1
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Guo X, Song J, Liu M, Ou X, Guo Y. The interplay between the tumor microenvironment and tumor-derived small extracellular vesicles in cancer development and therapeutic response. Cancer Biol Ther 2024; 25:2356831. [PMID: 38767879 PMCID: PMC11110713 DOI: 10.1080/15384047.2024.2356831] [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: 10/22/2023] [Accepted: 05/14/2024] [Indexed: 05/22/2024] Open
Abstract
The tumor microenvironment (TME) plays an essential role in tumor cell survival by profoundly influencing their proliferation, metastasis, immune evasion, and resistance to treatment. Extracellular vesicles (EVs) are small particles released by all cell types and often reflect the state of their parental cells and modulate other cells' functions through the various cargo they transport. Tumor-derived small EVs (TDSEVs) can transport specific proteins, nucleic acids and lipids tailored to propagate tumor signals and establish a favorable TME. Thus, the TME's biological characteristics can affect TDSEV heterogeneity, and this interplay can amplify tumor growth, dissemination, and resistance to therapy. This review discusses the interplay between TME and TDSEVs based on their biological characteristics and summarizes strategies for targeting cancer cells. Additionally, it reviews the current issues and challenges in this field to offer fresh insights into comprehending tumor development mechanisms and exploring innovative clinical applications.
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Affiliation(s)
- Xuanyu Guo
- The Affiliated Hospital, Southwest Medical University, Luzhou, PR China
| | - Jiajun Song
- Department of Clinical Laboratory Medicine, the Affiliated Hospital, Southwest Medical University, Luzhou, PR China
| | - Miao Liu
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, PR China
| | - Xinyi Ou
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, PR China
| | - Yongcan Guo
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, PR China
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2
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Nickerson JA, Momen-Heravi F. Long non-coding RNAs: roles in cellular stress responses and epigenetic mechanisms regulating chromatin. Nucleus 2024; 15:2350180. [PMID: 38773934 PMCID: PMC11123517 DOI: 10.1080/19491034.2024.2350180] [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: 01/18/2024] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Most of the genome is transcribed into RNA but only 2% of the sequence codes for proteins. Non-coding RNA transcripts include a very large number of long noncoding RNAs (lncRNAs). A growing number of identified lncRNAs operate in cellular stress responses, for example in response to hypoxia, genotoxic stress, and oxidative stress. Additionally, lncRNA plays important roles in epigenetic mechanisms operating at chromatin and in maintaining chromatin architecture. Here, we address three lncRNA topics that have had significant recent advances. The first is an emerging role for many lncRNAs in cellular stress responses. The second is the development of high throughput screening assays to develop causal relationships between lncRNAs across the genome with cellular functions. Finally, we turn to recent advances in understanding the role of lncRNAs in regulating chromatin architecture and epigenetics, advances that build on some of the earliest work linking RNA to chromatin architecture.
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Affiliation(s)
- Jeffrey A Nickerson
- Division of Genes & Development, Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Fatemeh Momen-Heravi
- College of Dental Medicine, Columbia University Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
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3
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Tran NT, Graf R, Acevedo-Ochoa E, Trombke J, Weber T, Sommermann T, Salomon C, Kühn R, Rajewsky K, Chu VT. In vivo CRISPR/Cas9-mediated screen reveals a critical function of TFDP1 and E2F4 transcription factors in hematopoiesis. Leukemia 2024:10.1038/s41375-024-02357-w. [PMID: 39043964 DOI: 10.1038/s41375-024-02357-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 07/10/2024] [Accepted: 07/15/2024] [Indexed: 07/25/2024]
Abstract
Hematopoiesis is a continuous process of blood cell production driven by hematopoietic stem and progenitor cells (HSPCs) in the bone marrow. Proliferation and differentiation of HSPCs are regulated by complex transcriptional networks. In order to identify transcription factors with key roles in HSPC-mediated hematopoietic reconstitution, we developed an efficient and robust CRISPR/Cas9-based in vivo genetic screen. Using this experimental system, we identified the TFDP1 transcription factor to be essential for HSPC proliferation and post-transplant hematopoiesis. We further discovered that E2F4, an E2F transcription factor, serves as a binding partner of TFDP1 and is required for HSPC proliferation. Deletion of TFDP1 caused downregulation of genes associated with the cell cycle, with around 50% of these genes being identified as direct targets of TFDP1 and E2F4. Thus, our study expands the transcriptional network governing hematopoietic development through an in vivo CRISPR/Cas9-based genetic screen and identifies TFDP1/E2F4 as positive regulators of cell cycle genes in HSPCs.
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Affiliation(s)
- Ngoc Tung Tran
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany.
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Robin Graf
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, 13125, Germany
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin, Berlin, Germany
| | - Ernesto Acevedo-Ochoa
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
| | - Janine Trombke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
| | - Timm Weber
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
- Biobank OWL (BOWL), Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Thomas Sommermann
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
- Dynamic42 GmbH, Jena, Germany
| | - Claudia Salomon
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
| | - Ralf Kühn
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Genome Engineering & Disease Models, Berlin, Germany
| | - Klaus Rajewsky
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany.
| | - Van Trung Chu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany.
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Genome Engineering & Disease Models, Berlin, Germany.
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4
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Lebenzon JE, Toxopeus J. Knock down to level up: Reframing RNAi for invertebrate ecophysiology. Comp Biochem Physiol A Mol Integr Physiol 2024; 297:111703. [PMID: 39029617 DOI: 10.1016/j.cbpa.2024.111703] [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: 02/21/2024] [Revised: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
Comparative ecophysiologists strive to understand physiological problems in non-model organisms, but molecular tools such as RNA interference (RNAi) are under-used in our field. Here, we provide a framework for invertebrate ecophysiologists to use RNAi to answer questions focused on physiological processes, rather than as a tool to investigate gene function. We specifically focus on non-model invertebrates, in which the use of other genetic tools (e.g., genetic knockout lines) is less likely. We argue that because RNAi elicits a temporary manipulation of gene expression, and resources to carry out RNAi are technically and financially accessible, it is an effective tool for invertebrate ecophysiologists. We cover the terminology and basic mechanisms of RNA interference as an accessible introduction for "non-molecular" physiologists, include a suggested workflow for identifying RNAi gene targets and validating biologically relevant gene knockdowns, and present a hypothesis-testing framework for using RNAi to answer common questions in the realm of invertebrate ecophysiology. This review encourages invertebrate ecophysiologists to use these tools and workflows to explore physiological processes and bridge genotypes to phenotypes in their animal(s) of interest.
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Affiliation(s)
- Jacqueline E Lebenzon
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4.
| | - Jantina Toxopeus
- Department of Biology, St. Francis Xavier University, 2321 Notre Dame Ave, Antigonish, NS, Canada B2G 2W5
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5
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Jin SE, Sung JH. Delivery Strategies of siRNA Therapeutics for Hair Loss Therapy. Int J Mol Sci 2024; 25:7612. [PMID: 39062852 PMCID: PMC11277092 DOI: 10.3390/ijms25147612] [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: 05/01/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024] Open
Abstract
Therapeutic needs for hair loss are intended to find small interfering ribonucleic acid (siRNA) therapeutics for breakthrough. Since naked siRNA is restricted to meet a druggable target in clinic,, delivery systems are indispensable to overcome intrinsic and pathophysiological barriers, enhancing targetability and persistency to ensure safety, efficacy, and effectiveness. Diverse carriers repurposed from small molecules to siRNA can be systematically or locally employed in hair loss therapy, followed by the adoption of new compositions associated with structural and environmental modification. The siRNA delivery systems have been extensively studied via conjugation or nanoparticle formulation to improve their fate in vitro and in vivo. In this review, we introduce clinically tunable siRNA delivery systems for hair loss based on design principles, after analyzing clinical trials in hair loss and currently approved siRNA therapeutics. We further discuss a strategic research framework for optimized siRNA delivery in hair loss from the scientific perspective of clinical translation.
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Affiliation(s)
- Su-Eon Jin
- Epi Biotech Co., Ltd., Incheon 21984, Republic of Korea
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6
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Gaude AA, Siqueira RH, Botelho SB, Jalmi SK. Epigenetic arsenal for stress mitigation in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130620. [PMID: 38636616 DOI: 10.1016/j.bbagen.2024.130620] [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: 11/07/2023] [Revised: 02/23/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Plant's ability to perceive, respond to, and ultimately adapt to various stressors is a testament to their remarkable resilience. In response to stresses, plants activate a complex array of molecular and physiological mechanisms. These include the rapid activation of stress-responsive genes, the manufacturing of protective compounds, modulation of cellular processes and alterations in their growth and development patterns to enhance their chances of survival. Epigenetic mechanisms play a pivotal role in shaping the responses of plants to environmental stressors. This review explores the intricate interplay between epigenetic regulation and plant stress mitigation. We delve into the dynamic landscape of epigenetic modifications, highlighting their influence on gene expression and ultimately stress tolerance. This review assembles current research, shedding light on the promising strategies within plants' epigenetic arsenal to thrive amidst adverse conditions.
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Affiliation(s)
- Aishwarya Ashok Gaude
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
| | - Roxiette Heromina Siqueira
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
| | - Savia Bernadette Botelho
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
| | - Siddhi Kashinath Jalmi
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
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7
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He L, Li Z, Su D, Du H, Zhang K, Zhang W, Wang S, Xie F, Qiu Y, Ma S, Shi G, Yu D, Lei X, Li W, Li M, Wang Z, Gu J, Zhang Y. Tumor Microenvironment-Responsive Nanocapsule Delivery CRISPR/Cas9 to Reprogram the Immunosuppressive Microenvironment in Hepatoma Carcinoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2403858. [PMID: 38704691 PMCID: PMC11234430 DOI: 10.1002/advs.202403858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Indexed: 05/07/2024]
Abstract
Cancer immunotherapy has demonstrated significant efficacy in various tumors, but its effectiveness in treating Hepatocellular Carcinoma (HCC) remains limited. Therefore, there is an urgent need to identify a new immunotherapy target and develop corresponding intervention strategies. Bioinformatics analysis has revealed that growth differentiation factor 15 (GDF15) is highly expressed in HCC and is closely related to poor prognosis of HCC patients. The previous study revealed that GDF15 can promote immunosuppression in the tumor microenvironment. Therefore, knocking out GDF15 through gene editing could potentially reverse the suppressive tumor immune microenvironment permanently. To deliver the CRISPR/Cas9 system specifically to HCC, nanocapsules (SNC) coated with HCC targeting peptides (SP94) on their surface is utilized. These nanocapsules incorporate disulfide bonds (SNCSS) that release their contents in the tumor microenvironment characterized by high levels of glutathione (GSH). In vivo, the SNCSS target HCC cells, exert a marked inhibitory effect on HCC progression, and promote HCC immunotherapy. Mechanistically, CyTOF analysis showed favorable changes in the immune microenvironment of HCC, immunocytes with killer function increased and immunocytes with inhibitive function decreased. These findings highlight the potential of the CRISPR-Cas9 gene editing system in modulating the immune microenvironment and improving the effectiveness of existing immunotherapy approaches for HCC.
