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Hofman T, Ng SW, Garcés-Lázaro I, Heigwer F, Boutros M, Cerwenka A. IFNγ mediates the resistance of tumor cells to distinct NK cell subsets. J Immunother Cancer 2024; 12:e009410. [PMID: 38955423 PMCID: PMC11218003 DOI: 10.1136/jitc-2024-009410] [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] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Immune checkpoint blockade targeting the adaptive immune system has revolutionized the treatment of cancer. Despite impressive clinical benefits observed, patient subgroups remain non-responsive underscoring the necessity for combinational therapies harnessing additional immune cells. Natural killer (NK) cells are emerging tools for cancer therapy. However, only subpopulations of NK cells that are differentially controlled by inhibitory receptors exert reactivity against particular cancer types. How to leverage the complete anti-tumor potential of all NK cell subsets without favoring the emergence of NK cell-resistant tumor cells remains unresolved. METHODS We performed a genome-wide CRISPR/Cas9 knockout resistance screen in melanoma cells in co-cultures with human primary NK cells. We comprehensively evaluated factors regulating tumor resistance and susceptibility by focusing on NK cell subsets in an allogenic setting. Moreover, we tested therapeutic blocking antibodies currently used in clinical trials. RESULTS Melanoma cells deficient in antigen-presenting or the IFNγ-signaling pathways were depleted in remaining NK cell-co-cultured melanoma cells and displayed enhanced sensitivity to NK cells. Treatment with IFNγ induced potent resistance of melanoma cells to resting, IL-2-cultured and ADCC-activated NK cells that depended on B2M required for the expression of both classical and non-classical MHC-I. IFNγ-induced expression of HLA-E mediated the resistance of melanoma cells to the NKG2A+ KIR- and partially to the NKG2A+ KIR+ NK cell subset. The expression of classical MHC-I by itself was sufficient for the inhibition of the NKG2A- KIR+, but not the NKG2A+ KIR+ NK cell subset. Treatment of NK cells with monalizumab, an NKG2A blocking mAb, enhanced the reactivity of a corresponding subset of NK cells. The combination of monalizumab with lirilumab, blocking KIR2 receptors, together with DX9, blocking KIR3DL1, was required to restore cytotoxicity of all NK cell subsets against IFNγ-induced resistant tumor cells in melanoma and tumors of different origins. CONCLUSION Our data reveal that in the context of NK cells, IFNγ induces the resistance of tumor cells by the upregulation of classical and non-classical MHC-I. Moreover, we reveal insights into NK cell subset reactivity and propose a therapeutic strategy involving combinational monalizumab/lirilumab/DX9 treatment to fully restore the antitumor response across NK cell subsets.
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Affiliation(s)
- Tomáš Hofman
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Siu Wang Ng
- Signalling and Functional Genomics, German Cancer Research Centre, Heidelberg, Germany
| | - Irene Garcés-Lázaro
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Florian Heigwer
- Signalling and Functional Genomics, German Cancer Research Centre, Heidelberg, Germany
- Department of Life Sciences and Engineering, University of Applied Sciences Bingen, Bingen am Rhein, Germany
| | - Michael Boutros
- Signalling and Functional Genomics, German Cancer Research Centre, Heidelberg, Germany
| | - Adelheid Cerwenka
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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2
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Vasconcelos Komninakis S, Domingues W, Saeed Sanabani S, Angelo Folgosi V, Neves Barbosa I, Casseb J. CRISPR/CAS as a Powerful Tool for Human Immunodeficiency Virus Cure: A Review. AIDS Res Hum Retroviruses 2024; 40:363-375. [PMID: 38164106 DOI: 10.1089/aid.2022.0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024] Open
Abstract
Despite care and the availability of effective antiretroviral treatment, some human immunodeficiency virus (HIV)-infected individuals suffer from neurocognitive disorders associated with HIV (HAND) that significantly affect their quality of life. The different types of HAND can be divided into asymptomatic neurocognitive impairment, mild neurocognitive disorder, and the most severe form known as HIV-associated dementia. Little is known about the mechanisms of HAND, but it is thought to be related to infection of astrocytes, microglial cells, and macrophages in the human brain. The formation of a viral reservoir that lies dormant as a provirus in resting CD4+ T lymphocytes and in refuge tissues such as the brain contributes significantly to HIV eradication. In recent years, a new set of tools have emerged: the gene editing based on the clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 system, which can alter genome segments by insertion, deletion, and replacement and has great therapeutic potential. This technology has been used in research to treat HIV and appears to offer hope for a possible cure for HIV infection and perhaps prevention of HAND. This approach has the potential to directly impact the quality of life of HIV-infected individuals, which is a very important topic to be known and discussed.
