dual-single guide RNA (sgRNA) strategies are efficient and that 67% of HTT editing events are leading to exon 1 deletion in HEK293T cells. In contrast, these sgRNA actively cleaved HTT in HU97/18 mice, but most editing events do not lead to exon 1 deletion (10% exon 1 deletion). We also showed that the in vivo editing pattern is not affected by CAG expansion but may potentially be due to the presence of multiple copies of wildtype (wt)/mHTT genes HU97/18 mice as well as the slow kinetics of AAV-mediated CRISPR/Cas9 delivery.
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Affiliation(s)
- Fábio Duarte
- Laboratory of Cellular and Molecular Neurotherapies, Department of Clinical Neurosciences (DNC)
- Laboratory of Cellular and Molecular Neurotherapies (LCMN), Neuroscience Research Center (CRN); Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Gabriel Vachey
- Laboratory of Cellular and Molecular Neurotherapies, Department of Clinical Neurosciences (DNC)
- Laboratory of Cellular and Molecular Neurotherapies (LCMN), Neuroscience Research Center (CRN); Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Nicholas S Caron
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital and Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Melanie Sipion
- Laboratory of Cellular and Molecular Neurotherapies, Department of Clinical Neurosciences (DNC)
- Laboratory of Cellular and Molecular Neurotherapies (LCMN), Neuroscience Research Center (CRN); Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Maria Rey
- Laboratory of Cellular and Molecular Neurotherapies, Department of Clinical Neurosciences (DNC)
- Laboratory of Cellular and Molecular Neurotherapies (LCMN), Neuroscience Research Center (CRN); Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Anselme L Perrier
- Université Paris-Saclay, CEA, CNRS, Laboratoire des Maladies Neurodégénératives: mécanismes, thérapies, imagerie, Fontenay-aux-Roses, France
- Université Paris-Saclay, CEA, Molecular Imaging Research Center, Fontenay-aux-Roses, France
| | - Michael R Hayden
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital and Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicole Déglon
- Laboratory of Cellular and Molecular Neurotherapies, Department of Clinical Neurosciences (DNC)
- Laboratory of Cellular and Molecular Neurotherapies (LCMN), Neuroscience Research Center (CRN); Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
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Deng C, Li S, Liu Y, Bao W, Xu C, Zheng W, Wang M, Ma X. Split-Cas9-based targeted gene editing and nanobody-mediated proteolysis-targeting chimeras optogenetically coordinated regulation of Survivin to control the fate of cancer cells. Clin Transl Med 2023; 13:e1382. [PMID: 37620295 PMCID: PMC10449816 DOI: 10.1002/ctm2.1382] [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: 02/25/2023] [Revised: 08/09/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Precise regulation of partial critical proteins in cancer cells, such as anti-apoptotic proteins, is one of the crucial strategies for treating cancer and discovering related molecular mechanisms. Still, it is also challenging in actual research and practice. The widely used CRISPR/Cas9-based gene editing technology and proteolysis-targeting chimeras (PROTACs) have played an essential role in regulating gene expression and protein function in cells. However, the accuracy and controllability of their targeting remain necessary. METHODS Construction of UMUC-3-EGFP stable transgenic cell lines using the Sleeping Beauty system, Flow cytometry, quantitative real-time PCR, western blot, fluorescence microplate reader and fluorescence inverted microscope analysis of EGFP intensity. Characterization of Survivin inhibition was done by using Annexin V-FITC/PI apoptosis, calcein/PI/DAPI cell viability/cytotoxicity assay, cloning formation assay and scratch assay. The cell-derived xenograft (CDX) model was constructed to assess the in vivo effects of reducing Survivin expression. RESULTS Herein, we established a synergistic control platform that coordinated photoactivatable split-Cas9 targeted gene editing and light-induced protein degradation, on which the Survivin gene in the nucleus was controllably edited by blue light irradiation (named paCas9-Survivin) and simultaneously the Survivin protein in the cytoplasm was degraded precisely by a nanobody-mediated target (named paProtacL-Survivin). Meanwhile, in vitro experiments demonstrated that reducing Survivin expression could effectively promote apoptosis and decrease the proliferation and migration of bladder cancerous cells. Furthermore, the CDX model was constructed using UMUC-3 cell lines, results from animal studies indicated that both the paCas9-Survivin system and paProtacL-Survivin significantly inhibited tumour growth, with higher inhibition rates when combined. CONCLUSIONS In short, the coordinated regulatory strategies and combinable technology platforms offer clear advantages in controllability and targeting, as well as an excellent reference value and universal applicability in controlling the fate of cancer cells through multi-level regulation of key intracellular factors.