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Affiliation(s)
- Lei He
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Zhaozhao Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Danjie Su
- Department of Obstetrics and GynecologyTangdu HospitalThe Fourth Military Medical UniversityXi'an710038China
| | - Haichen Du
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
- Department of Oncology940th HospitalJoint Logistic Support ForceLanzhou730050China
| | - Kuo Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Wangqian Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Shuning Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Fei Xie
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Yueyuan Qiu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Shuangxin Ma
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Gege Shi
- College of Life SciencesNorthwest UniversityXi'an710069China
| | - Duo Yu
- Department of NeurosurgeryGeneral Hospital of Central Theater CommandWuhan430012China
| | - Xiaoying Lei
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Weina Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Meng Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Zhaowei Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Jintao Gu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Yingqi Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
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8
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Campos TL, Korhonen PK, Young ND, Wang T, Song J, Marhoefer R, Chang BCH, Selzer PM, Gasser RB. Inference of Essential Genes of the Parasite Haemonchus contortus via Machine Learning. Int J Mol Sci 2024; 25:7015. [PMID: 39000124 PMCID: PMC11240989 DOI: 10.3390/ijms25137015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024] Open
Abstract
Over the years, comprehensive explorations of the model organisms Caenorhabditis elegans (elegant worm) and Drosophila melanogaster (vinegar fly) have contributed substantially to our understanding of complex biological processes and pathways in multicellular organisms generally. Extensive functional genomic-phenomic, genomic, transcriptomic, and proteomic data sets have enabled the discovery and characterisation of genes that are crucial for life, called 'essential genes'. Recently, we investigated the feasibility of inferring essential genes from such data sets using advanced bioinformatics and showed that a machine learning (ML)-based workflow could be used to extract or engineer features from DNA, RNA, protein, and/or cellular data/information to underpin the reliable prediction of essential genes both within and between C. elegans and D. melanogaster. As these are two distantly related species within the Ecdysozoa, we proposed that this ML approach would be particularly well suited for species that are within the same phylum or evolutionary clade. In the present study, we cross-predicted essential genes within the phylum Nematoda (evolutionary clade V)-between C. elegans and the pathogenic parasitic nematode H. contortus-and then ranked and prioritised H. contortus proteins encoded by these genes as intervention (e.g., drug) target candidates. Using strong, validated predictors, we inferred essential genes of H. contortus that are involved predominantly in crucial biological processes/pathways including ribosome biogenesis, translation, RNA binding/processing, and signalling and which are highly transcribed in the germline, somatic gonad precursors, sex myoblasts, vulva cell precursors, various nerve cells, glia, or hypodermis. The findings indicate that this in silico workflow provides a promising avenue to identify and prioritise panels/groups of drug target candidates in parasitic nematodes for experimental validation in vitro and/or in vivo.
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Affiliation(s)
- Túlio L Campos
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
- Bioinformatics Core Facility, Aggeu Magalhães Institute (Fiocruz), Recife 50740-465, PE, Brazil
| | - Pasi K Korhonen
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Neil D Young
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Tao Wang
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jiangning Song
- Department of Data Science and AI, Faculty of IT, Monash University, Melbourne, VIC 3800, Australia
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- Monash Data Futures Institute, Monash University, Clayton, VIC 3800, Australia
| | - Richard Marhoefer
- Boehringer Ingelheim Animal Health, Binger Strasse 173, 55216 Ingelheim am Rhein, Germany
| | - Bill C H Chang
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Paul M Selzer
- Boehringer Ingelheim Animal Health, Binger Strasse 173, 55216 Ingelheim am Rhein, Germany
| | - Robin B Gasser
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
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Mills J, Tessari A, Anastas V, Kumar DS, Rad NS, Lamba S, Cosentini I, Reers A, Zhu Z, Miles WO, Coppola V, Cocucci E, Magliery TJ, Shive H, Davies AE, Rizzotto L, Croce CM, Palmieri D. Nucleolin acute degradation reveals novel functions in cell cycle progression and division in TNBC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599429. [PMID: 38948867 PMCID: PMC11212942 DOI: 10.1101/2024.06.17.599429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Nucleoli are large nuclear sub-compartments where vital processes, such as ribosome assembly, take place. Technical obstacles still limit our understanding of the biological functions of nucleolar proteins in cell homeostasis and cancer pathogenesis. Since most nucleolar proteins are essential, their abrogation cannot be achieved through conventional approaches. Additionally, the biological activities of many nucleolar proteins are connected to their physiological concentration. Thus, artificial overexpression might not fully recapitulate their endogenous functions. Proteolysis-based approaches, such as the Auxin Inducible Degron (AID) system paired with CRISPR/Cas9 knock-in gene-editing, have the potential to overcome these limitations, providing unprecedented characterization of the biological activities of endogenous nucleolar proteins. We applied this system to endogenous nucleolin (NCL), one of the most abundant nucleolar proteins, and characterized the impact of its acute depletion on Triple-Negative Breast Cancer (TNBC) cell behavior. Abrogation of endogenous NCL reduced proliferation and caused defective cytokinesis, resulting in bi-nucleated tetraploid cells. Bioinformatic analysis of patient data, and quantitative proteomics using our experimental NCL-depleted model, indicated that NCL levels are correlated with the abundance of proteins involved in chromosomal segregation. In conjunction with its effects on sister chromatid dynamics, NCL abrogation enhanced the anti-proliferative effects of chemical inhibitors of mitotic modulators such as the Anaphase Promoting Complex. In summary, using the AID system in combination with CRISPR/Cas9 for endogenous gene editing, our findings indicate a novel role for NCL in supporting the completion of the cell division in TNBC models, and that its abrogation could enhance the therapeutic activity of mitotic-progression inhibitors.
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Affiliation(s)
- Joseph Mills
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, 43210, Columbus, OH, USA
| | - Anna Tessari
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Vollter Anastas
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Graduate School of Biomedical Sciences, Tufts University, 02155, Boston, MA, USA
| | - Damu Sunil Kumar
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Nastaran Samadi Rad
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Biomedical Sciences Graduate Program, The Ohio State University, 43210, Columbus, OH, USA
| | - Saranya Lamba
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Ilaria Cosentini
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Current address: Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), Palermo, Italy
| | - Ashley Reers
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Current address: Department of Ecology and Evolutionary Biology, Tulane University, 70118, New Orleans, LA, USA
| | - Zirui Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, 43210, Columbus, OH, USA
- Chemistry Graduate Program, The Ohio State University, 43210, Columbus, OH, USA
| | - Wayne O Miles
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University-James Cancer Hospital and Solove Research Institute, 43210, Columbus, OH, USA
| | - Emanuele Cocucci
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, 43210, Columbus, OH, USA
| | - Thomas J. Magliery
- Department of Chemistry and Biochemistry, The Ohio State University, 43210, Columbus, OH, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University-James Cancer Hospital and Solove Research Institute, 43210, Columbus, OH, USA
| | - Heather Shive
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, 43210, Columbus, OH, USA
- Current address: Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alexander E. Davies
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, 43210, Columbus, OH, USA
- Current address: Division of Oncological Sciences, Department of Pediatrics, Cancer Early Detection Advanced Research Center, School of Medicine, Oregon Health and Science University, 97239, Portland, OR, USA
| | - Lara Rizzotto
- Gene Editing Shared Resource, The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Dario Palmieri
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Gene Editing Shared Resource, The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
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10
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Di Marco T, Mazzoni M, Greco A, Cassinelli G. Non-oncogene dependencies: Novel opportunities for cancer therapy. Biochem Pharmacol 2024:116254. [PMID: 38704100 DOI: 10.1016/j.bcp.2024.116254] [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: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Targeting oncogene addictions have changed the history of subsets of malignancies and continues to represent an excellent therapeutic opportunity. Nonetheless, alternative strategies are required to treat malignancies driven by undruggable oncogenes or loss of tumor suppressor genes and to overcome drug resistance also occurring in cancers addicted to actionable drivers. The discovery of non-oncogene addiction (NOA) uncovered novel therapeutically exploitable "Achilles' heels". NOA refers to genes/pathways not oncogenic per sé but essential for the tumor cell growth/survival while dispensable for normal cells. The clinical success of several classes of conventional and molecular targeted agents can be ascribed to their impact on both tumor cell-associated intrinsic as well as microenvironment-related extrinsic NOA. The integration of genetic, computational and pharmacological high-throughput approaches led to the identification of an expanded repertoire of synthetic lethality interactions implicating NOA targets. Only a few of them have been translated into the clinics as most NOA vulnerabilities are not easily druggable or appealing targets. Nonetheless, their identification has provided in-depth knowledge of tumor pathobiology and suggested novel therapeutic opportunities. Here, we summarize conceptual framework of intrinsic and extrinsic NOA providing exploitable vulnerabilities. Conventional and emerging methodological approaches used to disclose NOA dependencies are reported together with their limits. We illustrate NOA paradigmatic and peculiar examples and outline the functional/mechanistic aspects, potential druggability and translational interest. Finally, we comment on difficulties in exploiting the NOA-generated knowledge to develop novel therapeutic approaches to be translated into the clinics and to fully harness the potential of clinically available drugs.
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Affiliation(s)
- Tiziana Di Marco
- Integrated Biology of Rare Tumors Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy
| | - Mara Mazzoni
- Integrated Biology of Rare Tumors Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy
| | - Angela Greco
- Integrated Biology of Rare Tumors Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy
| | - Giuliana Cassinelli
- Molecular Pharmacology Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy.
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11
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Yang F, Vincis Pereira Sanglard L, Lee CP, Ströher E, Singh S, Oh GGK, Millar AH, Small I, Colas des Francs-Small C. Mitochondrial atp1 mRNA knockdown by a custom-designed pentatricopeptide repeat protein alters ATP synthase. PLANT PHYSIOLOGY 2024; 194:2631-2647. [PMID: 38206203 PMCID: PMC10980415 DOI: 10.1093/plphys/kiae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/12/2024]
Abstract
Spontaneous mutations are rare in mitochondria and the lack of mitochondrial transformation methods has hindered genetic analyses. We show that a custom-designed RNA-binding pentatricopeptide repeat (PPR) protein binds and specifically induces cleavage of ATP synthase subunit1 (atp1) mRNA in mitochondria, significantly decreasing the abundance of the Atp1 protein and the assembled F1Fo ATP synthase in Arabidopsis (Arabidopsis thaliana). The transformed plants are characterized by delayed vegetative growth and reduced fertility. Five-fold depletion of Atp1 level was accompanied by a decrease in abundance of other ATP synthase subunits and lowered ATP synthesis rate of isolated mitochondria, but no change to mitochondrial electron transport chain complexes, adenylates, or energy charge in planta. Transcripts for amino acid transport and a variety of stress response processes were differentially expressed in lines containing the PPR protein, indicating changes to achieve cellular homeostasis when ATP synthase was highly depleted. Leaves of ATP synthase-depleted lines showed higher respiratory rates and elevated steady-state levels of numerous amino acids, most notably of the serine family. The results show the value of using custom-designed PPR proteins to influence the expression of specific mitochondrial transcripts to carry out reverse genetic studies on mitochondrial gene functions and the consequences of ATP synthase depletion on cellular functions in Arabidopsis.
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Affiliation(s)
- Fei Yang
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, P. R. China
| | - Lilian Vincis Pereira Sanglard
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Chun-Pong Lee
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Elke Ströher
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Swati Singh
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Glenda Guec Khim Oh
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - A Harvey Millar
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Catherine Colas des Francs-Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
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12
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He J, Li J, Liu Y, Li Y. Sperm-Associated Antigen 5 Knockout Reduces Doxorubicin and Docetaxel Resistance in Triple-Negative Breast Cancer MDA-MB-231 and BT549 Cells. Cancers (Basel) 2024; 16:1269. [PMID: 38610947 PMCID: PMC11010853 DOI: 10.3390/cancers16071269] [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: 02/24/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Sperm-associated antigen 5 (SPAG5), also known as Astrin, was previously demonstrated as a biomarker for cellular resistance to major breast cancer therapies, including chemo-, endocrine- and targeted therapy. However, the contribution of SPAG5 to anthracycline- and taxane-based chemotherapy in triple-negative breast cancer (TNBC) remains controversial. In the present study, the SPAG5 knockout cell model was established by using clustered regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system in MDA-MB-231 and BT549 TNBC cell lines. The knockout of SPAG5 was confirmed on both gene and protein levels using genomic PCR, DNA sequencing and western blotting. The functional loss of SPAG5 was determined by colony-formation assay. SPAG5-regulated doxorubicin- and docetaxel-resistance was assessed by MTT and apoptosis assays. The results indicated that all the SPAG5 knockout MDA-MB-231 and BT549 clones were biallelic, where one allele was replaced by the donor template, and the other allele had the same "T" insertion (indel) adjacent to the cutting sites of gRNAs at the exon 1 boundary, irrespective of the gRNAs and cell lines. The locus of indel interrupted the SPAG5 transcription by damaging the GT-AG mRNA processing rule. Deletion of SPAG5 decreased clonogenicity in both MDA-MB-231 and BT549 cells. SPAG5 was able to regulate the resistance and the drug-induced apoptosis of both doxorubicin and docetaxel. In conclusion, recombinant plasmid-based CRISPR-Cas9 technology can be used to delete the SPAG5 gene in the TNBC cell lines. SPAG5 has an important role in regulating cell proliferation and doxorubicin- and docetaxel-resistance in MDA-MB-231 and BT549 cells.
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Affiliation(s)
- Ji He
- School of Science, Auckland University of Technology, Auckland 1010, New Zealand; (J.H.); (J.L.); (Y.L.)
- Department of Food and Agriculture Technology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Jiawei Li
- School of Science, Auckland University of Technology, Auckland 1010, New Zealand; (J.H.); (J.L.); (Y.L.)