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Affiliation(s)
- Shirley Vasconcelos Komninakis
- Laboratory of Medical Investigation (LIM56) of the School of Medicine/Institute de Tropical Medicine, Department of Dermatology, São Paulo University, São Paulo, São Paulo, Brazil
| | - Wilson Domingues
- Laboratory of Medical Investigation (LIM56) of the School of Medicine/Institute de Tropical Medicine, Department of Dermatology, São Paulo University, São Paulo, São Paulo, Brazil
| | - Sabri Saeed Sanabani
- Laboratory of Medical Investigation (LIM56) of the School of Medicine/Institute de Tropical Medicine, Department of Dermatology, São Paulo University, São Paulo, São Paulo, Brazil
| | - Victor Angelo Folgosi
- Laboratory of Medical Investigation (LIM56) of the School of Medicine/Institute de Tropical Medicine, Department of Dermatology, São Paulo University, São Paulo, São Paulo, Brazil
| | - Igor Neves Barbosa
- Institute of Genetic Biology at the Biological Institute of São Paulo University, São Paulo, São Paulo, Brazil
| | - Jorge Casseb
- Laboratory of Medical Investigation (LIM56) of the School of Medicine/Institute de Tropical Medicine, Department of Dermatology, São Paulo University, São Paulo, São Paulo, Brazil
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3
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Qin M, Deng C, Wen L, Luo G, Meng Y. CRISPR-Cas and CRISPR-based screening system for precise gene editing and targeted cancer therapy. J Transl Med 2024; 22:516. [PMID: 38816739 PMCID: PMC11138051 DOI: 10.1186/s12967-024-05235-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/24/2024] [Indexed: 06/01/2024] Open
Abstract
Target cancer therapy has been developed for clinical cancer treatment based on the discovery of CRISPR (clustered regularly interspaced short palindromic repeat) -Cas system. This forefront and cutting-edge scientific technique improves the cancer research into molecular level and is currently widely utilized in genetic investigation and clinical precision cancer therapy. In this review, we summarized the genetic modification by CRISPR/Cas and CRISPR screening system, discussed key components for successful CRISPR screening, including Cas enzymes, guide RNA (gRNA) libraries, target cells or organs. Furthermore, we focused on the application for CAR-T cell therapy, drug target, drug screening, or drug selection in both ex vivo and in vivo with CRISPR screening system. In addition, we elucidated the advantages and potential obstacles of CRISPR system in precision clinical medicine and described the prospects for future genetic therapy.In summary, we provide a comprehensive and practical perspective on the development of CRISPR/Cas and CRISPR screening system for the treatment of cancer defects, aiming to further improve the precision and accuracy for clinical treatment and individualized gene therapy.
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Affiliation(s)
- Mingming Qin
- Reproductive Medical Center, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University (Foshan Women and Children Hospital), Foshan, Guangdong, 528000, China
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Chunhao Deng
- Chinese Medicine and Translational Medicine R&D center, Zhuhai UM Science & Technology Research Institute, Zhuhai, Guangdong, 519031, China
| | - Liewei Wen
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital, Zhuhai Clinical Medical College of Jinan University, Zhuhai, Guangdong, 519000, China
| | - Guoqun Luo
- Reproductive Medical Center, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University (Foshan Women and Children Hospital), Foshan, Guangdong, 528000, China.
| | - Ya Meng
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital, Zhuhai Clinical Medical College of Jinan University, Zhuhai, Guangdong, 519000, China.
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4
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Zhang S, Yun D, Yang H, Eckstein M, Elbait GD, Zhou Y, Lu Y, Yang H, Zhang J, Dörflein I, Britzen-Laurent N, Pfeffer S, Stemmler MP, Dahl A, Mukhopadhyay D, Chang D, He H, Zeng S, Lan B, Frey B, Hampel C, Lentsch E, Gollavilli PN, Büttner C, Ekici AB, Biankin A, Schneider-Stock R, Ceppi P, Grützmann R, Pilarsky C. Roflumilast inhibits tumor growth and migration in STK11/LKB1 deficient pancreatic cancer. Cell Death Discov 2024; 10:124. [PMID: 38461159 PMCID: PMC10924943 DOI: 10.1038/s41420-024-01890-y] [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: 12/20/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/11/2024] Open
Abstract
Pancreatic cancer is a malignant tumor of the digestive system. It is highly aggressive, easily metastasizes, and extremely difficult to treat. This study aimed to analyze the genes that might regulate pancreatic cancer migration to provide an essential basis for the prognostic assessment of pancreatic cancer and individualized treatment. A CRISPR knockout library directed against 915 murine genes was transfected into TB 32047 cell line to screen which gene loss promoted cell migration. Next-generation sequencing and PinAPL.py- analysis was performed to identify candidate genes. We then assessed the effect of serine/threonine kinase 11 (STK11) knockout on pancreatic cancer by wound-healing assay, chick agnosia (CAM) assay, and orthotopic mouse pancreatic cancer model. We performed RNA sequence and Western blotting for mechanistic studies to identify and verify the pathways. After accelerated Transwell migration screening, STK11 was identified as one of the top candidate genes. Further experiments showed that targeted knockout of STK11 promoted the cell migration and increased liver metastasis in mice. Mechanistic analyses revealed that STK11 knockout influences blood vessel morphogenesis and is closely associated with the enhanced expression of phosphodiesterases (PDEs), especially PDE4D, PDE4B, and PDE10A. PDE4 inhibitor Roflumilast inhibited STK11-KO cell migration and tumor size, further demonstrating that PDEs are essential for STK11-deficient cell migration. Our findings support the adoption of therapeutic strategies, including Roflumilast, for patients with STK11-mutated pancreatic cancer in order to improve treatment efficacy and ultimately prolong survival.