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Affiliation(s)
- Changping Deng
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghaiP. R. China
| | - Shihui Li
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghaiP. R. China
| | - Yuping Liu
- Shanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and TechnologyShanghaiP. R. China
| | - Wen Bao
- Shanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and TechnologyShanghaiP. R. China
| | - Chengnan Xu
- Shanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and TechnologyShanghaiP. R. China
| | - Wenyun Zheng
- Shanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and TechnologyShanghaiP. R. China
| | - Meiyan Wang
- Synthetic Biology and Biomedical Engineering LaboratoryBiomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory BiologyInstitute of BiomedicalSciences and School of Life SciencesEast China Normal UniversityShanghaiP. R. China
| | - Xingyuan Ma
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghaiP. R. China
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Zvintzou E, Xepapadaki E, Skroubis G, Mparnia V, Giannatou K, Benabdellah K, Kypreos KE. High-Density Lipoprotein in Metabolic Disorders and Beyond: An Exciting New World Full of Challenges and Opportunities. Pharmaceuticals (Basel) 2023; 16:855. [PMID: 37375802 DOI: 10.3390/ph16060855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/17/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
High-density lipoprotein (HDL) is an enigmatic member of the plasma lipid and lipoprotein transport system, best known for its ability to promote the reverse cholesterol efflux and the unloading of excess cholesterol from peripheral tissues. More recently, data in experimental mice and humans suggest that HDL may play important novel roles in other physiological processes associated with various metabolic disorders. Important parameters in the HDL functions are its apolipoprotein and lipid content, further reinforcing the principle that HDL structure defines its functionality. Thus, based on current evidence, low levels of HDL-cholesterol (HDL-C) or dysfunctional HDL particles contribute to the development of metabolic diseases such as morbid obesity, type 2 diabetes mellitus, and nonalcoholic fatty liver disease. Interestingly, low levels of HDL-C and dysfunctional HDL particles are observed in patients with multiple myeloma and other types of cancer. Therefore, adjusting HDL-C levels within the optimal range and improving HDL particle functionality is expected to benefit such pathological conditions. The failure of previous clinical trials testing various HDL-C-raising pharmaceuticals does not preclude a significant role for HDL in the treatment of atherosclerosis and related metabolic disorders. Those trials were designed on the principle of "the more the better", ignoring the U-shape relationship between HDL-C levels and morbidity and mortality. Thus, many of these pharmaceuticals should be retested in appropriately designed clinical trials. Novel gene-editing-based pharmaceuticals aiming at altering the apolipoprotein composition of HDL are expected to revolutionize the treatment strategies, improving the functionality of dysfunctional HDL.
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Affiliation(s)
- Evangelia Zvintzou
- Department of Pharmacology, School of Medicine, University of Patras, Rio Achaias, 26500 Patras, Greece
| | - Eva Xepapadaki
- Department of Pharmacology, School of Medicine, University of Patras, Rio Achaias, 26500 Patras, Greece
| | - George Skroubis
- Morbid Obesity Unit, Department of Surgery, School of Medicine, University of Patras, Rio Achaias, 26500 Patras, Greece
| | - Victoria Mparnia
- Department of Pharmacology, School of Medicine, University of Patras, Rio Achaias, 26500 Patras, Greece
| | - Katerina Giannatou
- Department of Pharmacology, School of Medicine, University of Patras, Rio Achaias, 26500 Patras, Greece
| | - Karim Benabdellah
- Department of Genomic Medicine, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), PTS, Avda. de la Ilustración 114, 18016 Granada, Spain
| | - Kyriakos E Kypreos
- Department of Pharmacology, School of Medicine, University of Patras, Rio Achaias, 26500 Patras, Greece
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404 Nicosia, Cyprus
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Lei Z, Meng H, Rao X, Zhao H, Yi C. Detect-seq, a chemical labeling and biotin pull-down approach for the unbiased and genome-wide off-target evaluation of programmable cytosine base editors. Nat Protoc 2023:10.1038/s41596-023-00837-4. [PMID: 37277562 DOI: 10.1038/s41596-023-00837-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 03/09/2023] [Indexed: 06/07/2023]
Abstract
Programmable cytosine base editors show promising approaches for correcting pathogenic mutations; yet, their off-target effects have been of great concern. Detect-seq (dU-detection enabled by C-to-T transition during sequencing) is an unbiased, sensitive method for the off-target evaluation of programmable cytosine base editors. It profiles the editome by tracing the editing intermediate dU, which is introduced inside living cells and edited by programmable cytosine base editors. The genomic DNA is extracted, preprocessed and labeled by successive chemical and enzymatic reactions, followed by biotin pull-down to enrich the dU-containing loci for sequencing. Here, we describe a detailed protocol for performing the Detect-seq experiment, and a customized, open-source, bioinformatic pipeline for analyzing the characteristic Detect-seq data is also provided. Unlike those previous whole-genome sequencing-based methods, Detect-seq uses an enrichment strategy and hence is endowed with great sensitivity, a higher signal-to-noise ratio and no requirement for high sequencing depth. Furthermore, Detect-seq is widely applicable for both mitotic and postmitotic biological systems. The entire protocol typically takes 5 d from the genomic DNA extraction to sequencing and ~1 week for data analysis.