- General Medicine Department, Shenzhen Longhua District Central Hospital, Shenzhen 518110, China
| | - Yanbiao Liu
- School of Science, Auckland University of Technology, Auckland 1010, New Zealand; (J.H.); (J.L.); (Y.L.)
| | - Yan Li
- School of Science, Auckland University of Technology, Auckland 1010, New Zealand; (J.H.); (J.L.); (Y.L.)
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13
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Spisak S, Chen D, Likasitwatanakul P, Doan P, Li Z, Bala P, Vizkeleti L, Tisza V, De Silva P, Giannakis M, Wolpin B, Qi J, Sethi NS. Identifying regulators of aberrant stem cell and differentiation activity in colorectal cancer using a dual endogenous reporter system. Nat Commun 2024; 15:2230. [PMID: 38472198 PMCID: PMC10933491 DOI: 10.1038/s41467-024-46285-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: 02/02/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators of these key cellular programs, we engineer a dual endogenous reporter system by genome-editing the SOX9 and KRT20 loci of human CRC cell lines to express fluorescent reporters, broadcasting aberrant stem cell-like and differentiation activity, respectively. By applying a CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs to this platform, we identify factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominate SMARCB1 of the BAF complex (also known as SWI/SNF) as a negative regulator of differentiation across an array of neoplastic colon models. SMARCB1 is a dependency and required for in vivo growth of human CRC models. These studies highlight the utility of biologically designed endogenous reporter platforms to uncover regulators with therapeutic potential.
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Affiliation(s)
- Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - David Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Pornlada Likasitwatanakul
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Paul Doan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Zhixin Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Pratyusha Bala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Laura Vizkeleti
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, 1094, Budapest, Hungary
| | - Viktoria Tisza
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Pushpamali De Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nilay S Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA.
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA.
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14
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Luo J, Amin B, Wu B, Wu B, Huang W, Salmen SH, Fang Z. Blocking of awn development-related gene OsGAD1 coordinately boosts yield and quality of Kam Sweet Rice. PHYSIOLOGIA PLANTARUM 2024; 176:e14229. [PMID: 38413386 DOI: 10.1111/ppl.14229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/04/2024] [Accepted: 02/10/2024] [Indexed: 02/29/2024]
Abstract
Kam Sweet Rice is a high-quality local variety of Guizhou province in China, but most varieties have awns on lemma. In this study, we aimed to obtain awnless varieties of Kam Sweet Rice by blocking the awn development-related gene OsGAD1 using CRISPR/Cas9 technology. We determined that natural variations of the OsGAD1 triggered different lengths of awns of Kam Sweet Rice. We found that the awning rate of the CRISPR lines of OsGAD1 in Guxiangnuo, Goujingao and Gouhuanggang decreased by over 65%, and the number of grains per panicle and yield per plant increased by more than 17% and 20% compared to the wild-types. Furthermore, we indicated that blocking OsGAD1 resulted in an increase of over 2% in the brown rice rate and milled rice rate in these varieties. In addition, the analysis of the transcriptome revealed that the regulation of awn development and yield formation in CRISPR lines of OsGAD1 may involve genes associated with phytohormone and nitrogen pathways. These results suggest that blocking OsGAD1 in Kam Sweet Rice using CRISPR/Cas9 technology can be used for breeding programs seeking high yield and grain quality of Kam Sweet Rice.
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Affiliation(s)
- Jun Luo
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Bakht Amin
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Bilong Wu
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Bowen Wu
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, Guizhou, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
| | - Weiting Huang
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Saleh H Salmen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Zhongming Fang
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, Guizhou, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
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15
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Chariou PL, Minnar CM, Tandon M, Guest MR, Chari R, Schlom J, Gameiro SR. Generation of murine tumor models refractory to αPD-1/-L1 therapies due to defects in antigen processing/presentation or IFNγ signaling using CRISPR/Cas9. PLoS One 2024; 19:e0287733. [PMID: 38427670 PMCID: PMC10906908 DOI: 10.1371/journal.pone.0287733] [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: 01/25/2023] [Accepted: 06/12/2023] [Indexed: 03/03/2024] Open
Abstract
Immune checkpoint blockade (ICB) targeting the programmed cell death protein 1 (PD-1) and its ligand 1 (PD-L1) fails to provide clinical benefit for most cancer patients due to primary or acquired resistance. Drivers of ICB resistance include tumor antigen processing/presentation machinery (APM) and IFNγ signaling mutations. Thus, there is an unmet clinical need to develop alternative therapies for these patients. To this end, we have developed a CRISPR/Cas9 approach to generate murine tumor models refractory to PD-1/-L1 inhibition due to APM/IFNγ signaling mutations. Guide RNAs were employed to delete B2m, Jak1, or Psmb9 genes in ICB-responsive EMT6 murine tumor cells. B2m was deleted in ICB-responsive MC38 murine colon cancer cells. We report a detailed development and validation workflow including whole exome and Sanger sequencing, western blotting, and flow cytometry to assess target gene deletion. Tumor response to ICB and immune effects of gene deletion were assessed in syngeneic mice. This workflow can help accelerate the discovery and development of alternative therapies and a deeper understanding of the immune consequences of tumor mutations, with potential clinical implications.
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Affiliation(s)
- Paul L. Chariou
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Christine M. Minnar
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Mayank Tandon
- National Cancer Institute, CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Institutes of Health, Bethesda, MD, United States of America
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Mary R. Guest
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Raj Chari
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Jeffrey Schlom
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Sofia R. Gameiro
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
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16
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Macarrón Palacios A, Korus P, Wilkens BGC, Heshmatpour N, Patnaik SR. Revolutionizing in vivo therapy with CRISPR/Cas genome editing: breakthroughs, opportunities and challenges. Front Genome Ed 2024; 6:1342193. [PMID: 38362491 PMCID: PMC10867117 DOI: 10.3389/fgeed.2024.1342193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/11/2024] [Indexed: 02/17/2024] Open
Abstract
Genome editing using the CRISPR/Cas system has revolutionized the field of genetic engineering, offering unprecedented opportunities for therapeutic applications in vivo. Despite the numerous ongoing clinical trials focusing on ex vivo genome editing, recent studies emphasize the therapeutic promise of in vivo gene editing using CRISPR/Cas technology. However, it is worth noting that the complete attainment of the inherent capabilities of in vivo therapy in humans is yet to be accomplished. Before the full realization of in vivo therapeutic potential, it is crucial to achieve enhanced specificity in selectively targeting defective cells while minimizing harm to healthy cells. This review examines emerging studies, focusing on CRISPR/Cas-based pre-clinical and clinical trials for innovative therapeutic approaches for a wide range of diseases. Furthermore, we emphasize targeting cancer-specific sequences target in genes associated with tumors, shedding light on the diverse strategies employed in cancer treatment. We highlight the various challenges associated with in vivo CRISPR/Cas-based cancer therapy and explore their prospective clinical translatability and the strategies employed to overcome these obstacles.
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17
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Wang M, Ye X, Bi H, Shen Z. Microalgae biofuels: illuminating the path to a sustainable future amidst challenges and opportunities. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:10. [PMID: 38254224 PMCID: PMC10804497 DOI: 10.1186/s13068-024-02461-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
The development of microalgal biofuels is of significant importance in advancing the energy transition, alleviating food pressure, preserving the natural environment, and addressing climate change. Numerous countries and regions across the globe have conducted extensive research and strategic planning on microalgal bioenergy, investing significant funds and manpower into this field. However, the microalgae biofuel industry has faced a downturn due to the constraints of high costs. In the past decade, with the development of new strains, technologies, and equipment, the feasibility of large-scale production of microalgae biofuel should be re-evaluated. Here, we have gathered research results from the past decade regarding microalgae biofuel production, providing insights into the opportunities and challenges faced by this industry from the perspectives of microalgae selection, modification, and cultivation. In this review, we suggest that highly adaptable microalgae are the preferred choice for large-scale biofuel production, especially strains that can utilize high concentrations of inorganic carbon sources and possess stress resistance. The use of omics technologies and genetic editing has greatly enhanced lipid accumulation in microalgae. However, the associated risks have constrained the feasibility of large-scale outdoor cultivation. Therefore, the relatively controllable cultivation method of photobioreactors (PBRs) has made it the mainstream approach for microalgae biofuel production. Moreover, adjusting the performance and parameters of PBRs can also enhance lipid accumulation in microalgae. In the future, given the relentless escalation in demand for sustainable energy sources, microalgae biofuels should be deemed a pivotal constituent of national energy planning, particularly in the case of China. The advancement of synthetic biology helps reduce the risks associated with genetically modified (GM) microalgae and enhances the economic viability of their biofuel production.
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Affiliation(s)
- Min Wang
- Institute of Agricultural Remote Sensing and Information, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.
| | - Xiaoxue Ye
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, 572025, China
| | - Hongwen Bi
- Institute of Agricultural Remote Sensing and Information, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Zhongbao Shen
- Grass and Science Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.
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18
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Spisak S, Chen D, Likasitwatanakul P, Doan P, Li Z, Bala P, Vizkeleti L, Tisza V, De Silva P, Giannakis M, Wolpin B, Qi J, Sethi NS. Utilizing a dual endogenous reporter system to identify functional regulators of aberrant stem cell and differentiation activity in colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.21.545895. [PMID: 38293113 PMCID: PMC10827082 DOI: 10.1101/2023.06.21.545895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators that regulate these key cellular programs in CRC, we developed an endogenous reporter system by genome-editing human CRC cell lines with knock-in fluorescent reporters at the SOX9 and KRT20 locus to report aberrant stem cell-like activity and differentiation, respectively, and then performed pooled genetic perturbation screens. Constructing a dual reporter system that simultaneously monitored aberrant stem cell-like and differentiation activity in the same CRC cell line improved our signal to noise discrimination. Using a focused-library CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs, we identified factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominated SMARCB1 of the BAF complex (also known as SWI/SNF) as a negative regulator of differentiation across an array of neoplastic colon models. SMARCB1 is a dependency in CRC and required for in vivo growth of human CRC models. These studies highlight the utility of a biologically designed endogenous reporter system to uncover novel therapeutic targets for drug development.
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Affiliation(s)
- Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - David Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Pornlada Likasitwatanakul
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Bangkok, Thailand
| | - Paul Doan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Zhixin Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Pratyusha Bala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Laura Vizkeleti
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary
| | - Viktoria Tisza
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Pushpamail De Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nilay S. Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
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19
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Gil M, Hamann CA, Brunger JM, Gama V. Engineering a CRISPRoff Platform to Modulate Expression of Myeloid Cell Leukemia (MCL-1) in Committed Oligodendrocyte Neural Precursor Cells. Bio Protoc 2024; 14:e4913. [PMID: 38213321 PMCID: PMC10777056 DOI: 10.21769/bioprotoc.4913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 01/13/2024] Open
Abstract
In vitro differentiation of human pluripotent stem cell (hPSC) model systems has furthered our understanding of human development. Techniques used to elucidate gene function during early development have encountered technical challenges, especially when targeting embryonic lethal genes. The introduction of CRISPRoff by Nuñez and collaborators provides an opportunity to heritably silence genes during long-term differentiation. We modified CRISPRoff and sgRNA Sleeping Beauty transposon vectors that depend on tetracycline-controlled transcriptional activation to silence the expression of embryonic lethal genes at different stages of differentiation in a stable manner. We provide instructions on how to generate sgRNA transposon vectors that can be used in combination with our CRISPRoff transposon vector and a stable hPSC line. We validate the use of this tool by silencing MCL-1, an anti-apoptotic protein, which results in pre-implantation embryonic lethality in mice; this protein is necessary for oligodendrocyte and hematopoietic stem cell development and is required for the in vitro survival of hPSCs. In this protocol, we use an adapted version of the differentiation protocol published by Douvaras and Fossati (2015) to generate oligodendrocyte lineage cells from human embryonic stem cells (hESCs). After introduction of the CRISPRoff and sgRNAs transposon vectors in hESCs, we silence MCL-1 in committed oligodendrocyte neural precursor cells and describe methods to measure its expression. With the methods described here, users can design sgRNA transposon vectors targeting MCL-1 or other essential genes of interest to study human oligodendrocyte development or other differentiation protocols that use hPSC model systems. Key features • Generation of an inducible CRISPRoff Sleeping Beauty transposon system. • Experiments performed in vitro for generation of inducible CRISPRoff pluripotent stem cell line amenable to oligodendrocyte differentiation. • Strategy to downregulate an essential gene at different stages of oligodendrocyte development.