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Affiliation(s)
- Shuman Zhang
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Duo Yun
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Hao Yang
- Experimental Tumor pathology, Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Markus Eckstein
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Gihan Daw Elbait
- Department of Biology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Yaxing Zhou
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Yanxi Lu
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Hai Yang
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Jinping Zhang
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Isabella Dörflein
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Nathalie Britzen-Laurent
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Susanne Pfeffer
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Marc P Stemmler
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Andreas Dahl
- DRESDEN-concept Genome Center a DFG NGS Competence Center; TU Dresden, 01307, Dresden, Germany
| | - Debabrata Mukhopadhyay
- Departments of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Jacksonville, USA
| | - David Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - Hang He
- Department of Pancreatic Surgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Siyuan Zeng
- Department of Breast and Thyroid Surgery, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Bin Lan
- Department of Interventional Radiology and Vascular Surgery, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha, 410002, China
| | - Benjamin Frey
- Translational Radiobiology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Chuanpit Hampel
- Experimental Tumor pathology, Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Eva Lentsch
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Paradesi Naidu Gollavilli
- Department of Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Odense, Denmark
| | - Christian Büttner
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Andrew Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - Regine Schneider-Stock
- Experimental Tumor pathology, Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Paolo Ceppi
- Department of Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Odense, Denmark
| | - Robert Grützmann
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christian Pilarsky
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
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5
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Heo SJ, Enriquez LD, Federman S, Chang AY, Mace R, Shevade K, Nguyen P, Litterman AJ, Shafer S, Przybyla L, Chow ED. Compact CRISPR genetic screens enabled by improved guide RNA library cloning. Genome Biol 2024; 25:25. [PMID: 38243310 PMCID: PMC10797759 DOI: 10.1186/s13059-023-03132-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/29/2023] [Indexed: 01/21/2024] Open
Abstract
CRISPR genome editing approaches theoretically enable researchers to define the function of each human gene in specific cell types, but challenges remain to efficiently perform genetic perturbations in relevant models. In this work, we develop a library cloning protocol that increases sgRNA uniformity and greatly reduces bias in existing genome-wide libraries. We demonstrate that our libraries can achieve equivalent or better statistical power compared to previously reported screens using an order of magnitude fewer cells. This improved cloning protocol enables genome-scale CRISPR screens in technically challenging cell models and screen formats.
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Affiliation(s)
- Seok-Jin Heo
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Lauren D Enriquez
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Scot Federman
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Amy Y Chang
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Rachel Mace
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Kaivalya Shevade
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Phuong Nguyen
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Adam J Litterman
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Shawn Shafer
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- GSK, San Francisco, CA, 94158, USA
| | - Laralynne Przybyla
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Eric D Chow
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA.
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Groth C, Maric J, Garcés Lázaro I, Hofman T, Zhang Z, Ni Y, Keller F, Seufert I, Hofmann M, Neumann-Haefelin C, Sticht C, Rippe K, Urban S, Cerwenka A. Hepatitis D infection induces IFN-β-mediated NK cell activation and TRAIL-dependent cytotoxicity. Front Immunol 2023; 14:1287367. [PMID: 38143742 PMCID: PMC10739304 DOI: 10.3389/fimmu.2023.1287367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/23/2023] [Indexed: 12/26/2023] Open
Abstract
Background and aims The co-infection of hepatitis B (HBV) patients with the hepatitis D virus (HDV) causes the most severe form of viral hepatitis and thus drastically worsens the course of the disease. Therapy options for HBV/HDV patients are still limited. Here, we investigated the potential of natural killer (NK) cells that are crucial drivers of the innate immune response against viruses to target HDV-infected hepatocytes. Methods We established in vitro co-culture models using HDV-infected hepatoma cell lines and human peripheral blood NK cells. We determined NK cell activation by flow cytometry, transcriptome analysis, bead-based cytokine immunoassays, and NK cell-mediated effects on T cells by flow cytometry. We validated the mechanisms using CRISPR/Cas9-mediated gene deletions. Moreover, we assessed the frequencies and phenotype of NK cells in peripheral blood of HBV and HDV superinfected patients. Results Upon co-culture with HDV-infected hepatic cell lines, NK cells upregulated activation markers, interferon-stimulated genes (ISGs) including the death receptor ligand tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), produced interferon (IFN)-γ and eliminated HDV-infected cells via the TRAIL-TRAIL-R2 axis. We identified IFN-β released by HDV-infected cells as an important enhancer of NK cell activity. In line with our in vitro data, we observed activation of peripheral blood NK cells from HBV/HDV co-infected, but not HBV mono-infected patients. Conclusion Our data demonstrate NK cell activation in HDV infection and their potential to eliminate HDV-infected hepatoma cells via the TRAIL/TRAIL-R2 axis which implies a high relevance of NK cells for the design of novel anti-viral therapies.