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Affiliation(s)
- Zhixin Lei
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Haowei Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Xichen Rao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Huanan Zhao
- School of Life Sciences, Tsinghua University, Beijing, China
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China
| | - Chengqi Yi
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Peking University Genome Editing Research Center, Peking University, Beijing, China.
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Amariutei AE, Jeng JY, Safieddine S, Marcotti W. Recent advances and future challenges in gene therapy for hearing loss. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230644. [PMID: 37325593 PMCID: PMC10265000 DOI: 10.1098/rsos.230644] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 05/19/2023] [Indexed: 06/17/2023]
Abstract
Hearing loss is the most common sensory deficit experienced by humans and represents one of the largest chronic health conditions worldwide. It is expected that around 10% of the world's population will be affected by disabling hearing impairment by 2050. Hereditary hearing loss accounts for most of the known forms of congenital deafness, and over 25% of adult-onset or progressive hearing loss. Despite the identification of well over 130 genes associated with deafness, there is currently no curative treatment for inherited deafness. Recently, several pre-clinical studies in mice that exhibit key features of human deafness have shown promising hearing recovery through gene therapy involving the replacement of the defective gene with a functional one. Although the potential application of this therapeutic approach to humans is closer than ever, substantial further challenges need to be overcome, including testing the safety and longevity of the treatment, identifying critical therapeutic time windows and improving the efficiency of the treatment. Herein, we provide an overview of the recent advances in gene therapy and highlight the current hurdles that the scientific community need to overcome to ensure a safe and secure implementation of this therapeutic approach in clinical trials.
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Affiliation(s)
- Ana E. Amariutei
- School of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Jing-Yi Jeng
- School of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Saaid Safieddine
- Institut Pasteur, Université Paris Cité, Inserm, Institut de l'Audition, F-75012 Paris, France
| | - Walter Marcotti
- School of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, University of Sheffield, Sheffield S10 2TN, UK
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Fritzke M, Chen K, Tang W, Stinson S, Pham T, Wang Y, Xu L, Chen EY. The MYC-YBX1 Circuit in Maintaining Stem-like Vincristine-Resistant Cells in Rhabdomyosarcoma. Cancers (Basel) 2023; 15:2788. [PMID: 37345125 DOI: 10.3390/cancers15102788] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/03/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is a pediatric soft tissue sarcoma that causes significant devastation, with no effective therapy for relapsed disease. The mechanisms behind treatment failures are poorly understood. Our study showed that treatment of RMS cells with vincristine led to an increase in CD133-positive stem-like resistant cells. Single cell RNAseq analysis revealed that MYC and YBX1 were among the top-scoring transcription factors in CD133-high expressing cells. Targeting MYC and YBX1 using CRISPR/Cas9 reduced stem-like characteristics and viability of the vincristine-resistant cells. MYC and YBX1 showed mutual regulation, with MYC binding to the YBX1 promoter and YBX1 binding to MYC mRNA. The MYC inhibitor MYC361i synergized with vincristine to reduce tumor growth and stem-like cells in a zebrafish model of RMS. MYC and YBX expression showed a positive correlation in RMS patients, and high MYC expression correlated with poor survival. Targeting the MYC-YBX1 axis holds promise for improving survival in RMS patients.