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Affiliation(s)
- Melanie Gil
- Neuroscience Graduate Program, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | | | | | - Vivian Gama
- Neuroscience Graduate Program, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
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20
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Rinaldi G, Loukas A, Sotillo J. Trematode Genomics and Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1454:507-539. [PMID: 39008274 DOI: 10.1007/978-3-031-60121-7_13] [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: 07/16/2024]
Abstract
Trematode infections stand out as one of the frequently overlooked tropical diseases, despite their wide global prevalence and remarkable capacity to parasitize diverse host species and tissues. Furthermore, these parasites hold significant socio-economic, medical, veterinary and agricultural implications. Over the past decades, substantial strides have been taken to bridge the information gap concerning various "omic" tools, such as proteomics and genomics, in this field. In this edition of the book, we highlight recent progress in genomics and proteomics concerning trematodes with a particular focus on the advances made in the past 5 years. Additionally, we present insights into cutting-edge technologies employed in studying trematode biology and shed light on the available resources for exploring the molecular facets of this particular group of parasitic helminths.
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Affiliation(s)
- Gabriel Rinaldi
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
| | - Alex Loukas
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Javier Sotillo
- Laboratorio de Referencia e Investigación en Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain.
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21
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Javadi M, Sazegar H, Doosti A. Genome editing approaches with CRISPR/Cas9: the association of NOX4 expression in breast cancer patients and effectiveness evaluation of different strategies of CRISPR/Cas9 to knockout Nox4 in cancer cells. BMC Cancer 2023; 23:1155. [PMID: 38012557 PMCID: PMC10683234 DOI: 10.1186/s12885-023-11183-9] [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: 02/13/2023] [Accepted: 07/16/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND The increasing prevalence of cancer detection necessitated practical strategies to deliver highly accurate, beneficial, and dependable processed information together with experimental results. We deleted the cancer biomarker NOX4 using three novel genetic knockout (KO) methods. Homology-directed repair (HDR), Dual allele HITI (Du-HITI) and CRISPR-excision were utilized in this study. METHODS The predictive value of the NOX4 expression profile was assessed using a combined hazard ratio (HR) with a 95% confidence interval (CI). With a 95% confidence interval, a pooled odd ratio (OR) was used to calculate the relationship between NOX4 expression patterns and cancer metastasis. There were 1060 tumor patients in all sixteen research that made up this meta-analysis. To stop the NOX4 from being transcribed, we employed three different CRISPR/Cas9-mediated knockdown methods. The expression of RNA was assessed using RT-PCR. We employed the CCK-8 assay, colony formation assays, and the invasion transwell test for our experiments measuring cell proliferation and invasion. Using a sphere-formation test, the stemness was determined. Luciferase reporter tests were carried out to verify molecular adhesion. Utilizing RT-qPCR, MTT, and a colony formation assay, the functional effects of NOX4 genetic mutation in CRISPR-excision, CRISPR-HDR, and CRISPR du-HITI knockdown cell lines of breast cancer were verified. RESULTS There were 1060 malignant tumors in the 16 studies that made up this meta-analysis. In the meta-analysis, higher NOX4 expression was linked to both a shorter overall survival rate (HR = 1.93, 95% CI 1.49-2.49, P < 0.001) and a higher percentage of lymph node metastases (OR = 3.22, 95% CI 2.18-4.29, P < 0.001). In breast carcinoma cells, it was discovered that NOX4 was overexpressed, and this increase was linked to a poor prognosis. The gain and loss-of-function assays showed enhanced NOX4 breast carcinoma cell proliferation, sphere-forming capacity, and tumor development. To activate transcription, the transcriptional factor E2F1 also attaches to the promoter region of the Nanog gene. The treatment group (NOX4 ablation) had substantially more significant levels of proapoptotic gene expression than the control group (P < 0.01). Additionally, compared to control cells, mutant cells expressed fewer antiapoptotic genes (P < 0.001). The du-HITI technique incorporated a reporter and a transcription termination marker into the two target alleles. Both donor vector preparation and cell selection were substantially simpler using this approach than with "CRISPR HDR" or "CRISPR excision." Furthermore, single-cell knockouts for both genotypes were created when this method was applied in the initial transfection experiment. CONCLUSIONS The NOX4 Knockout cell lines generated in this research may be used for additional analytical studies to reveal the entire spectrum of NOX4 activities. The du-HITI method described in this study was easy to employ and could produce homozygous individuals who were knockout for a specific protein of interest.
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Affiliation(s)
- Marzieh Javadi
- Department of Biology, Faculty of Science, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Hossein Sazegar
- Department of Biology, Faculty of Science, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Abbas Doosti
- Biotechnology Research Center, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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22
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Lee SW, Frankston CM, Kim J. Epigenome editing in cancer: Advances and challenges for potential therapeutic options. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 383:191-230. [PMID: 38359969 DOI: 10.1016/bs.ircmb.2023.10.001] [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: 02/17/2024]
Abstract
Cancers are diseases caused by genetic and non-genetic environmental factors. Epigenetic alterations, some attributed to non-genetic factors, can lead to cancer development. Epigenetic changes can occur in tumor suppressors or oncogenes, or they may contribute to global cell state changes, making cells abnormal. Recent advances in gene editing technology show potential for cancer treatment. Herein, we will discuss our current knowledge of epigenetic alterations occurring in cancer and epigenetic editing technologies that can be applied to developing therapeutic options.
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Affiliation(s)
- Seung-Won Lee
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Connor Mitchell Frankston
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Biomedical Engineering Graduate Program, Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Jungsun Kim
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, United States; Cancer Biology Research Program, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States.
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Godbole N, Quinn A, Carrion F, Pelosi E, Salomon C. Extracellular vesicles as a potential delivery platform for CRISPR-Cas based therapy in epithelial ovarian cancer. Semin Cancer Biol 2023; 96:64-81. [PMID: 37820858 DOI: 10.1016/j.semcancer.2023.10.002] [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: 05/15/2023] [Revised: 08/27/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023]
Abstract
Ovarian Cancer (OC) is the most common gynecological malignancy and the eighth most diagnosed cancer in females worldwide. Presently, it ranks as the fifth leading cause of cancer-related mortality among patients globally. Major factors contributing to the lethality of OC worldwide include delayed diagnosis, chemotherapy resistance, high metastatic rates, and the heterogeneity of subtypes. Despite continuous efforts to develop novel targeted therapies and chemotherapeutic agents, challenges persist in the form of OC resistance and recurrence. In the last decade, CRISPR-Cas-based genome editing has emerged as a powerful tool for modifying genetic and epigenetic mechanisms, holding potential for treating numerous diseases. However, a significant challenge for therapeutic applications of CRISPR-Cas technology is the absence of an optimal vehicle for delivering CRISPR molecular machinery into targeted cells or tissues. Recently, extracellular vesicles (EVs) have gained traction as potential delivery vehicles for various therapeutic agents. These heterogeneous, membrane-derived vesicles are released by nearly all cells into extracellular spaces. They carry a molecular cargo of proteins and nucleic acids within their intraluminal space, encased by a cholesterol-rich phospholipid bilayer membrane. EVs actively engage in cell-to-cell communication by delivering cargo to both neighboring and distant cells. Their inherent ability to shield molecular cargo from degradation and cross biological barriers positions them ideally for delivering CRISPR-Cas ribonucleoproteins (RNP) to target cells. Furthermore, they exhibit higher biocompatibility, lower immunogenicity, and reduced toxicity compared to classical delivery platforms such as adeno-associated virus, lentiviruses, and synthetic nanoparticles. This review explores the potential of employing different CRISPR-Cas systems to target specific genes in OC, while also discussing various methods for engineering EVs to load CRISPR components and enhance their targeting capabilities.
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Affiliation(s)
- Nihar Godbole
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, UQ Centre for Clinical Research, Royal Brisbane and Women's Hospital, Faculty of Medicine, The University of Queensland, Australia
| | - Alexander Quinn
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia; CSIRO Agriculture and Food, Queensland Bioscience Precinct, Brisbane, QLD, Australia
| | - Flavio Carrion
- Departamento de Investigación, Postgrado y Educación Continua (DIPEC), Facultad de Ciencias de la Salud, Universidad del Alba, Santiago, Chile
| | - Emanuele Pelosi
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Carlos Salomon
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, UQ Centre for Clinical Research, Royal Brisbane and Women's Hospital, Faculty of Medicine, The University of Queensland, Australia; Departamento de Investigación, Postgrado y Educación Continua (DIPEC), Facultad de Ciencias de la Salud, Universidad del Alba, Santiago, Chile.
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24
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Sundaresan Y, Yacoub S, Kodati B, Amankwa CE, Raola A, Zode G. Therapeutic applications of CRISPR/Cas9 gene editing technology for the treatment of ocular diseases. FEBS J 2023; 290:5248-5269. [PMID: 36877952 PMCID: PMC10480348 DOI: 10.1111/febs.16771] [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: 05/24/2022] [Revised: 02/04/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023]
Abstract
Ocular diseases are a highly heterogeneous group of phenotypes, caused by a spectrum of genetic variants and environmental factors that exhibit diverse clinical symptoms. As a result of its anatomical location, structure and immune privilege, the eye is an ideal system to assess and validate novel genetic therapies. Advances in genome editing have revolutionized the field of biomedical science, enabling researchers to understand the biology behind disease mechanisms and allow the treatment of several health conditions, including ocular pathologies. The advent of clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing facilitates efficient and specific genetic modifications in the nucleic acid sequence, resulting in permanent changes at the genomic level. This approach has advantages over other treatment strategies and is promising for the treatment of various genetic and non-genetic ocular conditions. This review provides an overview of the CRISPR/CRISPR-associated protein 9 (Cas9) system and summarizes recent advances in the therapeutic application of CRISPR/Cas9 for the treatment of various ocular pathologies, as well as future challenges.
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Affiliation(s)
| | | | - Bindu Kodati
- Department of Pharmacology and Neuroscience, North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX 76107
| | - Charles E. Amankwa
- Department of Pharmacology and Neuroscience, North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX 76107
| | - Akash Raola
- Department of Pharmacology and Neuroscience, North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX 76107
| | - Gulab Zode
- Department of Pharmacology and Neuroscience, North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX 76107
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Li L, Vasan L, Kartono B, Clifford K, Attarpour A, Sharma R, Mandrozos M, Kim A, Zhao W, Belotserkovsky A, Verkuyl C, Schmitt-Ulms G. Advances in Recombinant Adeno-Associated Virus Vectors for Neurodegenerative Diseases. Biomedicines 2023; 11:2725. [PMID: 37893099 PMCID: PMC10603849 DOI: 10.3390/biomedicines11102725] [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: 09/08/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Recombinant adeno-associated virus (rAAV) vectors are gene therapy delivery tools that offer a promising platform for the treatment of neurodegenerative diseases. Keeping up with developments in this fast-moving area of research is a challenge. This review was thus written with the intention to introduce this field of study to those who are new to it and direct others who are struggling to stay abreast of the literature towards notable recent studies. In ten sections, we briefly highlight early milestones within this field and its first clinical success stories. We showcase current clinical trials, which focus on gene replacement, gene augmentation, or gene suppression strategies. Next, we discuss ongoing efforts to improve the tropism of rAAV vectors for brain applications and introduce pre-clinical research directed toward harnessing rAAV vectors for gene editing applications. Subsequently, we present common genetic elements coded by the single-stranded DNA of rAAV vectors, their so-called payloads. Our focus is on recent advances that are bound to increase treatment efficacies. As needed, we included studies outside the neurodegenerative disease field that showcased improved pre-clinical designs of all-in-one rAAV vectors for gene editing applications. Finally, we discuss risks associated with off-target effects and inadvertent immunogenicity that these technologies harbor as well as the mitigation strategies available to date to make their application safer.