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Affiliation(s)
- Christopher Groth
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jovana Maric
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Irene Garcés Lázaro
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tomáš Hofman
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Zhenfeng Zhang
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Yi Ni
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZFI) - Heidelberg Partner Site, Heidelberg, Germany
| | - Franziska Keller
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Isabelle Seufert
- Division of Chromatin Networks, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ) and Bioquant, Heidelberg, Germany
| | - Maike Hofmann
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Christoph Neumann-Haefelin
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Carsten Sticht
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ) and Bioquant, Heidelberg, Germany
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZFI) - Heidelberg Partner Site, Heidelberg, Germany
| | - Adelheid Cerwenka
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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Anvar NE, Lin C, Ma X, Wilson LL, Steger R, Sangree AK, Colic M, Wang SH, Doench JG, Hart T. Efficient gene knockout and genetic interactions: the IN4MER CRISPR/Cas12a multiplex knockout platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522655. [PMID: 36712129 PMCID: PMC9881895 DOI: 10.1101/2023.01.03.522655] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genetic interactions mediate the emergence of phenotype from genotype, but initial technologies for combinatorial genetic perturbation in mammalian cells suffer from inefficiency and are challenging to scale. Recent focus on paralog synthetic lethality in cancer cells offers an opportunity to evaluate different approaches and improve on the state of the art. Here we report a meta-analysis of CRISPR genetic interactions screens, identifying a candidate set of background-independent paralog synthetic lethals, and find that the Cas12a platform provides superior sensitivity and assay replicability. We demonstrate that Cas12a can independently target up to four genes from a single guide array, and we build on this knowledge by constructing a genome-scale library that expresses arrays of four guides per clone, a platform we call 'in4mer'. Our genome-scale human library, with only 49k clones, is substantially smaller than a typical CRISPR/Cas9 monogenic library while also targeting more than four thousand paralog pairs, triples, and quads. Proof of concept screens in four cell lines demonstrate discrimination of core and context-dependent essential genes similar to that of state-of-the-art CRISPR/Cas9 libraries, as well as detection of synthetic lethal and masking/buffering genetic interactions between paralogs of various family sizes, a capability not offered by any extant library. Importantly, the in4mer platform offers a fivefold reduction in the number of clones required to assay genetic interactions, dramatically improving the cost and effort required for these studies.
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Affiliation(s)
- Nazanin Esmaeili Anvar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth, Houston, TX, USA
| | - Chenchu Lin
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingdi Ma
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth, Houston, TX, USA
| | - Lori L. Wilson
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ryan Steger
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Annabel K. Sangree
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Medina Colic
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sidney H. Wang
- Center for Human Genetics, The Brown foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - John G. Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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8
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Flynn E, Almonte-Loya A, Fragiadakis GK. Single-Cell Multiomics. Annu Rev Biomed Data Sci 2023; 6:313-337. [PMID: 37159875 PMCID: PMC11146013 DOI: 10.1146/annurev-biodatasci-020422-050645] [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: 05/11/2023]
Abstract
Single-cell RNA sequencing methods have led to improved understanding of the heterogeneity and transcriptomic states present in complex biological systems. Recently, the development of novel single-cell technologies for assaying additional modalities, specifically genomic, epigenomic, proteomic, and spatial data, allows for unprecedented insight into cellular biology. While certain technologies collect multiple measurements from the same cells simultaneously, even when modalities are separately assayed in different cells, we can apply novel computational methods to integrate these data. The application of computational integration methods to multimodal paired and unpaired data results in rich information about the identities of the cells present and the interactions between different levels of biology, such as between genetic variation and transcription. In this review, we both discuss the single-cell technologies for measuring these modalities and describe and characterize a variety of computational integration methods for combining the resulting data to leverage multimodal information toward greater biological insight.
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Affiliation(s)
- Emily Flynn
- CoLabs, University of California, San Francisco, California, USA;
| | - Ana Almonte-Loya
- CoLabs, University of California, San Francisco, California, USA;
- Biomedical Informatics Program, University of California, San Francisco, California, USA
| | - Gabriela K Fragiadakis
- CoLabs, University of California, San Francisco, California, USA;
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
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9
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Ahmed M, Muffat J, Li Y. Understanding neural development and diseases using CRISPR screens in human pluripotent stem cell-derived cultures. Front Cell Dev Biol 2023; 11:1158373. [PMID: 37101616 PMCID: PMC10123288 DOI: 10.3389/fcell.2023.1158373] [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: 02/03/2023] [Accepted: 03/30/2023] [Indexed: 04/28/2023] Open
Abstract
The brain is arguably the most complex part of the human body in form and function. Much remains unclear about the molecular mechanisms that regulate its normal and pathological physiology. This lack of knowledge largely stems from the inaccessible nature of the human brain, and the limitation of animal models. As a result, brain disorders are difficult to understand and even more difficult to treat. Recent advances in generating human pluripotent stem cells (hPSCs)-derived 2-dimensional (2D) and 3-dimensional (3D) neural cultures have provided an accessible system to model the human brain. Breakthroughs in gene editing technologies such as CRISPR/Cas9 further elevate the hPSCs into a genetically tractable experimental system. Powerful genetic screens, previously reserved for model organisms and transformed cell lines, can now be performed in human neural cells. Combined with the rapidly expanding single-cell genomics toolkit, these technological advances culminate to create an unprecedented opportunity to study the human brain using functional genomics. This review will summarize the current progress of applying CRISPR-based genetic screens in hPSCs-derived 2D neural cultures and 3D brain organoids. We will also evaluate the key technologies involved and discuss their related experimental considerations and future applications.