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Affiliation(s)
- Madeline Fritzke
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Weiliang Tang
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Spencer Stinson
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Thao Pham
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
- Astellas US Technologies, Universal Cells, Inc., Seattle, WA 98121, USA
| | - Yadong Wang
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eleanor Y Chen
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
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Kraus C, Sontheimer EJ. Applications of Anti-CRISPR Proteins in Genome Editing and Biotechnology. J Mol Biol 2023; 435:168120. [PMID: 37100169 DOI: 10.1016/j.jmb.2023.168120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
Abstract
In the ten years since the discovery of the first anti-CRISPR (Acr) proteins, the number of validated Acrs has expanded rapidly, as has our understanding of the diverse mechanisms they employ to suppress natural CRISPR-Cas immunity. Many, though not all, function via direct, specific interaction with Cas protein effectors. The abilities of Acr proteins to modulate the activities and properties of CRISPR-Cas effectors have been exploited for an ever-increasing spectrum of biotechnological uses, most of which involve the establishment of control over genome editing systems. This control can be used to minimize off-target editing, restrict editing based on spatial, temporal, or conditional cues, limit the spread of gene drive systems, and select for genome-edited bacteriophages. Anti-CRISPRs have also been developed to overcome bacterial immunity, facilitate viral vector production, control synthetic gene circuits, and other purposes. The impressive and ever-growing diversity of Acr inhibitory mechanisms will continue to allow the tailored applications of Acrs.
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Affiliation(s)
| | - Erik J Sontheimer
- RNA Therapeutics Institute; Program in Molecular Medicine, and; Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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Sethi Y, Mahtani AU, Khehra N, Padda I, Patel N, Sebastian SA, Malhi G, Kaiwan O, Saith S, Johal G. Gene Editing as the Future of Cardiac Amyloidosis Therapeutics. Curr Probl Cardiol 2023; 48:101741. [PMID: 37059345 DOI: 10.1016/j.cpcardiol.2023.101741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 04/16/2023]
Abstract
BACKGROUND AND SIGNIFICANCE Cardiac Amyloidosis (CA) is a manifestation of a systemic disorder resulting from the deposition of the transthyretin (TTR) in the myocardium, resulting in a myriad manifestations ranging from conduction defects to heart failure. Several proteins, many of which have a genetic predisposition, are responsible for its presentation. Clustered Regularly Interspaced Short Palindromic Repeats of genetic information-Cas9 endonuclease (CRISPR-Cas9) is a RNA-guided endonuclease, which can be targeted using an RNA guide to specific locations in the genome. Until recently, CRISPR-Cas9 was studied in small animal models for its ability to decrease extracellular deposition and accumulation of amyloid in tissues. OBSERVATIONS Previously considered a rare disease, but recent advances in diagnostics and therapeutics have revealed the prevalence to be higher than estimated. There are two major classes of treatments for transthyretin cardiac amyloidosis (ATTR-CA): TTR stabilizers, such as tafamidis and AG10, and RNA interference (siRNA), such as patisiran and vutrisiran. Recently, gene editing has demonstrated some early clinical promise as an emerging therapeutic modality in the treatment of CA. CONCLUSIONS AND RELEVANCE In an introductory gene editing human trial involving 12 subjects with TTR amyloidosis and amyloid cardiomyopathy (ATTR-CM), CRISPR-Cas9 therapy has demonstrated a reduction of approximately 90% of serum TTR proteins after 28 days. In this article, the authors review the current literature on therapeutic gene editing as a prospective curative treatment modality for cardiac amyloidosis.
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Affiliation(s)
- Yashendra Sethi
- PearResearch, Dehradun, India; Government Doon Medical College, Dehradun, Uttarakhand, India.
| | - Arun Umesh Mahtani
- Richmond University Medical Center/Mount Sinai, Staten Island, New York, USA.
| | - Nimrat Khehra
- PearResearch, Dehradun, India; Saint James School of Medicine, St Vincent & Grenadines
| | - Inderbir Padda
- Richmond University Medical Center/Mount Sinai, Staten Island, New York, USA
| | - Neil Patel
- PearResearch, Dehradun, India; G.M.E.R.S. Medical College, Himmatnagar, Gujarat, India
| | | | - Gurnaaz Malhi
- Caribbean Medical University School of Medicine, Curacao, Willemstad
| | | | - Sunil Saith
- SUNY Downstate Medical Center, Brooklyn, New York, USA
| | - Gurpreet Johal
- University of Washington, Valley Medical Center, Seattle, Washington, USA
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Gunitseva N, Evteeva M, Borisova A, Patrushev M, Subach F. RNA-Dependent RNA Targeting by CRISPR-Cas Systems: Characterizations and Applications. Int J Mol Sci 2023; 24:ijms24086894. [PMID: 37108063 PMCID: PMC10138764 DOI: 10.3390/ijms24086894] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/01/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Genome editing technologies that are currently available and described have a fundamental impact on the development of molecular biology and medicine, industrial and agricultural biotechnology and other fields. However, genome editing based on detection and manipulation of the targeted RNA is a promising alternative to control the gene expression at the spatiotemporal transcriptomic level without complete elimination. The innovative CRISPR-Cas RNA-targeting systems changed the conception of biosensing systems and also allowed the RNA effectors to be used in various applications; for example, genomic editing, effective virus diagnostic tools, biomarkers, transcription regulations. In this review, we discussed the current state-of-the-art of specific CRISPR-Cas systems known to bind and cleave RNA substrates and summarized potential applications of the versatile RNA-targeting systems.