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Affiliation(s)
- Leyao Li
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
| | - Lakshmy Vasan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Bryan Kartono
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Kevan Clifford
- Institute of Medical Science, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Centre for Addiction and Mental Health (CAMH), 250 College St., Toronto, ON M5T 1R8, Canada
| | - Ahmadreza Attarpour
- Department of Medical Biophysics, University of Toronto, 101 College St., Toronto, ON M5G 1L7, Canada
| | - Raghav Sharma
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Matthew Mandrozos
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Ain Kim
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Wenda Zhao
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Ari Belotserkovsky
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Claire Verkuyl
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
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Kasi Viswanath K, Hamid A, Ateka E, Pappu HR. CRISPR/Cas, Multiomics, and RNA Interference in Virus Disease Management. PHYTOPATHOLOGY 2023; 113:1661-1676. [PMID: 37486077 DOI: 10.1094/phyto-01-23-0002-v] [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: 07/25/2023]
Abstract
Plant viruses infect a wide range of commercially important crop plants and cause significant crop production losses worldwide. Numerous alterations in plant physiology related to the reprogramming of gene expression may result from viral infections. Although conventional integrated pest management-based strategies have been effective in reducing the impact of several viral diseases, continued emergence of new viruses and strains, expanding host ranges, and emergence of resistance-breaking strains necessitate a sustained effort toward the development and application of new approaches for virus management that would complement existing tactics. RNA interference-based techniques, and more recently, clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing technologies have paved the way for precise targeting of viral transcripts and manipulation of viral genomes and host factors. In-depth knowledge of the molecular mechanisms underlying the development of disease would further expand the applicability of these recent methods. Advances in next-generation/high-throughput sequencing have made possible more intensive studies into host-virus interactions. Utilizing the omics data and its application has the potential to expedite fast-tracking traditional plant breeding methods, as well as applying modern molecular tools for trait enhancement, including virus resistance. Here, we summarize the recent developments in the CRISPR/Cas system, transcriptomics, endogenous RNA interference, and exogenous application of dsRNA in virus disease management.
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Affiliation(s)
| | - Aflaq Hamid
- Department of Plant Pathology, Washington State University, Pullman, WA, U.S.A
| | - Elijah Ateka
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, U.S.A
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Yuan R, Zhang W, You Y, Cui G, Gao Z, Wang X, Chen J. Vitamin D3 suppresses the cholesterol homeostasis pathway in patient-derived glioma cell lines. FEBS Open Bio 2023; 13:1789-1806. [PMID: 37489660 PMCID: PMC10476568 DOI: 10.1002/2211-5463.13679] [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: 02/03/2023] [Revised: 05/19/2023] [Accepted: 07/24/2023] [Indexed: 07/26/2023] Open
Abstract
Glioblastoma is one of the most common malignant brain tumors. Vitamin D, primarily its hormonally active form calcitriol, has been reported to have anti-cancer activity. In the present study, we used patient-derived glioma cell lines to examine the effect of vitamin D3 and calcitriol on glioblastoma. Surprisingly, vitamin D3 showed a more significant inhibitory effect than calcitriol on cell viability and proliferation. Vitamin D receptor (VDR) mediates most of the cellular effects of vitamin D, and thus we examined the expression level and function of VDR via gene silencing and gene knockout experiments. We observed that VDR does not affect the sensitivity of patient-derived glioma cell lines to vitamin D3, and the gene encoding VDR is not essential for growth of patient-derived glioma cell lines. RNA sequencing data analysis and sterolomics analysis revealed that vitamin D3 inhibits cholesterol synthesis and cholesterol homeostasis by inhibiting the expression level of 7-dehydrocholesterol reductase, which leads to the accumulation of 7-dehydrocholesterol and other sterol intermediates. In conclusion, our results suggest that vitamin D3, rather than calcitriol, inhibits growth of patient-derived glioma cell lines via inhibition of the cholesterol homeostasis pathway.
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Affiliation(s)
- Ran Yuan
- Institute of Functional Nano & Soft Materials (FUNSOM)Soochow UniversitySuzhouChina
- Chinese Institute for Brain ResearchBeijingChina
- Research Unit of Medical NeurobiologyChinese Academy of Medical SciencesBeijingChina
| | - Wei Zhang
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
| | - Yong‐Ping You
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityChina
| | - Gang Cui
- Department of Neurosurgery & Brain and Nerve Research LaboratoryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Zhengliang Gao
- Fundamental Research Center, Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of MedicineTongji UniversityShanghaiChina
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of MedicineShanghai UniversityNantongChina
| | - Xiuxing Wang
- National Health Commission Key Laboratory of Antibody Techniques, Department of Cell Biology, Jiangsu Provincial Key Laboratory of Human Functional Genomics, School of Basic Medical SciencesNanjing Medical UniversityChina
| | - Jian Chen
- Institute of Functional Nano & Soft Materials (FUNSOM)Soochow UniversitySuzhouChina
- Chinese Institute for Brain ResearchBeijingChina
- Research Unit of Medical NeurobiologyChinese Academy of Medical SciencesBeijingChina
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Cheng M, Tan C, Xiang B, Lin W, Cheng B, Peng X, Yang Y, Lin Y. Chain hybridization-based CRISPR-lateral flow assay enables accurate gene visual detection. Anal Chim Acta 2023; 1270:341437. [PMID: 37311609 DOI: 10.1016/j.aca.2023.341437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/22/2023] [Accepted: 05/26/2023] [Indexed: 06/15/2023]
Abstract
Visualized gene detection based on the CRISPR-Cas12/CRISPR-Cas13 technology and lateral flow assay device (CRISPR-LFA) has shown great potential in point-of-care testing sector. Current CRISPR-LFA methodology mainly utilizes conventional immuno-based LFA test strips, which could visualize whether the reporter probe is trans-cleaved by Cas protein, indicating the target positive detection. However, conventional CRISPR-LFA usually produces false-positive results in target negative assay. Herein, a nucleic acid Chain Hybridization-based Lateral Flow Assay platform, named CHLFA, has been developed to achieve the CRISPR-CHLFA concept. Different from the conventional CRISPR-LFA, the proposed CRISPR-CHLFA system was established based on the nucleic acid hybridization between the GNP-probe embedded in test strips and ssDNA (or ssRNA) reporter from CRISPR (LbaCas12a or LbuCas13a) reaction, which eliminated the requirement of immunoreaction in conventional immuno-based LFA. The assay realized the detection of 1-10 copy of target gene per reaction within 50 min. The CRISPR-CHLFA system achieved highly accurate visual detection of target negative samples, thus overcoming the false-positive problem that often produced in assays using conventional CRISPR-LFA. The CRISPR-CHLFA platform was further adopted for the visual detection of marker gene from SASR-CoV-2 Omicron variant and Mycobacterium tuberculosis (MTB), respectively, and 100% accuracy for the analysis of clinical specimens (45 SASR-CoV-2 specimens and 20 MTB specimens) was obtained. The proposed CRISPR-CHLFA system could provide an alternative platform for the development of POCT biosensors and can be widely adopted in accurate and visualized gene detection.
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Affiliation(s)
- Meng Cheng
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Caiwei Tan
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bo Xiang
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Weihong Lin
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bolin Cheng
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xuechun Peng
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yihao Yang
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yongping Lin
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China.
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Bouguenina H, Nicolaou S, Le Bihan YV, Bowling EA, Calderon C, Caldwell JJ, Harrington B, Hayes A, McAndrew PC, Mitsopoulos C, Sialana FJ, Scarpino A, Stubbs M, Thapaliya A, Tyagi S, Wang HZ, Wood F, Burke R, Raynaud F, Choudhary J, van Montfort RL, Sadok A, Westbrook TF, Collins I, Chopra R. iTAG an optimized IMiD-induced degron for targeted protein degradation in human and murine cells. iScience 2023; 26:107059. [PMID: 37360684 PMCID: PMC10285648 DOI: 10.1016/j.isci.2023.107059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/18/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
To address the limitation associated with degron based systems, we have developed iTAG, a synthetic tag based on IMiDs/CELMoDs mechanism of action that improves and addresses the limitations of both PROTAC and previous IMiDs/CeLMoDs based tags. Using structural and sequence analysis, we systematically explored native and chimeric degron containing domains (DCDs) and evaluated their ability to induce degradation. We identified the optimal chimeric iTAG(DCD23 60aa) that elicits robust degradation of targets across cell types and subcellular localizations without exhibiting the well documented "hook effect" of PROTAC-based systems. We showed that iTAG can also induce target degradation by murine CRBN and enabled the exploration of natural neo-substrates that can be degraded by murine CRBN. Hence, the iTAG system constitutes a versatile tool to degrade targets across the human and murine proteome.
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Affiliation(s)
- Habib Bouguenina
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Stephanos Nicolaou
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Yann-Vaï Le Bihan
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Elizabeth A. Bowling
- Therapeutic Innovation Centre (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cheyenne Calderon
- Therapeutic Innovation Centre (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - John J. Caldwell
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Brinley Harrington
- Therapeutic Innovation Centre (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Angela Hayes
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - P. Craig McAndrew
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Costas Mitsopoulos
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Fernando Jr. Sialana
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
- Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, UK
| | - Andrea Scarpino
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Mark Stubbs
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Arjun Thapaliya
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Siddhartha Tyagi
- Therapeutic Innovation Centre (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hannah Z. Wang
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Francesca Wood
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Rosemary Burke
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Florence Raynaud
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Jyoti Choudhary
- Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, UK
| | - Rob L.M. van Montfort
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Amine Sadok
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Thomas F. Westbrook
- Therapeutic Innovation Centre (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ian Collins
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Rajesh Chopra
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
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Idris SH, Mat Jalaluddin NS, Chang LW, 曾 立纬. Ethical and legal implications of gene editing in plant breeding: a systematic literature review. J Zhejiang Univ Sci B 2023; 24:1093-1105. [PMID: 38057267 PMCID: PMC10710910 DOI: 10.1631/jzus.b2200601] [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: 11/28/2022] [Accepted: 03/30/2023] [Indexed: 07/11/2023]
Abstract
Biotechnology policies and regulations must be revised and updated to reflect the most recent advances in plant-breeding technology. New Plant Breeding Techniques (NPBT) such as gene editing have been applied to address the myriad of challenges in plant breeding, while the use of NPBT as emerging biotechnological tools raises legal and ethical concerns. This study aims to highlight how gene editing is operationalized in the existing literature and examine the critical issues of ethical and legal issues of gene editing for plant breeding. We carried out a systematic literature review (SLR) to provide the current states of ethical and legal discourses surrounding this topic. We also identified critical research priority areas and policy gaps that must be addressed when designing the future governance of gene editing in plant breeding.
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Affiliation(s)
- Siti Hafsyah Idris
- Faculty of Law, Universiti Teknologi MARA, Jalan Sarjana 1/2, Shah Alam 40450, Selangor, Malaysia
| | - Nurzatil Sharleeza Mat Jalaluddin
- Centre for Research in Biotechnology for Agriculture (CEBAR), Level 3, Research Management and Innovation Complex, Universiti Malaya, Kuala Lumpur 50603, Malaysia.
| | - Lee Wei Chang
- Faculty of Law, Universiti Teknologi MARA, Jalan Sarjana 1/2, Shah Alam 40450, Selangor, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), Level 3, Research Management and Innovation Complex, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Centre for Civilisational Dialogue, Level 1, High Impact Research Building, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - 立 纬 曾
- Centre for Civilisational Dialogue, Level 1, High Impact Research Building, Universiti Malaya, Kuala Lumpur 50603, Malaysia
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31
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Ivanov KI, Samuilova OV, Zamyatnin AA. The emerging roles of long noncoding RNAs in lymphatic vascular development and disease. Cell Mol Life Sci 2023; 80:197. [PMID: 37407839 PMCID: PMC10322780 DOI: 10.1007/s00018-023-04842-4] [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: 11/08/2022] [Revised: 06/06/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
Recent advances in RNA sequencing technologies helped uncover what was once uncharted territory in the human genome-the complex and versatile world of long noncoding RNAs (lncRNAs). Previously thought of as merely transcriptional "noise", lncRNAs have now emerged as essential regulators of gene expression networks controlling development, homeostasis and disease progression. The regulatory functions of lncRNAs are broad and diverse, and the underlying molecular mechanisms are highly variable, acting at the transcriptional, post-transcriptional, translational, and post-translational levels. In recent years, evidence has accumulated to support the important role of lncRNAs in the development and functioning of the lymphatic vasculature and associated pathological processes such as tumor-induced lymphangiogenesis and cancer metastasis. In this review, we summarize the current knowledge on the role of lncRNAs in regulating the key genes and pathways involved in lymphatic vascular development and disease. Furthermore, we discuss the potential of lncRNAs as novel therapeutic targets and outline possible strategies for the development of lncRNA-based therapeutics to treat diseases of the lymphatic system.
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Affiliation(s)
- Konstantin I Ivanov
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, Russian Federation.