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Affiliation(s)
- Mai Ahmed
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Julien Muffat
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Yun Li
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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10
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Khabarova A, Koksharova G, Salnikov P, Belokopytova P, Mungalov R, Pristyazhnuk I, Nurislamov A, Gridina M, Fishman V. A Cre-LoxP-based approach for combinatorial chromosome rearrangements in human HAP1 cells. Chromosome Res 2023; 31:11. [PMID: 36842155 DOI: 10.1007/s10577-023-09719-7] [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: 12/15/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/27/2023]
Abstract
Alterations of human karyotype caused by chromosomal rearrangements are often associated with considerable phenotypic effects. Studying molecular mechanisms underlying these effects requires an efficient and scalable experimental model. Here, we propose a Cre-LoxP-based approach for the generation of combinatorial diversity of chromosomal rearrangements. We demonstrate that using the developed system, both intra- and inter-chromosomal rearrangements can be induced in the human haploid HAP1 cells, although the latter is significantly less effective. The obtained genetically modified HAP1 cell line can be used to dissect genomic effects associated with intra-chromosomal structural variations.
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Affiliation(s)
| | - Galina Koksharova
- Institute of Cytology and Genetics, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
| | - Pavel Salnikov
- Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Polina Belokopytova
- Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | | | - Artem Nurislamov
- Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Maria Gridina
- Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Veniamin Fishman
- Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- Artificial Intelligence Research Institute, AIRI, Moscow, Russia
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11
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Fasullo M, Dolan M. The continuing evolution of barcode applications: Functional toxicology to cell lineage. Exp Biol Med (Maywood) 2022; 247:2119-2127. [PMID: 36113119 PMCID: PMC9837303 DOI: 10.1177/15353702221121600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
DNA barcoding is a method to identify biological entities, including individual cells, tissues, organs, or species, by unique DNA sequences. With the advent of next generation sequencing (NGS), there has been an exponential increase in data acquisition pertaining to medical diagnosis, genetics, toxicology, ecology, cancer, and developmental biology. While barcoding first gained wide access in identifying species, signature tagged mutagenesis has been useful in elucidating gene function, particularly in microbes. With the advent of CRISPR/CAS9, methodology to profile eukaryotic genes has made a broad impact in toxicology and cancer biology. Designed homing guide RNAs (hgRNAs) that self-target DNA sequences facilitate cell lineage barcoding by introducing stochastic mutations within cell identifiers. While each of these applications has their limitations, the potential of sequence barcoding has yet to be realized. This review will focus on signature-tagged mutagenesis and briefly discuss the history of barcoding, experimental problems, novel detection methods, and future directions.
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Affiliation(s)
- Michael Fasullo
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
| | - Michael Dolan
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
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12
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Holcomb EA, Pearson AN, Jungles KM, Tate A, James J, Jiang L, Huber AK, Green MD. High-content CRISPR screening in tumor immunology. Front Immunol 2022; 13:1041451. [PMID: 36479127 PMCID: PMC9721350 DOI: 10.3389/fimmu.2022.1041451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/21/2022] [Indexed: 11/22/2022] Open
Abstract
CRISPR screening is a powerful tool that links specific genetic alterations to corresponding phenotypes, thus allowing for high-throughput identification of novel gene functions. Pooled CRISPR screens have enabled discovery of innate and adaptive immune response regulators in the setting of viral infection and cancer. Emerging methods couple pooled CRISPR screens with parallel high-content readouts at the transcriptomic, epigenetic, proteomic, and optical levels. These approaches are illuminating cancer immune evasion mechanisms as well as nominating novel targets that augment T cell activation, increase T cell infiltration into tumors, and promote enhanced T cell cytotoxicity. This review details recent methodological advances in high-content CRISPR screens and highlights the impact this technology is having on tumor immunology.
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Affiliation(s)
- Erin A. Holcomb
- Graduate Program in Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Ashley N. Pearson
- Graduate Program in Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Kassidy M. Jungles
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Department of Pharmacology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
| | - Akshay Tate
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Jadyn James
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Long Jiang
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China
| | - Amanda K. Huber
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Michael D. Green
- Graduate Program in Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
- Department of Microbiology and Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Department of Radiation Oncology, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, MI, United States
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13
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Walton RT, Singh A, Blainey PC. Pooled genetic screens with image-based profiling. Mol Syst Biol 2022; 18:e10768. [PMID: 36366905 PMCID: PMC9650298 DOI: 10.15252/msb.202110768] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
Spatial structure in biology, spanning molecular, organellular, cellular, tissue, and organismal scales, is encoded through a combination of genetic and epigenetic factors in individual cells. Microscopy remains the most direct approach to exploring the intricate spatial complexity defining biological systems and the structured dynamic responses of these systems to perturbations. Genetic screens with deep single-cell profiling via image features or gene expression programs have the capacity to show how biological systems work in detail by cataloging many cellular phenotypes with one experimental assay. Microscopy-based cellular profiling provides information complementary to next-generation sequencing (NGS) profiling and has only recently become compatible with large-scale genetic screens. Optical screening now offers the scale needed for systematic characterization and is poised for further scale-up. We discuss how these methodologies, together with emerging technologies for genetic perturbation and microscopy-based multiplexed molecular phenotyping, are powering new approaches to reveal genotype-phenotype relationships.