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Affiliation(s)
- Natalia Gunitseva
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Marta Evteeva
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Anna Borisova
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Maxim Patrushev
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Fedor Subach
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", 123182 Moscow, Russia
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45
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Jiménez C, Crosetto N. Discovering CRISPR-Cas off-target breaks. Nat Methods 2023; 20:641-642. [PMID: 37024652 DOI: 10.1038/s41592-023-01847-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Affiliation(s)
| | - Nicola Crosetto
- Human Technopole, Milan, Italy.
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
- Science for Life Laboratory, Solna, Sweden.
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Hu S, Xu S, Lu W, Si Y, Wang Y, Du Z, Wang Y, Feng Z, Tang X. The research on the treatment of primary immunodeficiency diseases by hematopoietic stem cell transplantation: A bibliometric analysis from 2013 to 2022. Medicine (Baltimore) 2023; 102:e33295. [PMID: 37000105 PMCID: PMC10063298 DOI: 10.1097/md.0000000000033295] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 04/01/2023] Open
Abstract
Hematopoietic stem cell transplantation (HSCT) is curative in patients with primary immunodeficiency syndrome. The safety and efficacy of HSCT as a therapeutic option for primary immunodeficiency diseases (PID) have been studied by many research groups. The purpose of our study was to perform a bibliometric analysis of research on HSCT for the treatment of PID, to assess research trends in this field, and note future research priorities. The Web of Science Core Collection (WOSCC) was used to identify relevant publications. VOSviewer and CiteSpace software were used to analyze bibliometric parameters, such as yearly records, authors, grouped authors, countries, institutions, categories and keywords. There are 602 relevant records for the last decade (2013-2022). The top 5 productive authors and high-quality paper journals are listed. Reference co-citations analysis demonstrated recent research trends were "inborn errors of immunity," "gene editing," and "enteropathy." Research on HSCT for the treatment of PID has increased rapidly in the last decade, and bibliometrics are valuable for researchers to obtain an overview of hot categories, academic collaborations and trends in this study field.
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Affiliation(s)
- Siqi Hu
- Faculty of Pediatrics, the Chinese PLA General Hospital, Beijing, China
- Institute of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Shixia Xu
- Department of Pediatrics, Eden Hospital, Beijing, China
| | - Wei Lu
- Institute of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
- Department of Hematology and Transplantation, Faculty of Pediatrics, the Chinese PLA General Hospital, Beijing, China
- Department of Children’s Internal Medicine, Faculty of Pediatrics, the Chinese PLA General Hospital, Beijing, China
| | - Yingjian Si
- Institute of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
- Department of Hematology and Transplantation, Faculty of Pediatrics, the Chinese PLA General Hospital, Beijing, China
- Department of Children’s Internal Medicine, Faculty of Pediatrics, the Chinese PLA General Hospital, Beijing, China
| | - Ya Wang
- Institute of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
- Department of Hematology and Transplantation, Faculty of Pediatrics, the Chinese PLA General Hospital, Beijing, China
- Department of Children’s Internal Medicine, Faculty of Pediatrics, the Chinese PLA General Hospital, Beijing, China
| | - Zhenlan Du
- Institute of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
- Department of Hematology and Transplantation, Faculty of Pediatrics, the Chinese PLA General Hospital, Beijing, China
- Department of Children’s Internal Medicine, Faculty of Pediatrics, the Chinese PLA General Hospital, Beijing, China
| | - Yi Wang
- Faculty of Pediatrics, the Chinese PLA General Hospital, Beijing, China
- Institute of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Zhichun Feng
- Faculty of Pediatrics, the Chinese PLA General Hospital, Beijing, China
- Institute of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Xiangfeng Tang
- Institute of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
- Department of Hematology and Transplantation, Faculty of Pediatrics, the Chinese PLA General Hospital, Beijing, China
- Department of Children’s Internal Medicine, Faculty of Pediatrics, the Chinese PLA General Hospital, Beijing, China
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47
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Towards the Clinical Application of Gene Therapy for Genetic Inner Ear Diseases. J Clin Med 2023; 12:jcm12031046. [PMID: 36769694 PMCID: PMC9918244 DOI: 10.3390/jcm12031046] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Hearing loss, the most common human sensory defect worldwide, is a major public health problem. About 70% of congenital forms and 25% of adult-onset forms of deafness are of genetic origin. In total, 136 deafness genes have already been identified and there are thought to be several hundred more awaiting identification. However, there is currently no cure for sensorineural deafness. In recent years, translational research studies have shown gene therapy to be effective against inherited inner ear diseases, and the application of this technology to humans is now within reach. We provide here a comprehensive and practical overview of current advances in gene therapy for inherited deafness, with and without an associated vestibular defect. We focus on the different gene therapy approaches, considering their prospects, including the viral vector used, and the delivery route. We also discuss the clinical application of the various strategies, their strengths, weaknesses, and the challenges to be overcome.