- Department of Microbiology, University of Helsinki, Helsinki, Finland.
| | - Olga V Samuilova
- Department of Biochemistry, Sechenov First Moscow State Medical University, Moscow, Russian Federation
- HSE University, Moscow, Russian Federation
| | - Andrey A Zamyatnin
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, Russian Federation
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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32
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Bendixen L, Jensen TI, Bak RO. CRISPR-Cas-mediated transcriptional modulation: The therapeutic promises of CRISPRa and CRISPRi. Mol Ther 2023; 31:1920-1937. [PMID: 36964659 PMCID: PMC10362391 DOI: 10.1016/j.ymthe.2023.03.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/09/2023] [Accepted: 03/21/2023] [Indexed: 03/26/2023] Open
Abstract
The CRISPR-Cas system is commonly known for its ability to cleave DNA in a programmable manner, which has democratized gene editing and facilitated recent breakthroughs in gene therapy. However, newer iterations of the technology using nuclease-disabled Cas enzymes have spurred a variety of different types of genetic engineering platforms such as transcriptional modulation using the CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) systems. This review introduces the creation of these programmable transcriptional modulators, various methods of delivery utilized for these systems, and recent technological developments. CRISPRa and CRISPRi have also been implemented in genetic screens for interrogating gene function and discovering genes involved in various biological pathways. We describe recent compelling examples of how these tools have become powerful means to unravel genetic networks and uncovering important information about devastating diseases. Finally, we provide an overview of preclinical studies in which transcriptional modulation has been used therapeutically, and we discuss potential future directions of these novel modalities.
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Affiliation(s)
- Louise Bendixen
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Trine I Jensen
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark.
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Junaid M, Thirapanmethee K, Khuntayaporn P, Chomnawang MT. CRISPR-Based Gene Editing in Acinetobacter baumannii to Combat Antimicrobial Resistance. Pharmaceuticals (Basel) 2023; 16:920. [PMID: 37513832 PMCID: PMC10384873 DOI: 10.3390/ph16070920] [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: 05/25/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance (AMR) poses a significant threat to the health, social, environment, and economic sectors on a global scale and requires serious attention to addressing this issue. Acinetobacter baumannii was given top priority among infectious bacteria because of its extensive resistance to nearly all antibiotic classes and treatment options. Carbapenem-resistant A. baumannii is classified as one of the critical-priority pathogens on the World Health Organization (WHO) priority list of antibiotic-resistant bacteria for effective drug development. Although available genetic manipulation approaches are successful in A. baumannii laboratory strains, they are limited when employed on newly acquired clinical strains since such strains have higher levels of AMR than those used to select them for genetic manipulation. Recently, the CRISPR-Cas (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) system has emerged as one of the most effective, efficient, and precise methods of genome editing and offers target-specific gene editing of AMR genes in a specific bacterial strain. CRISPR-based genome editing has been successfully applied in various bacterial strains to combat AMR; however, this strategy has not yet been extensively explored in A. baumannii. This review provides detailed insight into the progress, current scenario, and future potential of CRISPR-Cas usage for AMR-related gene manipulation in A. baumannii.
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Affiliation(s)
- Muhammad Junaid
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Krit Thirapanmethee
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Piyatip Khuntayaporn
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Mullika Traidej Chomnawang
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
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Berardinelli SJ, Sillato AR, Grady RC, Neupane S, Ito A, Haltiwanger RS, Holdener BC. O-fucosylation of thrombospondin type I repeats is dispensable for trafficking thrombospondin 1 to platelet secretory granules. Glycobiology 2023; 33:301-310. [PMID: 36721988 PMCID: PMC10191222 DOI: 10.1093/glycob/cwad006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/02/2023] Open
Abstract
Thrombospondin 1 (THBS1) is a secreted extracellular matrix glycoprotein that regulates a variety of cellular and physiological processes. THBS1's diverse functions are attributed to interactions between the modular domains of THBS1 with an array of proteins found in the extracellular matrix. THBS1's three Thrombospondin type 1 repeats (TSRs) are modified with O-linked glucose-fucose disaccharide and C-mannose. It is unknown whether these modifications impact trafficking and/or function of THBS1 in vivo. The O-fucose is added by Protein O-fucosyltransferase 2 (POFUT2) and is sequentially extended to the disaccharide by β3glucosyltransferase (B3GLCT). The C-mannose is added by one or more of four C-mannosyltransferases. O-fucosylation by POFUT2/B3GLCT in the endoplasmic reticulum has been proposed to play a role in quality control by locking TSR domains into their three-dimensional fold, allowing for proper secretion of many O-fucosylated substrates. Prior studies showed the siRNA knockdown of POFUT2 in HEK293T cells blocked secretion of TSRs 1-3 from THBS1. Here we demonstrated that secretion of THBS1 TSRs 1-3 was not reduced by CRISPR-Cas9-mediated knockout of POFUT2 in HEK293T cells and demonstrated that knockout of Pofut2 or B3glct in mice did not reduce the trafficking of endogenous THBS1 to secretory granules of platelets, a major source of THBS1. Additionally, we demonstrated that all three TSRs from platelet THBS1 were highly C-mannosylated, which has been shown to stabilize TSRs in vitro. Combined, these results suggested that POFUT2 substrates with TSRs that are also modified by C-mannose may be less susceptible to trafficking defects resulting from the loss of the glucose-fucose disaccharide.
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Affiliation(s)
- Steven J Berardinelli
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Andrew R Sillato
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Richard C Grady
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Sanjiv Neupane
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Atsuko Ito
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Robert S Haltiwanger
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Bernadette C Holdener
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
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Glinšek K, Bozovičar K, Bratkovič T. CRISPR Technologies in Chinese Hamster Ovary Cell Line Engineering. Int J Mol Sci 2023; 24:ijms24098144. [PMID: 37175850 PMCID: PMC10179654 DOI: 10.3390/ijms24098144] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
The Chinese hamster ovary (CHO) cell line is a well-established platform for the production of biopharmaceuticals due to its ability to express complex therapeutic proteins with human-like glycopatterns in high amounts. The advent of CRISPR technology has opened up new avenues for the engineering of CHO cell lines for improved protein production and enhanced product quality. This review summarizes recent advances in the application of CRISPR technology for CHO cell line engineering with a particular focus on glycosylation modulation, productivity enhancement, tackling adventitious agents, elimination of problematic host cell proteins, development of antibiotic-free selection systems, site-specific transgene integration, and CRISPR-mediated gene activation and repression. The review highlights the potential of CRISPR technology in CHO cell line genome editing and epigenetic engineering for the more efficient and cost-effective development of biopharmaceuticals while ensuring the safety and quality of the final product.
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Affiliation(s)
- Katja Glinšek
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Krištof Bozovičar
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tomaž Bratkovič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
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Lu J, Wang S. CRISPR/Cas9-Mediated Gene Knockout in Cells and Tissues Using Lentivirus. Curr Protoc 2023; 3:e772. [PMID: 37222511 PMCID: PMC10234494 DOI: 10.1002/cpz1.772] [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] [Indexed: 05/25/2023]
Abstract
CRISPR-Cas9 has become a powerful and popular gene editing tool. However, successful application of this tool in the lab can still be quite daunting to many newcomers to molecular biology, mostly because it is a relatively lengthy process involving multiple steps with variations of each step. Here, we provide a reliable, stepwise, and newcomer-friendly protocol to knock out a target gene in wild-type human fibroblasts. This protocol involves sgRNA design using CRISPOR, construction of an "all-in-one" vector expressing both sgRNA and Cas9 using Golden Gate cloning, streamlined production of high-titer lentiviruses in 1 week after molecular cloning, and transduction of cells to generate a knockout cell pool. We further introduce a protocol for lentiviral transduction of ex vivo mouse embryonic salivary epithelial explants. In summary, our protocol is useful for new researchers to apply CRISPR-Cas9 to generate stable gene knockout cells and tissue explants using lentivirus. Published 2023. This article is a U.S. Government work and is in the public domain in the USA. Basic Protocol 1: sgRNA design Basic Protocol 2: Cloning sgRNA in plasmid vector containing Cas9 encoding sequence using golden gate cloning Basic Protocol 3: Lentivirus packaging Basic Protocol 4: Lentivirus transduction of cells Basic Protocol 5: Lentivirus transduction of salivary gland epithelial buds.
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Affiliation(s)
- Jiaoyang Lu
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Shaohe Wang
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
- Current address: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
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Jost P, Klein F, Brand B, Wahl V, Wyatt A, Yildiz D, Boehm U, Niemeyer BA, Vaeth M, Alansary D. Acute Downregulation but Not Genetic Ablation of Murine MCU Impairs Suppressive Capacity of Regulatory CD4 T Cells. Int J Mol Sci 2023; 24:ijms24097772. [PMID: 37175478 PMCID: PMC10178810 DOI: 10.3390/ijms24097772] [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: 03/17/2023] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
By virtue of mitochondrial control of energy production, reactive oxygen species (ROS) generation, and maintenance of Ca2+ homeostasis, mitochondria play an essential role in modulating T cell function. The mitochondrial Ca2+ uniporter (MCU) is the pore-forming unit in the main protein complex mediating mitochondrial Ca2+ uptake. Recently, MCU has been shown to modulate Ca2+ signals at subcellular organellar interfaces, thus fine-tuning NFAT translocation and T cell activation. The mechanisms underlying this modulation and whether MCU has additional T cell subpopulation-specific effects remain elusive. However, mice with germline or tissue-specific ablation of Mcu did not show impaired T cell responses in vitro or in vivo, indicating that 'chronic' loss of MCU can be functionally compensated in lymphocytes. The current work aimed to specifically investigate whether and how MCU influences the suppressive potential of regulatory CD4 T cells (Treg). We show that, in contrast to genetic ablation, acute siRNA-mediated downregulation of Mcu in murine Tregs results in a significant reduction both in mitochondrial Ca2+ uptake and in the suppressive capacity of Tregs, while the ratios of Treg subpopulations and the expression of hallmark transcription factors were not affected. These findings suggest that permanent genetic inactivation of MCU may result in compensatory adaptive mechanisms, masking the effects on the suppressive capacity of Tregs.
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Affiliation(s)
- Priska Jost
- Molecular Biophysics, Saarland University, 66421 Homburg, Germany
| | - Franziska Klein
- Molecular Biophysics, Saarland University, 66421 Homburg, Germany
| | - Benjamin Brand
- Würzburg Institute of Systems Immunology, Max Planck Research Group at Julius-Maximilians University of Würzburg, 97078 Würzburg, Germany
| | - Vanessa Wahl
- Experimental Pharmacology, Center for Molecular Signaling (PZMS), School of Medicine, Saarland University, 66421 Homburg, Germany
| | - Amanda Wyatt
- Experimental Pharmacology, Center for Molecular Signaling (PZMS), School of Medicine, Saarland University, 66421 Homburg, Germany
| | - Daniela Yildiz
- Experimental Pharmacology, Center for Molecular Signaling (PZMS), School of Medicine, Saarland University, 66421 Homburg, Germany
| | - Ulrich Boehm
- Experimental Pharmacology, Center for Molecular Signaling (PZMS), School of Medicine, Saarland University, 66421 Homburg, Germany
| | | | - Martin Vaeth
- Würzburg Institute of Systems Immunology, Max Planck Research Group at Julius-Maximilians University of Würzburg, 97078 Würzburg, Germany
| | - Dalia Alansary
- Molecular Biophysics, Saarland University, 66421 Homburg, Germany
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Zhang F, Guangchuan W, Chow R, He E, Majety M, Zhang Y, Chen S. Multiplexed inhibition of immunosuppressive genes with Cas13d for on-demand combinatorial cancer immunotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532668. [PMID: 36993222 PMCID: PMC10055084 DOI: 10.1101/2023.03.14.532668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Checkpoint blockade immunotherapy is a potent class of cancer treatment, however, the complex immunosuppressive tumor microenvironment (TME) often requires multi-agent combinations to be effective. Current cancer immunotherapy combination approaches are cumbersome, usually involving one-drug-at-a-time scheme. Here, we devise Multiplex Universal Combinatorial Immunotherapy via Gene-silencing (MUCIG), as a versatile approach for combinatorial cancer immunotherapy. We harness CRISPR-Cas13d to efficiently target multiple endogenous immunosuppressive genes on demand, allowing us to silence various combinations of multiple immunosuppressive factors in the TME. Intratumoral AAV-mediated administration of MUCIG (AAV-MUCIG) elicits significant anti-tumor activity with several Cas13d gRNA compositions. TME target expression analysis driven optimization led to a simplified off-the-shelf MUCIG targeting a four gene combination (PGGC: Pdl1, Galectin9, Galectin3 and Cd47 ). AAV-PGGC shows significant in vivo efficacy in syngeneic tumor models. Single cell and flow profiling revealed that AAV-PGGC remodeled the TME by increasing CD8 + T cell infiltration and reducing myeloid-derived immunosuppressive cells (MDSCs). MUCIG thus serves as a universal method to silence multiple immune genes in vivo, and can be delivered via AAV as a therapeutic approach.