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Affiliation(s)
- Russell T Walton
- Broad Institute of MIT and HarvardCambridgeMAUSA
- Department of Biological EngineeringMITCambridgeMAUSA
| | - Avtar Singh
- Broad Institute of MIT and HarvardCambridgeMAUSA
- Present address:
Department of Cellular and Tissue GenomicsGenentechSouth San FranciscoCAUSA
| | - Paul C Blainey
- Broad Institute of MIT and HarvardCambridgeMAUSA
- Department of Biological EngineeringMITCambridgeMAUSA
- Koch Institute for Integrative Cancer ResearchMITCambridgeMAUSA
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14
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Banerjee R, Sotero-Caio CG, Fu B, Yang F. Chromosomal instability (CIN) in HAP1 cell lines revealed by multiplex fluorescence in situ hybridisation (M-FISH). Mol Cytogenet 2022; 15:46. [PMID: 36289492 PMCID: PMC9609465 DOI: 10.1186/s13039-022-00625-x] [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: 08/17/2022] [Accepted: 10/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND HAP1, a near-haploid human leukemic cancer cell line is often used in combination with CRISPR-Cas9 gene editing technology for genetic screens. HAP1 carries the Philadelphia chromosome (Ph) and an additional ~ 30 Mb fragment of chromosome 15 inserted into chromosome 19. The potential use of an in vitro cell line as a model system in biomedical research studies depends on its ability to maintain genome stability. Being a cancer cell line with a near-haploid genome, HAP1 is prone to genetic instability, which is further compounded by its tendency to diploidise in culture spontaneously. Moreover, CRISPR-Cas9 gene editing coupled with prolonged in-vitro cell culturing has the potential to induce unintended 'off-target' cytogenetic mutations. To gain an insight into chromosomal instability (CIN) and karyotype heterogeneity, 19 HAP1 cell lines were cytogenetically characterised, 17 of which were near-haploids and two double-haploids, using multiplex fluorescence in situ hybridisation (M-FISH), at single cell resolution. We focused on novel numerical (N) and structural (S) CIN and discussed the potential causal factors for the observed instability. For each cell line we examined its ploidy, gene editing status and its length of in-vitro cell culturing. RESULTS Sixteen of the 19 cell lines had been gene edited with passage numbers ranging from 10 to 35. Diploidisation in 17 near-haploid cell lines ranged from 4 to 35% and percentage of N- and S-CIN in [1n] and [2n] metaphases ranged from 7 to 50% with two cell lines showing no CIN. Percentage of cells with CIN in the two double-haploid cell lines were 96% and 100% respectively. The most common S-CIN observed was deletion followed by translocation of both types, non-reciprocal and Robertsonian. Interestingly, we observed a prevalence of S-CIN associated with chromosome 13 in both near-and double-haploid cell lines, with a high incidence of Robertsonian translocation involving chromosome 13. Furthermore, locus-specific BAC (bacterial artificial chromosome) FISH enabled us to show for the first time that the additional chromosome 15 fragment is inserted into the p-arm rather than the q-arm of chromosome 19 of the HAP1 genome. CONCLUSION Our study revealed a high incidence of CIN leading to karyotype heterogeneity in majority of the HAP1 cell lines with the number of chromosomal aberrations varying between cell lines. A noteworthy observation was the high frequency of structural chromosomal aberrations associated with chromosome 13. We showed that CRISPR-Cas9 gene editing technology in combination with spontaneous diploidisation and prolonged in-vitro cell culturing is potentially instrumental in inducing further chromosomal rearrangements in the HAP1 cell lines with existing CIN. We highlight the importance of maintaining cell lines at low passage and the need for regular monitoring to prevent implications in downstream applications. Our study also established that the additional fragment of chromosome 15 in the HAP1 genome is inserted into chromosome 19p rather than 19q.