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48
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Milanese JS, Marcotte R, Costain WJ, Kablar B, Drouin S. Roles of Skeletal Muscle in Development: A Bioinformatics and Systems Biology Overview. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2023; 236:21-55. [PMID: 37955770 DOI: 10.1007/978-3-031-38215-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
The ability to assess various cellular events consequent to perturbations, such as genetic mutations, disease states and therapies, has been recently revolutionized by technological advances in multiple "omics" fields. The resulting deluge of information has enabled and necessitated the development of tools required to both process and interpret the data. While of tremendous value to basic researchers, the amount and complexity of the data has made it extremely difficult to manually draw inference and identify factors key to the study objectives. The challenges of data reduction and interpretation are being met by the development of increasingly complex tools that integrate disparate knowledge bases and synthesize coherent models based on current biological understanding. This chapter presents an example of how genomics data can be integrated with biological network analyses to gain further insight into the developmental consequences of genetic perturbations. State of the art methods for conducting similar studies are discussed along with modern methods used to analyze and interpret the data.
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Affiliation(s)
| | - Richard Marcotte
- Human Health Therapeutics, National Research Council of Canada , Montreal, QC, Canada
| | - Willard J Costain
- Human Health Therapeutics, National Research Council of Canada, Ottawa, ON, Canada
| | - Boris Kablar
- Department of Medical Neuroscience, Anatomy and Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Simon Drouin
- Human Health Therapeutics, National Research Council of Canada , Montreal, QC, Canada.
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Mencarelli G, Pieroni B, Murphy KM, Gargaro M. Use of CRISPR/CAS9 Technologies to Study the Role of TLR in Dendritic Cell Subsets. Methods Mol Biol 2023; 2700:77-92. [PMID: 37603175 DOI: 10.1007/978-1-0716-3366-3_4] [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] [Indexed: 08/22/2023]
Abstract
Dendritic cells (DCs) have a significant role in coordinating both innate and adaptive immunity by serving as sentinels that detect invaders and initiate immune responses to eliminate them, as well as presenting antigens to activate adaptive immune responses that are specific to the antigen and the context in which it was detected. The regulation of DC functions is complex and involves intracellular drivers such as transcription factors and signaling pathways, as well as intercellular interactions with adhesion molecules, chemokines, and their receptors in the microenvironment. Toll-like receptors (TLRs) are crucial for DCs to detect pathogen-associated molecular patterns (PAMPs) and initiate downstream signaling pathways that lead to DC maturation and education in bridging with adaptive immunity, including the upregulation of MHC class II expression, induction of CD80, CD86, and CD40, and production of innate cytokines. Understanding the TLR pathways that DCs use to respond to innate immune stimuli and convert them into adaptive responses is important for new therapeutic targets identification.We present a novel platform that offers a fast and affordable CRISPR-Cas9 screening of genes that are involved in dendritic cells' TLR-dependent activation. Using CRISPR/Cas9 screening to target individual TLR genes in different dendritic cell subsets allows the identification of TLR-dependent pathways that regulate dendritic cell activation and cytokine production. This approach offers the efficient targeting of TLR driver genes to modulate the immune response and identify novel immune response regulators, establishing a causal link between these regulators and functional phenotypes based on genotypes.
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Affiliation(s)
- Giulia Mencarelli
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Benedetta Pieroni
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Marco Gargaro
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy.
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