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Thoidingjam S, Sriramulu S, Freytag S, Brown SL, Kim JH, Chetty IJ, Siddiqui F, Movsas B, Nyati S. Oncolytic virus-based suicide gene therapy for cancer treatment: a perspective of the clinical trials conducted at Henry Ford Health. TRANSLATIONAL MEDICINE COMMUNICATIONS 2023; 8:11. [PMID: 37065938 PMCID: PMC10088621 DOI: 10.1186/s41231-023-00144-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Gene therapy manipulates or modifies a gene that provides a new cellular function to treat or correct a pathological condition, such as cancer. The approach of using gene manipulation to modify patient's cells to improve cancer therapy and potentially find a cure is gaining popularity. Currently, there are 12 gene therapy products approved by US-FDA, EMA and CFDA for cancer management, these include Rexin-G, Gendicine, Oncorine, Provange among other. The Radiation Biology Research group at Henry Ford Health has been actively developing gene therapy approaches for improving clinical outcome in cancer patients. The team was the first to test a replication-competent oncolytic virus armed with a therapeutic gene in humans, to combine this approach with radiation in humans, and to image replication-competent adenoviral gene expression/activity in humans. The adenoviral gene therapy products developed at Henry Ford Health have been evaluated in more than 6 preclinical studies and evaluated in 9 investigator initiated clinical trials treating more than100 patients. Two phase I clinical trials are currently following patients long term and a phase I trial for recurrent glioma was initiated in November 2022. This systematic review provides an overview of gene therapy approaches and products employed for treating cancer patients including the products developed at Henry Ford Health.
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Affiliation(s)
- Shivani Thoidingjam
- Department of Radiation Oncology, Henry Ford Health, 1 Ford Place, 5D-42, Detroit, MI 48202 USA
| | - Sushmitha Sriramulu
- Department of Radiation Oncology, Henry Ford Health, 1 Ford Place, 5D-42, Detroit, MI 48202 USA
| | - Svend Freytag
- Department of Radiation Oncology, Henry Ford Health, 1 Ford Place, 5D-42, Detroit, MI 48202 USA
| | - Stephen L. Brown
- Department of Radiation Oncology, Henry Ford Health, 1 Ford Place, 5D-42, Detroit, MI 48202 USA
- College of Human Medicine, Michigan State University, East Lansing, MI 48824 USA
| | - Jae Ho Kim
- Department of Radiation Oncology, Henry Ford Health, 1 Ford Place, 5D-42, Detroit, MI 48202 USA
| | - Indrin J. Chetty
- Department of Radiation Oncology, Henry Ford Health, 1 Ford Place, 5D-42, Detroit, MI 48202 USA
| | - Farzan Siddiqui
- Department of Radiation Oncology, Henry Ford Health, 1 Ford Place, 5D-42, Detroit, MI 48202 USA
| | - Benjamin Movsas
- Department of Radiation Oncology, Henry Ford Health, 1 Ford Place, 5D-42, Detroit, MI 48202 USA
- College of Human Medicine, Michigan State University, East Lansing, MI 48824 USA
| | - Shyam Nyati
- Department of Radiation Oncology, Henry Ford Health, 1 Ford Place, 5D-42, Detroit, MI 48202 USA
- College of Human Medicine, Michigan State University, East Lansing, MI 48824 USA
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Wang L, Liu C, Wang X, Ma S, Liu F, Zhang Y, Wang Y, Shen M, Wu X, Wu Q, Gong C. Tumor-specific activated nano-domino-CRISPR to amplify intrinsic oxidative and activate endogenous apoptosis for spatiotemporally specific therapy. Biomaterials 2023; 295:122056. [PMID: 36805243 DOI: 10.1016/j.biomaterials.2023.122056] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 01/29/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023]
Abstract
As a non-invasive modality with unique spatiotemporal selectivity, photodynamic therapy (PDT) is emerging as a candidate in cancer treatment. Nevertheless, intrinsic anti-oxidative stress factors represented by the up-regulated B cell lymphoma/leukemia-2 (Bcl-2) and the attenuated-PDT activity along the light path are still the major concerns, therefore exploring the PDT-based synergistic and augmented strategies is challenging but imperative. Here, a tumor-specific activated nano-domino-CRISPR (TAN) is fabricated and coloaded with chlorins e6 (Ce6) and CRISPR/Cas9 plasmid targeting Bcl-2 gene to amplify intrinsic oxidative and activate endogenous apoptosis for spatiotemporally specific therapy. Inert TAN acting as the first domino is activated in enzyme-abundant intracellular environment to strip the shell. The activated TAN pushes the subsequent dominos, encompassing orderly efficient lysosomal escape, gene delivery, precise disruption of Bcl-2 protein and PDT effect induced by the shell containing Ce6 with light to trigger further domino effects. For tumor cells located superficial sites, down-regulated Bcl-2 reduces cellular GSH content and potentiates oxidative stress of PDT. Cells located deep sites are triggered endogenous apoptosis by disruption of Bcl-2. The high anti-tumor efficacy of TAN is demonstrated both in vitro and in vivo. Overall, our work offers a valuable emerging approach for conquering the therapeutical deficiency of PDT.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Chao Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Xinxin Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Shuang Ma
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Furong Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Yi Zhang
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, 110004, PR China
| | - Yan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Meiling Shen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Xinyue Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Qinjie Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, PR China.
| | - Changyang Gong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, PR China.
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Jogdeo CM, Panja S, Kanvinde S, Kapoor E, Siddhanta K, Oupický D. Advances in Lipid-Based Codelivery Systems for Cancer and Inflammatory Diseases. Adv Healthc Mater 2023; 12:e2202400. [PMID: 36453542 PMCID: PMC10023350 DOI: 10.1002/adhm.202202400] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/13/2022] [Indexed: 12/03/2022]
Abstract
Combination therapy targeting multiple therapeutic targets is a favorable strategy to achieve better therapeutic outcomes in cancer and inflammatory diseases. Codelivery is a subfield of drug delivery that aims to achieve combined delivery of diverse therapeutic cargoes within the same delivery system, thereby ensuring delivery to the same site and providing an opportunity to tailor the release kinetics as desired. Among the wide range of materials being investigated in the design of codelivery systems, lipids have stood out on account of their low toxicity, biocompatibility, and ease of formulation scale-up. This review highlights the advances of the last decade in lipid-based codelivery systems focusing on the codelivery of drug-drug, drug-nucleic acid, nucleic acid-nucleic acid, and protein therapeutic-based combinations for targeted therapy in cancer and inflammatory diseases.
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Affiliation(s)
- Chinmay M. Jogdeo
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Sudipta Panja
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Shrey Kanvinde
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ekta Kapoor
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kasturi Siddhanta
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - David Oupický
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Genome editing in cancer: Challenges and potential opportunities. Bioact Mater 2023; 21:394-402. [PMID: 36185740 PMCID: PMC9483578 DOI: 10.1016/j.bioactmat.2022.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/21/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Ever since its mechanism was discovered back in 2012, the CRISPR/Cas9 system have revolutionized the field of genome editing. While at first it was seen as a therapeutic tool mostly relevant for curing genetic diseases, it has been recently shown to also hold the potential to become a clinically relevant therapy for cancer. However, there are multiple challenges that must be addressed prior to clinical testing. Predominantly, the safety of the system when used for in-vivo therapies, including off-target activity and the effects of the double strand break induction on genomic stability. Here, we will focus on the inherent challenges in the CRISPR/Cas9 system and discuss various opportunities to overcoming these challenges. In recent years, several works have shown that knocking down key genes by CRISPR/Cas9 based could potentially be a new type of cancer therapy. This has been made possible due to advances in the fields of In-vivo delivery, such as lentiviral vectors and lipid nanoparticles. Limiting CRISPR/Cas9 activity to the tumor and minimizing off-target activity are challenges that must be overcome before proceeding to the clinic. We review approaches arising from multiple disciplines that could overcome these challenges. The combination of these multi-disciplinary approaches should be able to overcome the different challenges and open the way to the clinic.
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Chitturi Suryaprakash RT, Shearston K, Farah CS, Fox SA, Iqbal MM, Kadolsky U, Zhong X, Saxena A, Kujan O. A Novel Preclinical In Vitro 3D Model of Oral Carcinogenesis for Biomarker Discovery and Drug Testing. Int J Mol Sci 2023; 24:ijms24044096. [PMID: 36835505 PMCID: PMC9967961 DOI: 10.3390/ijms24044096] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
This study aimed to develop an in vitro three-dimensional (3D) cell culture model of oral carcinogenesis for the rapid, scalable testing of chemotherapeutic agents. Spheroids of normal (HOK) and dysplastic (DOK) human oral keratinocytes were cultured and treated with 4-nitroquinoline-1-oxide (4NQO). A 3D invasion assay using Matrigel was performed to validate the model. RNA was extracted and subjected to transcriptomic analysis to validate the model and assess carcinogen-induced changes. The VEGF inhibitors pazopanib and lenvatinib were tested in the model and were validated by a 3D invasion assay, which demonstrated that changes induced by the carcinogen in spheroids were consistent with a malignant phenotype. Further validation was obtained by bioinformatic analyses, which showed the enrichment of pathways associated with hallmarks of cancer and VEGF signalling. Overexpression of common genes associated with tobacco-induced oral squamous cell carcinoma (OSCC), such as MMP1, MMP3, MMP9, YAP1, CYP1A1, and CYP1B1, was also observed. Pazopanib and lenvatinib inhibited the invasion of transformed spheroids. In summary, we successfully established a 3D spheroid model of oral carcinogenesis for biomarker discovery and drug testing. This model is a validated preclinical model for OSCC development and would be suitable for testing a range of chemotherapeutic agents.
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Affiliation(s)
| | - Kate Shearston
- UWA Dental School, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Camile S. Farah
- Australian Centre for Oral Oncology Research and Education, Nedlands, WA 6009, Australia
| | - Simon A. Fox
- UWA Dental School, The University of Western Australia, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Muhammad Munir Iqbal
- Genomics WA, Harry Perkins Institute of Medical Research, Telethon Kids Institute, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Ulrich Kadolsky
- Genomics WA, Harry Perkins Institute of Medical Research, Telethon Kids Institute, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Xiao Zhong
- Genomics WA, Harry Perkins Institute of Medical Research, Telethon Kids Institute, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Alka Saxena
- Genomics WA, Harry Perkins Institute of Medical Research, Telethon Kids Institute, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Omar Kujan
- UWA Dental School, The University of Western Australia, Nedlands, WA 6009, Australia
- Correspondence:
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Shirani-Bidabadi S, Tabatabaee A, Tavazohi N, Hariri A, Aref AR, Zarrabi A, Casarcia N, Bishayee A, Mirian M. CRISPR technology: A versatile tool to model, screen, and reverse drug resistance in cancer. Eur J Cell Biol 2023; 102:151299. [PMID: 36809688 DOI: 10.1016/j.ejcb.2023.151299] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND Drug resistance is a serious challenge in cancer treatment that can render chemotherapy a failure. Understanding the mechanisms behind drug resistance and developing novel therapeutic approaches are cardinal steps in overcoming this issue. Clustered regularly interspaced short palindrome repeats (CRISPR) gene-editing technology has proven to be a useful tool to study cancer drug resistance mechanisms and target the responsible genes. In this review, we evaluated original research studies that used the CRISPR tool in three areas related to drug resistance, namely screening resistance-related genes, generating modified models of resistant cells and animals, and removing resistance by genetic manipulation. We reported the targeted genes, study models, and drug groups in these studies. In addition to discussing different applications of CRISPR technology in cancer drug resistance, we analyzed drug resistance mechanisms and provided examples of CRISPR's role in studying them. Although CRISPR is a powerful tool for examining drug resistance and sensitizing resistant cells to chemotherapy, more studies are required to overcome its disadvantages, such as off-target effects, immunotoxicity, and inefficient delivery of CRISPR/cas9 into the cells.