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Affiliation(s)
- Ruby Banerjee
- grid.10306.340000 0004 0606 5382Molecular Cytogenetics Core Facility, Wellcome Sanger Institute, Cambridge, CB10 1SA UK
| | - Cibele G. Sotero-Caio
- grid.10306.340000 0004 0606 5382Molecular Cytogenetics Core Facility, Wellcome Sanger Institute, Cambridge, CB10 1SA UK
| | - Beiyuan Fu
- grid.10306.340000 0004 0606 5382Molecular Cytogenetics Core Facility, Wellcome Sanger Institute, Cambridge, CB10 1SA UK
| | - Fengtang Yang
- grid.10306.340000 0004 0606 5382Molecular Cytogenetics Core Facility, Wellcome Sanger Institute, Cambridge, CB10 1SA UK ,grid.412509.b0000 0004 1808 3414School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong People’s Republic of China
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15
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Braun CJ, Adames AC, Saur D, Rad R. Tutorial: design and execution of CRISPR in vivo screens. Nat Protoc 2022; 17:1903-1925. [PMID: 35840661 DOI: 10.1038/s41596-022-00700-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/22/2022] [Indexed: 11/09/2022]
Abstract
Here we provide a detailed tutorial on CRISPR in vivo screening. Using the mouse as the model organism, we introduce a range of CRISPR tools and applications, delineate general considerations for 'transplantation-based' or 'direct in vivo' screening design, and provide details on technical execution, sequencing readouts, computational analyses and data interpretation. In vivo screens face unique pitfalls and limitations, such as delivery issues or library bottlenecking, which must be counteracted to avoid screening failure or flawed conclusions. A broad variety of in vivo phenotypes can be interrogated such as organ development, hematopoietic lineage decision and evolutionary licensing in oncogenesis. We describe experimental strategies to address various biological questions and provide an outlook on emerging CRISPR applications, such as genetic interaction screening. These technological advances create potent new opportunities to dissect the molecular underpinnings of complex organismal phenotypes.
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Affiliation(s)
- Christian J Braun
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany. .,Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany. .,Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Andrés Carbonell Adames
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Dieter Saur
- Institute of Experimental Cancer Therapy, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany. .,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany. .,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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16
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Asmamaw Mengstie M. Viral Vectors for the in Vivo Delivery of CRISPR Components: Advances and Challenges. Front Bioeng Biotechnol 2022; 10:895713. [PMID: 35646852 PMCID: PMC9133430 DOI: 10.3389/fbioe.2022.895713] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/26/2022] [Indexed: 01/21/2023] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) and its accompanying protein (Cas9) are now the most effective, efficient, and precise genome editing techniques. Two essential components of the CRISPR/Cas9 system are guide RNA (gRNA) and CRISPR-associated (Cas9) proteins. Choosing and implementing safe and effective delivery systems in the therapeutic application of CRISPR/Cas9 has proven to be a significant problem. For in vivo CRISPR/Cas9 delivery, viral vectors are the natural specialists. Due to their higher delivery effectiveness than other delivery methods, vectors such as adenoviral vectors (AdVs), adeno-associated viruses (AAVs), and lentivirus vectors (LVs) are now commonly employed as delivery methods. This review thoroughly examined recent achievements in using a variety of viral vectors as a means of CRISPR/Cas9 delivery, as well as the benefits and limitations of each viral vector. Future thoughts for overcoming the current restrictions and adapting the technology are also discussed.
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17
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Siegler JJ, Correia MP, Hofman T, Prager I, Birgin E, Rahbari NN, Watzl C, Stojanovic A, Cerwenka A. Human ILC3 Exert TRAIL-Mediated Cytotoxicity Towards Cancer Cells. Front Immunol 2022; 13:742571. [PMID: 35300331 PMCID: PMC8921484 DOI: 10.3389/fimmu.2022.742571] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/02/2022] [Indexed: 12/29/2022] Open
Abstract
Group 3 helper Innate Lymphoid Cells (ILC3s) are cytokine-producing lymphocytes that respond to stress signals released during disturbed tissue homeostasis and infection. Upon activation, ILC3s secrete IL-22 and IL-17, and orchestrate immune responses against extracellular pathogens. Their role in cancer remains poorly explored. To determine their anti-cancer effector potential, we co-cultured cytokine-activated human ILC3s with cancer cells of different origins. ILC3s were able to directly respond to tumor cells, resulting in enhanced IFN-γ production. Upon tumor cell encounter, ILC3s maintained expression of the transcription factor RORγt, indicating that ILC3s preserved their identity. ILC3s were able to directly kill both hepatocellular carcinoma and melanoma tumor cells expressing cell-death receptor TRAILR2, through the activation of Caspase-8 in target cells. Moreover, liver-derived cytokine-activated ILC3s also expressed TRAIL and were able to eliminate hepatoblastoma cells. Together, our data reveal that ILC3s can participate in anti-tumor immune response through direct recognition of tumor cells resulting in IFN-γ release and TRAIL-dependent cytotoxicity. Thus, ILC3s might be ancillary players of anti-tumor immunity in tissues, acting as primary responders against transformed or metastasizing cells, which might be further exploited for therapies against cancer.
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Affiliation(s)
- Jana-Julia Siegler
- Department of Immunobiochemistry, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Margareta P Correia
- Department of Immunobiochemistry, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
| | - Tomáš Hofman
- Department of Immunobiochemistry, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Isabel Prager
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
| | - Emrullah Birgin
- Department of Surgery, University Clinics Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Nuh N Rahbari
- Department of Surgery, University Clinics Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carsten Watzl
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
| | - Ana Stojanovic
- Department of Immunobiochemistry, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Adelheid Cerwenka
- Department of Immunobiochemistry, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,European Center for Angioscience (ECAS), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
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18
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Schraivogel D, Kuhn TM, Rauscher B, Rodríguez-Martínez M, Paulsen M, Owsley K, Middlebrook A, Tischer C, Ramasz B, Ordoñez-Rueda D, Dees M, Cuylen-Haering S, Diebold E, Steinmetz LM. High-speed fluorescence image-enabled cell sorting. Science 2022; 375:315-320. [PMID: 35050652 PMCID: PMC7613231 DOI: 10.1126/science.abj3013] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fast and selective isolation of single cells with unique spatial and morphological traits remains a technical challenge. Here, we address this by establishing high-speed image-enabled cell sorting (ICS), which records multicolor fluorescence images and sorts cells based on measurements from image data at speeds up to 15,000 events per second. We show that ICS quantifies cell morphology and localization of labeled proteins and increases the resolution of cell cycle analyses by separating mitotic stages. We combine ICS with CRISPR-pooled screens to identify regulators of the nuclear factor κB (NF-κB) pathway, enabling the completion of genome-wide image-based screens in about 9 hours of run time. By assessing complex cellular phenotypes, ICS substantially expands the phenotypic space accessible to cell-sorting applications and pooled genetic screening.