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Affiliation(s)
- Shiva Shirani-Bidabadi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran
| | - Aliye Tabatabaee
- Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran
| | - Nazita Tavazohi
- Novel Drug Delivery Systems Research Centre, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran
| | - Amirali Hariri
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran
| | - Amir Reza Aref
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Translational Sciences, Xsphera Biosciences Inc., Boston, MA 02215, USA
| | - Ali Zarrabi
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Istanbul 34396, Turkey
| | - Nicolette Casarcia
- College of Osteopathic Medicine, Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA
| | - Anupam Bishayee
- College of Osteopathic Medicine, Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA.
| | - Mina Mirian
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran.
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Systemic Cytokines in Retinopathy of Prematurity. J Pers Med 2023; 13:jpm13020291. [PMID: 36836525 PMCID: PMC9966226 DOI: 10.3390/jpm13020291] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/30/2023] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
Retinopathy of prematurity (ROP), a vasoproliferative vitreoretinal disorder, is the leading cause of childhood blindness worldwide. Although angiogenic pathways have been the main focus, cytokine-mediated inflammation is also involved in ROP etiology. Herein, we illustrate the characteristics and actions of all cytokines involved in ROP pathogenesis. The two-phase (vaso-obliteration followed by vasoproliferation) theory outlines the evaluation of cytokines in a time-dependent manner. Levels of cytokines may even differ between the blood and the vitreous. Data from animal models of oxygen-induced retinopathy are also valuable. Although conventional cryotherapy and laser photocoagulation are well established and anti-vascular endothelial growth factor agents are available, less destructive novel therapeutics that can precisely target the signaling pathways are required. Linking the cytokines involved in ROP to other maternal and neonatal diseases and conditions provides insights into the management of ROP. Suppressing disordered retinal angiogenesis via the modulation of hypoxia-inducible factor, supplementation of insulin-like growth factor (IGF)-1/IGF-binding protein 3 complex, erythropoietin, and its derivatives, polyunsaturated fatty acids, and inhibition of secretogranin III have attracted the attention of researchers. Recently, gut microbiota modulation, non-coding RNAs, and gene therapies have shown promise in regulating ROP. These emerging therapeutics can be used to treat preterm infants with ROP.
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Sekiguchi R, Mehlferber M, Matsumoto K, Wang S. Efficient Gene Knockout in Salivary Gland Epithelial Explant Cultures. J Dent Res 2023; 102:197-206. [PMID: 36366748 PMCID: PMC9893391 DOI: 10.1177/00220345221128201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have developed methods to achieve efficient CRISPR-Cas9-mediated gene knockout in ex vivo mouse embryonic salivary epithelial explants. Salivary epithelial explants provide a valuable model for characterizing cell signaling, differentiation, and epithelial morphogenesis, but research has been limited by a paucity of efficient gene perturbation methods. Here, we demonstrate highly efficient gene perturbation by transient transduction of guide RNA-expressing lentiviruses into Cas9-expressing salivary epithelial buds isolated from Cas9 transgenic mice. We first show that salivary epithelial explants can be cultured in low-concentration, nonsolidified Matrigel suspensions in 96-well plates, which greatly increases sample throughput compared to conventional cultures embedded in solidified Matrigel. We further show that salivary epithelial explants can grow and branch with FGF7 alone, while supplementing with insulin, transferrin, and selenium (ITS) enhances growth and branching. We then describe an efficient workflow to produce experiment-ready, high-titer lentiviruses within 1 wk after molecular cloning. To track transduced cells, we designed the lentiviral vector to coexpress a nuclear fluorescent reporter with the guide RNA. We routinely achieved 80% transduction efficiency when antibiotic selection was used. Importantly, we detected robust loss of targeted protein products when testing 9 guide RNAs for 3 different genes. Moreover, targeting the β1 integrin gene (Itgb1) inhibited branching morphogenesis, which supports the importance of cell-matrix adhesion in driving branching morphogenesis. In summary, we have established a lentivirus-based method that can efficiently perturb genes of interest in salivary epithelial explants, which will greatly facilitate studies of specific gene functions using this system.
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Affiliation(s)
- R. Sekiguchi
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - M.M. Mehlferber
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
- Present address: Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - K. Matsumoto
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - S. Wang
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
- Present address: 4D Cellular Physiology, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
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Nucleic acid drug vectors for diagnosis and treatment of brain diseases. Signal Transduct Target Ther 2023; 8:39. [PMID: 36650130 PMCID: PMC9844208 DOI: 10.1038/s41392-022-01298-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/08/2022] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
Nucleic acid drugs have the advantages of rich target selection, simple in design, good and enduring effect. They have been demonstrated to have irreplaceable superiority in brain disease treatment, while vectors are a decisive factor in therapeutic efficacy. Strict physiological barriers, such as degradation and clearance in circulation, blood-brain barrier, cellular uptake, endosome/lysosome barriers, release, obstruct the delivery of nucleic acid drugs to the brain by the vectors. Nucleic acid drugs against a single target are inefficient in treating brain diseases of complex pathogenesis. Differences between individual patients lead to severe uncertainties in brain disease treatment with nucleic acid drugs. In this Review, we briefly summarize the classification of nucleic acid drugs. Next, we discuss physiological barriers during drug delivery and universal coping strategies and introduce the application methods of these universal strategies to nucleic acid drug vectors. Subsequently, we explore nucleic acid drug-based multidrug regimens for the combination treatment of brain diseases and the construction of the corresponding vectors. In the following, we address the feasibility of patient stratification and personalized therapy through diagnostic information from medical imaging and the manner of introducing contrast agents into vectors. Finally, we take a perspective on the future feasibility and remaining challenges of vector-based integrated diagnosis and gene therapy for brain diseases.
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Boti MA, Athanasopoulou K, Adamopoulos PG, Sideris DC, Scorilas A. Recent Advances in Genome-Engineering Strategies. Genes (Basel) 2023; 14:129. [PMID: 36672870 PMCID: PMC9859587 DOI: 10.3390/genes14010129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/25/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023] Open
Abstract
In October 2020, the chemistry Nobel Prize was awarded to Emmanuelle Charpentier and Jennifer A. Doudna for the discovery of a new promising genome-editing tool: the genetic scissors of CRISPR-Cas9. The identification of CRISPR arrays and the subsequent identification of cas genes, which together represent an adaptive immunological system that exists not only in bacteria but also in archaea, led to the development of diverse strategies used for precise DNA editing, providing new insights in basic research and in clinical practice. Due to their advantageous features, the CRISPR-Cas systems are already employed in several biological and medical research fields as the most suitable technique for genome engineering. In this review, we aim to describe the CRISPR-Cas systems that have been identified among prokaryotic organisms and engineered for genome manipulation studies. Furthermore, a comprehensive comparison between the innovative CRISPR-Cas methodology and the previously utilized ZFN and TALEN editing nucleases is also discussed. Ultimately, we highlight the contribution of CRISPR-Cas methodology in modern biomedicine and the current plethora of available applications for gene KO, repression and/or overexpression, as well as their potential implementation in therapeutical strategies that aim to improve patients' quality of life.
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Affiliation(s)
| | | | - Panagiotis G. Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
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49
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Bonamino MH, Correia EM. The CRISPR/Cas System in Human Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1429:59-71. [PMID: 37486516 DOI: 10.1007/978-3-031-33325-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
The use of CRISPR as a genetic editing tool modified the oncology field from its basic to applied research for opening a simple, fast, and cheaper way to manipulate the genome. This chapter reviews some of the major uses of this technique for in vitro- and in vivo-based biological screenings, for cellular and animal model generation, and new derivative tools applied to cancer research. CRISPR has opened new frontiers increasing the knowledge about cancer, pointing to new solutions to overcome several challenges to better understand the disease and design better treatments.
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50
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Edwards-Faret G, de Vin F, Slezak M, Gollenbeck L, Karaman R, Shinmyo Y, Batiuk MY, Pando CM, Urschitz J, Rincon MY, Moisyadi S, Schnütgen F, Kawasaki H, Schmucker D, Holt MG. A New Technical Approach for Cross-species Examination of Neuronal Wiring and Adult Neuron-glia Functions. Neuroscience 2023; 508:40-51. [PMID: 36464177 DOI: 10.1016/j.neuroscience.2022.11.029] [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: 03/21/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022]
Abstract
Advances in single cell sequencing have enabled the identification of a large number of genes, expressed in many different cell types, and across a variety of model organisms. In particular, the nervous system harbors an immense number of interacting cell types, which are poorly characterized. Future loss- and gain-of-function experiments will be essential in determining how novel genes play critical roles in diverse cellular, as well as evolutionarily adapted, contexts. However, functional analysis across species is often hampered by technical limitations, in non-genetic animal systems. Here, we describe a new single plasmid system, misPiggy. The system is based around the hyperactive piggyBac transposon system, which combines stable genomic integration of transgenes (for long-term expression) with large cargo capacity. Taking full advantage of these characteristics, we engineered novel expression modules into misPiggy that allow for cell-type specific loss- and gain-of-gene function. These modules work widely across species from frog to ferret. As a proof of principle, we present a loss-of-function analysis of the neuronal receptor Deleted in Colorectal Cancer (DCC) in retinal ganglion cells (RGCs) of Xenopus tropicalis tadpoles. Single axon tracings of mosaic knock-out cells reveal a specific cell-intrinsic requirement of DCC, specifically in axonal arborization within the frog tectum, rather than retina-to-brain axon guidance. Furthermore, we report additional technical advances that enable temporal control of knock-down or gain-of-function analysis. We applied this to visualize and manipulate labeled neurons, astrocytes and other glial cells in the central nervous system (CNS) of mouse, rat and ferret. We propose that misPiggy will be a valuable tool for rapid, flexible and cost-effective screening of gene function across a variety of animal models.
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Affiliation(s)
- Gabriela Edwards-Faret
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium; Neuronal Wiring Group, Life & Medical Sciences Institute, University of Bonn, Carl-Troll-Straße 31, Bonn D53115, Germany
| | - Filip de Vin
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium
| | - Michal Slezak
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium
| | - Lennart Gollenbeck
- Neuronal Wiring Group, Life & Medical Sciences Institute, University of Bonn, Carl-Troll-Straße 31, Bonn D53115, Germany
| | - Ruçhan Karaman
- VIB Center for Cancer Biology, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Oncology, Herestraat 49, Leuven 3000, Belgium
| | - Yohei Shinmyo
- Department of Medical Neuroscience, Graduate School of Medicine, Kanazawa University, Ishikawa 920-1192, Japan
| | - Mykhailo Y Batiuk
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium
| | - Carmen Menacho Pando
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium
| | - Johann Urschitz
- Institute for Biogenesis Research, University of Hawaii, 1960 East-West Rd. E-124, Honolulu, HI 96822, USA
| | - Melvin Y Rincon
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium
| | - Stefan Moisyadi
- Institute for Biogenesis Research, University of Hawaii, 1960 East-West Rd. E-124, Honolulu, HI 96822, USA
| | - Frank Schnütgen
- Department of Medicine 2, University Hospital Frankfurt, Goethe University, Theodor Stern Kai 7, Frankfurt am Main D60590, Germany; LOEWE Center for Cell and Gene Therapy, University Hospital Frankfurt, Goethe University, Theodor Stern Kai 7, Frankfurt am Main D60590, Germany; FCI, Frankfurt Cancer Institute, University Hospital Frankfurt, Goethe University, Theodor Stern Kai 7, Frankfurt am Main D60590, Germany
| | - Hiroshi Kawasaki
- Department of Medical Neuroscience, Graduate School of Medicine, Kanazawa University, Ishikawa 920-1192, Japan
| | - Dietmar Schmucker
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium; Neuronal Wiring Group, Life & Medical Sciences Institute, University of Bonn, Carl-Troll-Straße 31, Bonn D53115, Germany; Leuven Brain Institute, Herestraat 49, Leuven 3000, Belgium.
| | - Matthew G Holt
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium; KU Leuven Department of Neuroscience, Herestraat 49, Leuven 3000, Belgium; Leuven Brain Institute, Herestraat 49, Leuven 3000, Belgium; University of Porto, Instituto de Investigaçāo e Inovaçāo em Saúde (i3S), Rua Alfredo Allen 208, 4200-135 Porto, Portugal.
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