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Affiliation(s)
- Daniel Schraivogel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit; Heidelberg, Germany
| | - Terra M. Kuhn
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit; Heidelberg, Germany
| | - Benedikt Rauscher
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit; Heidelberg, Germany
| | | | - Malte Paulsen
- European Molecular Biology Laboratory (EMBL), Flow Cytometry Core Facility; Heidelberg, Germany
| | | | | | - Christian Tischer
- European Molecular Biology Laboratory (EMBL); Advanced Light Microscopy Core Facility, Heidelberg, Germany
| | - Beáta Ramasz
- European Molecular Biology Laboratory (EMBL), Flow Cytometry Core Facility; Heidelberg, Germany
| | - Diana Ordoñez-Rueda
- European Molecular Biology Laboratory (EMBL), Flow Cytometry Core Facility; Heidelberg, Germany
| | - Martina Dees
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit; Heidelberg, Germany
| | - Sara Cuylen-Haering
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit; Heidelberg, Germany
| | | | - Lars M. Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit; Heidelberg, Germany
- Department of Genetics, Stanford University School of Medicine; Stanford, CA, USA
- Stanford Genome Technology Center; Palo Alto, CA, USA
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19
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Genolet O, Ravid Lustig L, Schulz EG. Dissecting Molecular Phenotypes Through FACS-Based Pooled CRISPR Screens. Methods Mol Biol 2022; 2520:1-24. [PMID: 35218528 DOI: 10.1007/7651_2021_457] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Pooled CRISPR screens are emerging as a powerful tool to dissect regulatory networks, by assessing how a protein responds to genetic perturbations in a highly multiplexed manner. A large number of genes are perturbed in a cell population through genomic integration of one single-guide RNA (sgRNA) per cell. A subset of cells with the phenotype of interest can then be enriched through fluorescence-activated cell sorting (FACS). SgRNAs with altered abundance after phenotypic enrichment allow identification of genes that either promote or attenuate the investigated phenotype. Here we provide detailed guidelines on how to design and execute a pooled CRISPR screen to investigate molecular phenotypes. We describe how to generate a custom sgRNA library and how to perform a FACS-based screen using readouts such as intracellular antibody staining or Flow-FISH to assess phosphorylation levels or RNA abundance. Through the variety of available perturbation systems and readout options many different molecular and cellular phenotypes can now be tackled with pooled CRISPR screens.
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Affiliation(s)
- Oriana Genolet
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Liat Ravid Lustig
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Edda G Schulz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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20
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Abstract
The past 25 years of genomics research first revealed which genes are encoded by the human genome and then a detailed catalogue of human genome variation associated with many diseases. Despite this, the function of many genes and gene regulatory elements remains poorly characterized, which limits our ability to apply these insights to human disease. The advent of new CRISPR functional genomics tools allows for scalable and multiplexable characterization of genes and gene regulatory elements encoded by the human genome. These approaches promise to reveal mechanisms of gene function and regulation, and to enable exploration of how genes work together to modulate complex phenotypes.
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21
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Gonçalves E, Thomas M, Behan FM, Picco G, Pacini C, Allen F, Vinceti A, Sharma M, Jackson DA, Price S, Beaver CM, Dovey O, Parry-Smith D, Iorio F, Parts L, Yusa K, Garnett MJ. Minimal genome-wide human CRISPR-Cas9 library. Genome Biol 2021; 22:40. [PMID: 33478580 PMCID: PMC7818936 DOI: 10.1186/s13059-021-02268-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023] Open
Abstract
CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by mining existing large-scale gene loss-of-function datasets, resulting in a greater than 42% reduction in size compared to other CRISPR-Cas9 libraries while preserving assay sensitivity and specificity. MinLibCas9 provides backward compatibility with existing datasets, increases the dynamic range of CRISPR-Cas9 screens and extends their application to complex models and assays.
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Affiliation(s)
| | - Mark Thomas
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Fiona M Behan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Gabriele Picco
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Clare Pacini
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Felicity Allen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Mamta Sharma
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - David A Jackson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Stacey Price
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Oliver Dovey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Francesco Iorio
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Human Technopole, Via Cristina Belgioioso 147, 20157, Milan, Italy
| | - Leopold Parts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Computer Science, University of Tartu, 18 Narva St, Tartu, Estonia
| | - Kosuke Yusa
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
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